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remove bval bvecs files generated for SBRef on XA60/CMRR/dcm2niix #819

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remove bval bvecs files generated for SBRef on XA60/CMRR/dcm2niix #819

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05660cc
remove bval bvecs files for SBRef (now produced somewhere by the inte…
bpinsard Mar 24, 2025
f349ed2
fix warning and tests
bpinsard Mar 25, 2025
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10 changes: 3 additions & 7 deletions heudiconv/convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -61,9 +61,7 @@ class PopulateIntendedForOpts(TypedDict, total=False):


LOCKFILE = "heudiconv.lock"
DW_IMAGE_IN_FMAP_FOLDER_WARNING = (
"Diffusion-weighted image saved in non dwi folder ({folder})"
)
DW_IMAGE_WRONG_SUFFIX_WARNING = "Diffusion-weighted image saved as non dwi ({prefix})"
lgr = logging.getLogger(__name__)


Expand Down Expand Up @@ -896,7 +894,7 @@ def save_converted_files(
bvals, bvecs = res.outputs.bvals, res.outputs.bvecs
bvals = list(bvals) if isinstance(bvals, TraitListObject) else bvals
bvecs = list(bvecs) if isinstance(bvecs, TraitListObject) else bvecs
if prefix_dirname.endswith("dwi"):
if prefix.endswith("dwi"):
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Sorry for being anal -- just trying to get a better grasp.

With this change I think the else: warning on

                lgr.warning(
                    DW_IMAGE_IN_FMAP_FOLDER_WARNING.format(folder=prefix_dirname)
                )

might be confusing false positive since we might be finding _dwi somewhere else than dwi/ folder (e.g. due to a bug in heuristic or alike)

Also, how/where do we treat fmap/..._epi here -- from the code it seems we could also run into the warnings, can't we?

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I see you're right that the logic has drifted, so we can change that message to

DW_IMAGE_WRONG_SUFFIX_WARNING = (
    "Diffusion-weighted image saved as non dwi ({prefix})"
)

and

                lgr.warning(
                    DW_IMAGE_WRONG_SUFFIX_WARNING.format(prefix=prefix)
                )

outname_bvecs, outname_bvals = prefix + ".bvec", prefix + ".bval"
safe_movefile(bvecs, outname_bvecs, overwrite)
safe_movefile(bvals, outname_bvals, overwrite)
Expand All @@ -907,9 +905,7 @@ def save_converted_files(
os.remove(ftr)
lgr.debug("%s and %s were removed since not dwi", bvecs, bvals)
else:
lgr.warning(
DW_IMAGE_IN_FMAP_FOLDER_WARNING.format(folder=prefix_dirname)
)
lgr.warning(DW_IMAGE_WRONG_SUFFIX_WARNING.format(prefix=prefix))
lgr.warning(
".bvec and .bval files will be generated. This is NOT BIDS compliant"
)
Expand Down
6 changes: 3 additions & 3 deletions heudiconv/tests/test_convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
from heudiconv.cli.run import main as runner
import heudiconv.convert
from heudiconv.convert import (
DW_IMAGE_IN_FMAP_FOLDER_WARNING,
DW_IMAGE_WRONG_SUFFIX_WARNING,
bvals_are_zero,
update_complex_name,
update_multiecho_name,
Expand Down Expand Up @@ -170,8 +170,8 @@ def test_b0dwi_for_fmap(tmp_path: Path, caplog: pytest.LogCaptureFixture) -> Non

# assert that it raised a warning that the fmap directory will contain
# bvec and bval files.
expected_msg = DW_IMAGE_IN_FMAP_FOLDER_WARNING.format(
folder=op.join(tmp_path, f"sub-{subID}", "fmap")
expected_msg = DW_IMAGE_WRONG_SUFFIX_WARNING.format(
prefix=op.join(tmp_path, f"sub-{subID}", "fmap", f"sub-{subID}_acq-b0dwi_epi")
)
assert any(expected_msg in c.message for c in caplog.records)

Expand Down