From 745a2050cf2d39086a242dc9df7bb03f7001c941 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Tue, 30 Jan 2018 10:11:15 -0700 Subject: [PATCH 01/71] Add util. script for making MPAS to lat/lon mapping files --- .../make_mpas_to_lat_lon_mapping.py | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100755 utility_scripts/make_mpas_to_lat_lon_mapping.py diff --git a/utility_scripts/make_mpas_to_lat_lon_mapping.py b/utility_scripts/make_mpas_to_lat_lon_mapping.py new file mode 100755 index 000000000..00d508356 --- /dev/null +++ b/utility_scripts/make_mpas_to_lat_lon_mapping.py @@ -0,0 +1,39 @@ +#!/usr/bin/env python + +''' +Creates a mapping file that can be used with ncremap (NCO) to remap MPAS files +to a latitude/longitude grid. + +Usage: Copy this script into the main MPAS-Analysis directory (up one level). +Modify the grid name, the path to the MPAS grid file and the output grid +resolution. +''' + +from mpas_analysis.shared.interpolation import Remapper +from mpas_analysis.shared.grid import MpasMeshDescriptor +from mpas_analysis.shared.climatology import get_comparison_descriptor +from mpas_analysis.configuration import MpasAnalysisConfigParser + + +# replace with the MPAS mesh name +inGridName = 'oQU240' + +# replace with the path to the desired mesh or restart file +inGridFileName = '/media/xylar/extra_data/analysis/edison/G-QU240-master-intel/run/mpaso.rst.0001-01-06_00000.nc' + +config = MpasAnalysisConfigParser() +config.read('mpas_analysis/config.default') +# replace 1.0 with the desired resolution of the output mesh +config.set('climatology', 'comparisonLatResolution', '1.0') +config.set('climatology', 'comparisonLonResolution', '1.0') + +inDescriptor = MpasMeshDescriptor(inGridFileName, inGridName) + +outDescriptor = get_comparison_descriptor(config, 'latlon') +outGridName = outDescriptor.meshName + +mappingFileName = 'map_{}_to_{}.nc'.format(inGridName, outGridName) + +remapper = Remapper(inDescriptor, outDescriptor, mappingFileName) + +remapper.build_mapping_file(method='bilinear') From 4fb69cdcd8f37af484fce85e2136b7931b5f75fc Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Wed, 31 Jan 2018 11:42:19 -0700 Subject: [PATCH 02/71] Error if the requested config file(s) don't exist --- run_mpas_analysis | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/run_mpas_analysis b/run_mpas_analysis index 0472d9a1b..53d1de451 100755 --- a/run_mpas_analysis +++ b/run_mpas_analysis @@ -460,6 +460,10 @@ if __name__ == "__main__": type=str, nargs='*', help='config file') args = parser.parse_args() + for configFile in args.configFiles: + if not os.path.exists(configFile): + raise OSError('Config file {} not found.'.format(configFile)) + # add config.default to cover default not included in the config files # provided on the command line if pkg_resources.resource_exists('mpas_analysis', 'config.default'): From 9c5e01872046836e140415ba68ffc5fb9aec631f Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Wed, 31 Jan 2018 11:42:44 -0700 Subject: [PATCH 03/71] Plot the zero line across the full plot Before this merge, the zero line has the same extent as the first (valid) curve being plotted, whereas it should really have the full extent of the axis. (Thanks @vanroekel for finding this issue.) --- mpas_analysis/shared/plot/plotting.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/mpas_analysis/shared/plot/plotting.py b/mpas_analysis/shared/plot/plotting.py index eff883a41..bebeb6346 100644 --- a/mpas_analysis/shared/plot/plotting.py +++ b/mpas_analysis/shared/plot/plotting.py @@ -164,15 +164,14 @@ def timeseries_analysis_plot(config, dsvalues, N, title, xlabel, ylabel, 'color': config.get('plot', 'titleFontColor'), 'weight': config.get('plot', 'titleFontWeight')} + plot_xtick_format(plt, calendar, minDays, maxDays, maxXTicks) + # Add a y=0 line if y ranges between positive and negative values yaxLimits = ax.get_ylim() if yaxLimits[0]*yaxLimits[1] < 0: - indgood = np.where(np.logical_not(np.isnan(mean))) - x = mean['Time'][indgood] + x = ax.get_xlim() plt.plot(x, np.zeros(np.size(x)), 'k-', linewidth=1.2, zorder=1) - plot_xtick_format(plt, calendar, minDays, maxDays, maxXTicks) - if title is not None: plt.title(title, **title_font) if xlabel is not None: From 87ff9807e1112b4bea9cd71c31b84d9ff70f0058 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Mon, 12 Feb 2018 12:26:48 -0700 Subject: [PATCH 04/71] Switch from relative to absolute imports This is the recommended python standard. --- mpas_analysis/analysis_task_template.py | 7 ++-- mpas_analysis/configuration/__init__.py | 3 +- mpas_analysis/ocean/__init__.py | 33 +++++++++++-------- .../ocean/climatology_map_antarctic_melt.py | 15 +++++---- mpas_analysis/ocean/climatology_map_mld.py | 13 ++++---- mpas_analysis/ocean/climatology_map_sose.py | 16 +++++---- mpas_analysis/ocean/climatology_map_sss.py | 11 ++++--- mpas_analysis/ocean/climatology_map_sst.py | 11 ++++--- .../ocean/compute_anomaly_subtask.py | 11 ++++--- mpas_analysis/ocean/index_nino34.py | 16 ++++----- .../ocean/meridional_heat_transport.py | 14 ++++---- .../ocean/plot_climatology_map_subtask.py | 11 ++++--- ...ot_depth_integrated_time_series_subtask.py | 17 +++++----- mpas_analysis/ocean/plot_hovmoller_subtask.py | 11 ++++--- .../ocean/remap_depth_slices_subtask.py | 6 ++-- mpas_analysis/ocean/streamfunction_moc.py | 15 +++++---- .../ocean/time_series_antarctic_melt.py | 13 ++++---- .../ocean/time_series_ohc_anomaly.py | 8 ++--- .../ocean/time_series_salinity_anomaly.py | 6 ++-- mpas_analysis/ocean/time_series_sst.py | 17 +++++----- .../ocean/time_series_temperature_anomaly.py | 6 ++-- mpas_analysis/sea_ice/__init__.py | 8 +++-- .../sea_ice/climatology_map_sea_ice_conc.py | 11 ++++--- .../sea_ice/climatology_map_sea_ice_thick.py | 11 ++++--- .../sea_ice/plot_climatology_map_subtask.py | 9 ++--- mpas_analysis/sea_ice/time_series.py | 23 ++++++------- mpas_analysis/shared/__init__.py | 2 +- mpas_analysis/shared/analysis_task.py | 5 +-- mpas_analysis/shared/climatology/__init__.py | 15 +++++---- .../shared/climatology/climatology.py | 21 +++++++----- .../climatology/comparison_descriptors.py | 5 +-- .../climatology/mpas_climatology_task.py | 5 +-- .../remap_mpas_climatology_subtask.py | 19 ++++++----- .../remap_observed_climatology_subtask.py | 16 +++++---- mpas_analysis/shared/containers.py | 6 ++-- .../shared/generalized_reader/__init__.py | 3 +- .../generalized_reader/generalized_reader.py | 5 +-- mpas_analysis/shared/grid/__init__.py | 4 +-- mpas_analysis/shared/html/__init__.py | 5 +-- mpas_analysis/shared/html/image_xml.py | 2 +- mpas_analysis/shared/html/pages.py | 2 +- .../shared/interpolation/__init__.py | 2 +- .../shared/interpolation/remapper.py | 4 +-- mpas_analysis/shared/io/__init__.py | 10 +++--- mpas_analysis/shared/io/mpas_reader.py | 3 +- .../shared/io/namelist_streams_interface.py | 6 ++-- .../shared/mpas_xarray/mpas_xarray.py | 5 +-- mpas_analysis/shared/plot/plotting.py | 5 +-- mpas_analysis/shared/time_series/__init__.py | 10 +++--- mpas_analysis/shared/time_series/anomaly.py | 4 +-- .../time_series/mpas_time_series_task.py | 7 ++-- .../shared/time_series/time_series.py | 2 +- mpas_analysis/shared/timekeeping/utility.py | 3 +- mpas_analysis/test/test_mpas_config_parser.py | 2 +- 54 files changed, 278 insertions(+), 222 deletions(-) diff --git a/mpas_analysis/analysis_task_template.py b/mpas_analysis/analysis_task_template.py index 2ec02f293..0c53f46e7 100644 --- a/mpas_analysis/analysis_task_template.py +++ b/mpas_analysis/analysis_task_template.py @@ -42,11 +42,12 @@ # import mpas_analysis module here (those with relative paths starting with # dots) -from ..shared.analysis_task import AnalysisTask +from mpas_analysis.shared.analysis_task import AnalysisTask -from ..shared.html import write_image_xml +from mpas_analysis.shared.html import write_image_xml -from ..shared.climatology import update_climatology_bounds_from_file_names +from mpas_analysis.shared.climatology import \ + update_climatology_bounds_from_file_names # Everywhere in this template, change MyTask to the name of your task, starting diff --git a/mpas_analysis/configuration/__init__.py b/mpas_analysis/configuration/__init__.py index 114e54cb5..644ae9562 100644 --- a/mpas_analysis/configuration/__init__.py +++ b/mpas_analysis/configuration/__init__.py @@ -1 +1,2 @@ -from .mpas_analysis_config_parser import MpasAnalysisConfigParser +from mpas_analysis.configuration.mpas_analysis_config_parser import \ + MpasAnalysisConfigParser diff --git a/mpas_analysis/ocean/__init__.py b/mpas_analysis/ocean/__init__.py index a9e4f9c89..2a8097a67 100644 --- a/mpas_analysis/ocean/__init__.py +++ b/mpas_analysis/ocean/__init__.py @@ -1,16 +1,21 @@ -from .climatology_map_sst import ClimatologyMapSST -from .climatology_map_mld import ClimatologyMapMLD -from .climatology_map_sss import ClimatologyMapSSS -from .climatology_map_antarctic_melt import ClimatologyMapAntarcticMelt -from .climatology_map_sose import ClimatologyMapSoseTemperature, \ - ClimatologyMapSoseSalinity +from mpas_analysis.ocean.climatology_map_sst import ClimatologyMapSST +from mpas_analysis.ocean.climatology_map_mld import ClimatologyMapMLD +from mpas_analysis.ocean.climatology_map_sss import ClimatologyMapSSS +from mpas_analysis.ocean.climatology_map_antarctic_melt import \ + ClimatologyMapAntarcticMelt +from mpas_analysis.ocean.climatology_map_sose import \ + ClimatologyMapSoseTemperature, ClimatologyMapSoseSalinity -from .time_series_temperature_anomaly import TimeSeriesTemperatureAnomaly -from .time_series_salinity_anomaly import TimeSeriesSalinityAnomaly -from .time_series_ohc_anomaly import TimeSeriesOHCAnomaly +from mpas_analysis.ocean.time_series_temperature_anomaly import \ + TimeSeriesTemperatureAnomaly +from mpas_analysis.ocean.time_series_salinity_anomaly import \ + TimeSeriesSalinityAnomaly +from mpas_analysis.ocean.time_series_ohc_anomaly import TimeSeriesOHCAnomaly -from .time_series_sst import TimeSeriesSST -from .index_nino34 import IndexNino34 -from .streamfunction_moc import StreamfunctionMOC -from .meridional_heat_transport import MeridionalHeatTransport -from .time_series_antarctic_melt import TimeSeriesAntarcticMelt +from mpas_analysis.ocean.time_series_sst import TimeSeriesSST +from mpas_analysis.ocean.index_nino34 import IndexNino34 +from mpas_analysis.ocean.streamfunction_moc import StreamfunctionMOC +from mpas_analysis.ocean.meridional_heat_transport import \ + MeridionalHeatTransport +from mpas_analysis.ocean.time_series_antarctic_melt import \ + TimeSeriesAntarcticMelt diff --git a/mpas_analysis/ocean/climatology_map_antarctic_melt.py b/mpas_analysis/ocean/climatology_map_antarctic_melt.py index 47e4a82af..07002cc73 100644 --- a/mpas_analysis/ocean/climatology_map_antarctic_melt.py +++ b/mpas_analysis/ocean/climatology_map_antarctic_melt.py @@ -3,20 +3,21 @@ import xarray as xr -from ..shared import AnalysisTask +from mpas_analysis.shared import AnalysisTask -from ..shared.io.utility import build_config_full_path +from mpas_analysis.shared.io.utility import build_config_full_path -from ..shared.climatology import RemapMpasClimatologySubtask, \ +from mpas_analysis.shared.climatology import RemapMpasClimatologySubtask, \ RemapObservedClimatologySubtask, get_antarctic_stereographic_projection -from .plot_climatology_map_subtask import PlotClimatologyMapSubtask +from mpas_analysis.ocean.plot_climatology_map_subtask import \ + PlotClimatologyMapSubtask -from ..shared.mpas_xarray import mpas_xarray +from mpas_analysis.shared.mpas_xarray import mpas_xarray -from ..shared.constants import constants +from mpas_analysis.shared.constants import constants -from ..shared.grid import ProjectionGridDescriptor +from mpas_analysis.shared.grid import ProjectionGridDescriptor class ClimatologyMapAntarcticMelt(AnalysisTask): # {{{ diff --git a/mpas_analysis/ocean/climatology_map_mld.py b/mpas_analysis/ocean/climatology_map_mld.py index 174f065a6..6631d2c8e 100644 --- a/mpas_analysis/ocean/climatology_map_mld.py +++ b/mpas_analysis/ocean/climatology_map_mld.py @@ -4,18 +4,19 @@ import xarray as xr import numpy as np -from ..shared import AnalysisTask +from mpas_analysis.shared import AnalysisTask -from ..shared.io.utility import build_config_full_path +from mpas_analysis.shared.io.utility import build_config_full_path -from ..shared.climatology import RemapMpasClimatologySubtask, \ +from mpas_analysis.shared.climatology import RemapMpasClimatologySubtask, \ RemapObservedClimatologySubtask -from .plot_climatology_map_subtask import PlotClimatologyMapSubtask +from mpas_analysis.ocean.plot_climatology_map_subtask import \ + PlotClimatologyMapSubtask -from ..shared.grid import LatLonGridDescriptor +from mpas_analysis.shared.grid import LatLonGridDescriptor -from ..shared.mpas_xarray import mpas_xarray +from mpas_analysis.shared.mpas_xarray import mpas_xarray class ClimatologyMapMLD(AnalysisTask): # {{{ diff --git a/mpas_analysis/ocean/climatology_map_sose.py b/mpas_analysis/ocean/climatology_map_sose.py index 894b8ebd6..ef23524ab 100644 --- a/mpas_analysis/ocean/climatology_map_sose.py +++ b/mpas_analysis/ocean/climatology_map_sose.py @@ -9,20 +9,22 @@ import xarray as xr -from ..shared import AnalysisTask +from mpas_analysis.shared import AnalysisTask -from .remap_depth_slices_subtask import RemapDepthSlicesSubtask +from mpas_analysis.ocean.remap_depth_slices_subtask import \ + RemapDepthSlicesSubtask -from .plot_climatology_map_subtask import PlotClimatologyMapSubtask +from mpas_analysis.ocean.plot_climatology_map_subtask import \ + PlotClimatologyMapSubtask -from ..shared.io.utility import build_config_full_path +from mpas_analysis.shared.io.utility import build_config_full_path -from ..shared.climatology import RemapObservedClimatologySubtask, \ +from mpas_analysis.shared.climatology import RemapObservedClimatologySubtask, \ get_antarctic_stereographic_projection -from ..shared.grid import ProjectionGridDescriptor +from mpas_analysis.shared.grid import ProjectionGridDescriptor -from ..shared.mpas_xarray import mpas_xarray +from mpas_analysis.shared.mpas_xarray import mpas_xarray class ClimatologyMapSoseTemperature(AnalysisTask): # {{{ diff --git a/mpas_analysis/ocean/climatology_map_sss.py b/mpas_analysis/ocean/climatology_map_sss.py index 0fdc0877d..7e8f27a55 100644 --- a/mpas_analysis/ocean/climatology_map_sss.py +++ b/mpas_analysis/ocean/climatology_map_sss.py @@ -4,16 +4,17 @@ import xarray as xr import datetime -from ..shared import AnalysisTask +from mpas_analysis.shared import AnalysisTask -from ..shared.io.utility import build_config_full_path +from mpas_analysis.shared.io.utility import build_config_full_path -from ..shared.climatology import RemapMpasClimatologySubtask, \ +from mpas_analysis.shared.climatology import RemapMpasClimatologySubtask, \ RemapObservedClimatologySubtask -from .plot_climatology_map_subtask import PlotClimatologyMapSubtask +from mpas_analysis.ocean.plot_climatology_map_subtask import \ + PlotClimatologyMapSubtask -from ..shared.grid import LatLonGridDescriptor +from mpas_analysis.shared.grid import LatLonGridDescriptor class ClimatologyMapSSS(AnalysisTask): # {{{ diff --git a/mpas_analysis/ocean/climatology_map_sst.py b/mpas_analysis/ocean/climatology_map_sst.py index 0a5b1d699..b7c99a8f5 100644 --- a/mpas_analysis/ocean/climatology_map_sst.py +++ b/mpas_analysis/ocean/climatology_map_sst.py @@ -4,16 +4,17 @@ import xarray as xr import datetime -from ..shared import AnalysisTask +from mpas_analysis.shared import AnalysisTask -from ..shared.io.utility import build_config_full_path +from mpas_analysis.shared.io.utility import build_config_full_path -from ..shared.climatology import RemapMpasClimatologySubtask, \ +from mpas_analysis.shared.climatology import RemapMpasClimatologySubtask, \ RemapObservedClimatologySubtask -from .plot_climatology_map_subtask import PlotClimatologyMapSubtask +from mpas_analysis.ocean.plot_climatology_map_subtask import \ + PlotClimatologyMapSubtask -from ..shared.grid import LatLonGridDescriptor +from mpas_analysis.shared.grid import LatLonGridDescriptor class ClimatologyMapSST(AnalysisTask): # {{{ diff --git a/mpas_analysis/ocean/compute_anomaly_subtask.py b/mpas_analysis/ocean/compute_anomaly_subtask.py index befefbf8c..49773a538 100644 --- a/mpas_analysis/ocean/compute_anomaly_subtask.py +++ b/mpas_analysis/ocean/compute_anomaly_subtask.py @@ -5,15 +5,16 @@ import os -from ..shared import AnalysisTask +from mpas_analysis.shared import AnalysisTask -from ..shared.io import write_netcdf +from mpas_analysis.shared.io import write_netcdf -from ..shared.timekeeping.utility import get_simulation_start_time +from mpas_analysis.shared.timekeeping.utility import get_simulation_start_time -from ..shared.io.utility import build_config_full_path +from mpas_analysis.shared.io.utility import build_config_full_path -from ..shared.time_series import compute_moving_avg_anomaly_from_start +from mpas_analysis.shared.time_series import \ + compute_moving_avg_anomaly_from_start class ComputeAnomalySubtask(AnalysisTask): diff --git a/mpas_analysis/ocean/index_nino34.py b/mpas_analysis/ocean/index_nino34.py index 608621328..105342af2 100644 --- a/mpas_analysis/ocean/index_nino34.py +++ b/mpas_analysis/ocean/index_nino34.py @@ -10,19 +10,19 @@ from scipy import signal, stats import matplotlib.pyplot as plt -from ..shared.climatology import climatology -from ..shared.constants import constants -from ..shared.io.utility import build_config_full_path +from mpas_analysis.shared.climatology import climatology +from mpas_analysis.shared.constants import constants +from mpas_analysis.shared.io.utility import build_config_full_path -from ..shared.timekeeping.utility import datetime_to_days, \ +from mpas_analysis.shared.timekeeping.utility import datetime_to_days, \ string_to_days_since_date -from ..shared.io import open_mpas_dataset +from mpas_analysis.shared.io import open_mpas_dataset -from ..shared.plot.plotting import plot_xtick_format +from mpas_analysis.shared.plot.plotting import plot_xtick_format -from ..shared import AnalysisTask -from ..shared.html import write_image_xml +from mpas_analysis.shared import AnalysisTask +from mpas_analysis.shared.html import write_image_xml class IndexNino34(AnalysisTask): # {{{ diff --git a/mpas_analysis/ocean/meridional_heat_transport.py b/mpas_analysis/ocean/meridional_heat_transport.py index e6b139e76..f1dbfd0fc 100644 --- a/mpas_analysis/ocean/meridional_heat_transport.py +++ b/mpas_analysis/ocean/meridional_heat_transport.py @@ -6,16 +6,18 @@ import numpy as np import os -from ..shared.plot.plotting import plot_vertical_section,\ +from mpas_analysis.shared.plot.plotting import plot_vertical_section,\ setup_colormap, plot_1D -from ..shared.io.utility import build_config_full_path, make_directories -from ..shared.io import write_netcdf, subset_variables +from mpas_analysis.shared.io.utility import build_config_full_path, \ + make_directories +from mpas_analysis.shared.io import write_netcdf, subset_variables -from ..shared import AnalysisTask -from ..shared.html import write_image_xml +from mpas_analysis.shared import AnalysisTask +from mpas_analysis.shared.html import write_image_xml -from ..shared.climatology import get_unmasked_mpas_climatology_file_name +from mpas_analysis.shared.climatology import \ + get_unmasked_mpas_climatology_file_name class MeridionalHeatTransport(AnalysisTask): # {{{ diff --git a/mpas_analysis/ocean/plot_climatology_map_subtask.py b/mpas_analysis/ocean/plot_climatology_map_subtask.py index 826046a0f..34b11d39d 100644 --- a/mpas_analysis/ocean/plot_climatology_map_subtask.py +++ b/mpas_analysis/ocean/plot_climatology_map_subtask.py @@ -13,16 +13,17 @@ import xarray as xr import numpy as np -from ..shared import AnalysisTask +from mpas_analysis.shared import AnalysisTask -from ..shared.plot.plotting import plot_global_comparison, \ +from mpas_analysis.shared.plot.plotting import plot_global_comparison, \ setup_colormap, plot_polar_projection_comparison -from ..shared.html import write_image_xml +from mpas_analysis.shared.html import write_image_xml -from ..shared.grid import interp_extrap_corner +from mpas_analysis.shared.grid import interp_extrap_corner -from ..shared.climatology import get_remapped_mpas_climatology_file_name +from mpas_analysis.shared.climatology import \ + get_remapped_mpas_climatology_file_name def nans_to_numpy_mask(field): diff --git a/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py b/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py index 10f3b1bf2..ad98cd56c 100644 --- a/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py +++ b/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py @@ -6,20 +6,21 @@ import xarray as xr import os -from ..shared import AnalysisTask +from mpas_analysis.shared import AnalysisTask -from ..shared.plot.plotting import timeseries_analysis_plot +from mpas_analysis.shared.plot.plotting import timeseries_analysis_plot -from ..shared.generalized_reader import open_multifile_dataset -from ..shared.io import open_mpas_dataset +from mpas_analysis.shared.generalized_reader import open_multifile_dataset +from mpas_analysis.shared.io import open_mpas_dataset -from ..shared.timekeeping.utility import date_to_days, days_to_datetime +from mpas_analysis.shared.timekeeping.utility import date_to_days, \ + days_to_datetime -from ..shared.io.utility import build_config_full_path +from mpas_analysis.shared.io.utility import build_config_full_path -from ..shared.html import write_image_xml +from mpas_analysis.shared.html import write_image_xml -from ..shared.time_series import compute_moving_avg +from mpas_analysis.shared.time_series import compute_moving_avg class PlotDepthIntegratedTimeSeriesSubtask(AnalysisTask): diff --git a/mpas_analysis/ocean/plot_hovmoller_subtask.py b/mpas_analysis/ocean/plot_hovmoller_subtask.py index 2c802c8d7..96e54a284 100644 --- a/mpas_analysis/ocean/plot_hovmoller_subtask.py +++ b/mpas_analysis/ocean/plot_hovmoller_subtask.py @@ -6,15 +6,16 @@ import xarray as xr import os -from ..shared import AnalysisTask +from mpas_analysis.shared import AnalysisTask -from ..shared.plot.plotting import plot_vertical_section, setup_colormap +from mpas_analysis.shared.plot.plotting import plot_vertical_section, \ + setup_colormap -from ..shared.io import open_mpas_dataset +from mpas_analysis.shared.io import open_mpas_dataset -from ..shared.io.utility import build_config_full_path +from mpas_analysis.shared.io.utility import build_config_full_path -from ..shared.html import write_image_xml +from mpas_analysis.shared.html import write_image_xml class PlotHovmollerSubtask(AnalysisTask): diff --git a/mpas_analysis/ocean/remap_depth_slices_subtask.py b/mpas_analysis/ocean/remap_depth_slices_subtask.py index 6788fe43e..b2102ae59 100644 --- a/mpas_analysis/ocean/remap_depth_slices_subtask.py +++ b/mpas_analysis/ocean/remap_depth_slices_subtask.py @@ -4,11 +4,11 @@ import xarray as xr import numpy as np -from ..shared.climatology import RemapMpasClimatologySubtask +from mpas_analysis.shared.climatology import RemapMpasClimatologySubtask -from ..shared.mpas_xarray import mpas_xarray +from mpas_analysis.shared.mpas_xarray import mpas_xarray -from .utility import compute_zmid +from mpas_analysis.ocean.utility import compute_zmid class RemapDepthSlicesSubtask(RemapMpasClimatologySubtask): # {{{ diff --git a/mpas_analysis/ocean/streamfunction_moc.py b/mpas_analysis/ocean/streamfunction_moc.py index 974b32845..04c9d8a3a 100644 --- a/mpas_analysis/ocean/streamfunction_moc.py +++ b/mpas_analysis/ocean/streamfunction_moc.py @@ -8,19 +8,20 @@ import netCDF4 import os -from ..shared.constants.constants import m3ps_to_Sv -from ..shared.plot.plotting import plot_vertical_section,\ +from mpas_analysis.shared.constants.constants import m3ps_to_Sv +from mpas_analysis.shared.plot.plotting import plot_vertical_section,\ timeseries_analysis_plot, setup_colormap -from ..shared.io.utility import build_config_full_path, make_directories +from mpas_analysis.shared.io.utility import build_config_full_path, \ + make_directories -from ..shared.io import open_mpas_dataset +from mpas_analysis.shared.io import open_mpas_dataset -from ..shared.timekeeping.utility import days_to_datetime +from mpas_analysis.shared.timekeeping.utility import days_to_datetime -from ..shared import AnalysisTask +from mpas_analysis.shared import AnalysisTask -from ..shared.html import write_image_xml +from mpas_analysis.shared.html import write_image_xml class StreamfunctionMOC(AnalysisTask): # {{{ diff --git a/mpas_analysis/ocean/time_series_antarctic_melt.py b/mpas_analysis/ocean/time_series_antarctic_melt.py index 8c668826b..743da8af3 100644 --- a/mpas_analysis/ocean/time_series_antarctic_melt.py +++ b/mpas_analysis/ocean/time_series_antarctic_melt.py @@ -5,17 +5,18 @@ import xarray import numpy -from ..shared.analysis_task import AnalysisTask +from mpas_analysis.shared.analysis_task import AnalysisTask -from ..shared.constants import constants +from mpas_analysis.shared.constants import constants -from ..shared.plot.plotting import timeseries_analysis_plot +from mpas_analysis.shared.plot.plotting import timeseries_analysis_plot -from ..shared.io import open_mpas_dataset, write_netcdf +from mpas_analysis.shared.io import open_mpas_dataset, write_netcdf -from ..shared.io.utility import build_config_full_path, make_directories +from mpas_analysis.shared.io.utility import build_config_full_path, \ + make_directories -from ..shared.html import write_image_xml +from mpas_analysis.shared.html import write_image_xml import csv diff --git a/mpas_analysis/ocean/time_series_ohc_anomaly.py b/mpas_analysis/ocean/time_series_ohc_anomaly.py index 0592abaf5..00d6e3594 100644 --- a/mpas_analysis/ocean/time_series_ohc_anomaly.py +++ b/mpas_analysis/ocean/time_series_ohc_anomaly.py @@ -5,11 +5,11 @@ import xarray as xr -from ..shared import AnalysisTask +from mpas_analysis.shared import AnalysisTask -from .compute_anomaly_subtask import ComputeAnomalySubtask -from .plot_hovmoller_subtask import PlotHovmollerSubtask -from .plot_depth_integrated_time_series_subtask import \ +from mpas_analysis.ocean.compute_anomaly_subtask import ComputeAnomalySubtask +from mpas_analysis.ocean.plot_hovmoller_subtask import PlotHovmollerSubtask +from mpas_analysis.ocean.plot_depth_integrated_time_series_subtask import \ PlotDepthIntegratedTimeSeriesSubtask diff --git a/mpas_analysis/ocean/time_series_salinity_anomaly.py b/mpas_analysis/ocean/time_series_salinity_anomaly.py index dba021329..3f29492b3 100644 --- a/mpas_analysis/ocean/time_series_salinity_anomaly.py +++ b/mpas_analysis/ocean/time_series_salinity_anomaly.py @@ -3,10 +3,10 @@ from __future__ import absolute_import, division, print_function, \ unicode_literals -from ..shared import AnalysisTask +from mpas_analysis.shared import AnalysisTask -from .compute_anomaly_subtask import ComputeAnomalySubtask -from .plot_hovmoller_subtask import PlotHovmollerSubtask +from mpas_analysis.ocean.compute_anomaly_subtask import ComputeAnomalySubtask +from mpas_analysis.ocean.plot_hovmoller_subtask import PlotHovmollerSubtask class TimeSeriesSalinityAnomaly(AnalysisTask): diff --git a/mpas_analysis/ocean/time_series_sst.py b/mpas_analysis/ocean/time_series_sst.py index 947d2b881..9b889288d 100644 --- a/mpas_analysis/ocean/time_series_sst.py +++ b/mpas_analysis/ocean/time_series_sst.py @@ -2,18 +2,19 @@ from __future__ import absolute_import, division, print_function, \ unicode_literals -from ..shared import AnalysisTask +from mpas_analysis.shared import AnalysisTask -from ..shared.plot.plotting import timeseries_analysis_plot +from mpas_analysis.shared.plot.plotting import timeseries_analysis_plot -from ..shared.generalized_reader import open_multifile_dataset -from ..shared.io import open_mpas_dataset +from mpas_analysis.shared.generalized_reader import open_multifile_dataset +from mpas_analysis.shared.io import open_mpas_dataset -from ..shared.timekeeping.utility import date_to_days, days_to_datetime +from mpas_analysis.shared.timekeeping.utility import date_to_days, \ + days_to_datetime -from ..shared.io.utility import build_config_full_path, make_directories, \ - check_path_exists -from ..shared.html import write_image_xml +from mpas_analysis.shared.io.utility import build_config_full_path, \ + make_directories, check_path_exists +from mpas_analysis.shared.html import write_image_xml class TimeSeriesSST(AnalysisTask): diff --git a/mpas_analysis/ocean/time_series_temperature_anomaly.py b/mpas_analysis/ocean/time_series_temperature_anomaly.py index 4897795f3..9e61b2156 100644 --- a/mpas_analysis/ocean/time_series_temperature_anomaly.py +++ b/mpas_analysis/ocean/time_series_temperature_anomaly.py @@ -3,10 +3,10 @@ from __future__ import absolute_import, division, print_function, \ unicode_literals -from ..shared import AnalysisTask +from mpas_analysis.shared import AnalysisTask -from .compute_anomaly_subtask import ComputeAnomalySubtask -from .plot_hovmoller_subtask import PlotHovmollerSubtask +from mpas_analysis.ocean.compute_anomaly_subtask import ComputeAnomalySubtask +from mpas_analysis.ocean.plot_hovmoller_subtask import PlotHovmollerSubtask class TimeSeriesTemperatureAnomaly(AnalysisTask): diff --git a/mpas_analysis/sea_ice/__init__.py b/mpas_analysis/sea_ice/__init__.py index bc745d9d9..7f6a548b6 100644 --- a/mpas_analysis/sea_ice/__init__.py +++ b/mpas_analysis/sea_ice/__init__.py @@ -1,3 +1,5 @@ -from .climatology_map_sea_ice_conc import ClimatologyMapSeaIceConc -from .climatology_map_sea_ice_thick import ClimatologyMapSeaIceThick -from .time_series import TimeSeriesSeaIce +from mpas_analysis.sea_ice.climatology_map_sea_ice_conc import \ + ClimatologyMapSeaIceConc +from mpas_analysis.sea_ice.climatology_map_sea_ice_thick import \ + ClimatologyMapSeaIceThick +from mpas_analysis.sea_ice.time_series import TimeSeriesSeaIce diff --git a/mpas_analysis/sea_ice/climatology_map_sea_ice_conc.py b/mpas_analysis/sea_ice/climatology_map_sea_ice_conc.py index c749f5c9c..b1909dec0 100644 --- a/mpas_analysis/sea_ice/climatology_map_sea_ice_conc.py +++ b/mpas_analysis/sea_ice/climatology_map_sea_ice_conc.py @@ -4,16 +4,17 @@ import xarray as xr -from ..shared import AnalysisTask +from mpas_analysis.shared import AnalysisTask -from ..shared.climatology import RemapMpasClimatologySubtask, \ +from mpas_analysis.shared.climatology import RemapMpasClimatologySubtask, \ RemapObservedClimatologySubtask -from .plot_climatology_map_subtask import PlotClimatologyMapSubtask +from mpas_analysis.sea_ice.plot_climatology_map_subtask import \ + PlotClimatologyMapSubtask -from ..shared.io.utility import build_config_full_path +from mpas_analysis.shared.io.utility import build_config_full_path -from ..shared.grid import LatLonGridDescriptor +from mpas_analysis.shared.grid import LatLonGridDescriptor class ClimatologyMapSeaIceConc(AnalysisTask): # {{{ diff --git a/mpas_analysis/sea_ice/climatology_map_sea_ice_thick.py b/mpas_analysis/sea_ice/climatology_map_sea_ice_thick.py index 96c3f4f04..957b15830 100644 --- a/mpas_analysis/sea_ice/climatology_map_sea_ice_thick.py +++ b/mpas_analysis/sea_ice/climatology_map_sea_ice_thick.py @@ -4,16 +4,17 @@ import xarray as xr -from ..shared import AnalysisTask +from mpas_analysis.shared import AnalysisTask -from ..shared.climatology import RemapMpasClimatologySubtask, \ +from mpas_analysis.shared.climatology import RemapMpasClimatologySubtask, \ RemapObservedClimatologySubtask -from .plot_climatology_map_subtask import PlotClimatologyMapSubtask +from mpas_analysis.sea_ice.plot_climatology_map_subtask import \ + PlotClimatologyMapSubtask -from ..shared.io.utility import build_config_full_path +from mpas_analysis.shared.io.utility import build_config_full_path -from ..shared.grid import LatLonGridDescriptor +from mpas_analysis.shared.grid import LatLonGridDescriptor class ClimatologyMapSeaIceThick(AnalysisTask): # {{{ diff --git a/mpas_analysis/sea_ice/plot_climatology_map_subtask.py b/mpas_analysis/sea_ice/plot_climatology_map_subtask.py index 9d5bf9ad2..5ca70ff2e 100644 --- a/mpas_analysis/sea_ice/plot_climatology_map_subtask.py +++ b/mpas_analysis/sea_ice/plot_climatology_map_subtask.py @@ -7,14 +7,15 @@ import xarray as xr -from ..shared import AnalysisTask +from mpas_analysis.shared import AnalysisTask -from ..shared.plot.plotting import plot_polar_comparison, \ +from mpas_analysis.shared.plot.plotting import plot_polar_comparison, \ setup_colormap -from ..shared.html import write_image_xml +from mpas_analysis.shared.html import write_image_xml -from ..shared.climatology import get_remapped_mpas_climatology_file_name +from mpas_analysis.shared.climatology import \ + get_remapped_mpas_climatology_file_name class PlotClimatologyMapSubtask(AnalysisTask): # {{{ diff --git a/mpas_analysis/sea_ice/time_series.py b/mpas_analysis/sea_ice/time_series.py index c890964f3..67d34915b 100644 --- a/mpas_analysis/sea_ice/time_series.py +++ b/mpas_analysis/sea_ice/time_series.py @@ -5,23 +5,24 @@ import xarray as xr import os -from ..shared import AnalysisTask +from mpas_analysis.shared import AnalysisTask -from ..shared.plot.plotting import timeseries_analysis_plot, \ +from mpas_analysis.shared.plot.plotting import timeseries_analysis_plot, \ timeseries_analysis_plot_polar -from ..shared.io.utility import build_config_full_path, check_path_exists, \ - make_directories +from mpas_analysis.shared.io.utility import build_config_full_path, \ + check_path_exists, make_directories -from ..shared.timekeeping.utility import date_to_days, days_to_datetime, \ - datetime_to_days, get_simulation_start_time -from ..shared.timekeeping.MpasRelativeDelta import MpasRelativeDelta +from mpas_analysis.shared.timekeeping.utility import date_to_days, \ + days_to_datetime, datetime_to_days, get_simulation_start_time +from mpas_analysis.shared.timekeeping.MpasRelativeDelta import \ + MpasRelativeDelta -from ..shared.generalized_reader import open_multifile_dataset -from ..shared.io import open_mpas_dataset, write_netcdf -from ..shared.mpas_xarray.mpas_xarray import subset_variables +from mpas_analysis.shared.generalized_reader import open_multifile_dataset +from mpas_analysis.shared.io import open_mpas_dataset, write_netcdf +from mpas_analysis.shared.mpas_xarray.mpas_xarray import subset_variables -from ..shared.html import write_image_xml +from mpas_analysis.shared.html import write_image_xml class TimeSeriesSeaIce(AnalysisTask): diff --git a/mpas_analysis/shared/__init__.py b/mpas_analysis/shared/__init__.py index 27d9310c9..d6b130b6c 100644 --- a/mpas_analysis/shared/__init__.py +++ b/mpas_analysis/shared/__init__.py @@ -1 +1 @@ -from .analysis_task import AnalysisTask +from mpas_analysis.shared.analysis_task import AnalysisTask diff --git a/mpas_analysis/shared/analysis_task.py b/mpas_analysis/shared/analysis_task.py index f03625ecd..2e7b7d70b 100644 --- a/mpas_analysis/shared/analysis_task.py +++ b/mpas_analysis/shared/analysis_task.py @@ -16,8 +16,9 @@ import logging import sys -from .io import NameList, StreamsFile -from .io.utility import build_config_full_path, make_directories +from mpas_analysis.shared.io import NameList, StreamsFile +from mpas_analysis.shared.io.utility import build_config_full_path, \ + make_directories class AnalysisTask(Process): # {{{ diff --git a/mpas_analysis/shared/climatology/__init__.py b/mpas_analysis/shared/climatology/__init__.py index 3be6e13d9..afb8d7b4b 100644 --- a/mpas_analysis/shared/climatology/__init__.py +++ b/mpas_analysis/shared/climatology/__init__.py @@ -1,4 +1,4 @@ -from .climatology import get_remapper, \ +from mpas_analysis.shared.climatology.climatology import get_remapper, \ compute_monthly_climatology, compute_climatology, \ add_years_months_days_in_month, remap_and_write_climatology, \ get_unmasked_mpas_climatology_directory, \ @@ -6,8 +6,11 @@ get_masked_mpas_climatology_file_name, \ get_remapped_mpas_climatology_file_name -from .mpas_climatology_task import MpasClimatologyTask -from .remap_mpas_climatology_subtask import RemapMpasClimatologySubtask -from .remap_observed_climatology_subtask import RemapObservedClimatologySubtask -from .comparison_descriptors import get_comparison_descriptor, \ - get_antarctic_stereographic_projection +from mpas_analysis.shared.climatology.mpas_climatology_task import \ + MpasClimatologyTask +from mpas_analysis.shared.climatology.remap_mpas_climatology_subtask import \ + RemapMpasClimatologySubtask +from mpas_analysis.shared.climatology.remap_observed_climatology_subtask \ + import RemapObservedClimatologySubtask +from mpas_analysis.shared.climatology.comparison_descriptors import \ + get_comparison_descriptor, get_antarctic_stereographic_projection diff --git a/mpas_analysis/shared/climatology/climatology.py b/mpas_analysis/shared/climatology/climatology.py index a33469422..c2b411465 100644 --- a/mpas_analysis/shared/climatology/climatology.py +++ b/mpas_analysis/shared/climatology/climatology.py @@ -13,17 +13,19 @@ import os import numpy -from ..constants import constants +from mpas_analysis.shared.constants import constants -from ..timekeeping.utility import days_to_datetime +from mpas_analysis.shared.timekeeping.utility import days_to_datetime -from ..io.utility import build_config_full_path, make_directories, \ - fingerprint_generator -from ..io import write_netcdf +from mpas_analysis.shared.io.utility import build_config_full_path, \ + make_directories, fingerprint_generator +from mpas_analysis.shared.io import write_netcdf -from ..interpolation import Remapper -from ..grid import LatLonGridDescriptor, ProjectionGridDescriptor -from .comparison_descriptors import get_comparison_descriptor +from mpas_analysis.shared.interpolation import Remapper +from mpas_analysis.shared.grid import LatLonGridDescriptor, \ + ProjectionGridDescriptor +from mpas_analysis.shared.climatology.comparison_descriptors import \ + get_comparison_descriptor def get_remapper(config, sourceDescriptor, comparisonDescriptor, @@ -327,7 +329,8 @@ def remap_and_write_climatology(config, climatologyDataSet, useNcremap = config.getboolean('climatology', 'useNcremap') if (isinstance(remapper.sourceDescriptor, ProjectionGridDescriptor) or - isinstance(remapper.destinationDescriptor, ProjectionGridDescriptor)): + isinstance(remapper.destinationDescriptor, + ProjectionGridDescriptor)): # ncremap doesn't support projection grids useNcremap = False diff --git a/mpas_analysis/shared/climatology/comparison_descriptors.py b/mpas_analysis/shared/climatology/comparison_descriptors.py index 1c91c7476..ed553070f 100644 --- a/mpas_analysis/shared/climatology/comparison_descriptors.py +++ b/mpas_analysis/shared/climatology/comparison_descriptors.py @@ -12,9 +12,10 @@ import numpy import pyproj -from ..constants import constants +from mpas_analysis.shared.constants import constants -from ..grid import LatLonGridDescriptor, ProjectionGridDescriptor +from mpas_analysis.shared.grid import LatLonGridDescriptor, \ + ProjectionGridDescriptor def get_comparison_descriptor(config, comparisonGridName): # {{{ diff --git a/mpas_analysis/shared/climatology/mpas_climatology_task.py b/mpas_analysis/shared/climatology/mpas_climatology_task.py index fa5d05824..231bf3203 100644 --- a/mpas_analysis/shared/climatology/mpas_climatology_task.py +++ b/mpas_analysis/shared/climatology/mpas_climatology_task.py @@ -7,9 +7,10 @@ import subprocess from distutils.spawn import find_executable -from ..analysis_task import AnalysisTask +from mpas_analysis.shared.analysis_task import AnalysisTask -from .climatology import get_unmasked_mpas_climatology_directory, \ +from mpas_analysis.shared.climatology.climatology import \ + get_unmasked_mpas_climatology_directory, \ get_unmasked_mpas_climatology_file_name diff --git a/mpas_analysis/shared/climatology/remap_mpas_climatology_subtask.py b/mpas_analysis/shared/climatology/remap_mpas_climatology_subtask.py index 3e9d55067..771e97649 100644 --- a/mpas_analysis/shared/climatology/remap_mpas_climatology_subtask.py +++ b/mpas_analysis/shared/climatology/remap_mpas_climatology_subtask.py @@ -6,20 +6,23 @@ import numpy import os -from ..analysis_task import AnalysisTask +from mpas_analysis.shared.analysis_task import AnalysisTask -from ..constants import constants +from mpas_analysis.shared.constants import constants -from ..io.utility import build_config_full_path, make_directories -from ..io import write_netcdf +from mpas_analysis.shared.io.utility import build_config_full_path, \ + make_directories +from mpas_analysis.shared.io import write_netcdf -from .climatology import get_remapper, get_masked_mpas_climatology_file_name, \ +from mpas_analysis.shared.climatology.climatology import get_remapper, \ + get_masked_mpas_climatology_file_name, \ get_remapped_mpas_climatology_file_name -from .comparison_descriptors import get_comparison_descriptor +from mpas_analysis.shared.climatology.comparison_descriptors import \ + get_comparison_descriptor -from ..grid import MpasMeshDescriptor +from mpas_analysis.shared.grid import MpasMeshDescriptor -from ..mpas_xarray import mpas_xarray +from mpas_analysis.shared.mpas_xarray import mpas_xarray class RemapMpasClimatologySubtask(AnalysisTask): # {{{ diff --git a/mpas_analysis/shared/climatology/remap_observed_climatology_subtask.py b/mpas_analysis/shared/climatology/remap_observed_climatology_subtask.py index ac4c14af6..ba39e3cbf 100644 --- a/mpas_analysis/shared/climatology/remap_observed_climatology_subtask.py +++ b/mpas_analysis/shared/climatology/remap_observed_climatology_subtask.py @@ -5,17 +5,19 @@ import os.path import xarray as xr -from ..analysis_task import AnalysisTask +from mpas_analysis.shared.analysis_task import AnalysisTask -from ..constants import constants +from mpas_analysis.shared.constants import constants -from ..io.utility import build_config_full_path, make_directories -from ..io import write_netcdf +from mpas_analysis.shared.io.utility import build_config_full_path, \ + make_directories +from mpas_analysis.shared.io import write_netcdf -from .climatology import get_remapper, remap_and_write_climatology, \ - compute_climatology +from mpas_analysis.shared.climatology.climatology import get_remapper, \ + remap_and_write_climatology, compute_climatology -from .comparison_descriptors import get_comparison_descriptor +from mpas_analysis.shared.climatology.comparison_descriptors import \ + get_comparison_descriptor class RemapObservedClimatologySubtask(AnalysisTask): # {{{ diff --git a/mpas_analysis/shared/containers.py b/mpas_analysis/shared/containers.py index a0b30f004..8c2583a85 100644 --- a/mpas_analysis/shared/containers.py +++ b/mpas_analysis/shared/containers.py @@ -10,7 +10,9 @@ unicode_literals import collections -class ReadOnlyDict(collections.Mapping): #{{{ + + +class ReadOnlyDict(collections.Mapping): # {{{ """ Read only-dictionary http://stackoverflow.com/questions/19022868/how-to-make-dictionary-read-only-in-python 310/22/2016 @@ -28,6 +30,6 @@ def __len__(self): def __iter__(self): return iter(self._data) -#}}} +# }}} # vim: foldmethod=marker ai ts=4 sts=4 et sw=4 ft=python diff --git a/mpas_analysis/shared/generalized_reader/__init__.py b/mpas_analysis/shared/generalized_reader/__init__.py index 6db020e3b..4e5b85ce4 100644 --- a/mpas_analysis/shared/generalized_reader/__init__.py +++ b/mpas_analysis/shared/generalized_reader/__init__.py @@ -1 +1,2 @@ -from .generalized_reader import open_multifile_dataset \ No newline at end of file +from mpas_analysis.shared.generalized_reader.generalized_reader import \ + open_multifile_dataset diff --git a/mpas_analysis/shared/generalized_reader/generalized_reader.py b/mpas_analysis/shared/generalized_reader/generalized_reader.py index a7c1c4375..87b357baa 100644 --- a/mpas_analysis/shared/generalized_reader/generalized_reader.py +++ b/mpas_analysis/shared/generalized_reader/generalized_reader.py @@ -21,8 +21,9 @@ from functools import partial import resource -from ..mpas_xarray import mpas_xarray -from ..timekeeping.utility import string_to_days_since_date, days_to_datetime +from mpas_analysis.shared.mpas_xarray import mpas_xarray +from mpas_analysis.shared.timekeeping.utility import \ + string_to_days_since_date, days_to_datetime def open_multifile_dataset(fileNames, calendar, config, diff --git a/mpas_analysis/shared/grid/__init__.py b/mpas_analysis/shared/grid/__init__.py index beffc841f..4155437f5 100644 --- a/mpas_analysis/shared/grid/__init__.py +++ b/mpas_analysis/shared/grid/__init__.py @@ -1,2 +1,2 @@ -from .grid import MpasMeshDescriptor, LatLonGridDescriptor, \ - ProjectionGridDescriptor, interp_extrap_corner +from mpas_analysis.shared.grid.grid import MpasMeshDescriptor, \ + LatLonGridDescriptor, ProjectionGridDescriptor, interp_extrap_corner diff --git a/mpas_analysis/shared/html/__init__.py b/mpas_analysis/shared/html/__init__.py index 209d380a7..85962d2ac 100644 --- a/mpas_analysis/shared/html/__init__.py +++ b/mpas_analysis/shared/html/__init__.py @@ -1,2 +1,3 @@ -from .pages import MainPage, ComponentPage, generate_html -from .image_xml import write_image_xml +from mpas_analysis.shared.html.pages import MainPage, ComponentPage, \ + generate_html +from mpas_analysis.shared.html.image_xml import write_image_xml diff --git a/mpas_analysis/shared/html/image_xml.py b/mpas_analysis/shared/html/image_xml.py index 001e62602..a05a8c2f4 100644 --- a/mpas_analysis/shared/html/image_xml.py +++ b/mpas_analysis/shared/html/image_xml.py @@ -11,7 +11,7 @@ from lxml import etree from PIL import Image -from ..io.utility import build_config_full_path +from mpas_analysis.shared.io.utility import build_config_full_path def write_image_xml(config, filePrefix, componentName, componentSubdirectory, diff --git a/mpas_analysis/shared/html/pages.py b/mpas_analysis/shared/html/pages.py index 7c3640228..97edc12d5 100644 --- a/mpas_analysis/shared/html/pages.py +++ b/mpas_analysis/shared/html/pages.py @@ -8,7 +8,7 @@ from lxml import etree from collections import OrderedDict -from ..io.utility import build_config_full_path +from mpas_analysis.shared.io.utility import build_config_full_path def generate_html(config, analyses, refConfig=None): # {{{ diff --git a/mpas_analysis/shared/interpolation/__init__.py b/mpas_analysis/shared/interpolation/__init__.py index 1de243cde..adae7c0b9 100644 --- a/mpas_analysis/shared/interpolation/__init__.py +++ b/mpas_analysis/shared/interpolation/__init__.py @@ -1 +1 @@ -from .remapper import Remapper +from mpas_analysis.shared.interpolation.remapper import Remapper diff --git a/mpas_analysis/shared/interpolation/remapper.py b/mpas_analysis/shared/interpolation/remapper.py index cd15ad393..50b455a77 100644 --- a/mpas_analysis/shared/interpolation/remapper.py +++ b/mpas_analysis/shared/interpolation/remapper.py @@ -25,8 +25,8 @@ import xarray as xr import sys -from ..grid import MpasMeshDescriptor, LatLonGridDescriptor, \ - ProjectionGridDescriptor +from mpas_analysis.shared.grid import MpasMeshDescriptor, \ + LatLonGridDescriptor, ProjectionGridDescriptor class Remapper(object): diff --git a/mpas_analysis/shared/io/__init__.py b/mpas_analysis/shared/io/__init__.py index daa194070..d369a423e 100644 --- a/mpas_analysis/shared/io/__init__.py +++ b/mpas_analysis/shared/io/__init__.py @@ -1,4 +1,6 @@ -from .namelist_streams_interface import NameList, StreamsFile -from .utility import paths -from .write_netcdf import write_netcdf -from .mpas_reader import open_mpas_dataset, subset_variables +from mpas_analysis.shared.io.namelist_streams_interface import NameList, \ + StreamsFile +from mpas_analysis.shared.io.utility import paths +from mpas_analysis.shared.io.write_netcdf import write_netcdf +from mpas_analysis.shared.io.mpas_reader import open_mpas_dataset, \ + subset_variables diff --git a/mpas_analysis/shared/io/mpas_reader.py b/mpas_analysis/shared/io/mpas_reader.py index 720d9f2fd..783bb6099 100644 --- a/mpas_analysis/shared/io/mpas_reader.py +++ b/mpas_analysis/shared/io/mpas_reader.py @@ -13,7 +13,8 @@ import six import xarray -from ..timekeeping.utility import string_to_days_since_date, days_to_datetime +from mpas_analysis.shared.timekeeping.utility import \ + string_to_days_since_date, days_to_datetime def open_mpas_dataset(fileName, calendar, diff --git a/mpas_analysis/shared/io/namelist_streams_interface.py b/mpas_analysis/shared/io/namelist_streams_interface.py index c09f2f98c..f0156e114 100644 --- a/mpas_analysis/shared/io/namelist_streams_interface.py +++ b/mpas_analysis/shared/io/namelist_streams_interface.py @@ -16,9 +16,9 @@ import re import os.path -from ..containers import ReadOnlyDict -from .utility import paths -from ..timekeeping.utility import string_to_datetime +from mpas_analysis.shared.containers import ReadOnlyDict +from mpas_analysis.shared.io.utility import paths +from mpas_analysis.shared.timekeeping.utility import string_to_datetime def convert_namelist_to_dict(fname, readonly=True): diff --git a/mpas_analysis/shared/mpas_xarray/mpas_xarray.py b/mpas_analysis/shared/mpas_xarray/mpas_xarray.py index c704ee1ac..6b63ce905 100644 --- a/mpas_analysis/shared/mpas_xarray/mpas_xarray.py +++ b/mpas_analysis/shared/mpas_xarray/mpas_xarray.py @@ -7,8 +7,9 @@ import xarray from functools import partial -from ..timekeeping.utility import string_to_days_since_date, \ - string_to_datetime, days_to_datetime, datetime_to_days +from mpas_analysis.shared.timekeeping.utility import \ + string_to_days_since_date, string_to_datetime, days_to_datetime, \ + datetime_to_days """ Utility functions for importing MPAS files into xarray. diff --git a/mpas_analysis/shared/plot/plotting.py b/mpas_analysis/shared/plot/plotting.py index bebeb6346..d60a2cbb0 100644 --- a/mpas_analysis/shared/plot/plotting.py +++ b/mpas_analysis/shared/plot/plotting.py @@ -23,9 +23,10 @@ from functools import partial from mpl_toolkits.axes_grid1 import make_axes_locatable -from ..timekeeping.utility import days_to_datetime, date_to_days +from mpas_analysis.shared.timekeeping.utility import days_to_datetime, \ + date_to_days -from ..constants import constants +from mpas_analysis.shared.constants import constants from six.moves import configparser diff --git a/mpas_analysis/shared/time_series/__init__.py b/mpas_analysis/shared/time_series/__init__.py index 787036001..627ff0408 100644 --- a/mpas_analysis/shared/time_series/__init__.py +++ b/mpas_analysis/shared/time_series/__init__.py @@ -1,5 +1,7 @@ -from .time_series import cache_time_series -from .mpas_time_series_task import MpasTimeSeriesTask +from mpas_analysis.shared.time_series.time_series import cache_time_series +from mpas_analysis.shared.time_series.mpas_time_series_task import \ + MpasTimeSeriesTask -from .anomaly import compute_moving_avg_anomaly_from_start -from .moving_average import compute_moving_avg +from mpas_analysis.shared.time_series.anomaly import \ + compute_moving_avg_anomaly_from_start +from mpas_analysis.shared.time_series.moving_average import compute_moving_avg diff --git a/mpas_analysis/shared/time_series/anomaly.py b/mpas_analysis/shared/time_series/anomaly.py index 46a2d4ae8..0dfac5419 100644 --- a/mpas_analysis/shared/time_series/anomaly.py +++ b/mpas_analysis/shared/time_series/anomaly.py @@ -3,8 +3,8 @@ from __future__ import absolute_import, division, print_function, \ unicode_literals -from ..io import open_mpas_dataset -from .moving_average import compute_moving_avg +from mpas_analysis.shared.io import open_mpas_dataset +from mpas_analysis.shared.time_series.moving_average import compute_moving_avg def compute_moving_avg_anomaly_from_start(timeSeriesFileName, variableList, diff --git a/mpas_analysis/shared/time_series/mpas_time_series_task.py b/mpas_analysis/shared/time_series/mpas_time_series_task.py index 53c108daf..75755bcf8 100644 --- a/mpas_analysis/shared/time_series/mpas_time_series_task.py +++ b/mpas_analysis/shared/time_series/mpas_time_series_task.py @@ -8,10 +8,11 @@ import xarray as xr import numpy -from ..analysis_task import AnalysisTask +from mpas_analysis.shared.analysis_task import AnalysisTask -from ..io.utility import build_config_full_path, make_directories -from ..timekeeping.utility import get_simulation_start_time +from mpas_analysis.shared.io.utility import \ + build_config_full_path, make_directories +from mpas_analysis.shared.timekeeping.utility import get_simulation_start_time class MpasTimeSeriesTask(AnalysisTask): # {{{ diff --git a/mpas_analysis/shared/time_series/time_series.py b/mpas_analysis/shared/time_series/time_series.py index 76df1ab20..4dc1d6b85 100644 --- a/mpas_analysis/shared/time_series/time_series.py +++ b/mpas_analysis/shared/time_series/time_series.py @@ -13,7 +13,7 @@ import numpy import os -from ..timekeeping.utility import days_to_datetime +from mpas_analysis.shared.timekeeping.utility import days_to_datetime def cache_time_series(timesInDataSet, timeSeriesCalcFunction, cacheFileName, diff --git a/mpas_analysis/shared/timekeeping/utility.py b/mpas_analysis/shared/timekeeping/utility.py index 84a598cbc..7ddb49503 100644 --- a/mpas_analysis/shared/timekeeping/utility.py +++ b/mpas_analysis/shared/timekeeping/utility.py @@ -14,7 +14,8 @@ import numpy import six -from .MpasRelativeDelta import MpasRelativeDelta +from mpas_analysis.shared.timekeeping.MpasRelativeDelta import \ + MpasRelativeDelta def get_simulation_start_time(streams): diff --git a/mpas_analysis/test/test_mpas_config_parser.py b/mpas_analysis/test/test_mpas_config_parser.py index 38944f287..fca487ff5 100644 --- a/mpas_analysis/test/test_mpas_config_parser.py +++ b/mpas_analysis/test/test_mpas_config_parser.py @@ -13,7 +13,7 @@ from six.moves import configparser from mpas_analysis.test import TestCase, loaddatadir from mpas_analysis.configuration import MpasAnalysisConfigParser -from . import requires_numpy +from mpas_analysis.test import requires_numpy @pytest.mark.usefixtures("loaddatadir") From 3929ac011ceae1efda2996bd300a3599bf71084b Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Thu, 1 Feb 2018 18:08:01 -0700 Subject: [PATCH 05/71] Parse file-name templates from streams The filename_template attribute can now be parsed into a format that datetime.strptime can use to extract the year, month, etc. from a file name. --- mpas_analysis/ocean/streamfunction_moc.py | 12 ++++--- .../shared/io/namelist_streams_interface.py | 34 +++++++++++++++++++ 2 files changed, 42 insertions(+), 4 deletions(-) diff --git a/mpas_analysis/ocean/streamfunction_moc.py b/mpas_analysis/ocean/streamfunction_moc.py index 04c9d8a3a..2727909c0 100644 --- a/mpas_analysis/ocean/streamfunction_moc.py +++ b/mpas_analysis/ocean/streamfunction_moc.py @@ -9,7 +9,7 @@ import os from mpas_analysis.shared.constants.constants import m3ps_to_Sv -from mpas_analysis.shared.plot.plotting import plot_vertical_section,\ +from mpas_analysis.shared.plot.plotting import plot_vertical_section, \ timeseries_analysis_plot, setup_colormap from mpas_analysis.shared.io.utility import build_config_full_path, \ @@ -485,9 +485,13 @@ def _compute_moc_time_series_postprocess(self): # {{{ streamName, startDate=self.startDateTseries, endDate=self.endDateTseries, calendar=self.calendar)) - dates = sorted([fileName[-13:-6] for fileName in inputFilesTseries]) - years = np.array([int(date[0:4]) for date in dates]) - months = np.array([int(date[5:7]) for date in dates]) + template = self.historyStreams.read_datetime_template(streamName) + template = os.path.basename(template) + dts = [datetime.strptime(os.path.basename(fileName), template) for + fileName in inputFilesTseries] + + years = [dt.year for dt in dts] + months = [dt.month for dt in dts] mocRegion = np.zeros(len(inputFilesTseries)) times = np.zeros(len(inputFilesTseries)) diff --git a/mpas_analysis/shared/io/namelist_streams_interface.py b/mpas_analysis/shared/io/namelist_streams_interface.py index f0156e114..8ccf41c0c 100644 --- a/mpas_analysis/shared/io/namelist_streams_interface.py +++ b/mpas_analysis/shared/io/namelist_streams_interface.py @@ -329,6 +329,40 @@ def read(self, streamname, attribname): return stream.get(attribname) return None + def read_datetime_template(self, streamname): + """ + Get the value of the given attribute in the given stream + + Parameters + ---------- + streamname : str + The name of the stream + + Returns + ------- + value : str + The template for file names from this stream in a format accepted + by ``datetime.strptime``. This is useful for parsing the date + from a given file name. + + Authors + ------- + Xylar Asay-Davis + """ + template = self.read(streamname, 'filename_template') + replacements = {'$Y': '%Y', + '$M': '%m', + '$D': '%d', + '$S': '00000', # datetime doesn't handle seconds alone + '$h': '%H', + '$m': '%M', + '$s': '%S'} + + for old in replacements: + template = template.replace(old, replacements[old]) + + return template + def readpath(self, streamName, startDate=None, endDate=None, calendar=None): """ From 57c66aa58001b9bbc93e5f79e9191540aee52d92 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Thu, 1 Feb 2018 18:10:17 -0700 Subject: [PATCH 06/71] Use template to parse dates from monthly mean files Instead of relying on monthly mean files having the E3SM file format, parse the year and month using the filename_template attribute from the stream. --- mpas_analysis/ocean/streamfunction_moc.py | 12 ++---- .../climatology/mpas_climatology_task.py | 9 +++-- mpas_analysis/shared/io/utility.py | 40 ++++++++++++++++++- .../time_series/mpas_time_series_task.py | 25 +++++++----- 4 files changed, 63 insertions(+), 23 deletions(-) diff --git a/mpas_analysis/ocean/streamfunction_moc.py b/mpas_analysis/ocean/streamfunction_moc.py index 2727909c0..ef310ad3b 100644 --- a/mpas_analysis/ocean/streamfunction_moc.py +++ b/mpas_analysis/ocean/streamfunction_moc.py @@ -13,7 +13,7 @@ timeseries_analysis_plot, setup_colormap from mpas_analysis.shared.io.utility import build_config_full_path, \ - make_directories + make_directories, get_files_year_month from mpas_analysis.shared.io import open_mpas_dataset @@ -485,13 +485,9 @@ def _compute_moc_time_series_postprocess(self): # {{{ streamName, startDate=self.startDateTseries, endDate=self.endDateTseries, calendar=self.calendar)) - template = self.historyStreams.read_datetime_template(streamName) - template = os.path.basename(template) - dts = [datetime.strptime(os.path.basename(fileName), template) for - fileName in inputFilesTseries] - - years = [dt.year for dt in dts] - months = [dt.month for dt in dts] + years, months = get_files_year_month(inputFilesTseries, + self.historyStreams, + 'timeSeriesStatsMonthlyOutput') mocRegion = np.zeros(len(inputFilesTseries)) times = np.zeros(len(inputFilesTseries)) diff --git a/mpas_analysis/shared/climatology/mpas_climatology_task.py b/mpas_analysis/shared/climatology/mpas_climatology_task.py index 231bf3203..6c08faaa6 100644 --- a/mpas_analysis/shared/climatology/mpas_climatology_task.py +++ b/mpas_analysis/shared/climatology/mpas_climatology_task.py @@ -13,6 +13,8 @@ get_unmasked_mpas_climatology_directory, \ get_unmasked_mpas_climatology_file_name +from ..io.utility import get_files_year_month + class MpasClimatologyTask(AnalysisTask): # {{{ ''' @@ -262,9 +264,10 @@ def _update_climatology_bounds_from_file_names(self): # {{{ requestedStartYear = config.getint('climatology', 'startYear') requestedEndYear = config.getint('climatology', 'endYear') - dates = sorted([fileName[-13:-6] for fileName in self.inputFiles]) - years = [int(date[0:4]) for date in dates] - months = [int(date[5:7]) for date in dates] + fileNames = sorted(self.inputFiles) + years, months = get_files_year_month(fileNames, + self.historyStreams, + 'timeSeriesStatsMonthlyOutput') # search for the start of the first full year firstIndex = 0 diff --git a/mpas_analysis/shared/io/utility.py b/mpas_analysis/shared/io/utility.py index 1be5d61ca..0a8923216 100644 --- a/mpas_analysis/shared/io/utility.py +++ b/mpas_analysis/shared/io/utility.py @@ -11,6 +11,7 @@ import os import random import string +from datetime import datetime def paths(*args): # {{{ @@ -95,7 +96,7 @@ def make_directories(path): # {{{ def build_config_full_path(config, section, relativePathOption, relativePathSection=None, - defaultPath=None): # {{{ + defaultPath=None): # {{{ """ Returns a full path from a base directory and a relative path @@ -134,7 +135,7 @@ def build_config_full_path(config, section, relativePathOption, if defaultPath is not None and not os.path.exists(fullPath): fullPath = defaultPath - return fullPath # }}} + return fullPath # }}} def check_path_exists(path): # {{{ @@ -159,4 +160,39 @@ def check_path_exists(path): # {{{ raise OSError('Path {} not found'.format(path)) # }}} +def get_files_year_month(fileNames, streamsFile, streamName): # {{{ + """ + Extract the year and month from file names associated with a stream + + Parameters + ---------- + fileNames : list of str + The names of files with a year and month in their names. + + streamsFile : ``StreamsFile`` + The parsed streams file, used to get a template for the + + streamName : str + The name of the stream with a file-name template for ``fileNames`` + + Returns + ------- + years, months : list of int + The years and months for each file in ``fileNames`` + + Authors + ------- + Xylar Asay-Davis + """ + + template = streamsFile.read_datetime_template(streamName) + template = os.path.basename(template) + dts = [datetime.strptime(os.path.basename(fileName), template) for + fileName in fileNames] + + years = [dt.year for dt in dts] + months = [dt.month for dt in dts] + + return years, months # }}} + # vim: foldmethod=marker ai ts=4 sts=4 et sw=4 ft=python diff --git a/mpas_analysis/shared/time_series/mpas_time_series_task.py b/mpas_analysis/shared/time_series/mpas_time_series_task.py index 75755bcf8..2c194415a 100644 --- a/mpas_analysis/shared/time_series/mpas_time_series_task.py +++ b/mpas_analysis/shared/time_series/mpas_time_series_task.py @@ -10,8 +10,8 @@ from mpas_analysis.shared.analysis_task import AnalysisTask -from mpas_analysis.shared.io.utility import \ - build_config_full_path, make_directories +from mpas_analysis.shared.io.utility import build_config_full_path, \ + make_directories, get_files_year_month from mpas_analysis.shared.timekeeping.utility import get_simulation_start_time @@ -211,9 +211,10 @@ def _update_time_series_bounds_from_file_names(self): # {{{ requestedStartYear = config.getint(section, 'startYear') requestedEndYear = config.getint(section, 'endYear') - dates = sorted([fileName[-13:-6] for fileName in self.inputFiles]) - years = [int(date[0:4]) for date in dates] - months = [int(date[5:7]) for date in dates] + fileNames = sorted(self.inputFiles) + years, months = get_files_year_month(fileNames, + self.historyStreams, + 'timeSeriesStatsMonthlyOutput') # search for the start of the first full year firstIndex = 0 @@ -289,10 +290,14 @@ def _compute_time_series_with_ncrcat(self): if updateSubset: # add only input files wiht times that aren't already in # the output file - dates = sorted([fileName[-13:-6] for fileName in - self.inputFiles]) - inYears = numpy.array([int(date[0:4]) for date in dates]) - inMonths = numpy.array([int(date[5:7]) for date in dates]) + + fileNames = sorted(self.inputFiles) + inYears, inMonths = get_files_year_month( + fileNames, self.historyStreams, + 'timeSeriesStatsMonthlyOutput') + + inYears = numpy.array(inYears) + inMonths = numpy.array(inMonths) totalMonths = 12*inYears + inMonths dates = [bytes.decode(name) for name in @@ -304,7 +309,7 @@ def _compute_time_series_with_ncrcat(self): lastTotalMonths = 12*lastYear + lastMonth inputFiles = [] - for index, inputFile in enumerate(self.inputFiles): + for index, inputFile in enumerate(fileNames): if totalMonths[index] > lastTotalMonths: inputFiles.append(inputFile) From b1064cd64c42261d9b96d394724aaaa94e92a3db Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Thu, 1 Feb 2018 20:48:00 -0700 Subject: [PATCH 07/71] Create symlinks to timeSeriesStatsMonthly output This allows us to use ncclimo even when a standalone MPAS run has used different file-naming conventions than ncclimo supports. --- .../climatology/mpas_climatology_task.py | 39 ++++++++++++++++--- 1 file changed, 34 insertions(+), 5 deletions(-) diff --git a/mpas_analysis/shared/climatology/mpas_climatology_task.py b/mpas_analysis/shared/climatology/mpas_climatology_task.py index 6c08faaa6..e4d4d2e73 100644 --- a/mpas_analysis/shared/climatology/mpas_climatology_task.py +++ b/mpas_analysis/shared/climatology/mpas_climatology_task.py @@ -13,7 +13,8 @@ get_unmasked_mpas_climatology_directory, \ get_unmasked_mpas_climatology_file_name -from ..io.utility import get_files_year_month +from ..io.utility import build_config_full_path, make_directories, \ + get_files_year_month class MpasClimatologyTask(AnalysisTask): # {{{ @@ -170,7 +171,8 @@ def setup_and_check(self): # {{{ raise IOError('No files were found in stream {} between {} and ' '{}.'.format(streamName, startDate, endDate)) - self._update_climatology_bounds_from_file_names() + self.symlinkDirectory = \ + self._update_climatology_bounds_and_create_symlinks() # }}} @@ -219,7 +221,7 @@ def run_task(self): # {{{ if not allExist: self._compute_climatologies_with_ncclimo( - inDirectory=self.historyDirectory, + inDirectory=self.symlinkDirectory, outDirectory=climatologyDirectory) # }}} @@ -249,10 +251,18 @@ def get_file_name(self, season): # {{{ # }}} - def _update_climatology_bounds_from_file_names(self): # {{{ + def _update_climatology_bounds_and_create_symlinks(self): # {{{ """ Update the start and end years and dates for climatologies based on the - years actually available in the list of files. + years actually available in the list of files. Create symlinks to + monthly mean files so they have the expected file naming convention + for ncclimo. + + Returns + ------- + symlinkDirectory : str + The path to the symlinks created for each timeSeriesStatsMonthly + input file Authors ------- @@ -306,6 +316,25 @@ def _update_climatology_bounds_from_file_names(self): # {{{ self.startYear = startYear self.endYear = endYear + # now, create the symlinks + climatologyBaseDirectory = build_config_full_path( + config, 'output', 'mpasClimatologySubdirectory') + + symlinkDirectory = '{}/source_symlinks'.format( + climatologyBaseDirectory) + + make_directories(symlinkDirectory) + + for inFileName, year, month in zip(fileNames, years, months): + outFileName = '{}/{}.hist.am.timeSeriesStatsMonthly.{:04d}-' \ + '{:02d}-01.nc'.format(symlinkDirectory, self.ncclimoModel, + year, month) + + if not os.path.exists(outFileName): + os.symlink(inFileName, outFileName) + + return symlinkDirectory + # }}} def _compute_climatologies_with_ncclimo(self, inDirectory, outDirectory, From 7034195b2dbdad9b8515c478320a86543675d058 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Fri, 2 Feb 2018 16:28:15 -0700 Subject: [PATCH 08/71] Document setup for standalone MPAS Standalone MPAS runs need to be set up with the proper analysis members enabled and streams defined. These are now described in the documentation. Authors are now included at the end of the documentation. --- docs/authors.rst | 19 ++++++ docs/e3sm.rst | 20 ++++++ docs/index.rst | 20 +++++- docs/mpascice.rst | 63 +++++++++++++++++++ docs/mpaso.rst | 156 ++++++++++++++++++++++++++++++++++++++++++++++ 5 files changed, 277 insertions(+), 1 deletion(-) create mode 100644 docs/authors.rst create mode 100644 docs/e3sm.rst create mode 100644 docs/mpascice.rst create mode 100644 docs/mpaso.rst diff --git a/docs/authors.rst b/docs/authors.rst new file mode 100644 index 000000000..3b67178e5 --- /dev/null +++ b/docs/authors.rst @@ -0,0 +1,19 @@ +Main Authors +============ +* Xylar Asay-Davis +* Milena Veniziani +* Philip Wolfram + +Contributors +============ +* Luke Van Roekel +* Greg Streletz +* Mark Petersen +* Stephen Price +* Joseph Kennedy +* Adrian Turner +* Matthew Hoffman +* Jeremy Fyke + +For a list of all the contributions: +https://github.com/MPAS-Dev/MPAS-Analysis/graphs/contributors \ No newline at end of file diff --git a/docs/e3sm.rst b/docs/e3sm.rst new file mode 100644 index 000000000..435c79f7e --- /dev/null +++ b/docs/e3sm.rst @@ -0,0 +1,20 @@ +E3SM +==== + +The Energy Exascale Earth System Model (E3SM) project, previously known as +ACME, is central to ESM as well as many of the Climate and Environmental +Sciences Division activities, as it is developing a computationally advanced +coupled climate-energy model to investigate the challenges posed by the +interactions of weather-climate scale variability with energy and related +sectors. + +A Full description of E3SM is available at: +https://climatemodeling.science.energy.gov/projects/energy-exascale-earth-system-model + +Setting up E3SM runs +-------------------- + +All online analysis and output stream within MPAS components (MPAS-O and +MPAS-SeaIce) are configured to support MPAS-Analysis without any modifications +to namelists or streams files. + diff --git a/docs/index.rst b/docs/index.rst index 1bdbce629..0431d85e6 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -23,7 +23,25 @@ Documentation api design_docs +MPAS Components and E3SM +======================== + +.. toctree:: + :maxdepth: 2 + + mpaso + mpascice + e3sm + + Indices and tables ================== -* :ref:`genindex` \ No newline at end of file +* :ref:`genindex` + +Authors +======= +.. toctree:: + :maxdepth: 1 + + authors diff --git a/docs/mpascice.rst b/docs/mpascice.rst new file mode 100644 index 000000000..ce1a3c46f --- /dev/null +++ b/docs/mpascice.rst @@ -0,0 +1,63 @@ +MPAS Sea Ice +============ + +The Model for Prediction Across Scales Sea Ice (MPAS Sea Ice, sometimes called +MPAS-CICE because of the physics it has inherited from the CICE sea-ice model) +is designed for the simulations of sea ice on unstructured grids supported by +the MPAS framework. The model has not yet been publicly released and does not +have public documentation. + +Setting up Standalone MPAS Sea Ice Runs +--------------------------------------- + +In order to support all sea=ice analysis tasks from MPAS-Analysis, certain +"analysis members", Fortran modules that perform analysis during the +simulation, need to be enabled. + +The following is a list of suggested values for namelist options, typically +found in ``namelist.cice`` or ``mpas-cice_in``:: + + config_AM_timeSeriesStatsMonthly_enable = .true. + +Additionally, the duration of the run should be set to at least two years and +typically longer before most analysis is useful:: + + config_run_duration = '0002-00-00_00:00:00' + +Several streams must be defined in the streams file, typically +``streams.cice``, (even if they will not be written out -- +``output_interval=="none"``):: + + + + + + + + + + + + +The ``filename_tempalate`` can be modified as desired (these are the defalult +values from E3SM). For the ``timeSeriesStatsMonthlyOutput`` stream, both the +filename_interval and the output_interval must currently be monthly +(``"0000-01-00_00:00:00"``). + +Additional fields can be included in the ``timeSeriesStatsMonthlyOutput`` +streams. These are the minimum that allow the analysis to run successfully. diff --git a/docs/mpaso.rst b/docs/mpaso.rst new file mode 100644 index 000000000..f84e21d33 --- /dev/null +++ b/docs/mpaso.rst @@ -0,0 +1,156 @@ +MPAS Ocean +========== + +The Model for Prediction Across Scales Ocean (MPAS-O) is designed for the +simulation of the ocean system from time scales of months to millenia and +spatial scales from sub 1 km to global circulations. + +MPAS-O has demonstrated the ability to accurately reproduce mesoscale ocean +activity with a local mesh refinement strategy. + +In addition to faciliating the study of multiscale phenomena within the ocean +system, MPAS-O is intended for the study of anthropogenic climate change as +the ocean component of climate system models. + + +Full documentaiton is available at: +https://mpas-dev.github.io/ocean/ocean.html + +Setting up Standalone MPAS-O Runs +--------------------------------- + +In order to support all ocean analysis tasks from MPAS-Analysis, certain +"analysis members", Fortran modules that perform analysis during the +simulation, need to be enabled. + +The following is a list of suggested values for namelist options, typically +found in ``namelist.ocean`` or ``mpas-o_in``:: + + config_AM_surfaceAreaWeightedAverages_enable = .true. + config_AM_surfaceAreaWeightedAverages_compute_interval = '0000-00-00_01:00:00' + config_AM_layerVolumeWeightedAverage_enable = .true. + config_AM_layerVolumeWeightedAverage_compute_interval = '0000-00-00_01:00:00' + config_AM_meridionalHeatTransport_enable = .true. + config_AM_meridionalHeatTransport_compute_interval = '0000-00-00_01:00:00' + config_AM_mixedLayerDepths_enable = .true. + config_AM_timeSeriesStatsMonthly_enable = .true. + +Additionally, the duration of the run should be set to at least two years and +typically longer before most analysis is useful:: + + config_run_duration = '0002-00-00_00:00:00' + +Several streams must be defined in the streams file, typically +``streams.ocean``, (even if they will not be written out -- +``output_intervale=="none"``):: + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +The ``filename_tempalate`` can be modified as desired (in most cases, these are +the defalult values from E3SM). For the ``timeSeriesStatsMonthlyOutput`` +stream, both the filename_interval and the output_interval must currently be +monthly (``"0000-01-00_00:00:00"``). + +Additional fields can be included in the ``timeSeriesStatsMonthlyOutput`` +streams. These are the minimum that allow the analysis to run successfully. From e0dc22c8555e4255e75a4240480afaacff482353 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Sat, 3 Feb 2018 11:56:04 -0700 Subject: [PATCH 09/71] Update CI test based on recent changes --- mpas_analysis/test/test_mpas_climatology_task.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/mpas_analysis/test/test_mpas_climatology_task.py b/mpas_analysis/test/test_mpas_climatology_task.py index e336043cb..61e836856 100644 --- a/mpas_analysis/test/test_mpas_climatology_task.py +++ b/mpas_analysis/test/test_mpas_climatology_task.py @@ -112,7 +112,7 @@ def test_run_analysis(self): fileName = mpasClimatologyTask.get_file_name(season=season) assert(os.path.exists(fileName)) - def test_update_climatology_bounds_from_file_names(self): + def test_update_climatology_bounds_and_create_symlinks(self): mpasClimatologyTask = self.setup_task() config = mpasClimatologyTask.config @@ -123,7 +123,7 @@ def test_update_climatology_bounds_from_file_names(self): startDate = '{:04d}-01-01_00:00:00'.format(startYear) endDate = '{:04d}-12-31_23:59:59'.format(endYear) - mpasClimatologyTask._update_climatology_bounds_from_file_names() + mpasClimatologyTask._update_climatology_bounds_and_create_symlinks() assert(mpasClimatologyTask.startYear == startYear) assert(mpasClimatologyTask.endYear == endYear) @@ -142,7 +142,7 @@ def test_update_climatology_bounds_from_file_names(self): config.set('climatology', 'startDate', startDate) config.set('climatology', 'endDate', endDate) - mpasClimatologyTask._update_climatology_bounds_from_file_names() + mpasClimatologyTask._update_climatology_bounds_and_create_symlinks() startYear = 2 endYear = 2 From 73dc51d8fa6cc7bdacc1e8852a761f1d406a28ed Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Sun, 26 Nov 2017 18:01:22 +0100 Subject: [PATCH 10/71] Add a task for plotting the sea surface height vs. obs Uses the AVISO time series on the 1 degree grid. --- mpas_analysis/config.default | 27 +++ mpas_analysis/ocean/__init__.py | 1 + mpas_analysis/ocean/climatology_map_ssh.py | 209 +++++++++++++++++++++ run_mpas_analysis | 3 + 4 files changed, 240 insertions(+) create mode 100644 mpas_analysis/ocean/climatology_map_ssh.py diff --git a/mpas_analysis/config.default b/mpas_analysis/config.default index a96053572..292e78ddc 100644 --- a/mpas_analysis/config.default +++ b/mpas_analysis/config.default @@ -212,6 +212,7 @@ ninoSubdirectory = Nino mhtSubdirectory = MHT meltSubdirectory = Melt soseSubdirectory = SOSE +sshSubdirectory = SSH # first and last year of SST observational climatology (preferably one of the # two ranges given below) @@ -582,6 +583,32 @@ seasons = ['JFM', 'JAS', 'ANN'] # comparison grid(s) ('latlon', 'antarctic') on which to plot analysis comparisonGrids = ['latlon'] +[climatologyMapSSH] +## options related to plotting horizontally remapped climatologies of +## sea surface height (SSH) against reference model results and observations + +# colormap for model/observations +colormapNameResult = Spectral_r +# color indices into colormapName for filled contours +colormapIndicesResult = [0, 20, 40, 80, 100, 120, 160, 180, 200, 240, 255] +# colormap levels/values for contour boundaries +colorbarLevelsResult = [-2.4, -2, -1.6, -1.2, -0.8, -0.4, 0, 0.4, 0.8, 1.2] + +# colormap for differences +colormapNameDifference = RdBu_r +# color indices into colormapName for filled contours +colormapIndicesDifference = [0, 23, 46, 70, 93, 116, 128, 128, 139, 162, 185, 209, 232, 255] +# colormap levels/values for contour boundaries +colorbarLevelsDifference = [-1., -0.8, -0.6, -0.4, -0.2, -0.1, 0., 0.1, 0.2, 0.4, 0.6, 0.8, 1.] + +# Times for comparison times (Jan, Feb, Mar, Apr, May, Jun, Jul, Aug, Sep, Oct, +# Nov, Dec, JFM, AMJ, JAS, OND, ANN) +seasons = ['JFM', 'JAS', 'ANN'] + +# comparison grid(s) ('latlon', 'antarctic') on which to plot analysis +comparisonGrids = ['latlon'] + + [climatologyMapAntarcticMelt] ## options related to plotting horizontally regridded maps of Antarctic ## sub-ice-shelf melt rates against reference model results and observations diff --git a/mpas_analysis/ocean/__init__.py b/mpas_analysis/ocean/__init__.py index 2a8097a67..359795fb5 100644 --- a/mpas_analysis/ocean/__init__.py +++ b/mpas_analysis/ocean/__init__.py @@ -1,6 +1,7 @@ from mpas_analysis.ocean.climatology_map_sst import ClimatologyMapSST from mpas_analysis.ocean.climatology_map_mld import ClimatologyMapMLD from mpas_analysis.ocean.climatology_map_sss import ClimatologyMapSSS +from mpas_analysis.ocean.climatology_map_ssh import ClimatologyMapSSH from mpas_analysis.ocean.climatology_map_antarctic_melt import \ ClimatologyMapAntarcticMelt from mpas_analysis.ocean.climatology_map_sose import \ diff --git a/mpas_analysis/ocean/climatology_map_ssh.py b/mpas_analysis/ocean/climatology_map_ssh.py new file mode 100644 index 000000000..54be7bea2 --- /dev/null +++ b/mpas_analysis/ocean/climatology_map_ssh.py @@ -0,0 +1,209 @@ +from __future__ import absolute_import, division, print_function, \ + unicode_literals + +import xarray as xr + +from mpas_analysis.shared import AnalysisTask + +from mpas_analysis.shared.io.utility import build_config_full_path + +from mpas_analysis.shared.climatology import RemapMpasClimatologySubtask, \ + RemapObservedClimatologySubtask + +from mpas_analysis.ocean.plot_climatology_map_subtask import \ + PlotClimatologyMapSubtask + +from mpas_analysis.shared.grid import LatLonGridDescriptor + + +class ClimatologyMapSSH(AnalysisTask): # {{{ + """ + An analysis task for comparison of sea surface height (ssh) against + observations + + Authors + ------- + Xylar Asay-Davis + """ + def __init__(self, config, mpasClimatologyTask, + refConfig=None): # {{{ + """ + Construct the analysis task. + + Parameters + ---------- + config : ``MpasAnalysisConfigParser`` + Configuration options + + mpasClimatologyTask : ``MpasClimatologyTask`` + The task that produced the climatology to be remapped and plotted + + refConfig : ``MpasAnalysisConfigParser``, optional + Configuration options for a reference run (if any) + + Authors + ------- + Xylar Asay-Davis + """ + fieldName = 'ssh' + # call the constructor from the base class (AnalysisTask) + super(ClimatologyMapSSH, self).__init__( + config=config, taskName='climatologyMapSSH', + componentName='ocean', + tags=['climatology', 'horizontalMap', fieldName]) + + mpasFieldName = 'timeMonthly_avg_ssh' + iselValues = None + + sectionName = self.taskName + + # read in what seasons we want to plot + seasons = config.getExpression(sectionName, 'seasons') + + if len(seasons) == 0: + raise ValueError('config section {} does not contain valid list ' + 'of seasons'.format(sectionName)) + + comparisonGridNames = config.getExpression(sectionName, + 'comparisonGrids') + + if len(comparisonGridNames) == 0: + raise ValueError('config section {} does not contain valid list ' + 'of comparison grids'.format(sectionName)) + + # the variable mpasFieldName will be added to mpasClimatologyTask + # along with the seasons. + remapClimatologySubtask = RemapMpasClimatologySubtask( + mpasClimatologyTask=mpasClimatologyTask, + parentTask=self, + climatologyName=fieldName, + variableList=[mpasFieldName], + comparisonGridNames=comparisonGridNames, + seasons=seasons, + iselValues=iselValues) + + if refConfig is None: + + refTitleLabel = 'Observations (AVISO sea-level anomaly)' + + observationsDirectory = build_config_full_path( + config, 'oceanObservations', + '{}Subdirectory'.format(fieldName)) + + obsFileName = \ + "{}/zos_AVISO_L4_199210-201012.nc".format( + observationsDirectory) + refFieldName = 'zos' + outFileLabel = 'sshAVISO' + galleryName = 'Observations: AVISO' + + remapObservationsSubtask = RemapObservedSSHClimatology( + parentTask=self, seasons=seasons, fileName=obsFileName, + outFilePrefix=refFieldName, + comparisonGridNames=comparisonGridNames) + self.add_subtask(remapObservationsSubtask) + diffTitleLabel = 'Model - Observations' + + else: + remapObservationsSubtask = None + refRunName = refConfig.get('runs', 'mainRunName') + galleryName = None + refTitleLabel = 'Ref: {}'.format(refRunName) + + refFieldName = mpasFieldName + outFileLabel = 'ssh' + diffTitleLabel = 'Main - Reference' + + for comparisonGridName in comparisonGridNames: + for season in seasons: + # make a new subtask for this season and comparison grid + subtask = PlotClimatologyMapSubtask(self, season, + comparisonGridName, + remapClimatologySubtask, + remapObservationsSubtask, + refConfig) + + subtask.set_plot_info( + outFileLabel=outFileLabel, + fieldNameInTitle='SSH', + mpasFieldName=mpasFieldName, + refFieldName=refFieldName, + refTitleLabel=refTitleLabel, + diffTitleLabel=diffTitleLabel, + unitsLabel=r'm', + imageCaption='Mean Sea Surface Height', + galleryGroup='Sea Surface Height', + groupSubtitle=None, + groupLink='ssh', + galleryName=galleryName) + + self.add_subtask(subtask) + # }}} + # }}} + + +class RemapObservedSSHClimatology(RemapObservedClimatologySubtask): # {{{ + """ + A subtask for reading and remapping SSH observations + + Authors + ------- + Xylar Asay-Davis + """ + + def get_observation_descriptor(self, fileName): # {{{ + ''' + get a MeshDescriptor for the observation grid + + Parameters + ---------- + fileName : str + observation file name describing the source grid + + Returns + ------- + obsDescriptor : ``MeshDescriptor`` + The descriptor for the observation grid + + Authors + ------- + Xylar Asay-Davis + ''' + + # create a descriptor of the observation grid using the lat/lon + # coordinates + obsDescriptor = LatLonGridDescriptor.read(fileName=fileName, + latVarName='lat', + lonVarName='lon') + return obsDescriptor # }}} + + def build_observational_dataset(self, fileName): # {{{ + ''' + read in the data sets for observations, and possibly rename some + variables and dimensions + + Parameters + ---------- + fileName : str + observation file name + + Returns + ------- + dsObs : ``xarray.Dataset`` + The observational dataset + + Authors + ------- + Xylar Asay-Davis + ''' + + dsObs = xr.open_dataset(fileName) + dsObs.rename({'time': 'Time'}, inplace=True) + dsObs.coords['month'] = dsObs['Time.month'] + dsObs.coords['year'] = dsObs['Time.year'] + + return dsObs # }}} + + # }}} + +# vim: foldmethod=marker ai ts=4 sts=4 et sw=4 ft=python diff --git a/run_mpas_analysis b/run_mpas_analysis index 53d1de451..9c4aa4e1b 100755 --- a/run_mpas_analysis +++ b/run_mpas_analysis @@ -85,6 +85,8 @@ def build_analysis_list(config, refConfig): # {{{ refConfig)) analyses.append(ocean.ClimatologyMapSSS(config, oceanClimatolgyTask, refConfig)) + analyses.append(ocean.ClimatologyMapSSH(config, oceanClimatolgyTask, + refConfig)) analyses.append(ocean.ClimatologyMapSoseTemperature( config, oceanClimatolgyTask, refConfig)) analyses.append(ocean.ClimatologyMapSoseSalinity( @@ -107,6 +109,7 @@ def build_analysis_list(config, refConfig): # {{{ refConfig)) analyses.append(ocean.MeridionalHeatTransport(config, oceanClimatolgyTask, refConfig)) + analyses.append(ocean.StreamfunctionMOC(config, oceanClimatolgyTask)) analyses.append(ocean.IndexNino34(config, oceanIndexTask, refConfig)) From b89f6ebc4c9c98333707f83a6bbe4211c642916e Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Wed, 21 Feb 2018 20:59:44 -0700 Subject: [PATCH 11/71] Change diff color map to be white near zero This was not the case for SST, SSS and MLD, which could lead to meaningless blue/pink speckle. --- mpas_analysis/config.default | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/mpas_analysis/config.default b/mpas_analysis/config.default index a96053572..9d0573eea 100644 --- a/mpas_analysis/config.default +++ b/mpas_analysis/config.default @@ -521,9 +521,9 @@ colorbarLevelsResult = [-2, 0, 2, 6, 10, 16, 22, 26, 28, 32] # colormap for differences colormapNameDifference = RdBu_r # color indices into colormapName for filled contours -colormapIndicesDifference = [0, 28, 57, 85, 113, 142, 170, 198, 227, 255] +colormapIndicesDifference = [0, 28, 57, 85, 113, 128, 128, 142, 170, 198, 227, 255] # colormap levels/values for contour boundaries -colorbarLevelsDifference = [-5, -3, -2, -1, 0, 1, 2, 3, 5] +colorbarLevelsDifference = [-5, -3, -2, -1, -0.1, 0, 0.1, 1, 2, 3, 5] # Times for comparison times (Jan, Feb, Mar, Apr, May, Jun, Jul, Aug, Sep, Oct, # Nov, Dec, JFM, AMJ, JAS, OND, ANN) @@ -546,9 +546,9 @@ colorbarLevelsResult = [28, 29, 30, 31, 32, 33, 34, 35, 36, 38] # colormap for differences colormapNameDifference = RdBu_r # color indices into colormapName for filled contours -colormapIndicesDifference = [0, 28, 57, 85, 113, 142, 170, 198, 227, 255] +colormapIndicesDifference = [0, 28, 57, 85, 113, 128, 128, 142, 170, 198, 227, 255] # colormap levels/values for contour boundaries -colorbarLevelsDifference = [-3, -2, -1, -0.5, 0, 0.5, 1, 2, 3] +colorbarLevelsDifference = [-3, -2, -1, -0.5, -0.02, 0, 0.02, 0.5, 1, 2, 3] # Times for comparison times (Jan, Feb, Mar, Apr, May, Jun, Jul, Aug, Sep, Oct, # Nov, Dec, JFM, AMJ, JAS, OND, ANN) @@ -571,9 +571,9 @@ colorbarLevelsResult = [0, 20, 40, 60, 80, 100, 150, 200, 400, 800] # colormap for differences colormapNameDifference = RdBu_r # color indices into colormapName for filled contours -colormapIndicesDifference = [0, 28, 57, 85, 113, 142, 170, 198, 227, 255] +colormapIndicesDifference = [0, 28, 57, 85, 113, 128, 128, 142, 170, 198, 227, 255] # colormap levels/values for contour boundaries -colorbarLevelsDifference = [-150, -80, -30, -10, 0, 10, 30, 80, 150] +colorbarLevelsDifference = [-150, -80, -30, -10, -1, 0, 1, 10, 30, 80, 150] # Times for comparison times (Jan, Feb, Mar, Apr, May, Jun, Jul, Aug, Sep, Oct, # Nov, Dec, JFM, AMJ, JAS, OND, ANN) @@ -711,9 +711,9 @@ colorbarLevelsResult = [0.15, 0.3, 0.5, 0.7, 0.8, 0.85, 0.9, 0.95, 1] # colormap for differences colormapNameDifference = RdBu_r # color indices into colormapName for filled contours -colormapIndicesDifference = [0, 32, 64, 96, 128, 128, 160, 192, 224, 255] +colormapIndicesDifference = [0, 32, 64, 96, 112, 128, 128, 144, 160, 192, 224, 255] # colormap levels/values for contour boundaries -colorbarLevelsDifference = [-1., -0.8, -0.6, -0.4, -0.2, 0, 0.2, 0.4, 0.6, 0.8, 1.] +colorbarLevelsDifference = [-1., -0.8, -0.6, -0.4, -0.2, -0.1, 0, 0.1, 0.2, 0.4, 0.6, 0.8, 1.] # Times for comparison times (These should be left unchanged, since # observations are only available for these seasons) @@ -747,9 +747,9 @@ colorbarLevelsResult = [0.15, 0.3, 0.5, 0.7, 0.8, 0.85, 0.9, 0.95, 1] # colormap for differences colormapNameDifference = RdBu_r # color indices into colormapName for filled contours -colormapIndicesDifference = [0, 32, 64, 96, 128, 128, 160, 192, 224, 255] +colormapIndicesDifference = [0, 32, 64, 96, 112, 128, 128, 144, 160, 192, 224, 255] # colormap levels/values for contour boundaries -colorbarLevelsDifference = [-1., -0.8, -0.6, -0.4, -0.2, 0, 0.2, 0.4, 0.6, 0.8, 1.] +colorbarLevelsDifference = [-1., -0.8, -0.6, -0.4, -0.2, -0.1, 0, 0.1, 0.2, 0.4, 0.6, 0.8, 1.] # Times for comparison times (These should be left unchanged, since # observations are only available for these seasons) From 3cf765c076a9d932e4cb03a6b9a85ee20348920b Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Wed, 21 Feb 2018 23:09:21 -0700 Subject: [PATCH 12/71] Optionally add bolus velocity to MOC By default, the bolus velocity is added as long as GM is turned on. --- mpas_analysis/config.default | 5 +++ mpas_analysis/ocean/streamfunction_moc.py | 43 ++++++++++++++++++++--- 2 files changed, 43 insertions(+), 5 deletions(-) diff --git a/mpas_analysis/config.default b/mpas_analysis/config.default index a96053572..bdae25598 100644 --- a/mpas_analysis/config.default +++ b/mpas_analysis/config.default @@ -442,6 +442,11 @@ movingAveragePoints = 1 ## options related to plotting the streamfunction of the meridional overturning ## circulation (MOC) +# Include the bolus velocity from the Gent-McWilliams parameterization? This +# only needs to be disabled if the simulation was run with GM turned on but +# the MOC shouldn't include the bolus term +includeBolus = True + # Region names for basin MOC calculation. # Supported options are Atlantic and IndoPacific regionNames = ['Atlantic'] diff --git a/mpas_analysis/ocean/streamfunction_moc.py b/mpas_analysis/ocean/streamfunction_moc.py index 04c9d8a3a..1af9c9cbc 100644 --- a/mpas_analysis/ocean/streamfunction_moc.py +++ b/mpas_analysis/ocean/streamfunction_moc.py @@ -112,8 +112,17 @@ def setup_and_check(self): # {{{ self.sectionName = 'streamfunctionMOC' + self.includeBolus = config.getboolean(self.sectionName, 'includeBolus') + if self.includeBolus: + # only add the bolus velocity if GM is enabled + self.includeBolus = self.namelist.getbool('config_use_standardgm') + self.variableList = ['timeMonthly_avg_normalVelocity', 'timeMonthly_avg_vertVelocityTop'] + if self.includeBolus: + self.variableList.extend( + ['timeMonthly_avg_normalGMBolusVelocity', + 'timeMonthly_avg_vertGMBolusVelocityTop']) self.mpasClimatologyTask.add_variables(variableList=self.variableList, seasons=['ANN']) @@ -351,11 +360,21 @@ def _compute_moc_climo_postprocess(self): # {{{ climatologyFileName = self.mpasClimatologyTask.get_file_name( season='ANN') annualClimatology = xr.open_dataset(climatologyFileName) - # rename some variables for convenience - annualClimatology = annualClimatology.rename( + annualClimatology = annualClimatology.isel(Time=0) + + if self.includeBolus: + annualClimatology['avgNormalVelocity'] = \ + annualClimatology['timeMonthly_avg_normalVelocity'] + \ + annualClimatology['timeMonthly_avg_normalGMBolusVelocity'] + + annualClimatology['avgVertVelocityTop'] = \ + annualClimatology['timeMonthly_avg_vertVelocityTop'] + \ + annualClimatology['timeMonthly_avg_vertGMBolusVelocityTop'] + else: + # rename some variables for convenience + annualClimatology = annualClimatology.rename( {'timeMonthly_avg_normalVelocity': 'avgNormalVelocity', 'timeMonthly_avg_vertVelocityTop': 'avgVertVelocityTop'}) - annualClimatology = annualClimatology.isel(Time=0) # Convert to numpy arrays # (can result in a memory error for large array size) @@ -534,8 +553,22 @@ def _compute_moc_time_series_postprocess(self): # {{{ self.logger.info(' date: {:04d}-{:02d}'.format(date.year, date.month)) - horizontalVel = dsLocal.timeMonthly_avg_normalVelocity.values - verticalVel = dsLocal.timeMonthly_avg_vertVelocityTop.values + if self.includeBolus: + dsLocal['avgNormalVelocity'] = \ + dsLocal['timeMonthly_avg_normalVelocity'] + \ + dsLocal['timeMonthly_avg_normalGMBolusVelocity'] + + dsLocal['avgVertVelocityTop'] = \ + dsLocal['timeMonthly_avg_vertVelocityTop'] + \ + dsLocal['timeMonthly_avg_vertGMBolusVelocityTop'] + else: + # rename some variables for convenience + dsLocal = dsLocal.rename( + {'timeMonthly_avg_normalVelocity': 'avgNormalVelocity', + 'timeMonthly_avg_vertVelocityTop': 'avgVertVelocityTop'}) + + horizontalVel = dsLocal.avgNormalVelocity.values + verticalVel = dsLocal.avgVertVelocityTop.values velArea = verticalVel * areaCell[:, np.newaxis] transportZ = self._compute_transport(maxEdgesInTransect, transectEdgeGlobalIDs, From 93ef78e4bc3a3bcd0a074c04f19fb91bf91303cf Mon Sep 17 00:00:00 2001 From: Luke Van Roekel Date: Thu, 22 Feb 2018 13:51:17 -0600 Subject: [PATCH 13/71] Fixes path to MOC mask on anvil --- .../anvil/config.20170926.FCT2.A_WCYCL1850S.ne30_oECv3.anvil | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/configs/anvil/config.20170926.FCT2.A_WCYCL1850S.ne30_oECv3.anvil b/configs/anvil/config.20170926.FCT2.A_WCYCL1850S.ne30_oECv3.anvil index 2768885a2..c96b7444a 100644 --- a/configs/anvil/config.20170926.FCT2.A_WCYCL1850S.ne30_oECv3.anvil +++ b/configs/anvil/config.20170926.FCT2.A_WCYCL1850S.ne30_oECv3.anvil @@ -142,4 +142,4 @@ polarPlot = False ## options related to ocean regions used in several analysis modules # Directory for region mask files -regionMaskDirectory = /global/project/projectdirs/acme/mapping/grids/ +regionMaskDirectory = /lcrc/group/acme/mpas_analysis/region_masks From c477e2983ba5d6d6fed290cfe44e9b9b54c11f20 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Thu, 22 Feb 2018 16:10:44 -0700 Subject: [PATCH 14/71] Switch from m to cm --- mpas_analysis/config.default | 4 +- mpas_analysis/ocean/climatology_map_ssh.py | 47 ++++++++++++++++++++- mpas_analysis/shared/constants/constants.py | 3 ++ 3 files changed, 50 insertions(+), 4 deletions(-) diff --git a/mpas_analysis/config.default b/mpas_analysis/config.default index 292e78ddc..2eb7f729c 100644 --- a/mpas_analysis/config.default +++ b/mpas_analysis/config.default @@ -592,14 +592,14 @@ colormapNameResult = Spectral_r # color indices into colormapName for filled contours colormapIndicesResult = [0, 20, 40, 80, 100, 120, 160, 180, 200, 240, 255] # colormap levels/values for contour boundaries -colorbarLevelsResult = [-2.4, -2, -1.6, -1.2, -0.8, -0.4, 0, 0.4, 0.8, 1.2] +colorbarLevelsResult = [-240., -200., -160., -120., -80., -40., 0., 40., 80., 120.] # colormap for differences colormapNameDifference = RdBu_r # color indices into colormapName for filled contours colormapIndicesDifference = [0, 23, 46, 70, 93, 116, 128, 128, 139, 162, 185, 209, 232, 255] # colormap levels/values for contour boundaries -colorbarLevelsDifference = [-1., -0.8, -0.6, -0.4, -0.2, -0.1, 0., 0.1, 0.2, 0.4, 0.6, 0.8, 1.] +colorbarLevelsDifference = [-100., -80., -60., -40., -20., -10., 0., 10., 20., 40., 60., 80., 100.] # Times for comparison times (Jan, Feb, Mar, Apr, May, Jun, Jul, Aug, Sep, Oct, # Nov, Dec, JFM, AMJ, JAS, OND, ANN) diff --git a/mpas_analysis/ocean/climatology_map_ssh.py b/mpas_analysis/ocean/climatology_map_ssh.py index 54be7bea2..fe59d3b4d 100644 --- a/mpas_analysis/ocean/climatology_map_ssh.py +++ b/mpas_analysis/ocean/climatology_map_ssh.py @@ -15,6 +15,8 @@ from mpas_analysis.shared.grid import LatLonGridDescriptor +from mpas_analysis.shared.constants import constants + class ClimatologyMapSSH(AnalysisTask): # {{{ """ @@ -73,7 +75,7 @@ def __init__(self, config, mpasClimatologyTask, # the variable mpasFieldName will be added to mpasClimatologyTask # along with the seasons. - remapClimatologySubtask = RemapMpasClimatologySubtask( + remapClimatologySubtask = RemapSSHClimatology( mpasClimatologyTask=mpasClimatologyTask, parentTask=self, climatologyName=fieldName, @@ -130,7 +132,7 @@ def __init__(self, config, mpasClimatologyTask, refFieldName=refFieldName, refTitleLabel=refTitleLabel, diffTitleLabel=diffTitleLabel, - unitsLabel=r'm', + unitsLabel=r'cm', imageCaption='Mean Sea Surface Height', galleryGroup='Sea Surface Height', groupSubtitle=None, @@ -142,6 +144,44 @@ def __init__(self, config, mpasClimatologyTask, # }}} +class RemapSSHClimatology(RemapMpasClimatologySubtask): # {{{ + """ + Change units from m to cm + + Authors + ------- + Xylar Asay-Davis + """ + + def customize_masked_climatology(self, climatology): # {{{ + """ + Mask the melt rates using ``landIceMask`` and rescale it to m/yr + + Parameters + ---------- + climatology : ``xarray.Dataset`` object + the climatology data set + + Returns + ------- + climatology : ``xarray.Dataset`` object + the modified climatology data set + + Authors + ------- + Xylar Asay-Davis + """ + + fieldName = self.variableList[0] + + # scale the field to cm from m + climatology[fieldName] = constants.cm_per_m * climatology[fieldName] + + return climatology # }}} + + # }}} + + class RemapObservedSSHClimatology(RemapObservedClimatologySubtask): # {{{ """ A subtask for reading and remapping SSH observations @@ -202,6 +242,9 @@ def build_observational_dataset(self, fileName): # {{{ dsObs.coords['month'] = dsObs['Time.month'] dsObs.coords['year'] = dsObs['Time.year'] + # scale the field to cm from m + dsObs['zos'] = constants.cm_per_m * dsObs['zos'] + return dsObs # }}} # }}} diff --git a/mpas_analysis/shared/constants/constants.py b/mpas_analysis/shared/constants/constants.py index 9f901aadf..7231fe7be 100644 --- a/mpas_analysis/shared/constants/constants.py +++ b/mpas_analysis/shared/constants/constants.py @@ -64,4 +64,7 @@ # kilograms per gigatonne kg_per_GT = 1e12 +# cm per m +cm_per_m = 100. + # vim: foldmethod=marker ai ts=4 sts=4 et sw=4 ft=python From d1fcf7df5d940cd58028b51feedf1da4a8de45d1 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Thu, 22 Feb 2018 12:54:20 -0800 Subject: [PATCH 15/71] Use common colormap setup for all plots with colormaps All support either contours (via indexed colormaps) or continuous plotting (via a norm). Tick marks can be specified (optionally) differently from contour levels. --- .../mpas_analysis_config_parser.py | 4 +- .../ocean/meridional_heat_transport.py | 25 +- .../ocean/plot_climatology_map_subtask.py | 22 +- mpas_analysis/ocean/plot_hovmoller_subtask.py | 20 +- mpas_analysis/ocean/streamfunction_moc.py | 18 +- .../sea_ice/plot_climatology_map_subtask.py | 13 +- mpas_analysis/shared/plot/plotting.py | 553 ++++++++++-------- 7 files changed, 340 insertions(+), 315 deletions(-) diff --git a/mpas_analysis/configuration/mpas_analysis_config_parser.py b/mpas_analysis/configuration/mpas_analysis_config_parser.py index 3bf3cf643..06f2472cf 100644 --- a/mpas_analysis/configuration/mpas_analysis_config_parser.py +++ b/mpas_analysis/configuration/mpas_analysis_config_parser.py @@ -22,8 +22,8 @@ if six.PY3: xrange = range -npallow = dict(linspace=np.linspace, xrange=xrange, range=range, - arange=np.arange, pi=np.pi, Pi=np.pi, __builtins__=None) +npallow = dict(linspace=np.linspace, xrange=xrange, range=range, array=np.array, + arange=np.arange, pi=np.pi, Pi=np.pi, int=int, __builtins__=None) class MpasAnalysisConfigParser(ConfigParser): diff --git a/mpas_analysis/ocean/meridional_heat_transport.py b/mpas_analysis/ocean/meridional_heat_transport.py index f1dbfd0fc..218203f41 100644 --- a/mpas_analysis/ocean/meridional_heat_transport.py +++ b/mpas_analysis/ocean/meridional_heat_transport.py @@ -6,8 +6,7 @@ import numpy as np import os -from mpas_analysis.shared.plot.plotting import plot_vertical_section,\ - setup_colormap, plot_1D +from mpas_analysis.shared.plot.plotting import plot_vertical_section, plot_1D from mpas_analysis.shared.io.utility import build_config_full_path, \ make_directories @@ -16,9 +15,6 @@ from mpas_analysis.shared import AnalysisTask from mpas_analysis.shared.html import write_image_xml -from mpas_analysis.shared.climatology import \ - get_unmasked_mpas_climatology_file_name - class MeridionalHeatTransport(AnalysisTask): # {{{ ''' @@ -174,7 +170,6 @@ def run_task(self): # {{{ '{}/meridionalHeatTransport_years{:04d}-{:04d}.nc'.format( outputDirectory, self.startYear, self.endYear) - if os.path.exists(outFileName): self.logger.info(' Reading results from previous analysis run...') annualClimatology = xr.open_dataset(outFileName) @@ -342,18 +337,12 @@ def run_task(self): # {{{ filePrefix = self.filePrefixes['mhtZ'] figureName = '{}/{}.png'.format(self.plotsDirectory, filePrefix) colorbarLabel = '[PW/m]' - contourLevels = config.getExpression(self.sectionName, - 'contourLevelsGlobal', - usenumpyfunc=True) - (colormapName, colorbarLevels) = setup_colormap(config, - self.sectionName, - suffix='Global') - plot_vertical_section(config, x, y, z, - colormapName, colorbarLevels, - contourLevels, colorbarLabel, - title, xLabel, yLabel, figureName, - xLim=xLimGlobal, yLim=depthLimGlobal, - invertYAxis=False, N=movingAveragePoints) + plot_vertical_section(config, x, y, z, self.sectionName, + suffix='', colorbarLabel=colorbarLabel, + title=title, xlabel=xLabel, ylabel=yLabel, + fileout=figureName, xLim=xLimGlobal, + yLim=depthLimGlobal, invertYAxis=False, + N=movingAveragePoints) self._write_xml(filePrefix) diff --git a/mpas_analysis/ocean/plot_climatology_map_subtask.py b/mpas_analysis/ocean/plot_climatology_map_subtask.py index 34b11d39d..66395a887 100644 --- a/mpas_analysis/ocean/plot_climatology_map_subtask.py +++ b/mpas_analysis/ocean/plot_climatology_map_subtask.py @@ -16,7 +16,7 @@ from mpas_analysis.shared import AnalysisTask from mpas_analysis.shared.plot.plotting import plot_global_comparison, \ - setup_colormap, plot_polar_projection_comparison + plot_polar_projection_comparison from mpas_analysis.shared.html import write_image_xml @@ -386,11 +386,6 @@ def _plot_latlon(self, remappedModelClimatology, remappedRefClimatology): mainRunName = config.get('runs', 'mainRunName') - (colormapResult, colorbarLevelsResult) = setup_colormap( - config, configSectionName, suffix='Result') - (colormapDifference, colorbarLevelsDifference) = setup_colormap( - config, configSectionName, suffix='Difference') - modelOutput = nans_to_numpy_mask( remappedModelClimatology[self.mpasFieldName].values) @@ -419,10 +414,7 @@ def _plot_latlon(self, remappedModelClimatology, remappedRefClimatology): modelOutput, refOutput, bias, - colormapResult, - colorbarLevelsResult, - colormapDifference, - colorbarLevelsDifference, + configSectionName, fileout=outFileName, title=title, modelTitle='{}'.format(mainRunName), @@ -483,15 +475,6 @@ def _plot_antarctic(self, remappedModelClimatology, self.fieldNameInTitle, season, self.startYear, self.endYear) - if config.has_option(configSectionName, 'colormapIndicesResult'): - colorMapType = 'indexed' - elif config.has_option(configSectionName, 'normTypeResult'): - colorMapType = 'norm' - else: - raise ValueError('config section {} contains neither the info' - 'for an indexed color map nor for computing a ' - 'norm'.format(configSectionName)) - plot_polar_projection_comparison( config, x, @@ -502,7 +485,6 @@ def _plot_antarctic(self, remappedModelClimatology, bias, fileout=outFileName, colorMapSectionName=configSectionName, - colorMapType=colorMapType, title=title, modelTitle='{}'.format(mainRunName), refTitle=self.refTitleLabel, diff --git a/mpas_analysis/ocean/plot_hovmoller_subtask.py b/mpas_analysis/ocean/plot_hovmoller_subtask.py index 96e54a284..8543325e8 100644 --- a/mpas_analysis/ocean/plot_hovmoller_subtask.py +++ b/mpas_analysis/ocean/plot_hovmoller_subtask.py @@ -8,8 +8,7 @@ from mpas_analysis.shared import AnalysisTask -from mpas_analysis.shared.plot.plotting import plot_vertical_section, \ - setup_colormap +from mpas_analysis.shared.plot.plotting import plot_vertical_section from mpas_analysis.shared.io import open_mpas_dataset @@ -260,18 +259,11 @@ def run_task(self): # {{{ figureName = '{}/{}.png'.format(self.plotsDirectory, self.filePrefix) - (colormapName, colorbarLevels) = setup_colormap(config, - self.sectionName) - - contourLevels = config.getExpression(self.sectionName, - 'contourLevels', - usenumpyfunc=True) - - plot_vertical_section(config, Time, depth, field, - colormapName, colorbarLevels, contourLevels, - self.unitsLabel, title, xLabel, yLabel, - figureName, linewidths=1, xArrayIsTime=True, - calendar=self.calendar) + plot_vertical_section(config, Time, depth, field, self.sectionName, + suffix='', colorbarLabel=self.unitsLabel, + title=title, xlabel=xLabel, ylabel=yLabel, + fileout=figureName, linewidths=1, + xArrayIsTime=True, calendar=self.calendar) write_image_xml( config=config, diff --git a/mpas_analysis/ocean/streamfunction_moc.py b/mpas_analysis/ocean/streamfunction_moc.py index ef310ad3b..5b7ec216c 100644 --- a/mpas_analysis/ocean/streamfunction_moc.py +++ b/mpas_analysis/ocean/streamfunction_moc.py @@ -9,8 +9,8 @@ import os from mpas_analysis.shared.constants.constants import m3ps_to_Sv -from mpas_analysis.shared.plot.plotting import plot_vertical_section, \ - timeseries_analysis_plot, setup_colormap +from mpas_analysis.shared.plot.plotting import plot_vertical_section,\ + timeseries_analysis_plot from mpas_analysis.shared.io.utility import build_config_full_path, \ make_directories, get_files_year_month @@ -197,20 +197,14 @@ def run_task(self): # {{{ mainRunName) filePrefix = self.filePrefixes[region] figureName = '{}/{}.png'.format(self.plotsDirectory, filePrefix) - contourLevels = \ - config.getExpression(self.sectionName, - 'contourLevels{}'.format(region), - usenumpyfunc=True) - (colormapName, colorbarLevels) = setup_colormap(config, - self.sectionName, - suffix=region) x = self.lat[region] y = self.depth z = self.moc[region] - plot_vertical_section(config, x, y, z, colormapName, - colorbarLevels, contourLevels, colorbarLabel, - title, xLabel, yLabel, figureName, + plot_vertical_section(config, x, y, z, self.sectionName, + suffix=region, colorbarLabel=colorbarLabel, + title=title, xlabel=xLabel, ylabel=yLabel, + fileout=figureName, N=movingAveragePointsClimatological) caption = '{} Meridional Overturning Streamfunction'.format(region) diff --git a/mpas_analysis/sea_ice/plot_climatology_map_subtask.py b/mpas_analysis/sea_ice/plot_climatology_map_subtask.py index 5ca70ff2e..5393ee826 100644 --- a/mpas_analysis/sea_ice/plot_climatology_map_subtask.py +++ b/mpas_analysis/sea_ice/plot_climatology_map_subtask.py @@ -9,8 +9,7 @@ from mpas_analysis.shared import AnalysisTask -from mpas_analysis.shared.plot.plotting import plot_polar_comparison, \ - setup_colormap +from mpas_analysis.shared.plot.plotting import plot_polar_comparison from mpas_analysis.shared.html import write_image_xml @@ -298,11 +297,6 @@ def run_task(self): # {{{ else: plotProjection = 'spstere' - (colormapResult, colorbarLevelsResult) = setup_colormap( - config, sectionName, suffix='Result') - (colormapDifference, colorbarLevelsDifference) = setup_colormap( - config, sectionName, suffix='Difference') - referenceLongitude = config.getfloat(sectionName, 'referenceLongitude') minimumLatitude = config.getfloat(sectionName, @@ -373,10 +367,7 @@ def run_task(self): # {{{ modelOutput, refOutput, difference, - colormapResult, - colorbarLevelsResult, - colormapDifference, - colorbarLevelsDifference, + sectionName, title=title, fileout=fileout, plotProjection=plotProjection, diff --git a/mpas_analysis/shared/plot/plotting.py b/mpas_analysis/shared/plot/plotting.py index d60a2cbb0..54d768322 100644 --- a/mpas_analysis/shared/plot/plotting.py +++ b/mpas_analysis/shared/plot/plotting.py @@ -13,6 +13,7 @@ from __future__ import absolute_import, division, print_function, \ unicode_literals +import matplotlib import matplotlib.pyplot as plt import matplotlib.colors as cols import xarray as xr @@ -261,7 +262,7 @@ def timeseries_analysis_plot_polar(config, dsvalues, N, title, majorTickLocs[month] = majorTickLocs[month-1] + \ ((constants.daysInMonth[month-1] * np.pi * 2.0) / 365.0) minorTickLocs[month] = minorTickLocs[month-1] + \ - (((constants.daysInMonth[month-1] + \ + (((constants.daysInMonth[month-1] + constants.daysInMonth[month]) * np.pi) / 365.0) ax.set_xticks(majorTickLocs) @@ -273,7 +274,6 @@ def timeseries_analysis_plot_polar(config, dsvalues, N, title, if titleFontSize is None: titleFontSize = config.get('plot', 'titleFontSize') - axis_font = {'size': config.get('plot', 'axisFontSize')} title_font = {'size': titleFontSize, 'color': config.get('plot', 'titleFontColor'), 'weight': config.get('plot', 'titleFontWeight')} @@ -294,10 +294,7 @@ def plot_polar_comparison( modelArray, refArray, diffArray, - cmapModelRef, - clevsModelRef, - cmapDiff, - clevsDiff, + colorMapSectionName, fileout, title=None, plotProjection='npstere', @@ -330,17 +327,8 @@ def plot_polar_comparison( diffArray : float array difference between modelArray and refArray - cmapModelRef : str - colormap of model and observations or reference run panel - - clevsModelRef : int array - colorbar values for model and observations or reference run panel - - cmapDiff : str - colormap of difference (bias) panel - - clevsDiff : int array - colorbar values for difference (bias) panel + colorMapSectionName : str + section name in ``config`` where color map info can be found. fileout : str the file name to be written @@ -383,7 +371,8 @@ def plot_polar_comparison( Xylar Asay-Davis, Milena Veneziani """ - def do_subplot(ax, field, title, cmap, norm, levels): + def do_subplot(ax, field, title, colormap, norm, levels, ticks, contours, + lineWidth, lineColor): """ Make a subplot within the figure. """ @@ -398,16 +387,28 @@ def do_subplot(ax, field, title, cmap, norm, levels): m.drawparallels(np.arange(-80., 81., 10.)) m.drawmeridians(np.arange(-180., 181., 20.), labels=[True, False, True, True]) - cs = m.contourf(x, y, field, cmap=cmap, norm=norm, - levels=levels) - cbar = m.colorbar(cs, location='right', pad="3%", spacing='uniform', - ticks=levels, boundaries=levels) + if levels is None: + plotHandle = m.pcolormesh(x, y, field, cmap=colormap, norm=norm) + else: + plotHandle = m.contourf(x, y, field, cmap=colormap, norm=norm, + levels=levels) + + if contours is not None: + matplotlib.rcParams['contour.negative_linestyle'] = 'solid' + m.contour(x, y, field, levels=contours, colors=lineColor, + linewidths=lineWidth) + + cbar = m.colorbar(plotHandle, location='right', pad="3%", + spacing='uniform', ticks=ticks, boundaries=levels) cbar.set_label(cbarlabel) if dpi is None: dpi = config.getint('plot', 'dpi') + dictModelRef = setup_colormap(config, colorMapSectionName, suffix='Result') + dictDiff = setup_colormap(config, colorMapSectionName, suffix='Difference') + if refArray is None: if figsize is None: figsize = (8, 8.5) @@ -432,21 +433,15 @@ def do_subplot(ax, field, title, cmap, norm, levels): fig.suptitle(title, y=0.95, **title_font) axis_font = {'size': config.get('plot', 'axisFontSize')} - normModelRef = cols.BoundaryNorm(clevsModelRef, cmapModelRef.N) - normDiff = cols.BoundaryNorm(clevsDiff, cmapDiff.N) - ax = plt.subplot(subplots[0]) - do_subplot(ax=ax, field=modelArray, title=modelTitle, cmap=cmapModelRef, - norm=normModelRef, levels=clevsModelRef) + do_subplot(ax=ax, field=modelArray, title=modelTitle, **dictModelRef) if refArray is not None: ax = plt.subplot(subplots[1]) - do_subplot(ax=ax, field=refArray, title=refTitle, cmap=cmapModelRef, - norm=normModelRef, levels=clevsModelRef) + do_subplot(ax=ax, field=refArray, title=refTitle, **dictModelRef) ax = plt.subplot(subplots[2]) - do_subplot(ax=ax, field=diffArray, title=diffTitle, cmap=cmapDiff, - norm=normDiff, levels=clevsDiff) + do_subplot(ax=ax, field=diffArray, title=diffTitle, **dictDiff) plt.tight_layout(pad=4.) if vertical: @@ -460,25 +455,24 @@ def do_subplot(ax, field, title, cmap, norm, levels): def plot_global_comparison( - config, - Lons, - Lats, - modelArray, - refArray, - diffArray, - cmapModelRef, - clevsModelRef, - cmapDiff, - clevsDiff, - fileout, - title=None, - modelTitle='Model', - refTitle='Observations', - diffTitle='Model-Observations', - cbarlabel='units', - titleFontSize=None, - figsize=(8, 13), - dpi=None): + config, + Lons, + Lats, + modelArray, + refArray, + diffArray, + colorMapSectionName, + fileout, + title=None, + modelTitle='Model', + refTitle='Observations', + diffTitle='Model-Observations', + cbarlabel='units', + titleFontSize=None, + figsize=(8, 13), + dpi=None, + lineWidth=1, + lineColor='black'): """ Plots a data set as a longitude/latitude map. @@ -498,17 +492,8 @@ def plot_global_comparison( diffArray : float array difference between modelArray and refArray - cmapModelRef : str - colormap of model and observations or reference run panel - - clevsModelRef : int array - colorbar values for model and observations or reference run panel - - cmapDiff : str - colormap of difference (bias) panel - - clevsDiff : int array - colorbar values for difference (bias) panel + colorMapSectionName : str + section name in ``config`` where color map info can be found. fileout : str the file name to be written @@ -538,11 +523,42 @@ def plot_global_comparison( the number of dots per inch of the figure, taken from section ``plot`` option ``dpi`` in the config file by default + lineWidth : int, optional + the line width of contour lines (if specified) + + lineColor : str, optional + the color contour lines (if specified) + Authors ------- Xylar Asay-Davis, Milena Veneziani """ + def plot_panel(title, array, colormap, norm, levels, ticks, contours, + lineWidth, lineColor): + plt.title(title, y=1.06, **axis_font) + m.drawcoastlines() + m.fillcontinents(color='grey', lake_color='white') + m.drawparallels(np.arange(-80., 80., 20.), + labels=[True, False, False, False]) + m.drawmeridians(np.arange(-180., 180., 60.), + labels=[False, False, False, True]) + + if levels is None: + plotHandle = m.pcolormesh(x, y, array, cmap=colormap, norm=norm) + else: + plotHandle = m.contourf(x, y, array, cmap=colormap, norm=norm, + levels=levels, extend='both') + + if contours is not None: + matplotlib.rcParams['contour.negative_linestyle'] = 'solid' + m.contour(x, y, array, levels=contours, colors=lineColor, + linewidths=lineWidth) + + cbar = m.colorbar(plotHandle, location='right', pad="5%", + spacing='uniform', ticks=ticks, boundaries=ticks) + cbar.set_label(cbarlabel) + # set up figure if dpi is None: dpi = config.getint('plot', 'dpi') @@ -560,52 +576,20 @@ def plot_global_comparison( urcrnrlon=181, resolution='l') x, y = m(Lons, Lats) # compute map proj coordinates - normModelRef = cols.BoundaryNorm(clevsModelRef, cmapModelRef.N) - normDiff = cols.BoundaryNorm(clevsDiff, cmapDiff.N) + dictModelRef = setup_colormap(config, colorMapSectionName, suffix='Result') + dictDiff = setup_colormap(config, colorMapSectionName, suffix='Difference') if refArray is not None: plt.subplot(3, 1, 1) - plt.title(modelTitle, y=1.06, **axis_font) - m.drawcoastlines() - m.fillcontinents(color='grey', lake_color='white') - m.drawparallels(np.arange(-80., 80., 20.), - labels=[True, False, False, False]) - m.drawmeridians(np.arange(-180., 180., 60.), - labels=[False, False, False, True]) - cs = m.contourf(x, y, modelArray, cmap=cmapModelRef, norm=normModelRef, - levels=clevsModelRef, extend='both') - cbar = m.colorbar(cs, location='right', pad="5%", spacing='uniform', - ticks=clevsModelRef, boundaries=clevsModelRef) - cbar.set_label(cbarlabel) + + plot_panel(modelTitle, modelArray, **dictModelRef) if refArray is not None: plt.subplot(3, 1, 2) - plt.title(refTitle, y=1.06, **axis_font) - m.drawcoastlines() - m.fillcontinents(color='grey', lake_color='white') - m.drawparallels(np.arange(-80., 80., 20.), - labels=[True, False, False, False]) - m.drawmeridians(np.arange(-180., 180., 40.), - labels=[False, False, False, True]) - cs = m.contourf(x, y, refArray, cmap=cmapModelRef, norm=normModelRef, - levels=clevsModelRef, extend='both') - cbar = m.colorbar(cs, location='right', pad="5%", spacing='uniform', - ticks=clevsModelRef, boundaries=clevsModelRef) - cbar.set_label(cbarlabel) + plot_panel(refTitle, refArray, **dictModelRef) plt.subplot(3, 1, 3) - plt.title(diffTitle, y=1.06, **axis_font) - m.drawcoastlines() - m.fillcontinents(color='grey', lake_color='white') - m.drawparallels(np.arange(-80., 80., 20.), - labels=[True, False, False, False]) - m.drawmeridians(np.arange(-180., 180., 40.), - labels=[False, False, False, True]) - cs = m.contourf(x, y, diffArray, cmap=cmapDiff, norm=normDiff, - levels=clevsDiff, extend='both') - cbar = m.colorbar(cs, location='right', pad="5%", spacing='uniform', - ticks=clevsDiff, boundaries=clevsModelRef) - cbar.set_label(cbarlabel) + plot_panel(diffTitle, diffArray, **dictDiff) if (fileout is not None): plt.savefig(fileout, dpi=dpi, bbox_inches='tight', pad_inches=0.1) @@ -624,7 +608,6 @@ def plot_polar_projection_comparison( diffArray, fileout, colorMapSectionName, - colorMapType='norm', title=None, modelTitle='Model', refTitle='Observations', @@ -662,22 +645,6 @@ def plot_polar_projection_comparison( colorMapSectionName : str section name in ``config`` where color map info can be found. - colorMapType : {'norm', 'indexed'}, optional - The type of color map, either a matplotlib norm or indices into a color - map. - - If 'norm', the following options must be defined for suffixes - ``Result`` and ``Difference``: - ``colormapName``, ``normType``, - ``normArgs``, ``colorbarTicks`` - - If 'indexed', these options are required: - ``colormapName``, ``colormapIndices``, - ``colorbarLevels`` - - The colorbar for each panel will be constructed from these options - - title : str, optional the subtitle of the plot @@ -716,21 +683,31 @@ def plot_polar_projection_comparison( Xylar Asay-Davis """ - def plot_panel(ax, title, array, cmap, norm, ticks): + def plot_panel(ax, title, array, colormap, norm, levels, ticks, contours, + lineWidth, lineColor): plt.title(title, y=1.06, **axis_font) - mesh = plt.pcolormesh(x, y, array, cmap=cmap, norm=norm) + if levels is None: + plotHandle = plt.pcolormesh(x, y, array, cmap=colormap, norm=norm) + else: + plotHandle = plt.contourf(x, y, array, cmap=colormap, norm=norm, + levels=levels, extend='both') plt.pcolormesh(x, y, landMask, cmap=landColorMap) plt.contour(xCenter, yCenter, landMask.mask, (0.5,), colors='k', linewidths=0.5) + if contours is not None: + matplotlib.rcParams['contour.negative_linestyle'] = 'solid' + plt.contour(x, y, array, levels=contours, colors=lineColor, + linewidths=lineWidth) + # create an axes on the right side of ax. The width of cax will be 5% # of ax and the padding between cax and ax will be fixed at 0.05 inch. divider = make_axes_locatable(ax) cax = divider.append_axes("right", size="5%", pad=0.05) - cbar = plt.colorbar(mesh, cax=cax) + cbar = plt.colorbar(plotHandle, cax=cax) cbar.set_label(cbarlabel) if ticks is not None: cbar.set_ticks(ticks) @@ -757,36 +734,8 @@ def plot_panel(ax, title, array, cmap, norm, ticks): figsize = (22, 7.5) subplots = [131, 132, 133] - if colorMapType == 'norm': - (cmapModelRef, normModelRef) = _setup_colormap_and_norm( - config, colorMapSectionName, suffix='Result') - (cmapDiff, normDiff) = _setup_colormap_and_norm( - config, colorMapSectionName, suffix='Difference') - - if config.has_option(colorMapSectionName, 'colorbarTicksResult'): - colorbarTicksResult = config.getExpression(colorMapSectionName, - 'colorbarTicksResult', - usenumpyfunc=True) - else: - colorbarTicksResult = None - if config.has_option(colorMapSectionName, 'colorbarTicksDifference'): - colorbarTicksDifference = config.getExpression( - colorMapSectionName, 'colorbarTicksDifference', - usenumpyfunc=True) - else: - colorbarTicksDifference = None - - elif colorMapType == 'indexed': - - (cmapModelRef, colorbarTicksResult) = setup_colormap( - config, colorMapSectionName, suffix='Result') - (cmapDiff, colorbarTicksDifference) = setup_colormap( - config, colorMapSectionName, suffix='Difference') - - normModelRef = cols.BoundaryNorm(colorbarTicksResult, cmapModelRef.N) - normDiff = cols.BoundaryNorm(colorbarTicksDifference, cmapDiff.N) - else: - raise ValueError('colorMapType must be one of {norm, indexed}') + dictModelRef = setup_colormap(config, colorMapSectionName, suffix='Result') + dictDiff = setup_colormap(config, colorMapSectionName, suffix='Difference') # set up figure fig = plt.figure(figsize=figsize, dpi=dpi) @@ -808,17 +757,14 @@ def plot_panel(ax, title, array, cmap, norm, ticks): yCenter = 0.5*(y[1:] + y[0:-1]) ax = plt.subplot(subplots[0]) - plot_panel(ax, modelTitle, modelArray, cmapModelRef, normModelRef, - colorbarTicksResult) + plot_panel(ax, modelTitle, modelArray, **dictModelRef) if refArray is not None: ax = plt.subplot(subplots[1]) - plot_panel(ax, refTitle, refArray, cmapModelRef, normModelRef, - colorbarTicksResult) + plot_panel(ax, refTitle, refArray, **dictModelRef) ax = plt.subplot(subplots[2]) - plot_panel(ax, diffTitle, diffArray, cmapDiff, normDiff, - colorbarTicksDifference) + plot_panel(ax, diffTitle, diffArray, **dictDiff) if (fileout is not None): plt.savefig(fileout, dpi=dpi, bbox_inches='tight', pad_inches=0.1) @@ -949,28 +895,27 @@ def plot_1D(config, xArrays, fieldArrays, errArrays, def plot_vertical_section( - config, - xArray, - depthArray, - fieldArray, - colormapName, - colorbarLevels, - contourLevels, - colorbarLabel=None, - title=None, - xlabel=None, - ylabel=None, - fileout='moc.png', - figsize=(10, 4), - dpi=None, - xLim=None, - yLim=None, - linewidths=2, - invertYAxis=True, - xArrayIsTime=False, - N=None, - maxXTicks=20, - calendar='gregorian'): # {{{ + config, + xArray, + depthArray, + fieldArray, + colorMapSectionName, + suffix='', + colorbarLabel=None, + title=None, + xlabel=None, + ylabel=None, + fileout='moc.png', + figsize=(10, 4), + dpi=None, + xLim=None, + yLim=None, + linewidths=2, + invertYAxis=True, + xArrayIsTime=False, + N=None, + maxXTicks=20, + calendar='gregorian'): # {{{ """ Plots a data set as a x distance (latitude, longitude, @@ -986,7 +931,8 @@ def plot_vertical_section( control plotting xArray : float array - x array (latitude, longitude, or spherical distance; or, time for a Hovmoller plot) + x array (latitude, longitude, or spherical distance; or, time for a + Hovmoller plot) depthArray : float array depth array [m] @@ -994,17 +940,11 @@ def plot_vertical_section( fieldArray : float array field array to plot - colormapName : str - colormap of plot - - colorbarLevels : int array - colorbar levels of plot - - contourLevels : int levels - levels of contours to be drawn + colorMapSectionName : str + section name in ``config`` where color map info can be found. - colorbarLabel : str, optional - label of the colorbar + suffix : str, optional + the suffix used for colorbar config options title : str, optional title of plot @@ -1040,9 +980,10 @@ def plot_vertical_section( N : int, optional the number of points over which to perform a moving average NOTE: this option is mostly intended for use when xArrayIsTime is True, - although it will work with other data as well. Also, the moving average - calculation is based on number of points, not actual x axis values, so for - best results, the values in the xArray should be equally spaced. + although it will work with other data as well. Also, the moving + average calculation is based on number of points, not actual x axis + values, so for best results, the values in the xArray should be equally + spaced. maxXTicks : int, optional the maximum number of tick marks that will be allowed along the x axis. @@ -1058,7 +999,8 @@ def plot_vertical_section( Milena Veneziani, Mark Petersen, Xylar Asay-Davis, Greg Streletz """ - # verify that the dimensions of fieldArray are consistent with those of xArray and depthArray + # verify that the dimensions of fieldArray are consistent with those of + # xArray and depthArray if len(xArray) != fieldArray.shape[1]: raise ValueError('size mismatch between xArray and fieldArray') elif len(depthArray) != fieldArray.shape[0]: @@ -1069,12 +1011,15 @@ def plot_vertical_section( dpi = config.getint('plot', 'dpi') plt.figure(figsize=figsize, dpi=dpi) - if N is not None and N != 1: # compute moving averages with respect to the x dimension + # compute moving averages with respect to the x dimension + if N is not None and N != 1: movingAverageDepthSlices = [] for nVertLevel in range(len(depthArray)): depthSlice = fieldArray[[nVertLevel]][0] - depthSlice = xr.DataArray(depthSlice) # in case it's not an xarray already - mean = pd.Series.rolling(depthSlice.to_series(), N, center=True).mean() + # in case it's not an xarray already + depthSlice = xr.DataArray(depthSlice) + mean = pd.Series.rolling(depthSlice.to_series(), N, + center=True).mean() mean = xr.DataArray.from_series(mean) mean = mean[int(N/2.0):-int(round(N/2.0)-1)] movingAverageDepthSlices.append(mean) @@ -1083,21 +1028,23 @@ def plot_vertical_section( x, y = np.meshgrid(xArray, depthArray) # change to zMid - if colorbarLevels is None: - normModelObs = None - else: - normModelObs = cols.BoundaryNorm(colorbarLevels, colormapName.N) + colormapDict = setup_colormap(config, colorMapSectionName, suffix=suffix) - cs = plt.contourf(x, y, fieldArray, cmap=colormapName, norm=normModelObs, - levels=colorbarLevels, extend='both') + cs = plt.contourf(x, y, fieldArray, cmap=colormapDict['colormap'], + norm=colormapDict['norm'], + levels=colormapDict['levels'], extend='both') + contourLevels = colormapDict['contours'] if contourLevels is not None: if len(contourLevels) == 0: - contourLevels = None # automatic calculation of contour levels - plt.contour(x, y, fieldArray, levels=contourLevels, colors='k', linewidths=linewidths) + # automatic calculation of contour levels + contourLevels = None + plt.contour(x, y, fieldArray, levels=contourLevels, colors='k', + linewidths=linewidths) cbar = plt.colorbar(cs, orientation='vertical', spacing='uniform', - ticks=colorbarLevels, boundaries=colorbarLevels) + ticks=colormapDict['ticks'], + boundaries=colormapDict['ticks']) if colorbarLabel is not None: cbar.set_label(colorbarLabel) @@ -1152,13 +1099,28 @@ def setup_colormap(config, configSectionName, suffix=''): suffix: str, optional suffix of colormap related options + colorMapType + Returns ------- - colormap : srt - new colormap + colormapDict : dict + A dictionary of colormap information. - colorbarLevels : int array - colorbar levels + 'colormap' specifies the name of the new colormap + + 'norm' is a matplotlib norm object used to normalize the colormap + + 'levels' is an array of contour levels or ``None`` if not using indexed + color map + + 'ticks' is an array of values where ticks should be placed + + 'contours' is an array of contour values to plot or ``None`` if none + have been specified + + 'lineWidth' is the width of contour lines or ``None`` if not specified + + 'lineColor' is the color of contour lines or ``None`` if not specified Authors ------- @@ -1167,38 +1129,42 @@ def setup_colormap(config, configSectionName, suffix=''): _register_custom_colormaps() - colormap = plt.get_cmap(config.get(configSectionName, - 'colormapName{}'.format(suffix))) - - indices = config.getExpression(configSectionName, - 'colormapIndices{}'.format(suffix), - usenumpyfunc=True) + if config.has_option(configSectionName, + 'colormapIndices{}'.format(suffix)): + (colormap, norm, levels, ticks) = _setup_indexed_colormap( + config, configSectionName, suffix=suffix) + elif config.has_option(configSectionName, 'normType{}'.format(suffix)): + (colormap, norm, ticks) = _setup_colormap_and_norm( + config, configSectionName, suffix=suffix) + levels = None + else: + raise ValueError('config section {} contains neither the info' + 'for an indexed color map nor for computing a ' + 'norm'.format(configSectionName)) + + option = 'contourLevels{}'.format(suffix) + if config.has_option(configSectionName, option): + contours = config.getExpression(configSectionName, + option, + usenumpyfunc=True) + else: + contours = None - try: - colorbarLevels = config.getExpression(configSectionName, - 'colorbarLevels{}'.format(suffix), - usenumpyfunc=True) - except(configparser.NoOptionError): - colorbarLevels = None + option = 'contourThickness{}'.format(suffix) + if config.has_option(configSectionName, option): + lineWidth = config.getfloat(configSectionName, option) + else: + lineWidth = None - if colorbarLevels is not None: - # set under/over values based on the first/last indices in the colormap - underColor = colormap(indices[0]) - overColor = colormap(indices[-1]) - if len(colorbarLevels)+1 == len(indices): - # we have 2 extra values for the under/over so make the colormap - # without these values - indices = indices[1:-1] - elif len(colorbarLevels)-1 != len(indices): - # indices list must be either one element shorter - # or one element longer than colorbarLevels list - raise ValueError('length mismatch between indices and colorbarLevels') - colormap = cols.ListedColormap(colormap(indices), - 'colormapName{}'.format(suffix)) - colormap.set_under(underColor) - colormap.set_over(overColor) + option = 'contourColor{}'.format(suffix) + if config.has_option(configSectionName, option): + lineColor = config.get(configSectionName, option) + else: + lineColor = None - return (colormap, colorbarLevels) + return {'colormap': colormap, 'norm': norm, 'levels': levels, + 'ticks': ticks, 'contours': contours, 'lineWidth': lineWidth, + 'lineColor': lineColor} def plot_xtick_format(plt, calendar, minDays, maxDays, maxXTicks): @@ -1273,6 +1239,9 @@ def _setup_colormap_and_norm(config, configSectionName, suffix=''): norm : ``SymLogNorm`` object the norm used to normalize the colormap + ticks : array of float + the tick marks on the colormap + Authors ------- Xylar Asay-Davis @@ -1296,7 +1265,93 @@ def _setup_colormap_and_norm(config, configSectionName, suffix=''): raise ValueError('Unsupported norm type {} in section {}'.format( normType, configSectionName)) - return (colormap, norm) + try: + ticks = config.getExpression( + configSectionName, 'colorbarTicks{}'.format(suffix), + usenumpyfunc=True) + except(configparser.NoOptionError): + ticks = None + + return (colormap, norm, ticks) + + +def _setup_indexed_colormap(config, configSectionName, suffix=''): + + ''' + Set up a colormap from the registry + + Parameters + ---------- + config : instance of ConfigParser + the configuration, containing a [plot] section with options that + control plotting + + configSectionName : str + name of config section + + suffix: str, optional + suffix of colormap related options + + colorMapType + + Returns + ------- + colormap : srt + new colormap + + norm : ``SymLogNorm`` object + the norm used to normalize the colormap + + ticks : array of float + the tick marks on the colormap + + Authors + ------- + Xylar Asay-Davis, Milena Veneziani, Greg Streletz + ''' + + colormap = plt.get_cmap(config.get(configSectionName, + 'colormapName{}'.format(suffix))) + + indices = config.getExpression(configSectionName, + 'colormapIndices{}'.format(suffix), + usenumpyfunc=True) + + try: + levels = config.getExpression( + configSectionName, 'colorbarLevels{}'.format(suffix), + usenumpyfunc=True) + except(configparser.NoOptionError): + levels = None + + if levels is not None: + # set under/over values based on the first/last indices in the colormap + underColor = colormap(indices[0]) + overColor = colormap(indices[-1]) + if len(levels)+1 == len(indices): + # we have 2 extra values for the under/over so make the colormap + # without these values + indices = indices[1:-1] + elif len(levels)-1 != len(indices): + # indices list must be either one element shorter + # or one element longer than colorbarLevels list + raise ValueError('length mismatch between indices and ' + 'colorbarLevels') + colormap = cols.ListedColormap(colormap(indices), + 'colormapName{}'.format(suffix)) + colormap.set_under(underColor) + colormap.set_over(overColor) + + norm = cols.BoundaryNorm(levels, colormap.N) + + try: + ticks = config.getExpression( + configSectionName, 'colorbarTicks{}'.format(suffix), + usenumpyfunc=True) + except(configparser.NoOptionError): + ticks = levels + + return (colormap, norm, levels, ticks) def _date_tick(days, pos, calendar='gregorian', includeMonth=True): @@ -1426,5 +1481,27 @@ def _register_custom_colormaps(): plt.register_cmap(name, colorMap) + name = 'Maximenko' + colorArray = np.array([ + [-1, 0., 0.45882352941, 0.76470588235], + [-0.666667, 0., 0.70196078431, 0.90588235294], + [-0.333333, 0.3294117647, 0.87058823529, 1.], + [0., 0.76470588235, 0.94509803921, 0.98039215686], + [0.333333, 1., 1., 0.], + [0.666667, 1., 0.29411764705, 0.], + [1, 1., 0., 0.]], float) + + colorCount = 255 + colorList = np.ones((colorCount, 4), float) + x = colorArray[:, 0] + for cIndex in range(3): + colorList[:, cIndex] = np.interp( + np.linspace(-1., 1., colorCount), + x, colorArray[:, cIndex+1]) + + colorMap = cols.LinearSegmentedColormap.from_list( + name, colorList, N=255) + + plt.register_cmap(name, colorMap) # vim: foldmethod=marker ai ts=4 sts=4 et sw=4 ft=python From 3768ba013677bda4eacb4e48e15961e342ec54d8 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Thu, 22 Feb 2018 22:34:21 -0700 Subject: [PATCH 16/71] Change SSH to match Maximenko dynamic topography --- mpas_analysis/config.default | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/mpas_analysis/config.default b/mpas_analysis/config.default index caba17636..6ae09c339 100644 --- a/mpas_analysis/config.default +++ b/mpas_analysis/config.default @@ -588,11 +588,21 @@ comparisonGrids = ['latlon'] ## sea surface height (SSH) against reference model results and observations # colormap for model/observations -colormapNameResult = Spectral_r +#colormapNameResult = Spectral_r +colormapNameResult = Maximenko # color indices into colormapName for filled contours -colormapIndicesResult = [0, 20, 40, 80, 100, 120, 160, 180, 200, 240, 255] +colormapIndicesResult = numpy.array(numpy.linspace(0, 255, 38), int) # colormap levels/values for contour boundaries -colorbarLevelsResult = [-240., -200., -160., -120., -80., -40., 0., 40., 80., 120.] +colorbarLevelsResult = numpy.arange(-240., 130., 10.) +# colormap levels/values for ticks (defaults to same as levels) +colorbarTicksResult = numpy.arange(-240., 160., 40.) + +# contour line levels +contourLevelsResult = numpy.arange(-240., 130., 10.) +# contour line thickness +contourThicknessResult = 0.25 +# contour color +contourColorResult = 0.25 # colormap for differences colormapNameDifference = RdBu_r From cf0f1b701e4efa2b14dff0fc886cbf8040619d44 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Fri, 23 Feb 2018 11:34:04 -0700 Subject: [PATCH 17/71] add SSH task to the docs --- docs/api.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/api.rst b/docs/api.rst index 5a240eff0..857656b6b 100644 --- a/docs/api.rst +++ b/docs/api.rst @@ -51,6 +51,7 @@ Ocean tasks ClimatologyMapSST ClimatologyMapSSS ClimatologyMapMLD + ClimatologyMapSSH ClimatologyMapAntarcticMelt IndexNino34 MeridionalHeatTransport From d1d5a8a2c02fc9622ebbc2ab8ea8b50d48dbf777 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Fri, 23 Feb 2018 12:00:55 -0700 Subject: [PATCH 18/71] Remove mean from SSH (model and obs) Also change to pressure-adjusted SSH and change some of the title text. --- mpas_analysis/ocean/climatology_map_ssh.py | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/mpas_analysis/ocean/climatology_map_ssh.py b/mpas_analysis/ocean/climatology_map_ssh.py index fe59d3b4d..c5e2c24ee 100644 --- a/mpas_analysis/ocean/climatology_map_ssh.py +++ b/mpas_analysis/ocean/climatology_map_ssh.py @@ -54,7 +54,8 @@ def __init__(self, config, mpasClimatologyTask, componentName='ocean', tags=['climatology', 'horizontalMap', fieldName]) - mpasFieldName = 'timeMonthly_avg_ssh' + mpasFieldName = 'timeMonthly_avg_pressureAdjustedSSH' + iselValues = None sectionName = self.taskName @@ -86,7 +87,8 @@ def __init__(self, config, mpasClimatologyTask, if refConfig is None: - refTitleLabel = 'Observations (AVISO sea-level anomaly)' + refTitleLabel = 'Observations (AVISO Dynamic ' \ + 'Topography, 1993-2010)' observationsDirectory = build_config_full_path( config, 'oceanObservations', @@ -127,7 +129,7 @@ def __init__(self, config, mpasClimatologyTask, subtask.set_plot_info( outFileLabel=outFileLabel, - fieldNameInTitle='SSH', + fieldNameInTitle='Zero-mean SSH', mpasFieldName=mpasFieldName, refFieldName=refFieldName, refTitleLabel=refTitleLabel, @@ -176,6 +178,9 @@ def customize_masked_climatology(self, climatology): # {{{ # scale the field to cm from m climatology[fieldName] = constants.cm_per_m * climatology[fieldName] + # remove the mean + climatology[fieldName] = climatology[fieldName] - \ + climatology[fieldName].mean() return climatology # }}} @@ -245,6 +250,9 @@ def build_observational_dataset(self, fileName): # {{{ # scale the field to cm from m dsObs['zos'] = constants.cm_per_m * dsObs['zos'] + # remove the mean + dsObs['zos'] = dsObs['zos'] -dsObs['zos'].mean() + return dsObs # }}} # }}} From 62196cf827e53d63cb7584f45be92df524c7f259 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Fri, 23 Feb 2018 11:58:09 -0800 Subject: [PATCH 19/71] Remove the mean from model and obs SSH with common mask This leads to a bias plot that just shows differences in spatial pattern, not mean offsets. --- mpas_analysis/ocean/climatology_map_ssh.py | 8 +---- .../ocean/plot_climatology_map_subtask.py | 35 ++++++++++++++++++- 2 files changed, 35 insertions(+), 8 deletions(-) diff --git a/mpas_analysis/ocean/climatology_map_ssh.py b/mpas_analysis/ocean/climatology_map_ssh.py index c5e2c24ee..bab7483f6 100644 --- a/mpas_analysis/ocean/climatology_map_ssh.py +++ b/mpas_analysis/ocean/climatology_map_ssh.py @@ -125,7 +125,7 @@ def __init__(self, config, mpasClimatologyTask, comparisonGridName, remapClimatologySubtask, remapObservationsSubtask, - refConfig) + refConfig, removeMean=True) subtask.set_plot_info( outFileLabel=outFileLabel, @@ -178,9 +178,6 @@ def customize_masked_climatology(self, climatology): # {{{ # scale the field to cm from m climatology[fieldName] = constants.cm_per_m * climatology[fieldName] - # remove the mean - climatology[fieldName] = climatology[fieldName] - \ - climatology[fieldName].mean() return climatology # }}} @@ -250,9 +247,6 @@ def build_observational_dataset(self, fileName): # {{{ # scale the field to cm from m dsObs['zos'] = constants.cm_per_m * dsObs['zos'] - # remove the mean - dsObs['zos'] = dsObs['zos'] -dsObs['zos'].mean() - return dsObs # }}} # }}} diff --git a/mpas_analysis/ocean/plot_climatology_map_subtask.py b/mpas_analysis/ocean/plot_climatology_map_subtask.py index 66395a887..3d68a766b 100644 --- a/mpas_analysis/ocean/plot_climatology_map_subtask.py +++ b/mpas_analysis/ocean/plot_climatology_map_subtask.py @@ -57,6 +57,13 @@ class PlotClimatologyMapSubtask(AnalysisTask): # {{{ The subtask for remapping the MPAS climatology for the reference run that this subtask will plot + removeMean : bool, optional + If True, a common mask for the model and reference data sets is + computed (where both are valid) and the mean over that mask is + subtracted from both the model and reference results. This is + useful for data sets where the desire is to compare the spatial + pattern but the mean offset is not meaningful (e.g. SSH) + outFileLabel : str The prefix on each plot and associated XML file @@ -106,7 +113,7 @@ class PlotClimatologyMapSubtask(AnalysisTask): # {{{ def __init__(self, parentTask, season, comparisonGridName, remapMpasClimatologySubtask, remapObsClimatologySubtask=None, - refConfig=None, depth=None): + refConfig=None, depth=None, removeMean=False): # {{{ ''' Construct one analysis subtask for each plot (i.e. each season and @@ -139,6 +146,13 @@ def __init__(self, parentTask, season, comparisonGridName, Depth the data is being plotted, 'top' for the sea surface 'bot' for the sea floor + removeMean : bool, optional + If True, a common mask for the model and reference data sets is + computed (where both are valid) and the mean over that mask is + subtracted from both the model and reference results. This is + useful for data sets where the desire is to compare the spatial + pattern but the mean offset is not meaningful (e.g. SSH) + Authors ------- Xylar Asay-Davis @@ -151,6 +165,7 @@ def __init__(self, parentTask, season, comparisonGridName, self.remapMpasClimatologySubtask = remapMpasClimatologySubtask self.remapObsClimatologySubtask = remapObsClimatologySubtask self.refConfig = refConfig + self.removeMean = removeMean subtaskName = 'plot{}_{}'.format(season, comparisonGridName) if depth is None: @@ -369,6 +384,24 @@ def run_task(self): # {{{ remappedRefClimatology = remappedRefClimatology.sel( depthSlice=str(depth), drop=True) + if self.removeMean: + if remappedRefClimatology is None: + remappedModelClimatology[self.mpasFieldName] = \ + remappedModelClimatology[self.mpasFieldName] - \ + remappedModelClimatology[self.mpasFieldName].mean() + else: + masked = remappedModelClimatology[self.mpasFieldName].where( + remappedRefClimatology[self.refFieldName].notnull()) + remappedModelClimatology[self.mpasFieldName] = \ + remappedModelClimatology[self.mpasFieldName] - \ + masked.mean() + + masked = remappedRefClimatology[self.refFieldName].where( + remappedModelClimatology[self.mpasFieldName].notnull()) + remappedRefClimatology[self.refFieldName] = \ + remappedRefClimatology[self.refFieldName] - \ + masked.mean() + if self.comparisonGridName == 'latlon': self._plot_latlon(remappedModelClimatology, remappedRefClimatology) elif self.comparisonGridName == 'antarctic': From 45146bf7053bea76c0d54f344d52b753f1bb1933 Mon Sep 17 00:00:00 2001 From: "Adrian K. Turner" Date: Mon, 26 Feb 2018 12:41:34 -0700 Subject: [PATCH 20/71] Minor modifications to MPAS-Seaice documentation --- docs/{mpascice.rst => mpasseaice.rst} | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) rename docs/{mpascice.rst => mpasseaice.rst} (93%) diff --git a/docs/mpascice.rst b/docs/mpasseaice.rst similarity index 93% rename from docs/mpascice.rst rename to docs/mpasseaice.rst index ce1a3c46f..78060d37b 100644 --- a/docs/mpascice.rst +++ b/docs/mpasseaice.rst @@ -1,8 +1,7 @@ -MPAS Sea Ice +MPAS-Seaice ============ -The Model for Prediction Across Scales Sea Ice (MPAS Sea Ice, sometimes called -MPAS-CICE because of the physics it has inherited from the CICE sea-ice model) +The Model for Prediction Across Scales Sea Ice (MPAS-Seaice) is designed for the simulations of sea ice on unstructured grids supported by the MPAS framework. The model has not yet been publicly released and does not have public documentation. From 5552d71e9c7e25433c76b53bebae101b778b218d Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Wed, 7 Mar 2018 14:31:49 -0700 Subject: [PATCH 21/71] Add ability to not use ncremap in MPAS remap task Also, switch the depth-slice remapping task to not use ncremap, since the depth coordinate seems to confuse ncremap. --- .../ocean/remap_depth_slices_subtask.py | 2 +- .../remap_mpas_climatology_subtask.py | 31 ++++++++++++++----- 2 files changed, 24 insertions(+), 9 deletions(-) diff --git a/mpas_analysis/ocean/remap_depth_slices_subtask.py b/mpas_analysis/ocean/remap_depth_slices_subtask.py index b2102ae59..7af2a7b35 100644 --- a/mpas_analysis/ocean/remap_depth_slices_subtask.py +++ b/mpas_analysis/ocean/remap_depth_slices_subtask.py @@ -86,7 +86,7 @@ def __init__(self, mpasClimatologyTask, parentTask, climatologyName, # (RemapMpasClimatologySubtask) super(RemapDepthSlicesSubtask, self).__init__( mpasClimatologyTask, parentTask, climatologyName, variableList, - seasons, comparisonGridNames, iselValues) + seasons, comparisonGridNames, iselValues, useNcremap=False) def run_task(self): # {{{ """ diff --git a/mpas_analysis/shared/climatology/remap_mpas_climatology_subtask.py b/mpas_analysis/shared/climatology/remap_mpas_climatology_subtask.py index 771e97649..999ba5795 100644 --- a/mpas_analysis/shared/climatology/remap_mpas_climatology_subtask.py +++ b/mpas_analysis/shared/climatology/remap_mpas_climatology_subtask.py @@ -58,6 +58,11 @@ class RemapMpasClimatologySubtask(AnalysisTask): # {{{ If ``comparisonGridName`` is not ``None``, the name of a restart file from which the MPAS mesh can be read. + useNcremap : bool, optional + Whether to use ncremap to do the remapping (the other option being + an internal python code that handles more grid types and extra + dimensions) + Authors ------- Xylar Asay-Davis @@ -65,7 +70,8 @@ class RemapMpasClimatologySubtask(AnalysisTask): # {{{ def __init__(self, mpasClimatologyTask, parentTask, climatologyName, variableList, seasons, comparisonGridNames=['latlon'], - iselValues=None, subtaskName='remapMpasClimatology'): + iselValues=None, subtaskName='remapMpasClimatology', + useNcremap=None): # {{{ ''' Construct the analysis task and adds it as a subtask of the @@ -104,6 +110,14 @@ def __init__(self, mpasClimatologyTask, parentTask, climatologyName, subtaskName : str, optional The name of the subtask + useNcremap : bool, optional + Whether to use ncremap to do the remapping (the other option being + an internal python code that handles more grid types and extra + dimensions). This defaults to the config option ``useNcremap`` + if it is not explicitly given. If a comparison grid other than + ``latlon`` is given, ncremap is not supported so this flag is set + to ``False``. + Authors ------- Xylar Asay-Davis @@ -133,6 +147,12 @@ def __init__(self, mpasClimatologyTask, parentTask, climatologyName, # correctly self._fillValue = -9.99999979021476795361e+33 + if useNcremap is None: + self.useNcremap = self.config.getboolean('climatology', + 'useNcremap') + else: + self.useNcremap = useNcremap + # }}} def setup_and_check(self): # {{{ @@ -511,16 +531,11 @@ def _remap(self, inFileName, outFileName, remapper, comparisonGridName): # no remapping is needed return - useNcremap = self.config.getboolean('climatology', 'useNcremap') - - if comparisonGridName != 'latlon': - # ncremap doesn't support grids other than lat/lon - useNcremap = False - renormalizationThreshold = self.config.getfloat( 'climatology', 'renormalizationThreshold') - if useNcremap: + # ncremap doesn't support grids other than lat/lon + if self.useNcremap and comparisonGridName == 'latlon': remapper.remap_file(inFileName=inFileName, outFileName=outFileName, overwrite=True, From 80206008ff3c27003a98d7207b446618bc9a2390 Mon Sep 17 00:00:00 2001 From: Luke Van Roekel Date: Wed, 7 Mar 2018 15:34:19 -0600 Subject: [PATCH 22/71] Adds ability to compare to ARGO data with depth This commit follows the SOSE level capability but compares globally to ARGO data from Roemmich-Gilson Argo Climatology. --- mpas_analysis/config.default | 70 +++ mpas_analysis/ocean/__init__.py | 2 + mpas_analysis/ocean/climatology_map_argo.py | 461 ++++++++++++++++++++ run_mpas_analysis | 5 + 4 files changed, 538 insertions(+) create mode 100644 mpas_analysis/ocean/climatology_map_argo.py diff --git a/mpas_analysis/config.default b/mpas_analysis/config.default index 5a5f93cfa..2a7632b2e 100644 --- a/mpas_analysis/config.default +++ b/mpas_analysis/config.default @@ -213,6 +213,7 @@ mhtSubdirectory = MHT meltSubdirectory = Melt soseSubdirectory = SOSE sshSubdirectory = SSH +argoSubdirectory = ARGO # first and last year of SST observational climatology (preferably one of the # two ranges given below) @@ -703,6 +704,41 @@ normArgsDifference = {'vmin': -2., 'vmax': 2.} # place the ticks automatically by default # colorbarTicksDifference = numpy.linspace(-2., 2., 9) +[climatologyMapArgoTemperature] +## options related to plotting climatology maps of Global +## potential temperature at various levels against +## reference model results and Roemmich-Gilson Argo Climatology + +# comparison grid(s) +comparisonGrids = ['latlon'] + +# Times for comparison times (Jan, Feb, Mar, Apr, May, Jun, Jul, Aug, Sep, Oct, +# Nov, Dec, JFM, AMJ, JAS, OND, ANN) +seasons = ['ANN','JAS','JFM'] + +# list of depths in meters (positive up) at which to analyze, 'top' for the +# sea surface, 'bot' for the sea floor +depths = ['top', -25, -50, -100, -150, -200, -400, -800, -1500] + + +# colormap for model/observations +colormapNameResult = RdBu_r +# the type of norm used in the colormap +normTypeResult = linear +# A dictionary with keywords for the SemiLogNorm +normArgsResult = {'vmin': -2., 'vmax': 30.} +# place the ticks automatically by default +# colorbarTicksResult = numpy.linspace(-2., 2., 9) + +# colormap for differences +colormapNameDifference = RdBu_r +# the type of norm used in the colormap +normTypeDifference = linear +# A dictionary with keywords for the SemiLogNorm +normArgsDifference = {'vmin': -2., 'vmax': 2.} +# place the ticks automatically by default +# colorbarTicksDifference = numpy.linspace(-2., 2., 9) + [climatologyMapSoseSalinity] ## options related to plotting climatology maps of Antarctic ## salinity at various levels, including the sea floor against @@ -738,6 +774,40 @@ normArgsDifference = {'vmin': -0.5, 'vmax': 0.5} # place the ticks automatically by default # colorbarTicksDifference = numpy.linspace(-0.5, 0.5, 9) +[climatologyMapArgoSalinity] +## options related to plotting climatology maps of Global +## salinity at various levels against +## reference model results and the Roemmich-Gilson Argo Climatology + +# comparison grid(s) +comparisonGrids = ['latlon'] + +# Times for comparison times (Jan, Feb, Mar, Apr, May, Jun, Jul, Aug, Sep, Oct, +# Nov, Dec, JFM, AMJ, JAS, OND, ANN) +seasons = ['ANN','JFM','JAS'] + +# list of depths in meters (positive up) at which to analyze, 'top' for the +# sea surface +depths = ['top', -25, -50, -100, -150, -200, -400, -600, -800, -1500] +#depths = ['top',-50] +# colormap for model/observations +colormapNameResult = BuOr +# the type of norm used in the colormap +normTypeResult = linear +# A dictionary with keywords for the SemiLogNorm +normArgsResult = {'vmin': 30, 'vmax': 39.0} +# place the ticks automatically by default +# colorbarTicksResult = numpy.linspace(34.2, 35.2, 9) + +# colormap for differences +colormapNameDifference = RdBu_r +# the type of norm used in the colormap +normTypeDifference = linear +# A dictionary with keywords for the SemiLogNorm +normArgsDifference = {'vmin': -0.5, 'vmax': 0.5} +# place the ticks automatically by default +# colorbarTicksDifference = numpy.linspace(-0.5, 0.5, 9) + [climatologyMapSeaIceConcNH] ## options related to plotting horizontally remapped climatologies of ## sea ice concentration against reference model results and observations diff --git a/mpas_analysis/ocean/__init__.py b/mpas_analysis/ocean/__init__.py index 359795fb5..f6f53384b 100644 --- a/mpas_analysis/ocean/__init__.py +++ b/mpas_analysis/ocean/__init__.py @@ -6,6 +6,8 @@ ClimatologyMapAntarcticMelt from mpas_analysis.ocean.climatology_map_sose import \ ClimatologyMapSoseTemperature, ClimatologyMapSoseSalinity +from mpas_analysis.ocean.climatology_map_argo import \ + ClimatologyMapArgoTemperature, ClimatologyMapArgoSalinity from mpas_analysis.ocean.time_series_temperature_anomaly import \ TimeSeriesTemperatureAnomaly diff --git a/mpas_analysis/ocean/climatology_map_argo.py b/mpas_analysis/ocean/climatology_map_argo.py new file mode 100644 index 000000000..e33b05b6a --- /dev/null +++ b/mpas_analysis/ocean/climatology_map_argo.py @@ -0,0 +1,461 @@ +''' +Analysis tasks for comparing Global climatology maps against ARGO data. + +Authors +------- +Luke Van Roekel +''' + +import xarray as xr +import numpy as np + +from mpas_analysis.shared import AnalysisTask + +from mpas_analysis.ocean.remap_depth_slices_subtask import \ + RemapDepthSlicesSubtask + +from mpas_analysis.ocean.plot_climatology_map_subtask import \ + PlotClimatologyMapSubtask + +from mpas_analysis.shared.io.utility import build_config_full_path + +from mpas_analysis.shared.climatology import RemapObservedClimatologySubtask, \ + RemapMpasClimatologySubtask + +from mpas_analysis.shared.grid import LatLonGridDescriptor + +from mpas_analysis.shared.mpas_xarray import mpas_xarray + + +class ClimatologyMapArgoTemperature(AnalysisTask): # {{{ + """ + An analysis task for comparison of antarctic temperature against SOSE + fields + + Authors + ------- + Luke Van Roekel, Xylar Asay-Davis + """ + + def __init__(self, config, mpasClimatologyTask, + refConfig=None): # {{{ + """ + Construct the analysis task. + + Parameters + ---------- + config : ``MpasAnalysisConfigParser`` + Configuration options + + mpasClimatologyTask : ``MpasClimatologyTask`` + The task that produced the climatology to be remapped and plotted + + refConfig : ``MpasAnalysisConfigParser``, optional + Configuration options for a reference run (if any) + + Authors + ------- + Luke Van Roekel, Xylar Asay-Davis + """ + fieldName = 'temperature' + # call the constructor from the base class (AnalysisTask) + super(ClimatologyMapArgoTemperature, self).__init__( + config=config, taskName='climatologyMapArgoTemperature', + componentName='ocean', + tags=['climatology', 'horizontalMap', 'argo', fieldName]) + + sectionName = self.taskName + + mpasFieldName = 'timeMonthly_avg_activeTracers_temperature' + iselValues = None + + # read in what seasons we want to plot + seasons = config.getExpression(sectionName, 'seasons') + + if len(seasons) == 0: + raise ValueError('config section {} does not contain valid list ' + 'of seasons'.format(sectionName)) + + comparisonGridNames = config.getExpression(sectionName, + 'comparisonGrids') + + if len(comparisonGridNames) == 0: + raise ValueError('config section {} does not contain valid list ' + 'of comparison grids'.format(sectionName)) + + depths = config.getExpression(sectionName, 'depths') + + if len(depths) == 0: + raise ValueError('config section {} does not contain valid ' + 'list of depths'.format(sectionName)) + + # the variable 'timeMonthly_avg_landIceFreshwaterFlux' will be added to + # mpasClimatologyTask along with the seasons. + remapClimatologySubtask = RemapDepthSlicesSubtask( + mpasClimatologyTask=mpasClimatologyTask, + parentTask=self, + climatologyName=fieldName, + variableList=[mpasFieldName], + seasons=seasons, + depths=depths, + comparisonGridNames=comparisonGridNames, + iselValues=iselValues) + + if refConfig is None: + + refTitleLabel = 'Roemmich-Gilson Argo Climatology: Temperature' + + observationsDirectory = build_config_full_path( + config, 'oceanObservations', 'argoSubdirectory') + + obsFileName = \ + '{}/ArgoClimatology_TS.nc'.format( + observationsDirectory) + refFieldName = 'theta' + outFileLabel = 'tempArgo' + galleryName = 'Roemmich-Gilson Climatology: ARGO' + diffTitleLabel = 'Model - Argo' + + remapObservationsSubtask = RemapArgoClimatology( + parentTask=self, seasons=seasons, fileName=obsFileName, + outFilePrefix=refFieldName, + fieldName=refFieldName, + depths=depths, + comparisonGridNames=comparisonGridNames) + + self.add_subtask(remapObservationsSubtask) + + else: + remapObservationsSubtask = None + refRunName = refConfig.get('runs', 'mainRunName') + galleryName = 'Ref: {}'.format(refRunName) + refTitleLabel = galleryName + + refFieldName = mpasFieldName + outFileLabel = 'temp' + diffTitleLabel = 'Main - Reference' + + for comparisonGridName in comparisonGridNames: + for season in seasons: + for depth in depths: + subtask = PlotClimatologyMapSubtask( + parentTask=self, + season=season, + comparisonGridName=comparisonGridName, + remapMpasClimatologySubtask=remapClimatologySubtask, + remapObsClimatologySubtask=remapObservationsSubtask, + refConfig=refConfig, + depth=depth) + + subtask.set_plot_info( + outFileLabel=outFileLabel, + fieldNameInTitle='Temperature', + mpasFieldName=mpasFieldName, + refFieldName=refFieldName, + refTitleLabel=refTitleLabel, + diffTitleLabel=diffTitleLabel, + unitsLabel=r'$^\circ$C', + imageCaption='Temperature', + galleryGroup='Temperature', + groupSubtitle=None, + groupLink='temp', + galleryName=galleryName) + + self.add_subtask(subtask) + # }}} + + # }}} + + +class ClimatologyMapArgoSalinity(AnalysisTask): # {{{ + """ + An analysis task for comparison of Global Temperature against Argo + fields + + Authors + ------- + Xylar Asay-Davis, Luke Van Roekel + """ + + def __init__(self, config, mpasClimatologyTask, + refConfig=None): # {{{ + """ + Construct the analysis task. + + Parameters + ---------- + config : ``MpasAnalysisConfigParser`` + Configuration options + + mpasClimatologyTask : ``MpasClimatologyTask`` + The task that produced the climatology to be remapped and plotted + + refConfig : ``MpasAnalysisConfigParser``, optional + Configuration options for a reference run (if any) + + Authors + ------- + Xylar Asay-Davis, Luke Van Roekel + """ + fieldName = 'salinity' + # call the constructor from the base class (AnalysisTask) + super(ClimatologyMapArgoSalinity, self).__init__( + config=config, taskName='climatologyMapArgoSalinity', + componentName='ocean', + tags=['climatology', 'horizontalMap', 'argo', fieldName]) + + sectionName = self.taskName + + mpasFieldName = 'timeMonthly_avg_activeTracers_salinity' + iselValues = None + + # read in what seasons we want to plot + seasons = config.getExpression(sectionName, 'seasons') + + if len(seasons) == 0: + raise ValueError('config section {} does not contain valid list ' + 'of seasons'.format(sectionName)) + + comparisonGridNames = config.getExpression(sectionName, + 'comparisonGrids') + + if len(comparisonGridNames) == 0: + raise ValueError('config section {} does not contain valid list ' + 'of comparison grids'.format(sectionName)) + + depths = config.getExpression(sectionName, 'depths') + + if len(depths) == 0: + raise ValueError('config section {} does not contain valid ' + 'list of depths'.format(sectionName)) + + # the variable 'timeMonthly_avg_landIceFreshwaterFlux' will be added to + # mpasClimatologyTask along with the seasons. + remapClimatologySubtask = RemapDepthSlicesSubtask( + mpasClimatologyTask=mpasClimatologyTask, + parentTask=self, + climatologyName=fieldName, + variableList=[mpasFieldName], + seasons=seasons, + depths=depths, + comparisonGridNames=comparisonGridNames, + iselValues=iselValues) + + if refConfig is None: + + refTitleLabel = 'Roemmich-Gilson Argo Climatology: Salinity' + + observationsDirectory = build_config_full_path( + config, 'oceanObservations', 'argoSubdirectory') + + obsFileName = \ + '{}/ArgoClimatology_TS.nc'.format( + observationsDirectory) + refFieldName = 'salinity' + outFileLabel = 'salinArgo' + galleryName = 'Roemmich-Gilson Climatology: Argo' + diffTitleLabel = 'Model - Argo' + + remapObservationsSubtask = RemapArgoClimatology( + parentTask=self, seasons=seasons, fileName=obsFileName, + outFilePrefix=refFieldName, + fieldName=refFieldName, + depths=depths, + comparisonGridNames=comparisonGridNames) + + self.add_subtask(remapObservationsSubtask) + + else: + remapObservationsSubtask = None + refRunName = refConfig.get('runs', 'mainRunName') + galleryName = None + refTitleLabel = 'Ref: {}'.format(refRunName) + + refFieldName = mpasFieldName + outFileLabel = 'salin' + diffTitleLabel = 'Main - Reference' + + for comparisonGridName in comparisonGridNames: + for season in seasons: + for depth in depths: + subtask = PlotClimatologyMapSubtask( + parentTask=self, + season=season, + comparisonGridName=comparisonGridName, + remapMpasClimatologySubtask=remapClimatologySubtask, + remapObsClimatologySubtask=remapObservationsSubtask, + refConfig=refConfig, + depth=depth) + + subtask.set_plot_info( + outFileLabel=outFileLabel, + fieldNameInTitle='Salinity', + mpasFieldName=mpasFieldName, + refFieldName=refFieldName, + refTitleLabel=refTitleLabel, + diffTitleLabel=diffTitleLabel, + unitsLabel=r'PSU', + imageCaption='Salinity', + galleryGroup='Salinity', + groupSubtitle=None, + groupLink='salin', + galleryName=galleryName) + + self.add_subtask(subtask) + # }}} + + # }}} + + +class RemapArgoClimatology(RemapObservedClimatologySubtask): + # {{{ + """ + A subtask for reading and remapping SOSE fields to the comparison grid + + Authors + ------- + Xylar Asay-Davis, Luke Van Roekel + """ + + def __init__(self, parentTask, seasons, fileName, outFilePrefix, + fieldName, depths, + comparisonGridNames=['latlon'], + subtaskName='remapObservations'): + # {{{ + ''' + Construct one analysis subtask for each plot (i.e. each season and + comparison grid) and a subtask for computing climatologies. + + Parameters + ---------- + parentTask : ``AnalysisTask`` + The parent (master) task for this subtask + + seasons : list of str + A list of seasons (keys in ``constants.monthDictionary``) over + which the climatology should be computed. + + fileName : str + The name of the observation file + + outFilePrefix : str + The prefix in front of output files and mapping files, typically + the name of the field being remapped + + fieldName : str + The name of the 3D field to remap + + depths : list of {None, float, 'top', 'bot'} + A list of depths at which the climatology will be sliced in the + vertical. + + comparisonGridNames : list of {'latlon', 'antarctic'}, optional + The name(s) of the comparison grid to use for remapping. + + subtaskName : str, optional + The name of the subtask + + Authors + ------- + Xylar Asay-Davis, Luke Van Roekel + + ''' + + self.fieldName = fieldName + self.depths = depths + + # call the constructor from the base class + # (RemapObservedClimatologySubtask) + super(RemapArgoClimatology, self).__init__( + parentTask, seasons, fileName, outFilePrefix, + comparisonGridNames, subtaskName) + # }}} + + def get_observation_descriptor(self, fileName): # {{{ + ''' + get a MeshDescriptor for the observation grid + + Parameters + ---------- + fileName : str + observation file name describing the source grid + + Returns + ------- + obsDescriptor : ``MeshDescriptor`` + The descriptor for the observation grid + + Authors + ------- + Xylar Asay-Davis, Luke Van Roekel + ''' + + # Load Argo observational Data + dsObs = self.build_observational_dataset(fileName) + + # create a descriptor of the observation grid using Lat/Lon + # coordinates + obsDescriptor = LatLonGridDescriptor.read(ds=dsObs, + latVarName='latCoord', + lonVarName='lonCoord') + dsObs.close() + return obsDescriptor # }}} + + def build_observational_dataset(self, fileName): # {{{ + ''' + read in the data sets for observations, and possibly rename some + variables and dimensions + + Parameters + ---------- + fileName : str + observation file name + + Returns + ------- + dsObs : ``xarray.Dataset`` + The observational dataset + + Authors + ------- + Xylar Asay-Davis, Luke Van Roekel + ''' + + # Load Argo observational data + dsObs = xr.open_dataset(fileName) + + # Rename coordinates to be consistent with other datasets + dsObs.rename({'month':'calmonth', 'LATITUDE': 'latCoord', + 'LONGITUDE':'lonCoord', 'DEPTH': 'depth'}, inplace=True) + dsObs.coords['LATITUDE'] = dsObs['latCoord'] + dsObs.coords['LONGITUDE'] = dsObs['lonCoord'] + dsObs.coords['DEPTH'] = dsObs['depth'] + dsObs.coords['month'] = ('Time', np.array(dsObs['calmonth'], int)) + + # no meaningful year since this is already a climatology + dsObs.coords['year'] = ('Time', np.ones(dsObs.dims['Time'], int)) + dsObs = mpas_xarray.subset_variables(dsObs, [self.fieldName, 'month']) + + slices = [] + field = dsObs[self.fieldName] + for depth in self.depths: + if depth == 'top': + slices.append(field.sel(method='nearest', depth=0.).drop( + 'depth')) + elif depth == 'bot': + slices.append(botField) + else: + slices.append(field.sel(method='nearest', depth=depth).drop( + 'depth')) + + depthNames = [str(depth) for depth in self.depths] + field = xr.concat(slices, dim='depthSlice') + + dsObs = xr.Dataset(data_vars={self.fieldName: field}, + coords={'depthSlice': depthNames}) + + return dsObs # }}} + + # }}} + +# vim: foldmethod=marker ai ts=4 sts=4 et sw=4 ft=python diff --git a/run_mpas_analysis b/run_mpas_analysis index 9c4aa4e1b..87d608229 100755 --- a/run_mpas_analysis +++ b/run_mpas_analysis @@ -91,6 +91,11 @@ def build_analysis_list(config, refConfig): # {{{ config, oceanClimatolgyTask, refConfig)) analyses.append(ocean.ClimatologyMapSoseSalinity( config, oceanClimatolgyTask, refConfig)) + analyses.append(ocean.ClimatologyMapArgoTemperature( + config, oceanClimatolgyTask, refConfig)) + analyses.append(ocean.ClimatologyMapArgoSalinity( + config, oceanClimatolgyTask, refConfig)) + analyses.append(ocean.ClimatologyMapAntarcticMelt(config, oceanClimatolgyTask, refConfig)) From 3cc66652a0038c97003b269f7a3c35381de2f815 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Wed, 7 Mar 2018 17:46:43 -0600 Subject: [PATCH 23/71] Add support for specifying the anomaly ref year This is useful for runs that include a spin-up phase and anomalies are only of interest after the spin-up has completed (e.g. the last CORE-II cycle in a G-case E3SM run). --- mpas_analysis/config.default | 5 +++++ mpas_analysis/ocean/compute_anomaly_subtask.py | 8 ++++++-- .../shared/time_series/mpas_time_series_task.py | 15 ++++++++++----- 3 files changed, 21 insertions(+), 7 deletions(-) diff --git a/mpas_analysis/config.default b/mpas_analysis/config.default index 5a5f93cfa..dacd54d32 100644 --- a/mpas_analysis/config.default +++ b/mpas_analysis/config.default @@ -184,6 +184,11 @@ renormalizationThreshold = 0.01 ## options related to producing time series plots, often to compare against ## observations and previous runs +# the year from which to compute anomalies if not the start year of the +# simulation. This might be useful if a long spin-up cycle is performed and +# only the anomaly over a later span of years is of interest. +# anomalyRefYear = 249 + # start and end years for timeseries analysis. Using out-of-bounds values # like start_year = 1 and end_year = 9999 will be clipped to the valid range # of years, and is a good way of insuring that all values are used. diff --git a/mpas_analysis/ocean/compute_anomaly_subtask.py b/mpas_analysis/ocean/compute_anomaly_subtask.py index 49773a538..293ac7659 100644 --- a/mpas_analysis/ocean/compute_anomaly_subtask.py +++ b/mpas_analysis/ocean/compute_anomaly_subtask.py @@ -145,12 +145,16 @@ def run_task(self): # {{{ startDate = config.get('timeSeries', 'startDate') endDate = config.get('timeSeries', 'endDate') - simulationStartTime = get_simulation_start_time(self.runStreams) + if config.has_option('timeSeries', 'anomalyRefYear'): + anomalyYear = config.getint('timeSeries', 'anomalyRefYear') + anomalyRefDate = '{:04d}-01-01_00:00:00'.format(anomalyYear) + else: + anomalyRefDate = get_simulation_start_time(self.runStreams) ds = compute_moving_avg_anomaly_from_start( timeSeriesFileName=self.inputFile, variableList=self.variableList, - simulationStartTime=simulationStartTime, + simulationStartTime=anomalyRefDate, startDate=startDate, endDate=endDate, calendar=self.calendar, diff --git a/mpas_analysis/shared/time_series/mpas_time_series_task.py b/mpas_analysis/shared/time_series/mpas_time_series_task.py index 2c194415a..a6ef1fc1d 100644 --- a/mpas_analysis/shared/time_series/mpas_time_series_task.py +++ b/mpas_analysis/shared/time_series/mpas_time_series_task.py @@ -161,12 +161,17 @@ def setup_and_check(self): # {{{ os.path.basename(self.inputFiles[-1])) # Make sure first year of data is included for computing anomalies - simulationStartTime = get_simulation_start_time(self.runStreams) - firstYear = int(simulationStartTime[0:4]) - endDateFirstYear = '{:04d}-12-31_23:59:59'.format(firstYear) + if config.has_option('timeSeries', 'anomalyRefYear'): + anomalyYear = config.getint('timeSeries', 'anomalyRefYear') + anomalyStartDate = '{:04d}-01-01_00:00:00'.format(anomalyYear) + else: + anomalyStartDate = get_simulation_start_time(self.runStreams) + anomalyYear = int(anomalyStartDate[0:4]) + + anomalyEndDate = '{:04d}-12-31_23:59:59'.format(anomalyYear) firstYearInputFiles = self.historyStreams.readpath( - streamName, startDate=simulationStartTime, - endDate=endDateFirstYear, + streamName, startDate=anomalyStartDate, + endDate=anomalyEndDate, calendar=self.calendar) for fileName in firstYearInputFiles: if fileName not in self.inputFiles: From b477f1c6f623cd74d4f766474485751bbb638375 Mon Sep 17 00:00:00 2001 From: Luke Van Roekel Date: Thu, 8 Mar 2018 01:12:36 -0500 Subject: [PATCH 24/71] Fixes issue with remap file name the argo task caused an error when run with the SOSE task due to same name remap files and different depth slices --- mpas_analysis/ocean/climatology_map_argo.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/mpas_analysis/ocean/climatology_map_argo.py b/mpas_analysis/ocean/climatology_map_argo.py index e33b05b6a..724e8da1f 100644 --- a/mpas_analysis/ocean/climatology_map_argo.py +++ b/mpas_analysis/ocean/climatology_map_argo.py @@ -57,7 +57,7 @@ def __init__(self, config, mpasClimatologyTask, ------- Luke Van Roekel, Xylar Asay-Davis """ - fieldName = 'temperature' + fieldName = 'temperatureARGO' # call the constructor from the base class (AnalysisTask) super(ClimatologyMapArgoTemperature, self).__init__( config=config, taskName='climatologyMapArgoTemperature', @@ -155,8 +155,8 @@ def __init__(self, config, mpasClimatologyTask, refTitleLabel=refTitleLabel, diffTitleLabel=diffTitleLabel, unitsLabel=r'$^\circ$C', - imageCaption='Temperature', - galleryGroup='Temperature', + imageCaption='ARGO_Temperature', + galleryGroup='ARGO_Temperature', groupSubtitle=None, groupLink='temp', galleryName=galleryName) @@ -197,7 +197,7 @@ def __init__(self, config, mpasClimatologyTask, ------- Xylar Asay-Davis, Luke Van Roekel """ - fieldName = 'salinity' + fieldName = 'salinityARGO' # call the constructor from the base class (AnalysisTask) super(ClimatologyMapArgoSalinity, self).__init__( config=config, taskName='climatologyMapArgoSalinity', @@ -295,8 +295,8 @@ def __init__(self, config, mpasClimatologyTask, refTitleLabel=refTitleLabel, diffTitleLabel=diffTitleLabel, unitsLabel=r'PSU', - imageCaption='Salinity', - galleryGroup='Salinity', + imageCaption='ARGO_Salinity', + galleryGroup='ARGO_Salinity', groupSubtitle=None, groupLink='salin', galleryName=galleryName) From 8e63a93e88b094f9aa19862d4dd11b470db9b788 Mon Sep 17 00:00:00 2001 From: Luke Van Roekel Date: Thu, 8 Mar 2018 11:24:11 -0500 Subject: [PATCH 25/71] Changes formatting and variable naming for remap --- mpas_analysis/ocean/climatology_map_argo.py | 12 ++++++------ mpas_analysis/ocean/climatology_map_sose.py | 12 ++++++------ 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/mpas_analysis/ocean/climatology_map_argo.py b/mpas_analysis/ocean/climatology_map_argo.py index 724e8da1f..2eddda375 100644 --- a/mpas_analysis/ocean/climatology_map_argo.py +++ b/mpas_analysis/ocean/climatology_map_argo.py @@ -111,7 +111,7 @@ def __init__(self, config, mpasClimatologyTask, obsFileName = \ '{}/ArgoClimatology_TS.nc'.format( observationsDirectory) - refFieldName = 'theta' + refFieldName = 'thetaArgo' outFileLabel = 'tempArgo' galleryName = 'Roemmich-Gilson Climatology: ARGO' diffTitleLabel = 'Model - Argo' @@ -155,8 +155,8 @@ def __init__(self, config, mpasClimatologyTask, refTitleLabel=refTitleLabel, diffTitleLabel=diffTitleLabel, unitsLabel=r'$^\circ$C', - imageCaption='ARGO_Temperature', - galleryGroup='ARGO_Temperature', + imageCaption='Model temperature compared with ARGO observations', + galleryGroup='Argo Temperature', groupSubtitle=None, groupLink='temp', galleryName=galleryName) @@ -251,7 +251,7 @@ def __init__(self, config, mpasClimatologyTask, obsFileName = \ '{}/ArgoClimatology_TS.nc'.format( observationsDirectory) - refFieldName = 'salinity' + refFieldName = 'salinityArgo' outFileLabel = 'salinArgo' galleryName = 'Roemmich-Gilson Climatology: Argo' diffTitleLabel = 'Model - Argo' @@ -295,8 +295,8 @@ def __init__(self, config, mpasClimatologyTask, refTitleLabel=refTitleLabel, diffTitleLabel=diffTitleLabel, unitsLabel=r'PSU', - imageCaption='ARGO_Salinity', - galleryGroup='ARGO_Salinity', + imageCaption='Model Salinity compared with Argo observations', + galleryGroup='Argo Salinity', groupSubtitle=None, groupLink='salin', galleryName=galleryName) diff --git a/mpas_analysis/ocean/climatology_map_sose.py b/mpas_analysis/ocean/climatology_map_sose.py index ef23524ab..d3668947f 100644 --- a/mpas_analysis/ocean/climatology_map_sose.py +++ b/mpas_analysis/ocean/climatology_map_sose.py @@ -57,7 +57,7 @@ def __init__(self, config, mpasClimatologyTask, ------- Xylar Asay-Davis """ - fieldName = 'temperature' + fieldName = 'temperatureSOSE' # call the constructor from the base class (AnalysisTask) super(ClimatologyMapSoseTemperature, self).__init__( config=config, taskName='climatologyMapSoseTemperature', @@ -112,7 +112,7 @@ def __init__(self, config, mpasClimatologyTask, '{}/SOSE_2005-2010_monthly_pot_temp_6000.0x' \ '6000.0km_10.0km_Antarctic_stereo.nc'.format( observationsDirectory) - refFieldName = 'theta' + refFieldName = 'thetaSOSE' outFileLabel = 'tempSOSE' galleryName = 'State Estimate: SOSE' diffTitleLabel = 'Model - State Estimate' @@ -157,7 +157,7 @@ def __init__(self, config, mpasClimatologyTask, refTitleLabel=refTitleLabel, diffTitleLabel=diffTitleLabel, unitsLabel=r'$^\circ$C', - imageCaption='Temperature', + imageCaption='Temperature compared with SOSE', galleryGroup='Temperature', groupSubtitle=None, groupLink='temp', @@ -199,7 +199,7 @@ def __init__(self, config, mpasClimatologyTask, ------- Xylar Asay-Davis """ - fieldName = 'salinity' + fieldName = 'salinitySOSE' # call the constructor from the base class (AnalysisTask) super(ClimatologyMapSoseSalinity, self).__init__( config=config, taskName='climatologyMapSoseSalinity', @@ -254,7 +254,7 @@ def __init__(self, config, mpasClimatologyTask, '{}/SOSE_2005-2010_monthly_salinity_6000.0x' \ '6000.0km_10.0km_Antarctic_stereo.nc'.format( observationsDirectory) - refFieldName = 'salinity' + refFieldName = 'salinitySOSE' outFileLabel = 'salinSOSE' galleryName = 'State Estimate: SOSE' diffTitleLabel = 'Model - State Estimate' @@ -299,7 +299,7 @@ def __init__(self, config, mpasClimatologyTask, refTitleLabel=refTitleLabel, diffTitleLabel=diffTitleLabel, unitsLabel=r'PSU', - imageCaption='Salinity', + imageCaption='Salinity compared with SOSE', galleryGroup='Salinity', groupSubtitle=None, groupLink='salin', From e580a2470282bd8e22325b175ed4a84b729d2ffa Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Thu, 8 Mar 2018 10:50:55 -0700 Subject: [PATCH 26/71] Some formatting clean up and removing 'bot' Argo tasks don't (yet) support plotting the bottom T and S. --- mpas_analysis/config.default | 4 ++-- mpas_analysis/ocean/climatology_map_argo.py | 21 ++++++++++----------- 2 files changed, 12 insertions(+), 13 deletions(-) diff --git a/mpas_analysis/config.default b/mpas_analysis/config.default index 2a7632b2e..fc567efc7 100644 --- a/mpas_analysis/config.default +++ b/mpas_analysis/config.default @@ -717,7 +717,7 @@ comparisonGrids = ['latlon'] seasons = ['ANN','JAS','JFM'] # list of depths in meters (positive up) at which to analyze, 'top' for the -# sea surface, 'bot' for the sea floor +# sea surface depths = ['top', -25, -50, -100, -150, -200, -400, -800, -1500] @@ -789,7 +789,7 @@ seasons = ['ANN','JFM','JAS'] # list of depths in meters (positive up) at which to analyze, 'top' for the # sea surface depths = ['top', -25, -50, -100, -150, -200, -400, -600, -800, -1500] -#depths = ['top',-50] + # colormap for model/observations colormapNameResult = BuOr # the type of norm used in the colormap diff --git a/mpas_analysis/ocean/climatology_map_argo.py b/mpas_analysis/ocean/climatology_map_argo.py index 2eddda375..e56c9c994 100644 --- a/mpas_analysis/ocean/climatology_map_argo.py +++ b/mpas_analysis/ocean/climatology_map_argo.py @@ -19,10 +19,9 @@ from mpas_analysis.shared.io.utility import build_config_full_path -from mpas_analysis.shared.climatology import RemapObservedClimatologySubtask, \ - RemapMpasClimatologySubtask +from mpas_analysis.shared.climatology import RemapObservedClimatologySubtask -from mpas_analysis.shared.grid import LatLonGridDescriptor +from mpas_analysis.shared.grid import LatLonGridDescriptor from mpas_analysis.shared.mpas_xarray import mpas_xarray @@ -155,7 +154,8 @@ def __init__(self, config, mpasClimatologyTask, refTitleLabel=refTitleLabel, diffTitleLabel=diffTitleLabel, unitsLabel=r'$^\circ$C', - imageCaption='Model temperature compared with ARGO observations', + imageCaption='Model temperature compared with ARGO ' + 'observations', galleryGroup='Argo Temperature', groupSubtitle=None, groupLink='temp', @@ -295,7 +295,8 @@ def __init__(self, config, mpasClimatologyTask, refTitleLabel=refTitleLabel, diffTitleLabel=diffTitleLabel, unitsLabel=r'PSU', - imageCaption='Model Salinity compared with Argo observations', + imageCaption='Model Salinity compared with Argo ' + 'observations', galleryGroup='Argo Salinity', groupSubtitle=None, groupLink='salin', @@ -345,7 +346,7 @@ def __init__(self, parentTask, seasons, fileName, outFilePrefix, fieldName : str The name of the 3D field to remap - depths : list of {None, float, 'top', 'bot'} + depths : list of {None, float, 'top'} A list of depths at which the climatology will be sliced in the vertical. @@ -393,7 +394,7 @@ def get_observation_descriptor(self, fileName): # {{{ # Load Argo observational Data dsObs = self.build_observational_dataset(fileName) - # create a descriptor of the observation grid using Lat/Lon + # create a descriptor of the observation grid using Lat/Lon # coordinates obsDescriptor = LatLonGridDescriptor.read(ds=dsObs, latVarName='latCoord', @@ -425,8 +426,8 @@ def build_observational_dataset(self, fileName): # {{{ dsObs = xr.open_dataset(fileName) # Rename coordinates to be consistent with other datasets - dsObs.rename({'month':'calmonth', 'LATITUDE': 'latCoord', - 'LONGITUDE':'lonCoord', 'DEPTH': 'depth'}, inplace=True) + dsObs.rename({'month': 'calmonth', 'LATITUDE': 'latCoord', + 'LONGITUDE': 'lonCoord', 'DEPTH': 'depth'}, inplace=True) dsObs.coords['LATITUDE'] = dsObs['latCoord'] dsObs.coords['LONGITUDE'] = dsObs['lonCoord'] dsObs.coords['DEPTH'] = dsObs['depth'] @@ -442,8 +443,6 @@ def build_observational_dataset(self, fileName): # {{{ if depth == 'top': slices.append(field.sel(method='nearest', depth=0.).drop( 'depth')) - elif depth == 'bot': - slices.append(botField) else: slices.append(field.sel(method='nearest', depth=depth).drop( 'depth')) From cd66abe8200ab2c6c4d95c66a3b800d23193492d Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Thu, 8 Mar 2018 11:09:11 -0700 Subject: [PATCH 27/71] Fix SOSE and ARGO obs. field names Should the field names should be unchanged, but the file prefix should include SOSE or ARGO. --- mpas_analysis/ocean/climatology_map_argo.py | 8 ++++---- mpas_analysis/ocean/climatology_map_sose.py | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/mpas_analysis/ocean/climatology_map_argo.py b/mpas_analysis/ocean/climatology_map_argo.py index e56c9c994..17af5996c 100644 --- a/mpas_analysis/ocean/climatology_map_argo.py +++ b/mpas_analysis/ocean/climatology_map_argo.py @@ -110,14 +110,14 @@ def __init__(self, config, mpasClimatologyTask, obsFileName = \ '{}/ArgoClimatology_TS.nc'.format( observationsDirectory) - refFieldName = 'thetaArgo' + refFieldName = 'theta' outFileLabel = 'tempArgo' galleryName = 'Roemmich-Gilson Climatology: ARGO' diffTitleLabel = 'Model - Argo' remapObservationsSubtask = RemapArgoClimatology( parentTask=self, seasons=seasons, fileName=obsFileName, - outFilePrefix=refFieldName, + outFilePrefix='{}Argo'.format(refFieldName), fieldName=refFieldName, depths=depths, comparisonGridNames=comparisonGridNames) @@ -251,14 +251,14 @@ def __init__(self, config, mpasClimatologyTask, obsFileName = \ '{}/ArgoClimatology_TS.nc'.format( observationsDirectory) - refFieldName = 'salinityArgo' + refFieldName = 'salinity' outFileLabel = 'salinArgo' galleryName = 'Roemmich-Gilson Climatology: Argo' diffTitleLabel = 'Model - Argo' remapObservationsSubtask = RemapArgoClimatology( parentTask=self, seasons=seasons, fileName=obsFileName, - outFilePrefix=refFieldName, + outFilePrefix='{}Argo'.format(refFieldName), fieldName=refFieldName, depths=depths, comparisonGridNames=comparisonGridNames) diff --git a/mpas_analysis/ocean/climatology_map_sose.py b/mpas_analysis/ocean/climatology_map_sose.py index d3668947f..53a626622 100644 --- a/mpas_analysis/ocean/climatology_map_sose.py +++ b/mpas_analysis/ocean/climatology_map_sose.py @@ -112,14 +112,14 @@ def __init__(self, config, mpasClimatologyTask, '{}/SOSE_2005-2010_monthly_pot_temp_6000.0x' \ '6000.0km_10.0km_Antarctic_stereo.nc'.format( observationsDirectory) - refFieldName = 'thetaSOSE' + refFieldName = 'theta' outFileLabel = 'tempSOSE' galleryName = 'State Estimate: SOSE' diffTitleLabel = 'Model - State Estimate' remapObservationsSubtask = RemapSoseClimatology( parentTask=self, seasons=seasons, fileName=obsFileName, - outFilePrefix=refFieldName, + outFilePrefix='{}SOSE'.format(refFieldName), fieldName=refFieldName, botFieldName='botTheta', depths=depths, @@ -254,14 +254,14 @@ def __init__(self, config, mpasClimatologyTask, '{}/SOSE_2005-2010_monthly_salinity_6000.0x' \ '6000.0km_10.0km_Antarctic_stereo.nc'.format( observationsDirectory) - refFieldName = 'salinitySOSE' + refFieldName = 'salinity' outFileLabel = 'salinSOSE' galleryName = 'State Estimate: SOSE' diffTitleLabel = 'Model - State Estimate' remapObservationsSubtask = RemapSoseClimatology( parentTask=self, seasons=seasons, fileName=obsFileName, - outFilePrefix=refFieldName, + outFilePrefix='{}SOSE'.format(refFieldName), fieldName=refFieldName, botFieldName='botSalinity', depths=depths, From 08e3c4beaee75b33165389caddba58109be21ec7 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Thu, 8 Mar 2018 11:25:17 -0700 Subject: [PATCH 28/71] Fix group links --- mpas_analysis/ocean/climatology_map_argo.py | 4 ++-- mpas_analysis/ocean/climatology_map_sose.py | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/mpas_analysis/ocean/climatology_map_argo.py b/mpas_analysis/ocean/climatology_map_argo.py index 17af5996c..c8b625a81 100644 --- a/mpas_analysis/ocean/climatology_map_argo.py +++ b/mpas_analysis/ocean/climatology_map_argo.py @@ -158,7 +158,7 @@ def __init__(self, config, mpasClimatologyTask, 'observations', galleryGroup='Argo Temperature', groupSubtitle=None, - groupLink='temp', + groupLink='tempArgo', galleryName=galleryName) self.add_subtask(subtask) @@ -299,7 +299,7 @@ def __init__(self, config, mpasClimatologyTask, 'observations', galleryGroup='Argo Salinity', groupSubtitle=None, - groupLink='salin', + groupLink='salinArgo', galleryName=galleryName) self.add_subtask(subtask) diff --git a/mpas_analysis/ocean/climatology_map_sose.py b/mpas_analysis/ocean/climatology_map_sose.py index 53a626622..17b349e39 100644 --- a/mpas_analysis/ocean/climatology_map_sose.py +++ b/mpas_analysis/ocean/climatology_map_sose.py @@ -160,7 +160,7 @@ def __init__(self, config, mpasClimatologyTask, imageCaption='Temperature compared with SOSE', galleryGroup='Temperature', groupSubtitle=None, - groupLink='temp', + groupLink='tempSose', galleryName=galleryName) self.add_subtask(subtask) @@ -302,7 +302,7 @@ def __init__(self, config, mpasClimatologyTask, imageCaption='Salinity compared with SOSE', galleryGroup='Salinity', groupSubtitle=None, - groupLink='salin', + groupLink='salinSose', galleryName=galleryName) self.add_subtask(subtask) From c664fb4f978ad158c603012d090d025930f48dde Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Thu, 8 Mar 2018 12:38:38 -0800 Subject: [PATCH 29/71] State max depth of ARGO data --- mpas_analysis/config.default | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/mpas_analysis/config.default b/mpas_analysis/config.default index fc567efc7..8a4fe64f9 100644 --- a/mpas_analysis/config.default +++ b/mpas_analysis/config.default @@ -717,7 +717,7 @@ comparisonGrids = ['latlon'] seasons = ['ANN','JAS','JFM'] # list of depths in meters (positive up) at which to analyze, 'top' for the -# sea surface +# sea surface. Argo data is only available above -2000 m depths = ['top', -25, -50, -100, -150, -200, -400, -800, -1500] @@ -787,7 +787,7 @@ comparisonGrids = ['latlon'] seasons = ['ANN','JFM','JAS'] # list of depths in meters (positive up) at which to analyze, 'top' for the -# sea surface +# sea surface. Argo data is only available above -2000 m depths = ['top', -25, -50, -100, -150, -200, -400, -600, -800, -1500] # colormap for model/observations From 861d41399dea898e3c1658ed7cca8a35da64f058 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Sat, 25 Mar 2017 21:16:08 +0100 Subject: [PATCH 30/71] Make mpas_analysis an installable package --- docs/conf.py | 2 +- setup.cfg | 5 +++++ setup.py | 46 ++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 52 insertions(+), 1 deletion(-) create mode 100644 setup.cfg create mode 100755 setup.py diff --git a/docs/conf.py b/docs/conf.py index d9a7031e7..0ebe5270d 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -57,7 +57,7 @@ # General information about the project. project = u'MPAS-Analysis' -copyright = u'2016-2017, Los Alamos National Security, LLC (LANS) (Ocean: ' \ +copyright = u'2016-2018, Los Alamos National Security, LLC (LANS) (Ocean: ' \ u'LA-CC-13-047; Land Ice: LA-CC-13-117) and the University ' \ u'Corporation for Atmospheric Research (UCAR)' author = u'Xylar Asay-Davis, Milena Veneziani, Phillip Wolfram, ' \ diff --git a/setup.cfg b/setup.cfg new file mode 100644 index 000000000..44b0d881c --- /dev/null +++ b/setup.cfg @@ -0,0 +1,5 @@ +[wheel] +universal = 1 + +[tool:pytest] +python_files=test_*.py diff --git a/setup.py b/setup.py new file mode 100755 index 000000000..43f3c2e28 --- /dev/null +++ b/setup.py @@ -0,0 +1,46 @@ +#!/usr/bin/env python + +from setuptools import setup, find_packages +import warnings + +isrelease = True + +version = '0.7.0' + +if not isrelease: + import subprocess + try: + pipe = subprocess.Popen( + ["git", "describe", "--always", "--match", "v[0-9]*"], + stdout=subprocess.PIPE) + (version, stderr) = pipe.communicate() + except: + warnings.warn("WARNING: Couldn't get git revision, using generic " + "version string") + +setup(name='mpas_analysis', + version=version, + description='Analysis for Model for Prediction Across Scales (MPAS) ' + 'simulations.', + url='https://github.com/MPAS-Dev/MPAS-Analysis', + author='MPAS-Analysis Developers', + author_email='mpas-developers@googlegroups.com', + license='BSD', + classifiers=[ + 'Development Status :: 3 - Alpha', + 'License :: OSI Approved :: BSD License', + 'Operating System :: OS Independent', + 'Intended Audience :: Science/Research', + 'Programming Language :: Python', + 'Programming Language :: Python :: 2', + 'Programming Language :: Python :: 2.7', + 'Topic :: Scientific/Engineering', + ], + packages=find_packages(), + package_data={'mpas_analysis': ['config.default'], + 'mpas_analysis.shared.html': ['templates/*'], + 'mpas_analysis.test': ['test*/*', 'test*/*/*']}, + install_requires=['numpy', 'scipy', 'matplotlib', 'netCDF4', 'xarray', + 'dask', 'bottleneck', 'basemap', 'lxml', 'nco', + ' pyproj', 'pillow'], + scripts=['run_mpas_analysis']) From 7983de07afafcb17f9ffe1f907ffa8f6e530d43f Mon Sep 17 00:00:00 2001 From: Charles Doutriaux Date: Fri, 15 Sep 2017 09:48:55 -0700 Subject: [PATCH 31/71] adding conda recipe removing dependencies from setup install script, letting conda deal with it (for now) --- conda/recipe/build.sh | 2 ++ conda/recipe/meta.yaml | 47 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 conda/recipe/build.sh create mode 100644 conda/recipe/meta.yaml diff --git a/conda/recipe/build.sh b/conda/recipe/build.sh new file mode 100644 index 000000000..383455d82 --- /dev/null +++ b/conda/recipe/build.sh @@ -0,0 +1,2 @@ +#!/usr/bin/sh +python setup.py install --single-version-externally-managed --record=record.txt diff --git a/conda/recipe/meta.yaml b/conda/recipe/meta.yaml new file mode 100644 index 000000000..5b05b7b3c --- /dev/null +++ b/conda/recipe/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "0.7.0" %} + +package: + name: mpas_analysis + version: {{ version }} + +source: + path: ../.. + +build: + number: 0 + +test: + requires: + - pytest + imports: + - mpas_analysis + - pytest + commands: + - pytest --pyargs mpas_analysis + +requirements: + build: + - python + - setuptools + run: + - python + - numpy + - scipy + - matplotlib + - netcdf4 + - xarray >=0.10.0 + - dask + - bottleneck + - basemap + - lxml + - nco >=4.7.0 + - pillow + +about: + home: http://gitub.com/MPAS-Dev/MPAS-Analysis + +extra: + recipe-maintainers: + - doutriaux1 + - xylar + From f4fccf2889900aedf8fd4e648970517b7f9bf684 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Mon, 30 Oct 2017 13:25:08 -0600 Subject: [PATCH 32/71] Add licenses and code for adding licenses to source --- LICENSE | 39 ++++ licenses/A-PRIME_LICENSE.txt | 29 +++ licenses/NUMPY_LICENSE.txt | 30 +++ licenses/SEMENOV_LICENSE | 20 ++ licenses/XARRAY_LICENSE.txt | 191 +++++++++++++++++++ licenses/_headers/README.md | 91 +++++++++ licenses/_headers/header-css | 10 + licenses/_headers/header-css-full | 43 +++++ licenses/_headers/header-html | 10 + licenses/_headers/header-html-full | 43 +++++ licenses/_headers/header-ncl | 7 + licenses/_headers/header-ncl-full | 39 ++++ licenses/_headers/header-py | 7 + licenses/_headers/header-py-full | 39 ++++ licenses/_headers/license-bump-copyright.sh | 66 +++++++ licenses/_headers/license-find-missing.sh | 21 ++ licenses/_headers/license-prepend-missing.sh | 111 +++++++++++ licenses/_headers/license-setup.sh | 30 +++ 18 files changed, 826 insertions(+) create mode 100644 LICENSE create mode 100644 licenses/A-PRIME_LICENSE.txt create mode 100644 licenses/NUMPY_LICENSE.txt create mode 100644 licenses/SEMENOV_LICENSE create mode 100644 licenses/XARRAY_LICENSE.txt create mode 100755 licenses/_headers/README.md create mode 100755 licenses/_headers/header-css create mode 100755 licenses/_headers/header-css-full create mode 100755 licenses/_headers/header-html create mode 100755 licenses/_headers/header-html-full create mode 100755 licenses/_headers/header-ncl create mode 100755 licenses/_headers/header-ncl-full create mode 100755 licenses/_headers/header-py create mode 100755 licenses/_headers/header-py-full create mode 100755 licenses/_headers/license-bump-copyright.sh create mode 100755 licenses/_headers/license-find-missing.sh create mode 100755 licenses/_headers/license-prepend-missing.sh create mode 100755 licenses/_headers/license-setup.sh diff --git a/LICENSE b/LICENSE new file mode 100644 index 000000000..14f6b63cb --- /dev/null +++ b/LICENSE @@ -0,0 +1,39 @@ +Copyright (c) 2013, Los Alamos National Security, LLC (LANS) (Ocean: LA-CC-13-047; +Land Ice: LA-CC-13-117) and the University Corporation for Atmospheric Research (UCAR). + +All rights reserved. + +LANS is the operator of the Los Alamos National Laboratory under Contract No. +DE-AC52-06NA25396 with the U.S. Department of Energy. 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Submission of Contributions. + +Unless You explicitly state otherwise, any Contribution intentionally submitted +for inclusion in the Work by You to the Licensor shall be under the terms and +conditions of this License, without any additional terms or conditions. +Notwithstanding the above, nothing herein shall supersede or modify the terms of +any separate license agreement you may have executed with Licensor regarding +such Contributions. + +6. Trademarks. + +This License does not grant permission to use the trade names, trademarks, +service marks, or product names of the Licensor, except as required for +reasonable and customary use in describing the origin of the Work and +reproducing the content of the NOTICE file. + +7. 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Limitation of Liability. + +In no event and under no legal theory, whether in tort (including negligence), +contract, or otherwise, unless required by applicable law (such as deliberate +and grossly negligent acts) or agreed to in writing, shall any Contributor be +liable to You for damages, including any direct, indirect, special, incidental, +or consequential damages of any character arising as a result of this License or +out of the use or inability to use the Work (including but not limited to +damages for loss of goodwill, work stoppage, computer failure or malfunction, or +any and all other commercial damages or losses), even if such Contributor has +been advised of the possibility of such damages. + +9. Accepting Warranty or Additional Liability. + +While redistributing the Work or Derivative Works thereof, You may choose to +offer, and charge a fee for, acceptance of support, warranty, indemnity, or +other liability obligations and/or rights consistent with this License. However, +in accepting such obligations, You may act only on Your own behalf and on Your +sole responsibility, not on behalf of any other Contributor, and only if You +agree to indemnify, defend, and hold each Contributor harmless for any liability +incurred by, or claims asserted against, such Contributor by reason of your +accepting any such warranty or additional liability. + +END OF TERMS AND CONDITIONS + +APPENDIX: How to apply the Apache License to your work + +To apply the Apache License to your work, attach the following boilerplate +notice, with the fields enclosed by brackets "[]" replaced with your own +identifying information. (Don't include the brackets!) The text should be +enclosed in the appropriate comment syntax for the file format. We also +recommend that a file or class name and description of purpose be included on +the same "printed page" as the copyright notice for easier identification within +third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/licenses/_headers/README.md b/licenses/_headers/README.md new file mode 100755 index 000000000..79cd62ef9 --- /dev/null +++ b/licenses/_headers/README.md @@ -0,0 +1,91 @@ +# License Header Tools + +Before releasing software, it's important to ensure each "code" file has a license header, and that +header has an appropriate copyright date. Provided here are two main `bash` scripts to assist +developers in adding and updating the header files. + +* `license-prepend-missing.sh` finds "code" files which do not have a license header, and prepends + the relevant license header to the file. + + *Warning: Matlab uses the header of the file for its automatic help text. For Matlab files, + license files need to be appended to the file, or removed from the distribution entirely (LIVVkit + opted for the latter).* + +* `license-bump-copyright.sh` will find outdated copyright date statements, and replace them + (in place) with a current copyright statement. + +## Usage + +### `license-prepend-missing.sh` + +The `license-prepend-missing.sh` script will prepend a license header from a template to files with +these extensions: + +| Extension | Template file | +| --------- | ------------- | +| `.py` | `header-py` | +| `.sh` | `header-py` | +| `.bash` | `header-py` | +| `.html` | `header-html`| +| `.css` | `header-css` | +| `.js` | `header-css` | +| `.ncl` | `header-ncl` | + +*Note: Because comment syntax differs between these file types, files mush have one of the above +extensions --- extension-less files, and files without the above extensions are ignored.* + +This script work by first sourcing `license-setup.sh`, which sets the important search variables: + +* `SOURCE_DIR` sets the top level of the source repository, relative to the current working + directory. Currently, this is set as `../..` assuming the scripts will be run from this directory + (`docs/headers`). + +* `CURRENT` is a string that should be unique to the license header (e.g., `Copyright (c)`) and is + used to determine if the header is present in a file. + +* `ALWAYS_IGNORE` contains a set of regular expressions to match files which should always be + ignored by the find command (e.g., `*.git/*`). + +* `FILE_IGNORE` contains a set of regular expressions to match the types of files that don't need a + license header (e.g., `*.png`, `*.md`). + +* `PYTHON_IGNORE` contains a set of regular expressions to match python files which don't need a + license header, or are repackaged and licensed separately. + +* `CSS_IGNORE` contains a set of regular expressions to match web (CSS, Javascript, HTML) files + which don't need a license header, or are repackaged and licensed separately. + +The `license-prepend-missing.sh` script then goes through a number of find-and-modify blocks for +the above extensions, and appends a license header to the files missing a header. + +**Before** running the `license-prepend-missing.sh` script, it's important to ensure that the script +is finding the correct files. + +**First**, run the `license-find-missing.sh` script to verify the found files, which will output a list +of files without a license header. + +**Read through this output carefully!** This find command is generous and not restricted to the +above extensions. Files found with extensions differing from the list above will either need to be +added to the appropriate `*_IGNORE` variables in `license-setup.sh`, or added to the appropriate +find-and-modify block in `license-prepend-missing.sh` (or have a header added to it manually). *If +this file type's comment syntax differs from those found in the available templates, a new template +will need to be created and a new find-and-modify block added to `license-prepend-missing.sh`.* + +Once you're confident the `license-find-missing.sh` script is finding all the appropriate files, and +`license-prepend-missing.sh` has all the required find-and-modify blocks, simply run the +`liscense-prepend-missing.sh` script. You should now see a license header at the top of all your +"code" files. + +### `license-bump-copyright.sh` + +This script also uses the `*_IGNORE` variables from `license-setup.sh`, but instead of using the +`CURRENT` string to determine if a license header is present, it looks for the `OLD` string, which +is more restrictive, and replaces it (in place) with the `NEW` string. + +For example, `CURRENT` is typically set as `Copyright (c)`, which will match files with any copyright +statement, while `OLD` may be set as `Copyright (c) 2015, UT` to match files with the 2015 +copyright statement and `NEW` would set to `Copyright (c) 2015,2016, UT` to add 2016 to the +copyright statement. (`OLD` and `NEW` are found in `license-bump-copyright.sh`.) + +*Note: Like `license-find-missing.sh`, this script is not restricted to the above file types that +`license-prepend-missing.sh` is.* diff --git a/licenses/_headers/header-css b/licenses/_headers/header-css new file mode 100755 index 000000000..76537fd01 --- /dev/null +++ b/licenses/_headers/header-css @@ -0,0 +1,10 @@ +/* +/ Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +/ and the University Corporation for Atmospheric Research (UCAR). +/ +/ Unless noted otherwise source code is licensed under the BSD license. +/ Additional copyright and license information can be found in the LICENSE file +/ distributed with this code, or at http://mpas-dev.github.com/license.html +/ */ + + diff --git a/licenses/_headers/header-css-full b/licenses/_headers/header-css-full new file mode 100755 index 000000000..e0069d034 --- /dev/null +++ b/licenses/_headers/header-css-full @@ -0,0 +1,43 @@ +/* +/ Copyright (c) 2017, Los Alamos National Security, LLC (LANS) (Ocean: LA-CC-13-047; +/ Land Ice: LA-CC-13-117) and the University Corporation for Atmospheric Research (UCAR). +/ +/ All rights reserved. +/ +/ LANS is the operator of the Los Alamos National Laboratory under Contract No. +/ DE-AC52-06NA25396 with the U.S. Department of Energy. UCAR manages the National +/ Center for Atmospheric Research under Cooperative Agreement ATM-0753581 with the +/ National Science Foundation. The U.S. Government has rights to use, reproduce, +/ and distribute this software. NO WARRANTY, EXPRESS OR IMPLIED IS OFFERED BY +/ LANS, UCAR OR THE GOVERNMENT AND NONE OF THEM ASSUME ANY LIABILITY FOR THE USE +/ OF THIS SOFTWARE. If software is modified to produce derivative works, such +/ modified software should be clearly marked, so as not to confuse it with the +/ version available from LANS and UCAR. +/ +/ Additionally, redistribution and use in source and binary forms, with or without +/ modification, are permitted provided that the following conditions are met: +/ +/ 1) Redistributions of source code must retain the above copyright notice, this +/ list of conditions and the following disclaimer. +/ +/ 2) Redistributions in binary form must reproduce the above copyright notice, +/ this list of conditions and the following disclaimer in the documentation and/or +/ other materials provided with the distribution. +/ +/ 3) None of the names of LANS, UCAR or the names of its contributors, if any, may +/ be used to endorse or promote products derived from this software without +/ specific prior written permission. +/ +/ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +/ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +/ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +/ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR +/ ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +/ (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +/ LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON +/ ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +/ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +/ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +/ */ + + diff --git a/licenses/_headers/header-html b/licenses/_headers/header-html new file mode 100755 index 000000000..49114d2ef --- /dev/null +++ b/licenses/_headers/header-html @@ -0,0 +1,10 @@ + + + diff --git a/licenses/_headers/header-html-full b/licenses/_headers/header-html-full new file mode 100755 index 000000000..83a6f953e --- /dev/null +++ b/licenses/_headers/header-html-full @@ -0,0 +1,43 @@ + + + diff --git a/licenses/_headers/header-ncl b/licenses/_headers/header-ncl new file mode 100755 index 000000000..d501babe7 --- /dev/null +++ b/licenses/_headers/header-ncl @@ -0,0 +1,7 @@ +; Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +; and the University Corporation for Atmospheric Research (UCAR). +; +; Unless noted otherwise source code is licensed under the BSD license. +; Additional copyright and license information can be found in the LICENSE file +; distributed with this code, or at http://mpas-dev.github.com/license.html +; \ No newline at end of file diff --git a/licenses/_headers/header-ncl-full b/licenses/_headers/header-ncl-full new file mode 100755 index 000000000..1a923d9db --- /dev/null +++ b/licenses/_headers/header-ncl-full @@ -0,0 +1,39 @@ +; Copyright (c) 2017, Los Alamos National Security, LLC (LANS) (Ocean: LA-CC-13-047; +; Land Ice: LA-CC-13-117) and the University Corporation for Atmospheric Research (UCAR). +; +; All rights reserved. +; +; LANS is the operator of the Los Alamos National Laboratory under Contract No. +; DE-AC52-06NA25396 with the U.S. Department of Energy. UCAR manages the National +; Center for Atmospheric Research under Cooperative Agreement ATM-0753581 with the +; National Science Foundation. The U.S. Government has rights to use, reproduce, +; and distribute this software. NO WARRANTY, EXPRESS OR IMPLIED IS OFFERED BY +; LANS, UCAR OR THE GOVERNMENT AND NONE OF THEM ASSUME ANY LIABILITY FOR THE USE +; OF THIS SOFTWARE. If software is modified to produce derivative works, such +; modified software should be clearly marked, so as not to confuse it with the +; version available from LANS and UCAR. +; +; Additionally, redistribution and use in source and binary forms, with or without +; modification, are permitted provided that the following conditions are met: +; +; 1) Redistributions of source code must retain the above copyright notice, this +; list of conditions and the following disclaimer. +; +; 2) Redistributions in binary form must reproduce the above copyright notice, +; this list of conditions and the following disclaimer in the documentation and/or +; other materials provided with the distribution. +; +; 3) None of the names of LANS, UCAR or the names of its contributors, if any, may +; be used to endorse or promote products derived from this software without +; specific prior written permission. +; +; THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +; ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +; WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +; DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR +; ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +; (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON +; ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +; (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +; SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/licenses/_headers/header-py b/licenses/_headers/header-py new file mode 100755 index 000000000..49cdbd5a3 --- /dev/null +++ b/licenses/_headers/header-py @@ -0,0 +1,7 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# diff --git a/licenses/_headers/header-py-full b/licenses/_headers/header-py-full new file mode 100755 index 000000000..c4f3f2f54 --- /dev/null +++ b/licenses/_headers/header-py-full @@ -0,0 +1,39 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) (Ocean: LA-CC-13-047; +# Land Ice: LA-CC-13-117) and the University Corporation for Atmospheric Research (UCAR). +# +# All rights reserved. +# +# LANS is the operator of the Los Alamos National Laboratory under Contract No. +# DE-AC52-06NA25396 with the U.S. Department of Energy. UCAR manages the National +# Center for Atmospheric Research under Cooperative Agreement ATM-0753581 with the +# National Science Foundation. The U.S. Government has rights to use, reproduce, +# and distribute this software. NO WARRANTY, EXPRESS OR IMPLIED IS OFFERED BY +# LANS, UCAR OR THE GOVERNMENT AND NONE OF THEM ASSUME ANY LIABILITY FOR THE USE +# OF THIS SOFTWARE. If software is modified to produce derivative works, such +# modified software should be clearly marked, so as not to confuse it with the +# version available from LANS and UCAR. +# +# Additionally, redistribution and use in source and binary forms, with or without +# modification, are permitted provided that the following conditions are met: +# +# 1) Redistributions of source code must retain the above copyright notice, this +# list of conditions and the following disclaimer. +# +# 2) Redistributions in binary form must reproduce the above copyright notice, +# this list of conditions and the following disclaimer in the documentation and/or +# other materials provided with the distribution. +# +# 3) None of the names of LANS, UCAR or the names of its contributors, if any, may +# be used to endorse or promote products derived from this software without +# specific prior written permission. +# +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR +# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON +# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/licenses/_headers/license-bump-copyright.sh b/licenses/_headers/license-bump-copyright.sh new file mode 100755 index 000000000..e99eced52 --- /dev/null +++ b/licenses/_headers/license-bump-copyright.sh @@ -0,0 +1,66 @@ +#!/usr/bin/env bash +# +# Copyright (c) 2017, UT-BATTELLE, LLC +# All rights reserved. +# +# This software is released under the BSD license detailed +# in the file licenses/A-PRIME_LICENSE +# +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# +# Get the source dir and ignore variables +source license-setup.sh + +OLD="Copyright (c) 2015,2016, UT" +NEW="Copyright (c) 2017, UT" + +ALWAYS_IGNORE=(-not -path "*.git*" -not -path "*docs/*") +FILE_IGNORE=(-not -iname "*.md" -not -iname "*.json" -not -iname "*.txt" \ + -not -iname "*.png" -not -iname "*.jpg" -not -iname "*.svg" ) + +echo "--------------------------------------------------------------------------------" +echo " THESE FILES HAVE AN OUTDATED LICENSE HEADER:" +echo "--------------------------------------------------------------------------------" +find $SOURCE_DIR -type f "${ALWAYS_IGNORE[@]}" \ + "${FILE_IGNORE[@]}" \ + | xargs grep -l "$OLD" \ + | sort + +find ${SOURCE_DIR}/docs -type f \ + -not -path "*_build*" \ + -not -path "*source*" \ + "${FILE_IGNORE[@]}" \ + | xargs grep -l "$OLD" \ + | sort + + +echo "--------------------------------------------------------------------------------" +echo " UPDATING THE LICENSE HEADERS:" +echo "--------------------------------------------------------------------------------" +find $SOURCE_DIR -type f "${ALWAYS_IGNORE[@]}" \ + "${FILE_IGNORE[@]}" \ + | xargs grep -l "$OLD" \ + | sort \ + | while read SRC +do + echo "Bumping $SRC" + sed -i "s/$OLD/$NEW/g" $SRC +done + + +find ${SOURCE_DIR}/docs -type f \ + -not -path "*_build*" \ + -not -path "*source*" \ + "${FILE_IGNORE[@]}" \ + | xargs grep -l "$OLD" \ + | sort \ + | while read SRC +do + echo "Bumping $SRC" + sed -i "s/$OLD/$NEW/g" $SRC +done diff --git a/licenses/_headers/license-find-missing.sh b/licenses/_headers/license-find-missing.sh new file mode 100755 index 000000000..d80f0a140 --- /dev/null +++ b/licenses/_headers/license-find-missing.sh @@ -0,0 +1,21 @@ +#!/usr/bin/env bash +# +# Copyright (c) 2017, UT-BATTELLE, LLC +# All rights reserved. +# +# This software is released under the BSD license detailed +# in the file licenses/A-PRIME_LICENSE +# +# Get the source dir and ignore variables +source license-setup.sh + +echo "--------------------------------------------------------------------------------" +echo " THESE FILES ARE MISSING A CURRENT LICENSE HEADER:" +echo "--------------------------------------------------------------------------------" +find $SOURCE_DIR -type f "${ALWAYS_IGNORE[@]}" \ + "${FILE_IGNORE[@]}" \ + "${PYTHON_IGNORE[@]}" \ + "${CSS_IGNORE[@]}" \ + | xargs grep -L "$CURRENT" \ + | sort + diff --git a/licenses/_headers/license-prepend-missing.sh b/licenses/_headers/license-prepend-missing.sh new file mode 100755 index 000000000..361929298 --- /dev/null +++ b/licenses/_headers/license-prepend-missing.sh @@ -0,0 +1,111 @@ +#!/usr/bin/env bash +# +# Copyright (c) 2017, UT-BATTELLE, LLC +# All rights reserved. +# +# This software is released under the BSD license detailed +# in the file licenses/A-PRIME_LICENSE +# +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# +# Get the source dir and ignore variables +source license-setup.sh + +echo "--------------------------------------------------------------------------------" +echo " PREPENDING A LICENSE HEADER ONTO THESE FILES:" +echo "--------------------------------------------------------------------------------" +find $SOURCE_DIR -type f "${ALWAYS_IGNORE[@]}" \ + "${FILE_IGNORE[@]}" \ + "${PYTHON_IGNORE[@]}" \ + "${CSS_IGNORE[@]}" \ + | xargs grep -L "$CURRENT" \ + | sort + +echo "--------------------------------------------------------------------------------" +echo " BEGIN PREPENDING:" +echo "--------------------------------------------------------------------------------" +############################################################ +# Prepend license header to python files without a shebang. +# Will ignore files with a current license header. +############################################################ +GET=( -iname "*.py" ) + +find $SOURCE_DIR -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" "${PYTHON_IGNORE[@]}" \ + | xargs grep -L "#!" \ + | xargs grep -L "$CURRENT" \ + | while read SRC +do + BN=`basename ${SRC}` + echo HEADING ${SRC} + cp header-py /tmp/licHead + cat ${SRC} >> /tmp/licHead + chmod --reference=${SRC} /tmp/licHead + mv /tmp/licHead ${SRC} +done + +####################################################################### +# Prepend license header to python, bash, and sh files with a shebang. +# Will ignore files with a current license header. +####################################################################### +GET=( -iname "*.py" -or -iname "*.sh" -or -iname "*.bash" -or -iname "*.csh" -or -iname "*.pbs") + +find $SOURCE_DIR -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" "${PYTHON_IGNORE[@]}" \ + | xargs grep -l --max-count=1 "#!" \ + | xargs grep -L "$CURRENT" \ + | while read SRC +do + BN=`basename ${SRC}` + echo HEADING ${SRC} + cat ${SRC} | head -1 > /tmp/licHead + cat header-py >> /tmp/licHead + cat ${SRC} | tail -n +2 >> /tmp/licHead + chmod --reference=${SRC} /tmp/licHead + mv /tmp/licHead ${SRC} +done + + +#################################################### +# Prepend license header to html files. +# Will ignore files with a current license header. +#################################################### +GET=( -iname "*.html") + +find $SOURCE_DIR -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" \ + | xargs grep -L "$CURRENT" \ + | while read SRC +do + BN=`basename ${SRC}` + echo HEADING ${SRC} + cp header-html /tmp/licHead + cat ${SRC} >> /tmp/licHead + chmod --reference=${SRC} /tmp/licHead + mv /tmp/licHead ${SRC} +done + +#################################################### +# Prepend license header to css and js files. +# Will ignore files with a current license header. +#################################################### +GET=( -iname "*.css" -or -iname "*.js" ) + +find $SOURCE_DIR -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" "${CSS_IGNORE[@]}" \ + | xargs grep -L "$CURRENT" \ + | while read SRC +do + BN=`basename ${SRC}` + echo HEADING ${SRC} + cp header-css /tmp/licHead + cat ${SRC} >> /tmp/licHead + chmod --reference=${SRC} /tmp/licHead + mv /tmp/licHead ${SRC} +done + +echo "--------------------------------------------------------------------------------" +echo " DONE PREPENDING!" +echo "--------------------------------------------------------------------------------" + diff --git a/licenses/_headers/license-setup.sh b/licenses/_headers/license-setup.sh new file mode 100755 index 000000000..a2063e2d0 --- /dev/null +++ b/licenses/_headers/license-setup.sh @@ -0,0 +1,30 @@ +#!/usr/bin/env bash +# +# Copyright (c) 2017, UT-BATTELLE, LLC +# All rights reserved. +# +# This software is released under the BSD license detailed +# in the file licenses/A-PRIME_LICENSE +# +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html + +SOURCE_DIR="../.." + +CURRENT="Copyright (c)" + +ALWAYS_IGNORE=(-not -path "*.git*" -not -path "*docs/*" -not -path "build/*" \ + -not -path "dist/*" -not -path "*.egg-info/*" \ + -not -path "licenses/*" ) + +FILE_IGNORE=(-not -iname "*.md" -not -iname "*.json" -not -iname "*.txt" \ + -not -iname "*.png" -not -iname "*.jpg" -not -iname "*.svg" \ + -not -iname "config.*" -not -iname "*.nc"\ + -not -iname "*.pyc" \ + -not -iname "*.sl" -not -iname "*.ps1" -not -iname "*.yml" ) + +PYTHON_IGNORE=(-not -iname "__init__.py") From b506b8c23ad9ed3a5c1d0abdc2f6be277f28c4cf Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Sat, 10 Feb 2018 11:04:16 -0700 Subject: [PATCH 33/71] Add license headers to source files --- conda/recipe/build.sh | 7 +++++++ configs/anvil/job_script.anvil.bash | 7 +++++++ configs/cori/job_script.cori-haswell.bash | 7 +++++++ configs/cori/job_script.cori-knl.bash | 7 +++++++ configs/edison/job_script.edison.bash | 7 +++++++ configs/job_script.default.bash | 7 +++++++ configs/lanl/job_script.lanl.bash | 7 +++++++ configs/olcf/job_script.olcf.bash | 7 +++++++ configs/theta/job_script.theta.bash | 7 +++++++ mpas_analysis/analysis_task_template.py | 7 +++++++ .../configuration/mpas_analysis_config_parser.py | 7 +++++++ mpas_analysis/ocean/climatology_map_antarctic_melt.py | 7 +++++++ mpas_analysis/ocean/climatology_map_mld.py | 7 +++++++ mpas_analysis/ocean/climatology_map_sose.py | 7 +++++++ mpas_analysis/ocean/climatology_map_ssh.py | 7 +++++++ mpas_analysis/ocean/climatology_map_sss.py | 7 +++++++ mpas_analysis/ocean/climatology_map_sst.py | 7 +++++++ mpas_analysis/ocean/compute_anomaly_subtask.py | 7 +++++++ mpas_analysis/ocean/index_nino34.py | 7 +++++++ mpas_analysis/ocean/meridional_heat_transport.py | 7 +++++++ mpas_analysis/ocean/plot_climatology_map_subtask.py | 7 +++++++ .../ocean/plot_depth_integrated_time_series_subtask.py | 7 +++++++ mpas_analysis/ocean/plot_hovmoller_subtask.py | 7 +++++++ mpas_analysis/ocean/remap_depth_slices_subtask.py | 7 +++++++ mpas_analysis/ocean/streamfunction_moc.py | 7 +++++++ mpas_analysis/ocean/time_series_antarctic_melt.py | 7 +++++++ mpas_analysis/ocean/time_series_ohc_anomaly.py | 7 +++++++ mpas_analysis/ocean/time_series_salinity_anomaly.py | 7 +++++++ mpas_analysis/ocean/time_series_sst.py | 7 +++++++ mpas_analysis/ocean/time_series_temperature_anomaly.py | 7 +++++++ mpas_analysis/ocean/utility.py | 7 +++++++ mpas_analysis/sea_ice/climatology_map_sea_ice_conc.py | 7 +++++++ mpas_analysis/sea_ice/climatology_map_sea_ice_thick.py | 7 +++++++ mpas_analysis/sea_ice/plot_climatology_map_subtask.py | 7 +++++++ mpas_analysis/sea_ice/time_series.py | 7 +++++++ mpas_analysis/shared/analysis_task.py | 7 +++++++ mpas_analysis/shared/climatology/climatology.py | 7 +++++++ .../shared/climatology/comparison_descriptors.py | 7 +++++++ .../shared/climatology/mpas_climatology_task.py | 7 +++++++ .../climatology/remap_mpas_climatology_subtask.py | 7 +++++++ .../climatology/remap_observed_climatology_subtask.py | 7 +++++++ mpas_analysis/shared/constants/constants.py | 7 +++++++ mpas_analysis/shared/containers.py | 7 +++++++ .../shared/generalized_reader/generalized_reader.py | 7 +++++++ mpas_analysis/shared/grid/grid.py | 7 +++++++ mpas_analysis/shared/html/image_xml.py | 7 +++++++ mpas_analysis/shared/html/pages.py | 7 +++++++ .../shared/html/templates/component_gallery.html | 10 ++++++++++ .../shared/html/templates/component_group.html | 10 ++++++++++ .../shared/html/templates/component_image.html | 10 ++++++++++ .../shared/html/templates/component_quicklink.html | 10 ++++++++++ .../shared/html/templates/component_subtitle.html | 10 ++++++++++ mpas_analysis/shared/html/templates/index.js | 10 ++++++++++ .../shared/html/templates/main_component.html | 10 ++++++++++ mpas_analysis/shared/html/templates/main_page.html | 10 ++++++++++ mpas_analysis/shared/html/templates/style.css | 10 ++++++++++ mpas_analysis/shared/interpolation/remapper.py | 7 +++++++ mpas_analysis/shared/io/mpas_reader.py | 7 +++++++ mpas_analysis/shared/io/namelist_streams_interface.py | 7 +++++++ mpas_analysis/shared/io/utility.py | 7 +++++++ mpas_analysis/shared/io/write_netcdf.py | 7 +++++++ mpas_analysis/shared/mpas_xarray/mpas_xarray.py | 7 +++++++ mpas_analysis/shared/plot/plotting.py | 7 +++++++ mpas_analysis/shared/time_series/anomaly.py | 7 +++++++ mpas_analysis/shared/time_series/moving_average.py | 7 +++++++ .../shared/time_series/mpas_time_series_task.py | 7 +++++++ mpas_analysis/shared/time_series/time_series.py | 7 +++++++ mpas_analysis/shared/timekeeping/MpasRelativeDelta.py | 7 +++++++ mpas_analysis/shared/timekeeping/utility.py | 7 +++++++ mpas_analysis/test/test_analysis_task.py | 7 +++++++ mpas_analysis/test/test_climatology.py | 7 +++++++ mpas_analysis/test/test_generalized_reader.py | 7 +++++++ mpas_analysis/test/test_interpolate.py | 7 +++++++ mpas_analysis/test/test_io_utility.py | 7 +++++++ mpas_analysis/test/test_mpas_climatology_task.py | 7 +++++++ mpas_analysis/test/test_mpas_config_parser.py | 7 +++++++ mpas_analysis/test/test_mpas_xarray.py | 7 +++++++ mpas_analysis/test/test_namelist_streams_interface.py | 7 +++++++ mpas_analysis/test/test_open_mpas_dataset.py | 7 +++++++ mpas_analysis/test/test_remap_obs_clim_subtask.py | 7 +++++++ .../test/test_remap_obs_clim_subtask/remap_mld_obs.py | 7 +++++++ mpas_analysis/test/test_timekeeping.py | 7 +++++++ preprocess_masks/make_ice_shelf_masks.py | 7 +++++++ preprocess_observations/mds.py | 7 +++++++ preprocess_observations/remap_SOSE_T_S.py | 7 +++++++ preprocess_observations/remap_rignot.py | 7 +++++++ setup.py | 7 +++++++ utility_scripts/make_mpas_to_lat_lon_mapping.py | 7 +++++++ 88 files changed, 643 insertions(+) diff --git a/conda/recipe/build.sh b/conda/recipe/build.sh index 383455d82..2249089f8 100644 --- a/conda/recipe/build.sh +++ b/conda/recipe/build.sh @@ -1,2 +1,9 @@ #!/usr/bin/sh +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# python setup.py install --single-version-externally-managed --record=record.txt diff --git a/configs/anvil/job_script.anvil.bash b/configs/anvil/job_script.anvil.bash index 36f3d2e9a..49d7ff98c 100644 --- a/configs/anvil/job_script.anvil.bash +++ b/configs/anvil/job_script.anvil.bash @@ -1,4 +1,11 @@ #!/bin/bash +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# # comment out if using debug queue #PBS -q acme diff --git a/configs/cori/job_script.cori-haswell.bash b/configs/cori/job_script.cori-haswell.bash index aefa4fb46..8aa6f1cf9 100644 --- a/configs/cori/job_script.cori-haswell.bash +++ b/configs/cori/job_script.cori-haswell.bash @@ -1,4 +1,11 @@ #!/bin/bash -l +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# # comment out if using debug queue #SBATCH --partition=regular diff --git a/configs/cori/job_script.cori-knl.bash b/configs/cori/job_script.cori-knl.bash index b3936933b..2fe656738 100644 --- a/configs/cori/job_script.cori-knl.bash +++ b/configs/cori/job_script.cori-knl.bash @@ -1,4 +1,11 @@ #!/bin/bash -l +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# # comment out if using debug queue #SBATCH --partition=regular diff --git a/configs/edison/job_script.edison.bash b/configs/edison/job_script.edison.bash index f1098dc6e..922df234d 100644 --- a/configs/edison/job_script.edison.bash +++ b/configs/edison/job_script.edison.bash @@ -1,4 +1,11 @@ #!/bin/bash -l +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# # comment out if using debug queue #SBATCH --partition=regular diff --git a/configs/job_script.default.bash b/configs/job_script.default.bash index 565d423ab..f96ea54e3 100755 --- a/configs/job_script.default.bash +++ b/configs/job_script.default.bash @@ -1,4 +1,11 @@ #!/bin/bash +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# # MPAS/ACME job to be analyzed, including paths to simulation data and # observations. Change this name and path as needed diff --git a/configs/lanl/job_script.lanl.bash b/configs/lanl/job_script.lanl.bash index f42ffb377..19978ba92 100644 --- a/configs/lanl/job_script.lanl.bash +++ b/configs/lanl/job_script.lanl.bash @@ -1,4 +1,11 @@ #!/bin/bash +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# # change number of nodes to change the number of parallel tasks # (anything between 1 and the total number of tasks to run) diff --git a/configs/olcf/job_script.olcf.bash b/configs/olcf/job_script.olcf.bash index 42114f0e7..8d6c55f36 100644 --- a/configs/olcf/job_script.olcf.bash +++ b/configs/olcf/job_script.olcf.bash @@ -1,4 +1,11 @@ #!/bin/bash +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# # comment out if using debug queue #PBS -q batch diff --git a/configs/theta/job_script.theta.bash b/configs/theta/job_script.theta.bash index 0b681a7e9..3797f166e 100755 --- a/configs/theta/job_script.theta.bash +++ b/configs/theta/job_script.theta.bash @@ -1,4 +1,11 @@ #!/bin/bash +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# #COBALT -t 1:00:00 #COBALT -n 1 #COBALT -A OceanClimate diff --git a/mpas_analysis/analysis_task_template.py b/mpas_analysis/analysis_task_template.py index 0c53f46e7..8b1a93bbb 100644 --- a/mpas_analysis/analysis_task_template.py +++ b/mpas_analysis/analysis_task_template.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# ''' This is an example analysis task to be used as a template for new tasks. It should be copied into one of the component folders (`ocean`, `sea_ice`, diff --git a/mpas_analysis/configuration/mpas_analysis_config_parser.py b/mpas_analysis/configuration/mpas_analysis_config_parser.py index 06f2472cf..0440f4768 100644 --- a/mpas_analysis/configuration/mpas_analysis_config_parser.py +++ b/mpas_analysis/configuration/mpas_analysis_config_parser.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ A configuratin parser class for MPAS analysis. MpasAnalysisConfigParser adds the capabilities to get an option including a default value diff --git a/mpas_analysis/ocean/climatology_map_antarctic_melt.py b/mpas_analysis/ocean/climatology_map_antarctic_melt.py index 07002cc73..5d24b6f86 100644 --- a/mpas_analysis/ocean/climatology_map_antarctic_melt.py +++ b/mpas_analysis/ocean/climatology_map_antarctic_melt.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/ocean/climatology_map_mld.py b/mpas_analysis/ocean/climatology_map_mld.py index 6631d2c8e..e8f61b48b 100644 --- a/mpas_analysis/ocean/climatology_map_mld.py +++ b/mpas_analysis/ocean/climatology_map_mld.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/ocean/climatology_map_sose.py b/mpas_analysis/ocean/climatology_map_sose.py index ef23524ab..9ac4037d8 100644 --- a/mpas_analysis/ocean/climatology_map_sose.py +++ b/mpas_analysis/ocean/climatology_map_sose.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# ''' Analysis tasks for comparing Antarctic climatology maps against observations and reanalysis data. diff --git a/mpas_analysis/ocean/climatology_map_ssh.py b/mpas_analysis/ocean/climatology_map_ssh.py index bab7483f6..5838ba283 100644 --- a/mpas_analysis/ocean/climatology_map_ssh.py +++ b/mpas_analysis/ocean/climatology_map_ssh.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/ocean/climatology_map_sss.py b/mpas_analysis/ocean/climatology_map_sss.py index 7e8f27a55..069a34359 100644 --- a/mpas_analysis/ocean/climatology_map_sss.py +++ b/mpas_analysis/ocean/climatology_map_sss.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/ocean/climatology_map_sst.py b/mpas_analysis/ocean/climatology_map_sst.py index b7c99a8f5..35bcb6246 100644 --- a/mpas_analysis/ocean/climatology_map_sst.py +++ b/mpas_analysis/ocean/climatology_map_sst.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/ocean/compute_anomaly_subtask.py b/mpas_analysis/ocean/compute_anomaly_subtask.py index 49773a538..7b66bd125 100644 --- a/mpas_analysis/ocean/compute_anomaly_subtask.py +++ b/mpas_analysis/ocean/compute_anomaly_subtask.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# # -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function, \ diff --git a/mpas_analysis/ocean/index_nino34.py b/mpas_analysis/ocean/index_nino34.py index 105342af2..add345e69 100644 --- a/mpas_analysis/ocean/index_nino34.py +++ b/mpas_analysis/ocean/index_nino34.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# # -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function, \ diff --git a/mpas_analysis/ocean/meridional_heat_transport.py b/mpas_analysis/ocean/meridional_heat_transport.py index 218203f41..161f599fa 100644 --- a/mpas_analysis/ocean/meridional_heat_transport.py +++ b/mpas_analysis/ocean/meridional_heat_transport.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/ocean/plot_climatology_map_subtask.py b/mpas_analysis/ocean/plot_climatology_map_subtask.py index 3d68a766b..5ec9d73b6 100644 --- a/mpas_analysis/ocean/plot_climatology_map_subtask.py +++ b/mpas_analysis/ocean/plot_climatology_map_subtask.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ An analysis subtasks for plotting comparison of 2D model fields against observations. diff --git a/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py b/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py index ad98cd56c..e6b49d942 100644 --- a/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py +++ b/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# # -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function, \ diff --git a/mpas_analysis/ocean/plot_hovmoller_subtask.py b/mpas_analysis/ocean/plot_hovmoller_subtask.py index 8543325e8..c48018690 100644 --- a/mpas_analysis/ocean/plot_hovmoller_subtask.py +++ b/mpas_analysis/ocean/plot_hovmoller_subtask.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# # -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function, \ diff --git a/mpas_analysis/ocean/remap_depth_slices_subtask.py b/mpas_analysis/ocean/remap_depth_slices_subtask.py index b2102ae59..1debd1552 100644 --- a/mpas_analysis/ocean/remap_depth_slices_subtask.py +++ b/mpas_analysis/ocean/remap_depth_slices_subtask.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/ocean/streamfunction_moc.py b/mpas_analysis/ocean/streamfunction_moc.py index 59fc2d84f..77b7f50dc 100644 --- a/mpas_analysis/ocean/streamfunction_moc.py +++ b/mpas_analysis/ocean/streamfunction_moc.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# # -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function, \ diff --git a/mpas_analysis/ocean/time_series_antarctic_melt.py b/mpas_analysis/ocean/time_series_antarctic_melt.py index 743da8af3..fb0396401 100644 --- a/mpas_analysis/ocean/time_series_antarctic_melt.py +++ b/mpas_analysis/ocean/time_series_antarctic_melt.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/ocean/time_series_ohc_anomaly.py b/mpas_analysis/ocean/time_series_ohc_anomaly.py index 00d6e3594..bda379661 100644 --- a/mpas_analysis/ocean/time_series_ohc_anomaly.py +++ b/mpas_analysis/ocean/time_series_ohc_anomaly.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# # -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function, \ diff --git a/mpas_analysis/ocean/time_series_salinity_anomaly.py b/mpas_analysis/ocean/time_series_salinity_anomaly.py index 3f29492b3..f566415af 100644 --- a/mpas_analysis/ocean/time_series_salinity_anomaly.py +++ b/mpas_analysis/ocean/time_series_salinity_anomaly.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# # -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function, \ diff --git a/mpas_analysis/ocean/time_series_sst.py b/mpas_analysis/ocean/time_series_sst.py index 9b889288d..c49ead643 100644 --- a/mpas_analysis/ocean/time_series_sst.py +++ b/mpas_analysis/ocean/time_series_sst.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/ocean/time_series_temperature_anomaly.py b/mpas_analysis/ocean/time_series_temperature_anomaly.py index 9e61b2156..ab9c251f2 100644 --- a/mpas_analysis/ocean/time_series_temperature_anomaly.py +++ b/mpas_analysis/ocean/time_series_temperature_anomaly.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# # -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function, \ diff --git a/mpas_analysis/ocean/utility.py b/mpas_analysis/ocean/utility.py index 8600977ef..f58fc1e4a 100644 --- a/mpas_analysis/ocean/utility.py +++ b/mpas_analysis/ocean/utility.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ A utility for computing common ocean fields (e.g. zMid) from datasets diff --git a/mpas_analysis/sea_ice/climatology_map_sea_ice_conc.py b/mpas_analysis/sea_ice/climatology_map_sea_ice_conc.py index b1909dec0..8d48169ef 100644 --- a/mpas_analysis/sea_ice/climatology_map_sea_ice_conc.py +++ b/mpas_analysis/sea_ice/climatology_map_sea_ice_conc.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/sea_ice/climatology_map_sea_ice_thick.py b/mpas_analysis/sea_ice/climatology_map_sea_ice_thick.py index 957b15830..03c343278 100644 --- a/mpas_analysis/sea_ice/climatology_map_sea_ice_thick.py +++ b/mpas_analysis/sea_ice/climatology_map_sea_ice_thick.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/sea_ice/plot_climatology_map_subtask.py b/mpas_analysis/sea_ice/plot_climatology_map_subtask.py index 5393ee826..4af15d4cc 100644 --- a/mpas_analysis/sea_ice/plot_climatology_map_subtask.py +++ b/mpas_analysis/sea_ice/plot_climatology_map_subtask.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/sea_ice/time_series.py b/mpas_analysis/sea_ice/time_series.py index 67d34915b..00b77b6fd 100644 --- a/mpas_analysis/sea_ice/time_series.py +++ b/mpas_analysis/sea_ice/time_series.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/shared/analysis_task.py b/mpas_analysis/shared/analysis_task.py index 2e7b7d70b..6a06fed0a 100644 --- a/mpas_analysis/shared/analysis_task.py +++ b/mpas_analysis/shared/analysis_task.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# ''' Defines the base class for analysis tasks. diff --git a/mpas_analysis/shared/climatology/climatology.py b/mpas_analysis/shared/climatology/climatology.py index c2b411465..52a53433b 100644 --- a/mpas_analysis/shared/climatology/climatology.py +++ b/mpas_analysis/shared/climatology/climatology.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ Functions for creating climatologies from monthly time series data diff --git a/mpas_analysis/shared/climatology/comparison_descriptors.py b/mpas_analysis/shared/climatology/comparison_descriptors.py index ed553070f..a417de531 100644 --- a/mpas_analysis/shared/climatology/comparison_descriptors.py +++ b/mpas_analysis/shared/climatology/comparison_descriptors.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ Functions for creating climatologies from monthly time series data diff --git a/mpas_analysis/shared/climatology/mpas_climatology_task.py b/mpas_analysis/shared/climatology/mpas_climatology_task.py index e4d4d2e73..041ac12cb 100644 --- a/mpas_analysis/shared/climatology/mpas_climatology_task.py +++ b/mpas_analysis/shared/climatology/mpas_climatology_task.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/shared/climatology/remap_mpas_climatology_subtask.py b/mpas_analysis/shared/climatology/remap_mpas_climatology_subtask.py index 771e97649..21ba4f828 100644 --- a/mpas_analysis/shared/climatology/remap_mpas_climatology_subtask.py +++ b/mpas_analysis/shared/climatology/remap_mpas_climatology_subtask.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/shared/climatology/remap_observed_climatology_subtask.py b/mpas_analysis/shared/climatology/remap_observed_climatology_subtask.py index ba39e3cbf..49dd97957 100644 --- a/mpas_analysis/shared/climatology/remap_observed_climatology_subtask.py +++ b/mpas_analysis/shared/climatology/remap_observed_climatology_subtask.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/shared/constants/constants.py b/mpas_analysis/shared/constants/constants.py index 7231fe7be..584187063 100644 --- a/mpas_analysis/shared/constants/constants.py +++ b/mpas_analysis/shared/constants/constants.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ Constants that are common to all analysis tasks diff --git a/mpas_analysis/shared/containers.py b/mpas_analysis/shared/containers.py index 8c2583a85..27e725412 100644 --- a/mpas_analysis/shared/containers.py +++ b/mpas_analysis/shared/containers.py @@ -1,4 +1,11 @@ #!/usr/bin/env python +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ Module of custom container data types diff --git a/mpas_analysis/shared/generalized_reader/generalized_reader.py b/mpas_analysis/shared/generalized_reader/generalized_reader.py index 87b357baa..a97cf0ede 100644 --- a/mpas_analysis/shared/generalized_reader/generalized_reader.py +++ b/mpas_analysis/shared/generalized_reader/generalized_reader.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ Utility functions for importing MPAS files into xarray. These functions extend the capabilities of mpas_xarray to include mapping variable names from MPAS diff --git a/mpas_analysis/shared/grid/grid.py b/mpas_analysis/shared/grid/grid.py index ba7c4096d..cb33c5ae4 100644 --- a/mpas_analysis/shared/grid/grid.py +++ b/mpas_analysis/shared/grid/grid.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# ''' Classes for describing meshes and grids , including creating SCRIP files, used to create mapping files diff --git a/mpas_analysis/shared/html/image_xml.py b/mpas_analysis/shared/html/image_xml.py index a05a8c2f4..e2c1aa770 100644 --- a/mpas_analysis/shared/html/image_xml.py +++ b/mpas_analysis/shared/html/image_xml.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/shared/html/pages.py b/mpas_analysis/shared/html/pages.py index 97edc12d5..dd70a38a7 100644 --- a/mpas_analysis/shared/html/pages.py +++ b/mpas_analysis/shared/html/pages.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/shared/html/templates/component_gallery.html b/mpas_analysis/shared/html/templates/component_gallery.html index a016c5e8f..ee0400a57 100644 --- a/mpas_analysis/shared/html/templates/component_gallery.html +++ b/mpas_analysis/shared/html/templates/component_gallery.html @@ -1,3 +1,13 @@ + + + @galleryTitle
diff --git a/mpas_analysis/shared/html/templates/component_group.html b/mpas_analysis/shared/html/templates/component_group.html index a0287b305..5306017f9 100644 --- a/mpas_analysis/shared/html/templates/component_group.html +++ b/mpas_analysis/shared/html/templates/component_group.html @@ -1,3 +1,13 @@ + + +

@analysisGroupName

@groupSubtitle diff --git a/mpas_analysis/shared/html/templates/component_image.html b/mpas_analysis/shared/html/templates/component_image.html index 406b6ba9a..66f11b24f 100644 --- a/mpas_analysis/shared/html/templates/component_image.html +++ b/mpas_analysis/shared/html/templates/component_image.html @@ -1,3 +1,13 @@ + + +
@imageDescription diff --git a/mpas_analysis/shared/html/templates/component_quicklink.html b/mpas_analysis/shared/html/templates/component_quicklink.html index 5d4e2d118..ca6b0bebc 100644 --- a/mpas_analysis/shared/html/templates/component_quicklink.html +++ b/mpas_analysis/shared/html/templates/component_quicklink.html @@ -1,3 +1,13 @@ + + +
@analysisGroupName diff --git a/mpas_analysis/shared/html/templates/component_subtitle.html b/mpas_analysis/shared/html/templates/component_subtitle.html index 029b67a4f..c20bf8cb6 100644 --- a/mpas_analysis/shared/html/templates/component_subtitle.html +++ b/mpas_analysis/shared/html/templates/component_subtitle.html @@ -1 +1,11 @@ + + +

@subtitle

\ No newline at end of file diff --git a/mpas_analysis/shared/html/templates/index.js b/mpas_analysis/shared/html/templates/index.js index 61118b810..3ae19e5e9 100644 --- a/mpas_analysis/shared/html/templates/index.js +++ b/mpas_analysis/shared/html/templates/index.js @@ -1,3 +1,13 @@ +/* +/ Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +/ and the University Corporation for Atmospheric Research (UCAR). +/ +/ Unless noted otherwise source code is licensed under the BSD license. +/ Additional copyright and license information can be found in the LICENSE file +/ distributed with this code, or at http://mpas-dev.github.com/license.html +/ */ + + var initPhotoSwipeFromDOM = function(gallerySelector) { // parse slide data (url, title, size ...) from DOM elements diff --git a/mpas_analysis/shared/html/templates/main_component.html b/mpas_analysis/shared/html/templates/main_component.html index 209798c22..183d73e91 100644 --- a/mpas_analysis/shared/html/templates/main_component.html +++ b/mpas_analysis/shared/html/templates/main_component.html @@ -1,3 +1,13 @@ + + +
@componentName Analysis diff --git a/mpas_analysis/shared/html/templates/main_page.html b/mpas_analysis/shared/html/templates/main_page.html index be3d39190..fd85d9f25 100644 --- a/mpas_analysis/shared/html/templates/main_page.html +++ b/mpas_analysis/shared/html/templates/main_page.html @@ -1,3 +1,13 @@ + + + diff --git a/mpas_analysis/shared/html/templates/style.css b/mpas_analysis/shared/html/templates/style.css index 4d7ed76ea..d5a498973 100644 --- a/mpas_analysis/shared/html/templates/style.css +++ b/mpas_analysis/shared/html/templates/style.css @@ -1,3 +1,13 @@ +/* +/ Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +/ and the University Corporation for Atmospheric Research (UCAR). +/ +/ Unless noted otherwise source code is licensed under the BSD license. +/ Additional copyright and license information can be found in the LICENSE file +/ distributed with this code, or at http://mpas-dev.github.com/license.html +/ */ + + body { background:#EEE; font-family:"myriad-pro","Myriad Pro","Helvetica Neue",Helvetica,Arial,sans-serif; diff --git a/mpas_analysis/shared/interpolation/remapper.py b/mpas_analysis/shared/interpolation/remapper.py index 50b455a77..fb3d003e7 100644 --- a/mpas_analysis/shared/interpolation/remapper.py +++ b/mpas_analysis/shared/interpolation/remapper.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# ''' Functions for performing interpolation diff --git a/mpas_analysis/shared/io/mpas_reader.py b/mpas_analysis/shared/io/mpas_reader.py index 783bb6099..dcd9e5345 100644 --- a/mpas_analysis/shared/io/mpas_reader.py +++ b/mpas_analysis/shared/io/mpas_reader.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ Utility functions for reading a single MPAS file into xarray and for removing all but a given list of variables from a data set. diff --git a/mpas_analysis/shared/io/namelist_streams_interface.py b/mpas_analysis/shared/io/namelist_streams_interface.py index 8ccf41c0c..56d1508a6 100644 --- a/mpas_analysis/shared/io/namelist_streams_interface.py +++ b/mpas_analysis/shared/io/namelist_streams_interface.py @@ -1,4 +1,11 @@ #!/usr/bin/env python +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ Module of classes/routines to manipulate fortran namelist and streams files. diff --git a/mpas_analysis/shared/io/utility.py b/mpas_analysis/shared/io/utility.py index 0a8923216..0de779050 100644 --- a/mpas_analysis/shared/io/utility.py +++ b/mpas_analysis/shared/io/utility.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ IO utility functions diff --git a/mpas_analysis/shared/io/write_netcdf.py b/mpas_analysis/shared/io/write_netcdf.py index 03072bae5..e033248d3 100644 --- a/mpas_analysis/shared/io/write_netcdf.py +++ b/mpas_analysis/shared/io/write_netcdf.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/shared/mpas_xarray/mpas_xarray.py b/mpas_analysis/shared/mpas_xarray/mpas_xarray.py index 6b63ce905..e8dd1430b 100644 --- a/mpas_analysis/shared/mpas_xarray/mpas_xarray.py +++ b/mpas_analysis/shared/mpas_xarray/mpas_xarray.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/shared/plot/plotting.py b/mpas_analysis/shared/plot/plotting.py index 54d768322..c9d130900 100644 --- a/mpas_analysis/shared/plot/plotting.py +++ b/mpas_analysis/shared/plot/plotting.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ Plotting utilities, including routines for plotting: * time series (and comparing with reference data sets) diff --git a/mpas_analysis/shared/time_series/anomaly.py b/mpas_analysis/shared/time_series/anomaly.py index 0dfac5419..5449c4cfe 100644 --- a/mpas_analysis/shared/time_series/anomaly.py +++ b/mpas_analysis/shared/time_series/anomaly.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# # -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function, \ diff --git a/mpas_analysis/shared/time_series/moving_average.py b/mpas_analysis/shared/time_series/moving_average.py index 576c891ba..4d0290ffd 100644 --- a/mpas_analysis/shared/time_series/moving_average.py +++ b/mpas_analysis/shared/time_series/moving_average.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# # -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function, \ diff --git a/mpas_analysis/shared/time_series/mpas_time_series_task.py b/mpas_analysis/shared/time_series/mpas_time_series_task.py index 2c194415a..42148de20 100644 --- a/mpas_analysis/shared/time_series/mpas_time_series_task.py +++ b/mpas_analysis/shared/time_series/mpas_time_series_task.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/shared/time_series/time_series.py b/mpas_analysis/shared/time_series/time_series.py index 4dc1d6b85..a5e9163af 100644 --- a/mpas_analysis/shared/time_series/time_series.py +++ b/mpas_analysis/shared/time_series/time_series.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ Utility functions related to time-series data sets diff --git a/mpas_analysis/shared/timekeeping/MpasRelativeDelta.py b/mpas_analysis/shared/timekeeping/MpasRelativeDelta.py index 1b70041e2..c8353ee8c 100644 --- a/mpas_analysis/shared/timekeeping/MpasRelativeDelta.py +++ b/mpas_analysis/shared/timekeeping/MpasRelativeDelta.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/shared/timekeeping/utility.py b/mpas_analysis/shared/timekeeping/utility.py index 7ddb49503..e29574864 100644 --- a/mpas_analysis/shared/timekeeping/utility.py +++ b/mpas_analysis/shared/timekeeping/utility.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ Time keeping utility functions diff --git a/mpas_analysis/test/test_analysis_task.py b/mpas_analysis/test/test_analysis_task.py index e6eeab82e..6403e258e 100644 --- a/mpas_analysis/test/test_analysis_task.py +++ b/mpas_analysis/test/test_analysis_task.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ Unit tests for utility functions in run_mpas_analysis diff --git a/mpas_analysis/test/test_climatology.py b/mpas_analysis/test/test_climatology.py index bb3b1f3c8..7b090e209 100644 --- a/mpas_analysis/test/test_climatology.py +++ b/mpas_analysis/test/test_climatology.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ Unit test infrastructure for climatologies. diff --git a/mpas_analysis/test/test_generalized_reader.py b/mpas_analysis/test/test_generalized_reader.py index 1bc362831..5b0f271f3 100644 --- a/mpas_analysis/test/test_generalized_reader.py +++ b/mpas_analysis/test/test_generalized_reader.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ Unit test infrastructure for the generalized_reader. diff --git a/mpas_analysis/test/test_interpolate.py b/mpas_analysis/test/test_interpolate.py index 0b44d0a42..2b94ceeb4 100644 --- a/mpas_analysis/test/test_interpolate.py +++ b/mpas_analysis/test/test_interpolate.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# ''' Unit test infrastructure for horizontal interpolation. diff --git a/mpas_analysis/test/test_io_utility.py b/mpas_analysis/test/test_io_utility.py index df080401d..c1762d6f1 100644 --- a/mpas_analysis/test/test_io_utility.py +++ b/mpas_analysis/test/test_io_utility.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ Unit test infrastructure, adapted from approach of xarray. diff --git a/mpas_analysis/test/test_mpas_climatology_task.py b/mpas_analysis/test/test_mpas_climatology_task.py index 61e836856..0dfc7a81d 100644 --- a/mpas_analysis/test/test_mpas_climatology_task.py +++ b/mpas_analysis/test/test_mpas_climatology_task.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ Unit test infrastructure for MpasClimatologyTask. diff --git a/mpas_analysis/test/test_mpas_config_parser.py b/mpas_analysis/test/test_mpas_config_parser.py index fca487ff5..4b10f954d 100644 --- a/mpas_analysis/test/test_mpas_config_parser.py +++ b/mpas_analysis/test/test_mpas_config_parser.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ Unit test infrastructure for MpasAnalysisConfigParser diff --git a/mpas_analysis/test/test_mpas_xarray.py b/mpas_analysis/test/test_mpas_xarray.py index 0fe0b87b4..2f1d1c240 100644 --- a/mpas_analysis/test/test_mpas_xarray.py +++ b/mpas_analysis/test/test_mpas_xarray.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ Unit test infrastructure for mpas_xarray. diff --git a/mpas_analysis/test/test_namelist_streams_interface.py b/mpas_analysis/test/test_namelist_streams_interface.py index acb0cc756..0aefa1470 100644 --- a/mpas_analysis/test/test_namelist_streams_interface.py +++ b/mpas_analysis/test/test_namelist_streams_interface.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ Unit test infrastructure for namelist and streams readers, adapted from approach of xarray. diff --git a/mpas_analysis/test/test_open_mpas_dataset.py b/mpas_analysis/test/test_open_mpas_dataset.py index 3896f8f96..0cb95fe35 100644 --- a/mpas_analysis/test/test_open_mpas_dataset.py +++ b/mpas_analysis/test/test_open_mpas_dataset.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ Unit test infrastructure for the generalized_reader. diff --git a/mpas_analysis/test/test_remap_obs_clim_subtask.py b/mpas_analysis/test/test_remap_obs_clim_subtask.py index d0e0e55dc..fba32e6d1 100644 --- a/mpas_analysis/test/test_remap_obs_clim_subtask.py +++ b/mpas_analysis/test/test_remap_obs_clim_subtask.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ Unit test infrastructure for MpasClimatologyTask. diff --git a/mpas_analysis/test/test_remap_obs_clim_subtask/remap_mld_obs.py b/mpas_analysis/test/test_remap_obs_clim_subtask/remap_mld_obs.py index ff7ce2a20..e9027da63 100644 --- a/mpas_analysis/test/test_remap_obs_clim_subtask/remap_mld_obs.py +++ b/mpas_analysis/test/test_remap_obs_clim_subtask/remap_mld_obs.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# import numpy from mpas_analysis.shared.interpolation import Remapper diff --git a/mpas_analysis/test/test_timekeeping.py b/mpas_analysis/test/test_timekeeping.py index 362e16abf..5a459864c 100644 --- a/mpas_analysis/test/test_timekeeping.py +++ b/mpas_analysis/test/test_timekeeping.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ Unit test infrastructure for the Date class diff --git a/preprocess_masks/make_ice_shelf_masks.py b/preprocess_masks/make_ice_shelf_masks.py index 4e4136506..eb12f7473 100755 --- a/preprocess_masks/make_ice_shelf_masks.py +++ b/preprocess_masks/make_ice_shelf_masks.py @@ -1,4 +1,11 @@ #!/usr/bin/env python +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# ''' Make a mask file for a given mesh from ice-shelf geometric features. diff --git a/preprocess_observations/mds.py b/preprocess_observations/mds.py index 7e81bfa13..1088add70 100644 --- a/preprocess_observations/mds.py +++ b/preprocess_observations/mds.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# import sys import re import glob diff --git a/preprocess_observations/remap_SOSE_T_S.py b/preprocess_observations/remap_SOSE_T_S.py index 17587af55..9eb706e24 100644 --- a/preprocess_observations/remap_SOSE_T_S.py +++ b/preprocess_observations/remap_SOSE_T_S.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# import numpy import xarray import matplotlib.pyplot as plt diff --git a/preprocess_observations/remap_rignot.py b/preprocess_observations/remap_rignot.py index 3abaef9e0..336a23a8a 100644 --- a/preprocess_observations/remap_rignot.py +++ b/preprocess_observations/remap_rignot.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# import numpy import xarray import matplotlib.pyplot as plt diff --git a/setup.py b/setup.py index 43f3c2e28..e38cb21f4 100755 --- a/setup.py +++ b/setup.py @@ -1,4 +1,11 @@ #!/usr/bin/env python +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# from setuptools import setup, find_packages import warnings diff --git a/utility_scripts/make_mpas_to_lat_lon_mapping.py b/utility_scripts/make_mpas_to_lat_lon_mapping.py index 00d508356..4485e49e1 100755 --- a/utility_scripts/make_mpas_to_lat_lon_mapping.py +++ b/utility_scripts/make_mpas_to_lat_lon_mapping.py @@ -1,4 +1,11 @@ #!/usr/bin/env python +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# ''' Creates a mapping file that can be used with ncremap (NCO) to remap MPAS files From 6a0ea795f6ab3d2e221e4a0cba2bcbc48d5a8501 Mon Sep 17 00:00:00 2001 From: Luke Van Roekel Date: Mon, 19 Mar 2018 13:04:24 -0500 Subject: [PATCH 34/71] Fixes for ref start year Adds anomalyEndTime to open_mpas_dataset for reference end. --- mpas_analysis/ocean/compute_anomaly_subtask.py | 6 +++++- mpas_analysis/shared/time_series/anomaly.py | 7 ++++--- 2 files changed, 9 insertions(+), 4 deletions(-) diff --git a/mpas_analysis/ocean/compute_anomaly_subtask.py b/mpas_analysis/ocean/compute_anomaly_subtask.py index 293ac7659..76af86f62 100644 --- a/mpas_analysis/ocean/compute_anomaly_subtask.py +++ b/mpas_analysis/ocean/compute_anomaly_subtask.py @@ -148,13 +148,17 @@ def run_task(self): # {{{ if config.has_option('timeSeries', 'anomalyRefYear'): anomalyYear = config.getint('timeSeries', 'anomalyRefYear') anomalyRefDate = '{:04d}-01-01_00:00:00'.format(anomalyYear) + anomalyEndDate = '{:04d}-12-31_23:59:59'.format(anomalyYear) else: anomalyRefDate = get_simulation_start_time(self.runStreams) + anomalyYear = int(anomalyRefDate[0:4]) + anomalyEndDate = '{:04d}-12-31_23:59:59'.format(anomalyYear) ds = compute_moving_avg_anomaly_from_start( timeSeriesFileName=self.inputFile, variableList=self.variableList, - simulationStartTime=anomalyRefDate, + anomalyStartTime=anomalyRefDate, + anomalyEndTime=anomalyEndDate, startDate=startDate, endDate=endDate, calendar=self.calendar, diff --git a/mpas_analysis/shared/time_series/anomaly.py b/mpas_analysis/shared/time_series/anomaly.py index 0dfac5419..1ad3856fb 100644 --- a/mpas_analysis/shared/time_series/anomaly.py +++ b/mpas_analysis/shared/time_series/anomaly.py @@ -8,8 +8,8 @@ def compute_moving_avg_anomaly_from_start(timeSeriesFileName, variableList, - simulationStartTime, startDate, - endDate, calendar, + anomalyStartTime, anomalyEndTime, + startDate, endDate, calendar, movingAveragePoints=12, alter_dataset=None): # {{{ @@ -67,7 +67,8 @@ def compute_moving_avg_anomaly_from_start(timeSeriesFileName, variableList, fileName=timeSeriesFileName, calendar=calendar, variableList=variableList, - startDate=simulationStartTime) + startDate=anomalyStartTime, + endDate=anomalyEndTime) if alter_dataset is not None: dsStart = alter_dataset(dsStart) From 76a67d7be8fbb9b57afafc6b0cf01a9383c1bfa8 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Fri, 23 Mar 2018 10:26:32 +0100 Subject: [PATCH 35/71] Move encoding headers back to top of files These need to go before the license or they won't be recognized. --- mpas_analysis/ocean/climatology_map_argo.py | 7 +++++++ mpas_analysis/ocean/compute_anomaly_subtask.py | 3 ++- mpas_analysis/ocean/index_nino34.py | 3 ++- .../ocean/plot_depth_integrated_time_series_subtask.py | 3 ++- mpas_analysis/ocean/plot_hovmoller_subtask.py | 3 ++- mpas_analysis/ocean/streamfunction_moc.py | 3 ++- mpas_analysis/ocean/time_series_ohc_anomaly.py | 3 ++- mpas_analysis/ocean/time_series_salinity_anomaly.py | 3 ++- mpas_analysis/ocean/time_series_temperature_anomaly.py | 3 ++- mpas_analysis/shared/time_series/anomaly.py | 3 ++- mpas_analysis/shared/time_series/moving_average.py | 3 ++- 11 files changed, 27 insertions(+), 10 deletions(-) diff --git a/mpas_analysis/ocean/climatology_map_argo.py b/mpas_analysis/ocean/climatology_map_argo.py index c8b625a81..abf0402ce 100644 --- a/mpas_analysis/ocean/climatology_map_argo.py +++ b/mpas_analysis/ocean/climatology_map_argo.py @@ -1,3 +1,10 @@ +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# ''' Analysis tasks for comparing Global climatology maps against ARGO data. diff --git a/mpas_analysis/ocean/compute_anomaly_subtask.py b/mpas_analysis/ocean/compute_anomaly_subtask.py index 617420fcc..a2a35e162 100644 --- a/mpas_analysis/ocean/compute_anomaly_subtask.py +++ b/mpas_analysis/ocean/compute_anomaly_subtask.py @@ -1,3 +1,5 @@ +# -*- coding: utf-8 -*- +# # Copyright (c) 2017, Los Alamos National Security, LLC (LANS) # and the University Corporation for Atmospheric Research (UCAR). # @@ -5,7 +7,6 @@ # Additional copyright and license information can be found in the LICENSE file # distributed with this code, or at http://mpas-dev.github.com/license.html # -# -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/ocean/index_nino34.py b/mpas_analysis/ocean/index_nino34.py index add345e69..6c4653081 100644 --- a/mpas_analysis/ocean/index_nino34.py +++ b/mpas_analysis/ocean/index_nino34.py @@ -1,3 +1,5 @@ +# -*- coding: utf-8 -*- +# # Copyright (c) 2017, Los Alamos National Security, LLC (LANS) # and the University Corporation for Atmospheric Research (UCAR). # @@ -5,7 +7,6 @@ # Additional copyright and license information can be found in the LICENSE file # distributed with this code, or at http://mpas-dev.github.com/license.html # -# -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py b/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py index e6b49d942..58c8f0b5e 100644 --- a/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py +++ b/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py @@ -1,3 +1,5 @@ +# -*- coding: utf-8 -*- +# # Copyright (c) 2017, Los Alamos National Security, LLC (LANS) # and the University Corporation for Atmospheric Research (UCAR). # @@ -5,7 +7,6 @@ # Additional copyright and license information can be found in the LICENSE file # distributed with this code, or at http://mpas-dev.github.com/license.html # -# -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/ocean/plot_hovmoller_subtask.py b/mpas_analysis/ocean/plot_hovmoller_subtask.py index c48018690..108ce1d7f 100644 --- a/mpas_analysis/ocean/plot_hovmoller_subtask.py +++ b/mpas_analysis/ocean/plot_hovmoller_subtask.py @@ -1,3 +1,5 @@ +# -*- coding: utf-8 -*- +# # Copyright (c) 2017, Los Alamos National Security, LLC (LANS) # and the University Corporation for Atmospheric Research (UCAR). # @@ -5,7 +7,6 @@ # Additional copyright and license information can be found in the LICENSE file # distributed with this code, or at http://mpas-dev.github.com/license.html # -# -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/ocean/streamfunction_moc.py b/mpas_analysis/ocean/streamfunction_moc.py index 77b7f50dc..e673fec43 100644 --- a/mpas_analysis/ocean/streamfunction_moc.py +++ b/mpas_analysis/ocean/streamfunction_moc.py @@ -1,3 +1,5 @@ +# -*- coding: utf-8 -*- +# # Copyright (c) 2017, Los Alamos National Security, LLC (LANS) # and the University Corporation for Atmospheric Research (UCAR). # @@ -5,7 +7,6 @@ # Additional copyright and license information can be found in the LICENSE file # distributed with this code, or at http://mpas-dev.github.com/license.html # -# -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/ocean/time_series_ohc_anomaly.py b/mpas_analysis/ocean/time_series_ohc_anomaly.py index bda379661..45ff7e851 100644 --- a/mpas_analysis/ocean/time_series_ohc_anomaly.py +++ b/mpas_analysis/ocean/time_series_ohc_anomaly.py @@ -1,3 +1,5 @@ +# -*- coding: utf-8 -*- +# # Copyright (c) 2017, Los Alamos National Security, LLC (LANS) # and the University Corporation for Atmospheric Research (UCAR). # @@ -5,7 +7,6 @@ # Additional copyright and license information can be found in the LICENSE file # distributed with this code, or at http://mpas-dev.github.com/license.html # -# -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/ocean/time_series_salinity_anomaly.py b/mpas_analysis/ocean/time_series_salinity_anomaly.py index f566415af..c86e1a04c 100644 --- a/mpas_analysis/ocean/time_series_salinity_anomaly.py +++ b/mpas_analysis/ocean/time_series_salinity_anomaly.py @@ -1,3 +1,5 @@ +# -*- coding: utf-8 -*- +# # Copyright (c) 2017, Los Alamos National Security, LLC (LANS) # and the University Corporation for Atmospheric Research (UCAR). # @@ -5,7 +7,6 @@ # Additional copyright and license information can be found in the LICENSE file # distributed with this code, or at http://mpas-dev.github.com/license.html # -# -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/ocean/time_series_temperature_anomaly.py b/mpas_analysis/ocean/time_series_temperature_anomaly.py index ab9c251f2..f15c4b5e7 100644 --- a/mpas_analysis/ocean/time_series_temperature_anomaly.py +++ b/mpas_analysis/ocean/time_series_temperature_anomaly.py @@ -1,3 +1,5 @@ +# -*- coding: utf-8 -*- +# # Copyright (c) 2017, Los Alamos National Security, LLC (LANS) # and the University Corporation for Atmospheric Research (UCAR). # @@ -5,7 +7,6 @@ # Additional copyright and license information can be found in the LICENSE file # distributed with this code, or at http://mpas-dev.github.com/license.html # -# -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/shared/time_series/anomaly.py b/mpas_analysis/shared/time_series/anomaly.py index f20d0d157..29650fc45 100644 --- a/mpas_analysis/shared/time_series/anomaly.py +++ b/mpas_analysis/shared/time_series/anomaly.py @@ -1,3 +1,5 @@ +# -*- coding: utf-8 -*- +# # Copyright (c) 2017, Los Alamos National Security, LLC (LANS) # and the University Corporation for Atmospheric Research (UCAR). # @@ -5,7 +7,6 @@ # Additional copyright and license information can be found in the LICENSE file # distributed with this code, or at http://mpas-dev.github.com/license.html # -# -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/shared/time_series/moving_average.py b/mpas_analysis/shared/time_series/moving_average.py index 4d0290ffd..80e4cf498 100644 --- a/mpas_analysis/shared/time_series/moving_average.py +++ b/mpas_analysis/shared/time_series/moving_average.py @@ -1,3 +1,5 @@ +# -*- coding: utf-8 -*- +# # Copyright (c) 2017, Los Alamos National Security, LLC (LANS) # and the University Corporation for Atmospheric Research (UCAR). # @@ -5,7 +7,6 @@ # Additional copyright and license information can be found in the LICENSE file # distributed with this code, or at http://mpas-dev.github.com/license.html # -# -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function, \ unicode_literals From 45bedd3c135792a451c35d8ab8ca6305c43efb4c Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Fri, 23 Mar 2018 11:10:06 +0100 Subject: [PATCH 36/71] Update license prepend script to handle encoding The script now prepends headers only after the encoding in python file (and after the shebang and encodeing if both are present). Also, the -r flag was added to xarg calls to prevent issues when the incoming list of files is empty. --- licenses/_headers/license-prepend-missing.sh | 63 +++++++++++++++++--- 1 file changed, 56 insertions(+), 7 deletions(-) diff --git a/licenses/_headers/license-prepend-missing.sh b/licenses/_headers/license-prepend-missing.sh index 361929298..18c861692 100755 --- a/licenses/_headers/license-prepend-missing.sh +++ b/licenses/_headers/license-prepend-missing.sh @@ -16,10 +16,13 @@ # Get the source dir and ignore variables source license-setup.sh +GET=( -iname "*.py" -or -iname "*.sh" -or -iname "*.bash" -or -iname "*.csh" \ + -or -iname "*.pbs" -or -iname "*.html" -or -iname "*.css" -or -iname "*.js" ) + echo "--------------------------------------------------------------------------------" echo " PREPENDING A LICENSE HEADER ONTO THESE FILES:" echo "--------------------------------------------------------------------------------" -find $SOURCE_DIR -type f "${ALWAYS_IGNORE[@]}" \ +find $SOURCE_DIR -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" \ "${FILE_IGNORE[@]}" \ "${PYTHON_IGNORE[@]}" \ "${CSS_IGNORE[@]}" \ @@ -29,6 +32,51 @@ find $SOURCE_DIR -type f "${ALWAYS_IGNORE[@]}" \ echo "--------------------------------------------------------------------------------" echo " BEGIN PREPENDING:" echo "--------------------------------------------------------------------------------" + + +############################################################ +# Prepend license header to python files with a shebang and an encoding header. +# Will ignore files with a current license header. +############################################################ +GET=( -iname "*.py" ) + +find $SOURCE_DIR -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" "${PYTHON_IGNORE[@]}" \ + | xargs -r grep -l --max-count=1 "#!" \ + | xargs -r grep -l --max-count=1 "# -\*-" \ + | xargs -r grep -L "$CURRENT" \ + | while read SRC +do + BN=`basename ${SRC}` + echo HEADING ${SRC} + cat ${SRC} | head -n 2 > /tmp/licHead + cat header-py >> /tmp/licHead + cat ${SRC} | tail -n +3 >> /tmp/licHead + chmod --reference=${SRC} /tmp/licHead + mv /tmp/licHead ${SRC} +done + + +####################################################################### +# Prepend license header to python files with encoding header. +# Will ignore files with a current license header. +####################################################################### +GET=( -iname "*.py" ) + +find $SOURCE_DIR -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" "${PYTHON_IGNORE[@]}" \ + | xargs -r grep -l --max-count=1 "# -\*-" \ + | xargs -r grep -L "$CURRENT" \ + | while read SRC +do + BN=`basename ${SRC}` + echo HEADING ${SRC} + cat ${SRC} | head -n 1 > /tmp/licHead + cat header-py >> /tmp/licHead + cat ${SRC} | tail -n +2 >> /tmp/licHead + chmod --reference=${SRC} /tmp/licHead + mv /tmp/licHead ${SRC} +done + + ############################################################ # Prepend license header to python files without a shebang. # Will ignore files with a current license header. @@ -36,8 +84,8 @@ echo "-------------------------------------------------------------------------- GET=( -iname "*.py" ) find $SOURCE_DIR -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" "${PYTHON_IGNORE[@]}" \ - | xargs grep -L "#!" \ - | xargs grep -L "$CURRENT" \ + | xargs -r grep -L "#!" \ + | xargs -r grep -L "$CURRENT" \ | while read SRC do BN=`basename ${SRC}` @@ -48,6 +96,7 @@ do mv /tmp/licHead ${SRC} done + ####################################################################### # Prepend license header to python, bash, and sh files with a shebang. # Will ignore files with a current license header. @@ -55,8 +104,8 @@ done GET=( -iname "*.py" -or -iname "*.sh" -or -iname "*.bash" -or -iname "*.csh" -or -iname "*.pbs") find $SOURCE_DIR -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" "${PYTHON_IGNORE[@]}" \ - | xargs grep -l --max-count=1 "#!" \ - | xargs grep -L "$CURRENT" \ + | xargs -r grep -l --max-count=1 "#!" \ + | xargs -r grep -L "$CURRENT" \ | while read SRC do BN=`basename ${SRC}` @@ -76,7 +125,7 @@ done GET=( -iname "*.html") find $SOURCE_DIR -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" \ - | xargs grep -L "$CURRENT" \ + | xargs -r grep -L "$CURRENT" \ | while read SRC do BN=`basename ${SRC}` @@ -94,7 +143,7 @@ done GET=( -iname "*.css" -or -iname "*.js" ) find $SOURCE_DIR -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" "${CSS_IGNORE[@]}" \ - | xargs grep -L "$CURRENT" \ + | xargs -r grep -L "$CURRENT" \ | while read SRC do BN=`basename ${SRC}` From 9767a21540f99176a5bde8a21107f48c7a0a52de Mon Sep 17 00:00:00 2001 From: Joseph H Kennedy Date: Tue, 27 Mar 2018 09:07:44 -0400 Subject: [PATCH 37/71] Unify find in license scripts and use more inclusive search license-find-missing.sh, license-prepend-missing.sh, and license-bump-copyright.sh will all find the same set of files to examine for license issues. The find may be more inclusive than the set of files that will be modified by the license prepend script, and so a warning message has been added to describe how to fix missed files. Other small changes: * license-bump-copyright.sh will recognise the current copyright statement as the old copyright, and an expected future copyright statement has been set to the new statement * the -r flag was added to the xargs calls to prevent issues when the incoming list of files is empty * Curly braces have been added to all unquoted bash variables to prevent unintended expansion issues and follow best practices. * references to the non-existent CSS_IGNORE array has been removed --- licenses/_headers/license-bump-copyright.sh | 28 ++++++------ licenses/_headers/license-find-missing.sh | 5 +-- licenses/_headers/license-prepend-missing.sh | 46 ++++++++++++++------ 3 files changed, 47 insertions(+), 32 deletions(-) diff --git a/licenses/_headers/license-bump-copyright.sh b/licenses/_headers/license-bump-copyright.sh index e99eced52..4439e578b 100755 --- a/licenses/_headers/license-bump-copyright.sh +++ b/licenses/_headers/license-bump-copyright.sh @@ -16,51 +16,49 @@ # Get the source dir and ignore variables source license-setup.sh -OLD="Copyright (c) 2015,2016, UT" -NEW="Copyright (c) 2017, UT" - -ALWAYS_IGNORE=(-not -path "*.git*" -not -path "*docs/*") -FILE_IGNORE=(-not -iname "*.md" -not -iname "*.json" -not -iname "*.txt" \ - -not -iname "*.png" -not -iname "*.jpg" -not -iname "*.svg" ) +OLD="Copyright (c) 2017, UT" +NEW="Copyright (c) 2017-2018, UT" echo "--------------------------------------------------------------------------------" echo " THESE FILES HAVE AN OUTDATED LICENSE HEADER:" echo "--------------------------------------------------------------------------------" -find $SOURCE_DIR -type f "${ALWAYS_IGNORE[@]}" \ +find ${SOURCE_DIR} -type f "${ALWAYS_IGNORE[@]}" \ "${FILE_IGNORE[@]}" \ - | xargs grep -l "$OLD" \ + "${PYTHON_IGNORE[@]}" \ + | xargs -r grep -l "$OLD" \ | sort +# Also, bump any copyright statements in the documentation find ${SOURCE_DIR}/docs -type f \ -not -path "*_build*" \ -not -path "*source*" \ "${FILE_IGNORE[@]}" \ - | xargs grep -l "$OLD" \ + | xargs -r grep -l "$OLD" \ | sort echo "--------------------------------------------------------------------------------" echo " UPDATING THE LICENSE HEADERS:" echo "--------------------------------------------------------------------------------" -find $SOURCE_DIR -type f "${ALWAYS_IGNORE[@]}" \ +find ${SOURCE_DIR} -type f "${ALWAYS_IGNORE[@]}" \ "${FILE_IGNORE[@]}" \ - | xargs grep -l "$OLD" \ + | xargs -r grep -l "$OLD" \ | sort \ | while read SRC do echo "Bumping $SRC" - sed -i "s/$OLD/$NEW/g" $SRC + sed -i "s/$OLD/$NEW/g" ${SRC} done - +# Also, bump any copyright statements in the documentation find ${SOURCE_DIR}/docs -type f \ -not -path "*_build*" \ -not -path "*source*" \ "${FILE_IGNORE[@]}" \ - | xargs grep -l "$OLD" \ + | xargs -r grep -l "$OLD" \ | sort \ | while read SRC do echo "Bumping $SRC" - sed -i "s/$OLD/$NEW/g" $SRC + sed -i "s/$OLD/$NEW/g" ${SRC} done diff --git a/licenses/_headers/license-find-missing.sh b/licenses/_headers/license-find-missing.sh index d80f0a140..7b6ed7815 100755 --- a/licenses/_headers/license-find-missing.sh +++ b/licenses/_headers/license-find-missing.sh @@ -12,10 +12,9 @@ source license-setup.sh echo "--------------------------------------------------------------------------------" echo " THESE FILES ARE MISSING A CURRENT LICENSE HEADER:" echo "--------------------------------------------------------------------------------" -find $SOURCE_DIR -type f "${ALWAYS_IGNORE[@]}" \ +find ${SOURCE_DIR} -type f "${ALWAYS_IGNORE[@]}" \ "${FILE_IGNORE[@]}" \ "${PYTHON_IGNORE[@]}" \ - "${CSS_IGNORE[@]}" \ - | xargs grep -L "$CURRENT" \ + | xargs -r grep -L "$CURRENT" \ | sort diff --git a/licenses/_headers/license-prepend-missing.sh b/licenses/_headers/license-prepend-missing.sh index 18c861692..c74062570 100755 --- a/licenses/_headers/license-prepend-missing.sh +++ b/licenses/_headers/license-prepend-missing.sh @@ -16,17 +16,13 @@ # Get the source dir and ignore variables source license-setup.sh -GET=( -iname "*.py" -or -iname "*.sh" -or -iname "*.bash" -or -iname "*.csh" \ - -or -iname "*.pbs" -or -iname "*.html" -or -iname "*.css" -or -iname "*.js" ) - echo "--------------------------------------------------------------------------------" -echo " PREPENDING A LICENSE HEADER ONTO THESE FILES:" +echo " ATTEMPTING TO PREPEND A LICENSE HEADER ONTO THESE FILES:" echo "--------------------------------------------------------------------------------" -find $SOURCE_DIR -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" \ +find ${SOURCE_DIR} -type f "${ALWAYS_IGNORE[@]}" \ "${FILE_IGNORE[@]}" \ "${PYTHON_IGNORE[@]}" \ - "${CSS_IGNORE[@]}" \ - | xargs grep -L "$CURRENT" \ + | xargs -r grep -L "$CURRENT" \ | sort echo "--------------------------------------------------------------------------------" @@ -40,7 +36,7 @@ echo "-------------------------------------------------------------------------- ############################################################ GET=( -iname "*.py" ) -find $SOURCE_DIR -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" "${PYTHON_IGNORE[@]}" \ +find ${SOURCE_DIR} -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" "${PYTHON_IGNORE[@]}" \ | xargs -r grep -l --max-count=1 "#!" \ | xargs -r grep -l --max-count=1 "# -\*-" \ | xargs -r grep -L "$CURRENT" \ @@ -62,7 +58,7 @@ done ####################################################################### GET=( -iname "*.py" ) -find $SOURCE_DIR -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" "${PYTHON_IGNORE[@]}" \ +find ${SOURCE_DIR} -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" "${PYTHON_IGNORE[@]}" \ | xargs -r grep -l --max-count=1 "# -\*-" \ | xargs -r grep -L "$CURRENT" \ | while read SRC @@ -83,7 +79,7 @@ done ############################################################ GET=( -iname "*.py" ) -find $SOURCE_DIR -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" "${PYTHON_IGNORE[@]}" \ +find ${SOURCE_DIR} -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" "${PYTHON_IGNORE[@]}" \ | xargs -r grep -L "#!" \ | xargs -r grep -L "$CURRENT" \ | while read SRC @@ -103,7 +99,7 @@ done ####################################################################### GET=( -iname "*.py" -or -iname "*.sh" -or -iname "*.bash" -or -iname "*.csh" -or -iname "*.pbs") -find $SOURCE_DIR -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" "${PYTHON_IGNORE[@]}" \ +find ${SOURCE_DIR} -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" "${PYTHON_IGNORE[@]}" \ | xargs -r grep -l --max-count=1 "#!" \ | xargs -r grep -L "$CURRENT" \ | while read SRC @@ -124,7 +120,7 @@ done #################################################### GET=( -iname "*.html") -find $SOURCE_DIR -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" \ +find ${SOURCE_DIR} -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" \ | xargs -r grep -L "$CURRENT" \ | while read SRC do @@ -142,7 +138,7 @@ done #################################################### GET=( -iname "*.css" -or -iname "*.js" ) -find $SOURCE_DIR -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" "${CSS_IGNORE[@]}" \ +find ${SOURCE_DIR} -type f \( "${GET[@]}" \) "${ALWAYS_IGNORE[@]}" \ | xargs -r grep -L "$CURRENT" \ | while read SRC do @@ -156,5 +152,27 @@ done echo "--------------------------------------------------------------------------------" echo " DONE PREPENDING!" -echo "--------------------------------------------------------------------------------" + +MISSED=`find ${SOURCE_DIR} -type f "${ALWAYS_IGNORE[@]}" \ + "${FILE_IGNORE[@]}" \ + "${PYTHON_IGNORE[@]}" \ + | xargs -r grep -L "$CURRENT"` + +if [ "$MISSED" ] +then + echo "" + echo " WARNING: There is no method to prepend a license header onto the following" + echo " files. Please either manually add the license head to these files," + echo " add a method to prepend a license header onto these type of files," + echo " or set them to be ignored in 'license-setup.sh'. " + echo "--------------------------------------------------------------------------------" + find ${SOURCE_DIR} -type f "${ALWAYS_IGNORE[@]}" \ + "${FILE_IGNORE[@]}" \ + "${PYTHON_IGNORE[@]}" \ + | xargs -r grep -L "$CURRENT" \ + | sort + echo "--------------------------------------------------------------------------------" +else + echo "--------------------------------------------------------------------------------" +fi \ No newline at end of file From 1037f2a8cb44663ac80f993670dab4fca2e3f321 Mon Sep 17 00:00:00 2001 From: Joseph H Kennedy Date: Tue, 27 Mar 2018 09:20:58 -0400 Subject: [PATCH 38/71] Update ignore arrays for finding license issues The path directives in the ignore arrays now reference the SOURCE_DIR where appropriate to prevent too aggressive path matching, and a some more ignore directives have been added to better select files to examine for license issues. Added ignores: * The PyCharm .idea directory will always be ignored * *.ocean and *_in files will be ignored * conda/recipe/meta.yaml will be ignored * setup.cfg will be ignored --- licenses/_headers/license-setup.sh | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/licenses/_headers/license-setup.sh b/licenses/_headers/license-setup.sh index a2063e2d0..21c26b0eb 100755 --- a/licenses/_headers/license-setup.sh +++ b/licenses/_headers/license-setup.sh @@ -17,14 +17,21 @@ SOURCE_DIR="../.." CURRENT="Copyright (c)" -ALWAYS_IGNORE=(-not -path "*.git*" -not -path "*docs/*" -not -path "build/*" \ - -not -path "dist/*" -not -path "*.egg-info/*" \ - -not -path "licenses/*" ) +ALWAYS_IGNORE=(-not -path "*.git*" \ + -not -path "${SOURCE_DIR}/docs/*" \ + -not -path "${SOURCE_DIR}/licenses/*" \ + -not -path "${SOURCE_DIR}/build/*" \ + -not -path "${SOURCE_DIR}/dist/*" \ + -not -path "${SOURCE_DIR}/.idea/*" \ + -not -path "*.egg-info/*" \ + -not -path "${SOURCE_DIR}/conda/recipe/meta.yaml" \ + -not -path "${SOURCE_DIR}/setup.cfg") -FILE_IGNORE=(-not -iname "*.md" -not -iname "*.json" -not -iname "*.txt" \ +FILE_IGNORE=(-not -iname "*.ocean" -not -iname "*_in" \ + -not -iname "*.md" -not -iname "*.json" -not -iname "*.txt" \ -not -iname "*.png" -not -iname "*.jpg" -not -iname "*.svg" \ -not -iname "config.*" -not -iname "*.nc"\ -not -iname "*.pyc" \ - -not -iname "*.sl" -not -iname "*.ps1" -not -iname "*.yml" ) + -not -iname "*.sl" -not -iname "*.ps1" -not -iname "*.yml") PYTHON_IGNORE=(-not -iname "__init__.py") From daffb97314c740e4ecf188a1cc62d39700740729 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Tue, 27 Mar 2018 15:47:40 +0200 Subject: [PATCH 39/71] Manually add license to run_mpas_analysis --- run_mpas_analysis | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/run_mpas_analysis b/run_mpas_analysis index 87d608229..1782a1121 100755 --- a/run_mpas_analysis +++ b/run_mpas_analysis @@ -1,4 +1,11 @@ #!/usr/bin/env python +# Copyright (c) 2017, Los Alamos National Security, LLC (LANS) +# and the University Corporation for Atmospheric Research (UCAR). +# +# Unless noted otherwise source code is licensed under the BSD license. +# Additional copyright and license information can be found in the LICENSE file +# distributed with this code, or at http://mpas-dev.github.com/license.html +# """ Runs MPAS-Analysis via a configuration file (e.g. `config.analysis`) From 668f697887eeaf68d0ad281a32da874333d68671 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Sat, 31 Mar 2018 18:31:08 +0900 Subject: [PATCH 40/71] Fix moving average of preprocessed OHC data This is accomplished by writing out the multi-file data set and reading it in again as as single-file data set. --- ...ot_depth_integrated_time_series_subtask.py | 29 +++++++++++++++---- 1 file changed, 24 insertions(+), 5 deletions(-) diff --git a/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py b/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py index 58c8f0b5e..6e9fd4275 100644 --- a/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py +++ b/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py @@ -11,15 +11,15 @@ from __future__ import absolute_import, division, print_function, \ unicode_literals -import xarray as xr import os +import xarray from mpas_analysis.shared import AnalysisTask from mpas_analysis.shared.plot.plotting import timeseries_analysis_plot from mpas_analysis.shared.generalized_reader import open_multifile_dataset -from mpas_analysis.shared.io import open_mpas_dataset +from mpas_analysis.shared.io import open_mpas_dataset, write_netcdf from mpas_analysis.shared.timekeeping.utility import date_to_days, \ days_to_datetime @@ -216,6 +216,18 @@ def setup_and_check(self): # {{{ self.refFileName = '{}/{}'.format(baseDirectory, self.inFileName) + preprocessedReferenceRunName = config.get( + 'runs', 'preprocessedReferenceRunName') + if preprocessedReferenceRunName != 'None': + + assert(not os.path.isabs(self.inFileName)) + + baseDirectory = build_config_full_path( + config, 'output', 'timeSeriesSubdirectory') + + self.preprocessedFileName = '{}/preprocessed_{}'.format( + baseDirectory, self.inFileName) + if not os.path.isabs(self.inFileName): baseDirectory = build_config_full_path( config, 'output', 'timeSeriesSubdirectory') @@ -354,6 +366,13 @@ def run_task(self): # {{{ 'not be plotted.') preprocessedReferenceRunName = 'None' + # rolling mean seems to have trouble with dask data sets so we + # write out the data set and read it back as a single-file data set + # (without dask) + dsPreprocessed = dsPreprocessed.drop('xtime') + write_netcdf(dsPreprocessed, self.preprocessedFileName) + dsPreprocessed = xarray.open_dataset(self.preprocessedFileName) + if preprocessedReferenceRunName != 'None': color = 'r' title = '{} \n {} (red)'.format(title, @@ -369,13 +388,13 @@ def run_task(self): # {{{ divisionDepths] + ['btm'] # these preprocessed data are OHC *anomalies* + dsPreprocessed = compute_moving_avg(dsPreprocessed, + movingAveragePoints) for rangeIndex in range(len(suffixes)): variableName = '{}_{}'.format(preprocessedFieldPrefix, suffixes[rangeIndex]) if variableName in list(dsPreprocessed.data_vars.keys()): - field = dsPreprocessed[variableName] - field = compute_moving_avg(field, movingAveragePoints) - timeSeries.append(field) + timeSeries.append(dsPreprocessed[variableName]) else: self.logger.warning('Warning: Preprocessed variable {} ' 'not found. Skipping.'.format( From f8ddf79e36530a361b4edd1f6bc270fb7f758a51 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Mon, 16 Apr 2018 17:03:42 +0200 Subject: [PATCH 41/71] Update version and some missing task in docs --- docs/api.rst | 4 ++++ docs/conf.py | 4 ++-- docs/environment.yml | 3 +-- docs/index.rst | 2 +- 4 files changed, 8 insertions(+), 5 deletions(-) diff --git a/docs/api.rst b/docs/api.rst index 857656b6b..4aa18fc57 100644 --- a/docs/api.rst +++ b/docs/api.rst @@ -53,6 +53,10 @@ Ocean tasks ClimatologyMapMLD ClimatologyMapSSH ClimatologyMapAntarcticMelt + ClimatologyMapSoseTemperature + ClimatologyMapSoseSalinity + ClimatologyMapArgoTemperature + ClimatologyMapArgoSalinity IndexNino34 MeridionalHeatTransport StreamfunctionMOC diff --git a/docs/conf.py b/docs/conf.py index 0ebe5270d..c3b03a7da 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -69,9 +69,9 @@ # built documents. # # The short X.Y version. -version = u'0.6.5' +version = u'0.7.0' # The full version, including alpha/beta/rc tags. -release = u'0.6.5' +release = u'0.7.0' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/docs/environment.yml b/docs/environment.yml index 3500fb5e4..509b389e9 100644 --- a/docs/environment.yml +++ b/docs/environment.yml @@ -21,5 +21,4 @@ dependencies: - sphinx - sphinx_rtd_theme - numpydoc - - pip: - - recommonmark + - recommonmark diff --git a/docs/index.rst b/docs/index.rst index 0431d85e6..eea59046d 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -30,7 +30,7 @@ MPAS Components and E3SM :maxdepth: 2 mpaso - mpascice + mpasseaice e3sm From ec65c5909ec275d787c6e3906e39516f283e123c Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Mon, 16 Apr 2018 17:04:18 +0200 Subject: [PATCH 42/71] Move Authors out of docstrings Author info is not intended to be in docstrings (see numpydoc documentation) and a huge number of warnings when building the documentation. --- mpas_analysis/analysis_task_template.py | 37 ++--- .../mpas_analysis_config_parser.py | 23 ++- .../ocean/climatology_map_antarctic_melt.py | 65 ++++---- mpas_analysis/ocean/climatology_map_argo.py | 66 ++++---- mpas_analysis/ocean/climatology_map_mld.py | 37 ++--- mpas_analysis/ocean/climatology_map_sose.py | 66 ++++---- mpas_analysis/ocean/climatology_map_ssh.py | 51 +++--- mpas_analysis/ocean/climatology_map_sss.py | 37 ++--- mpas_analysis/ocean/climatology_map_sst.py | 37 ++--- .../ocean/compute_anomaly_subtask.py | 30 ++-- mpas_analysis/ocean/index_nino34.py | 90 +++++------ .../ocean/meridional_heat_transport.py | 31 ++-- .../ocean/plot_climatology_map_subtask.py | 45 +++--- ...ot_depth_integrated_time_series_subtask.py | 29 ++-- mpas_analysis/ocean/plot_hovmoller_subtask.py | 29 ++-- .../ocean/remap_depth_slices_subtask.py | 28 ++-- mpas_analysis/ocean/streamfunction_moc.py | 31 ++-- .../ocean/time_series_antarctic_melt.py | 45 +++--- .../ocean/time_series_ohc_anomaly.py | 15 +- .../ocean/time_series_salinity_anomaly.py | 15 +- mpas_analysis/ocean/time_series_sst.py | 30 ++-- .../ocean/time_series_temperature_anomaly.py | 15 +- mpas_analysis/ocean/utility.py | 14 +- .../sea_ice/climatology_map_sea_ice_conc.py | 37 ++--- .../sea_ice/climatology_map_sea_ice_thick.py | 37 ++--- .../sea_ice/plot_climatology_map_subtask.py | 38 ++--- mpas_analysis/sea_ice/time_series.py | 38 +++-- mpas_analysis/shared/analysis_task.py | 89 +++++------ .../shared/climatology/climatology.py | 107 ++++++------- .../climatology/comparison_descriptors.py | 39 +++-- .../climatology/mpas_climatology_task.py | 50 +++--- .../remap_mpas_climatology_subtask.py | 80 +++++----- .../remap_observed_climatology_subtask.py | 58 ++++--- mpas_analysis/shared/constants/constants.py | 11 +- .../generalized_reader/generalized_reader.py | 36 ++--- mpas_analysis/shared/grid/grid.py | 146 ++++++++---------- mpas_analysis/shared/html/image_xml.py | 16 +- mpas_analysis/shared/html/pages.py | 78 +++++----- .../shared/interpolation/remapper.py | 63 ++++---- mpas_analysis/shared/io/mpas_reader.py | 28 ++-- .../shared/io/namelist_streams_interface.py | 140 ++++++++--------- mpas_analysis/shared/io/utility.py | 46 +++--- mpas_analysis/shared/io/write_netcdf.py | 10 +- .../shared/mpas_xarray/mpas_xarray.py | 67 ++++---- mpas_analysis/shared/plot/plotting.py | 86 +++++------ mpas_analysis/shared/time_series/anomaly.py | 7 +- .../shared/time_series/moving_average.py | 7 +- .../time_series/mpas_time_series_task.py | 43 +++--- .../shared/time_series/time_series.py | 14 +- .../shared/timekeeping/MpasRelativeDelta.py | 7 +- mpas_analysis/shared/timekeeping/utility.py | 64 ++++---- .../test/test_remap_obs_clim_subtask.py | 21 ++- mpas_analysis/test/test_timekeeping.py | 7 +- run_mpas_analysis | 50 +++--- 54 files changed, 1080 insertions(+), 1306 deletions(-) diff --git a/mpas_analysis/analysis_task_template.py b/mpas_analysis/analysis_task_template.py index 8b1a93bbb..993205726 100644 --- a/mpas_analysis/analysis_task_template.py +++ b/mpas_analysis/analysis_task_template.py @@ -34,11 +34,10 @@ to be generated and is set up properly. Don't forget to remove this docstring. (It's not needed.) - -Authors -------- -Xylar Asay-Davis ''' +# Authors +# ------- +# Xylar Asay-Davis from __future__ import absolute_import, division, print_function, \ unicode_literals @@ -67,11 +66,10 @@ class MyTask(AnalysisTask): # {{{ ''' - - Authors - ------- - ''' + # Authors + # ------- + # # This function is the "constructor", which is called when you want to # create a new object from your class. Typically, it will just store a few @@ -114,12 +112,11 @@ def __init__(self, config, prerequsiteTask, myArg='myDefaultValue'): # {{{ myArg : str, optional - - Authors - ------- - - ''' + # Authors + # ------- + # + # first, call the constructor from the base class (AnalysisTask). # Modify MyTask, "myTask", "component" and ['tag1', 'tag2'] below: # taskName is the same as the class name but with a lowercase letter @@ -201,11 +198,10 @@ def setup_and_check(self): # {{{ Raises ------ ValueError: - - Authors - ------- - ''' + # Authors + # ------- + # # first, call setup_and_check from the base class (AnalysisTask), # which will perform some common setup, including storing: @@ -317,11 +313,10 @@ def setup_and_check(self): # {{{ def run_task(self): # {{{ ''' The main method of the task that performs the analysis task. - - Authors - ------- - ''' + # Authors + # ------- + # # Add the main contents of the analysis task below diff --git a/mpas_analysis/configuration/mpas_analysis_config_parser.py b/mpas_analysis/configuration/mpas_analysis_config_parser.py index 0440f4768..7cfae363c 100644 --- a/mpas_analysis/configuration/mpas_analysis_config_parser.py +++ b/mpas_analysis/configuration/mpas_analysis_config_parser.py @@ -10,11 +10,10 @@ the capabilities to get an option including a default value (``getWithDefault(section, option, default, ...)``) and to get options that are lists, tuples, dicts, etc (``getExpression(section, option)``). - -Authors -------- -Xylar Asay-Davis, Phillip J. Wolfram """ +# Authors +# ------- +# Xylar Asay-Davis, Phillip J. Wolfram from __future__ import absolute_import, division, print_function, \ unicode_literals @@ -53,11 +52,11 @@ def getWithDefault(self, section, option, default): to determine the type of the option if it *is* found. If ``default`` is a list, tuple, or dict, ``getExpression(...)`` is used if the option is present in the config file. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + if self.has_section(section): if self.has_option(section, option): if isinstance(default, bool): @@ -101,11 +100,11 @@ def getExpression(self, section, option, elementType=None, If ``True``, the expression is evaluated including functionality from the numpy package (which can be referenced either as ``numpy`` or ``np``). - - Authors - ------- - Xylar Asay-Davis, Phillip J. Wolfram """ + # Authors + # ------- + # Xylar Asay-Davis, Phillip J. Wolfram + expressionString = self.get(section, option) if usenumpyfunc: assert '__' not in expressionString, \ diff --git a/mpas_analysis/ocean/climatology_map_antarctic_melt.py b/mpas_analysis/ocean/climatology_map_antarctic_melt.py index 5d24b6f86..e9408dcdf 100644 --- a/mpas_analysis/ocean/climatology_map_antarctic_melt.py +++ b/mpas_analysis/ocean/climatology_map_antarctic_melt.py @@ -31,11 +31,11 @@ class ClimatologyMapAntarcticMelt(AnalysisTask): # {{{ """ An analysis task for comparison of Antarctic melt rates against observations - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + def __init__(self, config, mpasClimatologyTask, refConfig=None): # {{{ """ @@ -51,11 +51,11 @@ def __init__(self, config, mpasClimatologyTask, refConfig : ``MpasAnalysisConfigParser``, optional Configuration options for a reference run (if any) - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + fieldName = 'meltRate' # call the constructor from the base class (AnalysisTask) super(ClimatologyMapAntarcticMelt, self).__init__( @@ -155,11 +155,10 @@ def __init__(self, config, mpasClimatologyTask, def setup_and_check(self): # {{{ """ Perform steps to set up the analysis and check for errors in the setup. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis # first, call setup_and_check from the base class # (AnalysisTask), which will perform some common setup @@ -185,11 +184,10 @@ class RemapMpasAntarcticMeltClimatology(RemapMpasClimatologySubtask): # {{{ landIceMask : xarray.DataArray A mask indicating where there is land ice on the ocean grid (thus, where melt rates are valid) - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis def run_task(self): # {{{ """ @@ -198,11 +196,10 @@ def run_task(self): # {{{ This function has been overridden to load ``landIceMask`` from a restart file for later use in masking the melt rate. It then simply calls the run function from - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis # first, load the land-ice mask from the restart file dsLandIceMask = xr.open_dataset(self.restartFileName) @@ -230,11 +227,10 @@ def customize_masked_climatology(self, climatology): # {{{ ------- climatology : ``xarray.Dataset`` object the modified climatology data set - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis fieldName = self.variableList[0] @@ -252,11 +248,10 @@ class RemapObservedAntarcticMeltClimatology(RemapObservedClimatologySubtask): # {{{ """ A subtask for reading and remapping Antarctic melt-rate observations - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis def get_observation_descriptor(self, fileName): # {{{ ''' @@ -271,11 +266,10 @@ def get_observation_descriptor(self, fileName): # {{{ ------- obsDescriptor : ``MeshDescriptor`` The descriptor for the observation grid - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis # create a descriptor of the observation grid using the x/y polar # stereographic coordinates @@ -298,11 +292,10 @@ def build_observational_dataset(self, fileName): # {{{ ------- dsObs : ``xarray.Dataset`` The observational dataset - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis # Load MLD observational data dsObs = xr.open_dataset(fileName) diff --git a/mpas_analysis/ocean/climatology_map_argo.py b/mpas_analysis/ocean/climatology_map_argo.py index abf0402ce..8e976c8b8 100644 --- a/mpas_analysis/ocean/climatology_map_argo.py +++ b/mpas_analysis/ocean/climatology_map_argo.py @@ -7,11 +7,10 @@ # ''' Analysis tasks for comparing Global climatology maps against ARGO data. - -Authors -------- -Luke Van Roekel ''' +# Authors +# ------- +# Luke Van Roekel import xarray as xr import numpy as np @@ -37,11 +36,10 @@ class ClimatologyMapArgoTemperature(AnalysisTask): # {{{ """ An analysis task for comparison of antarctic temperature against SOSE fields - - Authors - ------- - Luke Van Roekel, Xylar Asay-Davis """ + # Authors + # ------- + # Luke Van Roekel, Xylar Asay-Davis def __init__(self, config, mpasClimatologyTask, refConfig=None): # {{{ @@ -58,11 +56,11 @@ def __init__(self, config, mpasClimatologyTask, refConfig : ``MpasAnalysisConfigParser``, optional Configuration options for a reference run (if any) - - Authors - ------- - Luke Van Roekel, Xylar Asay-Davis """ + # Authors + # ------- + # Luke Van Roekel, Xylar Asay-Davis + fieldName = 'temperatureARGO' # call the constructor from the base class (AnalysisTask) super(ClimatologyMapArgoTemperature, self).__init__( @@ -178,11 +176,10 @@ class ClimatologyMapArgoSalinity(AnalysisTask): # {{{ """ An analysis task for comparison of Global Temperature against Argo fields - - Authors - ------- - Xylar Asay-Davis, Luke Van Roekel """ + # Authors + # ------- + # Xylar Asay-Davis, Luke Van Roekel def __init__(self, config, mpasClimatologyTask, refConfig=None): # {{{ @@ -199,11 +196,11 @@ def __init__(self, config, mpasClimatologyTask, refConfig : ``MpasAnalysisConfigParser``, optional Configuration options for a reference run (if any) - - Authors - ------- - Xylar Asay-Davis, Luke Van Roekel """ + # Authors + # ------- + # Xylar Asay-Davis, Luke Van Roekel + fieldName = 'salinityARGO' # call the constructor from the base class (AnalysisTask) super(ClimatologyMapArgoSalinity, self).__init__( @@ -319,11 +316,10 @@ class RemapArgoClimatology(RemapObservedClimatologySubtask): # {{{ """ A subtask for reading and remapping SOSE fields to the comparison grid - - Authors - ------- - Xylar Asay-Davis, Luke Van Roekel """ + # Authors + # ------- + # Xylar Asay-Davis, Luke Van Roekel def __init__(self, parentTask, seasons, fileName, outFilePrefix, fieldName, depths, @@ -362,12 +358,10 @@ def __init__(self, parentTask, seasons, fileName, outFilePrefix, subtaskName : str, optional The name of the subtask - - Authors - ------- - Xylar Asay-Davis, Luke Van Roekel - ''' + # Authors + # ------- + # Xylar Asay-Davis, Luke Van Roekel self.fieldName = fieldName self.depths = depths @@ -392,11 +386,10 @@ def get_observation_descriptor(self, fileName): # {{{ ------- obsDescriptor : ``MeshDescriptor`` The descriptor for the observation grid - - Authors - ------- - Xylar Asay-Davis, Luke Van Roekel ''' + # Authors + # ------- + # Xylar Asay-Davis, Luke Van Roekel # Load Argo observational Data dsObs = self.build_observational_dataset(fileName) @@ -423,11 +416,10 @@ def build_observational_dataset(self, fileName): # {{{ ------- dsObs : ``xarray.Dataset`` The observational dataset - - Authors - ------- - Xylar Asay-Davis, Luke Van Roekel ''' + # Authors + # ------- + # Xylar Asay-Davis, Luke Van Roekel # Load Argo observational data dsObs = xr.open_dataset(fileName) diff --git a/mpas_analysis/ocean/climatology_map_mld.py b/mpas_analysis/ocean/climatology_map_mld.py index e8f61b48b..4ce53a9b6 100644 --- a/mpas_analysis/ocean/climatology_map_mld.py +++ b/mpas_analysis/ocean/climatology_map_mld.py @@ -30,11 +30,11 @@ class ClimatologyMapMLD(AnalysisTask): # {{{ """ An analysis task for comparison of mixed layer depth (mld) against observations - - Authors - ------- - Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani """ + # Authors + # ------- + # Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani + def __init__(self, config, mpasClimatologyTask, refConfig=None): # {{{ """ @@ -50,11 +50,11 @@ def __init__(self, config, mpasClimatologyTask, refConfig : ``MpasAnalysisConfigParser``, optional Configuration options for a reference run (if any) - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + fieldName = 'mld' # call the constructor from the base class (AnalysisTask) super(ClimatologyMapMLD, self).__init__( @@ -155,11 +155,10 @@ def __init__(self, config, mpasClimatologyTask, class RemapObservedMLDClimatology(RemapObservedClimatologySubtask): # {{{ """ A subtask for reading and remapping MLD observations - - Authors - ------- - Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani """ + # Authors + # ------- + # Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani def get_observation_descriptor(self, fileName): # {{{ ''' @@ -174,11 +173,10 @@ def get_observation_descriptor(self, fileName): # {{{ ------- obsDescriptor : ``MeshDescriptor`` The descriptor for the observation grid - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis # Load MLD observational data dsObs = self.build_observational_dataset(fileName) @@ -205,11 +203,10 @@ def build_observational_dataset(self, fileName): # {{{ ------- dsObs : ``xarray.Dataset`` The observational dataset - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis # Load MLD observational data dsObs = xr.open_dataset(fileName) diff --git a/mpas_analysis/ocean/climatology_map_sose.py b/mpas_analysis/ocean/climatology_map_sose.py index b99e43005..3c9cb2ee4 100644 --- a/mpas_analysis/ocean/climatology_map_sose.py +++ b/mpas_analysis/ocean/climatology_map_sose.py @@ -8,11 +8,10 @@ ''' Analysis tasks for comparing Antarctic climatology maps against observations and reanalysis data. - -Authors -------- -Xylar Asay-Davis ''' +# Authors +# ------- +# Xylar Asay-Davis import xarray as xr @@ -38,11 +37,10 @@ class ClimatologyMapSoseTemperature(AnalysisTask): # {{{ """ An analysis task for comparison of antarctic temperature against SOSE fields - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis def __init__(self, config, mpasClimatologyTask, refConfig=None): # {{{ @@ -59,11 +57,11 @@ def __init__(self, config, mpasClimatologyTask, refConfig : ``MpasAnalysisConfigParser``, optional Configuration options for a reference run (if any) - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + fieldName = 'temperatureSOSE' # call the constructor from the base class (AnalysisTask) super(ClimatologyMapSoseTemperature, self).__init__( @@ -180,11 +178,10 @@ class ClimatologyMapSoseSalinity(AnalysisTask): # {{{ """ An analysis task for comparison of antarctic salinity against SOSE fields - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis def __init__(self, config, mpasClimatologyTask, refConfig=None): # {{{ @@ -201,11 +198,11 @@ def __init__(self, config, mpasClimatologyTask, refConfig : ``MpasAnalysisConfigParser``, optional Configuration options for a reference run (if any) - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + fieldName = 'salinitySOSE' # call the constructor from the base class (AnalysisTask) super(ClimatologyMapSoseSalinity, self).__init__( @@ -322,11 +319,10 @@ class RemapSoseClimatology(RemapObservedClimatologySubtask): # {{{ """ A subtask for reading and remapping SOSE fields to the comparison grid - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis def __init__(self, parentTask, seasons, fileName, outFilePrefix, fieldName, botFieldName, depths, @@ -369,12 +365,10 @@ def __init__(self, parentTask, seasons, fileName, outFilePrefix, subtaskName : str, optional The name of the subtask - - Authors - ------- - Xylar Asay-Davis - ''' + # Authors + # ------- + # Xylar Asay-Davis self.fieldName = fieldName self.botFieldName = botFieldName @@ -400,11 +394,10 @@ def get_observation_descriptor(self, fileName): # {{{ ------- obsDescriptor : ``MeshDescriptor`` The descriptor for the observation grid - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis # create a descriptor of the observation grid using the x/y polar # stereographic coordinates @@ -427,11 +420,10 @@ def build_observational_dataset(self, fileName): # {{{ ------- dsObs : ``xarray.Dataset`` The observational dataset - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis # Load MLD observational data dsObs = xr.open_dataset(fileName) diff --git a/mpas_analysis/ocean/climatology_map_ssh.py b/mpas_analysis/ocean/climatology_map_ssh.py index 5838ba283..f7772b6cd 100644 --- a/mpas_analysis/ocean/climatology_map_ssh.py +++ b/mpas_analysis/ocean/climatology_map_ssh.py @@ -29,11 +29,11 @@ class ClimatologyMapSSH(AnalysisTask): # {{{ """ An analysis task for comparison of sea surface height (ssh) against observations - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + def __init__(self, config, mpasClimatologyTask, refConfig=None): # {{{ """ @@ -49,11 +49,11 @@ def __init__(self, config, mpasClimatologyTask, refConfig : ``MpasAnalysisConfigParser``, optional Configuration options for a reference run (if any) - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + fieldName = 'ssh' # call the constructor from the base class (AnalysisTask) super(ClimatologyMapSSH, self).__init__( @@ -156,11 +156,10 @@ def __init__(self, config, mpasClimatologyTask, class RemapSSHClimatology(RemapMpasClimatologySubtask): # {{{ """ Change units from m to cm - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis def customize_masked_climatology(self, climatology): # {{{ """ @@ -175,11 +174,10 @@ def customize_masked_climatology(self, climatology): # {{{ ------- climatology : ``xarray.Dataset`` object the modified climatology data set - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis fieldName = self.variableList[0] @@ -194,11 +192,10 @@ def customize_masked_climatology(self, climatology): # {{{ class RemapObservedSSHClimatology(RemapObservedClimatologySubtask): # {{{ """ A subtask for reading and remapping SSH observations - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis def get_observation_descriptor(self, fileName): # {{{ ''' @@ -213,11 +210,10 @@ def get_observation_descriptor(self, fileName): # {{{ ------- obsDescriptor : ``MeshDescriptor`` The descriptor for the observation grid - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis # create a descriptor of the observation grid using the lat/lon # coordinates @@ -240,11 +236,10 @@ def build_observational_dataset(self, fileName): # {{{ ------- dsObs : ``xarray.Dataset`` The observational dataset - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis dsObs = xr.open_dataset(fileName) dsObs.rename({'time': 'Time'}, inplace=True) diff --git a/mpas_analysis/ocean/climatology_map_sss.py b/mpas_analysis/ocean/climatology_map_sss.py index 069a34359..30359fc48 100644 --- a/mpas_analysis/ocean/climatology_map_sss.py +++ b/mpas_analysis/ocean/climatology_map_sss.py @@ -28,11 +28,11 @@ class ClimatologyMapSSS(AnalysisTask): # {{{ """ An analysis task for comparison of sea surface salinity (sss) against observations - - Authors - ------- - Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani """ + # Authors + # ------- + # Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani + def __init__(self, config, mpasClimatologyTask, refConfig=None): # {{{ """ @@ -48,11 +48,11 @@ def __init__(self, config, mpasClimatologyTask, refConfig : ``MpasAnalysisConfigParser``, optional Configuration options for a reference run (if any) - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + fieldName = 'sss' # call the constructor from the base class (AnalysisTask) super(ClimatologyMapSSS, self).__init__( @@ -154,11 +154,10 @@ def __init__(self, config, mpasClimatologyTask, class RemapObservedSSSClimatology(RemapObservedClimatologySubtask): # {{{ """ A subtask for reading and remapping SSS observations - - Authors - ------- - Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani """ + # Authors + # ------- + # Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani def get_observation_descriptor(self, fileName): # {{{ ''' @@ -173,11 +172,10 @@ def get_observation_descriptor(self, fileName): # {{{ ------- obsDescriptor : ``MeshDescriptor`` The descriptor for the observation grid - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis # create a descriptor of the observation grid using the lat/lon # coordinates @@ -200,11 +198,10 @@ def build_observational_dataset(self, fileName): # {{{ ------- dsObs : ``xarray.Dataset`` The observational dataset - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis timeStart = datetime.datetime(2011, 8, 1) timeEnd = datetime.datetime(2014, 12, 31) diff --git a/mpas_analysis/ocean/climatology_map_sst.py b/mpas_analysis/ocean/climatology_map_sst.py index 35bcb6246..48fb4c109 100644 --- a/mpas_analysis/ocean/climatology_map_sst.py +++ b/mpas_analysis/ocean/climatology_map_sst.py @@ -28,11 +28,11 @@ class ClimatologyMapSST(AnalysisTask): # {{{ """ An analysis task for comparison of sea surface temperature (sst) against observations - - Authors - ------- - Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani """ + # Authors + # ------- + # Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani + def __init__(self, config, mpasClimatologyTask, refConfig=None): # {{{ """ @@ -48,11 +48,11 @@ def __init__(self, config, mpasClimatologyTask, refConfig : ``MpasAnalysisConfigParser``, optional Configuration options for a reference run (if any) - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + fieldName = 'sst' # call the constructor from the base class (AnalysisTask) super(ClimatologyMapSST, self).__init__( @@ -164,11 +164,10 @@ def __init__(self, config, mpasClimatologyTask, class RemapObservedSSTClimatology(RemapObservedClimatologySubtask): # {{{ """ A subtask for reading and remapping SST observations - - Authors - ------- - Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani """ + # Authors + # ------- + # Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani def get_observation_descriptor(self, fileName): # {{{ ''' @@ -183,11 +182,10 @@ def get_observation_descriptor(self, fileName): # {{{ ------- obsDescriptor : ``MeshDescriptor`` The descriptor for the observation grid - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis # create a descriptor of the observation grid using the lat/lon # coordinates @@ -210,11 +208,10 @@ def build_observational_dataset(self, fileName): # {{{ ------- dsObs : ``xarray.Dataset`` The observational dataset - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis climStartYear = self.config.getint('oceanObservations', 'sstClimatologyStartYear') diff --git a/mpas_analysis/ocean/compute_anomaly_subtask.py b/mpas_analysis/ocean/compute_anomaly_subtask.py index a2a35e162..cac91ea65 100644 --- a/mpas_analysis/ocean/compute_anomaly_subtask.py +++ b/mpas_analysis/ocean/compute_anomaly_subtask.py @@ -52,11 +52,10 @@ class ComputeAnomalySubtask(AnalysisTask): variable computed from others). This operation is performed before computing moving averages and anomalies, so that these operations are also performed on any new variables added to the data set. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis def __init__(self, parentTask, mpasTimeSeriesTask, outFileName, variableList, movingAveragePoints, @@ -92,11 +91,11 @@ def __init__(self, parentTask, mpasTimeSeriesTask, outFileName, variable computed from others). This operation is performed before computing moving averages and anomalies, so that these operations are also performed on any new variables added to the data set. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + # first, call the constructor from the base class (AnalysisTask) super(ComputeAnomalySubtask, self).__init__( config=parentTask.config, @@ -120,11 +119,11 @@ def __init__(self, parentTask, mpasTimeSeriesTask, outFileName, def setup_and_check(self): # {{{ """ Perform steps to set up the analysis and check for errors in the setup. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + # first, call setup_and_check from the base class (AnalysisTask), # which will perform some common setup, including storing: # self.runDirectory , self.historyDirectory, self.plotsDirectory, @@ -141,11 +140,10 @@ def setup_and_check(self): # {{{ def run_task(self): # {{{ """ Performs analysis of ocean heat content (OHC) from time-series output. - - Authors - ------- - Xylar Asay-Davis, Milena Veneziani, Greg Streletz """ + # Authors + # ------- + # Xylar Asay-Davis, Milena Veneziani, Greg Streletz self.logger.info("\nComputing anomalies...") diff --git a/mpas_analysis/ocean/index_nino34.py b/mpas_analysis/ocean/index_nino34.py index 6c4653081..c414a7de0 100644 --- a/mpas_analysis/ocean/index_nino34.py +++ b/mpas_analysis/ocean/index_nino34.py @@ -46,11 +46,10 @@ class IndexNino34(AnalysisTask): # {{{ refConfig : ``MpasAnalysisConfigParser`` Configuration options for a reference run (if any) - - Authors - ------- - Luke Van Roekel, Xylar Asay-Davis ''' + # Authors + # ------- + # Luke Van Roekel, Xylar Asay-Davis def __init__(self, config, mpasTimeSeriesTask, refConfig=None): # {{{ @@ -67,12 +66,11 @@ def __init__(self, config, mpasTimeSeriesTask, refConfig=None): refConfig : ``MpasAnalysisConfigParser``, optional Configuration options for a reference run (if any) - - Authors - ------- - Xylar Asay-Davis - ''' + # Authors + # ------- + # Xylar Asay-Davis + # first, call the constructor from the base class (AnalysisTask) super(IndexNino34, self).__init__( config=config, @@ -90,11 +88,10 @@ def __init__(self, config, mpasTimeSeriesTask, refConfig=None): def setup_and_check(self): # {{{ ''' Perform steps to set up the analysis and check for errors in the setup. - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis # first, call setup_and_check from the base class (AnalysisTask), # which will perform some common setup, including storing: @@ -123,11 +120,10 @@ def run_task(self): # {{{ ''' Computes NINO34 index and plots the time series and power spectrum with 95 and 99% confidence bounds - - Authors - ------- - Luke Van Roekel, Xylar Asay-Davis ''' + # Authors + # ------- + # Luke Van Roekel, Xylar Asay-Davis self.logger.info("\nPlotting Nino3.4 time series and power " "spectrum....") @@ -300,11 +296,10 @@ def _compute_nino34_index(self, regionSST, calendar): # {{{ Returns ------- xarray.DataArray object containing the nino34index - - Authors - ------- - Luke Van Roekel, Xylar Asay-Davis """ + # Authors + # ------- + # Luke Van Roekel, Xylar Asay-Davis if not isinstance(regionSST, xr.core.dataarray.DataArray): raise ValueError('regionSST should be an xarray DataArray') @@ -360,11 +355,10 @@ def _compute_nino34_spectra(self, nino34Index): # {{{ mkov*scale*xHigh : numpy.array 99% confidence threshold from chi-squared test - - Authors - ------- - Luke Van Roekel, Xylar Asay-Davis """ + # Authors + # ------- + # Luke Van Roekel, Xylar Asay-Davis # Move nino34Index to numpy to allow functionality with scipy routines ninoIndex = nino34Index.values @@ -427,11 +421,10 @@ def _autocorr(self, x, t=1): # {{{ ------- Single value giving the lag one auto-correlation If t != 1, this is no longer a lag one auto-correlation - - Authors - ------- - Luke Van Roekel """ + # Authors + # ------- + # Luke Van Roekel return np.corrcoef(np.array([x[0:len(x)-t], x[t:len(x)]])) # }}} @@ -449,11 +442,10 @@ def _running_mean(self, inputData, wgts): # {{{ for the nino index this is a 5-point boxcar window for the nino power spectra this is a modified Daniell window (see https://www.ncl.ucar.edu/Document/Functions/Built-in/specx_anal.shtml) - - Authors - ------- - Luke Van Roekel, Xylar Asay-Davis """ + # Authors + # ------- + # Luke Van Roekel, Xylar Asay-Davis nt = len(inputData) sp = (len(wgts) - 1) // 2 @@ -508,11 +500,11 @@ def _nino34_spectra_plot(self, spectra, title, panelTitles, periodMin, periodMax : float, optional the maximum and minimum periods (in years) to be plotted - - Authors - ------- - Luke Van Roekel, Xylar Asay-Davis """ + # Authors + # ------- + # Luke Van Roekel, Xylar Asay-Davis + config = self.config if dpi is None: @@ -610,11 +602,11 @@ def _nino34_timeseries_plot(self, nino34s, title, panelTitles, outFileName, lineWidth : int, optional control line width - - Authors - ------- - Luke Van Roekel, Xylar Asay-Davis """ + # Authors + # ------- + # Luke Van Roekel, Xylar Asay-Davis + config = self.config calendar = self.calendar @@ -680,11 +672,11 @@ def _plot_nino_timeseries(self, ninoIndex, time, xlabel, ylabel, lineWidth : list of str control line width - - Authors - ------- - Luke Van Roekel, Xylar Asay-Davis ''' + # Authors + # ------- + # Luke Van Roekel, Xylar Asay-Davis + plt.title(panelTitle, y=1.06, **title_font) y1 = ninoIndex nt = np.size(ninoIndex) @@ -736,11 +728,11 @@ def _plot_size_y_axis(self, x, ys, xmin, xmax): xmax : float, optional The maximum x values - - Authors - ------- - Luke Van Roekel, Xylar Asay-Davis ''' + # Authors + # ------- + # Luke Van Roekel, Xylar Asay-Davis + mask = np.logical_and(x >= xmin, x <= xmax) # find maximum value of three curves plotted diff --git a/mpas_analysis/ocean/meridional_heat_transport.py b/mpas_analysis/ocean/meridional_heat_transport.py index 161f599fa..5dee1e3f8 100644 --- a/mpas_analysis/ocean/meridional_heat_transport.py +++ b/mpas_analysis/ocean/meridional_heat_transport.py @@ -35,11 +35,10 @@ class MeridionalHeatTransport(AnalysisTask): # {{{ refConfig : ``MpasAnalysisConfigParser`` Configuration options for a reference run (if any) - - Authors - ------- - Mark Petersen, Milena Veneziani, Xylar Asay-Davis ''' + # Authors + # ------- + # Mark Petersen, Milena Veneziani, Xylar Asay-Davis def __init__(self, config, mpasClimatologyTask, refConfig=None): # {{{ ''' @@ -55,12 +54,11 @@ def __init__(self, config, mpasClimatologyTask, refConfig=None): # {{{ refConfig : ``MpasAnalysisConfigParser``, optional Configuration options for a reference run (if any) - - Authors - ------- - Xylar Asay-Davis - ''' + # Authors + # ------- + # Xylar Asay-Davis + # first, call the constructor from the base class (AnalysisTask) super(MeridionalHeatTransport, self).__init__( config=config, @@ -78,11 +76,10 @@ def __init__(self, config, mpasClimatologyTask, refConfig=None): # {{{ def setup_and_check(self): # {{{ ''' Perform steps to set up the analysis and check for errors in the setup. - - Authors - ------- - Mark Petersen, Milena Veneziani, Xylar Asay-Davis ''' + # Authors + # ------- + # Mark Petersen, Milena Veneziani, Xylar Asay-Davis # first, call setup_and_check from the base class (AnalysisTask), # which will perform some common setup, including storing: @@ -151,11 +148,11 @@ def run_task(self): # {{{ Plots MHT as: 1D function of latitude 2D function of latitude and depth - - Authors - ------- - Mark Petersen, Milena Veneziani, Xylar Asay-Davis """ + # Authors + # ------- + # Mark Petersen, Milena Veneziani, Xylar Asay-Davis + self.logger.info("\nPlotting meridional heat transport (MHT)...") config = self.config diff --git a/mpas_analysis/ocean/plot_climatology_map_subtask.py b/mpas_analysis/ocean/plot_climatology_map_subtask.py index 5ec9d73b6..b1086302a 100644 --- a/mpas_analysis/ocean/plot_climatology_map_subtask.py +++ b/mpas_analysis/ocean/plot_climatology_map_subtask.py @@ -8,11 +8,10 @@ """ An analysis subtasks for plotting comparison of 2D model fields against observations. - -Authors -------- -Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani """ +# Authors +# ------- +# Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani from __future__ import absolute_import, division, print_function, \ unicode_literals @@ -112,11 +111,10 @@ class PlotClimatologyMapSubtask(AnalysisTask): # {{{ depth : {None, float, 'top', 'bot'} Depth at which to perform the comparison, 'top' for the sea surface 'bot' for the sea floor - - Authors - ------- - Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani """ + # Authors + # ------- + # Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani def __init__(self, parentTask, season, comparisonGridName, remapMpasClimatologySubtask, remapObsClimatologySubtask=None, @@ -159,12 +157,10 @@ def __init__(self, parentTask, season, comparisonGridName, subtracted from both the model and reference results. This is useful for data sets where the desire is to compare the spatial pattern but the mean offset is not meaningful (e.g. SSH) - - Authors - ------- - Xylar Asay-Davis - ''' + # Authors + # ------- + # Xylar Asay-Davis self.season = season self.depth = depth @@ -245,11 +241,11 @@ def set_plot_info(self, outFileLabel, fieldNameInTitle, mpasFieldName, diffTitleLabel : str, optional the title of the difference subplot - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + self.outFileLabel = outFileLabel self.fieldNameInTitle = fieldNameInTitle self.mpasFieldName = mpasFieldName @@ -285,11 +281,11 @@ def set_plot_info(self, outFileLabel, fieldNameInTitle, mpasFieldName, def setup_and_check(self): # {{{ """ Perform steps to set up the analysis and check for errors in the setup. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + # first, call setup_and_check from the base class (AnalysisTask), # which will perform some common setup, including storing: # self.runDirectory , self.historyDirectory, self.plotsDirectory, @@ -326,11 +322,10 @@ def run_task(self): # {{{ """ Plots a comparison of ACME/MPAS output to SST, MLD or SSS observations or a reference run - - Authors - ------- - Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani """ + # Authors + # ------- + # Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani season = self.season depth = self.depth diff --git a/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py b/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py index 6e9fd4275..93ffd4c40 100644 --- a/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py +++ b/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py @@ -83,11 +83,10 @@ class PlotDepthIntegratedTimeSeriesSubtask(AnalysisTask): refConfig : ``MpasAnalysisConfigParser`` The configuration options for the reference run (if any) - - Authors - ------- - Xylar Asay-Davis, Milena Veneziani, Greg Streletz """ + # Authors + # ------- + # Xylar Asay-Davis, Milena Veneziani, Greg Streletz def __init__(self, parentTask, regionName, inFileName, outFileLabel, fieldNameInTitle, mpasFieldName, yAxisLabel, sectionName, @@ -150,11 +149,10 @@ def __init__(self, parentTask, regionName, inFileName, outFileLabel, refConfig : ``MpasAnalysisConfigParser``, optional The configuration options for the reference run (if any) - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis if subtaskName is None: suffix = regionName[0].upper() + regionName[1:] @@ -191,11 +189,11 @@ def __init__(self, parentTask, regionName, inFileName, outFileLabel, def setup_and_check(self): # {{{ """ Perform steps to set up the analysis and check for errors in the setup. - - Authors - ------- - Xylar Asay-Davis, Greg Streletz """ + # Authors + # ------- + # Xylar Asay-Davis, Greg Streletz + # first, call setup_and_check from the base class (AnalysisTask), # which will perform some common setup, including storing: # self.runDirectory , self.historyDirectory, self.plotsDirectory, @@ -248,11 +246,10 @@ def setup_and_check(self): # {{{ def run_task(self): # {{{ """ Compute vertical agregates of the data and plot the time series - - Authors - ------- - Xylar Asay-Davis, Milena Veneziani, Greg Streletz """ + # Authors + # ------- + # Xylar Asay-Davis, Milena Veneziani, Greg Streletz self.logger.info("\nPlotting depth-integrated time series of " "{}...".format(self.fieldNameInTitle)) diff --git a/mpas_analysis/ocean/plot_hovmoller_subtask.py b/mpas_analysis/ocean/plot_hovmoller_subtask.py index 108ce1d7f..11eedb30a 100644 --- a/mpas_analysis/ocean/plot_hovmoller_subtask.py +++ b/mpas_analysis/ocean/plot_hovmoller_subtask.py @@ -75,11 +75,10 @@ class PlotHovmollerSubtask(AnalysisTask): galleryName : str The name of the gallery in which this plot belongs - - Authors - ------- - Xylar Asay-Davis, Milena Veneziani, Greg Streletz """ + # Authors + # ------- + # Xylar Asay-Davis, Milena Veneziani, Greg Streletz def __init__(self, parentTask, regionName, inFileName, outFileLabel, fieldNameInTitle, mpasFieldName, unitsLabel, sectionName, @@ -138,11 +137,10 @@ def __init__(self, parentTask, regionName, inFileName, outFileLabel, subtaskName : str The name of the subtask (``plotHovmoller`` by default) - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis if subtaskName is None: suffix = regionName[0].upper() + regionName[1:] @@ -177,11 +175,11 @@ def __init__(self, parentTask, regionName, inFileName, outFileLabel, def setup_and_check(self): # {{{ """ Perform steps to set up the analysis and check for errors in the setup. - - Authors - ------- - Xylar Asay-Davis, Greg Streletz """ + # Authors + # ------- + # Xylar Asay-Davis, Greg Streletz + # first, call setup_and_check from the base class (AnalysisTask), # which will perform some common setup, including storing: # self.runDirectory , self.historyDirectory, self.plotsDirectory, @@ -211,11 +209,10 @@ def setup_and_check(self): # {{{ def run_task(self): # {{{ """ Make the Hovmoller plot from the time series. - - Authors - ------- - Xylar Asay-Davis, Milena Veneziani, Greg Streletz """ + # Authors + # ------- + # Xylar Asay-Davis, Milena Veneziani, Greg Streletz self.logger.info("\nPlotting {} trends vs. depth...".format( self.fieldNameInTitle)) diff --git a/mpas_analysis/ocean/remap_depth_slices_subtask.py b/mpas_analysis/ocean/remap_depth_slices_subtask.py index 9dca2b54b..d8626ee2f 100644 --- a/mpas_analysis/ocean/remap_depth_slices_subtask.py +++ b/mpas_analysis/ocean/remap_depth_slices_subtask.py @@ -34,11 +34,10 @@ class RemapDepthSlicesSubtask(RemapMpasClimatologySubtask): # {{{ verticalIndices : xarray.DataArray The vertical indices of slice to be plotted - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis def __init__(self, mpasClimatologyTask, parentTask, climatologyName, variableList, seasons, depths, comparisonGridNames=['latlon'], @@ -81,11 +80,10 @@ def __init__(self, mpasClimatologyTask, parentTask, climatologyName, iselValues : dict, optional A dictionary of dimensions and indices (or ``None``) used to extract a slice of the MPAS field(s). - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis self.depths = depths @@ -104,11 +102,10 @@ def run_task(self): # {{{ ``verticalIndex`` is also computed for later indexing of the model level. It then simply calls the run function from ClimatologyMapOcean. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis # first, load the land-ice mask from the restart file ds = xr.open_dataset(self.restartFileName) @@ -190,11 +187,10 @@ def customize_masked_climatology(self, climatology): # {{{ ------- climatology : ``xarray.Dataset`` object the modified climatology data set - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis if self.depths is None: return climatology diff --git a/mpas_analysis/ocean/streamfunction_moc.py b/mpas_analysis/ocean/streamfunction_moc.py index e673fec43..66f3dd5f5 100644 --- a/mpas_analysis/ocean/streamfunction_moc.py +++ b/mpas_analysis/ocean/streamfunction_moc.py @@ -47,11 +47,10 @@ class StreamfunctionMOC(AnalysisTask): # {{{ mpasClimatologyTask : ``MpasClimatologyTask`` The task that produced the climatology to be remapped and plotted - - Authors - ------- - Milena Veneziani, Mark Petersen, Phillip Wolfram, Xylar Asay-Davis ''' + # Authors + # ------- + # Milena Veneziani, Mark Petersen, Phillip Wolfram, Xylar Asay-Davis def __init__(self, config, mpasClimatologyTask): # {{{ ''' @@ -64,12 +63,12 @@ def __init__(self, config, mpasClimatologyTask): # {{{ mpasClimatologyTask : ``MpasClimatologyTask`` The task that produced the climatology to be remapped and plotted - - Authors - ------- - Xylar Asay-Davis - ''' + # Authors + # ------- + # Xylar Asay-Davis + +# # first, call the constructor from the base class (AnalysisTask) super(StreamfunctionMOC, self).__init__( config=config, @@ -89,11 +88,10 @@ def setup_and_check(self): # {{{ ------ ValueError if timeSeriesStatsMonthly is not enabled in the MPAS run - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis # first, call setup_and_check from the base class (AnalysisTask), # which will perform some common setup, including storing: @@ -165,11 +163,10 @@ def run_task(self): # {{{ post-processing if not. Plots streamfunction climatolgoical sections as well as time series of max Atlantic MOC at 26.5N (latitude of RAPID MOC Array). - - Authors - ------- - Milena Veneziani, Mark Petersen, Phillip J. Wolfram, Xylar Asay-Davis ''' + # Authors + # ------- + # Milena Veneziani, Mark Petersen, Phillip J. Wolfram, Xylar Asay-Davis self.logger.info("\nPlotting streamfunction of Meridional Overturning " "Circulation (MOC)...") diff --git a/mpas_analysis/ocean/time_series_antarctic_melt.py b/mpas_analysis/ocean/time_series_antarctic_melt.py index fb0396401..be105e41c 100644 --- a/mpas_analysis/ocean/time_series_antarctic_melt.py +++ b/mpas_analysis/ocean/time_series_antarctic_melt.py @@ -41,11 +41,10 @@ class TimeSeriesAntarcticMelt(AnalysisTask): refConfig : ``MpasAnalysisConfigParser`` The configuration options for the reference run (if any) - - Authors - ------- - Xylar Asay-Davis, Stephen Price """ + # Authors + # ------- + # Xylar Asay-Davis, Stephen Price def __init__(self, config, mpasTimeSeriesTask, refConfig=None): # {{{ @@ -62,11 +61,11 @@ def __init__(self, config, mpasTimeSeriesTask, refConfig=None): refConfig : ``MpasAnalysisConfigParser``, optional Configuration options for a reference run (if any) - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + # first, call the constructor from the base class (AnalysisTask) super(TimeSeriesAntarcticMelt, self).__init__( config=config, @@ -89,11 +88,11 @@ def setup_and_check(self): # {{{ ------ IOError If files are not present - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + # first, call setup_and_check from the base class (AnalysisTask), # which will perform some common setup, including storing: # self.inDirectory, self.plotsDirectory, self.namelist, self.streams @@ -181,11 +180,10 @@ def run_task(self): # {{{ """ Performs analysis of the time-series output of Antarctic sub-ice-shelf melt rates. - - Authors - ------- - Xylar Asay-Davis, Stephen Price """ + # Authors + # ------- + # Xylar Asay-Davis, Stephen Price self.logger.info("\nPlotting Antarctic melt rate time series...") @@ -370,11 +368,10 @@ def _compute_ice_shelf_fluxes(self): # {{{ """ Reads melt flux time series and computes regional total melt flux and mean melt rate. - - Authors - ------- - Xylar Asay-Davis, Stephen Price """ + # Authors + # ------- + # Xylar Asay-Davis, Stephen Price mpasTimeSeriesTask = self.mpasTimeSeriesTask config = self.config @@ -464,11 +461,11 @@ def _load_ice_shelf_fluxes(self, config): # {{{ """ Reads melt flux time series and computes regional total melt flux and mean melt rate. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + baseDirectory = build_config_full_path( config, 'output', 'timeSeriesSubdirectory') diff --git a/mpas_analysis/ocean/time_series_ohc_anomaly.py b/mpas_analysis/ocean/time_series_ohc_anomaly.py index 45ff7e851..33128714f 100644 --- a/mpas_analysis/ocean/time_series_ohc_anomaly.py +++ b/mpas_analysis/ocean/time_series_ohc_anomaly.py @@ -24,11 +24,10 @@ class TimeSeriesOHCAnomaly(AnalysisTask): """ Performs analysis of ocean heat content (OHC) from time-series output. - - Authors - ------- - Xylar Asay-Davis, Milena Veneziani, Greg Streletz """ + # Authors + # ------- + # Xylar Asay-Davis, Milena Veneziani, Greg Streletz def __init__(self, config, mpasTimeSeriesTask, refConfig=None): # {{{ @@ -45,11 +44,11 @@ def __init__(self, config, mpasTimeSeriesTask, refConfig=None): refConfig : ``MpasAnalysisConfigParser``, optional Configuration options for a reference run (if any) - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + # first, call the constructor from the base class (AnalysisTask) super(TimeSeriesOHCAnomaly, self).__init__( config=config, diff --git a/mpas_analysis/ocean/time_series_salinity_anomaly.py b/mpas_analysis/ocean/time_series_salinity_anomaly.py index c86e1a04c..7c362dd50 100644 --- a/mpas_analysis/ocean/time_series_salinity_anomaly.py +++ b/mpas_analysis/ocean/time_series_salinity_anomaly.py @@ -21,11 +21,10 @@ class TimeSeriesSalinityAnomaly(AnalysisTask): """ Performs analysis of time series of salinity anomalies from the first simulation year as a function of depth. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis def __init__(self, config, mpasTimeSeriesTask): # {{{ """ @@ -38,11 +37,11 @@ def __init__(self, config, mpasTimeSeriesTask): # {{{ mpasTimeSeriesTask : ``MpasTimeSeriesTask`` The task that extracts the time series from MPAS monthly output - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + # first, call the constructor from the base class (AnalysisTask) super(TimeSeriesSalinityAnomaly, self).__init__( config=config, diff --git a/mpas_analysis/ocean/time_series_sst.py b/mpas_analysis/ocean/time_series_sst.py index c49ead643..029a64c36 100644 --- a/mpas_analysis/ocean/time_series_sst.py +++ b/mpas_analysis/ocean/time_series_sst.py @@ -37,11 +37,10 @@ class TimeSeriesSST(AnalysisTask): refConfig : ``MpasAnalysisConfigParser`` Configuration options for a reference run (if any) - - Authors - ------- - Xylar Asay-Davis, Milena Veneziani """ + # Authors + # ------- + # Xylar Asay-Davis, Milena Veneziani def __init__(self, config, mpasTimeSeriesTask, refConfig=None): # {{{ @@ -58,11 +57,11 @@ def __init__(self, config, mpasTimeSeriesTask, refConfig=None): refConfig : ``MpasAnalysisConfigParser``, optional Configuration options for a reference run (if any) - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + # first, call the constructor from the base class (AnalysisTask) super(TimeSeriesSST, self).__init__( config=config, @@ -85,11 +84,11 @@ def setup_and_check(self): # {{{ ------ OSError If files are not present - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + # first, call setup_and_check from the base class (AnalysisTask), # which will perform some common setup, including storing: # self.inDirectory, self.plotsDirectory, self.namelist, self.streams @@ -129,11 +128,10 @@ def run_task(self): # {{{ """ Performs analysis of the time-series output of sea-surface temperature (SST). - - Authors - ------- - Xylar Asay-Davis, Milena Veneziani """ + # Authors + # ------- + # Xylar Asay-Davis, Milena Veneziani self.logger.info("\nPlotting SST time series...") diff --git a/mpas_analysis/ocean/time_series_temperature_anomaly.py b/mpas_analysis/ocean/time_series_temperature_anomaly.py index f15c4b5e7..14f326cec 100644 --- a/mpas_analysis/ocean/time_series_temperature_anomaly.py +++ b/mpas_analysis/ocean/time_series_temperature_anomaly.py @@ -21,11 +21,10 @@ class TimeSeriesTemperatureAnomaly(AnalysisTask): """ Performs analysis of time series of temperature anomalies from the first simulation year as a function of depth. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis def __init__(self, config, mpasTimeSeriesTask): # {{{ """ @@ -38,11 +37,11 @@ def __init__(self, config, mpasTimeSeriesTask): # {{{ mpasTimeSeriesTask : ``MpasTimeSeriesTask`` The task that extracts the time series from MPAS monthly output - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + # first, call the constructor from the base class (AnalysisTask) super(TimeSeriesTemperatureAnomaly, self).__init__( config=config, diff --git a/mpas_analysis/ocean/utility.py b/mpas_analysis/ocean/utility.py index f58fc1e4a..f6efc927d 100644 --- a/mpas_analysis/ocean/utility.py +++ b/mpas_analysis/ocean/utility.py @@ -7,11 +7,10 @@ # """ A utility for computing common ocean fields (e.g. zMid) from datasets - -Authors -------- -Xylar Asay-Davis """ +# Authors +# ------- +# Xylar Asay-Davis from __future__ import absolute_import, division, print_function, \ unicode_literals @@ -41,11 +40,10 @@ def compute_zmid(bottomDepth, maxLevelCell, layerThickness): # {{{ zMid : ``xarray.DataArray`` the vertical coordinate defining the middle of each layer, masked below the bathymetry - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis nVertLevels = \ layerThickness.shape[layerThickness.dims.index('nVertLevels')] diff --git a/mpas_analysis/sea_ice/climatology_map_sea_ice_conc.py b/mpas_analysis/sea_ice/climatology_map_sea_ice_conc.py index 8d48169ef..88748ef2d 100644 --- a/mpas_analysis/sea_ice/climatology_map_sea_ice_conc.py +++ b/mpas_analysis/sea_ice/climatology_map_sea_ice_conc.py @@ -28,11 +28,11 @@ class ClimatologyMapSeaIceConc(AnalysisTask): # {{{ """ An analysis task for comparison of sea ice concentration against observations - - Authors - ------- - Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani """ + # Authors + # ------- + # Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani + def __init__(self, config, mpasClimatologyTask, hemisphere, refConfig=None): # {{{ """ @@ -51,11 +51,11 @@ def __init__(self, config, mpasClimatologyTask, hemisphere, refConfig : ``MpasAnalysisConfigParser``, optional Configuration options for a reference run (if any) - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + taskName = 'climatologyMapSeaIceConc{}'.format(hemisphere) fieldName = 'seaIceConc' @@ -226,11 +226,10 @@ def _add_ref_tasks(self, seasons, comparisonGridNames, hemisphere, class RemapObservedConcClimatology(RemapObservedClimatologySubtask): # {{{ """ A subtask for reading and remapping sea ice concentration observations - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis def get_observation_descriptor(self, fileName): # {{{ ''' @@ -245,11 +244,10 @@ def get_observation_descriptor(self, fileName): # {{{ ------- obsDescriptor : ``MeshDescriptor`` The descriptor for the observation grid - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis # create a descriptor of the observation grid using the lat/lon # coordinates @@ -272,11 +270,10 @@ def build_observational_dataset(self, fileName): # {{{ ------- dsObs : ``xarray.Dataset`` The observational dataset - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis dsObs = xr.open_dataset(fileName) dsObs.rename({'AICE': 'seaIceConc'}, inplace=True) diff --git a/mpas_analysis/sea_ice/climatology_map_sea_ice_thick.py b/mpas_analysis/sea_ice/climatology_map_sea_ice_thick.py index 03c343278..03bf9bc75 100644 --- a/mpas_analysis/sea_ice/climatology_map_sea_ice_thick.py +++ b/mpas_analysis/sea_ice/climatology_map_sea_ice_thick.py @@ -28,11 +28,11 @@ class ClimatologyMapSeaIceThick(AnalysisTask): # {{{ """ An analysis task for comparison of sea ice thickness against observations - - Authors - ------- - Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani """ + # Authors + # ------- + # Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani + def __init__(self, config, mpasClimatologyTask, hemisphere, refConfig=None): # {{{ """ @@ -51,11 +51,11 @@ def __init__(self, config, mpasClimatologyTask, hemisphere, refConfig : ``MpasAnalysisConfigParser``, optional Configuration options for a reference run (if any) - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + taskName = 'climatologyMapSeaIceThick{}'.format(hemisphere) fieldName = 'seaIceThick' @@ -171,11 +171,10 @@ def __init__(self, config, mpasClimatologyTask, hemisphere, class RemapObservedThickClimatology(RemapObservedClimatologySubtask): # {{{ """ A subtask for reading and remapping sea ice thickness observations - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis def get_observation_descriptor(self, fileName): # {{{ ''' @@ -190,11 +189,10 @@ def get_observation_descriptor(self, fileName): # {{{ ------- obsDescriptor : ``MeshDescriptor`` The descriptor for the observation grid - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis # create a descriptor of the observation grid using the lat/lon # coordinates @@ -217,11 +215,10 @@ def build_observational_dataset(self, fileName): # {{{ ------- dsObs : ``xarray.Dataset`` The observational dataset - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis dsObs = xr.open_dataset(fileName) dsObs.rename({'HI': 'seaIceThick'}, inplace=True) diff --git a/mpas_analysis/sea_ice/plot_climatology_map_subtask.py b/mpas_analysis/sea_ice/plot_climatology_map_subtask.py index 4af15d4cc..bf256b593 100644 --- a/mpas_analysis/sea_ice/plot_climatology_map_subtask.py +++ b/mpas_analysis/sea_ice/plot_climatology_map_subtask.py @@ -89,11 +89,10 @@ class PlotClimatologyMapSubtask(AnalysisTask): # {{{ galleryName : str the name of the gallery in which this plot belongs - - Authors - ------- - Xylar Asay-Davis, Milena Veneziani """ + # Authors + # ------- + # Xylar Asay-Davis, Milena Veneziani def __init__(self, parentTask, hemisphere, season, comparisonGridName, remapMpasClimatologySubtask, remapObsClimatologySubtask=None, @@ -132,12 +131,10 @@ def __init__(self, parentTask, hemisphere, season, comparisonGridName, subtaskSuffix : str, optional A suffix on the subtask to ensure that it is unique (e.g. the observations being plotted) - - Authors - ------- - Xylar Asay-Davis - ''' + # Authors + # ------- + # Xylar Asay-Davis self.hemisphere = hemisphere self.season = season @@ -219,11 +216,11 @@ def set_plot_info(self, outFileLabel, fieldNameInTitle, mpasFieldName, maskValue : float, optional a value to mask out in plots - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + self.outFileLabel = outFileLabel self.fieldNameInTitle = fieldNameInTitle self.mpasFieldName = mpasFieldName @@ -246,11 +243,11 @@ def set_plot_info(self, outFileLabel, fieldNameInTitle, mpasFieldName, def setup_and_check(self): # {{{ """ Perform steps to set up the analysis and check for errors in the setup. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + # first, call setup_and_check from the base class (AnalysisTask), # which will perform some common setup super(PlotClimatologyMapSubtask, self).setup_and_check() @@ -277,11 +274,10 @@ def run_task(self): # {{{ """ Performs analysis of sea-ice properties by comparing with previous model results and/or observations. - - Authors - ------- - Xylar Asay-Davis, Milena Veneziani """ + # Authors + # ------- + # Xylar Asay-Davis, Milena Veneziani config = self.config season = self.season diff --git a/mpas_analysis/sea_ice/time_series.py b/mpas_analysis/sea_ice/time_series.py index 00b77b6fd..3925afa25 100644 --- a/mpas_analysis/sea_ice/time_series.py +++ b/mpas_analysis/sea_ice/time_series.py @@ -45,11 +45,10 @@ class TimeSeriesSeaIce(AnalysisTask): refConfig : ``MpasAnalysisConfigParser`` Configuration options for a reference run (if any) - - Authors - ------- - Xylar Asay-Davis, Milena Veneziani """ + # Authors + # ------- + # Xylar Asay-Davis, Milena Veneziani def __init__(self, config, mpasTimeSeriesTask, refConfig=None): # {{{ @@ -66,11 +65,11 @@ def __init__(self, config, mpasTimeSeriesTask, refConfig : ``MpasAnalysisConfigParser``, optional Configuration options for a reference run (if any) - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + # first, call the constructor from the base class (AnalysisTask) super(TimeSeriesSeaIce, self).__init__( config=config, @@ -93,11 +92,11 @@ def setup_and_check(self): # {{{ ------ OSError If files are not present - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + # first, call setup_and_check from the base class (AnalysisTask), # which will perform some common setup, including storing: # self.runDirectory , self.historyDirectory, self.plotsDirectory, @@ -188,11 +187,10 @@ def setup_and_check(self): # {{{ def run_task(self): # {{{ """ Performs analysis of time series of sea-ice properties. - - Authors - ------- - Xylar Asay-Davis, Milena Veneziani """ + # Authors + # ------- + # Xylar Asay-Davis, Milena Veneziani self.logger.info("\nPlotting sea-ice area and volume time series...") @@ -498,11 +496,11 @@ def _replicate_cycle(self, ds, dsToReplicate, calendar): # {{{ -------- dsShift : a cyclicly repeated version of `dsToReplicte` covering the range of time of `ds`. - - Authors - ------- - Xylar Asay-Davis, Milena Veneziani """ + # Authors + # ------- + # Xylar Asay-Davis, Milena Veneziani + dsStartTime = days_to_datetime(ds.Time.min(), calendar=calendar) dsEndTime = days_to_datetime(ds.Time.max(), calendar=calendar) repStartTime = days_to_datetime(dsToReplicate.Time.min(), diff --git a/mpas_analysis/shared/analysis_task.py b/mpas_analysis/shared/analysis_task.py index 6a06fed0a..3d71f7d9b 100644 --- a/mpas_analysis/shared/analysis_task.py +++ b/mpas_analysis/shared/analysis_task.py @@ -7,12 +7,10 @@ # ''' Defines the base class for analysis tasks. - -Authors -------- -Xylar Asay-Davis - ''' +# Authors +# ------- +# Xylar Asay-Davis from __future__ import absolute_import, division, print_function, \ unicode_literals @@ -87,12 +85,10 @@ class AnalysisTask(Process): # {{{ logger : ``logging.Logger`` A logger for output during the run phase of an analysis task - - Authors - ------- - Xylar Asay-Davis - ''' + # Authors + # ------- + # Xylar Asay-Davis # flags for run status UNSET = 0 @@ -132,11 +128,11 @@ def __init__(self, config, taskName, componentName, tags=[], subtaskName : str, optional If this is a subtask of ``taskName``, the name of the subtask - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis + if subtaskName is None: self.fullTaskName = taskName self.printTaskName = taskName @@ -181,11 +177,10 @@ def setup_and_check(self): # {{{ analysis-specific setup. For example, this function could check if necessary observations and other data files are found, then, determine the list of files to be read when the analysis is run. - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis # read parameters from config file # the run directory contains the restart files @@ -235,11 +230,11 @@ def run_task(self): # {{{ ''' Run the analysis. Each task should override this function to do the work of computing and/or plotting analysis - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis + return # }}} def run_after(self, task): # {{{ @@ -254,11 +249,10 @@ def run_after(self, task): # {{{ ---------- task : ``AnalysisTask`` The task that should finish before this one begins - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis self.runAfterTasks.append(task) # }}} @@ -274,11 +268,10 @@ def add_subtask(self, subtask): # {{{ ---------- subtask : ``AnalysisTask`` The subtask to run as part of this task - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis if subtask not in self.subtasks: self.subtasks.append(subtask) @@ -295,11 +288,11 @@ def run(self, writeLogFile=True): # {{{ Otherwise, the internal logger ``self.logger`` points to stdout and no log file is created. The intention is for logging to take place in parallel mode but not in serial mode. - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis + # redirect output to a log file if writeLogFile: self.logger = logging.getLogger(self.fullTaskName) @@ -366,11 +359,10 @@ def check_generate(self): ------ ValueError : If one of ``self.taskName``, ``self.componentName`` or ``self.tags`` has not been set. - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis for memberName in ['taskName', 'componentName', 'tags']: if not hasattr(self, memberName): @@ -444,11 +436,10 @@ def check_analysis_enabled(self, analysisOptionName, default=False, If the given analysis option is not found and ``default`` is not ``True`` or if the analysis option is found and is ``False``. The exception is only raised if ``raiseException = True``. - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis try: optionName = analysisOptionName @@ -481,11 +472,10 @@ def set_start_end_date(self, section): # {{{ The name of a section in the config file containing ``startYear`` and ``endYear`` options. ``section`` is typically one of ``climatology``, ``timeSeries`` or ``index`` - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis if not self.config.has_option(section, 'startDate'): startDate = '{:04d}-01-01_00:00:00'.format( @@ -505,11 +495,10 @@ class AnalysisFormatter(logging.Formatter): # {{{ Modified from: https://stackoverflow.com/a/8349076/7728169 - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis # printing error messages without a prefix because they are sometimes # errors and sometimes only warnings sent to stderr diff --git a/mpas_analysis/shared/climatology/climatology.py b/mpas_analysis/shared/climatology/climatology.py index 52a53433b..c8d0599f3 100644 --- a/mpas_analysis/shared/climatology/climatology.py +++ b/mpas_analysis/shared/climatology/climatology.py @@ -7,11 +7,10 @@ # """ Functions for creating climatologies from monthly time series data - -Authors -------- -Xylar Asay-Davis """ +# Authors +# ------- +# Xylar Asay-Davis from __future__ import absolute_import, division, print_function, \ unicode_literals @@ -70,11 +69,10 @@ def get_remapper(config, sourceDescriptor, comparisonDescriptor, remapper : ``Remapper`` object A remapper that can be used to remap files or data sets from the source grid or mesh to the comparison grid. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis mappingFileName = None @@ -146,11 +144,10 @@ def compute_monthly_climatology(ds, calendar=None, maskVaries=True): # {{{ A data set without the ``'Time'`` coordinate containing the mean of ds over all months in monthValues, weighted by the number of days in each month. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis def compute_one_month_climatology(ds): monthValues = list(ds.month.values) @@ -200,11 +197,10 @@ def compute_climatology(ds, monthValues, calendar=None, A data set without the ``'Time'`` coordinate containing the mean of ds over all months in monthValues, weighted by the number of days in each month. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis ds = add_years_months_days_in_month(ds, calendar) @@ -243,11 +239,10 @@ def add_years_months_days_in_month(ds, calendar=None): # {{{ ds : object of same type as ``ds`` The data set with ``year``, ``month`` and ``daysInMonth`` data arrays added (if not already present) - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis if ('year' in ds.coords and 'month' in ds.coords and 'daysInMonth' in ds.coords): @@ -328,11 +323,11 @@ def remap_and_write_climatology(config, climatologyDataSet, ------- remappedClimatology : ``xarray.DataSet`` or ``xarray.DataArray`` object A data set containing the remapped climatology - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + useNcremap = config.getboolean('climatology', 'useNcremap') if (isinstance(remapper.sourceDescriptor, ProjectionGridDescriptor) or @@ -373,11 +368,10 @@ def get_unmasked_mpas_climatology_directory(config): # {{{ ---------- config : ``MpasAnalysisConfigParser`` configuration options - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis climatologyBaseDirectory = build_config_full_path( config, 'output', 'mpasClimatologySubdirectory') @@ -406,11 +400,10 @@ def get_unmasked_mpas_climatology_file_name(config, season, componentName): componentName : {'ocean', 'seaIce'} The MPAS component for which the climatology is being computed - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis startYear = config.getint('climatology', 'startYear') endYear = config.getint('climatology', 'endYear') @@ -460,11 +453,10 @@ def get_masked_mpas_climatology_file_name(config, season, componentName, climatologyName : str The name of the climatology (typically the name of a field to mask and later remap) - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis startYear = config.getint('climatology', 'startYear') endYear = config.getint('climatology', 'endYear') @@ -528,11 +520,10 @@ def get_remapped_mpas_climatology_file_name(config, season, componentName, comparisonGridName : {'latlon', 'antarctic'} The name of the comparison grid to use for remapping - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis startYear = config.getint('climatology', 'startYear') endYear = config.getint('climatology', 'endYear') @@ -581,11 +572,11 @@ def _compute_masked_mean(ds, maskVaries): # {{{ Compute the time average of data set, masked out where the variables in ds are NaN and, if ``maskVaries == True``, weighting by the number of days used to compute each monthly mean time in ds. - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis + def ds_to_weights(ds): # make an identical data set to ds but replacing all data arrays with # nonnull applied to that data array @@ -622,11 +613,10 @@ def ds_to_weights(ds): def _matches_comparison(obsDescriptor, comparisonDescriptor): # {{{ ''' Determine if the two meshes are the same - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis if isinstance(obsDescriptor, ProjectionGridDescriptor) and \ isinstance(comparisonDescriptor, ProjectionGridDescriptor): @@ -663,11 +653,10 @@ def _setup_climatology_caching(ds, startYearClimo, endYearClimo, ''' Determine which cache files already exist, which are incomplete and which years are present in each cache file (whether existing or to be created). - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis cacheInfo = [] @@ -726,11 +715,10 @@ def _cache_individual_climatologies(ds, cacheInfo, printProgress, calendar): # {{{ ''' Cache individual climatologies for later aggregation. - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis for cacheIndex, info in enumerate(cacheInfo): outputFileClimo, done, yearString = info @@ -763,11 +751,10 @@ def _cache_aggregated_climatology(startYearClimo, endYearClimo, cachePrefix, cacheInfo): # {{{ ''' Cache aggregated climatology from individual climatologies. - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis yearString, fileSuffix = _get_year_string(startYearClimo, endYearClimo) outputFileClimo = '{}_{}.nc'.format(cachePrefix, fileSuffix) diff --git a/mpas_analysis/shared/climatology/comparison_descriptors.py b/mpas_analysis/shared/climatology/comparison_descriptors.py index a417de531..24bbaf65b 100644 --- a/mpas_analysis/shared/climatology/comparison_descriptors.py +++ b/mpas_analysis/shared/climatology/comparison_descriptors.py @@ -7,11 +7,10 @@ # """ Functions for creating climatologies from monthly time series data - -Authors -------- -Xylar Asay-Davis """ +# Authors +# ------- +# Xylar Asay-Davis from __future__ import absolute_import, division, print_function, \ unicode_literals @@ -41,11 +40,11 @@ def get_comparison_descriptor(config, comparisonGridName): # {{{ ------ ValueError If comparisonGridName does not describe a known comparions grid - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + if comparisonGridName == 'latlon': comparisonDescriptor = \ _get_lat_lon_comparison_descriptor(config) @@ -66,11 +65,11 @@ def get_antarctic_stereographic_projection(): # {{{ ------- projection : ``pyproj.Proj`` object The projection - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + projection = pyproj.Proj('+proj=stere +lat_ts=-71.0 +lat_0=-90 +lon_0=0.0 ' '+k_0=1.0 +x_0=0.0 +y_0=0.0 +ellps=WGS84') @@ -91,11 +90,11 @@ def _get_lat_lon_comparison_descriptor(config): # {{{ ------- descriptor : ``LatLonGridDescriptor`` object A descriptor of the lat/lon grid - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + climSection = 'climatology' comparisonLatRes = config.getWithDefault(climSection, @@ -129,11 +128,11 @@ def _get_antarctic_stereographic_comparison_descriptor(config): # {{{ ------- descriptor : ``ProjectionGridDescriptor`` object A descriptor of the Antarctic comparison grid - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + climSection = 'climatology' comparisonStereoWidth = config.getfloat(climSection, diff --git a/mpas_analysis/shared/climatology/mpas_climatology_task.py b/mpas_analysis/shared/climatology/mpas_climatology_task.py index 041ac12cb..bd55d5cf5 100644 --- a/mpas_analysis/shared/climatology/mpas_climatology_task.py +++ b/mpas_analysis/shared/climatology/mpas_climatology_task.py @@ -52,11 +52,10 @@ class MpasClimatologyTask(AnalysisTask): # {{{ startYear, endYear : int The start and end years of the climatology - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis def __init__(self, config, componentName, taskName=None): # {{{ ''' @@ -74,11 +73,11 @@ def __init__(self, config, componentName, taskName=None): # {{{ taskName : str, optional the name of the task, defaults to mpasClimatology - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis + self.variableList = [] self.seasons = [] @@ -121,11 +120,10 @@ def add_variables(self, variableList, seasons=None): # {{{ A list of seasons (keys in ``shared.constants.monthDictionary``) to be computed or ['none'] (not ``None``) if only monthly climatologies are needed. - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis for variable in variableList: if variable not in self.variableList: @@ -148,11 +146,10 @@ def setup_and_check(self): # {{{ If a restart file is not available from which to read mesh information or if no history files are available from which to compute the climatology in the desired time range. - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis # first, call setup_and_check from the base class (AnalysisTask), # which will perform some common setup, including storing: @@ -186,11 +183,10 @@ def setup_and_check(self): # {{{ def run_task(self): # {{{ ''' Compute the requested climatologies - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis if len(self.variableList) == 0: # nothing to do @@ -247,11 +243,10 @@ def get_file_name(self, season): # {{{ ------- fileName : str The path to the climatology file for the specified season. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis return get_unmasked_mpas_climatology_file_name(self.config, season, self.componentName) @@ -270,11 +265,10 @@ def _update_climatology_bounds_and_create_symlinks(self): # {{{ symlinkDirectory : str The path to the symlinks created for each timeSeriesStatsMonthly input file - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis config = self.config diff --git a/mpas_analysis/shared/climatology/remap_mpas_climatology_subtask.py b/mpas_analysis/shared/climatology/remap_mpas_climatology_subtask.py index 4b39c2492..5a7f6b99d 100644 --- a/mpas_analysis/shared/climatology/remap_mpas_climatology_subtask.py +++ b/mpas_analysis/shared/climatology/remap_mpas_climatology_subtask.py @@ -69,11 +69,10 @@ class RemapMpasClimatologySubtask(AnalysisTask): # {{{ Whether to use ncremap to do the remapping (the other option being an internal python code that handles more grid types and extra dimensions) - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis def __init__(self, mpasClimatologyTask, parentTask, climatologyName, variableList, seasons, comparisonGridNames=['latlon'], @@ -124,11 +123,11 @@ def __init__(self, mpasClimatologyTask, parentTask, climatologyName, if it is not explicitly given. If a comparison grid other than ``latlon`` is given, ncremap is not supported so this flag is set to ``False``. - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis + tags = ['climatology'] # call the constructor from the base class (AnalysisTask) @@ -172,11 +171,10 @@ def setup_and_check(self): # {{{ If a restart file is not available from which to read mesh information or if no history files are available from which to compute the climatology in the desired time range. - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis # first, call setup_and_check from the base class (AnalysisTask), # which will perform some common setup, including storing: @@ -211,11 +209,10 @@ def setup_and_check(self): # {{{ def run_task(self): # {{{ ''' Compute the requested climatologies - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis self.logger.info('\nRemapping climatology {}'.format( self.climatologyName)) @@ -264,11 +261,10 @@ def get_masked_file_name(self, season): # {{{ ------- fileName : str The path to the climatology file for the specified season. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis fileName = get_masked_mpas_climatology_file_name(self.config, season, @@ -295,11 +291,10 @@ def get_remapped_file_name(self, season, comparisonGridName): # {{{ ------- fileName : str The path to the climatology file for the specified season. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis fileName = get_remapped_mpas_climatology_file_name( self.config, season, self.componentName, self.climatologyName, @@ -311,11 +306,11 @@ def _setup_remappers(self): # {{{ """ Set up the remappers for remapping from the MPAS to the comparison grids. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + config = self.config # make reamppers @@ -356,11 +351,10 @@ def customize_masked_climatology(self, climatology): # {{{ climatology : ``xarray.Dataset``` The same data set with any custom fields added or modifications made - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis return climatology # }}} @@ -378,22 +372,20 @@ def customize_remapped_climatology(self, climatology): # {{{ climatology : ``xarray.Dataset``` The same data set with any custom fields added or modifications made - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis return climatology # }}} def _setup_file_names(self): # {{{ """ Create a dictionary of file names and directories for this climatology - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis config = self.config climatologyBaseDirectory = build_config_full_path( @@ -529,11 +521,11 @@ def _remap(self, inFileName, outFileName, remapper, comparisonGridName): comparisonGridNames : {'latlon', 'antarctic'} The name of the comparison grid to use for remapping. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + if remapper.mappingFileName is None: # no remapping is needed return diff --git a/mpas_analysis/shared/climatology/remap_observed_climatology_subtask.py b/mpas_analysis/shared/climatology/remap_observed_climatology_subtask.py index 49dd97957..532490916 100644 --- a/mpas_analysis/shared/climatology/remap_observed_climatology_subtask.py +++ b/mpas_analysis/shared/climatology/remap_observed_climatology_subtask.py @@ -46,10 +46,10 @@ class RemapObservedClimatologySubtask(AnalysisTask): # {{{ comparisonGridNames : list of {'latlon', 'antarctic'} The name(s) of the comparison grid to use for remapping. - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis def __init__(self, parentTask, seasons, fileName, outFilePrefix, comparisonGridNames=['latlon'], @@ -80,12 +80,10 @@ def __init__(self, parentTask, seasons, fileName, outFilePrefix, subtaskName : str, optional The name of the subtask - - Authors - ------- - Xylar Asay-Davis - ''' + # Authors + # ------- + # Xylar Asay-Davis self.seasons = seasons self.fileName = fileName @@ -106,11 +104,11 @@ def __init__(self, parentTask, seasons, fileName, outFilePrefix, def setup_and_check(self): # {{{ """ Perform steps to set up the analysis and check for errors in the setup. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + # call setup_and_check from the base class (AnalysisTask), # which will perform some common setup, including storing: # self.runDirectory , self.historyDirectory, self.plotsDirectory, @@ -134,11 +132,10 @@ def setup_and_check(self): # {{{ def run_task(self): # {{{ """ Performs remapping of obsrevations to the comparsion grid - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis config = self.config @@ -207,11 +204,10 @@ def get_observation_descriptor(self, fileName): # {{{ ------- obsDescriptor : ``MeshDescriptor`` The descriptor for the observation grid - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis return None # }}} @@ -230,11 +226,10 @@ def build_observational_dataset(self, fileName): # {{{ ------- dsObs : ``xarray.Dataset`` The observational dataset - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis return None # }}} @@ -262,11 +257,10 @@ def get_file_name(self, stage, season=None, comparisonGridName=None): ------- fileName : str The path to the climatology file for the specified season. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis config = self.config obsSection = '{}Observations'.format(self.componentName) @@ -323,11 +317,11 @@ def _setup_remappers(self, fileName): # {{{ ---------- fileName : str The name of the observation file used to determine the source grid - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + config = self.config sectionName = '{}Observations'.format(self.componentName) diff --git a/mpas_analysis/shared/constants/constants.py b/mpas_analysis/shared/constants/constants.py index 584187063..7635ca678 100644 --- a/mpas_analysis/shared/constants/constants.py +++ b/mpas_analysis/shared/constants/constants.py @@ -7,15 +7,10 @@ # """ Constants that are common to all analysis tasks - -Authors -------- -Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani - -Last modified -------------- -03/15/2017 """ +# Authors +# ------- +# Luke Van Roekel, Xylar Asay-Davis, Milena Veneziani from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/mpas_analysis/shared/generalized_reader/generalized_reader.py b/mpas_analysis/shared/generalized_reader/generalized_reader.py index a97cf0ede..419e74a2b 100644 --- a/mpas_analysis/shared/generalized_reader/generalized_reader.py +++ b/mpas_analysis/shared/generalized_reader/generalized_reader.py @@ -14,11 +14,10 @@ open_multifile_dataset : opens a data set, maps variable names, preprocess the data set removes repeated time indices, and slices the time coordinate to lie between desired start and end dates. - -Authors -------- -Xylar Asay-Davis """ +# Authors +# ------- +# Xylar Asay-Davis from __future__ import absolute_import, division, print_function, \ unicode_literals @@ -124,11 +123,10 @@ def open_multifile_dataset(fileNames, calendar, config, If the time variable is not found in the data set or if the time variable is a number of days since the start of the simulation but simulationStartTime is None. - - Authors - ------- - Xylar Asay-Davis, Phillip J. Wolfram """ + # Authors + # ------- + # Xylar Asay-Davis, Phillip J. Wolfram preprocess_partial = partial(_preprocess, calendar=calendar, @@ -278,11 +276,10 @@ def _preprocess(ds, calendar, simulationStartTime, timeVariableName, ds : xarray.DataSet object A copy of the data set with the time coordinate set and which has been sliced. - - Authors - ------- - Xylar Asay-Davis, Phillip J. Wolfram """ + # Authors + # ------- + # Xylar Asay-Davis, Phillip J. Wolfram submap = variableMap @@ -350,11 +347,11 @@ def _map_variable_name(variableName, ds, variableMap): # {{{ ValueError If none of the possible variable names in `variableMap[variableName]` can be found in `ds`. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + possibleVariables = variableMap[variableName] for variable in possibleVariables: if isinstance(variable, (list, tuple)): @@ -398,11 +395,10 @@ def _rename_variables(ds, variableMap): # {{{ Returns ------- outDataSEt : A new `xarray.DataSet` object with the variable renamed. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis renameDict = {} for datasetVariable in ds.data_vars: diff --git a/mpas_analysis/shared/grid/grid.py b/mpas_analysis/shared/grid/grid.py index cb33c5ae4..26fe38032 100644 --- a/mpas_analysis/shared/grid/grid.py +++ b/mpas_analysis/shared/grid/grid.py @@ -17,12 +17,10 @@ ProjectionGridDescriptor - describes a logically rectangular grid on a pyproj projection - -Authors -------- -Xylar Asay-Davis - ''' +# Authors +# ------- +# Xylar Asay-Davis from __future__ import absolute_import, division, print_function, \ unicode_literals @@ -37,23 +35,20 @@ class MeshDescriptor(object): # {{{ ''' A class for describing a mesh - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis def __init__(self): # {{{ ''' Constructor creates a common ``meshName`` member variable, ``None`` by default. Each Subclass should define or use input arguments to set ``meshName`` to a short description of the mesh or grid. - - Authors - ------- - Xylar Asay-Davis - ''' + # Authors + # ------- + # Xylar Asay-Davis self.meshName = None # }}} @@ -66,11 +61,10 @@ def to_scrip(self, scripFileName): # {{{ ---------- scripFileName : str The path to which the SCRIP file should be written - - Authors - ------ - Xylar Asay-Davis ''' + # Authors + # ------ + # Xylar Asay-Davis return # }}} @@ -80,11 +74,10 @@ def to_scrip(self, scripFileName): # {{{ class MpasMeshDescriptor(MeshDescriptor): # {{{ ''' A class for describing an MPAS mesh - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis def __init__(self, fileName, meshName=None): # {{{ ''' @@ -100,11 +93,10 @@ def __init__(self, fileName, meshName=None): # {{{ ``'oRRS18to6'``). If not provided, the data set in ``fileName`` must have a global attribute ``meshName`` that will be used instead. - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis ds = xarray.open_dataset(fileName) @@ -137,11 +129,11 @@ def to_scrip(self, scripFileName): # {{{ ---------- scripFileName : str The path to which the SCRIP file should be written - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis + self.scripFileName = scripFileName inFile = netCDF4.Dataset(self.fileName, 'r') @@ -202,11 +194,11 @@ def to_scrip(self, scripFileName): # {{{ class LatLonGridDescriptor(MeshDescriptor): # {{{ ''' A class for describing a lat-lon grid - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis + def __init__(self): # {{{ ''' Constructor stores the file name @@ -215,11 +207,11 @@ def __init__(self): # {{{ ---------- fileName : str The path of the file containing the MPAS mesh - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis + self.regional = False self.meshName = None # }}} @@ -241,11 +233,11 @@ def read(cls, fileName=None, ds=None, latVarName='lat', latVarName, lonVarName : str, optional The name of the latitude and longitude variables in the grid file - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis + if ds is None: ds = xarray.open_dataset(fileName) @@ -289,11 +281,11 @@ def create(cls, latCorner, lonCorner, units='degrees'): # {{{ units : {'degrees', 'radians'}, optional The units of `latCorner` and `lonCorner` - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis + descriptor = cls() descriptor.latCorner = latCorner @@ -313,11 +305,11 @@ def to_scrip(self, scripFileName): # {{{ ---------- scripFileName : str The path to which the SCRIP file should be written - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis + self.scripFileName = scripFileName outFile = netCDF4.Dataset(scripFileName, 'w') @@ -382,11 +374,10 @@ class ProjectionGridDescriptor(MeshDescriptor): # {{{ ''' A class for describing a general logically rectangular grid that can be defined by a `pyproj` projection. - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis def __init__(self, projection): # {{{ ''' @@ -397,11 +388,11 @@ def __init__(self, projection): # {{{ projection : ``pyproj.Proj`` object The projection used to map from grid x-y space to latitude and longitude - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis + self.projection = projection self.latLonProjection = pyproj.Proj(proj='latlong', datum='WGS84') self.regional = True @@ -430,11 +421,11 @@ def read(cls, projection, fileName, meshName=None, xVarName='x', xVarName, yVarName : str, optional The name of the x and y (in meters) variables in the grid file - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis + descriptor = cls(projection) ds = xarray.open_dataset(fileName) @@ -480,11 +471,11 @@ def create(cls, projection, x, y, meshName): # {{{ meshName : str The name of the grid (e.g. ``'10km_Antarctic_stereo'``) - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis + descriptor = cls(projection) descriptor.meshName = meshName @@ -508,11 +499,11 @@ def to_scrip(self, scripFileName): # {{{ ---------- scripFileName : str The path to which the SCRIP file should be written - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis + self.scripFileName = scripFileName outFile = netCDF4.Dataset(scripFileName, 'w') @@ -560,11 +551,10 @@ def project_to_lat_lon(self, X, Y): # {{{ ------- Lat, Lon : numpy.array with same shape as X and Y the latitude and longitude in degrees of the points - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis Lon, Lat = pyproj.transform(self.projection, self.latLonProjection, X, Y, radians=False) @@ -634,11 +624,11 @@ def _create_scrip(outFile, grid_size, grid_corners, grid_rank, units, meshName : str The name of the mesh - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis + # Write to output file # Dimensions outFile.createDimension("grid_size", grid_size) diff --git a/mpas_analysis/shared/html/image_xml.py b/mpas_analysis/shared/html/image_xml.py index e2c1aa770..b16c80a82 100644 --- a/mpas_analysis/shared/html/image_xml.py +++ b/mpas_analysis/shared/html/image_xml.py @@ -81,11 +81,11 @@ def write_image_xml(config, filePrefix, componentName, componentSubdirectory, kwargs : dict additional keyword arguments will be used to add additional xml tags with the associated values - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + imageFileName = '{}.png'.format(filePrefix) plotsDirectory = build_config_full_path(config, 'output', 'plotsSubdirectory') @@ -148,11 +148,11 @@ def write_image_xml(config, filePrefix, componentName, componentSubdirectory, def _provenance_command(root, history): # {{{ """ Utility funciton for provenance of xml file associated with a plot. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + call = ' '.join(sys.argv) if history is None: history = call diff --git a/mpas_analysis/shared/html/pages.py b/mpas_analysis/shared/html/pages.py index dd70a38a7..ea9a7a03c 100644 --- a/mpas_analysis/shared/html/pages.py +++ b/mpas_analysis/shared/html/pages.py @@ -36,11 +36,11 @@ def generate_html(config, analyses, refConfig=None): # {{{ refConfig : ``MpasAnalysisConfigParser``, optional Config options for a reference run - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + generateHTML = config.getboolean('html', 'generate') if not generateHTML: return @@ -95,11 +95,11 @@ class MainPage(object): components : OrederdDict of dict Each component has a name, subdirectory and image name used to find the appropriate thumbnail. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + def __init__(self, config, refConfig=None): """ Create a MainPage object, reading in the templates @@ -111,11 +111,10 @@ def __init__(self, config, refConfig=None): refConfig : ``MpasAnalysisConfigParser``, optional Config options for a reference run - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis self.config = config self.refConfig = refConfig @@ -155,11 +154,11 @@ def add_component(self, name, subdirectory, imageFileName): The name of an image file (without path) that will be used as the thumbnail for the gallery. Typically, this is the first image from the first gallery. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + self.components[name] = {'subdirectory': subdirectory, 'imageFileName': imageFileName} @@ -167,11 +166,11 @@ def generate(self): """ Generate the webpage from templates and components, and write it out to the HTML directory. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + runName = self.config.get('runs', 'mainRunName') if self.refConfig is None: @@ -260,11 +259,11 @@ class ComponentPage(object): groups : tree of OrederdDict A tree of information describing the the gallery groups in the page, the galleries in each group and the images in each gallery. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + def __init__(self, config, name, subdirectory, refConfig=None): """ Create a ComponentPage object, reading in the templates @@ -284,11 +283,10 @@ def __init__(self, config, name, subdirectory, refConfig=None): refConfig : ``MpasAnalysisConfigParser``, optional Config options for a reference run - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis self.config = config self.refConfig = refConfig @@ -338,11 +336,11 @@ def add_image(xmlFileName, config, components, refConfig=None): refConfig : ``MpasAnalysisConfigParser``, optional Config options for a reference run - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + xmlRoot = etree.parse(xmlFileName).getroot() componentName = ComponentPage._get_required_xml_text(xmlRoot, @@ -405,11 +403,11 @@ def generate(self): """ Generate the webpage from templates and groups, and write it out to the HTML directory. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + runName = self.config.get('runs', 'mainRunName') if self.refConfig is None: @@ -451,11 +449,11 @@ def get_first_image(self): ------- firstImageFilename : str The name (with out path) of the first image in the first gallery - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + # get the first image name firstGroup = next(iter(self.groups.values())) firstGallery = next(iter(firstGroup['galleries'].values())) diff --git a/mpas_analysis/shared/interpolation/remapper.py b/mpas_analysis/shared/interpolation/remapper.py index fb3d003e7..67af6e618 100644 --- a/mpas_analysis/shared/interpolation/remapper.py +++ b/mpas_analysis/shared/interpolation/remapper.py @@ -14,11 +14,10 @@ weights needed to perform horizontal interpolation remap - perform horizontal interpolation on a data sets, given a mapping file - -Authors -------- -Xylar Asay-Davis ''' +# Authors +# ------- +# Xylar Asay-Davis from __future__ import absolute_import, division, print_function, \ unicode_literals @@ -41,11 +40,10 @@ class Remapper(object): A class for remapping fields using a given mapping file. The weights and indices from the mapping file can be loaded once and reused multiple times to map several fields between the same source and destination grids. - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis def __init__(self, sourceDescriptor, destinationDescriptor, mappingFileName=None): # {{{ @@ -70,11 +68,10 @@ def __init__(self, sourceDescriptor, destinationDescriptor, This is useful if the source and destination grids are determined to be the same (though the Remapper does not attempt to determine if this is the case). - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis if not isinstance(sourceDescriptor, (MpasMeshDescriptor, LatLonGridDescriptor, @@ -122,11 +119,10 @@ def build_mapping_file(self, method='bilinear', ValueError If sourceDescriptor or destinationDescriptor is of an unknown type - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis if self.mappingFileName is None or \ os.path.exists(self.mappingFileName): @@ -242,11 +238,10 @@ def remap_file(self, inFileName, outFileName, variableList=None, ValueError If ``mappingFileName`` is ``None`` (meaning no remapping is needed). - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis if self.mappingFileName is None: raise ValueError('No mapping file was given because remapping is ' @@ -371,11 +366,10 @@ def remap(self, ds, renormalizationThreshold=None): # {{{ (``self.src_grid_dims``). TypeError If ds is not an ``xarray.Dataset`` or ``xarray.DataArray`` object - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis if self.mappingFileName is None: # No remapping is needed @@ -420,11 +414,10 @@ def _load_mapping(self): # {{{ ''' Load weights and indices from a mapping file, if this has not already been done - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis if self.mappingLoaded: return @@ -491,11 +484,10 @@ def _check_drop(self, dataArray): # {{{ def _remap_data_array(self, dataArray, renormalizationThreshold): # {{{ ''' Remap a single xarray data array - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis sourceDims = self.sourceDescriptor.dims destDims = self.destinationDescriptor.dims @@ -562,11 +554,10 @@ def _remap_numpy_array(self, inField, remapAxes, renormalizationThreshold): # {{{ ''' Remap a single numpy array - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis # permute the dimensions of inField so the axes to remap are first, # then flatten the remapping and the extra dimensions separately for diff --git a/mpas_analysis/shared/io/mpas_reader.py b/mpas_analysis/shared/io/mpas_reader.py index dcd9e5345..2c824406a 100644 --- a/mpas_analysis/shared/io/mpas_reader.py +++ b/mpas_analysis/shared/io/mpas_reader.py @@ -8,11 +8,10 @@ """ Utility functions for reading a single MPAS file into xarray and for removing all but a given list of variables from a data set. - -Authors -------- -Xylar Asay-Davis """ +# Authors +# ------- +# Xylar Asay-Davis from __future__ import absolute_import, division, print_function, \ unicode_literals @@ -64,11 +63,10 @@ def open_mpas_dataset(fileName, calendar, ValueError If the time variable is not found in the data set - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis ds = xarray.open_dataset(fileName, decode_cf=True, decode_times=False, lock=False) @@ -121,11 +119,10 @@ def subset_variables(ds, variableList): # {{{ ------ ValueError If the resulting data set is empty. - - Authors - ------- - Phillip J. Wolfram, Xylar Asay-Davis """ + # Authors + # ------- + # Phillip J. Wolfram, Xylar Asay-Davis allvars = ds.data_vars.keys() @@ -204,11 +201,10 @@ def _parse_dataset_time(ds, inTimeVariableName, calendar, TypeError If the time variable has an unsupported type (not a date string or a floating-pont number of days since the start of the simulatio). - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis if isinstance(inTimeVariableName, (tuple, list)): # we want to average the two diff --git a/mpas_analysis/shared/io/namelist_streams_interface.py b/mpas_analysis/shared/io/namelist_streams_interface.py index 56d1508a6..ce77de203 100644 --- a/mpas_analysis/shared/io/namelist_streams_interface.py +++ b/mpas_analysis/shared/io/namelist_streams_interface.py @@ -9,11 +9,10 @@ """ Module of classes/routines to manipulate fortran namelist and streams files. - -Authors -------- -Phillip Wolfram, Xylar Asay-Davis """ +# Authors +# ------- +# Phillip Wolfram, Xylar Asay-Davis from __future__ import absolute_import, division, print_function, \ unicode_literals @@ -39,11 +38,11 @@ def convert_namelist_to_dict(fname, readonly=True): readonly : bool, optional Should the resulting dictionary read-only? - - Authors - ------- - Phillip J Wolfram """ + # Authors + # ------- + # Phillip J Wolfram + # form dictionary nml = dict() @@ -64,11 +63,10 @@ class NameList: """ Class for fortran manipulation of namelist files, provides read and write functionality - - Authors - ------- - Phillip Wolfram, Xylar Asay-Davis """ + # Authors + # ------- + # Phillip Wolfram, Xylar Asay-Davis # constructor def __init__(self, fname, path=None): @@ -83,11 +81,11 @@ def __init__(self, fname, path=None): path : str, optional If ``fname`` contains a relative path, ``fname`` is relative to ``path``, rather than the current working directory - - Authors - ------- - Phillip Wolfram, Xylar Asay-Davis """ + # Authors + # ------- + # Phillip Wolfram, Xylar Asay-Davis + if not os.path.isabs(fname) and path is not None: # only the file name was given, not the absolute path, and # a path was provided, so we will assume the namelist @@ -113,11 +111,11 @@ def __getattr__(self, key): ------- value : str The value associated with ``key`` - - Authors - ------- - Phillip Wolfram, Xylar Asay-Davis """ + # Authors + # ------- + # Phillip Wolfram, Xylar Asay-Davis + return self.nml[key] # provide accessor for dictionary notation (returns string) @@ -134,11 +132,11 @@ def __getitem__(self, key): ------- value : str The value associated with ``key`` - - Authors - ------- - Phillip Wolfram, Xylar Asay-Davis """ + # Authors + # ------- + # Phillip Wolfram, Xylar Asay-Davis + return self.nml[key] # provide accessors for get, getint, getfloat, getbool with appropriate @@ -156,11 +154,11 @@ def get(self, key): ------- value : str The value associated with ``key`` - - Authors - ------- - Phillip Wolfram, Xylar Asay-Davis """ + # Authors + # ------- + # Phillip Wolfram, Xylar Asay-Davis + return self.nml[key] def getint(self, key): @@ -176,11 +174,11 @@ def getint(self, key): ------- value : int The value associated with ``key`` - - Authors - ------- - Phillip Wolfram, Xylar Asay-Davis """ + # Authors + # ------- + # Phillip Wolfram, Xylar Asay-Davis + return int(self.nml[key]) def getfloat(self, key): @@ -196,11 +194,11 @@ def getfloat(self, key): ------- value : float The value associated with ``key`` - - Authors - ------- - Phillip Wolfram, Xylar Asay-Davis """ + # Authors + # ------- + # Phillip Wolfram, Xylar Asay-Davis + return float(self.nml[key]) def getbool(self, key): @@ -216,11 +214,11 @@ def getbool(self, key): ------- value : bool The value associated with ``key`` - - Authors - ------- - Phillip Wolfram, Xylar Asay-Davis """ + # Authors + # ------- + # Phillip Wolfram, Xylar Asay-Davis + if 'True' in self.nml[key] or 'true' in self.nml[key]: return True else: @@ -246,11 +244,10 @@ def find_option(self, possibleOptions): ------ ValueError If no match is found. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis for optionName in possibleOptions: if optionName in self.nml.keys(): @@ -266,11 +263,10 @@ class StreamsFile: """ Class to read in streams configuration file, provdies read and write functionality - - Authors - ------- - Phillip Wolfram, Xylar Asay-Davis """ + # Authors + # ------- + # Phillip Wolfram, Xylar Asay-Davis def __init__(self, fname, streamsdir=None): """ @@ -284,11 +280,11 @@ def __init__(self, fname, streamsdir=None): streamsdir : str, optional The base path to both the output streams data and the sreams file (the latter only if ``fname`` is a relative path). - - Authors - ------- - Phillip Wolfram, Xylar Asay-Davis """ + # Authors + # ------- + # Phillip Wolfram, Xylar Asay-Davis + if not os.path.isabs(fname) and streamsdir is not None: # only the file name was given, not the absolute path, and # a streamsdir was provided, so we will assume the streams @@ -325,11 +321,11 @@ def read(self, streamname, attribname): value : str The value associated with the attribute, or ``None`` if the attribute was not found - - Authors - ------- - Phillip Wolfram, Xylar Asay-Davis """ + # Authors + # ------- + # Phillip Wolfram, Xylar Asay-Davis + for stream in self.root: # assumes streamname is unique in XML if stream.get('name') == streamname: @@ -351,11 +347,11 @@ def read_datetime_template(self, streamname): The template for file names from this stream in a format accepted by ``datetime.strptime``. This is useful for parsing the date from a given file name. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + template = self.read(streamname, 'filename_template') replacements = {'$Y': '%Y', '$M': '%m', @@ -404,11 +400,11 @@ def readpath(self, streamName, startDate=None, endDate=None, ------ ValueError If no files from the stream are found. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + template = self.read(streamName, 'filename_template') if template is None: raise ValueError('Stream {} not found in streams file {}.'.format( @@ -492,11 +488,11 @@ def has_stream(self, streamName): streamFound : bool ``True`` if the stream was found in the stream file, ``False`` otherwise - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + for stream in self.root: # assumes streamname is unique in XML if stream.get('name') == streamName: @@ -523,11 +519,11 @@ def find_stream(self, possibleStreams): ------ ValueError If no match is found. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + for streamName in possibleStreams: if self.has_stream(streamName): return streamName diff --git a/mpas_analysis/shared/io/utility.py b/mpas_analysis/shared/io/utility.py index 0de779050..1f69bd1f3 100644 --- a/mpas_analysis/shared/io/utility.py +++ b/mpas_analysis/shared/io/utility.py @@ -35,11 +35,11 @@ def paths(*args): # {{{ ------- paths : list of str A list of file paths - - Authors - ------- - Phillip J. Wolfram """ + # Authors + # ------- + # Phillip J. Wolfram + paths = [] for aargs in args: paths += sorted(glob.glob(aargs)) @@ -67,11 +67,11 @@ def fingerprint_generator(size=12, Reference --------- http://stackoverflow.com/questions/2257441/random-string-generation-with-upper-case-letters-and-digits-in-python - - Authors - ------- - Phillip J. Wolfram """ + # Authors + # ------- + # Phillip J. Wolfram + return ''.join(random.choice(chars) for _ in range(size)) # }}} @@ -88,11 +88,10 @@ def make_directories(path): # {{{ ------- path : str the path unchanged - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis try: os.makedirs(path) @@ -125,11 +124,11 @@ def build_config_full_path(config, section, relativePathOption, defaultPath : str, optional the name of a path to return if the resulting path doesn't exist. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + if relativePathSection is None: relativePathSection = section @@ -158,11 +157,11 @@ def check_path_exists(path): # {{{ ------ OSError If the path does not exist - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + if not (os.path.isdir(path) or os.path.isfile(path)): raise OSError('Path {} not found'.format(path)) # }}} @@ -186,11 +185,10 @@ def get_files_year_month(fileNames, streamsFile, streamName): # {{{ ------- years, months : list of int The years and months for each file in ``fileNames`` - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis template = streamsFile.read_datetime_template(streamName) template = os.path.basename(template) diff --git a/mpas_analysis/shared/io/write_netcdf.py b/mpas_analysis/shared/io/write_netcdf.py index e033248d3..4cfc6c695 100644 --- a/mpas_analysis/shared/io/write_netcdf.py +++ b/mpas_analysis/shared/io/write_netcdf.py @@ -28,12 +28,12 @@ def write_netcdf(ds, fileName, fillValues=netCDF4.default_fillvals): # {{{ A dictionary of fill values for each supported data type. By default, this is the dictionary used by the netCDF4 package. Key entries should be of the form 'f8' (for float64), 'i4' (for int32), etc. - - Authors - ------- - Xylar Asay-Davis - ''' + # Authors + # ------- + # Xylar Asay-Davis + +# encodingDict = {} variableNames = list(ds.data_vars.keys()) + list(ds.coords.keys()) for variableName in variableNames: diff --git a/mpas_analysis/shared/mpas_xarray/mpas_xarray.py b/mpas_analysis/shared/mpas_xarray/mpas_xarray.py index e8dd1430b..133468465 100644 --- a/mpas_analysis/shared/mpas_xarray/mpas_xarray.py +++ b/mpas_analysis/shared/mpas_xarray/mpas_xarray.py @@ -25,11 +25,10 @@ subset_variables : Keep only a subset of variables in a dataset preprocess : preprocess a single file of an xarray dataset remove_repeated_time_index : remove redundant indices in the 'Time' coordinate - -Authors -------- -Phillip J. Wolfram, Xylar Asay-Davis """ +# Authors +# ------- +# Phillip J. Wolfram, Xylar Asay-Davis def open_multifile_dataset(fileNames, calendar, @@ -99,11 +98,10 @@ def open_multifile_dataset(fileNames, calendar, If the time variable is not found in the data set or if the time variable is a number of days since the start of the simulation but simulationStartTime is None. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis preprocess_partial = partial(preprocess, calendar=calendar, @@ -145,11 +143,10 @@ def subset_variables(ds, variableList): # {{{ ------ ValueError If the resulting data set is empty. - - Authors - ------- - Phillip J. Wolfram, Xylar Asay-Davis """ + # Authors + # ------- + # Phillip J. Wolfram, Xylar Asay-Davis allvars = ds.data_vars.keys() @@ -237,12 +234,11 @@ def preprocess(ds, calendar, simulationStartTime, timeVariableName, ds : ``xarray.DataSet`` object A copy of the data set with the time coordinate set and which has been sliced. - - Authors - ------- - Phillip J. Wolfram, Milena Veneziani, Luke van Roekel - and Xylar Asay-Davis """ + # Authors + # ------- + # Phillip J. Wolfram, Milena Veneziani, Luke van Roekel + # and Xylar Asay-Davis ds = _parse_dataset_time(ds=ds, inTimeVariableName=timeVariableName, @@ -280,11 +276,11 @@ def remove_repeated_time_index(ds): # {{{ ------- ds : ``xarray.DataSet`` object A copy of the original data set with any repeated time indices removed. - - Authors - ------- - Phillip J. Wolfram, Xylar Asay-Davis """ + # Authors + # ------- + # Phillip J. Wolfram, Xylar Asay-Davis + # get repeated indices times = ds.Time.values indices = list(range(len(times))) @@ -317,11 +313,11 @@ def _assert_valid_selections(ds, selvals, iselvals): # {{{ and iselvals are unique. Additionally, keys for selvals and iselvals are tested to make sure they are dataset dimensions that can be used for selection. - - Authors - ------- - Phillip J. Wolfram, Xylar Asay-Davis """ + # Authors + # ------- + # Phillip J. Wolfram, Xylar Asay-Davis + def test_vals_in_ds(vals, dims): if vals is not None: for val in vals.keys(): @@ -345,11 +341,10 @@ def test_vals_in_ds(vals, dims): def _ensure_list(alist): # {{{ """ Ensure that variables used as a list are actually lists. - - Authors - ------- - Phillip J. Wolfram, Xylar Asay-Davis """ + # Authors + # ------- + # Phillip J. Wolfram, Xylar Asay-Davis if isinstance(alist, six.string_types): # print 'Warning, converting %s to a list'%(alist) @@ -426,11 +421,10 @@ def _parse_dataset_time(ds, inTimeVariableName, calendar, ValueError If the time variable is a number of days since the start of the simulation but simulationStartTime is None. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis if isinstance(inTimeVariableName, (tuple, list)): # we want to average the two @@ -542,11 +536,10 @@ def process_chunking(ds, chunking): # {{{ ValueError If chunking value used is not an acceptable value. - - Authors - ------- - Phillip J. Wolfram """ + # Authors + # ------- + # Phillip J. Wolfram if isinstance(chunking, int): chunks = {} diff --git a/mpas_analysis/shared/plot/plotting.py b/mpas_analysis/shared/plot/plotting.py index c9d130900..f70c593d7 100644 --- a/mpas_analysis/shared/plot/plotting.py +++ b/mpas_analysis/shared/plot/plotting.py @@ -11,11 +11,10 @@ * remapped horizontal fields (and comparing with reference data sets) * vertical sections on native grid * NINO34 time series and spectra - -Authors -------- -Xylar Asay-Davis, Milena Veneziani, Luke Van Roekel, Greg Streletz """ +# Authors +# ------- +# Xylar Asay-Davis, Milena Veneziani, Luke Van Roekel, Greg Streletz from __future__ import absolute_import, division, print_function, \ unicode_literals @@ -108,11 +107,10 @@ def timeseries_analysis_plot(config, dsvalues, N, title, xlabel, ylabel, legendLocation : str, optional The location of the legend (see ``pyplot.legend()`` for details) - - Authors - ------- - Xylar Asay-Davis, Milena Veneziani, Stephen Price """ + # Authors + # ------- + # Xylar Asay-Davis, Milena Veneziani, Stephen Price if dpi is None: dpi = config.getint('plot', 'dpi') @@ -233,11 +231,11 @@ def timeseries_analysis_plot_polar(config, dsvalues, N, title, dpi : int, optional the number of dots per inch of the figure, taken from section ``plot`` option ``dpi`` in the config file by default - - Authors - ------- - Adrian K. Turner, Xylar Asay-Davis """ + # Authors + # ------- + # Adrian K. Turner, Xylar Asay-Davis + if dpi is None: dpi = config.getint('plot', 'dpi') plt.figure(figsize=figsize, dpi=dpi) @@ -372,11 +370,10 @@ def plot_polar_comparison( vertical : bool, optional whether the subplots should be stacked vertically rather than horizontally - - Authors - ------- - Xylar Asay-Davis, Milena Veneziani """ + # Authors + # ------- + # Xylar Asay-Davis, Milena Veneziani def do_subplot(ax, field, title, colormap, norm, levels, ticks, contours, lineWidth, lineColor): @@ -535,11 +532,10 @@ def plot_global_comparison( lineColor : str, optional the color contour lines (if specified) - - Authors - ------- - Xylar Asay-Davis, Milena Veneziani """ + # Authors + # ------- + # Xylar Asay-Davis, Milena Veneziani def plot_panel(title, array, colormap, norm, levels, ticks, contours, lineWidth, lineColor): @@ -684,11 +680,10 @@ def plot_polar_projection_comparison( vertical : bool, optional whether the subplots should be stacked vertically rather than horizontally - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis def plot_panel(ax, title, array, colormap, norm, levels, ticks, contours, lineWidth, lineColor): @@ -837,11 +832,10 @@ def plot_1D(config, xArrays, fieldArrays, errArrays, invertYAxis : logical, optional if True, invert Y axis - - Authors - ------- - Mark Petersen, Milena Veneziani """ + # Authors + # ------- + # Mark Petersen, Milena Veneziani # set up figure if dpi is None: @@ -1000,11 +994,10 @@ def plot_vertical_section( calendar : str, optional the calendar to use for formatting the time axis NOTE: calendar is only used if xArrayIsTime is True - - Authors - ------- - Milena Veneziani, Mark Petersen, Xylar Asay-Davis, Greg Streletz """ + # Authors + # ------- + # Milena Veneziani, Mark Petersen, Xylar Asay-Davis, Greg Streletz # verify that the dimensions of fieldArray are consistent with those of # xArray and depthArray @@ -1128,11 +1121,10 @@ def setup_colormap(config, configSectionName, suffix=''): 'lineWidth' is the width of contour lines or ``None`` if not specified 'lineColor' is the color of contour lines or ``None`` if not specified - - Authors - ------- - Xylar Asay-Davis, Milena Veneziani, Greg Streletz ''' + # Authors + # ------- + # Xylar Asay-Davis, Milena Veneziani, Greg Streletz _register_custom_colormaps() @@ -1188,11 +1180,11 @@ def plot_xtick_format(plt, calendar, minDays, maxDays, maxXTicks): minDays : start time for labels maxDays : end time for labels - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis + ax = plt.gca() start = days_to_datetime(np.amin(minDays), calendar=calendar) @@ -1248,11 +1240,10 @@ def _setup_colormap_and_norm(config, configSectionName, suffix=''): ticks : array of float the tick marks on the colormap - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis _register_custom_colormaps() @@ -1311,11 +1302,10 @@ def _setup_indexed_colormap(config, configSectionName, suffix=''): ticks : array of float the tick marks on the colormap - - Authors - ------- - Xylar Asay-Davis, Milena Veneziani, Greg Streletz ''' + # Authors + # ------- + # Xylar Asay-Davis, Milena Veneziani, Greg Streletz colormap = plt.get_cmap(config.get(configSectionName, 'colormapName{}'.format(suffix))) diff --git a/mpas_analysis/shared/time_series/anomaly.py b/mpas_analysis/shared/time_series/anomaly.py index 29650fc45..cfa6def98 100644 --- a/mpas_analysis/shared/time_series/anomaly.py +++ b/mpas_analysis/shared/time_series/anomaly.py @@ -56,11 +56,10 @@ def compute_moving_avg_anomaly_from_start(timeSeriesFileName, variableList, ------- ds : ``xarray.Dataset`` The anomaly of the rolling time mean from the start of the simulation - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis ds = open_mpas_dataset(fileName=timeSeriesFileName, calendar=calendar, diff --git a/mpas_analysis/shared/time_series/moving_average.py b/mpas_analysis/shared/time_series/moving_average.py index 80e4cf498..3196f6aec 100644 --- a/mpas_analysis/shared/time_series/moving_average.py +++ b/mpas_analysis/shared/time_series/moving_average.py @@ -30,11 +30,10 @@ def compute_moving_avg(ds, movingAveragePoints=12): # {{{ ------- ds : ``xarray.Dataset`` The anomaly of the rolling time mean from the start of the simulation - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis ds = ds.rolling(Time=movingAveragePoints, center=True).mean().dropna('Time') diff --git a/mpas_analysis/shared/time_series/mpas_time_series_task.py b/mpas_analysis/shared/time_series/mpas_time_series_task.py index 0d063d032..e0e18710b 100644 --- a/mpas_analysis/shared/time_series/mpas_time_series_task.py +++ b/mpas_analysis/shared/time_series/mpas_time_series_task.py @@ -42,11 +42,10 @@ class MpasTimeSeriesTask(AnalysisTask): # {{{ startYear, endYear : int The start and end years of the time series - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis def __init__(self, config, componentName, taskName=None, subtaskName=None, section='timeSeries'): # {{{ @@ -72,11 +71,11 @@ def __init__(self, config, componentName, taskName=None, section : str, optional The section of the config file from which to read the start and end times for the time series, also added as a tag - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis + self.variableList = [] self.section = section tags = [section] @@ -105,11 +104,10 @@ def add_variables(self, variableList): # {{{ variableList : list of str A list of variable names in ``timeSeriesStatsMonthly`` to be included in the time series - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis for variable in variableList: if variable not in self.variableList: @@ -120,11 +118,10 @@ def add_variables(self, variableList): # {{{ def setup_and_check(self): # {{{ ''' Perform steps to set up the analysis and check for errors in the setup. - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis # first, call setup_and_check from the base class (AnalysisTask), # which will perform some common setup, including storing: @@ -191,11 +188,10 @@ def setup_and_check(self): # {{{ def run_task(self): # {{{ ''' Compute the requested time series - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis if len(self.variableList) == 0: # nothing to do @@ -211,11 +207,10 @@ def _update_time_series_bounds_from_file_names(self): # {{{ """ Update the start and end years and dates for time series based on the years actually available in the list of files. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis config = self.config section = self.section diff --git a/mpas_analysis/shared/time_series/time_series.py b/mpas_analysis/shared/time_series/time_series.py index a5e9163af..3f2b2c187 100644 --- a/mpas_analysis/shared/time_series/time_series.py +++ b/mpas_analysis/shared/time_series/time_series.py @@ -7,11 +7,10 @@ # """ Utility functions related to time-series data sets - -Authors -------- -Xylar Asay-Davis """ +# Authors +# ------- +# Xylar Asay-Davis from __future__ import absolute_import, division, print_function, \ unicode_literals @@ -70,11 +69,10 @@ def cache_time_series(timesInDataSet, timeSeriesCalcFunction, cacheFileName, A data set without the ``'Time'`` coordinate containing the mean of ds over all months in monthValues, weighted by the number of days in each month. - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis timesProcessed = numpy.zeros(len(timesInDataSet), bool) # figure out which files to load and which years go in each file diff --git a/mpas_analysis/shared/timekeeping/MpasRelativeDelta.py b/mpas_analysis/shared/timekeeping/MpasRelativeDelta.py index c8353ee8c..72d1f082a 100644 --- a/mpas_analysis/shared/timekeeping/MpasRelativeDelta.py +++ b/mpas_analysis/shared/timekeeping/MpasRelativeDelta.py @@ -24,11 +24,10 @@ class MpasRelativeDelta(relativedelta): of ``datetime.datetime`` objects or other ``MpasRelativeDelta`` (but currently not ``datetime.date``, ``datetime.timedelta`` or other related objects) is supported. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis def __init__(self, dt1=None, dt2=None, years=0, months=0, days=0, hours=0, minutes=0, seconds=0, calendar='gregorian'): diff --git a/mpas_analysis/shared/timekeeping/utility.py b/mpas_analysis/shared/timekeeping/utility.py index e29574864..d16e2d2a1 100644 --- a/mpas_analysis/shared/timekeeping/utility.py +++ b/mpas_analysis/shared/timekeeping/utility.py @@ -7,11 +7,10 @@ # """ Time keeping utility functions - -Authors -------- -Xylar Asay-Davis """ +# Authors +# ------- +# Xylar Asay-Davis from __future__ import absolute_import, division, print_function, \ unicode_literals @@ -45,11 +44,10 @@ def get_simulation_start_time(streams): ------ IOError If no restart file can be found. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis try: restartFile = streams.readpath('restart')[0] @@ -100,11 +98,10 @@ def string_to_datetime(dateString): # {{{ ------ ValueError If an invalid ``dateString`` is supplied. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis (year, month, day, hour, minute, second) = \ _parse_date_string(dateString, isInterval=False) @@ -149,11 +146,10 @@ def string_to_relative_delta(dateString, calendar='gregorian'): # {{{ ------ ValueError If an invalid ``dateString`` is supplied. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis (years, months, days, hours, minutes, seconds) = \ _parse_date_string(dateString, isInterval=True) @@ -211,11 +207,10 @@ def string_to_days_since_date(dateString, calendar='gregorian', ------ ValueError If an invalid ``dateString`` or ``calendar`` is supplied. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis isSingleString = isinstance(dateString, six.string_types) @@ -262,11 +257,10 @@ def days_to_datetime(days, calendar='gregorian', referenceDate='0001-01-01'): ------ ValueError If an invalid ``days``, ``referenceDate`` or ``calendar`` is supplied. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis datetimes = netCDF4.num2date(days, 'days since {}'.format(referenceDate), @@ -317,11 +311,10 @@ def datetime_to_days(dates, calendar='gregorian', referenceDate='0001-01-01'): ValueError If an invalid ``datetimes``, ``referenceDate`` or ``calendar`` is supplied. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis isSingleDate = False if isinstance(dates, datetime.datetime): @@ -367,11 +360,10 @@ def date_to_days(year=1, month=1, day=1, hour=0, minute=0, second=0, ------ ValueError If an invalid ``referenceDate`` or ``calendar`` is supplied. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis calendar = _mpas_to_netcdf_calendar(calendar) @@ -419,11 +411,11 @@ def _parse_date_string(dateString, isInterval=False): # {{{ ------ ValueError If an invalid ``dateString`` is supplied. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + if isInterval: offset = 0 else: diff --git a/mpas_analysis/test/test_remap_obs_clim_subtask.py b/mpas_analysis/test/test_remap_obs_clim_subtask.py index fba32e6d1..06433de1c 100644 --- a/mpas_analysis/test/test_remap_obs_clim_subtask.py +++ b/mpas_analysis/test/test_remap_obs_clim_subtask.py @@ -32,11 +32,10 @@ class RemapObservedMLDClimatology(RemapObservedClimatologySubtask): # {{{ """ A subtask for reading and remapping MLD observations - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis def get_observation_descriptor(self, fileName): # {{{ ''' @@ -51,11 +50,10 @@ def get_observation_descriptor(self, fileName): # {{{ ------- obsDescriptor : ``MeshDescriptor`` The descriptor for the observation grid - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis # create a descriptor of the observation grid using the lat/lon # coordinates @@ -78,11 +76,10 @@ def build_observational_dataset(self, fileName): # {{{ ------- dsObs : ``xarray.Dataset`` The observational dataset - - Authors - ------- - Xylar Asay-Davis ''' + # Authors + # ------- + # Xylar Asay-Davis # Load MLD observational data dsObs = xarray.open_dataset(fileName) diff --git a/mpas_analysis/test/test_timekeeping.py b/mpas_analysis/test/test_timekeeping.py index 5a459864c..9b83077c0 100644 --- a/mpas_analysis/test/test_timekeeping.py +++ b/mpas_analysis/test/test_timekeeping.py @@ -7,11 +7,10 @@ # """ Unit test infrastructure for the Date class - -Authors -------- -Xylar Asay-Davis """ +# Authors +# ------- +# Xylar Asay-Davis from __future__ import absolute_import, division, print_function, \ unicode_literals diff --git a/run_mpas_analysis b/run_mpas_analysis index 1782a1121..974246001 100755 --- a/run_mpas_analysis +++ b/run_mpas_analysis @@ -10,11 +10,10 @@ """ Runs MPAS-Analysis via a configuration file (e.g. `config.analysis`) specifying analysis options. - -Authors -------- -Xylar Asay-Davis, Phillip J. Wolfram """ +# Authors +# ------- +# Xylar Asay-Davis, Phillip J. Wolfram from __future__ import absolute_import, division, print_function, \ unicode_literals @@ -56,11 +55,10 @@ def build_analysis_list(config, refConfig): # {{{ ------- analyses : list of ``AnalysisTask`` objects A list of all analysis tasks - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis # choose the right rendering backend, depending on whether we're displaying # to the screen @@ -168,11 +166,10 @@ def determine_analyses_to_generate(analyses): # {{{ ------- analysesToGenerate : list of ``AnalysisTask`` objects A list of analysis tasks to run - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis analysesToGenerate = OrderedDict() # check which analysis we actually want to generate and only keep those @@ -205,11 +202,10 @@ def add_task_and_subtasks(analysisTask, analysesToGenerate, see if it has been requested. We skip this for subtasks and prerequisites, since they are needed by another task regardless of whether the user specifically requested them. - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis key = (analysisTask.taskName, analysisTask.subtaskName) if key in analysesToGenerate.keys(): @@ -287,11 +283,10 @@ def update_generate(config, generate): # {{{ a comma-separated string of generate flags: either names of analysis tasks or commands of the form ``all_`` or ``no_`` indicating that analysis with a given tag should be included or excluded). - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis # overwrite the 'generate' in config with a string that parses to # a list of string @@ -314,11 +309,10 @@ def run_analysis(config, analyses): # {{{ analyses : OrderedDict of ``AnalysisTask`` objects A dictionary of analysis tasks to run with (task, subtask) names as keys - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis # write the config file the log directory logsDirectory = build_config_full_path(config, 'output', @@ -438,11 +432,11 @@ def wait_for_task(runningTasks, timeout=0.1): # {{{ ------- analysisTask : ``AnalysisTasks`` A task that finished - - Authors - ------- - Xylar Asay-Davis """ + # Authors + # ------- + # Xylar Asay-Davis + # necessary to have a timeout so we can kill the whole thing # with a keyboard interrupt while True: From fcb60ffd7afe24df80ef670981f7c251fcc18f44 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Mon, 16 Apr 2018 22:03:24 +0200 Subject: [PATCH 43/71] In mpas_xarray, make coords from non-time-dependent vars This prevents them from being expanded by xarray.open_mfdataset() to have a Time dimension, which we don't want. --- mpas_analysis/shared/mpas_xarray/mpas_xarray.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/mpas_analysis/shared/mpas_xarray/mpas_xarray.py b/mpas_analysis/shared/mpas_xarray/mpas_xarray.py index e8dd1430b..ac5d32eee 100644 --- a/mpas_analysis/shared/mpas_xarray/mpas_xarray.py +++ b/mpas_analysis/shared/mpas_xarray/mpas_xarray.py @@ -244,6 +244,12 @@ def preprocess(ds, calendar, simulationStartTime, timeVariableName, and Xylar Asay-Davis """ + # following a suggestion by @rabernat + # https://github.com/pydata/xarray/issues/2064#issuecomment-381717472 + concat_dim = 'Time' + coord_vars = [v for v in ds.data_vars if concat_dim not in ds[v].dims] + ds = ds.set_coords(coord_vars) + ds = _parse_dataset_time(ds=ds, inTimeVariableName=timeVariableName, calendar=calendar, From fb515dfdb7dbe348a911ac5b30ae53384e2fb201 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Mon, 16 Apr 2018 22:05:09 +0200 Subject: [PATCH 44/71] Update unit tests with vars --> coords Update the unit tests to handle the fact that some variables are now treated as coords because they don't have a time variable. --- mpas_analysis/test/test_generalized_reader.py | 7 +++++-- mpas_analysis/test/test_mpas_xarray.py | 19 ++++++++++++++----- 2 files changed, 19 insertions(+), 7 deletions(-) diff --git a/mpas_analysis/test/test_generalized_reader.py b/mpas_analysis/test/test_generalized_reader.py index 5b0f271f3..fe01b1a43 100644 --- a/mpas_analysis/test/test_generalized_reader.py +++ b/mpas_analysis/test/test_generalized_reader.py @@ -15,6 +15,7 @@ from __future__ import absolute_import, division, print_function, \ unicode_literals +import numpy import pytest from mpas_analysis.test import TestCase, loaddatadir from mpas_analysis.shared.generalized_reader.generalized_reader \ @@ -71,7 +72,8 @@ def test_variableMap(self): variableMap=variableMap) # make sure the remapping happened as expected - self.assertEqual(sorted(ds.data_vars.keys()), sorted(variableList)) + dsVarList = list(ds.data_vars.keys()) + list(ds.coords.keys()) + assert(numpy.all([var in dsVarList for var in variableList])) def test_open_dataset_fn(self): fileName = str(self.datadir.join('example_jan.nc')) @@ -87,7 +89,8 @@ def test_open_dataset_fn(self): config=config, timeVariableName=timestr, variableList=variableList) - self.assertEqual(list(ds.data_vars.keys()), variableList) + dsVarList = list(ds.data_vars.keys()) + list(ds.coords.keys()) + assert(numpy.all([var in dsVarList for var in variableList])) def test_start_end(self): fileName = str(self.datadir.join('example_jan_feb.nc')) diff --git a/mpas_analysis/test/test_mpas_xarray.py b/mpas_analysis/test/test_mpas_xarray.py index 2f1d1c240..8d1190cfd 100644 --- a/mpas_analysis/test/test_mpas_xarray.py +++ b/mpas_analysis/test/test_mpas_xarray.py @@ -15,6 +15,8 @@ from __future__ import absolute_import, division, print_function, \ unicode_literals +import numpy + import pytest from mpas_analysis.test import TestCase, loaddatadir from mpas_analysis.shared.mpas_xarray import mpas_xarray @@ -38,7 +40,8 @@ def test_subset_variables(self): calendar=calendar, timeVariableName=timestr) ds = mpas_xarray.subset_variables(ds, variableList) - self.assertEqual(sorted(ds.data_vars.keys()), sorted(variableList)) + dsVarList = list(ds.data_vars.keys()) + list(ds.coords.keys()) + assert(numpy.all([var in dsVarList for var in variableList])) self.assertEqual(days_to_datetime(days=ds.Time.values, referenceDate='0001-01-01', calendar=calendar), @@ -76,7 +79,8 @@ def test_iselvals(self): variableList=variableList, iselValues=iselvals) - self.assertEqual(sorted(ds.data_vars.keys()), sorted(variableList)) + dsVarList = list(ds.data_vars.keys()) + list(ds.coords.keys()) + assert(numpy.all([var in dsVarList for var in variableList])) self.assertEqual(ds[variableList[0]].shape, (1, 7, 3)) self.assertEqual(ds['refBottomDepth'].shape, (3,)) self.assertApproxEqual(ds['refBottomDepth'][-1], @@ -102,7 +106,9 @@ def test_no_units(self): simulationStartTime=simulationStartTime, timeVariableName=timestr, variableList=variableList) - self.assertEqual(sorted(ds.data_vars.keys()), sorted(variableList)) + + dsVarList = list(ds.data_vars.keys()) + list(ds.coords.keys()) + assert(numpy.all([var in dsVarList for var in variableList])) self.assertEqual(days_to_datetime(days=ds.Time.values[0], referenceDate='0001-01-01', @@ -157,7 +163,9 @@ def test_selvals(self): variableList=variableList, selValues=selvals) - self.assertEqual(list(ds.data_vars.keys()), variableList) + dsVarList = list(ds.data_vars.keys()) + list(ds.coords.keys()) + assert(numpy.all([var in dsVarList for var in variableList])) + self.assertEqual(ds[variableList[0]].shape, (1, 7)) self.assertEqual(ds['refBottomDepth'], dsRef['refBottomDepth'][vertIndex]) @@ -176,7 +184,8 @@ def test_remove_repeated_time_index(self): timeVariableName=timestr, variableList=variableList) - self.assertEqual(sorted(ds.data_vars.keys()), sorted(variableList)) + dsVarList = list(ds.data_vars.keys()) + list(ds.coords.keys()) + assert(numpy.all([var in dsVarList for var in variableList])) # There would be 3 time indices if repeat indices had not been removed. # Make sure there are 2. self.assertEqual(len(ds.Time.values), 2) From 30f3c72a8e2fe736dd23a30ddf32864a0e007de9 Mon Sep 17 00:00:00 2001 From: "Phillip J. Wolfram" Date: Mon, 16 Apr 2018 15:38:49 -0600 Subject: [PATCH 45/71] Adds xml-based functionality to keep track of data --- docs/Makefile | 7 +++- docs/environment.yml | 4 ++- docs/index.rst | 5 +++ docs/observations.rst | 9 ++++++ docs/parse_table.py | 48 +++++++++++++++++++++++++++ docs/tier1a.xml | 75 +++++++++++++++++++++++++++++++++++++++++++ 6 files changed, 146 insertions(+), 2 deletions(-) create mode 100644 docs/observations.rst create mode 100755 docs/parse_table.py create mode 100644 docs/tier1a.xml diff --git a/docs/Makefile b/docs/Makefile index 1489bead0..a229e0ef3 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -12,9 +12,14 @@ BUILDDIR = _build help: @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) +clean: + rm -rf tier1a.rst + @$(SPHINXBUILD) -M clean "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + .PHONY: help Makefile # Catch-all target: route all unknown targets to Sphinx using the new # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). %: Makefile - @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) \ No newline at end of file + python parse_table.py -x tier1a.xml -r tier1a.rst + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/environment.yml b/docs/environment.yml index 509b389e9..76d97501f 100644 --- a/docs/environment.yml +++ b/docs/environment.yml @@ -21,4 +21,6 @@ dependencies: - sphinx - sphinx_rtd_theme - numpydoc - - recommonmark + - tabulate + - pip: + - recommonmark diff --git a/docs/index.rst b/docs/index.rst index eea59046d..e5d0002d8 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -14,6 +14,11 @@ Analysis for simulations produced with Model for Prediction Across Scales (MPAS) components and the Accelerated Climate Model for Energy (ACME), which used those components. +Observations +============ +.. toctree:: + + observations Documentation ============= diff --git a/docs/observations.rst b/docs/observations.rst new file mode 100644 index 000000000..86a3af9f8 --- /dev/null +++ b/docs/observations.rst @@ -0,0 +1,9 @@ +Observations +========== + +A variety of observational datasets are used within MPAS-Analysis: + +Tier1a metrics +-------------- + +.. include:: tier1a.rst diff --git a/docs/parse_table.py b/docs/parse_table.py new file mode 100755 index 000000000..690dac9a7 --- /dev/null +++ b/docs/parse_table.py @@ -0,0 +1,48 @@ +#!/usr/bin/env python +""" +This script is used to convert an xml-based table into an rst table for +python documentation and pythonic parsing. + +Phillip J. Wolfram +04/16/2018 +""" + +import xml.etree.ElementTree as ET +import tabulate +import argparse + +def build_rst_table_from_xml(xmlfile, rstfile): + + # open xml file for reading + xml = ET.parse(xmlfile) + + # open rst file for writing + rst = open(rstfile, 'w') + + # get headers and build list to write entries + headers = xml.getroot().attrib['headers'].replace(' ','').split(',') + headernames = [aname.strip() for aname in xml.getroot().attrib['headernames'].split(',')] + data = [] + for entry in xml.findall('aobs'): + line = [] + for aheader in headers: + line.append(entry.findall(aheader)[0].text.strip().replace('\n', ' ')) + data.append(line) + + rst.write(tabulate.tabulate(data, headernames, tablefmt='rst')) + + rst.close() + +if __name__ == "__main__": + parser = argparse.ArgumentParser( + description=__doc__, formatter_class=argparse.RawTextHelpFormatter) + parser.add_argument("-x", "--xml_table", dest="xml_table", + help="Path to file containing xml description of table", + metavar="FILE", required=True) + parser.add_argument("-r", "--rst_table", dest="rst_table", + help="Path to file containing rst description of table for output", + metavar="FILE", required=True) + + args = parser.parse_args() + + build_rst_table_from_xml(args.xml_table, args.rst_table) diff --git a/docs/tier1a.xml b/docs/tier1a.xml new file mode 100644 index 000000000..8094bc6e2 --- /dev/null +++ b/docs/tier1a.xml @@ -0,0 +1,75 @@ + + + + + sst Hadley-NOAA + + + ocean + + + SST global annual climatology and trend + + + Global latitude/longitude plot on ocean native grid. Annual climatologies + computed over 5-10 year periods at regular intervals throughout the run. + Time series of area-weighted (AW) global mean (1-year running average). + + + Merged Hadley Center-NOAA/OI data set from Hurrell et al. 2008 + (https://climatedataguide.ucar.edu/climate-data/merged-hadley-noaaoi-sea-surface-temperature-sea-ice-concentration-hurrell-et-al-2008) + + Update 4/11/18: emailed UCAR to ask about their release policy. + + + + 1. CESM Atm diagnostic package, 2. Gent et al. (2011, Fig.1) + + + + + + + + + + SSS NASA Aquarius + + + ocean + + + SSS global annual climatology + + + Global latitude/longitude plot on ocean native grid . Annual climatologies + computed over 5-10 year periods at regular intervals throughout the run. + + + NASA Aquarius satellite data ~4 years until Jun 2015 + (ftp://podaac-ftp.jpl.nasa.gov/allData/aquarius/L3/mapped/V4/7day_running/SCI/) + + This statement is from the NASA daac (Distributed + Active Archive Center) website: "NASA data are not copyrighted; however, + when you publish our data or results derived therefrom, we request that + you include an acknowledgment within the text of the publication and + reference list." This should apply to all NASA data sets. + + + + PHC (http://psc.apl.washington.edu/nonwp_projects/PHC/Climatology.html) + or WOA13 climatology (https://www.nodc.noaa.gov/OC5/woa13/) + + + 1. Large and Danabasoglu (2006, Fig.1), 2. Griffies et al. (2009, Fig. 8) + + + + + + + + + From eb28e36e8320cc105890583af40beb334bbcd27d Mon Sep 17 00:00:00 2001 From: "Phillip J. Wolfram" Date: Mon, 16 Apr 2018 15:39:09 -0600 Subject: [PATCH 46/71] Fixes author name and whitespace typos --- docs/authors.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/authors.rst b/docs/authors.rst index 3b67178e5..5f5711aa6 100644 --- a/docs/authors.rst +++ b/docs/authors.rst @@ -2,7 +2,7 @@ Main Authors ============ * Xylar Asay-Davis * Milena Veniziani -* Philip Wolfram +* Phillip J. Wolfram Contributors ============ @@ -16,4 +16,4 @@ Contributors * Jeremy Fyke For a list of all the contributions: -https://github.com/MPAS-Dev/MPAS-Analysis/graphs/contributors \ No newline at end of file +https://github.com/MPAS-Dev/MPAS-Analysis/graphs/contributors From eec997249dec941bf7438a46e342042b8efd729f Mon Sep 17 00:00:00 2001 From: "Phillip J. Wolfram" Date: Tue, 17 Apr 2018 08:51:05 -0600 Subject: [PATCH 47/71] Supports Markdown urls in xml --- docs/Makefile | 4 ++-- docs/{tier1a.xml => observations.xml} | 10 ++++------ docs/parse_table.py | 24 +++++++++++++++++++++++- 3 files changed, 29 insertions(+), 9 deletions(-) rename docs/{tier1a.xml => observations.xml} (83%) diff --git a/docs/Makefile b/docs/Makefile index a229e0ef3..eef84e754 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -13,7 +13,7 @@ help: @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) clean: - rm -rf tier1a.rst + rm -rf observations.rst @$(SPHINXBUILD) -M clean "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) .PHONY: help Makefile @@ -21,5 +21,5 @@ clean: # Catch-all target: route all unknown targets to Sphinx using the new # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). %: Makefile - python parse_table.py -x tier1a.xml -r tier1a.rst + python parse_table.py -x observations.xml -r observations.rst @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/tier1a.xml b/docs/observations.xml similarity index 83% rename from docs/tier1a.xml rename to docs/observations.xml index 8094bc6e2..6021b50d7 100644 --- a/docs/tier1a.xml +++ b/docs/observations.xml @@ -18,8 +18,7 @@ Time series of area-weighted (AW) global mean (1-year running average). - Merged Hadley Center-NOAA/OI data set from Hurrell et al. 2008 - (https://climatedataguide.ucar.edu/climate-data/merged-hadley-noaaoi-sea-surface-temperature-sea-ice-concentration-hurrell-et-al-2008) + [Merged Hadley Center-NOAA/OI data set from Hurrell et al. 2008](https://climatedataguide.ucar.edu/climate-data/merged-hadley-noaaoi-sea-surface-temperature-sea-ice-concentration-hurrell-et-al-2008) Update 4/11/18: emailed UCAR to ask about their release policy. @@ -48,8 +47,7 @@ computed over 5-10 year periods at regular intervals throughout the run. - NASA Aquarius satellite data ~4 years until Jun 2015 - (ftp://podaac-ftp.jpl.nasa.gov/allData/aquarius/L3/mapped/V4/7day_running/SCI/) + [NASA Aquarius satellite data ~4 years until Jun 2015](ftp://podaac-ftp.jpl.nasa.gov/allData/aquarius/L3/mapped/V4/7day_running/SCI/) This statement is from the NASA daac (Distributed Active Archive Center) website: "NASA data are not copyrighted; however, @@ -59,8 +57,8 @@ - PHC (http://psc.apl.washington.edu/nonwp_projects/PHC/Climatology.html) - or WOA13 climatology (https://www.nodc.noaa.gov/OC5/woa13/) + [PHC](http://psc.apl.washington.edu/nonwp_projects/PHC/Climatology.html) + or [WOA13 climatology](https://www.nodc.noaa.gov/OC5/woa13/). 1. Large and Danabasoglu (2006, Fig.1), 2. Griffies et al. (2009, Fig. 8) diff --git a/docs/parse_table.py b/docs/parse_table.py index 690dac9a7..817f13658 100755 --- a/docs/parse_table.py +++ b/docs/parse_table.py @@ -10,6 +10,24 @@ import xml.etree.ElementTree as ET import tabulate import argparse +import re + +def markdown_links(data, footer): + urlscmd = re.findall(r"\[.*?\]\(.*?\)", data) + urls = re.findall(r"\[.*?\]\((.*?)\)", data) + linknames = re.findall(r"\[(.*?)\]\(.*?\)", data) + + for alinkname, aurl, aurlscmd in zip(linknames, urls, urlscmd): + data = data.replace(aurlscmd, '`' + alinkname +'`_') + footer += ".. _`" + alinkname + "`: " + aurl + "\n" + + return data, footer + +def cleanup(linedata, footer): + cleanups = [markdown_links] + for acleanup in cleanups: + cleandata, footer = acleanup(linedata, footer) + return cleandata, footer def build_rst_table_from_xml(xmlfile, rstfile): @@ -23,13 +41,17 @@ def build_rst_table_from_xml(xmlfile, rstfile): headers = xml.getroot().attrib['headers'].replace(' ','').split(',') headernames = [aname.strip() for aname in xml.getroot().attrib['headernames'].split(',')] data = [] + footer = '\n' for entry in xml.findall('aobs'): line = [] for aheader in headers: - line.append(entry.findall(aheader)[0].text.strip().replace('\n', ' ')) + linedata = entry.findall(aheader)[0].text.strip().replace('\n', ' ') + linedata, footer = cleanup(linedata, footer) + line.append(linedata) data.append(line) rst.write(tabulate.tabulate(data, headernames, tablefmt='rst')) + rst.write(footer) rst.close() From d83f13ef0161cf6d264618c1194d03b429afa64c Mon Sep 17 00:00:00 2001 From: "Phillip J. Wolfram" Date: Tue, 17 Apr 2018 10:41:37 -0600 Subject: [PATCH 48/71] Adds list capability and component filtering --- docs/Makefile | 6 +- docs/environment.yml | 2 +- docs/observations.rst | 17 ++++- docs/observations.xml | 73 ------------------ docs/observationstable.xml | 153 +++++++++++++++++++++++++++++++++++++ docs/parse_table.py | 24 ++++-- 6 files changed, 189 insertions(+), 86 deletions(-) delete mode 100644 docs/observations.xml create mode 100644 docs/observationstable.xml diff --git a/docs/Makefile b/docs/Makefile index eef84e754..299240787 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -13,7 +13,7 @@ help: @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) clean: - rm -rf observations.rst + rm -rf *observationstable.rst @$(SPHINXBUILD) -M clean "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) .PHONY: help Makefile @@ -21,5 +21,7 @@ clean: # Catch-all target: route all unknown targets to Sphinx using the new # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). %: Makefile - python parse_table.py -x observations.xml -r observations.rst + python parse_table.py -x observationstable.xml -r landicobservationstable.rst -c landice + python parse_table.py -x observationstable.xml -r oceanobservationstable.rst -c ocean + python parse_table.py -x observationstable.xml -r seaicobservationstable.rst -c seaice @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/environment.yml b/docs/environment.yml index 76d97501f..d67f332fb 100644 --- a/docs/environment.yml +++ b/docs/environment.yml @@ -21,6 +21,6 @@ dependencies: - sphinx - sphinx_rtd_theme - numpydoc - - tabulate + - tabulate >= 0.8.2 - pip: - recommonmark diff --git a/docs/observations.rst b/docs/observations.rst index 86a3af9f8..487135fbc 100644 --- a/docs/observations.rst +++ b/docs/observations.rst @@ -1,9 +1,18 @@ Observations -========== +============ A variety of observational datasets are used within MPAS-Analysis: -Tier1a metrics --------------- +Land Ice metrics +---------------- +.. include:: landicobservationstable.rst + +Ocean metrics +------------- + +.. include:: oceanobservationstable.rst + +Sea Ice metrics +--------------- +.. include:: seaicobservationstable.rst -.. include:: tier1a.rst diff --git a/docs/observations.xml b/docs/observations.xml deleted file mode 100644 index 6021b50d7..000000000 --- a/docs/observations.xml +++ /dev/null @@ -1,73 +0,0 @@ - - - - - sst Hadley-NOAA - - - ocean - - - SST global annual climatology and trend - - - Global latitude/longitude plot on ocean native grid. Annual climatologies - computed over 5-10 year periods at regular intervals throughout the run. - Time series of area-weighted (AW) global mean (1-year running average). - - - [Merged Hadley Center-NOAA/OI data set from Hurrell et al. 2008](https://climatedataguide.ucar.edu/climate-data/merged-hadley-noaaoi-sea-surface-temperature-sea-ice-concentration-hurrell-et-al-2008) - - Update 4/11/18: emailed UCAR to ask about their release policy. - - - - 1. CESM Atm diagnostic package, 2. Gent et al. (2011, Fig.1) - - - - - - - - - - SSS NASA Aquarius - - - ocean - - - SSS global annual climatology - - - Global latitude/longitude plot on ocean native grid . Annual climatologies - computed over 5-10 year periods at regular intervals throughout the run. - - - [NASA Aquarius satellite data ~4 years until Jun 2015](ftp://podaac-ftp.jpl.nasa.gov/allData/aquarius/L3/mapped/V4/7day_running/SCI/) - - This statement is from the NASA daac (Distributed - Active Archive Center) website: "NASA data are not copyrighted; however, - when you publish our data or results derived therefrom, we request that - you include an acknowledgment within the text of the publication and - reference list." This should apply to all NASA data sets. - - - - [PHC](http://psc.apl.washington.edu/nonwp_projects/PHC/Climatology.html) - or [WOA13 climatology](https://www.nodc.noaa.gov/OC5/woa13/). - - - 1. Large and Danabasoglu (2006, Fig.1), 2. Griffies et al. (2009, Fig. 8) - - - - - - - - - diff --git a/docs/observationstable.xml b/docs/observationstable.xml new file mode 100644 index 000000000..f222a7153 --- /dev/null +++ b/docs/observationstable.xml @@ -0,0 +1,153 @@ + + + + + + sst Hadley-NOAA + + + ocean + + + SST global annual climatology and trend + + + - Global latitude/longitude plot on ocean native grid. Annual climatologies computed over 5-10 year periods at regular intervals throughout the run. + - Time series of area-weighted (AW) global mean (1-year running average). + + + [Merged Hadley Center-NOAA/OI data set from Hurrell et al. 2008](https://climatedataguide.ucar.edu/climate-data/merged-hadley-noaaoi-sea-surface-temperature-sea-ice-concentration-hurrell-et-al-2008) + + Update 4/11/18: emailed UCAR to ask about their release policy. + + + + - CESM Atm diagnostic package + - Gent et al. (2011, Fig.1) + + + + + + + + + + SSS NASA Aquarius + + + ocean + + + SSS global annual climatology + + + - Global latitude/longitude plot on ocean native grid . Annual climatologies computed over 5-10 year periods at regular intervals throughout the run. + + + [NASA Aquarius satellite data ~4 years until Jun 2015](ftp://podaac-ftp.jpl.nasa.gov/allData/aquarius/L3/mapped/V4/7day_running/SCI/) + + This statement is from the NASA daac (Distributed + Active Archive Center) website: "NASA data are not copyrighted; however, + when you publish our data or results derived therefrom, we request that + you include an acknowledgment within the text of the publication and + reference list." This should apply to all NASA data sets. + + + + [PHC](http://psc.apl.washington.edu/nonwp_projects/PHC/Climatology.html) + or [WOA13 climatology](https://www.nodc.noaa.gov/OC5/woa13/). + + + - Large and Danabasoglu (2006, Fig.1) + - Griffies et al. (2009, Fig. 8) + + + + + + + + + + + Ice area/extent annual climatology, and annual and seasonal trends + + + seaice + + + Sea ice concentration + + + - Arctic and Antarctic seasonal and annual climatologies (maps) of ice area and extent. Annual climatologies computed over 5-10 year periods at regular intervals throughout the run. + - Daily, monthly and 1-year average time series of area-weighted ice area and extent. + + + - [Ice concentration: SSM/I, NASATeam algorithm(both NH and SH)](http://nsidc.org/data/NSIDC-0051) + - [Ice concentration: SSM/I, Bootstrap algorithm (both NH and SH)](http://nsidc.org/data/NSIDC-0079) + - [Ice area time series: SSM/I derived (both NH and SH)](http://neptune.gsfc.nasa.gov/csb/index.php?section=59) + + Same as all NASA data. + + + + - [Antarctic ship-based data](http://aspect.antarctica.gov.au/data) + - [Ice type, and drift](http://marine.copernicus.eu/services-portfolio/access-to-products/?option=com_csw&view=details&product_id=SEAICE_GLO_SEAICE_L4_NRT_OBSERVATIONS_011_001) + - [MANY data sets available for both ocean and sea ice, both global and regional](high-reshttp://marine.copernicus.edu) + + + - CESM CICE diagnostics + - Ivanova et al. (2012) + - Worby et al. (2008) + + + See CESM sea ice diagnostic package + + + + + + + + + Present-day ice sheet area and volume (scalar) + + + landice + + + Land ice area / volume + + + - Difference between modeled and observed values. + + + Greenland ice thickness at bed topography at 1 km posting + - [Bedmap2 paper](http://www.the-cryosphere.net/7/375/2013/), [Bedmap2 data](https://www.bas.ac.uk/project/bedmap-2/) + - [R-Topo2 paper](http://www.earth-syst-sci-data-discuss.net/essd-2016-3/), [R-Topo2 data](https://www.pangaea.de/PHP/hs.php?s=Maps&d=RTopo-2.0&ID=856844) + Antarctic ice thickness and bed topography at 1 km posting + + Same as all NASA data. + + + + - [Antarctic ship-based data](http://aspect.antarctica.gov.au/data) + - [Ice type, and drift](http://marine.copernicus.eu/services-portfolio/access-to-products/?option=com_csw&view=details&product_id=SEAICE_GLO_SEAICE_L4_NRT_OBSERVATIONS_011_001) + - [MANY data sets available for both ocean and sea ice, both global and regional](high-reshttp://marine.copernicus.edu) + + + - Bamber et al. (2013) + - Fretwell et al. (2013) + + + validate initial conditions + + + + + + + diff --git a/docs/parse_table.py b/docs/parse_table.py index 817f13658..e6a7988ee 100755 --- a/docs/parse_table.py +++ b/docs/parse_table.py @@ -23,13 +23,20 @@ def markdown_links(data, footer): return data, footer +def spurious_newline_whitespace(data, _): + whitespace = re.findall('\n\s*', data) + if len(whitespace) > 0: + astr = min(whitespace) + data = data.replace(astr, "\n") + return data, _ + def cleanup(linedata, footer): - cleanups = [markdown_links] + cleanups = [spurious_newline_whitespace, markdown_links] for acleanup in cleanups: - cleandata, footer = acleanup(linedata, footer) - return cleandata, footer + linedata, footer = acleanup(linedata, footer) + return linedata, footer -def build_rst_table_from_xml(xmlfile, rstfile): +def build_rst_table_from_xml(xmlfile, rstfile, component): # open xml file for reading xml = ET.parse(xmlfile) @@ -43,9 +50,11 @@ def build_rst_table_from_xml(xmlfile, rstfile): data = [] footer = '\n' for entry in xml.findall('aobs'): + if component != 'all' and entry.findall('component')[0].text.strip() != component: + continue line = [] for aheader in headers: - linedata = entry.findall(aheader)[0].text.strip().replace('\n', ' ') + linedata = entry.findall(aheader)[0].text.strip() linedata, footer = cleanup(linedata, footer) line.append(linedata) data.append(line) @@ -64,7 +73,10 @@ def build_rst_table_from_xml(xmlfile, rstfile): parser.add_argument("-r", "--rst_table", dest="rst_table", help="Path to file containing rst description of table for output", metavar="FILE", required=True) + parser.add_argument("-c", "--component", dest="component", + help="Component for parsing of table, 'landice', 'ocean', " + "'seaice', or 'all'", metavar="STRING", default="all") args = parser.parse_args() - build_rst_table_from_xml(args.xml_table, args.rst_table) + build_rst_table_from_xml(args.xml_table, args.rst_table, args.component) From c1aed90d665fd136a6af863d4078a0ff95415480 Mon Sep 17 00:00:00 2001 From: "Phillip J. Wolfram" Date: Tue, 17 Apr 2018 10:44:26 -0600 Subject: [PATCH 49/71] Moves observations xml to python code location --- docs/Makefile | 6 +++--- {docs => mpas_analysis/obs}/observationstable.xml | 0 2 files changed, 3 insertions(+), 3 deletions(-) rename {docs => mpas_analysis/obs}/observationstable.xml (100%) diff --git a/docs/Makefile b/docs/Makefile index 299240787..b417471f9 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -21,7 +21,7 @@ clean: # Catch-all target: route all unknown targets to Sphinx using the new # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). %: Makefile - python parse_table.py -x observationstable.xml -r landicobservationstable.rst -c landice - python parse_table.py -x observationstable.xml -r oceanobservationstable.rst -c ocean - python parse_table.py -x observationstable.xml -r seaicobservationstable.rst -c seaice + python parse_table.py -x ../mpas_analysis/obs/observationstable.xml -r landicobservationstable.rst -c landice + python parse_table.py -x ../mpas_analysis/obs/observationstable.xml -r oceanobservationstable.rst -c ocean + python parse_table.py -x ../mpas_analysis/obs/observationstable.xml -r seaicobservationstable.rst -c seaice @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/observationstable.xml b/mpas_analysis/obs/observationstable.xml similarity index 100% rename from docs/observationstable.xml rename to mpas_analysis/obs/observationstable.xml From 83ffba6317a8f7bc37f06a903c8f79d38efa474b Mon Sep 17 00:00:00 2001 From: "Phillip J. Wolfram" Date: Tue, 17 Apr 2018 10:48:49 -0600 Subject: [PATCH 50/71] Fixes aobs to observations --- docs/parse_table.py | 2 +- mpas_analysis/obs/observationstable.xml | 16 ++++++++-------- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/docs/parse_table.py b/docs/parse_table.py index e6a7988ee..a609ff3c0 100755 --- a/docs/parse_table.py +++ b/docs/parse_table.py @@ -49,7 +49,7 @@ def build_rst_table_from_xml(xmlfile, rstfile, component): headernames = [aname.strip() for aname in xml.getroot().attrib['headernames'].split(',')] data = [] footer = '\n' - for entry in xml.findall('aobs'): + for entry in xml.findall('observation'): if component != 'all' and entry.findall('component')[0].text.strip() != component: continue line = [] diff --git a/mpas_analysis/obs/observationstable.xml b/mpas_analysis/obs/observationstable.xml index f222a7153..bd202df5d 100644 --- a/mpas_analysis/obs/observationstable.xml +++ b/mpas_analysis/obs/observationstable.xml @@ -3,7 +3,7 @@ headers="shortdesc, obsDataSet, references" headernames="Dataset, Observational Dataset, References"> - + sst Hadley-NOAA @@ -32,8 +32,8 @@ - - + + SSS NASA Aquarius @@ -69,9 +69,9 @@ - + - + Ice area/extent annual climatology, and annual and seasonal trends @@ -109,9 +109,9 @@ - + - + Present-day ice sheet area and volume (scalar) @@ -148,6 +148,6 @@ - + From 8e593dee3280c73a132f0f0354d6038ca89e3e82 Mon Sep 17 00:00:00 2001 From: "Phillip J. Wolfram" Date: Tue, 17 Apr 2018 10:51:07 -0600 Subject: [PATCH 51/71] Adds support for MD url tags on sep lines [title](http://example.com) and [title] (http://example.com) both now work --- docs/parse_table.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/parse_table.py b/docs/parse_table.py index a609ff3c0..3eff90416 100755 --- a/docs/parse_table.py +++ b/docs/parse_table.py @@ -13,9 +13,9 @@ import re def markdown_links(data, footer): - urlscmd = re.findall(r"\[.*?\]\(.*?\)", data) - urls = re.findall(r"\[.*?\]\((.*?)\)", data) - linknames = re.findall(r"\[(.*?)\]\(.*?\)", data) + urlscmd = re.findall(r"\[.*?\]\n*\(.*?\)", data) + urls = re.findall(r"\[.*?\]\n*\((.*?)\)", data) + linknames = re.findall(r"\[(.*?)\]\n*\(.*?\)", data) for alinkname, aurl, aurlscmd in zip(linknames, urls, urlscmd): data = data.replace(aurlscmd, '`' + alinkname +'`_') From 55650c770bfc8adf3f8e9ba7379f34de0903aa84 Mon Sep 17 00:00:00 2001 From: "Phillip J. Wolfram" Date: Tue, 17 Apr 2018 10:58:15 -0600 Subject: [PATCH 52/71] PEP8 cleanup --- docs/parse_table.py | 26 ++++++++++++++++++-------- 1 file changed, 18 insertions(+), 8 deletions(-) diff --git a/docs/parse_table.py b/docs/parse_table.py index 3eff90416..105edb91a 100755 --- a/docs/parse_table.py +++ b/docs/parse_table.py @@ -12,17 +12,19 @@ import argparse import re + def markdown_links(data, footer): urlscmd = re.findall(r"\[.*?\]\n*\(.*?\)", data) urls = re.findall(r"\[.*?\]\n*\((.*?)\)", data) linknames = re.findall(r"\[(.*?)\]\n*\(.*?\)", data) for alinkname, aurl, aurlscmd in zip(linknames, urls, urlscmd): - data = data.replace(aurlscmd, '`' + alinkname +'`_') + data = data.replace(aurlscmd, '`' + alinkname + '`_') footer += ".. _`" + alinkname + "`: " + aurl + "\n" return data, footer + def spurious_newline_whitespace(data, _): whitespace = re.findall('\n\s*', data) if len(whitespace) > 0: @@ -30,12 +32,14 @@ def spurious_newline_whitespace(data, _): data = data.replace(astr, "\n") return data, _ + def cleanup(linedata, footer): cleanups = [spurious_newline_whitespace, markdown_links] for acleanup in cleanups: linedata, footer = acleanup(linedata, footer) return linedata, footer + def build_rst_table_from_xml(xmlfile, rstfile, component): # open xml file for reading @@ -45,12 +49,14 @@ def build_rst_table_from_xml(xmlfile, rstfile, component): rst = open(rstfile, 'w') # get headers and build list to write entries - headers = xml.getroot().attrib['headers'].replace(' ','').split(',') - headernames = [aname.strip() for aname in xml.getroot().attrib['headernames'].split(',')] + headers = xml.getroot().attrib['headers'].replace(' ', '').split(',') + headernames = [aname.strip() for aname in + xml.getroot().attrib['headernames'].split(',')] data = [] footer = '\n' for entry in xml.findall('observation'): - if component != 'all' and entry.findall('component')[0].text.strip() != component: + if (component != 'all' and + entry.findall('component')[0].text.strip() != component): continue line = [] for aheader in headers: @@ -64,18 +70,22 @@ def build_rst_table_from_xml(xmlfile, rstfile, component): rst.close() + if __name__ == "__main__": parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.RawTextHelpFormatter) parser.add_argument("-x", "--xml_table", dest="xml_table", - help="Path to file containing xml description of table", + help="Path to file containing " + "xml description of table", metavar="FILE", required=True) parser.add_argument("-r", "--rst_table", dest="rst_table", - help="Path to file containing rst description of table for output", + help="Path to file containing rst description " + "of table for output", metavar="FILE", required=True) parser.add_argument("-c", "--component", dest="component", - help="Component for parsing of table, 'landice', 'ocean', " - "'seaice', or 'all'", metavar="STRING", default="all") + help="Component for parsing of table: " + "'landice', 'ocean', 'seaice', or 'all'", + metavar="STRING", default="all") args = parser.parse_args() From 7c3bb1d2e31e806c84ada80b44006348277e4cee Mon Sep 17 00:00:00 2001 From: "Phillip J. Wolfram" Date: Tue, 17 Apr 2018 11:00:10 -0600 Subject: [PATCH 53/71] Cleans up order of observations in docs --- docs/index.rst | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/docs/index.rst b/docs/index.rst index e5d0002d8..1df535021 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -14,12 +14,6 @@ Analysis for simulations produced with Model for Prediction Across Scales (MPAS) components and the Accelerated Climate Model for Energy (ACME), which used those components. -Observations -============ -.. toctree:: - - observations - Documentation ============= .. toctree:: @@ -38,6 +32,11 @@ MPAS Components and E3SM mpasseaice e3sm +Observations +============ +.. toctree:: + + observations Indices and tables ================== From 31dfbe1478efc681e088ae2c786029d44509fa04 Mon Sep 17 00:00:00 2001 From: "Phillip J. Wolfram" Date: Tue, 17 Apr 2018 11:18:15 -0600 Subject: [PATCH 54/71] Fixes line issue warning building doc --- docs/parse_table.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/parse_table.py b/docs/parse_table.py index 105edb91a..c44ab3c30 100755 --- a/docs/parse_table.py +++ b/docs/parse_table.py @@ -53,7 +53,7 @@ def build_rst_table_from_xml(xmlfile, rstfile, component): headernames = [aname.strip() for aname in xml.getroot().attrib['headernames'].split(',')] data = [] - footer = '\n' + footer = '' for entry in xml.findall('observation'): if (component != 'all' and entry.findall('component')[0].text.strip() != component): @@ -65,8 +65,10 @@ def build_rst_table_from_xml(xmlfile, rstfile, component): line.append(linedata) data.append(line) - rst.write(tabulate.tabulate(data, headernames, tablefmt='rst')) + rst.writelines(tabulate.tabulate(data, headernames, tablefmt='rst') + '\n') + rst.write('\n') rst.write(footer) + rst.write('\n') rst.close() From d46209302a7f20d30d37f0b1c77814bfa651ff6e Mon Sep 17 00:00:00 2001 From: "Phillip J. Wolfram" Date: Tue, 17 Apr 2018 11:49:38 -0600 Subject: [PATCH 55/71] White space fix --- docs/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/environment.yml b/docs/environment.yml index d67f332fb..8d5b05f2c 100644 --- a/docs/environment.yml +++ b/docs/environment.yml @@ -21,6 +21,6 @@ dependencies: - sphinx - sphinx_rtd_theme - numpydoc - - tabulate >= 0.8.2 + - tabulate >= 0.8.2 - pip: - recommonmark From c4f1d21a38b0d8cb6ac68c5aee61504c84a5ee11 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Thu, 5 Apr 2018 19:23:53 +0200 Subject: [PATCH 56/71] Rename cice to seaice Everywhere except where used by ncclimo. Use old input and streams file names in config files for existing E3SM. --- README.md | 17 ++++++++++++----- ....20170926.FCT2.A_WCYCL1850S.ne30_oECv3.anvil | 7 +++++++ ...fault.GMPAS-IAF.T62_oRRS30to10v3wLI.cori-knl | 7 +++++++ .../config.20170807.beta1.G_oQU240.edison | 7 +++++++ ...0171102.beta3rc02_1850.ne30_oECv3_ICG.edison | 7 +++++++ ...ow_res_ice_shelves_1696_JWolfe_layout_Edison | 7 +++++++ ...onfig.20170207.MPAS-SeaIce.QU60km_polar.wolf | 7 +++++++ configs/lanl/config.MatchBoth_orig | 7 +++++++ ...313.beta1.A_WCYCL1850S.ne30_oECv3_ICG.edison | 7 +++++++ configs/olcf/config.GMPAS-IAF_oRRS18to6v3.titan | 7 +++++++ ...t.GMPAS-IAF.T62_oEC60to30v3wLI.60layer.theta | 7 +++++++ docs/mpasseaice.rst | 11 ++++++----- mpas_analysis/config.default | 4 ++-- 13 files changed, 90 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index b3f208287..f3982d569 100644 --- a/README.md +++ b/README.md @@ -103,12 +103,19 @@ for more details. * `mpaso.rst.0002-01-01_00000.nc` (or any other mpas-o restart file) * `streams.ocean` * `mpas-o_in` - * mpas-cice files: - * `mpascice.hist.am.timeSeriesStatsMonthly.*.nc` - * `mpascice.rst.0002-01-01_00000.nc` (or any other mpas-cice restart + * mpas-seaice files: + * `mpasseaice.hist.am.timeSeriesStatsMonthly.*.nc` + * `mpasseaice.rst.0002-01-01_00000.nc` (or any other mpas-seaice restart file) - * `streams.cice` - * `mpas-cice_in` + * `streams.seaice` + * `mpas-seaice_in` + +Note: for older runs, mpas-seaice files will be named: + * `mpascice.hist.am.timeSeriesStatsMonthly.*.nc` + * `mpascice.rst.0002-01-01_00000.nc` + * `streams.cice` + * `mpas-cice_in` + ## Purge Old Analysis diff --git a/configs/anvil/config.20170926.FCT2.A_WCYCL1850S.ne30_oECv3.anvil b/configs/anvil/config.20170926.FCT2.A_WCYCL1850S.ne30_oECv3.anvil index c96b7444a..035d50c55 100644 --- a/configs/anvil/config.20170926.FCT2.A_WCYCL1850S.ne30_oECv3.anvil +++ b/configs/anvil/config.20170926.FCT2.A_WCYCL1850S.ne30_oECv3.anvil @@ -32,6 +32,13 @@ mpasMeshName = oEC60to30v3 # placed in the output mappingSubdirectory mappingDirectory = /lcrc/group/acme/mpas_analysis/mapping +# names of namelist and streams files, either a path relative to baseDirectory +# or an absolute path. +oceanNamelistFileName = mpas-o_in +oceanStreamsFileName = streams.ocean +seaIceNamelistFileName = mpas-cice_in +seaIceStreamsFileName = streams.cice + [output] ## options related to writing out plots, intermediate cached data sets, logs, ## etc. diff --git a/configs/cori/config.20171201.default.GMPAS-IAF.T62_oRRS30to10v3wLI.cori-knl b/configs/cori/config.20171201.default.GMPAS-IAF.T62_oRRS30to10v3wLI.cori-knl index d7e31c660..e32a02ef0 100644 --- a/configs/cori/config.20171201.default.GMPAS-IAF.T62_oRRS30to10v3wLI.cori-knl +++ b/configs/cori/config.20171201.default.GMPAS-IAF.T62_oRRS30to10v3wLI.cori-knl @@ -43,6 +43,13 @@ mpasMeshName = oRRS30to10v3wLI # placed in the output mappingSubdirectory mappingDirectory = /global/project/projectdirs/acme/mpas_analysis/mapping +# names of namelist and streams files, either a path relative to baseDirectory +# or an absolute path. +oceanNamelistFileName = mpas-o_in +oceanStreamsFileName = streams.ocean +seaIceNamelistFileName = mpas-cice_in +seaIceStreamsFileName = streams.cice + [output] ## options related to writing out plots, intermediate cached data sets, logs, ## etc. diff --git a/configs/edison/config.20170807.beta1.G_oQU240.edison b/configs/edison/config.20170807.beta1.G_oQU240.edison index 15176e615..a5ebc0465 100644 --- a/configs/edison/config.20170807.beta1.G_oQU240.edison +++ b/configs/edison/config.20170807.beta1.G_oQU240.edison @@ -32,6 +32,13 @@ mpasMeshName = oQU240 # placed in the output mappingSubdirectory # mappingDirectory = /dir/for/mapping/files +# names of namelist and streams files, either a path relative to baseDirectory +# or an absolute path. +oceanNamelistFileName = mpas-o_in +oceanStreamsFileName = streams.ocean +seaIceNamelistFileName = mpas-cice_in +seaIceStreamsFileName = streams.cice + [output] ## options related to writing out plots, intermediate cached data sets, logs, ## etc. diff --git a/configs/edison/config.20171102.beta3rc02_1850.ne30_oECv3_ICG.edison b/configs/edison/config.20171102.beta3rc02_1850.ne30_oECv3_ICG.edison index c98f76515..c4d7fb149 100644 --- a/configs/edison/config.20171102.beta3rc02_1850.ne30_oECv3_ICG.edison +++ b/configs/edison/config.20171102.beta3rc02_1850.ne30_oECv3_ICG.edison @@ -33,6 +33,13 @@ mpasMeshName = oEC60to30v3 # placed in the output mappingSubdirectory mappingDirectory = /global/project/projectdirs/acme/mpas_analysis/mapping +# names of namelist and streams files, either a path relative to baseDirectory +# or an absolute path. +oceanNamelistFileName = mpas-o_in +oceanStreamsFileName = streams.ocean +seaIceNamelistFileName = mpas-cice_in +seaIceStreamsFileName = streams.cice + [output] ## options related to writing out plots, intermediate cached data sets, logs, ## etc. diff --git a/configs/edison/config.B_low_res_ice_shelves_1696_JWolfe_layout_Edison b/configs/edison/config.B_low_res_ice_shelves_1696_JWolfe_layout_Edison index 8a76e16bd..3cb7742d2 100644 --- a/configs/edison/config.B_low_res_ice_shelves_1696_JWolfe_layout_Edison +++ b/configs/edison/config.B_low_res_ice_shelves_1696_JWolfe_layout_Edison @@ -43,6 +43,13 @@ mpasMeshName = oEC60to30v3wLI # placed in the output mappingSubdirectory mappingDirectory = /global/project/projectdirs/acme/mpas_analysis/mapping +# names of namelist and streams files, either a path relative to baseDirectory +# or an absolute path. +oceanNamelistFileName = mpas-o_in +oceanStreamsFileName = streams.ocean +seaIceNamelistFileName = mpas-cice_in +seaIceStreamsFileName = streams.cice + [output] ## options related to writing out plots, intermediate cached data sets, logs, ## etc. diff --git a/configs/lanl/config.20170207.MPAS-SeaIce.QU60km_polar.wolf b/configs/lanl/config.20170207.MPAS-SeaIce.QU60km_polar.wolf index 51cf6628f..d019a4c00 100644 --- a/configs/lanl/config.20170207.MPAS-SeaIce.QU60km_polar.wolf +++ b/configs/lanl/config.20170207.MPAS-SeaIce.QU60km_polar.wolf @@ -32,6 +32,13 @@ mpasMeshName = QU60 # placed in the output mappingSubdirectory # mappingDirectory = /dir/for/mapping/files +# names of namelist and streams files, either a path relative to baseDirectory +# or an absolute path. +oceanNamelistFileName = mpas-o_in +oceanStreamsFileName = streams.ocean +seaIceNamelistFileName = mpas-cice_in +seaIceStreamsFileName = streams.cice + [output] ## options related to writing out plots, intermediate cached data sets, logs, ## etc. diff --git a/configs/lanl/config.MatchBoth_orig b/configs/lanl/config.MatchBoth_orig index 2c04fc127..c0d36a3ee 100644 --- a/configs/lanl/config.MatchBoth_orig +++ b/configs/lanl/config.MatchBoth_orig @@ -32,6 +32,13 @@ mpasMeshName = oEC60to30v3 # placed in the output mappingSubdirectory mappingDirectory = /turquoise/usr/projects/climate/SHARED_CLIMATE/mpas_analysis/mapping/ +# names of namelist and streams files, either a path relative to baseDirectory +# or an absolute path. +oceanNamelistFileName = mpas-o_in +oceanStreamsFileName = streams.ocean +seaIceNamelistFileName = mpas-cice_in +seaIceStreamsFileName = streams.cice + [output] ## options related to writing out plots, intermediate cached data sets, logs, ## etc. diff --git a/configs/olcf/config.20170313.beta1.A_WCYCL1850S.ne30_oECv3_ICG.edison b/configs/olcf/config.20170313.beta1.A_WCYCL1850S.ne30_oECv3_ICG.edison index c4b567970..3d93c3a80 100644 --- a/configs/olcf/config.20170313.beta1.A_WCYCL1850S.ne30_oECv3_ICG.edison +++ b/configs/olcf/config.20170313.beta1.A_WCYCL1850S.ne30_oECv3_ICG.edison @@ -32,6 +32,13 @@ mpasMeshName = oEC60to30v3 # placed in the output mappingSubdirectory mappingDirectory = /lustre/atlas/proj-shared/cli115/mpas_analysis/mapping/ +# names of namelist and streams files, either a path relative to baseDirectory +# or an absolute path. +oceanNamelistFileName = mpas-o_in +oceanStreamsFileName = streams.ocean +seaIceNamelistFileName = mpas-cice_in +seaIceStreamsFileName = streams.cice + [output] ## options related to writing out plots, intermediate cached data sets, logs, ## etc. diff --git a/configs/olcf/config.GMPAS-IAF_oRRS18to6v3.titan b/configs/olcf/config.GMPAS-IAF_oRRS18to6v3.titan index b38ae1983..33585854f 100644 --- a/configs/olcf/config.GMPAS-IAF_oRRS18to6v3.titan +++ b/configs/olcf/config.GMPAS-IAF_oRRS18to6v3.titan @@ -32,6 +32,13 @@ mpasMeshName = oRRS18to6v3 # placed in the output mappingSubdirectory mappingDirectory = /lustre/atlas/proj-shared/cli115/mpas_analysis/mapping +# names of namelist and streams files, either a path relative to baseDirectory +# or an absolute path. +oceanNamelistFileName = mpas-o_in +oceanStreamsFileName = streams.ocean +seaIceNamelistFileName = mpas-cice_in +seaIceStreamsFileName = streams.cice + [output] ## options related to writing out plots, intermediate cached data sets, logs, ## etc. diff --git a/configs/theta/config.20171031.tenYearTest.GMPAS-IAF.T62_oEC60to30v3wLI.60layer.theta b/configs/theta/config.20171031.tenYearTest.GMPAS-IAF.T62_oEC60to30v3wLI.60layer.theta index 2d87a8b84..190e7c374 100644 --- a/configs/theta/config.20171031.tenYearTest.GMPAS-IAF.T62_oEC60to30v3wLI.60layer.theta +++ b/configs/theta/config.20171031.tenYearTest.GMPAS-IAF.T62_oEC60to30v3wLI.60layer.theta @@ -45,6 +45,13 @@ mpasMeshName = oEC60to30v3wLI # placed in the output mappingSubdirectory mappingDirectory = /projects/OceanClimate/mpas-analysis_data/mpas_analysis/mapping +# names of namelist and streams files, either a path relative to baseDirectory +# or an absolute path. +oceanNamelistFileName = mpas-o_in +oceanStreamsFileName = streams.ocean +seaIceNamelistFileName = mpas-cice_in +seaIceStreamsFileName = streams.cice + [output] ## options related to writing out plots, intermediate cached data sets, logs, ## etc. diff --git a/docs/mpasseaice.rst b/docs/mpasseaice.rst index 78060d37b..248209ad7 100644 --- a/docs/mpasseaice.rst +++ b/docs/mpasseaice.rst @@ -14,7 +14,8 @@ In order to support all sea=ice analysis tasks from MPAS-Analysis, certain simulation, need to be enabled. The following is a list of suggested values for namelist options, typically -found in ``namelist.cice`` or ``mpas-cice_in``:: +found in ``namelist.seaice`` or ``mpas-seaice_in`` (or ``mpas-cice_in`` in +older E3SM runs):: config_AM_timeSeriesStatsMonthly_enable = .true. @@ -24,13 +25,13 @@ typically longer before most analysis is useful:: config_run_duration = '0002-00-00_00:00:00' Several streams must be defined in the streams file, typically -``streams.cice``, (even if they will not be written out -- -``output_interval=="none"``):: +``streams.seaice`` or ``streams.cice`` in older E3SM runs, (even if they will +not be written out -- ``output_interval=="none"``):: Date: Sat, 14 Apr 2018 11:18:57 +0200 Subject: [PATCH 57/71] Check for requested variables in timeSeriesStatsMonthly Before calling NCO tools, raise exceptions if the requested variables are not available so only tasks requesting unavailable variables fail, not the full analysis. --- .../climatology/mpas_climatology_task.py | 29 +++++++++++++++++++ .../time_series/mpas_time_series_task.py | 29 +++++++++++++++++++ 2 files changed, 58 insertions(+) diff --git a/mpas_analysis/shared/climatology/mpas_climatology_task.py b/mpas_analysis/shared/climatology/mpas_climatology_task.py index bd55d5cf5..fe5d4e269 100644 --- a/mpas_analysis/shared/climatology/mpas_climatology_task.py +++ b/mpas_analysis/shared/climatology/mpas_climatology_task.py @@ -36,6 +36,10 @@ class MpasClimatologyTask(AnalysisTask): # {{{ A list of variable names in ``timeSeriesStatsMonthly`` to be included in the climatologies + allVariables : list of str + A list of all available variable names in ``timeSeriesStatsMonthly`` + used to raise an exception when an unavailable variable is requested + seasons : list of str A list of seasons (keys in ``shared.constants.monthDictionary``) over which the climatology should be computed or ['none'] if only @@ -96,6 +100,8 @@ def __init__(self, config, componentName, taskName=None): # {{{ suffix = componentName[0].upper() + componentName[1:] taskName = 'mpasClimatology{}'.format(suffix) + self.allVariables = None + # call the constructor from the base class (AnalysisTask) super(MpasClimatologyTask, self).__init__( config=config, @@ -120,12 +126,32 @@ def add_variables(self, variableList, seasons=None): # {{{ A list of seasons (keys in ``shared.constants.monthDictionary``) to be computed or ['none'] (not ``None``) if only monthly climatologies are needed. + + Raises + ------ + ValueError + if this funciton is called before this task has been set up (so + the list of available variables has not yet been set) or if one + or more of the requested variables is not available in the + ``timeSeriesStatsMonthly`` output. ''' # Authors # ------- # Xylar Asay-Davis + if self.allVariables is None: + raise ValueError('add_variables() can only be called after ' + 'setup_and_check() in MpasClimatologyTask.\n' + 'Presumably tasks were added in the wrong order ' + 'or add_variables() is being called in the wrong ' + 'place.') + for variable in variableList: + if variable not in self.allVariables: + raise ValueError( + '{} is not available in timeSeriesStatsMonthly ' + 'output:\n{}'.format(variable, self.allVariables)) + if variable not in self.variableList: self.variableList.append(variable) @@ -178,6 +204,9 @@ def setup_and_check(self): # {{{ self.symlinkDirectory = \ self._update_climatology_bounds_and_create_symlinks() + with xarray.open_dataset(self.inputFiles[0]) as ds: + self.allVariables = list(ds.data_vars.keys()) + # }}} def run_task(self): # {{{ diff --git a/mpas_analysis/shared/time_series/mpas_time_series_task.py b/mpas_analysis/shared/time_series/mpas_time_series_task.py index e0e18710b..260b59165 100644 --- a/mpas_analysis/shared/time_series/mpas_time_series_task.py +++ b/mpas_analysis/shared/time_series/mpas_time_series_task.py @@ -34,6 +34,10 @@ class MpasTimeSeriesTask(AnalysisTask): # {{{ A list of variable names in ``timeSeriesStatsMonthly`` to be included in the time series + allVariables : list of str + A list of all available variable names in ``timeSeriesStatsMonthly`` + used to raise an exception when an unavailable variable is requested + inputFiles : list of str A list of input files from which to extract the time series. @@ -80,6 +84,8 @@ def __init__(self, config, componentName, taskName=None, self.section = section tags = [section] + self.allVariables = None + if taskName is None: suffix = section[0].upper() + section[1:] + \ componentName[0].upper() + componentName[1:] @@ -104,12 +110,32 @@ def add_variables(self, variableList): # {{{ variableList : list of str A list of variable names in ``timeSeriesStatsMonthly`` to be included in the time series + + Raises + ------ + ValueError + if this funciton is called before this task has been set up (so + the list of available variables has not yet been set) or if one + or more of the requested variables is not available in the + ``timeSeriesStatsMonthly`` output. ''' # Authors # ------- # Xylar Asay-Davis + if self.allVariables is None: + raise ValueError('add_variables() can only be called after ' + 'setup_and_check() in MpasTimeSeriesTask.\n' + 'Presumably tasks were added in the wrong order ' + 'or add_variables() is being called in the wrong ' + 'place.') + for variable in variableList: + if variable not in self.allVariables: + raise ValueError( + '{} is not available in timeSeriesStatsMonthly ' + 'output:\n{}'.format(variable, self.allVariables)) + if variable not in self.variableList: self.variableList.append(variable) @@ -183,6 +209,9 @@ def setup_and_check(self): # {{{ self.inputFiles = sorted(self.inputFiles) + with xr.open_dataset(self.inputFiles[0]) as ds: + self.allVariables = list(ds.data_vars.keys()) + # }}} def run_task(self): # {{{ From 86f1d0a252b03c5d0a2b69954a9f501846d80613 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Sat, 14 Apr 2018 12:07:41 +0200 Subject: [PATCH 58/71] In MLD task, check if MLD analysis member is enabled --- mpas_analysis/ocean/climatology_map_mld.py | 23 ++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/mpas_analysis/ocean/climatology_map_mld.py b/mpas_analysis/ocean/climatology_map_mld.py index 4ce53a9b6..bdd3148ad 100644 --- a/mpas_analysis/ocean/climatology_map_mld.py +++ b/mpas_analysis/ocean/climatology_map_mld.py @@ -149,6 +149,29 @@ def __init__(self, config, mpasClimatologyTask, self.add_subtask(subtask) # }}} + + def setup_and_check(self): # {{{ + ''' + Check if MLD capability was turned on in the run. + + Authors + ------- + Xylar Asay-Davis + ''' + + # first, call setup_and_check from the base class (AnalysisTask), + # which will perform some common setup, including storing: + # self.runDirectory , self.historyDirectory, self.plotsDirectory, + # self.namelist, self.runStreams, self.historyStreams, + # self.calendar + super(ClimatologyMapMLD, self).setup_and_check() + + self.check_analysis_enabled( + analysisOptionName='config_am_mixedlayerdepths_enable', + raiseException=True) + + # }}} + # }}} From c3bc56ea32eb2520e87aca479a8f0880563c8815 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Wed, 18 Apr 2018 13:56:37 +0200 Subject: [PATCH 59/71] Small fix to env that got messed up in a merge --- docs/environment.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/environment.yml b/docs/environment.yml index 8d5b05f2c..694b5e6d6 100644 --- a/docs/environment.yml +++ b/docs/environment.yml @@ -22,5 +22,4 @@ dependencies: - sphinx_rtd_theme - numpydoc - tabulate >= 0.8.2 - - pip: - - recommonmark + - recommonmark From 7c8d92d88f9ddf5c6d8836b69e20942596374c22 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Wed, 18 Apr 2018 13:58:24 +0200 Subject: [PATCH 60/71] Generate tables in conf.py To avoid a complicated custom build on ReadTheDocs, the 3 obs. tables are now built in conf.py since the Makefile is not used. The rst files have been renamed for easier readability. --- docs/.gitignore | 1 + docs/Makefile | 3 --- docs/__init__.py | 0 docs/conf.py | 8 ++++++++ docs/index.rst | 4 ++-- docs/observations.rst | 23 +++++++++-------------- 6 files changed, 20 insertions(+), 19 deletions(-) create mode 100644 docs/__init__.py diff --git a/docs/.gitignore b/docs/.gitignore index 86d4c2dd3..1cc1ca4d3 100644 --- a/docs/.gitignore +++ b/docs/.gitignore @@ -1 +1,2 @@ generated +*_obs_table.rst diff --git a/docs/Makefile b/docs/Makefile index b417471f9..609aaa947 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -21,7 +21,4 @@ clean: # Catch-all target: route all unknown targets to Sphinx using the new # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). %: Makefile - python parse_table.py -x ../mpas_analysis/obs/observationstable.xml -r landicobservationstable.rst -c landice - python parse_table.py -x ../mpas_analysis/obs/observationstable.xml -r oceanobservationstable.rst -c ocean - python parse_table.py -x ../mpas_analysis/obs/observationstable.xml -r seaicobservationstable.rst -c seaice @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/__init__.py b/docs/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/docs/conf.py b/docs/conf.py index c3b03a7da..77c8deb5d 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -16,6 +16,7 @@ import sys sys.path.insert(0, os.path.abspath('..')) import mpas_analysis +from docs.parse_table import build_rst_table_from_xml # -- General configuration ------------------------------------------------ @@ -181,3 +182,10 @@ 'python': ('https://docs.python.org/', None), 'numpy': ('http://docs.scipy.org/doc/numpy/', None), 'xarray': ('http://xarray.pydata.org/en/stable/', None)} + + +# Build some custom rst files +xmlFileName = '../mpas_analysis/obs/observationstable.xml' +for component in ['ocean', 'seaice', 'landice']: + build_rst_table_from_xml(xmlFileName, '{}_obs_table.rst'.format(component), + component) \ No newline at end of file diff --git a/docs/index.rst b/docs/index.rst index 1df535021..07e7ace11 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -32,8 +32,8 @@ MPAS Components and E3SM mpasseaice e3sm -Observations -============ +Observational Data Sets +======================= .. toctree:: observations diff --git a/docs/observations.rst b/docs/observations.rst index 487135fbc..0a9475b55 100644 --- a/docs/observations.rst +++ b/docs/observations.rst @@ -1,18 +1,13 @@ -Observations -============ - A variety of observational datasets are used within MPAS-Analysis: -Land Ice metrics ----------------- -.. include:: landicobservationstable.rst - -Ocean metrics -------------- - -.. include:: oceanobservationstable.rst +Ocean Observations +------------------ +.. include:: ocean_obs_table.rst -Sea Ice metrics ---------------- -.. include:: seaicobservationstable.rst +Sea Ice Observations +-------------------- +.. include:: seaice_obs_table.rst +Land Ice Observations +--------------------- +.. include:: landice_obs_table.rst From 5dfb8b82c21bc625f3ed41f7269037661669bf87 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Thu, 19 Apr 2018 12:24:36 +0200 Subject: [PATCH 61/71] User-specified tick start and stride for time axes A config file can now be used to specify firstYearXTicks and yearStrideXTicks to control how ticks are set for a time axis, e.g.: [hovmollerOHCAnomaly] firstYearXTicks = 2 yearStrideXTicks = 2 [hovmollerTemperatureAnomaly] firstYearXTicks = 2 yearStrideXTicks = 2 [hovmollerSalinityAnomaly] firstYearXTicks = 2 yearStrideXTicks = 2 [timeSeriesSeaIceAreaVol] firstYearXTicks = 2 yearStrideXTicks = 2 [timeSeriesSST] firstYearXTicks = 2 yearStrideXTicks = 2 [streamfunctionMOC] firstYearXTicks = 2 yearStrideXTicks = 2 --- mpas_analysis/config.default | 48 +++++++++++++++ mpas_analysis/ocean/index_nino34.py | 2 +- ...ot_depth_integrated_time_series_subtask.py | 16 ++++- mpas_analysis/ocean/plot_hovmoller_subtask.py | 16 ++++- mpas_analysis/ocean/streamfunction_moc.py | 17 +++++- .../ocean/time_series_antarctic_melt.py | 16 ++++- mpas_analysis/ocean/time_series_sst.py | 16 ++++- mpas_analysis/sea_ice/time_series.py | 17 +++++- mpas_analysis/shared/plot/plotting.py | 60 +++++++++++++++---- 9 files changed, 189 insertions(+), 19 deletions(-) diff --git a/mpas_analysis/config.default b/mpas_analysis/config.default index a7a60d05c..d0ef1258b 100644 --- a/mpas_analysis/config.default +++ b/mpas_analysis/config.default @@ -328,6 +328,12 @@ preprocessedFieldPrefix = ohc # window) movingAveragePoints = 12 +# An optional first year for the tick marks on the x axis +# firstYearXTicks = 1 + +# An optional number of years between tick marks on the x axis +# yearStrideXTicks = 1 + [hovmollerOHCAnomaly] ## options related to time vs. depth Hovmoller plots of ocean heat content ## (OHC) anomalies from year 1 @@ -344,6 +350,12 @@ colorbarLevels = [-2.4, -0.8, -0.4, -0.2, 0, 0.2, 0.4, 0.8, 2.4] # contour line levels contourLevels = np.arange(-2.5, 2.6, 0.5) +# An optional first year for the tick marks on the x axis +# firstYearXTicks = 1 + +# An optional number of years between tick marks on the x axis +# yearStrideXTicks = 1 + [hovmollerTemperatureAnomaly] ## options related to plotting time series of temperature vs. depth @@ -364,6 +376,12 @@ colorbarLevels = [-1, -0.5, -0.2, -0.05, 0, 0.05, 0.2, 0.5, 1] # contour line levels contourLevels = np.arange(-1.0, 1.26, 0.25) +# An optional first year for the tick marks on the x axis +# firstYearXTicks = 1 + +# An optional number of years between tick marks on the x axis +# yearStrideXTicks = 1 + [hovmollerSalinityAnomaly] ## options related to plotting time series of salinity vs. depth @@ -384,6 +402,12 @@ colorbarLevels = [-0.1, -0.02, -0.003, -0.001, 0, 0.001, 0.003, 0.02, 0.1] # contour line levels contourLevels = np.arange(-0.1, 0.11, 0.02) +# An optional first year for the tick marks on the x axis +# firstYearXTicks = 1 + +# An optional number of years between tick marks on the x axis +# yearStrideXTicks = 1 + [timeSeriesSST] ## options related to plotting time series of sea surface temperature (SST) @@ -396,6 +420,12 @@ regions = ['global'] # window) movingAveragePoints = 12 +# An optional first year for the tick marks on the x axis +# firstYearXTicks = 1 + +# An optional number of years between tick marks on the x axis +# yearStrideXTicks = 1 + [indexNino34] ## options related to plotting time series of the El Nino 3.4 index @@ -504,6 +534,12 @@ movingAveragePoints = 12 # latitude) for climatological MOC plots movingAveragePointsClimatological = 1 +# An optional first year for the tick marks on the x axis +# firstYearXTicks = 1 + +# An optional number of years between tick marks on the x axis +# yearStrideXTicks = 1 + [timeSeriesSeaIceAreaVol] ## options related to plotting time series of sea ice area and volume @@ -518,6 +554,12 @@ titleFontSize = 18 # plot on polar plot polarPlot = False +# An optional first year for the tick marks on the x axis +# firstYearXTicks = 1 + +# An optional number of years between tick marks on the x axis +# yearStrideXTicks = 1 + [climatologyMapSST] ## options related to plotting horizontally remapped climatologies of ## sea surface temperature (SST) against reference model results and @@ -673,6 +715,12 @@ iceShelvesToPlot = ['Antarctica'] # Number of months over which to compute moving average movingAverageMonths = 1 +# An optional first year for the tick marks on the x axis +# firstYearXTicks = 1 + +# An optional number of years between tick marks on the x axis +# yearStrideXTicks = 1 + [climatologyMapSoseTemperature] ## options related to plotting climatology maps of Antarctic ## potential temperature at various levels, including the sea floor against diff --git a/mpas_analysis/ocean/index_nino34.py b/mpas_analysis/ocean/index_nino34.py index c414a7de0..b54c5d81f 100644 --- a/mpas_analysis/ocean/index_nino34.py +++ b/mpas_analysis/ocean/index_nino34.py @@ -635,7 +635,7 @@ def _nino34_timeseries_plot(self, nino34s, title, panelTitles, outFileName, minDays = time.min() maxDays = time.max() - plot_xtick_format(plt, calendar, minDays, maxDays, maxXTicks) + plot_xtick_format(calendar, minDays, maxDays, maxXTicks) plt.tight_layout(rect=[0, 0.03, 1, 0.90]) diff --git a/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py b/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py index 93ffd4c40..b070f5336 100644 --- a/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py +++ b/mpas_analysis/ocean/plot_depth_integrated_time_series_subtask.py @@ -437,11 +437,25 @@ def run_task(self): # {{{ maxPoints.append(points[rangeIndex]) legendText.append(None) + if config.has_option(self.taskName, 'firstYearXTicks'): + firstYearXTicks = config.getint(self.taskName, + 'firstYearXTicks') + else: + firstYearXTicks = None + + if config.has_option(self.taskName, 'yearStrideXTicks'): + yearStrideXTicks = config.getint(self.taskName, + 'yearStrideXTicks') + else: + yearStrideXTicks = None + timeseries_analysis_plot(config=config, dsvalues=timeSeries, N=None, title=title, xlabel=xLabel, ylabel=yLabel, fileout=figureName, lineStyles=lineStyles, lineWidths=lineWidths, maxPoints=maxPoints, - legendText=legendText, calendar=calendar) + legendText=legendText, calendar=calendar, + firstYearXTicks=firstYearXTicks, + yearStrideXTicks=yearStrideXTicks) write_image_xml( config=config, diff --git a/mpas_analysis/ocean/plot_hovmoller_subtask.py b/mpas_analysis/ocean/plot_hovmoller_subtask.py index 11eedb30a..3fe7d927a 100644 --- a/mpas_analysis/ocean/plot_hovmoller_subtask.py +++ b/mpas_analysis/ocean/plot_hovmoller_subtask.py @@ -264,11 +264,25 @@ def run_task(self): # {{{ figureName = '{}/{}.png'.format(self.plotsDirectory, self.filePrefix) + if config.has_option(self.sectionName, 'firstYearXTicks'): + firstYearXTicks = config.getint(self.sectionName, + 'firstYearXTicks') + else: + firstYearXTicks = None + + if config.has_option(self.sectionName, 'yearStrideXTicks'): + yearStrideXTicks = config.getint(self.sectionName, + 'yearStrideXTicks') + else: + yearStrideXTicks = None + plot_vertical_section(config, Time, depth, field, self.sectionName, suffix='', colorbarLabel=self.unitsLabel, title=title, xlabel=xLabel, ylabel=yLabel, fileout=figureName, linewidths=1, - xArrayIsTime=True, calendar=self.calendar) + xArrayIsTime=True, calendar=self.calendar, + firstYearXTicks=firstYearXTicks, + yearStrideXTicks=yearStrideXTicks) write_image_xml( config=config, diff --git a/mpas_analysis/ocean/streamfunction_moc.py b/mpas_analysis/ocean/streamfunction_moc.py index 66f3dd5f5..0753da5b2 100644 --- a/mpas_analysis/ocean/streamfunction_moc.py +++ b/mpas_analysis/ocean/streamfunction_moc.py @@ -68,7 +68,6 @@ def __init__(self, config, mpasClimatologyTask): # {{{ # ------- # Xylar Asay-Davis -# # first, call the constructor from the base class (AnalysisTask) super(StreamfunctionMOC, self).__init__( config=config, @@ -242,11 +241,25 @@ def run_task(self): # {{{ figureName = '{}/{}.png'.format(self.plotsDirectory, filePrefix) + if config.has_option(self.taskName, 'firstYearXTicks'): + firstYearXTicks = config.getint(self.taskName, + 'firstYearXTicks') + else: + firstYearXTicks = None + + if config.has_option(self.taskName, 'yearStrideXTicks'): + yearStrideXTicks = config.getint(self.taskName, + 'yearStrideXTicks') + else: + yearStrideXTicks = None + timeseries_analysis_plot(config, [dsMOCTimeSeries.mocAtlantic26], movingAveragePoints, title, xLabel, yLabel, figureName, lineStyles=['k-'], lineWidths=[2], - legendText=[None], calendar=self.calendar) + legendText=[None], calendar=self.calendar, + firstYearXTicks=firstYearXTicks, + yearStrideXTicks=yearStrideXTicks) caption = u'Time Series of maximum Meridional Overturning ' \ u'Circulation at 26.5°N' diff --git a/mpas_analysis/ocean/time_series_antarctic_melt.py b/mpas_analysis/ocean/time_series_antarctic_melt.py index be105e41c..79225fd82 100644 --- a/mpas_analysis/ocean/time_series_antarctic_melt.py +++ b/mpas_analysis/ocean/time_series_antarctic_melt.py @@ -340,6 +340,18 @@ def run_task(self): # {{{ lineWidths.append(1.2) legendText.append(refRunName) + if config.has_option(self.taskName, 'firstYearXTicks'): + firstYearXTicks = config.getint(self.taskName, + 'firstYearXTicks') + else: + firstYearXTicks = None + + if config.has_option(self.taskName, 'yearStrideXTicks'): + yearStrideXTicks = config.getint(self.taskName, + 'yearStrideXTicks') + else: + yearStrideXTicks = None + timeseries_analysis_plot(config, fields, movingAverageMonths, title, xLabel, yLabel, figureName, lineStyles=lineStyles, @@ -347,7 +359,9 @@ def run_task(self): # {{{ legendText=legendText, calendar=calendar, obsMean=obsMeltRate, obsUncertainty=obsMeltRateUnc, - obsLegend=list(obsDict.keys())) + obsLegend=list(obsDict.keys()), + firstYearXTicks=firstYearXTicks, + yearStrideXTicks=yearStrideXTicks) caption = 'Running Mean of Area-averaged Melt Rate under Ice ' \ 'Shelves in the {} Region'.format(title) diff --git a/mpas_analysis/ocean/time_series_sst.py b/mpas_analysis/ocean/time_series_sst.py index 029a64c36..1695ea684 100644 --- a/mpas_analysis/ocean/time_series_sst.py +++ b/mpas_analysis/ocean/time_series_sst.py @@ -252,11 +252,25 @@ def run_task(self): # {{{ lineWidths.append(1.5) legendText.append(preprocessedReferenceRunName) + if config.has_option(self.taskName, 'firstYearXTicks'): + firstYearXTicks = config.getint(self.taskName, + 'firstYearXTicks') + else: + firstYearXTicks = None + + if config.has_option(self.taskName, 'yearStrideXTicks'): + yearStrideXTicks = config.getint(self.taskName, + 'yearStrideXTicks') + else: + yearStrideXTicks = None + timeseries_analysis_plot(config, fields, movingAveragePoints, title, xLabel, yLabel, figureName, lineStyles=lineStyles, lineWidths=lineWidths, - legendText=legendText, calendar=calendar) + legendText=legendText, calendar=calendar, + firstYearXTicks=firstYearXTicks, + yearStrideXTicks=yearStrideXTicks) caption = 'Running Mean of {} Sea Surface Temperature'.format( region) diff --git a/mpas_analysis/sea_ice/time_series.py b/mpas_analysis/sea_ice/time_series.py index 3925afa25..deca1ac27 100644 --- a/mpas_analysis/sea_ice/time_series.py +++ b/mpas_analysis/sea_ice/time_series.py @@ -418,6 +418,18 @@ def run_task(self): # {{{ lineStyles.append('g-') lineWidths.append(1.2) + if config.has_option(self.taskName, 'firstYearXTicks'): + firstYearXTicks = config.getint(self.taskName, + 'firstYearXTicks') + else: + firstYearXTicks = None + + if config.has_option(self.taskName, 'yearStrideXTicks'): + yearStrideXTicks = config.getint(self.taskName, + 'yearStrideXTicks') + else: + yearStrideXTicks = None + # separate plots for nothern and southern hemispheres timeseries_analysis_plot(config, dsvalues, movingAveragePoints, @@ -428,7 +440,10 @@ def run_task(self): # {{{ lineWidths=lineWidths, legendText=legendText, titleFontSize=titleFontSize, - calendar=calendar) + calendar=calendar, + firstYearXTicks=firstYearXTicks, + yearStrideXTicks=yearStrideXTicks) + filePrefix = '{}{}_{}'.format(variableName, hemisphere, mainRunName) diff --git a/mpas_analysis/shared/plot/plotting.py b/mpas_analysis/shared/plot/plotting.py index f70c593d7..5918b9346 100644 --- a/mpas_analysis/shared/plot/plotting.py +++ b/mpas_analysis/shared/plot/plotting.py @@ -41,7 +41,8 @@ def timeseries_analysis_plot(config, dsvalues, N, title, xlabel, ylabel, fileout, lineStyles, lineWidths, legendText, calendar, maxPoints=None, titleFontSize=None, - figsize=(15, 6), dpi=None, maxXTicks=20, + figsize=(15, 6), dpi=None, firstYearXTicks=None, + yearStrideXTicks=None, maxXTicks=20, obsMean=None, obsUncertainty=None, obsLegend=None, legendLocation='lower left'): @@ -92,6 +93,14 @@ def timeseries_analysis_plot(config, dsvalues, N, title, xlabel, ylabel, the number of dots per inch of the figure, taken from section ``plot`` option ``dpi`` in the config file by default + firstYearXTicks : int, optional + The year of the first tick on the x axis. By default, the first time + entry is the first tick. + + yearStrideXTicks : int, optional + The number of years between x ticks. By default, the stride is chosen + automatically to have ``maxXTicks`` tick marks or fewer. + maxXTicks : int, optional the maximum number of tick marks that will be allowed along the x axis. This may need to be adjusted depending on the figure size and aspect @@ -171,7 +180,11 @@ def timeseries_analysis_plot(config, dsvalues, N, title, xlabel, ylabel, 'color': config.get('plot', 'titleFontColor'), 'weight': config.get('plot', 'titleFontWeight')} - plot_xtick_format(plt, calendar, minDays, maxDays, maxXTicks) + if firstYearXTicks is not None: + minDays = date_to_days(year=firstYearXTicks, calendar=calendar) + + plot_xtick_format(calendar, minDays, maxDays, maxXTicks, + yearStride=yearStrideXTicks) # Add a y=0 line if y ranges between positive and negative values yaxLimits = ax.get_ylim() @@ -915,6 +928,8 @@ def plot_vertical_section( invertYAxis=True, xArrayIsTime=False, N=None, + firstYearXTicks=None, + yearStrideXTicks=None, maxXTicks=20, calendar='gregorian'): # {{{ @@ -986,6 +1001,14 @@ def plot_vertical_section( values, so for best results, the values in the xArray should be equally spaced. + firstYearXTicks : int, optional + The year of the first tick on the x axis. By default, the first time + entry is the first tick. + + yearStrideXTicks : int, optional + The number of years between x ticks. By default, the stride is chosen + automatically to have ``maxXTicks`` tick marks or fewer. + maxXTicks : int, optional the maximum number of tick marks that will be allowed along the x axis. This may need to be adjusted depending on the figure size and aspect @@ -1069,9 +1092,14 @@ def plot_vertical_section( plt.ylim(yLim) if xArrayIsTime: - minDays = [xArray[0]] + if firstYearXTicks is None: + minDays = [xArray[0]] + else: + minDays = date_to_days(year=firstYearXTicks, calendar=calendar) maxDays = [xArray[-1]] - plot_xtick_format(plt, calendar, minDays, maxDays, maxXTicks) + + plot_xtick_format(calendar, minDays, maxDays, maxXTicks, + yearStride=yearStrideXTicks) if (fileout is not None): plt.savefig(fileout, dpi=dpi, bbox_inches='tight', pad_inches=0.1) @@ -1166,20 +1194,28 @@ def setup_colormap(config, configSectionName, suffix=''): 'lineColor': lineColor} -def plot_xtick_format(plt, calendar, minDays, maxDays, maxXTicks): +def plot_xtick_format(calendar, minDays, maxDays, maxXTicks, yearStride=None): ''' Formats tick labels and positions along the x-axis for time series / index plots Parameters ---------- - plt : plt handle on which to change ticks + calendar : str + the calendar to use for formatting the time axis + + minDays : float + start time for labels - calendar : specified calendar for the plot + maxDays : float + end time for labels - minDays : start time for labels + maxXTicks : int + the maximum number of tick marks to display, used to sub-sample ticks + if there are too many - maxDays : end time for labels + stride : int, optionoal + the number of months or years to skip over between ticks ''' # Authors # ------- @@ -1190,9 +1226,11 @@ def plot_xtick_format(plt, calendar, minDays, maxDays, maxXTicks): start = days_to_datetime(np.amin(minDays), calendar=calendar) end = days_to_datetime(np.amax(maxDays), calendar=calendar) - if (end.year - start.year > maxXTicks/2): + if yearStride is not None or end.year - start.year > maxXTicks/2: + if yearStride is None: + yearStride = 1 major = [date_to_days(year=year, calendar=calendar) - for year in np.arange(start.year, end.year+1)] + for year in np.arange(start.year, end.year+1, yearStride)] formatterFun = partial(_date_tick, calendar=calendar, includeMonth=False) else: From d9b4291b813eff1acd7373702298e239891c17cf Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Fri, 20 Apr 2018 17:23:40 +0200 Subject: [PATCH 62/71] Add ARGO preprocessing jupyter notebook --- .../Process_RG_Argo_climatology.ipynb | 184 ++++++++++++++++++ 1 file changed, 184 insertions(+) create mode 100644 preprocess_observations/Process_RG_Argo_climatology.ipynb diff --git a/preprocess_observations/Process_RG_Argo_climatology.ipynb b/preprocess_observations/Process_RG_Argo_climatology.ipynb new file mode 100644 index 000000000..d36a6d4c3 --- /dev/null +++ b/preprocess_observations/Process_RG_Argo_climatology.ipynb @@ -0,0 +1,184 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "import matplotlib.pyplot as plt\n", + "import numpy as np\n", + "import xarray as xr\n", + "import glob\n", + "import matplotlib\n", + "from netCDF4 import Dataset\n", + "import sys\n", + "import os\n", + "\n", + "# define plot dimensions\n", + "%matplotlib inline \n", + "plt.rcParams[\"figure.figsize\"] = (8.,8.)\n", + "\n", + "from mpl_toolkits.basemap import Basemap\n", + "import matplotlib.colors as cols\n", + "plt.rcParams[\"figure.figsize\"] = (20,12)\n", + "\n", + "### axis_font = {'fontname':'Arial', 'size':'18'} \n", + "title_font = {'fontname':'Arial', 'size':'32', 'color':'black', 'weight':'normal'}\n", + "matplotlib.rc('xtick', labelsize=28)\n", + "matplotlib.rc('ytick', labelsize=28)" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [], + "source": [ + "#path to raw ARGO file downloaded from http://sio-argo.ucsd.edu/RG_Climatology.html\n", + "#Note that script expects files named RG_ArgoClim_Temperature_2017.nc and RG_ArgoClim_Salinity_2017.nc\n", + "\n", + "basePath = '/lcrc/group/acme/lvanroe'\n", + "nameOfOutputFile = 'ArgoClimatology_TS.nc'" + ] + }, + { + "cell_type": "code", + "execution_count": 33, + "metadata": {}, + "outputs": [], + "source": [ + "ncidT = Dataset(basePath+'/RG_ArgoClim_Temperature_2017.nc','r')\n", + "ncidS = Dataset(basePath+'/RG_ArgoClim_Salinity_2017.nc','r')\n", + "\n", + "lon = ncidT.variables['LONGITUDE'][:]\n", + "lat = ncidT.variables['LATITUDE'][:]\n", + "\n", + "anomT = ncidT.variables['ARGO_TEMPERATURE_ANOMALY'][:,:,:,:]\n", + "meanT = ncidT.variables['ARGO_TEMPERATURE_MEAN'][:,:,:]\n", + "\n", + "anomS = ncidS.variables['ARGO_SALINITY_ANOMALY'][:,:,:,:]\n", + "meanS = ncidS.variables['ARGO_SALINITY_MEAN'][:,:,:]\n", + "\n", + "bmask = ncidT.variables['BATHYMETRY_MASK'][:]\n", + "\n", + "depth = -ncidT.variables['PRESSURE'][:]" + ] + }, + { + "cell_type": "code", + "execution_count": 34, + "metadata": {}, + "outputs": [], + "source": [ + "#forms monthly averages of T and S\n", + "monthV = np.zeros(12);\n", + "nx = len(lon)\n", + "ny = len(lat)\n", + "nz = len(depth)\n", + "\n", + "theta = np.zeros((12,nz,ny,nx))\n", + "salinity = np.zeros((12,nz,ny,nx))\n", + "\n", + "for i in range(12):\n", + " monthV[i] = i\n", + " theta[i,:,:,:] = anomT[i::12,:,:,:].mean(axis=0)+meanT\n", + " salinity[i,:,:,:] = anomS[i::12,:,:,:].mean(axis=0)+meanS" + ] + }, + { + "cell_type": "code", + "execution_count": 35, + "metadata": {}, + "outputs": [], + "source": [ + "#Mask bathymetry\n", + "bmask = np.roll(bmask,20,axis=2)\n", + "for i in range(nz):\n", + " inds1=np.where(bmask[i,:,:] != 1.0)[0]\n", + " inds2=np.where(bmask[i,:,:] != 1.0)[1]\n", + " salinity[:,i,inds1,inds2] = np.nan\n", + " theta[:,i,inds1,inds2] = np.nan" + ] + }, + { + "cell_type": "code", + "execution_count": 36, + "metadata": {}, + "outputs": [], + "source": [ + "#need to append a few rows to have a 180 x 360 matrix\n", + "theta2 = np.zeros((12,58,180,360))\n", + "salt2 = np.zeros((12,58,180,360))" + ] + }, + { + "cell_type": "code", + "execution_count": 37, + "metadata": {}, + "outputs": [], + "source": [ + "theta2[:,:,25:170,:] = theta\n", + "salt2[:,:,25:170,:] = salinity\n", + "\n", + "theta2[:,:,:25,:] = np.nan\n", + "theta2[:,:,170:,:] = np.nan\n", + "\n", + "salt2[:,:,:25,:] = np.nan\n", + "salt2[:,:,170:,:] = np.nan" + ] + }, + { + "cell_type": "code", + "execution_count": 38, + "metadata": {}, + "outputs": [], + "source": [ + "if os.path.isfile(basePath+'/'+nameOfOutputFile):\n", + " os.remove(basePath+'/'+nameOfOutputFile)\n", + "ncid = Dataset(basePath+'/'+nameOfOutputFile,'w')\n", + "ncid.createDimension('Time',None)\n", + "ncid.createDimension('LATITUDE',180)\n", + "ncid.createDimension('LONGITUDE',360)\n", + "ncid.createDimension('DEPTH',58)\n", + "\n", + "month = ncid.createVariable('month','i4',('Time'))\n", + "lat = ncid.createVariable('LATITUDE','f8',('LATITUDE'))\n", + "lonV = ncid.createVariable('LONGITUDE','f8',('LONGITUDE'))\n", + "dep = ncid.createVariable('DEPTH','f8',('DEPTH'))\n", + "thet=ncid.createVariable('theta','f8',('Time','DEPTH','LATITUDE','LONGITUDE'))\n", + "sal=ncid.createVariable('salinity','f8',('Time','DEPTH','LATITUDE','LONGITUDE'))\n", + "\n", + "lat[:] = np.arange(-89.5,90,1)\n", + "lonV[:] = lon[:]\n", + "thet[:,:,:,:] = theta2\n", + "sal[:,:,:,:] = salt2\n", + "dep[:] = depth[:]\n", + "month[:] = monthV[:]\n", + "\n", + "ncid.close()" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python [conda root]", + "language": "python", + "name": "conda-root-py" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.14" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} From e29260e45625933ff6d83b0de664ec9c8ecb4a56 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Fri, 20 Apr 2018 18:39:39 +0200 Subject: [PATCH 63/71] Fix capitalization ARGO --> Argo --- mpas_analysis/ocean/climatology_map_argo.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/mpas_analysis/ocean/climatology_map_argo.py b/mpas_analysis/ocean/climatology_map_argo.py index 8e976c8b8..5dc2271f8 100644 --- a/mpas_analysis/ocean/climatology_map_argo.py +++ b/mpas_analysis/ocean/climatology_map_argo.py @@ -6,7 +6,7 @@ # distributed with this code, or at http://mpas-dev.github.com/license.html # ''' -Analysis tasks for comparing Global climatology maps against ARGO data. +Analysis tasks for comparing Global climatology maps against Argo data. ''' # Authors # ------- @@ -61,7 +61,7 @@ def __init__(self, config, mpasClimatologyTask, # ------- # Luke Van Roekel, Xylar Asay-Davis - fieldName = 'temperatureARGO' + fieldName = 'temperatureArgo' # call the constructor from the base class (AnalysisTask) super(ClimatologyMapArgoTemperature, self).__init__( config=config, taskName='climatologyMapArgoTemperature', @@ -117,7 +117,7 @@ def __init__(self, config, mpasClimatologyTask, observationsDirectory) refFieldName = 'theta' outFileLabel = 'tempArgo' - galleryName = 'Roemmich-Gilson Climatology: ARGO' + galleryName = 'Roemmich-Gilson Climatology: Argo' diffTitleLabel = 'Model - Argo' remapObservationsSubtask = RemapArgoClimatology( @@ -159,7 +159,7 @@ def __init__(self, config, mpasClimatologyTask, refTitleLabel=refTitleLabel, diffTitleLabel=diffTitleLabel, unitsLabel=r'$^\circ$C', - imageCaption='Model temperature compared with ARGO ' + imageCaption='Model temperature compared with Argo ' 'observations', galleryGroup='Argo Temperature', groupSubtitle=None, @@ -201,7 +201,7 @@ def __init__(self, config, mpasClimatologyTask, # ------- # Xylar Asay-Davis, Luke Van Roekel - fieldName = 'salinityARGO' + fieldName = 'salinityArgo' # call the constructor from the base class (AnalysisTask) super(ClimatologyMapArgoSalinity, self).__init__( config=config, taskName='climatologyMapArgoSalinity', From d2ed189e161c9c9f67f0796e9937da06410efb34 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Fri, 20 Apr 2018 19:24:32 +0200 Subject: [PATCH 64/71] Remove landice component There are no tasks that relate to it yet. --- docs/conf.py | 4 ++-- docs/observations.rst | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index 77c8deb5d..f1d8c9453 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -185,7 +185,7 @@ # Build some custom rst files -xmlFileName = '../mpas_analysis/obs/observationstable.xml' -for component in ['ocean', 'seaice', 'landice']: +xmlFileName = '../mpas_analysis/obs/observational_datasets.xml' +for component in ['ocean', 'seaice']: build_rst_table_from_xml(xmlFileName, '{}_obs_table.rst'.format(component), component) \ No newline at end of file diff --git a/docs/observations.rst b/docs/observations.rst index 0a9475b55..8c5ea35b6 100644 --- a/docs/observations.rst +++ b/docs/observations.rst @@ -1,3 +1,6 @@ +Observations +============ + A variety of observational datasets are used within MPAS-Analysis: Ocean Observations @@ -8,6 +11,3 @@ Sea Ice Observations -------------------- .. include:: seaice_obs_table.rst -Land Ice Observations ---------------------- -.. include:: landice_obs_table.rst From 0212f86ea27d6f2fe1390ea49f7956c58fc9a384 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Fri, 20 Apr 2018 19:25:24 +0200 Subject: [PATCH 65/71] Update obs. database with a number of new data sets Also, rename the file (it is not a table) and modify the requested fields for each entry. --- mpas_analysis/obs/observational_datasets.xml | 947 +++++++++++++++++++ mpas_analysis/obs/observationstable.xml | 153 --- 2 files changed, 947 insertions(+), 153 deletions(-) create mode 100644 mpas_analysis/obs/observational_datasets.xml delete mode 100644 mpas_analysis/obs/observationstable.xml diff --git a/mpas_analysis/obs/observational_datasets.xml b/mpas_analysis/obs/observational_datasets.xml new file mode 100644 index 000000000..d40ffc122 --- /dev/null +++ b/mpas_analysis/obs/observational_datasets.xml @@ -0,0 +1,947 @@ + + + + + + + + SST merged Hadley Center-NOAA/OI data set + + + ocean + + + The merged Hadley-OI sea surface temperature (SST) and sea ice + concentration (SIC) data sets were specifically developed as surface + forcing data sets for AMIP style uncoupled simulations of the Community + Atmosphere Model (CAM). The Hadley Centre's SST/SIC version 1.1 + (HADISST1), which is derived gridded, bias-adjusted in situ observations, + were merged with the NOAA-Optimal Interpolation (version 2; OI.v2) + analyses. The HADISST1 spanned 1870 onward but the OI.v2, which started + in November 1981, better resolved features such as the Gulf Stream and + Kuroshio Current which are important components of the climate system. + Since the two data sets used different development methods, anomalies + from a base period were used to create a more homogeneous record. Also, + additional adjustments were made to the SIC data set. + + + [NCAR Hadley-NOAA/OI SST website] + (https://climatedataguide.ucar.edu/climate-data/merged-hadley-noaaoi-sea-surface-temperature-sea-ice-concentration-hurrell-et-al-2008) + + + Unknown + + + [Hurrell et al. (2008)](https://doi.org/10.1175/2008JCLI2292.1) + + + @article{Hurrell2008, + author = {James W. Hurrell and James J. Hack and Dennis Shea and Julie M. Caron and James Rosinski}, + title = {A New Sea Surface Temperature and Sea Ice Boundary Dataset for the Community Atmosphere Model}, + journal = {Journal of Climate}, + volume = {21}, + number = {19}, + pages = {5145-5153}, + year = {2008}, + doi = {10.1175/2008JCLI2292.1}, + URL = {https://doi.org/10.1175/2008JCLI2292.1} + } + + + - ftp://ftp.cgd.ucar.edu/archive/SSTICE/MODEL.SST.HAD187001-198110.OI198111-201712.nc + + + + + - climatologyMapSST + + + + + + SSS from NASA Aquarius satellite + + + ocean + + + Level 3 Aquarius sea surface salinity (SSS) data products have a temporal + resolutions of daily, 8 day, monthly, 3 months, and annual. Monthly and + seasonal climatology + products from Aqaurius are also available. The Aquarius instrument + provides global coverage every 7 days. L3 products are gridded at 1 + degree spatial resolution. + + + [NASA Aquarius FTP server] + (ftp://podaac-ftp.jpl.nasa.gov/allData/aquarius/L3/mapped/V4/7day_running/SCI/) + + + NASA data are not copyrighted; however, when you publish our data or + results derived therefrom, we request that you include an acknowledgment + within the text of the publication and reference list. + [Data Citation and Acknowledgements] + (https://podaac.jpl.nasa.gov/CitingPODAAC) + + + [Lagerloef et al. (2015)](ftp://podaac.jpl.nasa.gov/SalinityDensity/aquarius/docs/v4/AQ-014-PS-0016_AquariusSalinityDataValidationAnalysis_DatasetVersion4.0and3.0.pdf) + + + + + (missing) + + + (missing) + + + - climatologyMapSSS + + + + + + AVISO Absolute Dynamic Topography + + + ocean + + + [NASA JPL AVISO website](https://podaac.jpl.nasa.gov/dataset/AVISO_L4_DYN_TOPO_1DEG_1MO) + This dataset contains absolute dynamic topography (similar to sea level + but with respect to the geoid) binned and averaged monthly on 1 degree + grids. The coverage is from October 1992 to December 2010. These data + were provided by AVISO (French space agency data provider) to support the + CMIP5 (Coupled Model Intercomparison Project Phase 5) under the World + Climate Research Program (WCRP) and was first made available via the JPL + Earth System Grid. The dynamic topography are derived from sea surface + height measured by several satellites including Envisat, TOPEX/Poseidon, + Jason-1 and OSTM/Jason-2, and referenced to the geoid. Along with this + dataset, two additional ancillary data files are included in the same + directory which contain the number of observations and standard error + co-located on the same 1 degree grids. + + + - [AVISO+ website](https://www.aviso.altimetry.fr/en/data/products/sea-surface-height-products/global/madt-h-uv.html) + - [NASA JPL AVISO website](https://podaac.jpl.nasa.gov/dataset/AVISO_L4_DYN_TOPO_1DEG_1MO) + + + When using Ssalto/Duacs data (NRT or DT along-track Absolute Dynamic + Topography (ADT), maps of SLA geostrophic currents (MSLA UV) or maps of + ADT heights and currents (MADT H and UV), climatologies and averages of + MSLA-H), please cite: "The altimeter products were produced by + Ssalto/Duacs and distributed by Aviso, with support from Cnes + (http://www.aviso.altimetry.fr/duacs/)" + + + (missing) + + + + + - ftp://podaac-ftp.jpl.nasa.gov/allData/aviso/L4/dynamic_topo_1deg_1mo/zos_AVISO_L4_199210-201012.nc + + + + + - climatologyMapSSH + + + + + + Argo Mixed Layer Depth (MLD) climatology + + + ocean + + + A mixed layer climatology and database (described in Holte et al. 2017) + using Argo profiles and a hybrid method (Holte and Talley 2009) for + finding the mixed layer depth (MLD). The climatology incorporates over + 1,385,000 Argo profiles (through February 2017). The new hybrid algorithm + models the general shape of each profile, searches for physical features + in the profile, and calculates threshold and gradient MLDs to assemble a + suite of possible MLD values. It then analyzes the patterns in the suite + to select a final MLD estimate. Results are also presented for MLDs + calculated using de Boyer Montegut et al.'s (2004) threshold values. + + + [UCSD Mixed Layer Website](http://mixedlayer.ucsd.edu/) + + + [Acknowledgment:](http://mixedlayer.ucsd.edu/) If you use this data, + please cite it as: Holte, J., L. D. Talley, J. Gilson, and D. Roemmich + (2017), An Argo mixed layer climatology and database, Geophys. Res. + Lett., 44, 5618–5626, doi:10.1002/2017GL073426. + + + - [Holte et al. (2017)](http://onlinelibrary.wiley.com/doi/10.1002/2017GL073426/full) + - [Holte and Talley (2009)](http://journals.ametsoc.org/doi/abs/10.1175/2009JTECHO543.1) + - [de Boyer Montegut et al. (2004)](https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2004JC002378) + + + @article{Holte2017, + author = {James Holte and Lynne D. Talley and John Gilson and Dean Roemmich}, + title = {An Argo mixed layer climatology and database}, + journal = {Geophysical Research Letters}, + year = {2017}, + volume = {44}, + number = {11}, + pages = {5618-5626}, + keywords = {Argo, mixed layer, climatology, global}, + doi = {10.1002/2017GL073426}, + url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2017GL073426} + } + + @article{Holte2009, + author = { James Holte and Lynne Talley }, + title = {A New Algorithm for Finding Mixed Layer Depths with Applications to Argo Data and Subantarctic Mode Water Formation}, + journal = {Journal of Atmospheric and Oceanic Technology}, + volume = {26}, + number = {9}, + pages = {1920-1939}, + year = {2009}, + doi = {10.1175/2009JTECHO543.1}, + URL = {https://doi.org/10.1175/2009JTECHO543.1} + } + + @article{deBoyerMontegut2004, + author = {Cl\'{e}ment {de Boyer Mont\'{e}gut} and Gurvan Madec and Albert S. Fischer and Alban Lazar and Daniele Iudicone}, + title = {Mixed layer depth over the global ocean: An examination of profile data and a profile‐based climatology}, + journal = {Journal of Geophysical Research: Oceans}, + volume = {109}, + number = {C12}, + pages = {}, + year = {2004}, + keywords = {mixed layer, mixed layer depth criterion, density compensation}, + doi = {10.1029/2004JC002378}, + url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2004JC002378} + } + + + - http://mixedlayer.ucsd.edu/data/Argo_mixedlayers_monthlyclim_03192017.nc + + + + + - climatologyMapMLD + + + + + + Meridional Heat Transport (MHT) + + + ocean + + + (missing) + + + (missing) + + + (missing) + + + [Trenberth and Caron (2000)](https://doi.org/10.1175/1520-0442%282000%29013<4358%3ATSORSL>2.0.CO%3B2) + + + @article{Trenberth2000, + author = { Kevin E. Trenberth and Julie M. Caron }, + title = {The Southern Oscillation Revisited: Sea Level Pressures, Surface Temperatures, and Precipitation}, + journal = {Journal of Climate}, + volume = {13}, + number = {24}, + pages = {4358-4365}, + year = {2000}, + doi = {10.1175/1520-0442(2000)013<4358:TSORSL>2.0.CO;2}, + URL = {https://doi.org/10.1175/1520-0442(2000)013<4358:TSORSL>2.0.CO;2} + } + + + (missing) + + + (missing) + + + - meridionalHeatTransport + + + + + + Roemmich-Gilson Argo Climatology + + + ocean + + + This new version of the Roemmich-Gilson Argo Climatology extends the + analysis of Argo-only derived temperature and salinity fields through + 2016. Several marginal seas and the Artic Oean have been added. The + analysis method is similar to what was descibed in the Progress In + Oceanography Roemmich and Gilson paper (2009). The only modification has + been to scale the zonal equatorial correlation of the optimal estimation + step, by 8 times, versus 4 times as in the 2009 paper. The additional + Argo data utilized in the analysis results in a longer monthly record as + well as better estimates of the mean and variability fields. Monthly + updates are available in between major yearly re-analyses. + + + [Scripps Roemmich-Gilson Argo Website](http://sio-argo.ucsd.edu/RG_Climatology.html) + + + [Acknowledgment:](http://sio-argo.ucsd.edu/RG_Climatology.html) Roemmich, + D. and J. Gilson, 2009: The 2004-2008 mean and annual cycle of + temperature, salinity, and steric height in the global ocean from the + Argo Program. Progress in Oceanography, 82, 81-100. + + + [Roemmich and Gilson (2009)](http://www.sciencedirect.com/science/article/pii/S0079661109000160) + + + @article{Roemmich2009, + title = "The 2004–2008 mean and annual cycle of temperature, salinity, and steric height in the global ocean from the Argo Program", + journal = "Progress in Oceanography", + volume = "82", + number = "2", + pages = "81 - 100", + year = "2009", + issn = "0079-6611", + doi = "10.1016/j.pocean.2009.03.004", + url = "http://www.sciencedirect.com/science/article/pii/S0079661109000160", + author = "Dean Roemmich and John Gilson" + } + + + - ftp://kakapo.ucsd.edu/pub/gilson/argo_climatology/RG_ArgoClim_Temperature_2017.nc.gz + - ftp://kakapo.ucsd.edu/pub/gilson/argo_climatology/RG_ArgoClim_Salinity_2017.nc.gz + + + preprocess_observations/Process_RG_Argo_climatology.ipynb + + + - climatologyMapArgoTemperature + - climatologyMapArgoSalinity + + + + + + SOSE potential temperature and salinity + + + ocean + + + Monthly potential temperature and salinity output from the Southern Ocean + State Estimate (SOSE) covering years 2005-2010 + + + [SOSE Website at UCSD] + (http://sose.ucsd.edu/sose_stateestimation_data_05to10.html) + + + [Conditions of use] + (http://sose.ucsd.edu/sose_stateestimation_disclaimer.html): The data on + these webpages are made freely available for scientific, bona fide, + not-for-profit research only. If your use of the data is different (e.g. + commercial), you must contact the data providers and receive written + permission for your use of the data prior to any such use. The user must + acknowledge SOSE data in all products or publications that use them, e.g. + by including the following written note: "Computational resources for the + SOSE were provided by NSF XSEDE resource grant OCE130007." An appropriate + citation should also be made. + + + [Mazloff et al. (2010)](http://doi.org/10.1175/2009JPO4236.1) + + + @article{Mazloff2010, + author = {Matthew R. Mazloff and Patrick Heimbach and Carl Wunsch}, + title = {An Eddy-Permitting Southern Ocean State Estimate}, + journal = {Journal of Physical Oceanography}, + volume = {40}, + number = {5}, + pages = {880-899}, + year = {2010}, + doi = {10.1175/2009JPO4236.1}, + URL = {https://doi.org/10.1175/2009JPO4236.1} + } + + + - http://sose.ucsd.edu/DATA/SO6_V2/THETA_mnthlyBar.0000000100.data.gz + - http://sose.ucsd.edu/DATA/SO6_V2/THETA_mnthlyBar.0000000100.meta + - http://sose.ucsd.edu/DATA/SO6_V2/SALT_mnthlyBar.0000000100.data.gz + - http://sose.ucsd.edu/DATA/SO6_V2/SALT_mnthlyBar.0000000100.meta + + + preprocess_observations/remap_SOSE_T_S.py + + + - climatologyMapSoseTemperature + - climatologyMapSoseSalinity + + + + + + Antarctic melt rates and fluxes + + + ocean + + + Melt rates and melt fluxes from Rignot et al. (2013) + + + [Ice-Shelf Melting Around Antarctica](http://science.sciencemag.org/content/341/6143/266) + + + Data available upon request from co-author J. Mouginot. + + + [Rignot et al. (2013)](http://science.sciencemag.org/content/341/6143/266) + + + @article{Rignot2013, + title = {Ice-{Shelf} {Melting} {Around} {Antarctica}}, + volume = {341}, + url = {http://www.ncbi.nlm.nih.gov/pubmed/23765278}, + doi = {10.1126/science.1235798}, + number = {6143}, + journal = {Science}, + author = {Rignot, E. and Jacobs, S. and Mouginot, J. and Scheuchl, B.}, + month = jul, + year = {2013}, + pages = {266--270} + } + + + - http://science.sciencemag.org/highwire/filestream/594977/field_highwire_adjunct_files/0/1235798tableS1.xlsx + - (data available upon request from J. Mouginot) + + + preprocess_observations/remap_rignot.py + + + - climatologyMapAntarcticMelt + - timeSeriesAntarcticMelt + + + + + + HadISST Nino 3.4 Index + + + ocean + + + (missing) + + + (missing) + + + (missing) + + + (missing) + + + (missing) + + + (missing) + + + (missing) + + + - indexNino34 + + + + + + ERS SSTv4 Nino 3.4 Index + + + ocean + + + (missing) + + + (missing) + + + (missing) + + + (missing) + + + (missing) + + + (missing) + + + (missing) + + + - indexNino34 + + + + + + + + + + Ice concentration: SSM/I, NASATeam algorithm + + + seaice + + + This data set is generated from brightness temperature data and is + designed to provide a consistent time series of sea ice concentrations + spanning the coverage of several passive microwave instruments. The data + are provided in the polar stereographic projection at a grid cell size of + 25 x 25 km. + + + [NSIDC NASATeam Website](http://nsidc.org/data/NSIDC-0051) + + + NASA data are not copyrighted; however, when you publish our data or + results derived therefrom, we request that you include an acknowledgment + within the text of the publication and reference list. + [Data Citation and Acknowledgements] + (https://podaac.jpl.nasa.gov/CitingPODAAC) + + + [Cavalieri et al. (1996)](https://doi.org/10.5067/8GQ8LZQVL0VL) + + + @misc{Cavalieri1996, + author = {D. J. Cavalieri, and C. L. Parkinson and P. Gloersen and H. J. Zwally}, + title = {Sea Ice Concentrations from Nimbus-7 SMMR and DMSP SSM/I-SSMIS Passive Microwave Data, Version 1}, + year = {1996}, + doi = {10.5067/8GQ8LZQVL0VL}, + notes = {updated yearly}, + url = {https://doi.org/10.5067/8GQ8LZQVL0VL} + } + + + (missing, requires registration with NSIDC) + + + (missing) + + + - climatologyMapSeaIceConcNH + - climatologyMapSeaIceConcSH + + + + + + Ice concentration: SSM/I, Bootstrap algorithm + + + seaice + + + This sea ice concentration data set was derived using measurements from + the Scanning Multichannel Microwave Radiometer (SMMR) on the Nimbus-7 + satellite and from the Special Sensor Microwave/Imager (SSM/I) sensors on + the Defense Meteorological Satellite Program's (DMSP) -F8, -F11, and -F13 + satellites. Measurements from the Special Sensor Microwave Imager/Sounder + (SSMIS) aboard DMSP-F17 are also included. The data set has been + generated using the Advanced Microwave Scanning Radiometer - Earth + Observing System (AMSR-E) Bootstrap Algorithm with daily varying + tie-points. Daily (every other day prior to July 1987) and monthly data + are available for both the north and south polar regions. Data are + gridded on the SSM/I polar stereographic grid (25 x 25 km) and provided + in two-byte integer format. Data are available via FTP. + + + [NSIDC Bootstrap Website](http://nsidc.org/data/NSIDC-0079) + + + NASA data are not copyrighted; however, when you publish our data or + results derived therefrom, we request that you include an acknowledgment + within the text of the publication and reference list. + [Data Citation and Acknowledgements] + (https://podaac.jpl.nasa.gov/CitingPODAAC) + + + [Comiso (2017)](https://doi.org/10.5067/7Q8HCCWS4I0R) + + + @misc{Comiso1996, + author = {J. C. Comiso}, + title = {Bootstrap Sea Ice Concentrations from Nimbus-7 SMMR and DMSP SSM/I-SSMIS, Version 3}, + year = {2017}, + doi = {10.5067/7Q8HCCWS4I0R}, + notes = {updated yearly}, + url = {https://doi.org/10.5067/7Q8HCCWS4I0R} + } + + + (missing, requires registration with NSIDC) + + + (missing) + + + - climatologyMapSeaIceConcNH + - climatologyMapSeaIceConcSH + + + + + + Ice area and extent time series: SSM/I derived + + + seaice + + + The sea ice data presented here were derived from satellite + passive-microwave radiometers, specifically, the Scanning Multichannel + Microwave Radiometer (SMMR) on NASA's Nimbus 7 satellite, for November + 1978-August 1987, a sequence of Special Sensor Microwave Imagers (SSMIs) + on the F8, F11, and F13 satellites of the Defense Meteorological + Satellite Program (DMSP), for August 1987-December 2007, and the Special + Sensor Microwave Imager Sounder (SSMIS) on the DMSP F17 satellite for + January 2008-December 2012. The baseline data used were daily maps of + sea ice concentration. The maps are polar stereographic projections with + individual grid elements of approximately 25 km x 25 km; and the ice + concentration data are also archived at the National Snow and Ice Data + Center (NSIDC) at http://nsidc.org. The concentrations are calculated for + each ocean grid element and are used to derive 'sea ice extent', which is + calculated as the sum of all ocean elements having a sea ice + concentration of at least 15%, and 'sea ice area', which is calculated as + the sum over all ocean grid elements of the product of ice concentration + and grid element area. The data sets provided here include the + hemispheric totals and additionally the values for nine regions in the + Arctic and five regions in the Antarctic. These regions are identified in + Figures 1 and 2 respectively. Figures 3 and 4 provide plots of the trends + in the Arctic and Antarctic sea ice extents, along with monthly + deviations and 12-month running means. The monthly deviations are + calculated by taking the individual month's ice extent/area and + subtracting from it the average over the course of the data set of the + extents/areas for that month. + + + [NASA Ice area and extent website](https://neptune.gsfc.nasa.gov/csb/index.php?section=59) + + + NASA data are not copyrighted; however, when you publish our data or + results derived therefrom, we request that you include an acknowledgment + within the text of the publication and reference list. + [Data Citation and Acknowledgements] + (https://podaac.jpl.nasa.gov/CitingPODAAC) + + + - [Cavalieri et al. (1999)](https://doi.org/10.1029/1999JC900081) + - [Cavalieri et al. (2012)](https://doi.org/10.1109/LGRS.2011.2166754) + - [Cavalieri and Parkinson (2012)](https://doi.org/10.5194/tc-6-881-2012) + - [Parkinson et al. (1999)](https://doi.org/0.1029/1999JC900082) + - [Parkinson and Cavalieri (2012)](https://doi.org/10.5194/tc-6-871-2012) + - [Zwally et al. (2002)](https://doi.org/10.1029/2000JC000733) + + + @article{Cavalieri1999, + author = {D. J. Cavalieri and C. L. Parkinson and P. Gloersen and J. C. Comiso and H. J. Zwally}, + title = {Deriving long‐term time series of sea ice cover from satellite passive‐microwave multisensor data sets}, + journal = {Journal of Geophysical Research: Oceans}, + volume = {104}, + number = {C7}, + year = {1999}, + pages = {15803-15814}, + doi = {10.1029/1999JC900081}, + url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/1999JC900081} + } + @article{Cavalieri2012a, + author={D. J. Cavalieri and C. L. Parkinson and N. DiGirolamo and A. Ivanoff}, + journal={IEEE Geoscience and Remote Sensing Letters}, + title={Intersensor Calibration Between F13 SSMI and F17 SSMIS for Global Sea Ice Data Records}, + year={2012}, + volume={9}, + number={2}, + pages={233-236}, + doi={10.1109/LGRS.2011.2166754}, + ISSN={1545-598X}, + month={March} + } + @Article{Cavalieri2012b, + AUTHOR = {Cavalieri, D. J. and Parkinson, C. L.}, + TITLE = {Arctic sea ice variability and trends, 1979--2010}, + JOURNAL = {The Cryosphere}, + VOLUME = {6}, + YEAR = {2012}, + NUMBER = {4}, + PAGES = {881--889}, + URL = {https://www.the-cryosphere.net/6/881/2012/}, + DOI = {10.5194/tc-6-881-2012} + } + @article{Parkinson1999, + author = {Claire L. Parkinson and Donald J. Cavalieri and Per Gloersen and H. Jay Zwally and Josefino C. Comiso}, + title = {Arctic sea ice extents, areas, and trends, 1978–1996}, + journal = {Journal of Geophysical Research: Oceans}, + volume = {104}, + number = {C9}, + year = {1999}, + pages = {20837-20856}, + doi = {10.1029/1999JC900082}, + url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/1999JC900082} + } + @Article{Parkinson2012, + AUTHOR = {Parkinson, C. L. and Cavalieri, D. J.}, + TITLE = {Antarctic sea ice variability and trends, 1979--2010}, + JOURNAL = {The Cryosphere}, + VOLUME = {6}, + YEAR = {2012}, + NUMBER = {4}, + PAGES = {871--880}, + URL = {https://www.the-cryosphere.net/6/871/2012/}, + DOI = {10.5194/tc-6-871-2012} + } + @article{Zwally2002, + author = {H. Jay Zwally and Josefino C. Comiso and Claire L. Parkinson and Donald J. Cavalieri and Per Gloersen}, + title = {Variability of Antarctic sea ice 1979–1998}, + journal = {Journal of Geophysical Research: Oceans}, + volume = {107}, + number = {C5}, + pages = {9-1-9-19}, + keywords = {sea ice, Antarctic, climate, passive microwave, Southern Ocean}, + doi = {10.1029/2000JC000733}, + url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2000JC000733}, + year = {2002} + } + + + - https://neptune.gsfc.nasa.gov/uploads/files/NH_IceArea_Monthly_1978-2012.txt + - https://neptune.gsfc.nasa.gov/uploads/files/NH_IceExt_Monthly_1978-2012.txt + - https://neptune.gsfc.nasa.gov/uploads/files/SH_IceArea_Monthly_1978-2012.txt + - https://neptune.gsfc.nasa.gov/uploads/files/SH_IceExt_Monthly_1978-2012.txt + + + (missing) + + + - timeSeriesSeaIceAreaVol + + + + + + IceSat Ice Thickness + + + seaice + + + This data set provides measurements of sea ice freeboard and sea ice + thickness for the Arctic region. The data were derived from measurements + made by from the Ice, Cloud, and land Elevation Satellite (ICESat) + Geoscience Laser Altimeter System (GLAS) instrument, the Special Sensor + Microwave/Imager (SSM/I), and climatologies of snow and drift of ice. + + + [NASA: Arctic Sea Ice Freeboard and Thickness](http://nsidc.org/data/NSIDC-0393) + + + NASA data are not copyrighted; however, when you publish our data or + results derived therefrom, we request that you include an acknowledgment + within the text of the publication and reference list. + [Data Citation and Acknowledgements] + (https://podaac.jpl.nasa.gov/CitingPODAAC) + + + [Yi and Zwally (2009)](https://doi.org/10.5067/SXJVJ3A2XIZT) + + + @misc{Yi2009, + author = {D. Yi and H. J. Zwally}, + title = {Arctic Sea Ice Freeboard and Thickness, Version 1}, + year = {2009}, + doi = {10.5067/7Q8HCCWS4I0R}, + url = {https://doi.org/10.5067/SXJVJ3A2XIZT} + } + + + (missing, requires registration with NSIDC) + + + + + - timeSeriesSeaIceAreaVol + + + + + + PIOMAS Arctic Sea Ice Volume Reanalysis + + + seaice + + + Sea Ice Volume is calculated using the Pan-Arctic Ice Ocean Modeling and + Assimilation System (PIOMAS, Zhang and Rothrock, 2003) developed at + APL/PSC. Anomalies for each day are calculated relative to the average + over the 1979 -2016 period for that day of the year to remove the annual + cycle. The model mean annual cycle of sea ice volume over this period + ranges from 28,000 km3 in April to 11,500 km3 in September. + + + [PIOMAS website](http://psc.apl.uw.edu/research/projects/arctic-sea-ice-volume-anomaly/) + + + Data is public, but they optionally ask for basic information about the + person downloading the data (name, e-mail, and affiliation). + + + - [Schweiger et al. (2011)](https://doi.org/10.1029/2011JC007084) + - [Zhang and Rothrock (2003)](https://doi.org/10.1175/1520-0493%282003%29131<0845:MGSIWA>2.0.CO;2) + + + @article{Schweiger2011, + author = {Axel Schweiger and Ron Lindsay and Jinlun Zhang and Mike Steele and Harry Stern and Ron Kwok}, + title = {Uncertainty in modeled Arctic sea ice volume}, + journal = {Journal of Geophysical Research: Oceans}, + volume = {116}, + number = {C8}, + pages = {}, + keywords = {Arctic, climate change, ice volume, modelling, sea ice}, + doi = {10.1029/2011JC007084}, + url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2011JC007084}, + year = {2011} + } + @article{Zhang2003, + author = { Jinlun Zhang and D. A. Rothrock }, + title = {Modeling Global Sea Ice with a Thickness and Enthalpy Distribution Model in Generalized Curvilinear Coordinates}, + journal = {Monthly Weather Review}, + volume = {131}, + number = {5}, + pages = {845-861}, + year = {2003}, + doi = {10.1175/1520-0493(2003)131<0845:MGSIWA>2.0.CO;2}, + URL = {https://doi.org/10.1175/1520-0493(2003)131<0845:MGSIWA>2.0.CO;2} + } + + + - http://psc.apl.uw.edu/wordpress/wp-content/uploads/schweiger/ice_volume/PIOMAS.2sst.monthly.Current.v2.1.txt + + + (missing) + + + - timeSeriesSeaIceAreaVol + + + + + + + + + diff --git a/mpas_analysis/obs/observationstable.xml b/mpas_analysis/obs/observationstable.xml deleted file mode 100644 index bd202df5d..000000000 --- a/mpas_analysis/obs/observationstable.xml +++ /dev/null @@ -1,153 +0,0 @@ - - - - - - sst Hadley-NOAA - - - ocean - - - SST global annual climatology and trend - - - - Global latitude/longitude plot on ocean native grid. Annual climatologies computed over 5-10 year periods at regular intervals throughout the run. - - Time series of area-weighted (AW) global mean (1-year running average). - - - [Merged Hadley Center-NOAA/OI data set from Hurrell et al. 2008](https://climatedataguide.ucar.edu/climate-data/merged-hadley-noaaoi-sea-surface-temperature-sea-ice-concentration-hurrell-et-al-2008) - - Update 4/11/18: emailed UCAR to ask about their release policy. - - - - - CESM Atm diagnostic package - - Gent et al. (2011, Fig.1) - - - - - - - - - - SSS NASA Aquarius - - - ocean - - - SSS global annual climatology - - - - Global latitude/longitude plot on ocean native grid . Annual climatologies computed over 5-10 year periods at regular intervals throughout the run. - - - [NASA Aquarius satellite data ~4 years until Jun 2015](ftp://podaac-ftp.jpl.nasa.gov/allData/aquarius/L3/mapped/V4/7day_running/SCI/) - - This statement is from the NASA daac (Distributed - Active Archive Center) website: "NASA data are not copyrighted; however, - when you publish our data or results derived therefrom, we request that - you include an acknowledgment within the text of the publication and - reference list." This should apply to all NASA data sets. - - - - [PHC](http://psc.apl.washington.edu/nonwp_projects/PHC/Climatology.html) - or [WOA13 climatology](https://www.nodc.noaa.gov/OC5/woa13/). - - - - Large and Danabasoglu (2006, Fig.1) - - Griffies et al. (2009, Fig. 8) - - - - - - - - - - - Ice area/extent annual climatology, and annual and seasonal trends - - - seaice - - - Sea ice concentration - - - - Arctic and Antarctic seasonal and annual climatologies (maps) of ice area and extent. Annual climatologies computed over 5-10 year periods at regular intervals throughout the run. - - Daily, monthly and 1-year average time series of area-weighted ice area and extent. - - - - [Ice concentration: SSM/I, NASATeam algorithm(both NH and SH)](http://nsidc.org/data/NSIDC-0051) - - [Ice concentration: SSM/I, Bootstrap algorithm (both NH and SH)](http://nsidc.org/data/NSIDC-0079) - - [Ice area time series: SSM/I derived (both NH and SH)](http://neptune.gsfc.nasa.gov/csb/index.php?section=59) - - Same as all NASA data. - - - - - [Antarctic ship-based data](http://aspect.antarctica.gov.au/data) - - [Ice type, and drift](http://marine.copernicus.eu/services-portfolio/access-to-products/?option=com_csw&view=details&product_id=SEAICE_GLO_SEAICE_L4_NRT_OBSERVATIONS_011_001) - - [MANY data sets available for both ocean and sea ice, both global and regional](high-reshttp://marine.copernicus.edu) - - - - CESM CICE diagnostics - - Ivanova et al. (2012) - - Worby et al. (2008) - - - See CESM sea ice diagnostic package - - - - - - - - - Present-day ice sheet area and volume (scalar) - - - landice - - - Land ice area / volume - - - - Difference between modeled and observed values. - - - Greenland ice thickness at bed topography at 1 km posting - - [Bedmap2 paper](http://www.the-cryosphere.net/7/375/2013/), [Bedmap2 data](https://www.bas.ac.uk/project/bedmap-2/) - - [R-Topo2 paper](http://www.earth-syst-sci-data-discuss.net/essd-2016-3/), [R-Topo2 data](https://www.pangaea.de/PHP/hs.php?s=Maps&d=RTopo-2.0&ID=856844) - Antarctic ice thickness and bed topography at 1 km posting - - Same as all NASA data. - - - - - [Antarctic ship-based data](http://aspect.antarctica.gov.au/data) - - [Ice type, and drift](http://marine.copernicus.eu/services-portfolio/access-to-products/?option=com_csw&view=details&product_id=SEAICE_GLO_SEAICE_L4_NRT_OBSERVATIONS_011_001) - - [MANY data sets available for both ocean and sea ice, both global and regional](high-reshttp://marine.copernicus.edu) - - - - Bamber et al. (2013) - - Fretwell et al. (2013) - - - validate initial conditions - - - - - - - From da72b6f98fff7266ea5298fe5e9380a5c97e420e Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Tue, 24 Apr 2018 22:00:37 +0200 Subject: [PATCH 66/71] A few small fixes to x ticks Some typos in the docstring are fixed. If yearStride is specified, maxXTicks will be ignored so the user's request will be honored. --- mpas_analysis/shared/plot/plotting.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/mpas_analysis/shared/plot/plotting.py b/mpas_analysis/shared/plot/plotting.py index 5918b9346..7c5ca9811 100644 --- a/mpas_analysis/shared/plot/plotting.py +++ b/mpas_analysis/shared/plot/plotting.py @@ -1214,8 +1214,8 @@ def plot_xtick_format(calendar, minDays, maxDays, maxXTicks, yearStride=None): the maximum number of tick marks to display, used to sub-sample ticks if there are too many - stride : int, optionoal - the number of months or years to skip over between ticks + yearStride : int, optional + the number of years to skip over between ticks ''' # Authors # ------- @@ -1229,6 +1229,8 @@ def plot_xtick_format(calendar, minDays, maxDays, maxXTicks, yearStride=None): if yearStride is not None or end.year - start.year > maxXTicks/2: if yearStride is None: yearStride = 1 + else: + maxXTicks = None major = [date_to_days(year=year, calendar=calendar) for year in np.arange(start.year, end.year+1, yearStride)] formatterFun = partial(_date_tick, calendar=calendar, From a916406505c2f5f620204b0d0b8b441671acc546 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Tue, 24 Apr 2018 22:11:56 +0200 Subject: [PATCH 67/71] Expand comments on manual ticks in config.default --- mpas_analysis/config.default | 61 ++++++++++++++++++++++++++---------- 1 file changed, 45 insertions(+), 16 deletions(-) diff --git a/mpas_analysis/config.default b/mpas_analysis/config.default index d0ef1258b..966d9c71f 100644 --- a/mpas_analysis/config.default +++ b/mpas_analysis/config.default @@ -328,10 +328,12 @@ preprocessedFieldPrefix = ohc # window) movingAveragePoints = 12 -# An optional first year for the tick marks on the x axis +# An optional first year for the tick marks on the x axis. Leare commented out +# to start at the beginning of the time series. # firstYearXTicks = 1 -# An optional number of years between tick marks on the x axis +# An optional number of years between tick marks on the x axis. Leave +# commented out to determine the distance between ticks automatically. # yearStrideXTicks = 1 [hovmollerOHCAnomaly] @@ -350,10 +352,13 @@ colorbarLevels = [-2.4, -0.8, -0.4, -0.2, 0, 0.2, 0.4, 0.8, 2.4] # contour line levels contourLevels = np.arange(-2.5, 2.6, 0.5) -# An optional first year for the tick marks on the x axis +# An optional first year for the tick marks on the x axis. Leare commented out +# to start at the beginning of the time series. + # firstYearXTicks = 1 -# An optional number of years between tick marks on the x axis +# An optional number of years between tick marks on the x axis. Leave +# commented out to determine the distance between ticks automatically. # yearStrideXTicks = 1 [hovmollerTemperatureAnomaly] @@ -376,10 +381,14 @@ colorbarLevels = [-1, -0.5, -0.2, -0.05, 0, 0.05, 0.2, 0.5, 1] # contour line levels contourLevels = np.arange(-1.0, 1.26, 0.25) -# An optional first year for the tick marks on the x axis +# An optional first year for the tick marks on the x axis. Leare commented out +# to start at the beginning of the time series. + # firstYearXTicks = 1 -# An optional number of years between tick marks on the x axis +# An optional number of years between tick marks on the x axis. Leave +# commented out to determine the distance between ticks automatically. + # yearStrideXTicks = 1 [hovmollerSalinityAnomaly] @@ -402,10 +411,14 @@ colorbarLevels = [-0.1, -0.02, -0.003, -0.001, 0, 0.001, 0.003, 0.02, 0.1] # contour line levels contourLevels = np.arange(-0.1, 0.11, 0.02) -# An optional first year for the tick marks on the x axis +# An optional first year for the tick marks on the x axis. Leare commented out +# to start at the beginning of the time series. + # firstYearXTicks = 1 -# An optional number of years between tick marks on the x axis +# An optional number of years between tick marks on the x axis. Leave +# commented out to determine the distance between ticks automatically. + # yearStrideXTicks = 1 [timeSeriesSST] @@ -420,10 +433,14 @@ regions = ['global'] # window) movingAveragePoints = 12 -# An optional first year for the tick marks on the x axis +# An optional first year for the tick marks on the x axis. Leare commented out +# to start at the beginning of the time series. + # firstYearXTicks = 1 -# An optional number of years between tick marks on the x axis +# An optional number of years between tick marks on the x axis. Leave +# commented out to determine the distance between ticks automatically. + # yearStrideXTicks = 1 [indexNino34] @@ -534,10 +551,14 @@ movingAveragePoints = 12 # latitude) for climatological MOC plots movingAveragePointsClimatological = 1 -# An optional first year for the tick marks on the x axis +# An optional first year for the tick marks on the x axis. Leare commented out +# to start at the beginning of the time series. + # firstYearXTicks = 1 -# An optional number of years between tick marks on the x axis +# An optional number of years between tick marks on the x axis. Leave +# commented out to determine the distance between ticks automatically. + # yearStrideXTicks = 1 [timeSeriesSeaIceAreaVol] @@ -554,10 +575,14 @@ titleFontSize = 18 # plot on polar plot polarPlot = False -# An optional first year for the tick marks on the x axis +# An optional first year for the tick marks on the x axis. Leare commented out +# to start at the beginning of the time series. + # firstYearXTicks = 1 -# An optional number of years between tick marks on the x axis +# An optional number of years between tick marks on the x axis. Leave +# commented out to determine the distance between ticks automatically. + # yearStrideXTicks = 1 [climatologyMapSST] @@ -715,10 +740,14 @@ iceShelvesToPlot = ['Antarctica'] # Number of months over which to compute moving average movingAverageMonths = 1 -# An optional first year for the tick marks on the x axis +# An optional first year for the tick marks on the x axis. Leare commented out +# to start at the beginning of the time series. + # firstYearXTicks = 1 -# An optional number of years between tick marks on the x axis +# An optional number of years between tick marks on the x axis. Leave +# commented out to determine the distance between ticks automatically. + # yearStrideXTicks = 1 [climatologyMapSoseTemperature] From d3db91348137efa0d955c78b0df4d7e47d583ac0 Mon Sep 17 00:00:00 2001 From: Milena Veneziani Date: Tue, 24 Apr 2018 19:59:31 -0400 Subject: [PATCH 68/71] Update obs. database. Add Milena's matlab pre-process sea-ice scripts --- mpas_analysis/obs/observational_datasets.xml | 12 ++- .../Bootstrap_Antarctic_compute_climo.m | 73 +++++++++++++ .../Bootstrap_Arctic_compute_climo.m | 73 +++++++++++++ .../ICESat_Arctic_compute_climo.m | 95 ++++++++++++++++ preprocess_observations/IceaArea_txt2netcdf.m | 96 +++++++++++++++++ .../NASATeam_Antarctic_compute_climo.m | 74 +++++++++++++ .../NASATeam_Arctic_compute_climo.m | 74 +++++++++++++ preprocess_observations/PIOMAS_txt2netcdf.m | 101 ++++++++++++++++++ preprocess_observations/notes4seaiceData.txt | 13 +++ 9 files changed, 606 insertions(+), 5 deletions(-) create mode 100644 preprocess_observations/Bootstrap_Antarctic_compute_climo.m create mode 100644 preprocess_observations/Bootstrap_Arctic_compute_climo.m create mode 100644 preprocess_observations/ICESat_Arctic_compute_climo.m create mode 100644 preprocess_observations/IceaArea_txt2netcdf.m create mode 100644 preprocess_observations/NASATeam_Antarctic_compute_climo.m create mode 100644 preprocess_observations/NASATeam_Arctic_compute_climo.m create mode 100644 preprocess_observations/PIOMAS_txt2netcdf.m create mode 100644 preprocess_observations/notes4seaiceData.txt diff --git a/mpas_analysis/obs/observational_datasets.xml b/mpas_analysis/obs/observational_datasets.xml index d40ffc122..bfcafc2c2 100644 --- a/mpas_analysis/obs/observational_datasets.xml +++ b/mpas_analysis/obs/observational_datasets.xml @@ -31,7 +31,9 @@ (https://climatedataguide.ucar.edu/climate-data/merged-hadley-noaaoi-sea-surface-temperature-sea-ice-concentration-hurrell-et-al-2008) - Unknown + [Acknowledgment:] Hurrell, J. W., J. J. Hack, D. Shea, J. M. Caron, and J. Rosinski, + 2008: A New Sea Surface Temperature and Sea Ice Boundary Dataset for the Community + Atmosphere Model. Journal of Climate, 21, 5145-5153. [Hurrell et al. (2008)](https://doi.org/10.1175/2008JCLI2292.1) @@ -76,7 +78,8 @@ [NASA Aquarius FTP server] - (ftp://podaac-ftp.jpl.nasa.gov/allData/aquarius/L3/mapped/V4/7day_running/SCI/) + (https://podaac.jpl.nasa.gov/dataset/AQUARIUS_L4_OISSS_IPRC_7DAY_V4) + NASA data are not copyrighted; however, when you publish our data or @@ -91,7 +94,7 @@ - (missing) + (ftp://podaac-ftp.jpl.nasa.gov/allData/aquarius/L4/IPRC/v4/7day/) (missing) @@ -124,7 +127,6 @@ co-located on the same 1 degree grids. - - [AVISO+ website](https://www.aviso.altimetry.fr/en/data/products/sea-surface-height-products/global/madt-h-uv.html) - [NASA JPL AVISO website](https://podaac.jpl.nasa.gov/dataset/AVISO_L4_DYN_TOPO_1DEG_1MO) @@ -136,7 +138,7 @@ (http://www.aviso.altimetry.fr/duacs/)" - (missing) + [ftp://podaac.jpl.nasa.gov/allData/aviso/L4/dynamic_topo_1deg_1mo/docs/zosTechNote_AVISO_L4_199210-201012.pdf] diff --git a/preprocess_observations/Bootstrap_Antarctic_compute_climo.m b/preprocess_observations/Bootstrap_Antarctic_compute_climo.m new file mode 100644 index 000000000..af13bb614 --- /dev/null +++ b/preprocess_observations/Bootstrap_Antarctic_compute_climo.m @@ -0,0 +1,73 @@ +% +% Combined SSM/I-SSMIS and SMMR sea-ice concentration data for both the +% Arctic and Antarctic. +% *** Bootstrap algorithm *** +% +% Source: http://nsidc.org/data/NSIDC-0079 +% +clear all; +close all; + +homedir = getenv('HOME'); + +maindir = [homedir '/ACME/observations/obsdir/SeaIce/SSMI/'... + 'Bootstrap_NSIDC0079']; +datadir = [maindir '/final-gsfc/south/monthly']; +griddir = [homedir '/ACME/observations/obsdir/SeaIce/ICESat/Antarctic/climo']; +lonlatfile = 'spring_ICESat_gridded_mean_thickness'; +months4climo = [12 1 2; % (boreal) winter months + 3 4 5; % (boreal) spring months + 6 7 8; % (boreal) summer months + 9 10 11]; % (boreal) fall months +seasons = {'djf','mam','jja','son'}; + +M = 332; % Polar Stereographic grid for Antarctica, # of rows +N = 316; % Polar Stereographic grid for Antarctica, # of columns + +[err,cwd] = unix('pwd'); +% Read in lon,lat: +eval(sprintf('cd %s;',griddir)); +eval(sprintf('load %s.txt',lonlatfile)); +eval(sprintf('cd %s;',cwd)); +eval(sprintf('lat = %s(:,1);',lonlatfile)); +eval(sprintf('lon = %s(:,2);',lonlatfile)); +x = reshape(lon,M,N); +y = reshape(lat,M,N); + +eval(sprintf('cd %s;',datadir)); +for is=1:length(seasons), + season = char(seasons(is)); + + % Get list of files to compute seasonal climatologies from: + filenames = sprintf('bt_????%02d*',months4climo(is,1)); + for i=2:size(months4climo,2), + filenames = [filenames sprintf(' bt_????%02d*',months4climo(is,i))]; + end + eval(sprintf('[err,filelist] = unix(''/bin/ls %s'');',filenames)); + filelist = strsplit(filelist); % convert to cell of strings + filelist = filelist(2:end-1); % remove redudant first and last space chars + + % Compute seasonal climatology: + for ifile=1:length(filelist); + infile = char(filelist(ifile)); + % Read in binary data: + fid = fopen(infile,'r','l'); + aice(ifile,:,:) = fread(fid,[N M],'int16'); + fclose(fid); + aice(find(aice>1000)) = nan; + aice(find(aice==0))=nan; + end + aice = squeeze(nanmean(aice,1)); + aice = aice/1000; + aice(find(isnan(aice)==1)) = -999; + aice = aice'; + + % Write to file: + outfile = ['SSMI_Bootstrap_gridded_concentration_SH_' season]; + fid = fopen(sprintf('%s/%s.txt',maindir,outfile),'w'); + fprintf(fid,'%12.4f %12.4f %12.5f\n',[y(:)'; x(:)'; aice(:)']); + fclose(fid); + + clear aice +end +eval(sprintf('cd %s;',cwd)); diff --git a/preprocess_observations/Bootstrap_Arctic_compute_climo.m b/preprocess_observations/Bootstrap_Arctic_compute_climo.m new file mode 100644 index 000000000..3e53121db --- /dev/null +++ b/preprocess_observations/Bootstrap_Arctic_compute_climo.m @@ -0,0 +1,73 @@ +% +% Combined SSM/I-SSMIS and SMMR sea-ice concentration data for both the +% Arctic and Antarctic. +% *** Bootstrap algorithm *** +% +% Source: http://nsidc.org/data/NSIDC-0079 +% +clear all; +close all; + +homedir = getenv('HOME'); + +maindir = [homedir '/ACME/observations/obsdir/SeaIce/SSMI/'... + 'Bootstrap_NSIDC0079']; +datadir = [maindir '/final-gsfc/north/monthly']; +griddir = [homedir '/ACME/observations/obsdir/SeaIce/ICESat/Arctic/' ... + 'NSIDC0393_GLAS_SI_Freeboard_v01/glas_seaice_grids']; +lonfile = [griddir '/PS25km_north_lon.img']; +latfile = [griddir '/PS25km_north_lat.img']; +months4climo = [ 1 2 3; % (boreal) winter months + 4 5 6; % (boreal) spring months + 7 8 9; % (boreal) summer months + 10 11 12]; % (boreal) fall months +seasons = {'jfm','amj','jas','ond'}; + +M = 304; % Polar Stereographic grid for the Arctic, # of rows +N = 448; % Polar Stereographic grid for the Arctic, # of columns + +% Read in lon,lat: +fid = fopen(lonfile,'r','l'); +x = fread(fid,[M N],'single'); +fclose(fid); +fid = fopen(latfile,'r','l'); +y = fread(fid,[M N],'single'); +fclose(fid); + +[err,cwd] = unix('pwd'); +eval(sprintf('cd %s;',datadir)); +for is=1:length(seasons), + season = char(seasons(is)); + + % Get list of files to compute seasonal climatologies from: + filenames = sprintf('bt_????%02d*',months4climo(is,1)); + for i=2:size(months4climo,2), + filenames = [filenames sprintf(' bt_????%02d*',months4climo(is,i))]; + end + eval(sprintf('[err,filelist] = unix(''/bin/ls %s'');',filenames)); + filelist = strsplit(filelist); % convert to cell of strings + filelist = filelist(2:end-1); % remove redudant first and last space chars + + % Compute seasonal climatology: + for ifile=1:length(filelist); + infile = char(filelist(ifile)); + % Read in binary data: + fid = fopen(infile,'r','l'); + aice(ifile,:,:) = fread(fid,[M N],'int16'); + fclose(fid); + aice(find(aice>1000)) = nan; + aice(find(aice==0))=nan; + end + aice = squeeze(nanmean(aice,1)); + aice = aice/1000; + aice(find(isnan(aice)==1)) = -999; + + % Write to file: + outfile = ['SSMI_Bootstrap_gridded_concentration_NH_' season]; + fid = fopen(sprintf('%s/%s.txt',maindir,outfile),'w'); + fprintf(fid,'%12.4f %12.4f %12.5f\n',[y(:)'; x(:)'; aice(:)']); + fclose(fid); + + clear aice +end +eval(sprintf('cd %s;',cwd)); diff --git a/preprocess_observations/ICESat_Arctic_compute_climo.m b/preprocess_observations/ICESat_Arctic_compute_climo.m new file mode 100644 index 000000000..2dcae49a7 --- /dev/null +++ b/preprocess_observations/ICESat_Arctic_compute_climo.m @@ -0,0 +1,95 @@ +% +% ICESat sea-ice thickness data for the Arctic. +% +% Source: http://nsidc.org/data/NSIDC-0393 +% +clear all; +close all; + +homedir = getenv('HOME'); + +datadir = [homedir '/ACME/observations/obsdir/SeaIce/ICESat/Arctic/' ... + 'NSIDC0393_GLAS_SI_Freeboard_v01/glas_seaice_grids']; +% Infile names (austral spring (Oct-Nov), max Antarctic ice extent; +% austral late summer (Feb-Mar), min Antarctic ice extent): +on_files_th = {'laser2a_thickness_mskd.img','laser3a_thickness_mskd.img',... + 'laser3d_thickness_mskd.img','laser3g_thickness_mskd.img',... + 'laser3i_thickness_mskd.img','laser3k_thickness_mskd.img'}; +fm_files_th = {'laser1_thickness_mskd.img' ,'laser2b_thickness_mskd.img',... + 'laser3b_thickness_mskd.img','laser3e_thickness_mskd.img',... + 'laser3h_thickness_mskd.img','laser3j_thickness_mskd.img'}; +on_files_fb = {'laser2a_freeboard_mskd.img','laser3a_freeboard_mskd.img',... + 'laser3d_freeboard_mskd.img','laser3g_freeboard_mskd.img',... + 'laser3i_freeboard_mskd.img','laser3k_freeboard_mskd.img'}; +fm_files_fb = {'laser1_freeboard_mskd.img' ,'laser2b_freeboard_mskd.img',... + 'laser3b_freeboard_mskd.img','laser3e_freeboard_mskd.img',... + 'laser3h_freeboard_mskd.img','laser3j_freeboard_mskd.img'}; +outfiles = {'ICESat_gridded_mean_thickness_NH_on',... + 'ICESat_gridded_mean_thickness_NH_fm'}; +lonfile = 'PS25km_north_lon.img'; +latfile = 'PS25km_north_lat.img'; + +M = 304; % Polar Stereographic grid for the Arctic, # of rows +N = 448; % Polar Stereographic grid for the Arctic, # of columns + +eval(sprintf('cd %s;',datadir)); + +% Read in lon,lat: +fid = fopen(lonfile,'r','l'); +x = fread(fid,[M N],'single'); +fclose(fid); +fid = fopen(latfile,'r','l'); +y = fread(fid,[M N],'single'); +fclose(fid); + +% Compute Oct-Nov climatologies: +for ifile=1:length(on_files_th), + on_file = char(on_files_th(ifile)); + fid = fopen(on_file,'r','l'); + hi(ifile,:,:) = fread(fid,[M N],'single'); + fclose(fid); +end +hi(find(hi<0)) = nan; +hi = squeeze(nanmean(hi,1)); +hi(find(isnan(hi)==1)) = -999; +for ifile=1:length(on_files_fb), + on_file = char(on_files_fb(ifile)); + fid = fopen(on_file,'r','l'); + fb(ifile,:,:) = fread(fid,[M N],'single'); + fclose(fid); +end +fb(find(fb<0)) = nan; +fb = squeeze(nanmean(fb,1)); +fb(find(isnan(fb)==1)) = -999; +% Write to file: +outfile = char(outfiles(1)); +fid = fopen(sprintf('%s.txt',outfile),'w'); +fprintf(fid,'%12.4f %12.4f %12.5f %12.5f\n',[y(:)'; x(:)'; fb(:)'; hi(:)']); +fclose(fid); + +clear hi fb + +% Compute Feb-Mar climatologies: +for ifile=1:length(fm_files_th), + fm_file = char(fm_files_th(ifile)); + fid = fopen(fm_file,'r','l'); + hi(ifile,:,:) = fread(fid,[M N],'single'); + fclose(fid); +end +hi(find(hi<0)) = nan; +hi = squeeze(nanmean(hi,1)); +hi(find(isnan(hi)==1)) = -999; +for ifile=1:length(fm_files_fb), + fm_file = char(fm_files_fb(ifile)); + fid = fopen(fm_file,'r','l'); + fb(ifile,:,:) = fread(fid,[M N],'single'); + fclose(fid); +end +fb(find(fb<0)) = nan; +fb = squeeze(nanmean(fb,1)); +fb(find(isnan(fb)==1)) = -999; +% Write to file: +outfile = char(outfiles(2)); +fid = fopen(sprintf('%s.txt',outfile),'w'); +fprintf(fid,'%12.4f %12.4f %12.5f %12.5f\n',[y(:)'; x(:)'; fb(:)'; hi(:)']); +fclose(fid); diff --git a/preprocess_observations/IceaArea_txt2netcdf.m b/preprocess_observations/IceaArea_txt2netcdf.m new file mode 100644 index 000000000..573f12b81 --- /dev/null +++ b/preprocess_observations/IceaArea_txt2netcdf.m @@ -0,0 +1,96 @@ +% Converts txt IceArea files to netcdf files +% +% Data source: http://neptune.gsfc.nasa.gov/csb/index.php?section=59 +% + +workdir = '/lustre/atlas1/cli115/proj-shared/milena/observations/SeaIce/IceArea_timeseries'; +files = {'iceAreaNH','iceAreaSH'}; + +cwd = pwd; +eval(sprintf('cd %s;',workdir)); + +for i=1:length(files), + varname = char(files(i)); + infile = sprintf('%s_year.txt',varname); + outfile1 = sprintf('%s_year.nc', varname); + outfile2 = sprintf('%s_climo.nc', varname); + varname = [varname '_year']; + + % the following loads t (yyyy.yearfraction),icearea (km^2) + eval(sprintf('load %s;',infile)); + + % First create netcdf file with original data: + % + % create netcdf file + ncid = netcdf.create(outfile1,'clobber'); + % define dimension(s) + t_dimid = netcdf.defDim(ncid,'Time',netcdf.getConstant('NC_UNLIMITED')); + strLen_dimid = netcdf.defDim(ncid,'StrLen',64); + % define variables and attributes + t_varid = netcdf.defVar(ncid,'xtime','NC_CHAR',[strLen_dimid,t_dimid]); + %t_varid = netcdf.defVar(ncid,'time','NC_DOUBLE',t_dimid); + icearea_varid = netcdf.defVar(ncid,'IceArea','NC_DOUBLE',t_dimid); + netcdf.putAtt(ncid,t_varid,'long_name','calendar date'); + %netcdf.putAtt(ncid,t_varid,'long_name','days since 0001-01-01'); + netcdf.putAtt(ncid,t_varid,'format','YYYY-MM-DD_HH:MM:SS character string'); + netcdf.putAtt(ncid,icearea_varid,'long_name','SSM/I derived ice area'); + netcdf.putAtt(ncid,icearea_varid,'units','km^2'); + + % leave define mode and enter data mode to write data + netcdf.endDef(ncid); + + % add variables + eval(sprintf('t = %s(:,1);',varname)); + eval(sprintf('var = %s(:,2);',varname)); + % go from year.fraction_of_year to date (string format) + tdate = yf2num(t); + date = datestr(tdate,'yyyy-mm-dd_HH:MM:SS'); + ntot = length(t); + %netcdf.putVar(ncid,t_varid,0,ntot,t); + for n=1:ntot, + netcdf.putVar(ncid,t_varid,[0,n-1],[size(date,2),1],date(n,:)); + end + netcdf.putVar(ncid,icearea_varid,0,ntot,var); + + % close netcdf file + netcdf.close(ncid); + + % Then create netcdf file with climatological annual cycle: + % + % create netcdf file + ncid = netcdf.create(outfile2,'clobber'); + % define dimension(s) + t_dimid = netcdf.defDim(ncid,'Time',netcdf.getConstant('NC_UNLIMITED')); + strLen_dimid = netcdf.defDim(ncid,'StrLen',64); + % define variables and attributes + t_varid = netcdf.defVar(ncid,'xtime','NC_CHAR',[strLen_dimid,t_dimid]); + %t_varid = netcdf.defVar(ncid,'time','NC_DOUBLE',t_dimid); + icearea_varid = netcdf.defVar(ncid,'IceArea','NC_DOUBLE',t_dimid); + netcdf.putAtt(ncid,t_varid,'long_name','climatological date'); + %netcdf.putAtt(ncid,t_varid,'long_name','days since 0001-01-01'); + netcdf.putAtt(ncid,t_varid,'format','YYYY-MM-DD_HH:MM:SS character string'); + netcdf.putAtt(ncid,icearea_varid,'long_name','SSM/I derived ice area'); + netcdf.putAtt(ncid,icearea_varid,'units','km^2'); + + % leave define mode and enter data mode to write data + netcdf.endDef(ncid); + + % add variables + tdatevec = datevec(tdate); + for im=1:12, + indmonth = find(tdatevec(:,2)==im); + var_climo(im) = nanmean(var(indmonth)); + end + tdate = datenum(1,1:12,15); + date = datestr(tdate,'yyyy-mm-dd_HH:MM:SS'); + %netcdf.putVar(ncid,t_varid,0,ntot,t); + for n=1:12, + netcdf.putVar(ncid,t_varid,[0,n-1],[size(date,2),1],date(n,:)); + end + netcdf.putVar(ncid,icearea_varid,0,12,var_climo); + + % close netcdf file + netcdf.close(ncid); +end % loop on data files + +eval(sprintf('cd %s;',cwd)); diff --git a/preprocess_observations/NASATeam_Antarctic_compute_climo.m b/preprocess_observations/NASATeam_Antarctic_compute_climo.m new file mode 100644 index 000000000..cd8fcee37 --- /dev/null +++ b/preprocess_observations/NASATeam_Antarctic_compute_climo.m @@ -0,0 +1,74 @@ +% +% Combined SSM/I-SSMIS and SMMR sea-ice concentration data for both the +% Arctic and Antarctic. +% *** NASA Team algorithm *** +% +% Source: http://nsidc.org/data/NSIDC-0051 +% +clear all; +close all; + +homedir = getenv('HOME'); + +maindir = [homedir '/ACME/observations/obsdir/SeaIce/SSMI/'... + 'NASATeam_NSIDC0051']; +datadir = [maindir '/south/monthly']; +griddir = [homedir '/ACME/observations/obsdir/SeaIce/ICESat/Antarctic/climo']; +lonlatfile = 'spring_ICESat_gridded_mean_thickness'; +months4climo = [12 1 2; % (boreal) winter months + 3 4 5; % (boreal) spring months + 6 7 8; % (boreal) summer months + 9 10 11]; % (boreal) fall months +seasons = {'djf','mam','jja','son'}; + +M = 332; % Polar Stereographic grid for Antarctica, # of rows +N = 316; % Polar Stereographic grid for Antarctica, # of columns + +[err,cwd] = unix('pwd'); +% Read in lon,lat: +eval(sprintf('cd %s;',griddir)); +eval(sprintf('load %s.txt',lonlatfile)); +eval(sprintf('cd %s;',cwd)); +eval(sprintf('lat = %s(:,1);',lonlatfile)); +eval(sprintf('lon = %s(:,2);',lonlatfile)); +x = reshape(lon,M,N); +y = reshape(lat,M,N); + +eval(sprintf('cd %s;',datadir)); +for is=1:length(seasons), + season = char(seasons(is)); + + % Get list of files to compute seasonal climatologies from: + filenames = sprintf('nt_????%02d*',months4climo(is,1)); + for i=2:size(months4climo,2), + filenames = [filenames sprintf(' nt_????%02d*',months4climo(is,i))]; + end + eval(sprintf('[err,filelist] = unix(''/bin/ls %s'');',filenames)); + filelist = strsplit(filelist); % convert to cell of strings + filelist = filelist(2:end-1); % remove redudant first and last space chars + + % Compute seasonal climatology: + for ifile=1:length(filelist); + infile = char(filelist(ifile)); + % Read in binary data: + fid = fopen(infile,'r'); + header = fread(fid,300,'char=>char'); + aice(ifile,:,:) = fread(fid,[N M],'uint8'); + fclose(fid); + aice(find(aice>250)) = nan; + aice(find(aice==0))=nan; + end + aice = squeeze(nanmean(aice,1)); + aice = aice/250; + aice(find(isnan(aice)==1)) = -999; + aice = aice'; + + % Write to file: + outfile = ['SSMI_NASATeam_gridded_concentration_SH_' season]; + fid = fopen(sprintf('%s/%s.txt',maindir,outfile),'w'); + fprintf(fid,'%12.4f %12.4f %12.5f\n',[y(:)'; x(:)'; aice(:)']); + fclose(fid); + + clear aice +end +eval(sprintf('cd %s;',cwd)); diff --git a/preprocess_observations/NASATeam_Arctic_compute_climo.m b/preprocess_observations/NASATeam_Arctic_compute_climo.m new file mode 100644 index 000000000..73e3cfe2b --- /dev/null +++ b/preprocess_observations/NASATeam_Arctic_compute_climo.m @@ -0,0 +1,74 @@ +% +% Combined SSM/I-SSMIS and SMMR sea-ice concentration data for both the +% Arctic and Antarctic. +% *** NASA Team algorithm *** +% +% Source: http://nsidc.org/data/NSIDC-0051 +% +clear all; +close all; + +homedir = getenv('HOME'); + +maindir = [homedir '/ACME/observations/obsdir/SeaIce/SSMI/'... + 'NASATeam_NSIDC0051']; +datadir = [maindir '/north/monthly']; +griddir = [homedir '/ACME/observations/obsdir/SeaIce/ICESat/Arctic/' ... + 'NSIDC0393_GLAS_SI_Freeboard_v01/glas_seaice_grids']; +lonfile = [griddir '/PS25km_north_lon.img']; +latfile = [griddir '/PS25km_north_lat.img']; +months4climo = [ 1 2 3; % (boreal) winter months + 4 5 6; % (boreal) spring months + 7 8 9; % (boreal) summer months + 10 11 12]; % (boreal) fall months +seasons = {'jfm','amj','jas','ond'}; + +M = 304; % Polar Stereographic grid for the Arctic, # of rows +N = 448; % Polar Stereographic grid for the Arctic, # of columns + +% Read in lon,lat: +fid = fopen(lonfile,'r','l'); +x = fread(fid,[M N],'single'); +fclose(fid); +fid = fopen(latfile,'r','l'); +y = fread(fid,[M N],'single'); +fclose(fid); + +[err,cwd] = unix('pwd'); +eval(sprintf('cd %s;',datadir)); +for is=1:length(seasons), + season = char(seasons(is)); + + % Get list of files to compute seasonal climatologies from: + filenames = sprintf('nt_????%02d*',months4climo(is,1)); + for i=2:size(months4climo,2), + filenames = [filenames sprintf(' nt_????%02d*',months4climo(is,i))]; + end + eval(sprintf('[err,filelist] = unix(''/bin/ls %s'');',filenames)); + filelist = strsplit(filelist); % convert to cell of strings + filelist = filelist(2:end-1); % remove redudant first and last space chars + + % Compute seasonal climatology: + for ifile=1:length(filelist); + infile = char(filelist(ifile)); + % Read in binary data: + fid = fopen(infile,'r'); + header = fread(fid,300,'char=>char'); + aice(ifile,:,:) = fread(fid,[M N],'uint8'); + fclose(fid); + aice(find(aice>250)) = nan; + aice(find(aice==0))=nan; + end + aice = squeeze(nanmean(aice,1)); + aice = aice/250; + aice(find(isnan(aice)==1)) = -999; + + % Write to file: + outfile = ['SSMI_NASATeam_gridded_concentration_NH_' season]; + fid = fopen(sprintf('%s/%s.txt',maindir,outfile),'w'); + fprintf(fid,'%12.4f %12.4f %12.5f\n',[y(:)'; x(:)'; aice(:)']); + fclose(fid); + + clear aice +end +eval(sprintf('cd %s;',cwd)); diff --git a/preprocess_observations/PIOMAS_txt2netcdf.m b/preprocess_observations/PIOMAS_txt2netcdf.m new file mode 100644 index 000000000..f00adfbf6 --- /dev/null +++ b/preprocess_observations/PIOMAS_txt2netcdf.m @@ -0,0 +1,101 @@ +% Converts txt PIOMAS data to netcdf files +% +% Data source: http://psc.apl.uw.edu/research/projects/arctic-sea-ice-volume-anomaly/ +% + +clear all; +close all; + +workdir = '/lustre/atlas1/cli115/proj-shared/milena/observations/SeaIce/PIOMAS'; +infile = 'PIOMASvolume_monthly'; +outfile1 = [infile '.nc']; +outfile2 = [infile '_climo.nc']; + +cwd = pwd; +eval(sprintf('cd %s;',workdir)); + +% the following loads year (first column) and ice volume (in 10^3 km^3) +% for each month of that year (subsequent 12 columns): +eval(sprintf('load %s.txt;',infile)); + +eval(sprintf('years = %s(:,1);',infile)); +eval(sprintf('obs = %s(:,2:13);',infile)); + +obs(find(obs==-1)) = nan; + +% Reorganize monthly observations: +ind = 1; +for iy=1:length(years), + for im=1:12, + tdate(ind) = datenum(years(iy),im,15); + date(ind,:) = datestr(tdate(ind),'yyyy-mm-dd_HH:MM:SS'); + icevol(ind) = obs(iy,im); + ind = ind+1; + end +end + +% Compute climatological annual cycle: +tdatevec = datevec(tdate); +for im=1:12, + indmonth = find(tdatevec(:,2)==im); + icevol_climo(im) = nanmean(icevol(indmonth)); +end +tdate_climo = datenum(1,1:12,15); +date_climo = datestr(tdate_climo,'yyyy-mm-dd_HH:MM:SS'); + +% First create netcdf file with monthly data: +% +% create netcdf file +ncid = netcdf.create(outfile1,'clobber'); +% define dimension(s) +t_dimid = netcdf.defDim(ncid,'Time',netcdf.getConstant('NC_UNLIMITED')); +strLen_dimid = netcdf.defDim(ncid,'StrLen',64); +% define variables and attributes +t_varid = netcdf.defVar(ncid,'xtime','NC_CHAR',[strLen_dimid,t_dimid]); +icevol_varid = netcdf.defVar(ncid,'IceVol','NC_DOUBLE',t_dimid); +netcdf.putAtt(ncid,t_varid,'long_name','calendar date'); +netcdf.putAtt(ncid,t_varid,'format','YYYY-MM-DD_HH:MM:SS character string'); +netcdf.putAtt(ncid,icevol_varid,'long_name','PIOMAS ice volume'); +netcdf.putAtt(ncid,icevol_varid,'units','10^3 km^3'); + +% leave define mode and enter data mode to write data +netcdf.endDef(ncid); + +% add variables +ntot = ind-1; +for n=1:ntot, + netcdf.putVar(ncid,t_varid,[0,n-1],[size(date,2),1],date(n,:)); +end +netcdf.putVar(ncid,icevol_varid,0,ntot,icevol); + +% close netcdf file +netcdf.close(ncid); + +% Then create netcdf file with climatological annual cycle: +% +% create netcdf file +ncid = netcdf.create(outfile2,'clobber'); +% define dimension(s) +t_dimid = netcdf.defDim(ncid,'Time',netcdf.getConstant('NC_UNLIMITED')); +strLen_dimid = netcdf.defDim(ncid,'StrLen',64); +% define variables and attributes +t_varid = netcdf.defVar(ncid,'xtime','NC_CHAR',[strLen_dimid,t_dimid]); +icevol_varid = netcdf.defVar(ncid,'IceVol','NC_DOUBLE',t_dimid); +netcdf.putAtt(ncid,t_varid,'long_name','climatological date'); +netcdf.putAtt(ncid,t_varid,'format','YYYY-MM-DD_HH:MM:SS character string'); +netcdf.putAtt(ncid,icevol_varid,'long_name','PIOMAS ice volume'); +netcdf.putAtt(ncid,icevol_varid,'units','10^3 km^3'); + +% leave define mode and enter data mode to write data +netcdf.endDef(ncid); + +% add variables +for n=1:12, + netcdf.putVar(ncid,t_varid,[0,n-1],[size(date_climo,2),1],date_climo(n,:)); +end +netcdf.putVar(ncid,icevol_varid,0,12,icevol_climo); + +% close netcdf file +netcdf.close(ncid); + +eval(sprintf('cd %s;',cwd)); diff --git a/preprocess_observations/notes4seaiceData.txt b/preprocess_observations/notes4seaiceData.txt new file mode 100644 index 000000000..2194632bd --- /dev/null +++ b/preprocess_observations/notes4seaiceData.txt @@ -0,0 +1,13 @@ +SSMI NASATeam or Bootstrap: Milena computed climatologies from the binary files +using the compute_climo.m scripts. The resulting netcdf files contain the fields +on the original stereographic projection. Mat then interpolated these +fields onto regular lat/lon grids. + +ICESat Arctic: a similar procedure as the SSMI data was taken. + +ICESat Antarctic: this data was only available for Feb/Mar and Oct/Nov, in ASCII +format. Milena cannot find preprocessing scripts for this data, so she is thinking +that probably Mat processed the ASCII data (already FM/ON climos) directly. + +IceArea_timeseries: Milena used the txt2netcdf.m scripts to go from the ASCII +files to netcdf. From da66005f8aa342c63b3f7241258d5422488f939e Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Wed, 25 Apr 2018 09:28:40 +0200 Subject: [PATCH 69/71] Add Matlab scripts to preprocessing steps in database The scripts were added to the repo but not listed in the database. --- mpas_analysis/obs/observational_datasets.xml | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) diff --git a/mpas_analysis/obs/observational_datasets.xml b/mpas_analysis/obs/observational_datasets.xml index bfcafc2c2..2ebb06340 100644 --- a/mpas_analysis/obs/observational_datasets.xml +++ b/mpas_analysis/obs/observational_datasets.xml @@ -32,7 +32,7 @@ [Acknowledgment:] Hurrell, J. W., J. J. Hack, D. Shea, J. M. Caron, and J. Rosinski, - 2008: A New Sea Surface Temperature and Sea Ice Boundary Dataset for the Community + 2008: A New Sea Surface Temperature and Sea Ice Boundary Dataset for the Community Atmosphere Model. Journal of Climate, 21, 5145-5153. @@ -79,7 +79,7 @@ [NASA Aquarius FTP server] (https://podaac.jpl.nasa.gov/dataset/AQUARIUS_L4_OISSS_IPRC_7DAY_V4) - + NASA data are not copyrighted; however, when you publish our data or @@ -577,7 +577,9 @@ (missing, requires registration with NSIDC) - (missing) + preprocess_observations/NASATeam_Antarctic_compute_climo.m + preprocess_observations/NASATeam_Arctic_compute_climo.m + (missing remapping from stereographic to lat/lon) - climatologyMapSeaIceConcNH @@ -633,7 +635,9 @@ (missing, requires registration with NSIDC) - (missing) + preprocess_observations/Bootstrap_Antarctic_compute_climo.m + preprocess_observations/Bootstrap_Arctic_compute_climo.m + (missing remapping from stereographic to lat/lon) - climatologyMapSeaIceConcNH @@ -770,7 +774,7 @@ - https://neptune.gsfc.nasa.gov/uploads/files/SH_IceExt_Monthly_1978-2012.txt - (missing) + preprocess_observations/IceaArea_txt2netcdf.m - timeSeriesSeaIceAreaVol @@ -817,6 +821,9 @@ (missing, requires registration with NSIDC) + ICESat_Arctic_compute_climo.m + (missing Antarctic climo) + (missing remapping from stereographic to lat/lon) - timeSeriesSeaIceAreaVol @@ -878,7 +885,7 @@ - http://psc.apl.uw.edu/wordpress/wp-content/uploads/schweiger/ice_volume/PIOMAS.2sst.monthly.Current.v2.1.txt - (missing) + preprocess_observations/PIOMAS_txt2netcdf.m - timeSeriesSeaIceAreaVol From 9fd3910f046d9d64c3e97879123bd666ad1ad995 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Wed, 25 Apr 2018 09:44:24 +0200 Subject: [PATCH 70/71] Some clean-up to the obs database --- mpas_analysis/obs/observational_datasets.xml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/mpas_analysis/obs/observational_datasets.xml b/mpas_analysis/obs/observational_datasets.xml index 2ebb06340..a5d5675ba 100644 --- a/mpas_analysis/obs/observational_datasets.xml +++ b/mpas_analysis/obs/observational_datasets.xml @@ -31,7 +31,7 @@ (https://climatedataguide.ucar.edu/climate-data/merged-hadley-noaaoi-sea-surface-temperature-sea-ice-concentration-hurrell-et-al-2008) - [Acknowledgment:] Hurrell, J. W., J. J. Hack, D. Shea, J. M. Caron, and J. Rosinski, + Acknowledgment: Hurrell, J. W., J. J. Hack, D. Shea, J. M. Caron, and J. Rosinski, 2008: A New Sea Surface Temperature and Sea Ice Boundary Dataset for the Community Atmosphere Model. Journal of Climate, 21, 5145-5153. @@ -77,7 +77,7 @@ degree spatial resolution. - [NASA Aquarius FTP server] + [NASA Aquarius Website] (https://podaac.jpl.nasa.gov/dataset/AQUARIUS_L4_OISSS_IPRC_7DAY_V4) @@ -94,7 +94,7 @@ - (ftp://podaac-ftp.jpl.nasa.gov/allData/aquarius/L4/IPRC/v4/7day/) + ftp://podaac-ftp.jpl.nasa.gov/allData/aquarius/L4/IPRC/v4/7day/ (missing) @@ -138,7 +138,8 @@ (http://www.aviso.altimetry.fr/duacs/)" - [ftp://podaac.jpl.nasa.gov/allData/aviso/L4/dynamic_topo_1deg_1mo/docs/zosTechNote_AVISO_L4_199210-201012.pdf] + [AVISO: Sea Surface Height above Geoid] + (ftp://podaac.jpl.nasa.gov/allData/aviso/L4/dynamic_topo_1deg_1mo/docs/zosTechNote_AVISO_L4_199210-201012.pdf) From fc2de2f2a12b22c0392c79300aeb35e54004482f Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Tue, 17 Apr 2018 13:29:28 +0200 Subject: [PATCH 71/71] update to v0.7.5 in docs, setup and recipe --- conda/recipe/meta.yaml | 2 +- docs/conf.py | 4 ++-- setup.py | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/conda/recipe/meta.yaml b/conda/recipe/meta.yaml index 5b05b7b3c..6403dae78 100644 --- a/conda/recipe/meta.yaml +++ b/conda/recipe/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.0" %} +{% set version = "0.7.5" %} package: name: mpas_analysis diff --git a/docs/conf.py b/docs/conf.py index f1d8c9453..658d713e2 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -70,9 +70,9 @@ # built documents. # # The short X.Y version. -version = u'0.7.0' +version = u'0.7.5' # The full version, including alpha/beta/rc tags. -release = u'0.7.0' +release = u'0.7.5' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/setup.py b/setup.py index e38cb21f4..df6010a42 100755 --- a/setup.py +++ b/setup.py @@ -12,7 +12,7 @@ isrelease = True -version = '0.7.0' +version = '0.7.5' if not isrelease: import subprocess