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ENH: Large refactor of the orchestration workflow [wipe phdiff_*]
This PR: - [x] Refines the work in nipreps#53 addressing nipreps#40. - [x] Adds tests to cover the orchestration workflow. - [x] Fixes nipreps#7 (added regression tests for this bug). - [x] Updates the interface of phdiff workflows: removes the metadata input, which was defined for this workflow solely. - [x] Makes it trivial to extend the phdiff workflow to phase1/phase2 workflows (nipreps#15).
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,140 @@ | ||
| """Test base workflows.""" | ||
| import pytest | ||
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| from ..base import init_sdc_estimate_wf | ||
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| EPI_METADATA = { | ||
| 'MultibandAccelerationFactor': 8, | ||
| 'PhaseEncodingDirection': 'i', | ||
| 'RepetitionTime': 0.72, | ||
| 'TaskName': 'Resting-state fMRI', | ||
| } | ||
| EPI_FMAP_METADATA_1 = { | ||
| 'BandwidthPerPixelPhaseEncode': 2290, | ||
| 'EPIFactor': 90, | ||
| 'EffectiveEchoSpacing': 0.00058, | ||
| 'IntendedFor': ['func/sub-HCP101006_task-rest_dir-LR_bold.nii.gz', | ||
| 'func/sub-HCP101006_task-rest_dir-LR_sbref.nii.gz'], | ||
| 'MultibandAccelerationFactor': 1, | ||
| 'PhaseEncodingDirection': 'i-', | ||
| } | ||
| EPI_FMAP_METADATA_2 = EPI_FMAP_METADATA_1.copy() | ||
| EPI_FMAP_METADATA_2['PhaseEncodingDirection'] = 'i' | ||
|
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| PHDIFF_METADATA = { | ||
| 'EchoTime1': 0.00492, | ||
| 'EchoTime2': 0.00738, | ||
| } | ||
| PHASE1_METADATA = { | ||
| 'EchoTime': 0.00492, | ||
| } | ||
| PHASE2_METADATA = { | ||
| 'EchoTime': 0.00738, | ||
| } | ||
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| FMAP_DICT_ELEMENTS = { | ||
| 'epi1': [('sub-HCP101006/fmap/sub-HCP101006_dir-RL_epi.nii.gz', | ||
| EPI_FMAP_METADATA_1.copy())], | ||
| 'epi2': [('sub-HCP101006/fmap/sub-HCP101006_dir-RL_epi.nii.gz', | ||
| EPI_FMAP_METADATA_1.copy()), | ||
| ('sub-HCP101006/fmap/sub-HCP101006_dir-LR_epi.nii.gz', | ||
| EPI_FMAP_METADATA_2.copy())], | ||
| 'phdiff1': { | ||
| 'magnitude': [('sub-HCP101006/fmap/sub-HCP101006_magnitude1.nii.gz', {}), | ||
| ('sub-HCP101006/fmap/sub-HCP101006_magnitude2.nii.gz', {})], | ||
| 'phases': [('sub-HCP101006/fmap/sub-HCP101006_phasediff.nii.gz', PHDIFF_METADATA)], | ||
| }, | ||
| 'phdiff2': { | ||
| 'magnitude': [('sub-HCP101006/fmap/sub-HCP101006_magnitude1.nii.gz', {}), | ||
| ('sub-HCP101006/fmap/sub-HCP101006_magnitude2.nii.gz', {})], | ||
| 'phases': [('sub-HCP101006/fmap/sub-HCP101006_phase1.nii.gz', | ||
| PHASE1_METADATA.copy()), | ||
| ('sub-HCP101006/fmap/sub-HCP101006_phase2.nii.gz', | ||
| PHASE2_METADATA.copy())], | ||
| }, | ||
| 'fmap1': { | ||
| 'magnitude': [('sub-HCP101006/fmap/sub-HCP101006_magnitude.nii.gz', {})], | ||
| 'fieldmap': [('sub-HCP101006/fmap/sub-HCP101006_fieldmap.nii.gz', {})], | ||
| }, | ||
| 'syn': { | ||
| 't1w': [('sub-HCP101006/fmap/sub-HCP101006_T1w.nii.gz', {})] | ||
| } | ||
| } | ||
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| @pytest.mark.parametrize('method', ['skip', 'phasediff', 'pepolar', 'fieldmap', 'syn']) | ||
| def test_base(method): | ||
| """Check the heuristics are correctly applied.""" | ||
| fieldmaps = { | ||
| 'epi': FMAP_DICT_ELEMENTS['epi1'].copy(), | ||
| 'fieldmap': FMAP_DICT_ELEMENTS['fmap1'].copy(), | ||
| 'phasediff': FMAP_DICT_ELEMENTS['phdiff1'].copy(), | ||
| } | ||
| epi_meta = EPI_METADATA.copy() | ||
|
|
||
| if method == 'skip': | ||
| wf = init_sdc_estimate_wf(fmaps=[], epi_meta=epi_meta) | ||
| assert wf.inputs.outputnode.method == 'None' | ||
|
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| wf = init_sdc_estimate_wf(fmaps=fieldmaps, epi_meta=epi_meta, ignore=('fieldmaps', )) | ||
| assert wf.inputs.outputnode.method == 'None' | ||
|
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||
| with pytest.raises(ValueError): | ||
| wf = init_sdc_estimate_wf(fmaps={'unsupported': None}, epi_meta=epi_meta) | ||
| elif method == 'pepolar': | ||
| wf = init_sdc_estimate_wf(fmaps=fieldmaps, epi_meta=epi_meta) | ||
| assert 'PEPOLAR' in wf.inputs.outputnode.method | ||
|
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| fieldmaps['epi'][0][1].pop('PhaseEncodingDirection') | ||
| with pytest.raises(ValueError): | ||
| wf = init_sdc_estimate_wf(fmaps=fieldmaps, epi_meta=epi_meta) | ||
|
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| fieldmaps['epi'][0][1]['PhaseEncodingDirection'] = \ | ||
| EPI_FMAP_METADATA_1['PhaseEncodingDirection'] | ||
| epi_meta.pop('PhaseEncodingDirection') | ||
| with pytest.raises(ValueError): | ||
| wf = init_sdc_estimate_wf(fmaps=fieldmaps, epi_meta=epi_meta) | ||
| epi_meta = EPI_METADATA.copy() | ||
|
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| fieldmaps['epi'] = FMAP_DICT_ELEMENTS['epi2'] | ||
| wf = init_sdc_estimate_wf(fmaps=fieldmaps, epi_meta=epi_meta) | ||
| assert 'PEPOLAR' in wf.inputs.outputnode.method | ||
|
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| elif method == 'fieldmap': | ||
| fieldmaps = { | ||
| 'fieldmap': FMAP_DICT_ELEMENTS['fmap1'].copy(), | ||
| 'phasediff': FMAP_DICT_ELEMENTS['phdiff1'].copy(), | ||
| } | ||
| wf = init_sdc_estimate_wf(fmaps=fieldmaps, epi_meta=epi_meta) | ||
| assert 'directly measured B0 map' in wf.inputs.outputnode.method | ||
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| elif method == 'phasediff': | ||
| fieldmaps = { | ||
| 'phasediff': FMAP_DICT_ELEMENTS['phdiff1'].copy(), | ||
| } | ||
|
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| wf = init_sdc_estimate_wf(fmaps=fieldmaps, epi_meta=epi_meta) | ||
| assert 'phase-difference' in wf.inputs.outputnode.method | ||
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| epi_meta.pop('PhaseEncodingDirection') | ||
| with pytest.raises(ValueError): | ||
| wf = init_sdc_estimate_wf(fmaps=fieldmaps, epi_meta=epi_meta) | ||
|
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| elif method == 'syn': | ||
| fmaps_onlysyn = {'syn': FMAP_DICT_ELEMENTS['syn']} | ||
| wf = init_sdc_estimate_wf(fmaps=fmaps_onlysyn, epi_meta=epi_meta) | ||
| assert 'SyN' in wf.inputs.outputnode.method | ||
|
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| epi_pe = epi_meta.pop('PhaseEncodingDirection') | ||
| wf = init_sdc_estimate_wf(fmaps=fmaps_onlysyn, epi_meta=epi_meta) | ||
| assert 'SyN' in wf.inputs.outputnode.method | ||
|
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| # Emulate --force-syn | ||
| fieldmaps.update(fmaps_onlysyn) | ||
| with pytest.raises(ValueError): | ||
| wf = init_sdc_estimate_wf(fmaps=fieldmaps, epi_meta=epi_meta) | ||
|
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| epi_meta['PhaseEncodingDirection'] = epi_pe | ||
| wf = init_sdc_estimate_wf(fmaps=fieldmaps, epi_meta=epi_meta) | ||
| assert 'PEPOLAR' in wf.inputs.outputnode.method |
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