def test_missing_confound(self):
for confound_name in [
'white_matter', 'csf', 'global_signal', 'motion', 'acompcor'
]:
del self.pipeline['confounds'][confound_name]
self.assertFalse(is_valid(self.pipeline, silent=True))
self.setUp()
def parse_pipelines(pipelines_args: str or set = "all") -> set:
"""
Parses all possible pipeline options:
:param pipelines_args: set or str, only valid string argument is 'all'.
If argument is set it can containing both names of pipelines from
fmridenoise.pipelines directory or path(s) to valid json file(s)
containing of valid pipeline description.
:return: set of valid pipelines paths.
"""
if type(pipelines_args) is str:
if pipelines_args != "all":
raise ValueError("Only valid string argument is 'all'")
else:
return get_pipelines_paths()
known_pipelines = get_pipelines_names()
pipelines_args = set(pipelines_args)
if pipelines_args <= known_pipelines:
return get_pipelines_paths(pipelines_args)
ret = set()
for p in pipelines_args:
if p in known_pipelines:
ret.add(get_pipeline_path(p))
elif p not in known_pipelines and is_valid(load_pipeline_from_json(p)):
ret.add(p)
else:
raise ValueError(f"File: '{p} is not a valid pipeline")
return ret
def test_incorrect_spikes_dict_values(self):
for fd_val in [-1, True, False, None, 'True', '1', '2.15']:
for dvars_val in [-1, True, False, None, 'True', '1', '2.15']:
self.pipeline['spikes'] = {
'fd_th': fd_val,
'dvars_th': dvars_val
}
self.assertFalse(is_valid(self.pipeline, silent=True))
def test_correct_spikes_dict_values(self):
for fd_val in [0.01, 1, 2.165, 5.94, 20]:
for dvars_val in [0.01, 1, 2.165, 5.94, 20]:
self.pipeline['spikes'] = {
'fd_th': fd_val,
'dvars_th': dvars_val
}
self.assertTrue(is_valid(self.pipeline, silent=True))
def test_correct_confound_dict_values(self):
'''Test all combinations of True / False values for confound dict.'''
for confound_name in [
'white_matter', 'csf', 'global_signal', 'motion'
]:
for c in itertools.combinations_with_replacement([True, False], 4):
confound_dict = self.pipeline['confounds'][confound_name]
confound_dict.update(zip(confound_dict, c))
self.assertTrue(is_valid(self.pipeline, silent=True))
def _run_interface(self, runtime):
js = load_pipeline_from_json(self.inputs.pipeline_path)
if not is_valid(js):
raise ValueError("""
Json file {} is not a valid pipeline,
check schema at fmridenoise.utils.json_validator.py
""".format(os.path.basename(self.inputs.pipeline_path)))
self._results['pipeline'] = js
return runtime
def test_incorrect_confound_dict_values(self):
'''Test wrong values for confound dict options.'''
for confound_name in [
'white_matter', 'csf', 'global_signal', 'motion'
]:
for type_ in [
'raw', 'derivative1', 'power2', 'derivative1_power2'
]:
for val in [1, 0, 'False', 'True', None]:
self.pipeline['confounds'][confound_name][type_] = val
self.assertFalse(is_valid(self.pipeline, silent=True))
self.setUp()
def test_missing_confound_type(self):
'''Keys 'raw', 'derivative1', 'power2' and 'derivative1_power2' are
mandatory for confound dict.'''
for confound_name in [
'white_matter', 'csf', 'global_signal', 'motion'
]:
for type_ in [
'raw', 'derivative1', 'power2', 'derivative1_power2'
]:
del self.pipeline['confounds'][confound_name][type_]
self.assertFalse(is_valid(self.pipeline, silent=True))
self.setUp()
def test_incorrect_spikes_value(self):
'''Value for 'spikes' key can be either False or spikes dict'''
for val in [True, None, 'True', 'False', 0, 1.321]:
self.pipeline['spikes'] = val
self.assertFalse(is_valid(self.pipeline, silent=True))
def test_incorrect_aroma(self):
for val in [1, 0, 'False', 'True', None, {'key': True}, 0.1, list()]:
self.pipeline['aroma'] = val
self.assertFalse(is_valid(self.pipeline, silent=True))
def test_correct_aroma(self):
self.pipeline['aroma'] = True
self.assertTrue(is_valid(self.pipeline, silent=True))
self.pipeline['aroma'] = False
self.assertTrue(is_valid(self.pipeline, silent=True))
def test_incorrect_acompcor(self):
for val in [1, 0, 'False', 'True', None, {'key': True}, 0.1, list()]:
self.pipeline['confounds']['acompcor'] = val
self.assertFalse(is_valid(self.pipeline, silent=True))
def test_correct_acompcor(self):
self.pipeline['confounds']['acompcor'] = True
self.assertTrue(is_valid(self.pipeline, silent=True))
self.pipeline['confounds']['acompcor'] = False
self.assertTrue(is_valid(self.pipeline, silent=True))
def test_missing_spikes_dict_key(self):
for key in ['fd_th', 'dvars_th']:
self.pipeline['spikes'] = {key: 1.321}
self.assertFalse(is_valid(self.pipeline, silent=True))
def test_null_pipeline(self):
'''Ensure that null pipeline is valid.'''
self.assertTrue(is_valid(self.pipeline, silent=True))
def test_missing_description(self):
'''Missing description should be valid.'''
del self.pipeline['description']
self.assertTrue(is_valid(self.pipeline, silent=True))
def test_pipeline_name_empty_string(self):
self.pipeline['name'] = ''
self.assertFalse(is_valid(self.pipeline, silent=True))
def test_pipeline_name_missing(self):
del self.pipeline['name']
self.assertFalse(is_valid(self.pipeline, silent=True))
