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FIX: Collate fieldmap coefficients into list of lists #317

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merged 2 commits into from
Dec 9, 2022
Merged

FIX: Collate fieldmap coefficients into list of lists #317

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433d2a0
FIX: Do not flatten fieldmaps or coefficients into single list
effigies Dec 7, 2022
16df78c
TEST: Add regression test for merge nodes
effigies Dec 8, 2022
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6 changes: 5 additions & 1 deletion sdcflows/workflows/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -87,11 +87,15 @@ def init_fmap_preproc_wf(

workflow = Workflow(name=name)

out_fields = ("fmap", "fmap_ref", "fmap_coeff", "fmap_mask", "fmap_id", "method")
out_fields = ("fmap", "fmap_coeff", "fmap_ref", "fmap_mask", "fmap_id", "method")
out_merge = {
f: pe.Node(niu.Merge(len(estimators)), name=f"out_merge_{f}")
for f in out_fields
}
# Fieldmaps and coefficient files can come in pairs, ensure they are not flattened
out_merge["fmap"].inputs.no_flatten = True
out_merge["fmap_coeff"].inputs.no_flatten = True

outputnode = pe.Node(niu.IdentityInterface(fields=out_fields), name="outputnode")

workflow.connect(
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14 changes: 12 additions & 2 deletions sdcflows/workflows/tests/test_base.py
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Expand Up @@ -62,5 +62,15 @@ def test_fmap_wf(tmpdir, workdir, outdir, bids_layouts, dataset, subject):
if workdir:
wf.base_dir = str(workdir)

if os.getenv("GITHUB_ACTIONS") != "true":
wf.run(plugin="Linear")
if os.getenv("GITHUB_ACTIONS") == "true":
return

res = wf.run(plugin="Linear")

# Regression test for when out_merge_fmap_coeff was flattened and would
# have twice as many elements as the other nodes
assert all(
len(node.result.outputs.out) == len(estimators)
for node in res.nodes
if node.name.startswith("out_merge_")
)