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properly remove GE multiecho bvals/bvecs #728

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merged 5 commits into from
Feb 24, 2024
Merged

properly remove GE multiecho bvals/bvecs #728

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636eb16
fix GE hyperband multi-echo bvecs/bvals
bpinsard Jan 11, 2024
758628d
add missing import
bpinsard Jan 11, 2024
2ea5c82
import from nipype to avoid adding traits to mypy ignores
bpinsard Jan 11, 2024
18d5e68
Update heudiconv/convert.py
bpinsard Jan 23, 2024
bc4ce42
cast to list first, add unit test for bvals_are_zero
bpinsard Jan 23, 2024
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14 changes: 12 additions & 2 deletions heudiconv/convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@

import filelock
from nipype import Node
from nipype.interfaces.base import TraitListObject

from .bids import (
BIDS_VERSION,
Expand Down Expand Up @@ -886,8 +887,13 @@
safe_movefile(res.outputs.bvals, outname_bvals, overwrite)
else:
if bvals_are_zero(res.outputs.bvals):
os.remove(res.outputs.bvecs)
os.remove(res.outputs.bvals)
to_remove = []
if isinstance(res.outputs.bvals, str):
to_remove = [res.outputs.bvals, res.outputs.bvecs]

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heudiconv/convert.py#L890-L892 

Added lines #L890 - L892 were not covered by tests
else:
to_remove = list(res.outputs.bvals) + list(res.outputs.bvecs)
for ftr in to_remove:
os.remove(ftr)

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heudiconv/convert.py#L894-L896 

Added lines #L894 - L896 were not covered by tests
lgr.debug(
"%s and %s were removed since not dwi",
res.outputs.bvecs,
Expand Down Expand Up @@ -1077,6 +1083,10 @@
True if all are all 0 or 5; False otherwise.
"""

# GE hyperband multi-echo containing diffusion info
if isinstance(bval_file, TraitListObject):
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return all([bvals_are_zero(bvf) for bvf in bval_file])

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Added line #L1088 was not covered by tests
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with open(bval_file) as f:
bvals = f.read().split()

Expand Down