def test_process_matching_templates_acquisition_file(self):
""" """
# Define context
context = {
'container_type': 'file',
'parent_container_type': 'acquisition',
'project': {'label': 'testproject'},
'subject': {'code': '12345'},
'session': {'label': 'haha', 'info': {'BIDS': {'Label': 'haha', 'Subject': '12345'}}},
'acquisition':{'label': 'blue', u'id': u'ID'},
'file': {u'type': u'image', u'name': u'fname'},
'ext': '.jpg'
}
# Won't match if not on upload
container = bidsify_flywheel.process_matching_templates(context)
# Define expected container
container_expected = {u'type': u'image', u'name': u'fname'}
self.assertEqual(container, container_expected)
# Call function
container = bidsify_flywheel.process_matching_templates(context, upload=True)
# Define expected container
container_expected = {
'info': {
'BIDS': {
'template': 'acquisition_file',
'Filename': '', 'Folder': 'acq-blue', 'Path': 'sub-12345/ses-haha/acq-blue',
'ignore': False
}
},
u'type': u'image',
u'name': u'fname'
}
self.assertEqual(container, container_expected)
def test_process_matching_templates_BIDS_NA(self):
""" """
# Define context
context = {
'container_type': 'file',
'parent_container_type': 'acquisition',
'project': None,
'subject': {u'code': u'001'},
'session': {u'label': u'sesTEST', 'info': {'BIDS': {'Label': u'sesTEST', 'Subject': u'001'}}},
'run_counters': utils.RunCounterMap(),
'acquisition': {u'label': u'acq_task-TEST_run+'},
'file': {u'classification': {u'Intent': u'Functional'},
u'type': u'nifti','info': {'BIDS': 'NA'}
},
'ext': '.nii.gz'
}
# Call function
container = bidsify_flywheel.process_matching_templates(context)
# Define expected container
container_expected = {
u'classification': {u'Intent': u'Functional'},
u'type': u'nifti',
'info': {'BIDS': 'NA'}
}
self.assertEqual(container, container_expected)
def test_process_matching_templates_project_file_multiple_measurements(self):
""" """
# Define context
context = {
'container_type': 'file',
'parent_container_type': 'acquisition',
'project': None,
'subject': {u'code': u'001'},
'session': {u'label': u'sesTEST', 'info': {'BIDS': {'Label': u'sesTEST', 'Subject': u'001'}}},
'acquisition': {u'label': u'acqTEST'},
'file': {
u'classification': {u'Measurement': [u'T1', u'T2'], u'Intent': u'Structural'},
u'type': u'nifti'
},
'ext': '.nii.gz'
}
# Call function
container = bidsify_flywheel.process_matching_templates(context)
# Define expected container
container_expected = {
'info': {
'BIDS': {
'template': 'anat_file',
'Filename': u'sub-001_ses-sesTEST_T1w.nii.gz',
'Path': u'sub-001/ses-sesTEST/anat', 'Folder': 'anat',
'Run': '', 'Acq': '', 'Ce': '', 'Rec': '',
'Modality': 'T1w', 'Mod': '',
'ignore': False
}
},
u'classification': {u'Measurement': [u'T1', u'T2'], u'Intent': u'Structural'}, u'type': u'nifti'}
print(container)
self.assertEqual(container, container_expected)
def test_process_matching_templates_project_file(self):
""" """
# Define context
context = {
'container_type': 'file',
'parent_container_type': 'project',
'project': None,
'subject': None,
'session': None,
'acquisition': None,
'file': {u'classification': {},
u'type': u'archive'},
'ext': '.zip'
}
# Call function
container = bidsify_flywheel.process_matching_templates(context)
# Define expected container
container_expected = {
'info': {
'BIDS': {
'template': 'project_file',
'Filename': '', 'Folder': '', 'Path': '',
'ignore': False
}
},
u'classification': {}, u'type': u'archive'}
self.assertEqual(container, container_expected)
def test_process_matching_templates_project(self):
""" """
# Define context
context = {
'container_type': 'project',
'parent_container_type': 'group',
'project': {'label': 'Project_Label_Test'},
'subject': None,
'session': None,
'acquisition': None,
'file': {},
'ext': '.zip'
}
# Call function
container = bidsify_flywheel.process_matching_templates(context)
# Define expected container
container_expected = {
'info': {
'BIDS': {
'Acknowledgements': '',
'Authors': [],
'BIDSVersion': '1.0.2',
'DatasetDOI': '',
'Funding': '',
'HowToAcknowledge': '',
'License': '',
'Name': 'Project_Label_Test',
'ReferencesAndLinks': [],
'template': 'project'
}
},
'label': 'Project_Label_Test'
}
self.assertEqual(container, container_expected)
def test_process_matching_templates_session_file(self):
""" """
# Define context
context = {
'container_type': 'file',
'parent_container_type': 'session',
'project': {'label': 'testproject'},
'subject': {'code': '12345'},
'session': {'label': u'sesTEST', 'info': {'BIDS': {'Label': u'sesTEST', 'Subject': u'12345'}}},
'acquisition': None,
'file': {u'type': u'tabular'},
'ext': '.tsv'
}
# Call function
container = bidsify_flywheel.process_matching_templates(context)
# Define expected container
container_expected = {
'info': {
'BIDS': {
'template': 'session_file',
'Filename': '', 'Folder': 'ses-sesTEST', 'Path': 'sub-12345/ses-sesTEST',
'ignore': False
}
},
u'type': u'tabular'}
self.assertEqual(container, container_expected)
def test_process_matching_templates_session(self):
""" """
# Define context
context = {
'container_type': 'session',
'parent_container_type': 'project',
'project': {'label': 'Project_Label_Test'},
'subject': {'code' : '12345'},
'session': {'label': 'Session_Label_Test'},
'acquisition': None,
'file': {},
'ext': '.zip'
}
# Call function
container = bidsify_flywheel.process_matching_templates(context)
# Define expected container
container_expected = {
'info': {
'BIDS': {
'Label': 'SessionLabelTest',
'Subject': '12345',
'template': 'session',
'ignore': False
}
},
'label': 'Session_Label_Test'
}
self.assertEqual(container, container_expected)
def test_resolve_initial_dicom_field_values_from_filename(self):
# Define context
context = {
'container_type': 'file',
'parent_container_type': 'acquisition',
'project': {u'label': 'hello'},
'subject': {u'code': u'001'},
'session': {u'label': u'sesTEST', 'info': {'BIDS': {'Label': u'sesTEST', 'Subject': u'001'}}},
'acquisition': {u'label': u'acqTEST'},
'file': {
u'name': u'09 cmrr_mbepi_task-spatialfrequency_s6_2mm_66sl_PA_TR1.0.dcm.zip',
u'classification': {u'Measurement': u'Diffusion', u'Intent': u'Structural'},
u'type': u'dicom'
},
'ext': '.dcm.zip'
}
# Call function
container = bidsify_flywheel.process_matching_templates(context)
# Define expected container
container_expected = {'info': {'BIDS': {
'template': 'dicom_file',
'Filename': u'09 cmrr_mbepi_task-spatialfrequency_s6_2mm_66sl_PA_TR1.0.dcm.zip',
'Folder': 'sourcedata',
'Path': u'sourcedata/sub-001/ses-sesTEST',
'ignore': False
}},
u'name': u'09 cmrr_mbepi_task-spatialfrequency_s6_2mm_66sl_PA_TR1.0.dcm.zip',
u'classification': {u'Measurement': u'Diffusion', u'Intent': u'Structural'},
u'type': u'dicom'}
self.assertEqual(container, container_expected)
def test_process_matching_templates_non_bids_dicom(self):
# Define context
context = {
'container_type': 'file',
'parent_container_type': 'acquisition',
'project': {u'label': 'hello'},
'subject': {u'code': u'001'},
'session': {u'label': u'sesTEST', 'info': {'BIDS': {'Label': u'sesTEST', 'Subject': u'001'}}},
'acquisition': {u'label': u'acqTEST', u'id': u'09090'},
'file': {
u'name': u'4784_1_1_localizer',
u'classification': {u'Measurement': u'T2', u'Intent': u'Localizer'},
u'type': u'dicom'
},
'ext': '.dcm.zip'
}
# Call function
container = bidsify_flywheel.process_matching_templates(context)
print(container)
# Define expected container
container_expected = {
u'name': u'4784_1_1_localizer',
u'classification': {u'Measurement': u'T2', u'Intent': u'Localizer'},
u'type': u'dicom'
}
self.assertEqual(container, container_expected)
def test_process_matching_templates_fieldmap_phase_encoded(self):
""""""
# Define context
context = {
'container_type': 'file',
'parent_container_type': 'acquisition',
'project': None,
'subject': {u'code': u'001'},
'session': {u'label': u'sesTEST', 'info': {'BIDS': {'Label': u'sesTEST', 'Subject': u'001'}}},
'acquisition': {u'label': u'acqTEST Topup PA'}, # Acquisition label needs to contain
'file': {u'classification': {u'Intent': u'Fieldmap'},
u'type': u'nifti'
},
'ext': '.nii.gz'
}
# Call function
container = bidsify_flywheel.process_matching_templates(context)
# Define expected container
container_expected = {
'info': {
'BIDS': {
'template': 'fieldmap_phase_encoded_file',
'Filename': u'sub-001_ses-sesTEST_dir-PA_epi.nii.gz',
'Folder': 'fmap', 'Path': u'sub-001/ses-sesTEST/fmap',
'Acq': '', 'Run': '', 'Dir': 'PA', 'Modality': 'epi',
'IntendedFor': [
{'Folder': 'anat'},
{'Folder': 'func'}
],
'ignore': False
}
},
u'classification': {u'Intent': u'Fieldmap'}, u'type': u'nifti'}
self.assertEqual(container, container_expected)
def test_process_matching_templates_dwi_bvec(self):
""" """
# Define context
context = {
'container_type': 'file',
'parent_container_type': 'acquisition',
'project': None,
'subject': {u'code': u'001'},
'session': {u'label': u'sesTEST', 'info': {'BIDS': {'Label': u'sesTEST', 'Subject': u'001'}}},
'acquisition': {u'label': u'acqTEST'},
'file': {u'classification': {u'Measurement': u'Diffusion', u'Intent': u'Structural'},
u'type': u'bvec'
},
'ext': '.bvec'
}
# Call function
container = bidsify_flywheel.process_matching_templates(context)
# Define expected container
container_expected = {
'info': {
'BIDS': {
'template': 'diffusion_file',
'Filename': u'sub-001_ses-sesTEST_dwi.bvec',
'Path': u'sub-001/ses-sesTEST/dwi', 'Folder': 'dwi',
'Modality': 'dwi', 'Acq': '', 'Run': '',
'ignore': False
}
},
u'classification': {u'Measurement': u'Diffusion', u'Intent': u'Structural'}, u'type': u'bvec'}
self.assertEqual(container, container_expected)
def test_process_matching_templates_physio_task_events(self):
""""""
# Define context
context = {
'container_type': 'file',
'parent_container_type': 'acquisition',
'project': None,
'subject': {u'code': u'001'},
'session': {u'label': u'sesTEST', 'info': {'BIDS': {'Label': u'sesTEST', 'Subject': u'001'}}},
'acquisition': {u'label': u'acqTEST'},
'file': {u'classification': {u'Custom': u'Physio'},
u'type': u'tabular data',
},
'ext': '.tsv'
}
# Call function
container = bidsify_flywheel.process_matching_templates(context)
# Define expected container
container_expected = {
'info': {
'BIDS': {
'template': 'physio_task_file',
'Filename': u'sub-001_ses-sesTEST_task-{file.info.BIDS.Task}_physio.tsv',
'Folder': 'func', 'Path': u'sub-001/ses-sesTEST/func',
'Acq': '', 'Task': '',
'Modality': 'physio',
'Rec': '',
'Recording': '',
'Run': '',
'Echo': '',
'ignore': False
}
},
u'classification': {u'Custom': u'Physio'}, u'type': u'tabular data'}
self.assertEqual(container, container_expected)
def test_process_matching_templates_func(self):
""" """
# Define context
context = {
'container_type': 'file',
'parent_container_type': 'acquisition',
'project': None,
'subject': {u'code': u'001'},
'session': {u'label': u'sesTEST', 'info': {'BIDS': {'Label': u'sesTEST', 'Subject': u'001'}}},
'run_counters': utils.RunCounterMap(),
'acquisition': {u'label': u'acq_task-TEST_run+'},
'file': {u'classification': {u'Intent': u'Functional'},
u'type': u'nifti',
},
'ext': '.nii.gz'
}
# Call function
container = bidsify_flywheel.process_matching_templates(context)
# Define expected container
container_expected = {
'info': {
'BIDS': {
'template': 'func_file',
'Filename': u'sub-001_ses-sesTEST_task-TEST_run-1_bold.nii.gz',
'Folder': 'func', 'Path': u'sub-001/ses-sesTEST/func',
'Acq': '', 'Task': 'TEST', 'Modality': 'bold',
'Rec': '', 'Run': '1', 'Echo': '',
'ignore': False
}
},
u'classification': {u'Intent': u'Functional'}, u'type': u'nifti'}
self.assertEqual(container, container_expected)