def __init__(self, path=None, string=None):
"""
Initialisation of BifReader object
Parameters
----------------
path : file or str
File of bif data
string : str
String of bif data
Examples
-----------------
# dog-problem.bif file is present at
# http://www.cs.cmu.edu/~javabayes/Examples/DogProblem/dog-problem.bif
>>> from pgmpy.readwrite import BIFReader
>>> reader = BIFReader("bif_test.bif")
>>> reader = BIFReader("bif_test.bif")
<pgmpy.readwrite.BIF.BIFReader object at 0x7f2375621cf8>
"""
if path:
with open(path, 'r') as network:
self.network = network.read()
elif string:
self.network = string
else:
raise ValueError("Must specify either path or string")
if '"' in self.network:
# Replacing quotes by spaces to remove case sensitivity like:
# "Dog-Problem" and Dog-problem
# or "true""false" and "true" "false" and true false
self.network = self.network.replace('"', ' ')
if '/*' in self.network or '//' in self.network:
self.network = cppStyleComment.suppress().transformString(
self.network) # removing comments from the file
self.name_expr, self.state_expr, self.property_expr = self.get_variable_grammar(
)
self.probability_expr, self.cpd_expr = self.get_probability_grammar()
self.network_name = self.get_network_name()
self.variable_names = self.get_variables()
self.variable_states = self.get_states()
self.variable_properties = self.get_property()
self.variable_parents = self.get_parents()
self.variable_cpds = self.get_values()
self.variable_edges = self.get_edges()
def __init__(self, path=None, string=None):
"""
Initialisation of BifReader object
Parameters
----------------
path : file or str
File of bif data
string : str
String of bif data
Examples
-----------------
# dog-problem.bif file is present at
# http://www.cs.cmu.edu/~javabayes/Examples/DogProblem/dog-problem.bif
>>> from pgmpy.readwrite import BIFReader
>>> reader = BIFReader("bif_test.bif")
>>> reader = BIFReader("bif_test.bif")
<pgmpy.readwrite.BIF.BIFReader object at 0x7f2375621cf8>
"""
if path:
with open(path, 'r') as network:
self.network = network.read()
elif string:
self.network = string
else:
raise ValueError("Must specify either path or string")
if '"' in self.network:
# Replacing quotes by spaces to remove case sensitivity like:
# "Dog-Problem" and Dog-problem
# or "true""false" and "true" "false" and true false
self.network = self.network.replace('"', ' ')
if '/*' in self.network or '//' in self.network:
self.network = cppStyleComment.suppress().transformString(self.network) # removing comments from the file
self.name_expr, self.state_expr, self.property_expr = self.get_variable_grammar()
self.probability_expr, self.cpd_expr = self.get_probability_grammar()
self.network_name = self.get_network_name()
self.variable_names = self.get_variables()
self.variable_states = self.get_states()
self.variable_properties = self.get_property()
self.variable_parents = self.get_parents()
self.variable_cpds = self.get_cpd()
self.variable_edges = self.get_edges()
def removeCommentsGo(fStr, fName='', removePrint=False):
returnStr = fStr
raw_lookup_table = ''
lookup_table = ''
fixStr = ''
# First remove the large blobs of data so we don't hit memory faults :-/
raw_lookup_table_query = re.compile(r' raw_lookup_table.*?\n', re.I)
lookup_table_query = re.compile(r' lookup_table.*?\n', re.I)
try:
raw_lookup_table = re.search(raw_lookup_table_query, returnStr).group()
except:
raw_lookup_table = ''
try:
lookup_table = re.search(lookup_table_query, returnStr).group()
except:
lookup_table = ''
if raw_lookup_table:
returnStr = re.sub(raw_lookup_table_query,
' raw_lookup_table := ""\n', returnStr)
if lookup_table:
returnStr = re.sub(lookup_table_query, ' lookup_table := ""\n',
returnStr)
#####
cppStyleComment.ignore(dblQuotedString)
v1 = cppStyleComment.suppress().transformString(returnStr)
if removePrint:
comp2 = re.compile(r'^\s*fmt.P.*?\n', re.MULTILINE)
v2 = re.sub(comp2, "", v1)
returnStr = v2
#Check for the case of fmt.Sprintf or other fmt modifications that are not printing
if not "fmt." in v2:
comp3 = re.compile(r'^\s*\"fmt\".*?\n', re.MULTILINE)
v3 = re.sub(comp3, "", v2)
returnStr = v3
#Ugggggh deal with the C import types :(
if "import \"C\"" in returnStr:
#print "In Import C Section"
comp4 = re.compile(r'^import \"C\".*?\n', re.MULTILINE)
repVal = '''/*
#cgo CFLAGS: -IMemoryModule
#cgo LDFLAGS: MemoryModule/build/MemoryModule.a
#include "MemoryModule/MemoryModule.h"
*/
import "C"
'''
v4 = re.sub(comp4, repVal, returnStr)
returnStr = v4
else:
returnStr = v1
#### Inject back in the blobs
returnStr = re.sub(raw_lookup_table_query, raw_lookup_table, returnStr)
returnStr = re.sub(lookup_table_query, lookup_table, returnStr)
#######
if fName:
try:
myOut = open(fileN + '_clean', 'w')
myOut.write(returnStr)
myOut.close()
except:
print("[!] Can not write output file")
else:
return returnStr
def __init__(self,
path=None,
string=None,
include_properties=False,
n_jobs=-1):
"""
Initializes a BIFReader object.
Parameters
----------
path : file or str
File of bif data
string : str
String of bif data
include_properties: boolean
If True, gets the properties tag from the file and stores in graph properties.
n_jobs: int (default: -1)
Number of jobs to run in parallel. `-1` means use all processors.
Examples
--------
# dog-problem.bif file is present at
# http://www.cs.cmu.edu/~javabayes/Examples/DogProblem/dog-problem.bif
>>> from ProbabilityModel.readwrite import BIFReader
>>> reader = BIFReader("bif_test.bif")
>>> reader = BIFReader("bif_test.bif")
<ProbabilityModel.readwrite.BIF.BIFReader object at 0x7f2375621cf8>
"""
if path:
with open(path, "r") as network:
self.network = network.read()
elif string:
self.network = string
else:
raise ValueError("Must specify either path or string")
self.n_jobs = n_jobs
self.include_properties = include_properties
if '"' in self.network:
# Replacing quotes by spaces to remove case sensitivity like:
# "Dog-Problem" and Dog-problem
# or "true""false" and "true" "false" and true false
self.network = self.network.replace('"', " ")
if "/*" in self.network or "//" in self.network:
self.network = cppStyleComment.suppress().transformString(
self.network) # removing comments from the file
(
self.name_expr,
self.state_expr,
self.property_expr,
) = self.get_variable_grammar()
self.probability_expr, self.cpd_expr = self.get_probability_grammar()
self.network_name = self.get_network_name()
self.variable_names = self.get_variables()
self.variable_states = self.get_states()
if self.include_properties:
self.variable_properties = self.get_property()
self.variable_parents = self.get_parents()
self.variable_cpds = self.get_values()
self.variable_edges = self.get_edges()
def removeCommentsGo(fStr,fName='',removePrint=False): returnStr = fStr raw_lookup_table = '' lookup_table='' fixStr = '' # First remove the large blobs of data so we don't hit memory faults :-/ raw_lookup_table_query = re.compile(r' raw_lookup_table.*?\n',re.I) lookup_table_query = re.compile(r' lookup_table.*?\n',re.I) try: raw_lookup_table = re.search(raw_lookup_table_query,returnStr).group() except: raw_lookup_table = '' try: lookup_table = re.search(lookup_table_query,returnStr).group() except: lookup_table = '' if raw_lookup_table: returnStr = re.sub(raw_lookup_table_query,' raw_lookup_table := ""\n',returnStr) if lookup_table: returnStr = re.sub(lookup_table_query,' lookup_table := ""\n',returnStr) ##### cppStyleComment.ignore(dblQuotedString) v1 = cppStyleComment.suppress().transformString(returnStr) if removePrint: comp2 = re.compile(r'^\s*fmt.P.*?\n',re.MULTILINE) v2 = re.sub(comp2,"",v1) returnStr = v2 #Check for the case of fmt.Sprintf or other fmt modifications that are not printing if not "fmt." in v2: comp3 = re.compile(r'^\s*\"fmt\".*?\n',re.MULTILINE) v3 = re.sub(comp3,"",v2) returnStr = v3 #Ugggggh deal with the C import types :( if "import \"C\"" in returnStr: #print "In Import C Section" comp4 = re.compile(r'^import \"C\".*?\n',re.MULTILINE) repVal = '''/* #cgo CFLAGS: -IMemoryModule #cgo LDFLAGS: MemoryModule/build/MemoryModule.a #include "MemoryModule/MemoryModule.h" */ import "C" ''' v4 = re.sub(comp4,repVal,returnStr) returnStr = v4 else: returnStr = v1 #### Inject back in the blobs returnStr = re.sub(raw_lookup_table_query,raw_lookup_table,returnStr) returnStr = re.sub(lookup_table_query,lookup_table,returnStr) ####### if fName: try: myOut = open(fileN+'_clean','w') myOut.write(returnStr) myOut.close() except: print "[!] Can not write output file" else: return returnStr
def header_parser():
identifier = Regex("[a-zA-Z_][a-zA-Z0-9_\$]*")
comment = cppStyleComment.suppress()
size = Group(
Optional( Suppress('[') + SkipTo(']') + Suppress(']') )
)
# Params
end_param = Literal(',') + 'parameter' | Literal(')') + '('
ptype = Optional( oneOf('integer real realtime time') )
# NOTE: this isn't completely right, good enough for parsing valid Verilog
param = Group(
'parameter' + ptype + size + identifier +
Suppress('=') + SkipTo(end_param)
)
list_of_params = Group(
Suppress('#(') + delimitedList( param ) + Suppress(')')
)
# Ports
dir_ = Optional( oneOf('input output inout') )
type_ = Optional( oneOf('wire reg') )
port = Group(
dir_ + type_ + size + identifier
)
list_of_ports = Group(
Suppress('(') + delimitedList( port ) + Suppress(')')
)
# Module
module_identifier = identifier
module = Group(
Suppress('module') +
module_identifier('module_name') +
Optional( list_of_params('params') ) +
Optional( list_of_ports ('ports' ) ) +
Suppress(';') +
SkipTo('endmodule') + Suppress('endmodule')
)
# Debug
#print
#module_identifier.setParseAction( dbg('modname') )#.setDebug()
#param .setParseAction( dbg('param') )#.setDebug()
#port .setParseAction( dbg('port' ) )#.setDebug()
#module .setParseAction( dbg('module', 1) )#.setDebug()
file_ = SkipTo('module', ignore=comment ).suppress() + \
OneOrMore( module ).ignore( comment ) + \
SkipTo( StringEnd() ).suppress()
return file_