"{}:{}".format(subj_id, visit_id)) if subj_id == 'subject1' and visit_id == 'visit3': self.assertNotIn( 'ten', [d.name for d in session.filesets], "'ten' should not be generated for " "subject1:visit3 as hundred and thousand are " "already present") test1_format = FileFormat('test1', extension='.t1') test2_format = FileFormat('test2', extension='.t2', converters={'test1': IdentityConverter}) test3_format = FileFormat('test3', extension='.t3') FileFormat.register(test1_format) FileFormat.register(test2_format) FileFormat.register(test3_format) class TestInputValidationStudy(with_metaclass(StudyMetaClass, Study)): add_data_specs = [ AcquiredFilesetSpec('a', (test1_format, test2_format)), AcquiredFilesetSpec('b', test3_format), FilesetSpec('c', test2_format, 'identity_pipeline'), FilesetSpec('d', test3_format, 'identity_pipeline') ] def identity_pipeline(self, **name_maps): pipeline = self.pipeline(
png_format = FileFormat(name='png', extension='.png') jpg_format = FileFormat(name='jpg', extension='.jpg') # PET formats list_mode_format = FileFormat(name='pet_list_mode', extension='.bf') # Raw formats dat_format = FileFormat(name='dat', extension='.dat') # MRS format rda_format = FileFormat(name='raw', extension='.rda') # Record list of all data formats registered by module (not really # used currently but could be useful in future) registered_file_formats = [] # Register all data formats in module for file_format in copy(globals()).values(): if isinstance(file_format, FileFormat): FileFormat.register(file_format) registered_file_formats.append(file_format.name) # Since the conversion from DICOM->NIfTI is unfortunately slightly # different between MRConvert and Dcm2niix, these data formats can # be used in pipeline input specs that need to use MRConvert instead # of Dcm2niix (i.e. motion-detection pipeline) mrconvert_nifti_format = deepcopy(nifti_format) mrconvert_nifti_format._converters['dicom'] = MrtrixConverter mrconvert_nifti_gz_format = deepcopy(nifti_gz_format) mrconvert_nifti_gz_format._converters['dicom'] = MrtrixConverter