Update tasks for standard region names

mpas_analysis/default.cfg

@@ -358,11 +358,11 @@ endYear = 20
 
 # list of region names (needs to be in the same order as region indices in
 # time-series stats)
-regions = ['arctic', 'equatorial', 'so', 'nino3', 'nino4', 'nino3.4', 'global']
-# list of plot titles (needs to be in the same order as region indices in
-# time-series stats)
-plotTitles = ['Arctic', 'Equatorial (15S-15N)', 'Southern Ocean', 'Nino 3',
-              'Nino 4', 'Nino 3.4', 'Global Ocean']
+regionShortNames = ['arctic', 'equatorial', 'so', 'nino3', 'nino4', 'nino3.4',
+                    'global']
+# list of full names (e.g. for plot titles) same order as regionShortNames
+regionNames = ['Arctic', 'Equatorial (15S-15N)', 'Southern Ocean', 'Nino 3',
+               'Nino 4', 'Nino 3.4', 'Global Ocean']
 
 
 [plot]
@@ -608,8 +608,8 @@ concentrationAltibergSH = Altiberg/Altiberg_1991-2017_20180308.nc
 ## options related to plotting time series of ocean heat content (OHC)
 ## anomalies from year 1
 
-# list of regions to plot from the region list in [regions] below
-regions = ['global']
+# list of region shrot names to plot from the region list in [regions] above
+regionShortNames = ['global']
 
 # approximate depths (m) separating plots of the upper, middle and lower ocean
 depths = [700, 2000]
@@ -672,8 +672,8 @@ movingAveragePoints = 12
 [hovmollerTemperatureAnomaly]
 ## options related to plotting time series of potential temperature vs. depth
 
-# list of regions to plot from the region list in [regions] below
-regions = ['global']
+# list of region short names to plot from the region list in [regions] above
+regionShortNames = ['global']
 
 # Number of points over which to compute moving average(e.g., for monthly
 # output, movingAveragePoints=12 corresponds to a 12-month moving average
@@ -706,8 +706,8 @@ contourLevelsResult = np.arange(-5.0, 5.51, 0.5)
 [hovmollerSalinityAnomaly]
 ## options related to plotting time series of salinity vs. depth
 
-# list of regions to plot from the region list in [regions] below
-regions = ['global']
+# list of region short names to plot from the region list in [regions] above
+regionShortNames = ['global']
 
 # Number of points over which to compute moving average(e.g., for monthly
 # output, movingAveragePoints=12 corresponds to a 12-month moving average
@@ -743,7 +743,7 @@ contourLevelsResult = np.arange(-2., 2.01, 0.2)
 ## options related to plotting time series of sea surface temperature (SST)
 
 # list of regions to plot from the region list in [regions] below
-regions = ['global']
+regionShortNames = ['global']
 
 # Number of points over which to compute moving average (e.g., for monthly
 # output, movingAveragePoints=12 corresponds to a 12-month moving average

mpas_analysis/ocean/index_nino34.py

@@ -38,6 +38,8 @@
 from mpas_analysis.shared import AnalysisTask
 from mpas_analysis.shared.html import write_image_xml
 
+from mpas_analysis.ocean.utility import add_standard_regions_and_subset
+
 
 class IndexNino34(AnalysisTask):
     """
@@ -129,7 +131,7 @@ def setup_and_check(self):
         regionToPlot = config.get('indexNino34', 'region')
 
         if regionToPlot not in ['nino3.4', 'nino3', 'nino4']:
-            raise ValueError('Unexpectes El Nino Index region {}'.format(
+            raise ValueError('Unexpected El Nino Index region {}'.format(
                 regionToPlot))
         ninoIndexNumber = regionToPlot[4:]
 
@@ -193,9 +195,7 @@ def run_task(self):
 
         # regionIndex should correspond to NINO34 in surface weighted Average
         # AM
-        regions = config.getexpression('regions', 'regions')
         regionToPlot = config.get('indexNino34', 'region')
-        regionIndex = regions.index(regionToPlot)
 
         # Load data:
         ds = open_mpas_dataset(fileName=self.inputFile,
@@ -204,6 +204,9 @@ def run_task(self):
                                startDate=startDate,
                                endDate=endDate)
 
+        ds = add_standard_regions_and_subset(ds, config,
+                                             regionShortNames=[regionToPlot])
+
         # Observations have been processed to the nino34Index prior to reading
         dsObs = xr.open_dataset(dataPath, decode_cf=False, decode_times=False)
         # add the days between 0001-01-01 and the refDate so we have a new
@@ -215,7 +218,7 @@ def run_task(self):
         self.logger.info('  Compute El Nino {} Index...'.format(
             ninoIndexNumber))
         varName = self.variableList[0]
-        regionSST = ds[varName].isel(nOceanRegions=regionIndex)
+        regionSST = ds[varName]
         nino34Main = self._compute_nino34_index(regionSST, calendar)
 
         # Compute the observational index over the entire time range
@@ -262,7 +265,10 @@ def run_task(self):
                 calendar=calendar,
                 variableList=self.variableList)
 
-            regionSSTRef = dsRef[varName].isel(nOceanRegions=regionIndex)
+            dsRef = add_standard_regions_and_subset(
+                dsRef, self.controlConfig, regionShortNames=[regionToPlot])
+
+            regionSSTRef = dsRef[varName]
             nino34Ref = self._compute_nino34_index(regionSSTRef, calendar)
 
             nino34s = [nino34Subset, nino34Main[2:-3], nino34Ref[2:-3]]

mpas_analysis/ocean/time_series_ohc_anomaly.py

@@ -25,6 +25,7 @@
     PlotDepthIntegratedTimeSeriesSubtask
 
 from mpas_analysis.shared.constants import constants as mpas_constants
+from mpas_analysis.ocean.utility import get_standard_region_names
 
 
 class TimeSeriesOHCAnomaly(AnalysisTask):
@@ -63,7 +64,8 @@ def __init__(self, config, mpasTimeSeriesTask, controlConfig=None):
             tags=['timeSeries', 'ohc', 'publicObs', 'anomaly'])
 
         sectionName = 'timeSeriesOHCAnomaly'
-        regionNames = config.getexpression(sectionName, 'regions')
+        regionShortNames = config.getexpression(sectionName,
+                                                'regionShortNames')
         movingAveragePoints = config.getint(sectionName, 'movingAveragePoints')
 
         self.variableDict = {}
@@ -85,6 +87,7 @@ def __init__(self, config, mpasTimeSeriesTask, controlConfig=None):
             alter_dataset=self._compute_ohc)
         self.add_subtask(anomalyTask)
 
+        regionNames = get_standard_region_names(config, regionShortNames)
         for regionName in regionNames:
             caption = 'Trend of {} OHC Anomaly vs depth'.format(
                 regionName)
@@ -133,10 +136,6 @@ def _compute_ohc(self, ds):
         """
         Compute the OHC time series.
         """
-
-        # regionNames = self.config.getexpression('regions', 'regions')
-        # ds['regionNames'] = ('nOceanRegionsTmp', regionNames)
-
         # for convenience, rename the variables to simpler, shorter names
         ds = ds.rename(self.variableDict)
 

mpas_analysis/ocean/time_series_salinity_anomaly.py

@@ -16,6 +16,8 @@
 from mpas_analysis.ocean.compute_anomaly_subtask import ComputeAnomalySubtask
 from mpas_analysis.ocean.plot_hovmoller_subtask import PlotHovmollerSubtask
 
+from mpas_analysis.ocean.utility import get_standard_region_names
+
 
 class TimeSeriesSalinityAnomaly(AnalysisTask):
     """
@@ -50,7 +52,8 @@ def __init__(self, config, mpasTimeSeriesTask):
             tags=['timeSeries', 'salinity', 'publicObs', 'anomaly'])
 
         sectionName = 'hovmollerSalinityAnomaly'
-        regionNames = config.getexpression(sectionName, 'regions')
+        regionShortNames = config.getexpression(sectionName,
+                                                'regionShortNames')
         movingAveragePoints = config.getint(sectionName, 'movingAveragePoints')
 
         mpasFieldName = 'timeMonthly_avg_avgValueWithinOceanLayerRegion_' \
@@ -66,9 +69,10 @@ def __init__(self, config, mpasTimeSeriesTask):
             movingAveragePoints=movingAveragePoints)
         self.add_subtask(anomalyTask)
 
+        regionNames = get_standard_region_names(config, regionShortNames)
+
         for regionName in regionNames:
-            caption = 'Trend of {} Salinity Anomaly vs depth'.format(
-                regionName)
+            caption = f'Trend of {regionName} Salinity Anomaly vs depth'
             plotTask = PlotHovmollerSubtask(
                 parentTask=self,
                 regionName=regionName,

mpas_analysis/ocean/time_series_sst.py

@@ -23,6 +23,11 @@
     make_directories, check_path_exists
 from mpas_analysis.shared.html import write_image_xml
 
+from mpas_analysis.ocean.utility import (
+    add_standard_regions_and_subset,
+    get_standard_region_names
+)
+
 
 class TimeSeriesSST(AnalysisTask):
     """
@@ -109,13 +114,16 @@ def setup_and_check(self):
         self.inputFile = self.mpasTimeSeriesTask.outputFile
 
         mainRunName = config.get('runs', 'mainRunName')
-        regions = config.getexpression('timeSeriesSST', 'regions')
+        regionShortNames = config.getexpression('timeSeriesSST',
+                                                'regionShortNames')
 
         self.xmlFileNames = []
         self.filePrefixes = {}
 
+        regions = get_standard_region_names(config, regionShortNames)
         for region in regions:
-            filePrefix = 'sst_{}_{}'.format(region, mainRunName)
+            regionSuffix = region.replace(' ', '_')
+            filePrefix = 'sst_{}_{}'.format(regionSuffix, mainRunName)
             self.xmlFileNames.append('{}/{}.xml'.format(self.plotsDirectory,
                                                         filePrefix))
             self.filePrefixes[region] = filePrefix
@@ -147,12 +155,8 @@ def run_task(self):
         movingAveragePoints = config.getint('timeSeriesSST',
                                             'movingAveragePoints')
 
-        regions = config.getexpression('regions', 'regions')
-        plotTitles = config.getexpression('regions', 'plotTitles')
-        regionsToPlot = config.getexpression('timeSeriesSST', 'regions')
-
-        regionIndicesToPlot = [regions.index(region) for region in
-                               regionsToPlot]
+        regionShortNames = config.getexpression('timeSeriesSST',
+                                                'regionShortNames')
 
         outputDirectory = build_config_full_path(config, 'output',
                                                  'timeseriesSubdirectory')
@@ -165,6 +169,9 @@ def run_task(self):
                                   startDate=self.startDate,
                                   endDate=self.endDate)
 
+        dsSST = add_standard_regions_and_subset(
+            dsSST, config, regionShortNames=regionShortNames)
+
         yearStart = days_to_datetime(dsSST.Time.min(), calendar=calendar).year
         yearEnd = days_to_datetime(dsSST.Time.max(), calendar=calendar).year
         timeStart = date_to_days(year=yearStart, month=1, day=1,
@@ -191,6 +198,9 @@ def run_task(self):
                 variableList=self.variableList,
                 startDate=controlStartDate,
                 endDate=controlEndDate)
+            dsRefSST = add_standard_regions_and_subset(
+                dsRefSST, self.controlConfig,
+                regionShortNames=regionShortNames)
         else:
             dsRefSST = None
 
@@ -221,17 +231,16 @@ def run_task(self):
                 preprocessedReferenceRunName = 'None'
 
         self.logger.info('  Make plots...')
-        for regionIndex in regionIndicesToPlot:
-            region = regions[regionIndex]
-
-            title = '{} SST'.format(plotTitles[regionIndex])
+        for regionName in dsSST.regionNames.values:
+            title = f'{regionName} SST'
             xLabel = 'Time [years]'
             yLabel = r'[$\degree$C]'
 
             varName = self.variableList[0]
-            SST = dsSST[varName].isel(nOceanRegions=regionIndex)
+            dsSST = dsSST.set_xindex('regionNames')
+            SST = dsSST[varName].sel(regionNames=regionName)
 
-            filePrefix = self.filePrefixes[region]
+            filePrefix = self.filePrefixes[regionName]
 
             outFileName = '{}/{}.png'.format(self.plotsDirectory, filePrefix)
 
@@ -242,7 +251,9 @@ def run_task(self):
             legendText = [mainRunName]
 
             if dsRefSST is not None:
-                refSST = dsRefSST[varName].isel(nOceanRegions=regionIndex)
+
+                dsRefSST = dsRefSST.set_xindex('regionNames')
+                refSST = dsRefSST[varName].sel(regionNames=regionName)
                 fields.append(refSST)
                 lineColors.append(config.get('timeSeries', 'controlColor'))
                 lineWidths.append(1.5)
@@ -279,16 +290,15 @@ def run_task(self):
 
             savefig(outFileName, config)
 
-            caption = 'Running Mean of {} Sea Surface Temperature'.format(
-                region)
+            caption = f'Running Mean of {regionName} Sea Surface Temperature'
             write_image_xml(
                 config=config,
                 filePrefix=filePrefix,
                 componentName='Ocean',
                 componentSubdirectory='ocean',
                 galleryGroup='Time Series',
                 groupLink='timeseries',
-                thumbnailDescription='{} SST'.format(region),
+                thumbnailDescription=f'{regionName} SST',
                 imageDescription=caption,
                 imageCaption=caption)
 

mpas_analysis/ocean/time_series_temperature_anomaly.py

@@ -16,6 +16,8 @@
 from mpas_analysis.ocean.compute_anomaly_subtask import ComputeAnomalySubtask
 from mpas_analysis.ocean.plot_hovmoller_subtask import PlotHovmollerSubtask
 
+from mpas_analysis.ocean.utility import get_standard_region_names
+
 
 class TimeSeriesTemperatureAnomaly(AnalysisTask):
     """
@@ -50,7 +52,8 @@ def __init__(self, config, mpasTimeSeriesTask):
             tags=['timeSeries', 'temperature', 'publicObs', 'anomaly'])
 
         sectionName = 'hovmollerTemperatureAnomaly'
-        regionNames = config.getexpression(sectionName, 'regions')
+        regionShortNames = config.getexpression(sectionName,
+                                                'regionShortNames')
         movingAveragePoints = config.getint(sectionName, 'movingAveragePoints')
 
         mpasFieldName = 'timeMonthly_avg_avgValueWithinOceanLayerRegion_' \
@@ -66,9 +69,11 @@ def __init__(self, config, mpasTimeSeriesTask):
             movingAveragePoints=movingAveragePoints)
         self.add_subtask(anomalyTask)
 
+        regionNames = get_standard_region_names(config, regionShortNames)
+
         for regionName in regionNames:
-            caption = 'Trend of {} Potential Temperature Anomaly vs ' \
-                      'Depth'.format(regionName)
+            caption = \
+                f'Trend of {regionName} Potential Temperature Anomaly vs Depth'
             plotTask = PlotHovmollerSubtask(
                 parentTask=self,
                 regionName=regionName,