def propertiesIni(self):
if os.path.exists(self.propertiesIniFile()):
return iniFile.iniFile(self.propertiesIniFile())
else:
ini = iniFile.iniFile()
ini.original_filename = self.propertiesIniFile()
return ini
def __init__(self, parent, ini):
QDialog.__init__(self, parent)
self.table = QTableWidget(self)
self.table.verticalHeader().hide()
layout = QGridLayout()
layout.addWidget(self.table, 0, 0)
button = QPushButton("Update")
self.connect(button, SIGNAL("clicked()"),
self.doUpdate)
layout.addWidget(button, 1, 0)
self.setLayout(layout)
self.setWindowTitle(self.tr('Settings'))
headers = ['parameter', 'value']
self.table.setColumnCount(len(headers))
self.table.setHorizontalHeaderLabels(headers)
self.table.verticalHeader().setVisible(False)
self.table.setSelectionBehavior(QAbstractItemView.SelectItems)
self.table.setSelectionMode(QAbstractItemView.SingleSelection)
names = iniFile(os.path.join(os.path.dirname(__file__), 'analysis_defaults.ini'))
items = []
self.ini = ini
for key in ini.readOrder:
if key in names.params:
items.append(key)
for key in ini.params:
if not key in items and key in names.params:
items.append(key)
nblank = 3
self.rows = len(items) + nblank
self.table.setRowCount(self.rows)
for irow, key in enumerate(items):
item = QTableWidgetItem(str(key))
item.setFlags(item.flags() ^ Qt.ItemIsEditable)
self.table.setItem(irow, 0, item)
item = QTableWidgetItem(ini.string(key))
self.table.setItem(irow, 1, item)
for i in range(nblank):
item = QTableWidgetItem(str(""))
irow = len(items) + i
self.table.setItem(irow, 0, item)
item = QTableWidgetItem(str(""))
self.table.setItem(irow, 1, item)
self.table.resizeRowsToContents()
self.table.resizeColumnsToContents()
self.table.horizontalHeader().setStretchLastSection(True);
self.table.setEditTriggers(QAbstractItemView.AllEditTriggers)
h = self.table.verticalHeader().length() + 40
h = min(QApplication.desktop().screenGeometry().height() * 4 / 5, h)
self.resize(300, h)
self.setAttribute(Qt.WA_DeleteOnClose)
def showSettings(self):
"""
Callback for action 'Show settings'
"""
if not self.plotter:
QMessageBox.warning(self, "settings", "Open chains first ")
return
if isinstance(self.iniFile, basestring): self.iniFile = iniFile(self.iniFile)
dlg = DialogSettings(self, self.iniFile)
dlg.show()
def __init__(self, path="xamppcontrolpanel.glade", root="PrefsWindow", domain=None, **kwargs):
path = os.path.join(glade_dir, path)
SimpleGladeApp.__init__(self, path, root, domain, **kwargs)
self.pathTextBox.set_text(self.parent.get_xampp_path())
self.HTTPD = self.parent.get_xampp_path().strip() + '/etc/httpd.conf'
self.MySQL = self.parent.get_xampp_path().strip() + '/etc/my.cnf'
self.BACKUP = self.parent.get_xampp_path().strip() + '/etc/bu_httpd.conf'
self.get_Apache_Setting()
self.sqlFile = iniFile(self.MySQL)
self.get_SQL_Setting()
self.modified = False
def __init__(self, path="xampp-control-panel.glade", root="MainWindow", domain=None, **kwargs):
path = os.path.join(glade_dir, path)
SimpleGladeApp.__init__(self, path, root, domain, **kwargs)
# default location of config file for this user (~/.xampp_cp);
# config file has format specified for ConfigParser module, e.g.
# [main]
# xampp_path=/opt/lampp
self.CONFIG_FILE_PATH = posix.environ['HOME'] + "/xampp_cp"
self.CONFIG_FILE = iniFile(self.CONFIG_FILE_PATH)
# set up the stop buttons that are hidden at the start - the execute buttons were created in glade :)
self.mainStopButton = gtk.Button(None, gtk.STOCK_MEDIA_STOP)
self.mainStopButton.set_border_width(5)
self.mainStopButton.connect("clicked", self.on_mainStopButton_clicked)
self.vbox1.pack_start(self.mainStopButton, True, False)
self.vbox1.reorder_child(self.mainStopButton, 0)
self.mainStopButton.hide()
self.apacheStopButton = gtk.Button(None, gtk.STOCK_MEDIA_STOP)
self.apacheStopButton.set_border_width(0)
self.apacheStopButton.connect("clicked", self.on_apacheStopButton_clicked)
self.table1.attach(self.apacheStopButton, 2, 3, 0, 1)
self.apacheStopButton.hide()
self.mysqlStopButton = gtk.Button(None, gtk.STOCK_MEDIA_STOP)
self.mysqlStopButton.set_border_width(0)
self.mysqlStopButton.connect("clicked", self.on_mysqlStopButton_clicked)
self.table1.attach(self.mysqlStopButton, 2, 3, 1, 2)
self.mysqlStopButton.hide()
self.proftpdStopButton = gtk.Button(None, gtk.STOCK_MEDIA_STOP)
self.proftpdStopButton.set_border_width(0)
self.proftpdStopButton.connect("clicked", self.on_proftpdStopButton_clicked)
self.table1.attach(self.proftpdStopButton, 2, 3, 2, 3)
self.proftpdStopButton.hide()
# get path configuration from .xcp file
xampppath = self.get_xampp_path()
if xampppath == "":
self.set_xampp_path("/opt/lampp")
# initialise the interface
self.init_interface()
def num_unequal(filename, cmpFcn):
"""
Check whether two files are numerically unequal for the given compare function.
:param filename: The base name of the files to check.
:param cmpFcn: The default comparison function. Can be overriden by the filetolmatrix.
:return: True, when the files do not match, false else.
"""
orig_name = os.path.join(args.ini_dir, args.diff_to, filename)
with open(orig_name) as f:
origMat = [[x for x in ln.split()] for ln in f]
# Check if the first row has one more column, which is the #
if len(origMat[0]) == len(origMat[1]) + 1:
origBase = 1
origMat[0] = origMat[0][1:]
else:
origBase = 0
new_name = os.path.join(args.ini_dir, args.out_files_dir, filename)
with open(new_name) as f:
newMat = [[x for x in ln.split()] for ln in f]
if len(newMat[0]) == len(newMat[1]) + 1:
newBase = 1
newMat[0] = newMat[0][1:]
else:
newBase = 0
if len(origMat) - origBase != len(newMat) - newBase:
if args.verbose_diff_output:
printlog('num rows do not match in %s: %d != %d' % (filename, len(origMat), len(newMat)))
return True
if newBase == 1:
cols = [s[0] + 'x' + s[1] if len(s) == 2 and s != 'nu' else s for s in newMat[0]]
else:
cols = range(len(newMat[0]))
tolerances = get_tolerance_vector(filename, cols)
row = 0
col = 0
try:
if tolerances:
inifilenameparts = filename.rsplit('_', 2)
inifilename = '_'.join(inifilenameparts[0:2]) if inifilenameparts[1] != 'transfer' else inifilenameparts[0]
inifilename += "_params.ini"
inifilename = os.path.join(args.ini_dir, args.out_files_dir, inifilename)
try:
# The following split fails for *_transfer_out.* files where it not needed anyway.
inifile = iniFile()
inifile.readFile(inifilename)
except:
printlog("Could not open inifilename: %s" % inifilename)
for o_row, n_row in zip(origMat[origBase:], newMat[newBase:]):
row += 1
if len(o_row) != len(n_row):
if args.verbose_diff_output:
printlog('num columns do not match in %s: %d != %d' % (filename, len(o_row), len(n_row)))
return True
col = 0
of_row = [float(f) for f in o_row]
nf_row = []
for f in n_row:
try:
nf_row += [float(f)]
except ValueError:
sp = customsplit(f)
nf_row += [ float(sp[0] + 'E' + sp[1]) ]
oldrowdict = False
newrowdict = False
for o, n in zip(of_row, nf_row):
if isinstance(tolerances[col], Ignore):
pass
else:
cond, tols = tolerances[col]
# When the column condition is bool (True or False) or a function
# returning False, then skip this column.
if isinstance(cond, bool) or not cond(inifile):
pass
else:
if isinstance(tols, float):
if not cmpFcn(o, n, tols):
if args.verbose_diff_output:
printlog('value mismatch at %d, %d ("%s") of %s: %s != %s' % (row, col + 1, cols[col], filename, o, n))
return True
elif not isinstance(tols, Ignore):
if not oldrowdict:
oldrowdict = dict(zip(cols, of_row))
newrowdict = dict(zip(cols, nf_row))
if isinstance(tols, list):
cand = False
for lim, rhs in tols:
if lim < newrowdict["L"]:
cand = rhs
else:
break
if isinstance(cand, float):
if not cmpFcn(o, n, cand):
if args.verbose_diff_output:
printlog('value mismatch at %d, %d ("%s") of %s: %s != %s' % (row, col + 1, cols[col], filename, o, n))
return True
elif not isinstance(cand, Ignore):
if not cand(oldrowdict, newrowdict):
if args.verbose_diff_output:
printlog('value mismatch at %d, %d ("%s") of %s: %s != %s' % (row, col + 1, cols[col], filename, o, n))
return True
else:
if not tols(oldrowdict, newrowdict):
if args.verbose_diff_output:
printlog('value mismatch at %d, %d ("%s") of %s: %s != %s' % (row, col + 1, cols[col], filename, o, n))
return True
col += 1
return False
else:
# if args.verbose_diff_output:
# printlog("Skipped file %s" % (filename))
return False
except ValueError as e:
printlog("ValueError: '%s' at %d, %d in file: %s" % (e.message, row, col + 1, filename))
return True
# the plotting matlab run is optional and only if you are using plot_ext=m in getdist
plot_types = ['.', '_2D.']
# you don't need these for python plots generated separately
# '_tri.m' is very slow for so many
if args.plot_data is None: data_dir = batch.batchPath + 'plot_data' + os.sep
else: data_dir = os.path.abspath(args.plot_data) + os.sep
ini_dir = batch.batchPath + 'getdist' + os.sep
checkDir(data_dir)
checkDir(ini_dir)
if not args.plots:
for jobItem in Opts.filteredBatchItems():
ini = iniFile.iniFile()
ini.params['file_root'] = jobItem.chainRoot
checkDir(jobItem.distPath)
ini.params['out_dir'] = jobItem.distPath
ini.params['plot_data_dir'] = data_dir
custom_plot = batch.commonPath + 'plots' + os.sep + jobItem.paramtag + '.ini'
custom_plot2 = batch.commonPath + 'plots' + os.sep + jobItem.name + '.ini'
if os.path.exists(custom_plot2):
ini.includes.append(custom_plot2)
elif os.path.exists(custom_plot):
ini.includes.append(custom_plot)
elif len(jobItem.param_set) > 0:
ini.params['plot_2D_param'] = jobItem.param_set[0]
ini.defaults.append(batch.commonPath + base_ini)
tag = ''
if jobItem.isImportanceJob or args.burn_removed:
# Get CAMB input parameters from best-fit .minimum file from cosmomc
import sys, os, iniFile
from getdist import ResultObjs
if len(sys.argv) < 3:
print 'Usage: python/bestFitCAMB.py chain_root iniName'
sys.exit()
root = os.path.abspath(sys.argv[1])
pars = {'ombh2':'omegabh2', 'omch2':'omegach2', 'omnuh2':'omeganuh2', 'hubble':'H0', 'w':'w',
'helium_fraction':'yheused', 'scalar_amp(1)':'A' , 'scalar_spectral_index(1)':'ns', 'scalar_nrun(1)':'nrun', 'initial_ratio(1)':'r',
're_optical_depth':'tau', 're_delta_redshift':'deltazrei', 'massless_neutrinos':'nnu'}
ini = iniFile.iniFile()
ini.params['re_use_optical_depth'] = True
ini.params['temp_cmb'] = 2.7255
ini.params['CMB_outputscale'] = 2.7255e6 ** 2.
ini.defaults.append('params.ini')
bf = ResultObjs.bestFit(root + '.minimum', setParamNameFile=root + '.paramnames', want_fixed=True)
for camb, cosmomc in pars.items():
par = bf.parWithName(cosmomc)
if par is not None: ini.params[camb] = par.best_fit
ini.params['scalar_amp(1)'] = float(ini.params['scalar_amp(1)']) / 1e9
nmassive = 1
neffstandard = 3.046 / 3
def loadDataset(self, froot):
if not '.dataset' in froot: froot += '.dataset'
ini = iniFile.iniFile(froot)
self.readIni(ini)
def num_unequal(filename, cmpFcn):
"""
Check whether two files are numerically unequal for the given compare function.
:param filename: The base name of the files to check.
:param cmpFcn: The default comparison function. Can be overriden by the filetolmatrix.
:return: True, when the files do not match, false else.
"""
orig_name = os.path.join(args.ini_dir, args.diff_to, filename)
with open(orig_name) as f:
origMat = [[x for x in ln.split()] for ln in f]
# Check if the first row has one more column, which is the #
if len(origMat[0]) == len(origMat[1]) + 1:
origBase = 1
origMat[0] = origMat[0][1:]
else:
origBase = 0
new_name = os.path.join(args.ini_dir, args.out_files_dir, filename)
with open(new_name) as f:
newMat = [[x for x in ln.split()] for ln in f]
if len(newMat[0]) == len(newMat[1]) + 1:
newBase = 1
newMat[0] = newMat[0][1:]
else:
newBase = 0
if len(origMat) - origBase != len(newMat) - newBase:
if args.verbose_diff_output:
printlog('num rows do not match in %s: %d != %d' %
(filename, len(origMat), len(newMat)))
return True
if newBase == 1:
cols = [
s[0] + 'x' + s[1] if len(s) == 2 and s != 'nu' else s
for s in newMat[0]
]
else:
cols = range(len(newMat[0]))
tolerances = get_tolerance_vector(filename, cols)
row = 0
col = 0
try:
if tolerances:
inifilenameparts = filename.rsplit('_', 2)
inifilename = '_'.join(
inifilenameparts[0:2]
) if inifilenameparts[1] != 'transfer' else inifilenameparts[0]
inifilename += "_params.ini"
inifilename = os.path.join(args.ini_dir, args.out_files_dir,
inifilename)
try:
# The following split fails for *_transfer_out.* files where it not needed anyway.
inifile = iniFile()
inifile.readFile(inifilename)
except:
printlog("Could not open inifilename: %s" % inifilename)
for o_row, n_row in zip(origMat[origBase:], newMat[newBase:]):
row += 1
if len(o_row) != len(n_row):
if args.verbose_diff_output:
printlog('num columns do not match in %s: %d != %d' %
(filename, len(o_row), len(n_row)))
return True
col = 0
of_row = [float(f) for f in o_row]
nf_row = []
for f in n_row:
try:
nf_row += [float(f)]
except ValueError:
sp = customsplit(f)
nf_row += [float(sp[0] + 'E' + sp[1])]
oldrowdict = False
newrowdict = False
for o, n in zip(of_row, nf_row):
if isinstance(tolerances[col], Ignore):
pass
else:
cond, tols = tolerances[col]
# When the column condition is bool (True or False) or a function
# returning False, then skip this column.
if isinstance(cond, bool) or not cond(inifile):
pass
else:
if isinstance(tols, float):
if not cmpFcn(o, n, tols):
if args.verbose_diff_output:
printlog(
'value mismatch at %d, %d ("%s") of %s: %s != %s'
% (row, col + 1, cols[col],
filename, o, n))
return True
elif not isinstance(tols, Ignore):
if not oldrowdict:
oldrowdict = dict(zip(cols, of_row))
newrowdict = dict(zip(cols, nf_row))
if isinstance(tols, list):
cand = False
for lim, rhs in tols:
if lim < newrowdict["L"]:
cand = rhs
else:
break
if isinstance(cand, float):
if not cmpFcn(o, n, cand):
if args.verbose_diff_output:
printlog(
'value mismatch at %d, %d ("%s") of %s: %s != %s'
% (row, col + 1, cols[col],
filename, o, n))
return True
elif not isinstance(cand, Ignore):
if not cand(oldrowdict, newrowdict):
if args.verbose_diff_output:
printlog(
'value mismatch at %d, %d ("%s") of %s: %s != %s'
% (row, col + 1, cols[col],
filename, o, n))
return True
else:
if not tols(oldrowdict, newrowdict):
if args.verbose_diff_output:
printlog(
'value mismatch at %d, %d ("%s") of %s: %s != %s'
% (row, col + 1, cols[col],
filename, o, n))
return True
col += 1
return False
else:
# if args.verbose_diff_output:
# printlog("Skipped file %s" % (filename))
return False
except ValueError as e:
printlog("ValueError: '%s' at %d, %d in file: %s" %
(e.message, row, col + 1, filename))
return True
def makeGrid(batchPath, settingName=None, settings=None, readOnly=False, interactive=False):
batchPath = os.path.abspath(batchPath) + os.sep
# 0: chains, 1: importance sampling, 2: best-fit, 3: best-fit and Hessian
cosmomcAction = 0
if not settings:
if not settingName:
if not pathIsGrid(batchPath):
raise Exception('Need to give name of setting file if batchPath/config does not exist')
readOnly = True
sys.path.insert(0, batchPath + 'config')
settings = __import__(iniFile.iniFile(batchPath + 'config/config.ini').params['setting_file'].replace('.py', ''))
else:
settings = __import__(settingName, fromlist=['dummy'])
batch = batchJob.batchJob(batchPath, settings.ini_dir)
# priors and widths for parameters which are varied
if not hasattr(settings, 'params'):
params = dict()
params['mnu'] = '0.02 0 5 0.1 0.03'
params['omegak'] = '-0.0008 -0.3 0.3 0.001 0.001' # starting exactly on flat seems to confuse minimizer
params['w'] = '-0.995 -3 -0.3 0.02 0.02'
params['nnu'] = '3.046 0.05 10 0.05 0.05'
params['nrun'] = '0 -1 1 0.005 0.001'
params['nrunrun'] = '0 -1 1 0.005 0.001'
params['r'] = '0 0 3 0.03 0.03'
params['Alens'] = '1 0 10 0.05 0.05'
params['yhe'] = '0.245 0.1 0.5 0.006 0.006'
params['alpha1'] = '0 -1 1 0.0003 0.0003'
params['deltazrei'] = '0.5 0.1 3 0.3 0.3'
params['wa'] = '0 -2 2 0.3 0.3'
params['meffsterile'] = '0.1 0 3 0.1 0.03'
params['Aphiphi'] = '1 0 10 0.02 0.02'
params['Alensf'] = '1 0 10 0.03 0.03'
params['nt'] = '0 -3 3 0.2 0.02'
settings.params = params
if hasattr(settings, 'skip'): batch.skip = settings.skip
batch.makeItems(settings, messages=not readOnly)
if readOnly:
for jobItem in [b for b in batch.jobItems]:
if not jobItem.chainExists():
batch.jobItems.remove(jobItem)
batch.save()
print 'OK, configured grid with %u existing chains' % (len(batch.jobItems))
return batch
else:
batch.makeDirectories(settings.__file__)
batch.save()
start_at_bestfit = getattr(settings, 'start_at_bestfit', False)
for jobItem in batch.items(wantSubItems=False):
jobItem.makeChainPath()
ini = iniFile.iniFile()
for param in jobItem.param_set:
ini.params['param[' + param + ']'] = settings.params[param]
if 'mnu' in jobItem.param_set:
ini.params['num_massive_neutrinos'] = 3
if 'meffsterile' in jobItem.param_set:
ini.params['param[mnu]'] = '0.06'
ini.params['param[nnu]'] = '3.1 3.046 10 0.05 0.05'
ini.params['num_massive_neutrinos'] = 1
ini.params['accuracy_level'] = 1.2 # to use 4 rather than 3 momentum modes
if 'yhe' in jobItem.param_set:
ini.params['bbn_consistency'] = False
if 'r' in jobItem.param_set:
ini.params['compute_tensors'] = True
if 'nt' in jobItem.param_set:
ini.params['inflation_consistency'] = False
ini.params['lmax_tensor'] = 1000
# ini.params['pivot_k'] = 0.002
if hasattr(settings, 'extra_opts'):
ini.params.update(settings.extra_opts)
ini.params['file_root'] = jobItem.chainRoot
cov_dir_name = getattr(settings, 'cov_dir', 'planck_covmats')
covdir = os.path.join(batch.basePath, cov_dir_name)
covmat = os.path.join(covdir, jobItem.name + '.covmat')
if not os.path.exists(covmat):
covNameMappings = getattr(settings, 'covNameMappings', None)
mapped_name_norm = jobItem.makeNormedName(covNameMappings)[0]
covmat_normed = os.path.join(covdir, mapped_name_norm + '.covmat')
covmat = covmat_normed
if not os.path.exists(covmat) and hasattr(jobItem.data_set, 'covmat'): covmat = batch.basePath + jobItem.data_set.covmat
if not os.path.exists(covmat) and hasattr(settings, 'covmat'): covmat = batch.basePath + settings.covmat
if os.path.exists(covmat):
ini.params['propose_matrix'] = covmat
if getattr(settings, 'newCovmats', True): ini.params['MPI_Max_R_ProposeUpdate'] = 20
else:
hasCov = False
ini.params['MPI_Max_R_ProposeUpdate'] = 20
covmat_try = []
if 'covRenamer' in dir(settings):
covmat_try += settings.covRenamer(jobItem.name)
covmat_try += settings.covRenamer(mapped_name_norm)
if hasattr(settings, 'covrenames'):
for aname in [jobItem.name, mapped_name_norm]:
covmat_try += [aname.replace(old, new, 1) for old, new in settings.covrenames if old in aname]
for new1, old1 in settings.covrenames:
if old1 in aname:
name = aname.replace(old1, new1, 1)
covmat_try += [name.replace(old, new, 1) for old, new in settings.covrenames if old in name]
if 'covWithoutNameOrder' in dir(settings):
if covNameMappings:
removes = copy.deepcopy(covNameMappings)
else: removes = dict()
for name in settings.covWithoutNameOrder:
if name in jobItem.data_set.names:
removes[name] = ''
covmat_try += [jobItem.makeNormedName(removes)[0]]
covdir2 = os.path.join(batch.basePath, getattr(settings, 'cov_dir_fallback', cov_dir_name))
for name in covmat_try:
covmat = os.path.join(batch.basePath, covdir2, name + '.covmat')
if os.path.exists(covmat):
ini.params['propose_matrix'] = covmat
print 'covmat ' + jobItem.name + ' -> ' + name
hasCov = True
break
if not hasCov: print 'WARNING: no matching specific covmat for ' + jobItem.name
ini.params['start_at_bestfit'] = start_at_bestfit
updateIniParams(ini, jobItem.data_set.params, batch.commonPath)
for deffile in settings.defaults:
ini.defaults.append(batch.commonPath + deffile)
if hasattr(settings, 'override_defaults'):
ini.defaults = [batch.commonPath + deffile for deffile in settings.override_defaults] + ini.defaults
ini.params['action'] = cosmomcAction
ini.saveFile(jobItem.iniFile())
if not start_at_bestfit:
setMinimize(jobItem, ini)
variant = '_minimize'
ini.saveFile(jobItem.iniFile(variant))
# add ini files for importance sampling runs
for imp in jobItem.importanceJobs():
if batch.hasName(imp.name.replace('_post', '')): raise Exception('importance sampling something you already have?')
for minimize in (False, True):
if minimize and not getattr(imp, 'want_minimize', True): continue
ini = iniFile.iniFile()
updateIniParams(ini, imp.importanceSettings, batch.commonPath)
if cosmomcAction == 0 and not minimize:
for deffile in settings.importanceDefaults:
ini.defaults.append(batch.commonPath + deffile)
ini.params['redo_outroot'] = imp.chainRoot
ini.params['action'] = 1
else:
ini.params['file_root'] = imp.chainRoot
if minimize:
setMinimize(jobItem, ini)
variant = '_minimize'
else: variant = ''
ini.defaults.append(jobItem.iniFile())
ini.saveFile(imp.iniFile(variant))
if cosmomcAction != 0: break
if not interactive: return batch
print 'Done... to run do: python python/runbatch.py ' + batchPath
if not start_at_bestfit:
print '....... for best fits: python python/runbatch.py ' + batchPath + ' --minimize'
print ''
print 'for importance sampled: python python/runbatch.py ' + batchPath + ' --importance'
print 'for best-fit for importance sampled: python python/runbatch.py ' + batchPath + ' --importance_minimize'
