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feat: Save mask to derivatives, pass derivatives to outputnode #506

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Merged
merged 6 commits into from
Sep 26, 2025
Merged

feat: Save mask to derivatives, pass derivatives to outputnode #506

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84777cb
sty: Use fmt:skip in workflows.base and workflows.outputs [ignore-rev]
effigies Sep 25, 2025
0120001
sty: Use trait_set, tuple(dictionary)
effigies Sep 26, 2025
e3bc6f5
feat: Pass datasink outputs to outputnodes
effigies Sep 26, 2025
4119e15
feat: Save fieldmap mask to output directory
effigies Sep 26, 2025
5cca67d
chore: Drop removed ruff rule from ignores
effigies Sep 26, 2025
38e9b63
chore: Patch file patterns to allow masks
effigies Sep 26, 2025
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1 change: 0 additions & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -193,7 +193,6 @@ ignore = [
"B019",
"SIM108",
"C901",
"UP038",
]

[tool.ruff.lint.flake8-quotes]
Expand Down
16 changes: 8 additions & 8 deletions sdcflows/workflows/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -137,6 +137,7 @@ def init_fmap_preproc_wf(
fmap_derivatives_wf = init_fmap_derivatives_wf(
output_dir=str(output_dir),
write_coeff=True,
write_mask=True,
bids_fmap_id=estimator.bids_id,
name=f'fmap_derivatives_wf_{estimator.sanitized_id}',
)
Expand All @@ -157,33 +158,32 @@ def init_fmap_preproc_wf(
niu.IdentityInterface(fields=fields),
name=f'in_{estimator.sanitized_id}',
)
# fmt:off
workflow.connect([
(inputnode, est_wf, [(f, f"inputnode.{f}") for f in fields])
])
# fmt:on
]) # fmt:skip

# fmt:off
workflow.connect([
(est_wf, fmap_derivatives_wf, [
("outputnode.fmap", "inputnode.fieldmap"),
("outputnode.fmap_ref", "inputnode.fmap_ref"),
("outputnode.fmap_coeff", "inputnode.fmap_coeff"),
("outputnode.fmap_mask", "inputnode.fmap_mask"),
]),
(est_wf, fmap_reports_wf, [
("outputnode.fmap", "inputnode.fieldmap"),
("outputnode.fmap_ref", "inputnode.fmap_ref"),
("outputnode.fmap_mask", "inputnode.fmap_mask"),
]),
(est_wf, out_map, [
("outputnode.fmap", "fmap"),
("outputnode.method", "method")
]),
(fmap_derivatives_wf, out_map, [
("outputnode.fieldmap", "fmap"),
("outputnode.fmap_ref", "fmap_ref"),
("outputnode.fmap_coeff", "fmap_coeff"),
("outputnode.fmap_mask", "fmap_mask"),
("outputnode.method", "method")
]),
])
# fmt:on
]) # fmt:skip

for field, mergenode in out_merge.items():
workflow.connect(out_map, field, mergenode, f'in{n}')
Expand Down
70 changes: 49 additions & 21 deletions sdcflows/workflows/outputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -98,23 +98,20 @@ def init_fmap_reports_wf(
suffix='fieldmap',
desc=fmap_type,
dismiss_entities=('fmap',),
allowed_entities=tuple(custom_entities.keys()),
allowed_entities=tuple(custom_entities),
),
name='ds_fmap_report',
)
for k, v in custom_entities.items():
setattr(ds_fmap_report.inputs, k, v)
ds_fmap_report.inputs.trait_set(**custom_entities)

# fmt:off
workflow.connect([
(inputnode, fmap_rpt, [(("fieldmap", _pop), "fieldmap"),
("fmap_ref", "reference"),
("fmap_mask", "mask")]),
(fmap_rpt, ds_fmap_report, [("out_report", "in_file")]),
(inputnode, ds_fmap_report, [("source_files", "source_file")]),

])
# fmt:on
]) # fmt:skip

return workflow

Expand All @@ -126,6 +123,7 @@ def init_fmap_derivatives_wf(
custom_entities=None,
name='fmap_derivatives_wf',
write_coeff=False,
write_mask=False,
):
"""
Set up datasinks to store derivatives in the right location.
Expand Down Expand Up @@ -162,10 +160,14 @@ def init_fmap_derivatives_wf(
workflow = pe.Workflow(name=name)
inputnode = pe.Node(
niu.IdentityInterface(
fields=['source_files', 'fieldmap', 'fmap_coeff', 'fmap_ref', 'fmap_meta']
fields=['source_files', 'fieldmap', 'fmap_coeff', 'fmap_ref', 'fmap_mask', 'fmap_meta']
),
name='inputnode',
)
outputnode = pe.Node(
niu.IdentityInterface(fields=['fieldmap', 'fmap_coeff', 'fmap_ref', 'fmap_mask']),
name='outputnode',
)

merge_fmap = pe.Node(MergeSeries(), name='merge_fmap')

Expand All @@ -176,7 +178,7 @@ def init_fmap_derivatives_wf(
suffix='fieldmap',
datatype='fmap',
dismiss_entities=('fmap',),
allowed_entities=tuple(custom_entities.keys()),
allowed_entities=tuple(custom_entities),
),
name='ds_reference',
)
Expand All @@ -188,19 +190,17 @@ def init_fmap_derivatives_wf(
suffix='fieldmap',
datatype='fmap',
compress=True,
allowed_entities=tuple(custom_entities.keys()),
allowed_entities=tuple(custom_entities),
),
name='ds_fieldmap',
)
ds_fieldmap.inputs.Units = 'Hz'
if bids_fmap_id:
ds_fieldmap.inputs.B0FieldIdentifier = bids_fmap_id

for k, v in custom_entities.items():
setattr(ds_reference.inputs, k, v)
setattr(ds_fieldmap.inputs, k, v)
ds_reference.inputs.trait_set(**custom_entities)
ds_fieldmap.inputs.trait_set(**custom_entities)

# fmt:off
workflow.connect([
(inputnode, merge_fmap, [("fieldmap", "in_files")]),
(inputnode, ds_reference, [("source_files", "source_file"),
Expand All @@ -213,8 +213,38 @@ def init_fmap_derivatives_wf(
(("out_file", _getname), "AnatomicalReference"),
]),
(inputnode, ds_fieldmap, [(("fmap_meta", _selectintent), "IntendedFor")]),
])
# fmt:on
(ds_fieldmap, outputnode, [("out_file", "fieldmap")]),
(ds_reference, outputnode, [("out_file", "fmap_ref")]),
]) # fmt:skip

if write_mask:
ds_mask = pe.Node(
DerivativesDataSink(
base_directory=output_dir,
compress=True,
desc='brain',
suffix='mask',
datatype='fmap',
dismiss_entities=('fmap',),
allowed_entities=tuple(custom_entities),
),
name='ds_mask',
)
ds_mask._interface._file_patterns += (
'sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/'
'sub-{subject}[_ses-{session}][_hash-{hash}][_acq-{acquisition}]'
'[_dir-{direction}][_run-{run}][_part-{part}][_space-{space}]'
'[_cohort-{cohort}][_res-{resolution}][_fmapid-{fmapid}]'
'[_desc-{desc}]_{suffix<mask>}{extension<.nii|.nii.gz|.json>|.nii.gz}',
)
Comment on lines +233 to +239
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@mgxd mgxd Sep 26, 2025

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opened nipreps/niworkflows#977 to make this less hacky


ds_mask.inputs.trait_set(**custom_entities)

workflow.connect([
(inputnode, ds_mask, [("source_files", "source_file"),
("fmap_mask", "in_file")]),
(ds_mask, outputnode, [("out_file", "fmap_mask")]),
]) # fmt:skip

if not write_coeff:
return workflow
Expand All @@ -225,26 +255,24 @@ def init_fmap_derivatives_wf(
suffix='fieldmap',
datatype='fmap',
compress=True,
allowed_entities=tuple(custom_entities.keys()),
allowed_entities=tuple(custom_entities),
),
name='ds_coeff',
iterfield=('in_file', 'desc'),
)

gen_desc = pe.Node(niu.Function(function=_gendesc), name='gen_desc')

for k, v in custom_entities.items():
setattr(ds_coeff.inputs, k, v)
ds_coeff.inputs.trait_set(**custom_entities)

# fmt:off
workflow.connect([
(inputnode, ds_coeff, [("source_files", "source_file"),
("fmap_coeff", "in_file")]),
(inputnode, gen_desc, [("fmap_coeff", "infiles")]),
(gen_desc, ds_coeff, [("out", "desc")]),
(ds_coeff, ds_fieldmap, [(("out_file", _getname), "AssociatedCoefficients")]),
])
# fmt:on
(ds_coeff, outputnode, [("out_file", "fmap_coeff")]),
]) # fmt:skip

return workflow

Expand Down
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