Merge pull request #271 from mgxd/enh/private

enh: fallback to private siemens header

Author: mgxd

heudiconv/dicoms.py

@@ -4,7 +4,7 @@
 import logging
 from collections import OrderedDict
 import tarfile
-
+from nibabel.nicom import csareader
 from heudiconv.external.pydicom import dcm
 
 from .utils import SeqInfo, load_json, set_readonly
@@ -73,6 +73,15 @@ def group_dicoms_into_seqinfos(files, file_filter, dcmfilter, grouping):
             lgr.info("File {} is missing any StudyInstanceUID".format(filename))
             file_studyUID = None
 
+        # Workaround for protocol name in private siemens csa header
+        try:
+            mw.dcm_data.ProtocolName
+        except AttributeError:
+            if not getattr(mw.dcm_data, 'ProtocolName', '').strip():
+                mw.dcm_data.ProtocolName = parse_private_csa_header(
+                    mw.dcm_data, 'ProtocolName', 'tProtocolName'
+                    ) if mw.is_csa else ''
+
         try:
             series_id = (int(mw.dcm_data.SeriesNumber),
                          mw.dcm_data.ProtocolName)
@@ -208,7 +217,7 @@ def group_dicoms_into_seqinfos(files, file_filter, dcmfilter, grouping):
             dcminfo.get('PatientID'),
             dcminfo.get('StudyDescription'),
             refphys,
-            dcminfo.get('SeriesDescription'),
+            series_desc,  # We try to set this further up.
             sequence_name,
             image_type,
             accession_number,
@@ -232,7 +241,7 @@ def group_dicoms_into_seqinfos(files, file_filter, dcmfilter, grouping):
         lgr.debug("%30s %30s %27s %27s %5s nref=%-2d nsrc=%-2d %s" % (
             key,
             info.series_id,
-            dcminfo.SeriesDescription,
+            series_desc,
             dcminfo.ProtocolName,
             info.is_derived,
             len(dcminfo.get('ReferencedImageSequence', '')),
@@ -483,3 +492,37 @@ def embed_metadata_from_dicoms(bids, item_dicoms, outname, outname_bids,
     except Exception as exc:
         lgr.error("Embedding failed: %s", str(exc))
         os.chdir(cwd)
+
+def parse_private_csa_header(dcm_data, public_attr, private_attr, default=None):
+    """
+    Parses CSA header in cases where value is not defined publicly
+
+    Parameters
+    ----------
+    dcm_data : pydicom Dataset object
+        DICOM metadata
+    public_attr : string
+        non-private DICOM attribute
+    private_attr : string
+        private DICOM attribute
+    default (optional)
+        default value if private_attr not found
+
+    Returns
+    -------
+    val (default: empty string)
+        private attribute value or default
+    """
+    # TODO: provide mapping to private_attr from public_attr
+    from nibabel.nicom import csareader
+    import dcmstack.extract as dsextract
+    try:
+        # TODO: test with attr besides ProtocolName
+        csastr = csareader.get_csa_header(dcm_data, 'series')['tags']['MrPhoenixProtocol']['items'][0]
+        csastr = csastr.replace("### ASCCONV BEGIN", "### ASCCONV BEGIN ### ")
+        parsedhdr = dsextract.parse_phoenix_prot('MrPhoenixProtocol', csastr)
+        val = parsedhdr[private_attr].replace(' ', '')
+    except Exception as e:
+        lgr.debug("Failed to parse CSA header: %s", str(e))
+        val = default if default else ''
+    return val

tests/data/axasc35.dcm

@@ -0,0 +1,25 @@
+import os.path as op
+
+import pytest
+
+from heudiconv.external.pydicom import dcm
+from heudiconv.cli.run import main as runner
+from heudiconv.dicoms import parse_private_csa_header
+from .utils import TESTS_DATA_PATH
+
+# Public: Private DICOM tags
+DICOM_FIELDS_TO_TEST = {
+    'ProtocolName': 'tProtocolName'
+}
+
+def test_private_csa_header(tmpdir):
+    dcm_file = op.join(TESTS_DATA_PATH, 'axasc35.dcm')
+    dcm_data = dcm.read_file(dcm_file)
+    for pub, priv in DICOM_FIELDS_TO_TEST.items():
+        # ensure missing public tag
+        with pytest.raises(AttributeError):
+            dcm.pub
+        # ensure private tag is found
+        assert parse_private_csa_header(dcm_data, pub, priv) != ''
+        # and quickly run heudiconv with no conversion
+        runner(['--files', dcm_file, '-c' 'none', '-f', 'reproin'])