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[ENH] filter dicoms earlier to avoid nibabel crash with XA ill-formed mutli-planar localizer dicoms #806

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[ENH] filter dicoms earlier to avoid nibabel crash with XA ill-formed mutli-planar localizer dicoms #806

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5493d65
filter dicoms earlier to avoid crash with XA mutli-planar dicoms
bpinsard Nov 29, 2024
357c109
make repronim dicom filter more robust, due to filtering earlier
bpinsard Dec 13, 2024
4ce1119
reorder again to improve testcov: clean signatures at the end
bpinsard Dec 13, 2024
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18 changes: 9 additions & 9 deletions heudiconv/dicoms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -169,12 +169,6 @@
Parse DICOM attributes. Returns None if not valid.
"""
mw = dw.wrapper_from_file(fl, force=True, stop_before_pixels=True)
# clean series signature
for sig in ("iop", "ICE_Dims", "SequenceName"):
try:
del mw.series_signature[sig]
except KeyError:
pass
# Workaround for protocol name in private siemens csa header
if not getattr(mw.dcm_data, "ProtocolName", "").strip():
mw.dcm_data.ProtocolName = (
Expand All @@ -189,9 +183,6 @@
except AttributeError as e:
lgr.warning('Ignoring %s since not quite a "normal" DICOM: %s', fl, e)
return None
if dcmfilter is not None and dcmfilter(mw.dcm_data):
lgr.warning("Ignoring %s because of DICOM filter", fl)
return None
if mw.dcm_data[0x0008, 0x0016].repval in (
"Raw Data Storage",
"GrayscaleSoftcopyPresentationStateStorage",
Expand All @@ -203,6 +194,15 @@
except AttributeError:
lgr.info("File {} is missing any StudyInstanceUID".format(fl))
file_studyUID = None
if dcmfilter is not None and dcmfilter(mw.dcm_data):
lgr.warning("Ignoring %s because of DICOM filter", fl)
return None

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heudiconv/dicoms.py#L198-L199 

Added lines #L198 - L199 were not covered by tests
# clean series signature
for sig in ("iop", "ICE_Dims", "SequenceName"):
try:
del mw.series_signature[sig]
except KeyError:
pass
return mw, series_id, file_studyUID


Expand Down
13 changes: 10 additions & 3 deletions heudiconv/heuristics/reproin.py
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Original file line number Diff line number Diff line change
Expand Up @@ -226,7 +226,7 @@

def filter_dicom(dcmdata: dcm.dataset.Dataset) -> bool:
"""Return True if a DICOM dataset should be filtered out, else False"""
return True if dcmdata.StudyInstanceUID in dicoms2skip else False
return True if dcmdata.get("StudyInstanceUID") in dicoms2skip else False


def filter_files(_fn: str) -> bool:
Expand Down Expand Up @@ -406,7 +406,11 @@
# XXX: skip derived sequences, we don't store them to avoid polluting
# the directory, unless it is the motion corrected ones
# (will get _rec-moco suffix)
if skip_derived and curr_seqinfo.is_derived and not curr_seqinfo.is_motion_corrected:
if (
skip_derived
and curr_seqinfo.is_derived
and not curr_seqinfo.is_motion_corrected
):
skipped.append(curr_seqinfo.series_id)
lgr.debug("Ignoring derived data %s", curr_seqinfo.series_id)
continue
Expand Down Expand Up @@ -552,7 +556,10 @@
# XXX if we have a known earlier study, we need to always
# increase the run counter for phasediff because magnitudes
# were not acquired
if get_study_hash([curr_seqinfo]) == "9d148e2a05f782273f6343507733309d":
if (

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get_study_hash([curr_seqinfo])
== "9d148e2a05f782273f6343507733309d"
):
current_run += 1
else:
raise RuntimeError(
Expand Down
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