def check_integrity(self, param, type=None):
"""
check integrity of each option type
if type is provided, use type instead of self.type_value --> allow recursive integrity checking
"""
type_option = self.type_value
if type is not None:
type_option = type
if type_option in self.OPTION_TYPES:
return self.checkStandardType(param,type)
elif type_option == "image_nifti":
return self.checkIfNifti(param)
elif type_option == "file":
return self.checkFile(param)
elif type_option == "file_output": # check if permission are required
if not sct.check_write_permission(param):
self.parser.usage.error("Error of writing permissions on file: "+param)
return param
elif type_option == "folder":
return self.checkFolder(param)
elif type_option == "folder_creation":
return self.checkFolderCreation(param)
elif type_option == "multiple_choice":
"""
the choices are listed in example variable
"""
if param not in self.example:
self.parser.usage.error(self.name + " only takes " + self.parser.usage.print_list_with_brackets(self.example) + " as potential arguments.")
return param
elif isinstance(type_option, list):
"""
This option is defined as a list delimited by a delimiter (that cannot be a space)
For now, only one-layer list are available
Examples:
[[','],'int']
[[':'],'coordinate']
"""
delimiter = type_option[0][0]
sub_type = type_option[1]
param_splitted = param.split(delimiter)
if len(param_splitted) != 0:
return list([self.check_integrity(val,sub_type) for val in param_splitted])
else:
self.parser.usage.error("ERROR: Option "+self.name+" must be correctly written. See usage.")
else:
# self.parser.usage.error("ERROR: Type of option \"" + str(self.type_value) +"\" is not supported by the parser.")
sct.printv("WARNING : Option "+str(self.type_value)+" does not exist and will have no effect on the execution of the script", "warining")
sct.printv("Type -h to see supported options", "warning")
def check_integrity(self, param, type=None):
"""
check integrity of each option type
if type is provided, use type instead of self.type_value --> allow recursive integrity checking
"""
type_option = self.type_value
if type is not None:
type_option = type
if type_option in self.OPTION_TYPES:
return self.checkStandardType(param,type)
elif type_option == "image_nifti":
return self.checkIfNifti(param)
elif type_option == "file":
return self.checkFile(param)
elif type_option == "file_output": # check if permission are required
if not sct.check_write_permission(param):
self.parser.usage.error("Error of writing permissions on file: "+param)
return param
elif type_option == "folder":
return self.checkFolder(param)
elif type_option == "folder_creation":
return self.checkFolderCreation(param)
elif type_option == "multiple_choice":
"""
the choices are listed in example variable
"""
if param not in self.example:
self.parser.usage.error(self.name + " only takes " + self.parser.usage.print_list_with_brackets(self.example) + " as potential arguments.")
return param
elif isinstance(type_option, list):
"""
This option is defined as a list delimited by a delimiter (that cannot be a space)
For now, only one-layer list are available
Examples:
[[','],'int']
[[':'],'coordinate']
"""
delimiter = type_option[0][0]
sub_type = type_option[1]
param_splitted = param.split(delimiter)
if len(param_splitted) != 0:
return list([self.check_integrity(val,sub_type) for val in param_splitted])
else:
self.parser.usage.error("ERROR: Option "+self.name+" must be correctly written. See usage.")
else:
# self.parser.usage.error("ERROR: Type of option \"" + str(self.type_value) +"\" is not supported by the parser.")
sct.printv("WARNING : Option "+str(self.type_value)+" does not exist and will have no effect on the execution of the script", "warining")
sct.printv("Type -h to see supported options", "warning")
def checkIntegrity(self, param, type=None):
"""
check integrity of each option type
:param param: option to test (could be a string, file name, etc.)
:param type: if provided, use type instead of self.type_value to allow recursive integrity checking
:return:
"""
type_option = self.type_value
if type is not None:
type_option = type
if type_option in self.OPTION_TYPES:
return self.checkStandardType(param, type)
elif type_option == "image_nifti":
return self.checkIfNifti(param)
elif type_option == "file":
return self.checkFile(param)
elif type_option == "file-transfo":
if param.startswith("-"):
self.checkFile(param[1:])
return param
else:
return self.checkFile(param)
elif type_option == "file_output": # check if permission are required
if not os.path.isdir(os.path.dirname(os.path.abspath(param))):
self.parser.usage.error(
"Option %s parent folder doesn't exist for file %s" %
(self.name, param))
if not sct.check_write_permission(param):
self.parser.usage.error(
"Option %s no write permission for file %s" %
(self.name, param))
return param
elif type_option == "folder":
return self.checkFolder(param)
elif type_option == "folder_creation":
return self.checkFolderCreation(param)
elif type_option == "multiple_choice":
"""
the choices are listed in example variable
"""
if param not in self.example:
self.parser.usage.error(
self.name + " only takes " +
self.parser.usage.print_list_with_brackets(self.example) +
" as potential arguments.")
return param
elif isinstance(type_option, list):
"""
This option is defined as a list delimited by a delimiter (that cannot be a space)
For now, only one-layer list are available
Examples:
[[','],'int']
[[':'],'coordinate']
"""
delimiter = type_option[0][0]
sub_type = type_option[1]
param_splitted = param.split(delimiter)
if len(param_splitted) != 0:
# check if files are separated by space (if "*" was used)
if not param_splitted[0].find(' ') == -1:
# if so, split and return list
param_splitted = param_splitted[0].split(' ')
return list([
self.checkIntegrity(val, sub_type)
for val in param_splitted
])
else:
self.parser.usage.error(
"Option " + self.name +
" must be correctly written. See usage.")
else:
# self.parser.usage.error("Type of option \"" + str(self.type_value) +"\" is not supported by the parser.")
sct.printv(
"Option " + str(self.type_value) +
" does not exist and will have no effect on the execution of the script",
1, "warning")
sct.printv("Type -h to see supported options", 1, "warning")
def checkIntegrity(self, param, type=None):
"""
check integrity of each option type
:param param: option to test (could be a string, file name, etc.)
:param type: if provided, use type instead of self.type_value to allow recursive integrity checking
:return:
"""
type_option = self.type_value
if type is not None:
type_option = type
if type_option in self.OPTION_TYPES:
return self.checkStandardType(param, type)
elif type_option == "image_nifti":
return self.checkIfNifti(param)
elif type_option == "file":
return self.checkFile(param)
elif type_option == "file-transfo":
if param.startswith("-"):
self.checkFile(param[1:])
return param
else:
return self.checkFile(param)
elif type_option == "file_output": # check if permission are required
if not os.path.isdir(os.path.dirname(os.path.abspath(param))):
self.parser.usage.error("Option %s parent folder doesn't exist for file %s" % (self.name, param))
if not sct.check_write_permission(param):
self.parser.usage.error("Option %s no write permission for file %s" % (self.name, param))
return param
elif type_option == "folder":
return self.checkFolder(param)
elif type_option == "folder_creation":
return self.checkFolderCreation(param)
elif type_option == "multiple_choice":
"""
the choices are listed in example variable
"""
if param not in self.example:
self.parser.usage.error(self.name + " only takes " + self.parser.usage.print_list_with_brackets(self.example) + " as potential arguments.")
return param
elif isinstance(type_option, list):
"""
This option is defined as a list delimited by a delimiter (that cannot be a space)
For now, only one-layer list are available
Examples:
[[','],'int']
[[':'],'coordinate']
"""
delimiter = type_option[0][0]
sub_type = type_option[1]
param_splitted = param.split(delimiter)
if len(param_splitted) != 0:
# check if files are separated by space (if "*" was used)
if not param_splitted[0].find(' ') == -1:
# if so, split and return list
param_splitted = param_splitted[0].split(' ')
return list([self.checkIntegrity(val, sub_type) for val in param_splitted])
else:
self.parser.usage.error("Option " + self.name + " must be correctly written. See usage.")
else:
# self.parser.usage.error("Type of option \"" + str(self.type_value) +"\" is not supported by the parser.")
sct.printv("Option " + str(self.type_value) + " does not exist and will have no effect on the execution of the script", 1, "warning")
sct.printv("Type -h to see supported options", 1, "warning")
