def use_table(self, tabletype, spacing=0.002):
"""Turn on the xvg table option, and generate a user-defined table
defined in self.xvg_lines, generated by the TableMaker object, with the specifications:showParams
OPTIONS
tabletype = a TableMaker.Dielectric derived class:
'Switch_Shift' (default) GROMACS-style tapered cutoffs
'SF3' ShenFreed 3 table
'ReactionField' rxn field dielectric solvent model
TableMaker examples:
# table=TableMaker(spacing=0.002)
# tabletype=SF3(length_scale=4.0)
# tabletype=Switch_Shift()
# tabletype=ReactionField(rc=1.0)
# settings for eps->Infinity
# tabletype.krf = 1.0 / ( 2.0 * tabletype.rc )
# tabletype.crf = 3.0 / ( 2.0 * tabletype.rc )
# table=table.make(tabletype)
# print table
"""
self.use_xvg = True
self.tabletype = tabletype
self.tablemaker = TableMaker(spacing=spacing)
self.tabletxt = self.tablemaker.make(self.tabletype)
# set the user-table flags in the the mdp file
self.setParameter('coulombtype', 'user')
self.setParameter('vdwtype', 'user')
def test():
"""To test code in imported modules"""
tableMaker.test()
boardAnalyser.test()
game.test()
player.test()
utils.test()
ui.test()
def use_table(self, tabletype, spacing=0.002):
"""Turn on the xvg table option, and generate a user-defined table
defined in self.xvg_lines, generated by the TableMaker object, with the specifications:showParams
OPTIONS
tabletype = a TableMaker.Dielectric derived class:
'Switch_Shift' (default) GROMACS-style tapered cutoffs
'SF3' ShenFreed 3 table
'ReactionField' rxn field dielectric solvent model
TableMaker examples:
# table=TableMaker(spacing=0.002)
# tabletype=SF3(length_scale=4.0)
# tabletype=Switch_Shift()
# tabletype=ReactionField(rc=1.0)
# settings for eps->Infinity
# tabletype.krf = 1.0 / ( 2.0 * tabletype.rc )
# tabletype.crf = 3.0 / ( 2.0 * tabletype.rc )
# table=table.make(tabletype)
# print table
"""
self.use_xvg = True
self.tabletype = tabletype
self.tablemaker = TableMaker(spacing=spacing)
self.tabletxt = self.tablemaker.make(self.tabletype)
# set the user-table flags in the the mdp file
self.setParameter('coulombtype','user')
self.setParameter('vdwtype','user')
# the command line option. If the file doesn't exist, execution will stop
net = kicad_netlist_reader.netlist(sys.argv[1])
Components = net.getInterestingComponents()
# Create the NetList and componentList lists
NetList = getNetList(net)
componentList = getComponentList(net)
# printNetList(NetList);
# printComponentList(componentList);
# Get an Anchor component and start Paths
Tables = []
tableCount = 0
while (len(componentList) > 0):
Tables.append(TableMaker())
table = Tables[tableCount]
Paths = CablePaths()
for component in componentList:
if (component['isAnchor'] == True):
# start Paths
for i, connection in enumerate(component['connections']):
position = connection['pin']
pathName = Paths.addPath(position, component['ref'],
connection['net'])
table.addPath(pathName)
table.sortTable()
# Add Headers
for path in Paths.getPaths():
table.addComponent(component, path, Components,
Paths.getPaths(), NetList)
class MdpFile(object):
"""A class to store and manipulate Gromacs mdp files.
TODO
Can we make use of the Units class to allow user to specify parameters with units attached and automatically convert to/from gromacs units?
"""
# Class data
MAXSEED = 2**30 # maximum random number seed
def __init__(self, mdpfile=None, debug=False):
"""Constructor to initialize mdp file container.
OPTIONAL ARGUMENTS
mdpfile filename (string) or contents (list of strings) of a gromacs .mdp file to be read
"""
# set debug flag
self.debug = debug
# store filename of .mdp file initialized from, if any
self.templatefile = None
if type(mdpfile) == str:
self.templatefile = mdpfile
# initialize internal storage
self.lines = []
self.params = {
} # {keyword:value} dictionary. NOTE: All values are stored as strings: i.e. {'rlist':'4.0'}
self.keywords = [
] # keep a list of the keyword order, just so we can write oiut *.mdp files in the same order as the template
# read .mdp file or process contents, if give
if mdpfile:
[self.lines, self.params, self.keywords,
self.keyword_line_index] = self.read(mdpfile)
# settings for user-defined tables
self.use_xvg = False
self.tablemaker = None
self.tabletype = None
self.tabletxt = None
return
def use_table(self, tabletype, spacing=0.002):
"""Turn on the xvg table option, and generate a user-defined table
defined in self.xvg_lines, generated by the TableMaker object, with the specifications:showParams
OPTIONS
tabletype = a TableMaker.Dielectric derived class:
'Switch_Shift' (default) GROMACS-style tapered cutoffs
'SF3' ShenFreed 3 table
'ReactionField' rxn field dielectric solvent model
TableMaker examples:
# table=TableMaker(spacing=0.002)
# tabletype=SF3(length_scale=4.0)
# tabletype=Switch_Shift()
# tabletype=ReactionField(rc=1.0)
# settings for eps->Infinity
# tabletype.krf = 1.0 / ( 2.0 * tabletype.rc )
# tabletype.crf = 3.0 / ( 2.0 * tabletype.rc )
# table=table.make(tabletype)
# print table
"""
self.use_xvg = True
self.tabletype = tabletype
self.tablemaker = TableMaker(spacing=spacing)
self.tabletxt = self.tablemaker.make(self.tabletype)
# set the user-table flags in the the mdp file
self.setParameter('coulombtype', 'user')
self.setParameter('vdwtype', 'user')
# NOTE: the acual 'table.xvg' file will be written by System.prepare()
def read(self, mdpfile):
"""Read the contents of a gromacs .mdp file.
ARGUMENTS
mdpfile (string or list of strings) - if a string is provided, the contents of the file are read;
if a list is provided, this is interpreted as the contents of an mdp file
"""
# handle multiple argument types
if (type(mdpfile) == list):
lines = mdpfile
elif (type(mdpfile) == str):
# if a filename is provided, get its contents
fin = open(mdpfile, 'r')
lines = fin.readlines()
# remove extraneous newlines
lines = map(lambda x: x.rstrip("\n"), lines)
fin.close()
else:
raise "Unrecognized argument: " + repr(mdpfile)
# build an initial dictionary of key:values from the lines
[params, keywords, keyword_line_index] = self.buildParameterDict(lines)
return [lines, params, keywords, keyword_line_index]
def write(self, filename):
"""Write contents of .mdp file to disk.
ARGUMENTS
filename (string) - the filename to write to
"""
fout = open(filename, 'w')
for line in self.lines:
fout.write(line + '\n')
fout.close()
return
def write_table(self, filename):
"""Writes the lines of self.tabletxt to user-supplied filename in correct directory -- should be 'table.xvg'
ARGUMENTS
filename (string) - the name of the file to be written
"""
fout = open(filename, 'w')
fout.write(self.tabletxt)
fout.close()
return
def buildParameterDict(self, lines):
"""Goes through each line of the file,and parses keywords into a key:value dictionary
ARGUMENTS
lines (list) - the contents of the .mdp file from which the dictionary is to be built
RETURNS
params (dict) - dictionary of key:value processed from contents of file
keywords (list) - list of keywords found in the file
keyword_line_index (dict) - keyword_line_index[keyword] is the line index on which 'keyword' appears
TODO
The processing here is very rudimentary -- may need to be modified to accomodate multiple arguments per line.
We should store the corresponding original line from the file, or store the complete contents of the line (including comments?)
"""
params = dict()
keywords = list()
keyword_line_index = dict()
line_index = 0
for line in lines:
# strip comments
index = line.find(';')
if index > -1:
line = line[0:index]
# strip whitespace from both ends of line
line = line.strip()
# split off keyword
fields = line.split()
# if key = values ... is found, store
if (len(fields) >= 3) and (fields[1] == '='):
# extract keywords
keyword = fields[0]
# extract value(s)
index = line.find('=')
values = line[index + 1:len(line)].strip()
# store
params[keyword] = values
keywords.append(keyword)
keyword_line_index[keyword] = line_index
# increment line index
line_index += 1
return [params, keywords, keyword_line_index]
def showParams(self):
"""Display dictionary of recognized key:value pairs from mdp file.
"""
outstr = ''
for key in self.keywords:
outstr = outstr + self.keyword2line(key)
print outstr
return
def showLines(self):
"""Display lines.
"""
contents = ''
for line in self.lines:
contents += line + '\n'
print contents
return
def keyword2line(self, keyword):
"""Takes in a parameter keyword and returns a formatted mdp file line.
ARGUMENTS
keyword (string) - the keyword specifying the formatted mdp line to retrieve
RETURNS
the formatted mdp line corresponding to the keyword, if found
TODO
What if keyword isn't found?
We should store the corresponding original line from the file, or store the complete contents of the line (including comments?)
"""
return '%-20s = %-20s\n' % (keyword, self.params[keyword])
def setParameter(self, keyword, valuestr):
"""Sets a particular mdp keyword to a value (string) in the parameter dictionary, updates mdp lines.
ARGUMENTS
keyword (string) - the keyword to which the parameter is to be assigned
valuestr (string) - the corresponding parameter value to assign to the keyword
TODO
Searching in the parameter file can be facilitated if we store a dictionary of which line a keyword is specified on.
"""
# determine whether the keyword already exists
keyword_exists = self.keyword_line_index.has_key(keyword)
# set keyword in dictionary (creating or overriding)
self.params[keyword] = valuestr
# create a new line from this keyword-value pair
line = self.keyword2line(keyword)
if keyword_exists:
# if keyword exists, replace the line
line_index = self.keyword_line_index[keyword]
self.lines[line_index] = line
else:
# if keyword does not exists, add a line
self.lines.append(line)
self.keywords.append(keyword) # add the keyword to the list
self.keyword_line_index[keyword] = len(
self.lines) - 1 # store line number of the appended line
return
def getParameter(self, keyword):
"""Returns the value associated with a particular parameter; or None if the parameter is not set"""
if keyword not in self.params:
return None
return self.params[keyword]
def setTemperature(self, temperature):
"""Set the temperature of the various options.
"""
# Set the temperature parameters
self.setParameter('gen_temp', temperature)
self.setParameter('ref_t', temperature)
return
def randomizeSeed(self):
"""Randomize the random seed, adding one if none exists.
TODO
Uses range from 1 to 2**30 for now, but should figure out acceptable range for gromacs.
"""
# choose a new random seed
import random
self.setParameter('gen_seed', str(random.randint(1, self.MAXSEED)))
self.setParameter('mc_seed', str(random.randint(1, self.MAXSEED)))
return
def setParametersFromDict(self, paramdict):
"""Takes in a set of parameters as a dictionary of {keyword:value} entries (values are strings) and sets parameters for each.
ARGUMENTS
paramdict (dict) - a dictionary of keyword:value pairs to be used to update parameters
"""
for [key, value] in paramdict.iteritems():
if self.debug: print 'DEBUG: key, value of paramdict{}', key, value
self.setParameter(key, value)
return
def delParameter(self, keyword):
"""Removes a particular mdp keyword (and its value (string)) from the parameter dictionary, and deletes mdp line.
ARGUMENTS
keyword (string) - the keyword to be cleared
TODO
Propose new name of clearParameter or removeParameter
"""
# remove keyword from dictionary
if self.params.has_key(keyword):
del self.params[keyword]
# replace instances of this 'keyword = value' in the mdp lines
i = 0
while i < len(self.lines):
fields = self.lines[i].strip().split()
if len(fields) > 0:
if fields[0] == keyword:
self.lines.pop(i)
else:
i = i + 1
else:
i = i + 1
return
process.start()
for process in p_plot:
process.join()
print '\n'
####################
### MAKE TABLES! ###
####################
if doYields:
doPresel = True
outFile = file('yields/.yields_tmp.tex', 'w')
categoryNames = []
yieldTable = TableMaker('fcncAnalysis/combined_histos/' + selection + '_cut1_' + period + batch + '.root', outFile, scale = LUMIDATA, delimiter = '&', doSumBG = True)
yieldTable.set_period(period)
yieldTable._columnList = ['higgs', 'Triboson', 'ttV', 'Diboson', 'top', 'VJets', 'BG', 'DATA', 'FCNH']#, 'Significance']
#yieldTable._columnList = ['BG', 'DATA', 'FCNH']#, 'Significance']
yieldTable.add_datasets(samples, Clear = True)
yieldTable.add_datasets('FCNH')
yieldTable.add_datasets('DATA')
print '\n\n Printing yields...\n'
if doOS:
categoryNames.extend(catOS)
if doSS:
### End of configuration for PlotProducer ###
for process in p_plot:
print 'Plotting {0}'.format(process.name)
process.start()
for process in p_plot:
process.join()
print '\n'
if doYields:
### Initialize table maker ###
tableFile = file('yields/.yields_tmp.tex', 'w')
yieldTable = TableMaker('fcncAnalysis/combined_histos/{0}_cut1_{1}_{2}.root'.format(selection, period, batch),
tableFile, scale = LUMIDATA,
delimiter = '&', doSumBG = True)
yieldTable.set_period(period)
yieldTable.add_datasets(samples['all'], Clear = True)
if not doPlots:
#yieldTable.get_scale_factors()
yieldTable.get_scale_factors(['FCNH', 'FCNHUp'])
if do3l:
yieldTable._columnList = ['Rare', 'WZJets3LNu', 'Fakes', 'BG', 'DATA', 'FCNH']
#yieldTable._columnList = ['Rare', 'WZJets3LNu', 'Fakes', 'BG', 'DATA', 'FCNHWW', 'FCNHTauTau', 'FCNHZZ']
#yieldTable._columnList = ['Rare', 'WZJets3LNu', 'Fakes', 'BG', 'DATA', 'FCNHUpWW', 'FCNHUpZZ', 'FCNHUpTauTau']
#yieldTable._columnList = ['Rare', 'WZJets3LNu', 'Fakes', 'BG', 'DATA', 'TTH_M-125']
#yieldTable._columnList = samples['3l_inclusive'] + ['BG', 'DATA', 'FCNH']
#yieldTable._columnList = ['BG', 'DATA', 'FCNHWW', 'FCNHZZ', 'FCNHTauTau']
#yieldTable._columnList = ['BG', 'DATA', 'FCNH']#, 'Significance']
# printNetList(NetList)
# printComponentList(componentList)
# Get an Anchor component and start Paths
Tables = []
tableCount = 0
# if componentList does not change between consecutive iterations, terminate Pathing
previousComponentList = []
while (len(componentList) > 0 and previousComponentList != componentList):
import copy
previousComponentList = copy.deepcopy(componentList)
Paths = CablePaths()
Tables.append(TableMaker(componentList, Paths, NetList))
table = Tables[tableCount]
tableCount += 1
for component in componentList:
if (component['isAnchor'] == True):
# start Paths
for i, connection in enumerate(component['connections']):
position = connection['pin']
pathName = Paths.addPath(position, component['ref'],
connection['net'])
table.addPath(pathName)
table.sortTable()
# Add Headers
for path in Paths.getPaths():
table.addComponent(component, path)
class MdpFile(object):
"""A class to store and manipulate Gromacs mdp files.
TODO
Can we make use of the Units class to allow user to specify parameters with units attached and automatically convert to/from gromacs units?
"""
# Class data
MAXSEED = 2**30 # maximum random number seed
def __init__(self, mdpfile = None, debug = False):
"""Constructor to initialize mdp file container.
OPTIONAL ARGUMENTS
mdpfile filename (string) or contents (list of strings) of a gromacs .mdp file to be read
"""
# set debug flag
self.debug = debug
# store filename of .mdp file initialized from, if any
self.templatefile = None
if type(mdpfile) == str:
self.templatefile = mdpfile
# initialize internal storage
self.lines = []
self.params = {} # {keyword:value} dictionary. NOTE: All values are stored as strings: i.e. {'rlist':'4.0'}
self.keywords = [] # keep a list of the keyword order, just so we can write oiut *.mdp files in the same order as the template
# read .mdp file or process contents, if give
if mdpfile:
[self.lines, self.params, self.keywords, self.keyword_line_index] = self.read(mdpfile)
# settings for user-defined tables
self.use_xvg = False
self.tablemaker = None
self.tabletype = None
self.tabletxt = None
return
def use_table(self, tabletype, spacing=0.002):
"""Turn on the xvg table option, and generate a user-defined table
defined in self.xvg_lines, generated by the TableMaker object, with the specifications:showParams
OPTIONS
tabletype = a TableMaker.Dielectric derived class:
'Switch_Shift' (default) GROMACS-style tapered cutoffs
'SF3' ShenFreed 3 table
'ReactionField' rxn field dielectric solvent model
TableMaker examples:
# table=TableMaker(spacing=0.002)
# tabletype=SF3(length_scale=4.0)
# tabletype=Switch_Shift()
# tabletype=ReactionField(rc=1.0)
# settings for eps->Infinity
# tabletype.krf = 1.0 / ( 2.0 * tabletype.rc )
# tabletype.crf = 3.0 / ( 2.0 * tabletype.rc )
# table=table.make(tabletype)
# print table
"""
self.use_xvg = True
self.tabletype = tabletype
self.tablemaker = TableMaker(spacing=spacing)
self.tabletxt = self.tablemaker.make(self.tabletype)
# set the user-table flags in the the mdp file
self.setParameter('coulombtype','user')
self.setParameter('vdwtype','user')
# NOTE: the acual 'table.xvg' file will be written by System.prepare()
def read(self, mdpfile):
"""Read the contents of a gromacs .mdp file.
ARGUMENTS
mdpfile (string or list of strings) - if a string is provided, the contents of the file are read;
if a list is provided, this is interpreted as the contents of an mdp file
"""
# handle multiple argument types
if (type(mdpfile) == list):
lines = mdpfile
elif (type(mdpfile) == str):
# if a filename is provided, get its contents
fin = open(mdpfile, 'r')
lines = fin.readlines()
# remove extraneous newlines
lines = map(lambda x:x.rstrip("\n"),lines)
fin.close()
else:
raise "Unrecognized argument: " + repr(mdpfile)
# build an initial dictionary of key:values from the lines
[params, keywords, keyword_line_index] = self.buildParameterDict(lines)
return [lines, params, keywords, keyword_line_index]
def write(self, filename):
"""Write contents of .mdp file to disk.
ARGUMENTS
filename (string) - the filename to write to
"""
fout = open(filename, 'w')
for line in self.lines:
fout.write(line + '\n')
fout.close()
return
def write_table(self, filename):
"""Writes the lines of self.tabletxt to user-supplied filename in correct directory -- should be 'table.xvg'
ARGUMENTS
filename (string) - the name of the file to be written
"""
fout = open(filename, 'w')
fout.write(self.tabletxt)
fout.close()
return
def buildParameterDict(self, lines):
"""Goes through each line of the file,and parses keywords into a key:value dictionary
ARGUMENTS
lines (list) - the contents of the .mdp file from which the dictionary is to be built
RETURNS
params (dict) - dictionary of key:value processed from contents of file
keywords (list) - list of keywords found in the file
keyword_line_index (dict) - keyword_line_index[keyword] is the line index on which 'keyword' appears
TODO
The processing here is very rudimentary -- may need to be modified to accomodate multiple arguments per line.
We should store the corresponding original line from the file, or store the complete contents of the line (including comments?)
"""
params = dict()
keywords = list()
keyword_line_index = dict()
line_index = 0
for line in lines:
# strip comments
index = line.find(';')
if index > -1:
line = line[0:index]
# strip whitespace from both ends of line
line = line.strip()
# split off keyword
fields = line.split()
# if key = values ... is found, store
if (len(fields) >= 3) and (fields[1] == '='):
# extract keywords
keyword = fields[0]
# extract value(s)
index = line.find('=')
values = line[index+1:len(line)].strip()
# store
params[keyword] = values
keywords.append(keyword)
keyword_line_index[keyword] = line_index
# increment line index
line_index += 1
return [params, keywords, keyword_line_index]
def showParams(self):
"""Display dictionary of recognized key:value pairs from mdp file.
"""
outstr = ''
for key in self.keywords:
outstr = outstr + self.keyword2line(key)
print outstr
return
def showLines(self):
"""Display lines.
"""
contents = ''
for line in self.lines:
contents += line + '\n'
print contents
return
def keyword2line(self, keyword):
"""Takes in a parameter keyword and returns a formatted mdp file line.
ARGUMENTS
keyword (string) - the keyword specifying the formatted mdp line to retrieve
RETURNS
the formatted mdp line corresponding to the keyword, if found
TODO
What if keyword isn't found?
We should store the corresponding original line from the file, or store the complete contents of the line (including comments?)
"""
return '%-20s = %-20s\n'%(keyword, self.params[keyword])
def setParameter(self, keyword, valuestr):
"""Sets a particular mdp keyword to a value (string) in the parameter dictionary, updates mdp lines.
ARGUMENTS
keyword (string) - the keyword to which the parameter is to be assigned
valuestr (string) - the corresponding parameter value to assign to the keyword
TODO
Searching in the parameter file can be facilitated if we store a dictionary of which line a keyword is specified on.
"""
# determine whether the keyword already exists
keyword_exists = self.keyword_line_index.has_key(keyword)
# set keyword in dictionary (creating or overriding)
self.params[keyword] = valuestr
# create a new line from this keyword-value pair
line = self.keyword2line(keyword)
if keyword_exists:
# if keyword exists, replace the line
line_index = self.keyword_line_index[keyword]
self.lines[line_index] = line
else:
# if keyword does not exists, add a line
self.lines.append(line)
self.keywords.append(keyword) # add the keyword to the list
self.keyword_line_index[keyword] = len(self.lines) - 1 # store line number of the appended line
return
def getParameter(self,keyword):
"""Returns the value associated with a particular parameter; or None if the parameter is not set"""
if keyword not in self.params:
return None
return self.params[keyword]
def setTemperature(self,temperature):
"""Set the temperature of the various options.
"""
# Set the temperature parameters
self.setParameter('gen_temp', temperature)
self.setParameter('ref_t', temperature)
return
def randomizeSeed(self):
"""Randomize the random seed, adding one if none exists.
TODO
Uses range from 1 to 2**30 for now, but should figure out acceptable range for gromacs.
"""
# choose a new random seed
import random
self.setParameter('gen_seed', str(random.randint(1, self.MAXSEED)))
self.setParameter('mc_seed', str(random.randint(1, self.MAXSEED)))
return
def setParametersFromDict(self, paramdict):
"""Takes in a set of parameters as a dictionary of {keyword:value} entries (values are strings) and sets parameters for each.
ARGUMENTS
paramdict (dict) - a dictionary of keyword:value pairs to be used to update parameters
"""
for [key,value] in paramdict.iteritems():
if self.debug: print 'DEBUG: key, value of paramdict{}', key, value
self.setParameter(key, value)
return
def delParameter(self, keyword):
"""Removes a particular mdp keyword (and its value (string)) from the parameter dictionary, and deletes mdp line.
ARGUMENTS
keyword (string) - the keyword to be cleared
TODO
Propose new name of clearParameter or removeParameter
"""
# remove keyword from dictionary
if self.params.has_key(keyword):
del self.params[keyword]
# replace instances of this 'keyword = value' in the mdp lines
i=0
while i < len(self.lines):
fields = self.lines[i].strip().split()
if len(fields) > 0:
if fields[0] == keyword:
self.lines.pop(i)
else:
i=i+1
else:
i=i+1
return
LUMIDATA += .3709
LUMIDATA += .6630
#LUMIDATA *= 1.0514
if period in ['Combined', '2011B']:
LUMIDATA += 2.511
elif selection in ['electron', 'eGamma']:
if period in ['Combined', '2011A']:
LUMIDATA += .2151
LUMIDATA += .7982
LUMIDATA += .3132
LUMIDATA += .6332
#LUMIDATA *= 1.053
if period in ['Combined', '2011B']:
LUMIDATA += 2.482
bTable = TableMaker('../HiggsAnalyzer/histos/higgsHistograms_'+dataSet+period+'.root', LUMIDATA)
samples = ['tW', 'ttbar', 'GluGluWW', 'WWJets', 'WZJets', 'ZZJets']
if selection in ['muGamma', 'eGamma']:
samples.append('PhotonJets')
elif selection == 'muEG':
samples.append('DYToTauTau')
elif doZJets:
samples.append('ZJets')
elif not doZJets:
if selection == 'muon':
samples.append('DYToMuMu')
samples.append('DYToTauTau')
if selection == 'electron':
samples.append('DYToEE')
samples.append('DYToTauTau')
