def __init__(self, root=None, ignore_rows=0, jobItem=None):
self.jobItem = jobItem
self.precision = '%.8e'
self.ignore_lines = ignore_rows
self.root = root
self.chains = []
self.samples = None
self.hasNames = os.path.exists(root + '.paramnames')
self.needs_update = True
if self.hasNames:
self.paramNames = paramNames.paramNames(root + '.paramnames')
self.getParamIndices()
def parseForBatch(self):
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('--plot_data', nargs='*', default=None, help='directory/ies containing getdist output plot_data')
self.parser.add_argument('--paramNameFile', default='clik_latex.paramnames', help=".paramnames file for custom labels for parameters")
self.parser.add_argument('--paramList', 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()
self.args = args
if args.batchPath:
self.batch = batchJob.readobject(args.batchPath)
if self.batch is None: raise Exception('batchPath does not exist or it not initialized with makeGrid.py')
if self.doplots:
import GetDistPlots
from getdist import paramNames
if args.paramList is not None: args.paramList = paramNames.paramNames(args.paramList)
if args.plot_data is not None:
g = GetDistPlots.GetDistPlotter(plot_data=args.plot_data)
else:
g = GetDistPlots.GetDistPlotter(chain_dir=self.batch.batchPath)
if args.size_inch is not None: g.settings.setWithSubplotSize(args.size_inch)
return (self.batch, self.args, g)
else:
return (self.batch, self.args)
else: return None, self.args
def loadWMAPChain(self, chainPath, namesFile, thinfac=1):
params = paramNames.paramNames(namesFile)
cols = []
self.weights = np.loadtxt(chainPath + 'weight', usecols=(1,))
self.loglikes = np.loadtxt(chainPath + 'neglnlike', usecols=(1,))
if thinfac <> 1:
thin_ix = self.thin_indices(thinfac)
self.weights = np.ones(len(thin_ix))
self.loglikes = self.loglikes[thin_ix]
else: thin_ix = None
usednames = []
for param in params.names:
if os.path.exists(chainPath + param.name):
col = np.loadtxt(chainPath + param.name, usecols=(1,))
if thin_ix is not None: col = col[thin_ix]
cols.append(col)
usednames.append(param)
params.names = usednames
self.paramNames = params
self.samples = np.vstack(cols).transpose()
self.numrows = self.samples.shape[0]
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 = ResultObjs.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)):
jobItem.loadJobItemResults(paramNameFile=None, bestfit=not args.nobestfits, noconverge=True, silent=True)
if jobItem.result_marge is not None:
# Just look at parameters being produced in single chain
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]
import batchJobArgs
from getdist import paramNames
Opts = batchJobArgs.batchArgs('rename parameter in all .paramnames files in grid', importance=True)
Opts.parser.add_argument('--old_new', nargs='+', help="list of oldname newname oldname2 newname2...")
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)
Opts.parser.add_argument('--blockEndParams', default=None)
Opts.parser.add_argument('--columns', type=int, nargs=1, default=3)
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="10in")
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: refResults = None
return ResultObjs.resultTable(args.columns, [content], blockEndParams=args.blockEndParams, formatter=formatter,
paramList=args.paramList, limit=args.limit,
refResults=refResults, shiftSigma_indep=args.shift_sigma_indep, shiftSigma_subset=args.shift_sigma_subset).lines
def paramResultTable(jobItem, deltaChisqJobItem=None, referenceDataJobItem=None):
