def parseForBatch(self, vals=None):
if self.importanceParameter:
self.parser.add_argument('--noimportance', action='store_true',
help='original chains only, no importance sampled')
self.parser.add_argument('--importance', nargs='*', default=None,
help='data names for importance sampling runs to include')
self.parser.add_argument('--importancetag', nargs='*', default=None,
help='importance tags for importance sampling runs to include')
self.parser.add_argument('--name', default=None, nargs='+',
help='specific chain full name only (base_paramx_data1_data2)')
self.parser.add_argument('--param', default=None, nargs='+',
help='runs including specific parameter only (paramx)')
self.parser.add_argument('--paramtag', default=None, nargs='+',
help='runs with specific parameter tag only (base_paramx)')
self.parser.add_argument('--data', nargs='+', default=None, help='runs including specific data only (data1)')
self.parser.add_argument('--datatag', nargs='+', default=None,
help='runs with specific data tag only (data1_data2)')
self.parser.add_argument('--musthave_data', nargs='+', default=None,
help='include only runs that include specific data (data1)')
self.parser.add_argument('--skip_data', nargs='+', default=None,
help='skip runs containing specific data (data1)')
self.parser.add_argument('--skip_param', nargs='+', default=None,
help='skip runs containing specific parameter (paramx)')
self.parser.add_argument('--group', default=None, nargs='+', help='include only runs with given group names')
self.parser.add_argument('--skip_group', default=None, nargs='+', help='exclude runs with given group names')
if self.notExist:
self.parser.add_argument('--notexist', action='store_true',
help='only include chains that don\'t already exist on disk')
if self.notall:
self.parser.add_argument('--notall', type=int, default=None,
help='only include chains where all N chains don\'t already exist on disk')
if self.doplots:
self.parser.add_argument('--paramNameFile', default='clik_latex.paramnames',
help=".paramnames file for custom labels for parameters")
self.parser.add_argument('--param_list', default=None,
help=".paramnames file listing specific parameters to include (only)")
self.parser.add_argument('--size_inch', type=float, default=None, help='output subplot size in inches')
self.parser.add_argument('--nx', default=None, help='number of plots per row')
self.parser.add_argument('--outputs', nargs='+', default=['pdf'], help='output file type (default: pdf)')
args = self.parser.parse_args(vals)
self.args = args
if args.batchPath:
self.batch = batchjob.readobject(args.batchPath)
if self.batch is None:
raise Exception('batchPath %s does not exist or is not initialized with makeGrid.py' % args.batchPath)
if self.doplots:
import getdist.plots as plots
from getdist import paramnames
if args.paramList is not None: args.paramList = paramnames.ParamNames(args.paramList)
g = plots.GetDistPlotter(chain_dir=self.batch.batchPath)
if args.size_inch is not None: g.settings.set_with_subplot_size(args.size_inch)
return self.batch, self.args, g
else:
return self.batch, self.args
else:
return None, self.args
Opts.parser.add_argument('--compare', nargs='+', default=None)
Opts.parser.add_argument('--titles', default=None) # for compare plots
Opts.parser.add_argument('--forpaper', action='store_true')
Opts.parser.add_argument('--separate_tex', action='store_true')
Opts.parser.add_argument('--header_tex', default=None)
Opts.parser.add_argument('--height', default="13in")
Opts.parser.add_argument('--width', default="12in")
(batch, args) = Opts.parseForBatch()
if args.blockEndParams is not None:
args.blockEndParams = args.blockEndParams.split(';')
if args.paramList is not None:
args.paramList = paramnames.ParamNames(args.paramList)
if args.forpaper:
formatter = planckStyle.planckStyleTableFormatter()
else:
formatter = None
def texEscapeText(string):
return string.replace('_', '{\\textunderscore}')
def getTableLines(content, referenceDataJobItem=None):
if referenceDataJobItem is not None:
refResults = referenceDataJobItem.result_marge
else:
Opts.parser.add_argument('--params', nargs='+')
Opts.parser.add_argument('--chain_name_params', nargs='+')
Opts.parser.add_argument('--compare', nargs='+', default=None)
Opts.parser.add_argument('--nobestfits', action='store_true')
Opts.parser.add_argument('--single_extparam', action='store_true')
Opts.parser.add_argument('--limit', type=int, default=2)
Opts.parser.add_argument('--latex_filename', default=None)
Opts.parser.add_argument('--mathColumns', action='store_true')
Opts.parser.add_argument('--endline', default='\\cr')
Opts.parser.add_argument('--paramNameFile', default='clik_latex.paramnames')
(batch, args) = Opts.parseForBatch()
formatter = types.TableFormatter()
names = paramnames.ParamNames(args.paramNameFile)
if args.chain_name_params is None: args.chain_name_params = args.params
if args.compare:
args.compare = [batch.normalizeDataTag(dat) for dat in args.compare]
table = dict()
paramtag_for_param = dict()
for par in args.params:
paramtag_for_param[par] = []
for jobItem in Opts.filteredBatchItems():
if (args.compare is None or jobItem.matchesDatatag(args.compare)) and (
not args.single_extparam or len(jobItem.param_set) == 1
and jobItem.hasParam(args.chain_name_params)):
Opts.parser.add_argument('--labelNames',
default=None,
help=".paramnames file for new param labels")
Opts.parser.add_argument('--map_file',
help="file with rows of oldname newname label")
Opts.parser.add_argument('--confirm',
action='store_true',
help="true to replace .paramnames files")
(batch, args) = Opts.parseForBatch()
if args.old_new and len(args.old_new) < 2:
raise Exception('Must have at least one pair of parameters to rename')
if args.labelNames:
labels = paramnames.ParamNames(args.labelNames)
else:
labels = None
mapper = dict()
if args.map_file:
with open(args.map_file) as f:
for line in f:
if line.strip():
old, new, label = [s.strip() for s in line.split(None, 2)]
mapper[old] = (new, label)
if args.old_new:
for old, new in zip(args.old_new[::2], args.old_new[1::2]):
mapper[old] = (new, None)
for jobItem in Opts.filteredBatchItems():
# Just look at parameters being produced in single chain
from __future__ import absolute_import
from __future__ import print_function
import os, sys
from getdist import paramnames
import numpy as np
if len(sys.argv) < 3:
print(
'Usage: python/chainPeek.py chains/chainroot paramname [chain_index]')
print('e.g. python/makeGrid.py chains/test omegabh2 1')
sys.exit()
chain = os.path.abspath(sys.argv[1])
param = sys.argv[2]
index = 1
if len(sys.argv) > 4: index = int(sys.argv[3])
d = np.loadtxt(chain + '_' + str(index) + '.txt')
names = paramnames.ParamNames(chain + '.paramnames')
print(d[:, names.numberOfName(param) + 2])