def write(self, path, config_list):
import ast
try:
f = open(path, 'w')
for item in config_list:
label = item.get_name()
value = item.get_selection()
dtype = item.get_datatype()
item_type = item.get_type()
sample_list = item.get_values()
comment = item.get_help()
for line in comment.split("\n"):
if line:
print>>f, "#", line
# prints setting names and values (ex. " runAnatomicalProcessing: [1] ") into the
# pipeline_config file, using a different set of code depending on the data type
# parameters that are strings (ex. " False " or a path)
if dtype == 0 or dtype == 1:
print >>f, label, ": ", str(value)
print >>f,"\n"
# parameters that are integers
elif dtype == 2:
# Add check for ReHo cluster
if label == 'clusterSize':
print 'Using ReHo cluster size of ', value
elif item_type == 0:
value = sample_list.index(value)
else:
if substitution_map.get(value) != None:
value = substitution_map.get(value)
elif value != 'None':
value = ast.literal_eval(str(value))
print >>f, label, ": ", value
print >>f,"\n"
# parameters that are lists (ex. " [False, False] ")
elif dtype == 3:
map = ast.literal_eval(str(value))
values = []
for x in range(0, len(map.keys())):
values.append(False)
for k, v in map.iteritems():
item, idx = k
values[idx] = v
print>>f, label, ": ", values
print>>f,"\n"
# parameters that are switches (ex. [0] or [1] )
elif dtype == 4:
values=[]
if isinstance(value, list):
value = ast.literal_eval(str(value))
else:
value = str(value).split(",")
for val in value:
val = val.strip()
sval = substitution_map.get(val)
if sval != None:
values.append(sval)
else:
values.append(val)
if values == [10]:
values = [1,0]
elif values == [11]:
values = ['ANTS','FSL']
elif values == [12]:
values = ['3dAutoMask','BET']
print>>f, label, ": ", values
print>>f,"\n"
# parameters that are bracketed numbers (int or float)
elif dtype == 5:
### parse user input ### can't use internal function type() here???
if value.find(',') != -1:
lvalue = value.split(',')
elif value.find(';') != -1:
lvalue = value.split(';')
elif value.find(':') != -1:
lvalue = value.split(':')
else:
lvalue = [value]
if value.find('.') != -1:
lvalue = [float(item) for item in lvalue]
elif len(value) > 0:
lvalue = [int(item) for item in lvalue]
else:
lvalue = 0
print>>f, label, ":", lvalue ###
print>>f, "\n"
# parameters that are ? (bandpass filter specs)
elif dtype == 6:
values = []
for val in ast.literal_eval(str(value)):
try:
val=ast.literal_eval(str(val))
except Exception as err:
print "Exception trying to translate: %s, %s, %s, %s"%(label,str(value),val,err)
print "value type: %s"%(type(val))
values.append(ast.literal_eval(str(val)))
print>>f, label, ":", values
print>>f, "\n"
# parameters that are whole words
# ALSO: the Nuisance Corrections lists
elif dtype == 8:
print>>f, label,":"
value = ast.literal_eval(str(value))
for val in value:
val = val.split(',')
f.write(" - ")
flag = 0
for sample in sample_list:
if flag == 0:
space = ""
flag = 1
else:
space = " "
if sample in val:
print>>f, space, sample, ": ", 1
else:
print>>f, space, sample, ": ", 0
print >>f, "\n"
else:
value = ast.literal_eval(str(value))
print>>f, label, ":", value
print>>f, "\n"
f.close()
except Exception, e:
print e
print "Error Writing the pipeline configuration file %s" % path
raise
def write(self, path, config_list):
import ast
import CPAC
try:
f = open(path, 'w')
print >> f, "# CPAC Pipeline Configuration YAML file"
print >> f, "# version %s\n" % str(CPAC.__version__)
for item in config_list:
label = item.get_name()
value = item.get_selection()
dtype = item.get_datatype()
item_type = item.get_type()
sample_list = item.get_values()
comment = item.get_help()
for line in comment.split("\n"):
if line:
print >> f, "#", line
# prints setting names and values (ex. " runAnatomicalProcessing: [1] ") into the
# pipeline_config file, using a different set of code depending on the data type
# parameters that are strings (ex. " False " or a path)
if dtype == 0 or dtype == 1:
print >> f, label, ": ", str(value)
print >> f, "\n"
# parameters that are integers
elif dtype == 2:
# Add check for ReHo cluster
if label == 'clusterSize':
#print 'Using ReHo cluster size of ', value
pass
elif item_type == 0:
value = sample_list.index(value)
else:
if substitution_map.get(value) != None:
value = substitution_map.get(value)
elif value != 'None':
value = ast.literal_eval(str(value))
print >> f, label, ": ", value
print >> f, "\n"
# parameters that are lists (ex. " [False, False] ")
elif dtype == 3:
map = ast.literal_eval(str(value))
values = []
for x in range(0, len(map.keys())):
values.append(False)
for k, v in map.iteritems():
item, idx = k
values[idx] = v
print >> f, label, ": ", values
print >> f, "\n"
# parameters that are switches (ex. [0] or [1] )
elif dtype == 4:
values = []
if isinstance(value, list):
value = ast.literal_eval(str(value))
else:
value = str(value).split(",")
for val in value:
val = val.strip()
sval = substitution_map.get(val)
if sval != None:
values.append(sval)
else:
values.append(val)
if values == [10]:
values = [1, 0]
elif values == [11]:
values = ['ANTS', 'FSL']
elif values == [12]:
values = ['3dAutoMask', 'BET']
print >> f, label, ": ", values
print >> f, "\n"
# parameters that are bracketed numbers (int or float)
elif dtype == 5:
### parse user input ### can't use internal function type() here???
if value.find(',') != -1:
lvalue = value.split(',')
elif value.find(';') != -1:
lvalue = value.split(';')
elif value.find(':') != -1:
lvalue = value.split(':')
else:
lvalue = [value]
if value.find('.') != -1:
lvalue = [float(item) for item in lvalue]
elif len(value) > 0:
lvalue = [int(item) for item in lvalue]
else:
lvalue = 0
print >> f, label, ":", lvalue ###
print >> f, "\n"
# parameters that are ? (bandpass filter specs)
elif dtype == 6:
values = []
for val in ast.literal_eval(str(value)):
try:
val = ast.literal_eval(str(val))
except Exception as err:
print "Exception trying to translate: %s, %s, %s, %s" % (
label, str(value), val, err)
print "value type: %s" % (type(val))
values.append(ast.literal_eval(str(val)))
print >> f, label, ":", values
print >> f, "\n"
# parameters that are whole words
# ALSO: the Nuisance Corrections lists
elif dtype == 8:
print >> f, label, ":"
value = ast.literal_eval(str(value))
for val in value:
val = val.split(',')
f.write(" - ")
flag = 0
for sample in sample_list:
if flag == 0:
space = ""
flag = 1
else:
space = " "
if sample in val:
print >> f, space, sample, ": ", 1
else:
print >> f, space, sample, ": ", 0
print >> f, "\n"
elif dtype == 9:
# checkbox grid (ROI extraction etc.)
string = gen_checkboxgrid_config_string(label, value)
print >> f, string
print >> f, "\n"
else:
value = ast.literal_eval(str(value))
print >> f, label, ":", value
print >> f, "\n"
f.close()
except Exception, e:
print e
print "Error Writing the pipeline configuration file %s" % path
raise
def write(self, path, config_list):
import ast
try:
f = open(path, 'w')
for item in config_list:
label = item.get_name()
value = item.get_selection()
dtype = item.get_datatype()
type = item.get_type()
'''
print "LABEL: ", label
print "VALUE: ", value
print "DTYPE: ", dtype
print "TYPE: ", type
print ""
'''
sample_list = item.get_values()
comment = item.get_help()
#print "*****label : type : value -->", label, " : ", dtype, " : ", value
for line in comment.split("\n"):
if line:
print >> f, "#", line
# prints setting names and values (ex. " runAnatomicalProcessing: [1] ") into the
# pipeline_config file, using a different set of code depending on the data type
# parameters that are strings (ex. " False " or a path)
if dtype == 0 or dtype == 1:
print >> f, label, ": ", str(value)
print >> f, "\n"
# parameters that are integers
elif dtype == 2:
if type == 0:
value = sample_list.index(value)
else:
if substitution_map.get(value) != None:
value = substitution_map.get(value)
elif value != 'None':
value = ast.literal_eval(str(value))
print >> f, label, ": ", value
print >> f, "\n"
# parameters that are lists (ex. " [False, False] ")
elif dtype == 3:
map = ast.literal_eval(str(value))
values = []
for x in range(0, len(map.keys())):
values.append(False)
for k, v in map.iteritems():
item, idx = k
values[idx] = v
print >> f, label, ": ", values
print >> f, "\n"
# parameters that are switches (ex. [0] or [1] )
elif dtype == 4:
values = []
if isinstance(value, list):
value = ast.literal_eval(str(value))
else:
value = str(value).split(",")
for val in value:
val = val.strip()
sval = substitution_map.get(val)
if sval != None:
values.append(sval)
else:
values.append(val)
if values == [10]:
values = [1, 0]
elif values == [11]:
values = ['ANTS', 'FSL']
print >> f, label, ": ", values
print >> f, "\n"
# parameters that are bracketed numbers (int or float)
elif dtype == 5:
'''
print "1: ", ast.literal_eval(value)
print "2: ", ast.literal_eval(str(value))
print "3: ", value
print "4: ", str(value)
print "5: ", [value]
print "6: ", list(value)
print "7: ", [sample_list.index(val) for val in value]
'''
'''
if isinstance(value, list):
value = ast.literal_eval(str(value))
else:
value = str(value)
'''
'''
if isinstance(value, tuple):
value = list(value)
elif isinstance(value, list):
value = [sample_list.index(val) for val in value]
else:
value = [value]
'''
### parse user input ### can't use internal function type() here???
if value.find(',') != -1:
lvalue = value.split(',')
elif value.find(';') != -1:
lvalue = value.split(';')
elif value.find(':') != -1:
lvalue = value.split(':')
else:
lvalue = [value]
#print 'split value: ', lvalue
if value.find('.') != -1:
lvalue = [float(item) for item in lvalue]
elif len(value) > 0:
lvalue = [int(item) for item in lvalue]
else:
lvalue = 0
#print 'final value: ', lvalue
"""
if len(value) > 1:
value = float(value)
elif len(value) == 1:
value = int(value)
else:
value = 0
valueList = []
valueList.append(value)
"""
print >> f, label, ":", lvalue ###
print >> f, "\n"
# parameters that are ? (bandpass filter specs)
elif dtype == 6:
values = []
for val in ast.literal_eval(str(value)):
values.append(ast.literal_eval(val))
print >> f, label, ":", values
print >> f, "\n"
# parameters that are whole words
elif dtype == 8:
print >> f, label, ":"
value = ast.literal_eval(str(value))
for val in value:
val = val.split(',')
f.write(" - ")
flag = 0
for sample in sample_list:
if flag == 0:
space = ""
flag = 1
else:
space = " "
if sample in val:
print >> f, space, sample, ": ", 1
else:
print >> f, space, sample, ": ", 0
print >> f, "\n"
else:
value = ast.literal_eval(str(value))
print >> f, label, ":", value
print >> f, "\n"
f.close()
except Exception, e:
print e
print "Error Writing the pipeline configuration file %s" % path
raise Exception
def write(self, path, config_list):
import ast
import CPAC
try:
f = open(path, 'w')
print >>f, "# CPAC Pipeline Configuration YAML file"
print >>f, "# Version %s\n#" % str(CPAC.__version__)
print >>f, "# http://fcp-indi.github.io for more info.\n#"
print >>f, "# Tip: This file can be edited manually with a " \
"text editor for quick modifications.\n\n"
for item in config_list:
label = item.get_name()
value = item.get_selection()
dtype = item.get_datatype()
item_type = item.get_type()
sample_list = item.get_values()
comment = item.get_help()
for line in comment.split("\n"):
if line:
print>>f, "#", line
# prints setting names and values (ex. " runAnatomicalProcessing: [1] ") into the
# pipeline_config file, using a different set of code depending on the data type
# parameters that are strings (ex. " False " or a path)
if dtype == 0 or dtype == 1:
print >>f, label, ": ", str(value)
print >>f,"\n"
# parameters that are integers
elif dtype == 2:
# Add check for ReHo cluster
if label == 'clusterSize':
#print 'Using ReHo cluster size of ', value
pass
elif item_type == 0:
value = sample_list.index(value)
else:
if substitution_map.get(value) != None:
value = substitution_map.get(value)
elif value != 'None':
try:
value = ast.literal_eval(str(value))
except Exception as e:
raise Exception("could not parse value: "
"{0}\n\n{1}"
"\n".format(str(value), e))
print >>f, label, ": ", value
print >>f,"\n"
# parameters that are lists (ex. " [False, False] ")
elif dtype == 3:
map = ast.literal_eval(str(value))
values = []
for x in range(0, len(map.keys())):
values.append(False)
for k, v in map.iteritems():
item, idx = k
values[idx] = v
print>>f, label, ": ", values
print>>f,"\n"
# parameters that are switches (ex. [0] or [1] )
elif dtype == 4:
values=[]
if isinstance(value, list):
value = ast.literal_eval(str(value))
else:
value = str(value).split(",")
for val in value:
val = val.strip()
sval = substitution_map.get(val)
if sval != None:
values.append(sval)
else:
values.append(val)
if values == [10]:
values = [1,0]
elif values == [11]:
values = ['ANTS','FSL']
elif values == [12]:
values = ['3dAutoMask','BET']
print>>f, label, ": ", values
print>>f, "\n"
# parameters that are bracketed numbers (int or float)
elif dtype == 5:
### parse user input ### can't use internal function
# type() here???
if value.find(',') != -1:
lvalue = value.split(',')
elif value.find(';') != -1:
lvalue = value.split(';')
elif value.find(':') != -1:
lvalue = value.split(':')
else:
lvalue = [value]
if value.find('.') != -1:
lvalue = [float(item) for item in lvalue]
elif len(value) > 0:
try:
new_lvalue = [int(item) for item in lvalue]
except ValueError:
# this trips only if user inputs a percentage for
# de-spiking/scrubbing motion threshold
new_lvalue = [str(item) for item in lvalue]
lvalue = new_lvalue
else:
lvalue = 0
print>>f, label, ":", lvalue ###
print>>f, "\n"
# parameters that are ? (bandpass filter specs)
elif dtype == 6:
values = []
for val in ast.literal_eval(str(value)):
try:
val=ast.literal_eval(str(val))
except Exception as err:
print "Exception trying to translate: " \
"%s, %s, %s, %s"%(label,str(value),val,err)
print "value type: %s"%(type(val))
values.append(ast.literal_eval(str(val)))
print>>f, label, ":", values
print>>f, "\n"
# parameters that are whole words
# ALSO: the Nuisance Corrections lists
elif dtype == 8:
print>>f, label,":"
value = ast.literal_eval(str(value))
for val in value:
val = val.split(',')
f.write(" - ")
flag = 0
for sample in sample_list:
if flag == 0:
space = ""
flag = 1
else:
space = " "
if sample in val:
print>>f, space, sample, ": ", 1
else:
print>>f, space, sample, ": ", 0
print >>f, "\n"
elif dtype == 9:
# checkbox grid (ROI extraction etc.)
string = gen_checkboxgrid_config_string(label, value)
print >>f, string
print >>f, "\n"
else:
value = ast.literal_eval(str(value))
print>>f, label, ":", value
print>>f, "\n"
f.close()
except Exception, e:
print e
print "Error Writing the pipeline configuration file %s" % path
raise
def write(self, path, config_list):
import ast
try:
f = open(path, 'w')
for item in config_list:
label = item.get_name()
value = item.get_selection()
dtype = item.get_datatype()
type = item.get_type()
'''
print "LABEL: ", label
print "VALUE: ", value
print "DTYPE: ", dtype
print "TYPE: ", type
print ""
'''
sample_list = item.get_values()
comment = item.get_help()
#print "*****label : type : value -->", label, " : ", dtype, " : ", value
for line in comment.split("\n"):
if line:
print>>f, "#", line
# prints setting names and values (ex. " runAnatomicalProcessing: [1] ") into the
# pipeline_config file, using a different set of code depending on the data type
# parameters that are strings (ex. " False " or a path)
if dtype == 0 or dtype == 1:
print >>f, label, ": ", str(value)
print >>f,"\n"
# parameters that are integers
elif dtype == 2:
if type == 0:
value = sample_list.index(value)
else:
if substitution_map.get(value) != None:
value = substitution_map.get(value)
elif value != 'None':
value = ast.literal_eval(str(value))
print >>f, label, ": ", value
print >>f,"\n"
# parameters that are lists (ex. " [False, False] ")
elif dtype == 3:
map = ast.literal_eval(str(value))
values = []
for x in range(0, len(map.keys())):
values.append(False)
for k, v in map.iteritems():
item, idx = k
values[idx] = v
print>>f, label, ": ", values
print>>f,"\n"
# parameters that are switches (ex. [0] or [1] )
elif dtype == 4:
values=[]
if isinstance(value, list):
value = ast.literal_eval(str(value))
else:
value = str(value).split(",")
for val in value:
val = val.strip()
sval = substitution_map.get(val)
if sval != None:
values.append(sval)
else:
values.append(val)
if values == [10]:
values = [1,0]
elif values == [11]:
values = ['ANTS','FSL']
elif values == [12]:
values = ['3dAutoMask','BET']
print>>f, label, ": ", values
print>>f,"\n"
# parameters that are bracketed numbers (int or float)
elif dtype == 5:
'''
print "1: ", ast.literal_eval(value)
print "2: ", ast.literal_eval(str(value))
print "3: ", value
print "4: ", str(value)
print "5: ", [value]
print "6: ", list(value)
print "7: ", [sample_list.index(val) for val in value]
'''
'''
if isinstance(value, list):
value = ast.literal_eval(str(value))
else:
value = str(value)
'''
'''
if isinstance(value, tuple):
value = list(value)
elif isinstance(value, list):
value = [sample_list.index(val) for val in value]
else:
value = [value]
'''
### parse user input ### can't use internal function type() here???
if value.find(',') != -1:
lvalue = value.split(',')
elif value.find(';') != -1:
lvalue = value.split(';')
elif value.find(':') != -1:
lvalue = value.split(':')
else:
lvalue = [value]
#print 'split value: ', lvalue
if value.find('.') != -1:
lvalue = [float(item) for item in lvalue]
elif len(value) > 0:
lvalue = [int(item) for item in lvalue]
else:
lvalue = 0
#print 'final value: ', lvalue
"""
if len(value) > 1:
value = float(value)
elif len(value) == 1:
value = int(value)
else:
value = 0
valueList = []
valueList.append(value)
"""
print>>f, label, ":", lvalue ###
print>>f, "\n"
# parameters that are ? (bandpass filter specs)
elif dtype == 6:
values = []
for val in ast.literal_eval(str(value)):
values.append(ast.literal_eval(val))
print>>f, label, ":", values
print>>f, "\n"
# parameters that are whole words
elif dtype == 8:
print>>f, label,":"
value = ast.literal_eval(str(value))
for val in value:
val = val.split(',')
f.write(" - ")
flag = 0
for sample in sample_list:
if flag == 0:
space = ""
flag = 1
else:
space = " "
if sample in val:
print>>f, space, sample, ": ", 1
else:
print>>f, space, sample, ": ", 0
print >>f, "\n"
else:
value = ast.literal_eval(str(value))
print>>f, label, ":", value
print>>f, "\n"
f.close()
except Exception, e:
print e
print "Error Writing the pipeline configuration file %s" % path
raise Exception
