def __init__(self, **kwargs):
""" Initialize the Process class.
"""
# Inheritance
super(Process, self).__init__()
# Initialize the process identifiers
self.name = self.__class__.__name__
self.id = self.__class__.__module__ + "." + self.name
# Parameter to store which tools will be used dusring the processing
self.versions = {
"capsul": get_tool_version("capsul")
}
# Initialize the log file name
self.log_file = None
self.study_config = None
default_values = getattr(self, 'default_values', None)
if default_values:
self.default_values = default_values.copy()
else:
self.default_values = {}
for k, v in six.iteritems(kwargs):
self.default_values[k] = v
def __init__(self, **kwargs):
""" Initialize the Process class.
"""
# Inheritance
super(Process, self).__init__()
# Initialize the process identifiers
self.name = self.__class__.__name__
self.id = self.__class__.__module__ + "." + self.name
# Parameter to store which tools will be used dusring the processing
self.versions = {
"capsul": get_tool_version("capsul")
}
# Initialize the log file name
self.log_file = None
default_values = getattr(self, 'default_values', None)
if default_values:
self.default_values = default_values.copy()
else:
self.default_values = {}
for k, v in kwargs.iteritems():
self.default_values[k] = v
def __init__(self):
""" Initialize the Process class.
"""
# Inheritance
super(Process, self).__init__()
# Initialize the process identifiers
self.name = self.__class__.__name__
self.id = self.__class__.__module__ + "." + self.name
# Parameter to store which tools will be used dusring the processing
self.versions = {
"capsul": get_tool_version("capsul")
}
# Initialize the log file name
self.log_file = None
def __init__(self, nipype_instance, *args, **kwargs):
""" Initialize the NipypeProcess class.
NipypeProcess instance get automatically an additional user trait
'output_directory'.
This class also fix also some lake of the nipye version '0.9.2'.
Parameters
----------
nipype_instance: nipype interface (mandatory)
the nipype interface we want to wrap in capsul.
Attributes
----------
_nipype_interface : Interface
private attribute to store the nipye interface
_nipype_module : str
private attribute to store the nipye module name
_nipype_class : str
private attribute to store the nipye class name
_nipype_interface_name : str
private attribute to store the nipye interface name
"""
# Set some class attributes that characterize the nipype interface
self._nipype_interface = nipype_instance
self._nipype_module = nipype_instance.__class__.__module__
self._nipype_class = nipype_instance.__class__.__name__
self._nipype_interface_name = self._nipype_module.split(".")[2]
# Inheritance: activate input files copy for spm interfaces.
if self._nipype_interface_name == "spm":
# Copy only 'copyfile' nipype traits
inputs_to_copy = self._nipype_interface.inputs.traits(
copyfile=True).keys()
super(NipypeProcess, self).__init__(
activate_copy=True, inputs_to_copy=inputs_to_copy, *args,
**kwargs)
else:
super(NipypeProcess, self).__init__(
activate_copy=False, *args, **kwargs)
# Replace the process name and identification attributes
self.id = ".".join([self._nipype_module, self._nipype_class])
self.name = self._nipype_interface.__class__.__name__
# Set the nipype and nipype interface versions
if self._nipype_interface_name != "spm":
self.versions.update({
"nipype": get_tool_version("nipype"),
self._nipype_interface_name: self._nipype_interface.version
})
else:
from nipype.interfaces.spm import SPMCommand
from nipype.interfaces.matlab import MatlabCommand
self.versions.update({
"nipype": get_tool_version("nipype"),
self._nipype_interface_name: "{0}-{1}|{2}-{3}".format(
SPMCommand._matlab_cmd, MatlabCommand._default_paths,
SPMCommand._paths, SPMCommand._use_mcr)
})
# Add a new trait to store the processing output directory
super(Process, self).add_trait(
"output_directory", Directory(Undefined, exists=True,
optional=True))
def test_version_python(self):
""" Method to test if we can get a python module version from
its string description and the nipype insterfaces versions.
"""
self.assertEqual(capsul.__version__, get_tool_version("capsul"))
self.assertEqual(get_tool_version("error_capsul"), None)
def test_version_python(self):
""" Method to test if we can get a python module version from
its string description and the nipype insterfaces versions.
"""
self.assertEqual(capsul.__version__, get_tool_version("capsul"))
self.assertEqual(get_tool_version("error_capsul"), None)
