CAMB and getdist updated

Author: cmbant

Diff for: batch3/outputs/fsig8-z.py

@@ -7,7 +7,7 @@
 import tempfile
 import pickle
 
-sys.path.insert(0, 'C:\Work\Dist\git\camb\pycamb')
+sys.path.insert(0, 'C:\Work\Dist\git\camb')
 from cosmomc_to_camb import get_camb_params
 import camb
 
@@ -43,7 +43,7 @@
             raise Exception('error')
         datapoints[i] *= rescale
         dataerrs[i] *= rescale
-    print dataredshifts[i], datapoints[i], dataerrs[i]
+    print(dataredshifts[i], datapoints[i], dataerrs[i])
 
 DR12 = np.loadtxt(batchjob.getCodeRootPath() + 'data/DR12/final_consensus_results_dM_Hz_fsig.dat',
                   usecols=[0, 1])

Diff for: camb

@@ -8,7 +8,7 @@
 <center>
 <h2>CosmoMC Readme </h2></center>
 
-<center><b>July 2018</b>. Check the <a href="http://cosmologist.info/cosmomc/">web
+<center><b>July 2019</b>. Check the <a href="http://cosmologist.info/cosmomc/">web
 page</a> for the latest version.<BR>
 </center>
 <P>

Diff for: docs/readme.html

@@ -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()