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Submodule camb
updated
7 files
| +3 −6 | .readthedocs.yml | |
| +2 −1 | camb/__init__.py | |
| + − | camb/cambdll.dll | |
| +16 −6 | camb/results.py | |
| +1 −1 | fortran/config.f90 | |
| +30 −24 | fortran/halofit.f90 | |
| +1 −2 | fortran/results.f90 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,363 +1,12 @@ | ||
| #!/usr/bin/env python | ||
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| from __future__ import absolute_import | ||
| from __future__ import print_function | ||
| import os | ||
| import subprocess | ||
| import getdist | ||
| import io | ||
| from getdist import MCSamples, chains, IniFile | ||
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| def runScript(fname): | ||
| subprocess.Popen(['python', fname]) | ||
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| def doError(msg): | ||
| if __name__ == '__main__': | ||
| import sys | ||
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| print(msg) | ||
| sys.exit() | ||
| raise ValueError(msg) | ||
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| def main(args): | ||
| no_plots = False | ||
| chain_root = args.chain_root | ||
| if args.ini_file is None and chain_root is None: | ||
| doError('Must give either a .ini file of parameters or a chain file root name. Run "GetDist.py -h" for help.') | ||
| if not '.ini' in args.ini_file and chain_root is None: | ||
| # use default settings acting on chain_root, no plots | ||
| chain_root = args.ini_file | ||
| args.ini_file = getdist.default_getdist_settings | ||
| no_plots = True | ||
| if not os.path.isfile(args.ini_file): | ||
| doError('Parameter file does not exist: ' + args.ini_file) | ||
| if chain_root and chain_root.endswith('.txt'): | ||
| chain_root = chain_root[:-4] | ||
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| if chain_root is not None and ('*' in chain_root or '?' in chain_root): | ||
| import glob, copy | ||
| for f in glob.glob(chain_root + '.paramnames'): | ||
| fileargs = copy.copy(args) | ||
| fileargs.chain_root = f.replace('.paramnames', '') | ||
| main(fileargs) | ||
| return | ||
|
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| # Input parameters | ||
| ini = IniFile(args.ini_file) | ||
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| # File root | ||
| if chain_root is not None: | ||
| in_root = chain_root | ||
| else: | ||
| in_root = ini.params['file_root'] | ||
| if not in_root: | ||
| doError('Chain Root file name not given ') | ||
| rootname = os.path.basename(in_root) | ||
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| if args.ignore_rows is not None: | ||
| ignorerows = args.ignore_rows | ||
| else: | ||
| ignorerows = ini.float('ignore_rows', 0.0) | ||
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| samples_are_chains = ini.bool('samples_are_chains', True) | ||
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| paramnames = ini.string('parameter_names', '') | ||
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| # Create instance of MCSamples | ||
| mc = MCSamples(in_root, ini=ini, files_are_chains=samples_are_chains, paramNamesFile=paramnames) | ||
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| if ini.bool('adjust_priors', False) or ini.bool('map_params', False): | ||
| doError( | ||
| 'To adjust priors or define new parameters, use a separate python script; see the python getdist docs for examples') | ||
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| plot_ext = ini.string('plot_ext', 'py') | ||
| finish_run_command = ini.string('finish_run_command', '') | ||
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| no_plots = ini.bool('no_plots', no_plots) | ||
| plots_only = ini.bool('plots_only', False) | ||
| no_tests = plots_only or ini.bool('no_tests', False) | ||
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| thin_factor = ini.int('thin_factor', 0) | ||
| thin_cool = ini.float('thin_cool', 1.0) | ||
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| make_single_samples = ini.bool('make_single_samples', False) | ||
| single_thin = ini.int('single_thin', 1) | ||
| cool = ini.float('cool', 1.0) | ||
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| chain_exclude = ini.int_list('exclude_chain') | ||
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| shade_meanlikes = ini.bool('shade_meanlikes', False) | ||
| plot_meanlikes = ini.bool('plot_meanlikes', False) | ||
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| dumpNDbins = ini.bool('dump_ND_bins', False) | ||
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| out_dir = ini.string('out_dir', './') | ||
| if out_dir: | ||
| if not os.path.isdir(out_dir): | ||
| os.mkdir(out_dir) | ||
| print('producing files in directory ', out_dir) | ||
| mc.out_dir = out_dir | ||
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| out_root = ini.string('out_root', '') | ||
| if out_root: | ||
| rootname = out_root | ||
| print('producing files with with root ', out_root) | ||
| mc.rootname = rootname | ||
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| rootdirname = os.path.join(out_dir, rootname) | ||
| mc.rootdirname = rootdirname | ||
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| if 'do_minimal_1d_intervals' in ini.params: | ||
| doError('do_minimal_1d_intervals no longer used; set credible_interval_threshold instead') | ||
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| line = ini.string('PCA_params', '') | ||
| if line.lower() == 'all': | ||
| PCA_params = mc.paramNames.list() | ||
| else: | ||
| PCA_params = line.split() | ||
| PCA_num = ini.int('PCA_num', len(PCA_params)) | ||
| if PCA_num != 0: | ||
| if PCA_num < 2: | ||
| doError('Can only do PCA for 2 or more parameters') | ||
| PCA_func = ini.string('PCA_func', '') | ||
| # Characters representing functional mapping | ||
| if PCA_func == '': | ||
| PCA_func = ['N'] * PCA_num # No mapping | ||
| PCA_NormParam = ini.string('PCA_normparam', '') or None | ||
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| make_scatter_samples = ini.bool('make_scatter_samples', False) | ||
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| # ============================================================================== | ||
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| first_chain = ini.int('first_chain', 0) | ||
| last_chain = ini.int('chain_num', -1) | ||
| # -1 means keep reading until one not found | ||
|
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| # Chain files | ||
| chain_files = chains.chainFiles(in_root, first_chain=first_chain, last_chain=last_chain, | ||
| chain_exclude=chain_exclude) | ||
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| mc.loadChains(in_root, chain_files) | ||
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| mc.removeBurnFraction(ignorerows) | ||
| if chains.print_load_details: | ||
| if ignorerows: | ||
| print('Removed %s as burn in' % ignorerows) | ||
| else: | ||
| print('Removed no burn in') | ||
| # Once installed this is not used, same as getdist script | ||
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| mc.deleteFixedParams() | ||
| mc.makeSingle() | ||
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| def filterParList(namestring, num=None): | ||
| if not namestring.strip(): | ||
| pars = mc.paramNames.list() | ||
| else: | ||
| pars = [] | ||
| for name in namestring.split(): | ||
| if '?' in name or '*' in name: | ||
| pars += mc.paramNames.getMatches(name, strings=True) | ||
| elif mc.paramNames.parWithName(name): | ||
| pars.append(name) | ||
| if num is not None and len(pars) != num: | ||
| print('%iD plot has missing parameter or wrong number of parameters: %s' % (num, pars)) | ||
| pars = None | ||
| return pars | ||
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| if cool != 1: | ||
| print('Cooling chains by ', cool) | ||
| mc.cool(cool) | ||
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| mc.updateBaseStatistics() | ||
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| if not no_tests: | ||
| mc.getConvergeTests(mc.converge_test_limit, writeDataToFile=True, feedback=True) | ||
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| mc.writeCovMatrix() | ||
| mc.writeCorrelationMatrix() | ||
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| # Output thinned data if requested | ||
| # Must do this with unsorted output | ||
| if thin_factor > 1: | ||
| thin_ix = mc.thin_indices(thin_factor) | ||
| filename = rootdirname + '_thin.txt' | ||
| mc.writeThinData(filename, thin_ix, thin_cool) | ||
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| print(mc.getNumSampleSummaryText().strip()) | ||
| if mc.likeStats: print(mc.likeStats.likeSummary().strip()) | ||
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| if PCA_num > 0 and not plots_only: | ||
| mc.PCA(PCA_params, PCA_func, PCA_NormParam, writeDataToFile=True) | ||
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| if not no_plots or dumpNDbins: | ||
| # set plot_data_dir before we generate the 1D densities below | ||
| plot_data_dir = ini.string('plot_data_dir', default='', allowEmpty=True) | ||
| if plot_data_dir and not os.path.isdir(plot_data_dir): | ||
| os.mkdir(plot_data_dir) | ||
| else: | ||
| plot_data_dir = None | ||
| mc.plot_data_dir = plot_data_dir | ||
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| # Do 1D bins | ||
| mc._setDensitiesandMarge1D(writeDataToFile=not no_plots and plot_data_dir, meanlikes=plot_meanlikes) | ||
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| if not no_plots: | ||
| # Output files for 1D plots | ||
| if plot_data_dir: print('Calculating plot data...') | ||
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| plotparams = [] | ||
| line = ini.string('plot_params', '') | ||
| if line not in ['', '0']: | ||
| plotparams = filterParList(line) | ||
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| line = ini.string('plot_2D_param', '').strip() | ||
| plot_2D_param = None | ||
| if line and line != '0': | ||
| plot_2D_param = line | ||
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| cust2DPlots = [] | ||
| if not plot_2D_param: | ||
| # Use custom array of specific plots | ||
| num_cust2D_plots = ini.int('plot_2D_num', 0) | ||
| for i in range(1, num_cust2D_plots + 1): | ||
| line = ini.string('plot' + str(i)) | ||
| pars = filterParList(line, 2) | ||
| if pars is not None: | ||
| cust2DPlots.append(pars) | ||
| else: | ||
| num_cust2D_plots -= 1 | ||
|
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| triangle_params = [] | ||
| triangle_plot = ini.bool('triangle_plot', False) | ||
| if triangle_plot: | ||
| line = ini.string('triangle_params', '') | ||
| triangle_params = filterParList(line) | ||
| triangle_num = len(triangle_params) | ||
| triangle_plot = triangle_num > 1 | ||
|
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| num_3D_plots = ini.int('num_3D_plots', 0) | ||
| plot_3D = [] | ||
| for ix in range(1, num_3D_plots + 1): | ||
| line = ini.string('3D_plot' + str(ix)) | ||
| pars = filterParList(line, 3) | ||
| if pars is not None: | ||
| plot_3D.append(pars) | ||
| else: | ||
| num_3D_plots -= 1 | ||
|
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| # Produce file of weight-1 samples if requested | ||
| if (num_3D_plots and not make_single_samples or make_scatter_samples) and not no_plots: | ||
| make_single_samples = True | ||
| single_thin = max(1, int(round(mc.norm / mc.max_mult)) // mc.max_scatter_points) | ||
|
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| if plot_data_dir: | ||
| if make_single_samples: | ||
| filename = os.path.join(plot_data_dir, rootname.strip() + '_single.txt') | ||
| mc.makeSingleSamples(filename, single_thin) | ||
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| # Write paramNames file | ||
| mc.getParamNames().saveAsText(os.path.join(plot_data_dir, rootname + '.paramnames')) | ||
| mc.getBounds().saveToFile(os.path.join(plot_data_dir, rootname + '.bounds')) | ||
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| make_plots = ini.bool('make_plots', False) or args.make_plots | ||
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| done2D = {} | ||
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| filename = rootdirname + '.' + plot_ext | ||
| mc.writeScriptPlots1D(filename, plotparams) | ||
| if make_plots: runScript(filename) | ||
|
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| # Do 2D bins | ||
| if plot_2D_param == 'corr': | ||
| # In this case output the most correlated variable combinations | ||
| print('...doing 2D plots for most correlated variables') | ||
| cust2DPlots = mc.getCorrelatedVariable2DPlots() | ||
| plot_2D_param = None | ||
| elif plot_2D_param: | ||
| mc.paramNames.parWithName(plot_2D_param, error=True) # just check | ||
|
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| if cust2DPlots or plot_2D_param: | ||
| print('...producing 2D plots') | ||
| filename = rootdirname + '_2D.' + plot_ext | ||
| done2D = mc.writeScriptPlots2D(filename, plot_2D_param, cust2DPlots, | ||
| writeDataToFile=plot_data_dir, shade_meanlikes=shade_meanlikes) | ||
| if make_plots: runScript(filename) | ||
|
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| if triangle_plot: | ||
| # Add the off-diagonal 2D plots | ||
| print('...producing triangle plot') | ||
| filename = rootdirname + '_tri.' + plot_ext | ||
| mc.writeScriptPlotsTri(filename, triangle_params) | ||
| for i, p2 in enumerate(triangle_params): | ||
| for p1 in triangle_params[i + 1:]: | ||
| if not done2D.get((p1, p2)) and plot_data_dir: | ||
| mc.get2DDensityGridData(p1, p2, writeDataToFile=True, meanlikes=shade_meanlikes) | ||
| if make_plots: runScript(filename) | ||
|
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| # Do 3D plots (i.e. 2D scatter plots with coloured points) | ||
| if num_3D_plots: | ||
| print('...producing ', num_3D_plots, '2D colored scatter plots') | ||
| filename = rootdirname + '_3D.' + plot_ext | ||
| mc.writeScriptPlots3D(filename, plot_3D) | ||
| if make_plots: runScript(filename) | ||
|
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| if not plots_only: | ||
| # Write out stats marginalized | ||
| mc.getMargeStats().saveAsText(rootdirname + '.margestats') | ||
|
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| # Limits from global likelihood | ||
| if mc.loglikes is not None: mc.getLikeStats().saveAsText(rootdirname + '.likestats') | ||
|
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| if dumpNDbins: | ||
| mc.num_bins_ND = ini.int('num_bins_ND', 10) | ||
| line = ini.string('ND_params', '') | ||
|
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| if line not in ["", '0']: | ||
| ND_params = filterParList(line) | ||
| print(ND_params) | ||
|
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| ND_dim = len(ND_params) | ||
| print(ND_dim) | ||
|
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| mc.getRawNDDensityGridData(ND_params, writeDataToFile=True, | ||
| meanlikes=shade_meanlikes) | ||
|
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| # System command | ||
| if finish_run_command: | ||
| finish_run_command = finish_run_command.replace('%ROOTNAME%', rootname) | ||
| finish_run_command = finish_run_command.replace('%PLOTDIR%', plot_data_dir) | ||
| finish_run_command = finish_run_command.replace('%PLOTROOT%', os.path.join(plot_data_dir, rootname)) | ||
| os.system(finish_run_command) | ||
| import sys | ||
| import os | ||
|
|
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| sys.path.append(os.path.realpath(os.path.dirname(__file__))) | ||
|
|
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| if __name__ == '__main__': | ||
| try: | ||
| import argparse | ||
| except ImportError: | ||
| print('Make sure you are using python 2.7+') | ||
| raise | ||
| from getdist.command_line import getdist_command | ||
|
|
||
| parser = argparse.ArgumentParser(description='GetDist sample analyser') | ||
| parser.add_argument('ini_file', nargs='?', | ||
| help='.ini file with analysis settings (optional, if omitted uses defaults)') | ||
| parser.add_argument('chain_root', nargs='?', | ||
| help='Root name of chain to analyse (e.g. chains/test), required unless file_root specified in ini_file') | ||
| parser.add_argument('--ignore_rows', | ||
| help='set initial fraction of chains to cut as burn in (fraction of total rows, or >1 number of rows); overrides any value in ini_file if set') | ||
| parser.add_argument('--make_param_file', | ||
| help='Produce a sample distparams.ini file that you can edit and use when running GetDist') | ||
| parser.add_argument('--make_plots', action='store_true', help='Make PDFs from any requested plot script files') | ||
| parser.add_argument('-V', '--version', action='version', version='%(prog)s ' + getdist.__version__) | ||
| args = parser.parse_args() | ||
| if args.make_param_file: | ||
| content = io.open(getdist.distparam_template).read() | ||
| analysis = io.open(getdist.default_getdist_settings).read() | ||
| content = content.replace('%%%ANALYSIS_DEFAULTS%%%', analysis) | ||
| with io.open(args.make_param_file, 'w') as f: | ||
| f.write(content) | ||
| print('Template .ini file written to ' + args.make_param_file) | ||
| else: | ||
| main(args) | ||
| getdist_command() |
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