-
Notifications
You must be signed in to change notification settings - Fork 68
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
62 changed files
with
8,597 additions
and
5,178 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,363 +1,12 @@ | ||
| #!/usr/bin/env python | ||
|
|
||
| from __future__ import absolute_import | ||
| from __future__ import print_function | ||
| import os | ||
| import subprocess | ||
| import getdist | ||
| import io | ||
| from getdist import MCSamples, chains, IniFile | ||
|
|
||
|
|
||
| def runScript(fname): | ||
| subprocess.Popen(['python', fname]) | ||
|
|
||
|
|
||
| def doError(msg): | ||
| if __name__ == '__main__': | ||
| import sys | ||
|
|
||
| print(msg) | ||
| sys.exit() | ||
| raise ValueError(msg) | ||
|
|
||
|
|
||
| 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] | ||
|
|
||
| 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 | ||
|
|
||
| # Input parameters | ||
| ini = IniFile(args.ini_file) | ||
|
|
||
| # 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) | ||
|
|
||
| if args.ignore_rows is not None: | ||
| ignorerows = args.ignore_rows | ||
| else: | ||
| ignorerows = ini.float('ignore_rows', 0.0) | ||
|
|
||
| samples_are_chains = ini.bool('samples_are_chains', True) | ||
|
|
||
| paramnames = ini.string('parameter_names', '') | ||
|
|
||
| # Create instance of MCSamples | ||
| mc = MCSamples(in_root, ini=ini, files_are_chains=samples_are_chains, paramNamesFile=paramnames) | ||
|
|
||
| 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') | ||
|
|
||
| plot_ext = ini.string('plot_ext', 'py') | ||
| finish_run_command = ini.string('finish_run_command', '') | ||
|
|
||
| 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) | ||
|
|
||
| thin_factor = ini.int('thin_factor', 0) | ||
| thin_cool = ini.float('thin_cool', 1.0) | ||
|
|
||
| make_single_samples = ini.bool('make_single_samples', False) | ||
| single_thin = ini.int('single_thin', 1) | ||
| cool = ini.float('cool', 1.0) | ||
|
|
||
| chain_exclude = ini.int_list('exclude_chain') | ||
|
|
||
| shade_meanlikes = ini.bool('shade_meanlikes', False) | ||
| plot_meanlikes = ini.bool('plot_meanlikes', False) | ||
|
|
||
| dumpNDbins = ini.bool('dump_ND_bins', False) | ||
|
|
||
| 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 | ||
|
|
||
| out_root = ini.string('out_root', '') | ||
| if out_root: | ||
| rootname = out_root | ||
| print('producing files with with root ', out_root) | ||
| mc.rootname = rootname | ||
|
|
||
| rootdirname = os.path.join(out_dir, rootname) | ||
| mc.rootdirname = rootdirname | ||
|
|
||
| if 'do_minimal_1d_intervals' in ini.params: | ||
| doError('do_minimal_1d_intervals no longer used; set credible_interval_threshold instead') | ||
|
|
||
| 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 | ||
|
|
||
| make_scatter_samples = ini.bool('make_scatter_samples', False) | ||
|
|
||
| # ============================================================================== | ||
|
|
||
| first_chain = ini.int('first_chain', 0) | ||
| last_chain = ini.int('chain_num', -1) | ||
| # -1 means keep reading until one not found | ||
|
|
||
| # Chain files | ||
| chain_files = chains.chainFiles(in_root, first_chain=first_chain, last_chain=last_chain, | ||
| chain_exclude=chain_exclude) | ||
|
|
||
| mc.loadChains(in_root, chain_files) | ||
|
|
||
| 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 | ||
|
|
||
| mc.deleteFixedParams() | ||
| mc.makeSingle() | ||
|
|
||
| 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 | ||
|
|
||
| if cool != 1: | ||
| print('Cooling chains by ', cool) | ||
| mc.cool(cool) | ||
|
|
||
| mc.updateBaseStatistics() | ||
|
|
||
| if not no_tests: | ||
| mc.getConvergeTests(mc.converge_test_limit, writeDataToFile=True, feedback=True) | ||
|
|
||
| mc.writeCovMatrix() | ||
| mc.writeCorrelationMatrix() | ||
|
|
||
| # 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) | ||
|
|
||
| print(mc.getNumSampleSummaryText().strip()) | ||
| if mc.likeStats: print(mc.likeStats.likeSummary().strip()) | ||
|
|
||
| if PCA_num > 0 and not plots_only: | ||
| mc.PCA(PCA_params, PCA_func, PCA_NormParam, writeDataToFile=True) | ||
|
|
||
| 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 | ||
|
|
||
| # Do 1D bins | ||
| mc._setDensitiesandMarge1D(writeDataToFile=not no_plots and plot_data_dir, meanlikes=plot_meanlikes) | ||
|
|
||
| if not no_plots: | ||
| # Output files for 1D plots | ||
| if plot_data_dir: print('Calculating plot data...') | ||
|
|
||
| plotparams = [] | ||
| line = ini.string('plot_params', '') | ||
| if line not in ['', '0']: | ||
| plotparams = filterParList(line) | ||
|
|
||
| line = ini.string('plot_2D_param', '').strip() | ||
| plot_2D_param = None | ||
| if line and line != '0': | ||
| plot_2D_param = line | ||
|
|
||
| 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 | ||
|
|
||
| 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 | ||
|
|
||
| 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 | ||
|
|
||
| # 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) | ||
|
|
||
| if plot_data_dir: | ||
| if make_single_samples: | ||
| filename = os.path.join(plot_data_dir, rootname.strip() + '_single.txt') | ||
| mc.makeSingleSamples(filename, single_thin) | ||
|
|
||
| # 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')) | ||
|
|
||
| make_plots = ini.bool('make_plots', False) or args.make_plots | ||
|
|
||
| done2D = {} | ||
|
|
||
| filename = rootdirname + '.' + plot_ext | ||
| mc.writeScriptPlots1D(filename, plotparams) | ||
| if make_plots: runScript(filename) | ||
|
|
||
| # 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 | ||
|
|
||
| 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) | ||
|
|
||
| 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) | ||
|
|
||
| # 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) | ||
|
|
||
| if not plots_only: | ||
| # Write out stats marginalized | ||
| mc.getMargeStats().saveAsText(rootdirname + '.margestats') | ||
|
|
||
| # Limits from global likelihood | ||
| if mc.loglikes is not None: mc.getLikeStats().saveAsText(rootdirname + '.likestats') | ||
|
|
||
| if dumpNDbins: | ||
| mc.num_bins_ND = ini.int('num_bins_ND', 10) | ||
| line = ini.string('ND_params', '') | ||
|
|
||
| if line not in ["", '0']: | ||
| ND_params = filterParList(line) | ||
| print(ND_params) | ||
|
|
||
| ND_dim = len(ND_params) | ||
| print(ND_dim) | ||
|
|
||
| mc.getRawNDDensityGridData(ND_params, writeDataToFile=True, | ||
| meanlikes=shade_meanlikes) | ||
|
|
||
| # 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 | ||
|
|
||
| sys.path.append(os.path.realpath(os.path.dirname(__file__))) | ||
|
|
||
| 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() |
Oops, something went wrong.