Merge pull request #806 from UNFmontreal/enh/filter_dicom_earlier

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

Author: yarikoptic

heudiconv/dicoms.py

@@ -169,12 +169,6 @@ def validate_dicom(
     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 = (
@@ -203,6 +197,12 @@ def validate_dicom(
     except AttributeError:
         lgr.info("File {} is missing any StudyInstanceUID".format(fl))
         file_studyUID = None
+    # 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
 
 

heudiconv/heuristics/reproin.py

@@ -406,7 +406,11 @@ def infotodict(
         # 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
@@ -552,7 +556,10 @@ def infotodict(
                         # 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 (
+                            get_study_hash([curr_seqinfo])
+                            == "9d148e2a05f782273f6343507733309d"
+                        ):
                             current_run += 1
                         else:
                             raise RuntimeError(