def test_clone_trait(self):
""" Method to test trait clone from string description.
"""
# Test first to build trait description from nipype traits and then
# to instanciate the trait
to_test_fields = {
"timing_units": "traits.Enum(('secs', 'scans'))",
"bases": ("traits.Dict(traits.Enum(('hrf', 'fourier', "
"'fourier_han', 'gamma', 'fir')), traits.Any())"),
"mask_image": "traits.File(Undefined)",
"microtime_onset": "traits.Float()",
"mask_threshold": ("traits.Either(traits.Enum(('-Inf',)), "
"traits.Float())")
}
i = spm.Level1Design()
for field, result in six.iteritems(to_test_fields):
# Test to build the trait expression
trait = i.inputs.trait(field)
expression = build_expression(trait)
self.assertEqual(expression, result)
# Try to clone the trait
trait = eval_trait(expression)()
self.assertEqual(build_expression(trait), result)
to_test_fields = {
"contrasts": (
"traits.List(traits.Either(traits.Tuple(traits.Str(), "
"traits.Enum(('T',)), traits.List(traits.Str()), "
"traits.List(traits.Float())), traits.Tuple(traits.Str(), "
"traits.Enum(('T',)), traits.List(traits.Str()), "
"traits.List(traits.Float()), traits.List(traits.Float())), "
"traits.Tuple(traits.Str(), traits.Enum(('F',)), "
"traits.List(traits.Either(traits.Tuple(traits.Str(), "
"traits.Enum(('T',)), traits.List(traits.Str()), "
"traits.List(traits.Float())), traits.Tuple(traits.Str(), "
"traits.Enum(('T',)), traits.List(traits.Str()), "
"traits.List(traits.Float()), traits.List(traits.Float())"
"))))))"),
"use_derivs": "traits.Bool()"
}
i = spm.EstimateContrast()
for field, result in six.iteritems(to_test_fields):
# Test to build the trait expression
trait = i.inputs.trait(field)
expression = build_expression(trait)
self.assertEqual(expression, result)
# Try to clone the trait
trait = eval_trait(expression)()
self.assertEqual(build_expression(trait), result)
# Test to clone some traits
trait_description = ["Float", "Int"]
handler = clone_trait(trait_description)
trait = handler.as_ctrait()
self.assertEqual(trait_description, trait_ids(trait))
def test_clone_trait(self):
""" Method to test trait clone from string description.
"""
# Test first to build trait description from nipype traits and then
# to instanciate the trait
to_test_fields = {
"timing_units":
"traits.Enum(('secs', 'scans'))",
"bases": ("traits.Dict(traits.Enum(('hrf', 'fourier', "
"'fourier_han', 'gamma', 'fir')), traits.Any())"),
"mask_image":
"traits.File(Undefined)",
"microtime_onset":
"traits.Float()",
"mask_threshold": ("traits.Either(traits.Enum(('-Inf',)), "
"traits.Float())")
}
i = spm.Level1Design()
for field, result in six.iteritems(to_test_fields):
# Test to build the trait expression
trait = i.inputs.trait(field)
expression = build_expression(trait)
self.assertEqual(expression, result)
# Try to clone the trait
trait = eval_trait(expression)()
self.assertEqual(build_expression(trait), result)
to_test_fields = {
"contrasts":
("traits.List(traits.Either(traits.Tuple(traits.Str(), "
"traits.Enum(('T',)), traits.List(traits.Str()), "
"traits.List(traits.Float())), traits.Tuple(traits.Str(), "
"traits.Enum(('T',)), traits.List(traits.Str()), "
"traits.List(traits.Float()), traits.List(traits.Float())), "
"traits.Tuple(traits.Str(), traits.Enum(('F',)), "
"traits.List(traits.Either(traits.Tuple(traits.Str(), "
"traits.Enum(('T',)), traits.List(traits.Str()), "
"traits.List(traits.Float())), traits.Tuple(traits.Str(), "
"traits.Enum(('T',)), traits.List(traits.Str()), "
"traits.List(traits.Float()), traits.List(traits.Float())"
"))))))"),
"use_derivs":
"traits.Bool()"
}
i = spm.EstimateContrast()
for field, result in six.iteritems(to_test_fields):
# Test to build the trait expression
trait = i.inputs.trait(field)
expression = build_expression(trait)
self.assertEqual(expression, result)
# Try to clone the trait
trait = eval_trait(expression)()
self.assertEqual(build_expression(trait), result)
# Test to clone some traits
trait_description = ["Float", "Int"]
handler = clone_trait(trait_description)
trait = handler.as_ctrait()
self.assertEqual(trait_description, trait_ids(trait))
def class_factory(func, destination_module_globals):
""" Dynamically create a process instance from a function
In order to make the class publicly accessible, we assign the result of
the function to a variable dynamically using globals().
Parameters
----------
func: @function (mandatory)
the function we want encapsulate in a process.
"""
# Create the process class name
class_name = title_for(func.__name__)
# Get the capsul prototype
capsul_proto = parse_docstring(func.__doc__)
# Create all the process input and output traits
process_traits = {}
for trait_item in capsul_proto:
# Create the trait
trait_desc = trait_item["type"]
trait = clone_trait([trait_desc])
# Specify the trait
trait.desc = trait_item.get("desc", "")
if trait_item.get("role", "") in ["return", "output"]:
trait.output = True
else:
trait.output = False
if trait_item.get("optional", "False") == "True":
trait.optional = True
else:
trait.optional = False
# Store the created trait
process_traits[trait_item["name"]] = trait
# Clean the docstring
docstring = func.__doc__
# python 2.7 only (not working on Centos 6.4)
# docstring = re.sub(r"<process>.*</process>", "", docstring,
# flags=re.DOTALL)
res = re.search(r"<process>.*</process>.*", docstring, flags=re.DOTALL)
if res:
docstring = docstring.replace(docstring[res.start():res.end()], "")
# Define the process class parameters
class_parameters = {
"__doc__": docstring,
"__module__": destination_module_globals["__name__"],
"_id": destination_module_globals["__name__"] + "." + class_name,
"_func_name": func.__name__,
"_func_module": func.__module__,
"_parameters": capsul_proto,
"_process_traits": process_traits
}
# Get the process instance associated to the function
destination_module_globals[class_name] = (
type(class_name, (AutoProcess, ), class_parameters))