updated code to match metadata access in fileformats

Australian-Imaging-Service · Mar 1, 2024 · dad811e · dad811e
1 parent 7351e26
commit dad811e
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Showing 4 changed files with 17 additions and 17 deletions.
diff --git a/xnat_ingest/cli/stage.py b/xnat_ingest/cli/stage.py
@@ -44,7 +44,7 @@
     help=("The keyword or tag of the DICOM field to extract the XNAT subject ID from "),
 )
 @click.option(
-    "--session-field",
+    "--visit-field",
     type=DicomField,
     default="AccessionNumber",
     envvar="XNAT_INGEST_SESSION",

diff --git a/xnat_ingest/session.py b/xnat_ingest/session.py
@@ -89,7 +89,7 @@ def make_session_id(cls, project_id, subject_id, visit_id):
 
     @cached_property
     def modalities(self) -> ty.Set[str]:
-        modalities = self["Modality"]
+        modalities = self.metadata["Modality"]
         if not isinstance(modalities, str):
             modalities = set(tuple(m) if not isinstance(m, str) else m for m in modalities)
         return modalities
@@ -180,10 +180,10 @@ def metadata(self):
         common_keys = [
             k for k in set(chain(*all_keys)) if all(k in keys for keys in all_keys)
         ]
-        collated = {k: all_dicoms[0][k] for k in common_keys}
+        collated = {k: all_dicoms[0].metadata[k] for k in common_keys}
         for i, series in enumerate(all_dicoms[1:], start=1):
             for key in common_keys:
-                val = series[key]
+                val = series.metadata[key]
                 if val != collated[key]:
                     # Check whether the value is the same as the values in the previous
                     # images in the series
@@ -266,7 +266,7 @@ def from_dicoms(
         ):
             # Restrict the metadata fields that are loaded (others are ignored),
             # for performance reasons
-            dicom_sessions[series["StudyInstanceUID"]].append(series)
+            dicom_sessions[series.metadata["StudyInstanceUID"]].append(series)
 
         # Construct sessions from sorted series
         logger.info("Searching for associated files ")
@@ -295,12 +295,12 @@ def get_id(field):
 
             scans = []
             for dicom_series in session_dicom_series:
-                series_description = dicom_series["SeriesDescription"]
+                series_description = dicom_series.metadata["SeriesDescription"]
                 if isinstance(series_description, list):
                     series_description = series_description[0]
                 scans.append(
                     ImagingScan(
-                        id=str(dicom_series["SeriesNumber"]),
+                        id=str(dicom_series.metadata["SeriesNumber"]),
                         type=str(series_description),
                         resources={"DICOM": dicom_series},
                     )

diff --git a/xnat_ingest/tests/test_dicom.py b/xnat_ingest/tests/test_dicom.py
@@ -15,7 +15,7 @@ def dicom_series(scope="module") -> ImagingSession:
     return DicomSeries(get_pet_image().iterdir())
 
 
-def test_mrtrix_dicom_metadata(dicom_series):
+def test_mrtrix_dicom_metadata(dicom_series: DicomSeries):
     keys = [
         "AccessionNumber",
         "PatientID",
@@ -27,10 +27,10 @@ def test_mrtrix_dicom_metadata(dicom_series):
     dicom_series.select_metadata(keys)
 
     assert sorted(dicom_series.metadata) == sorted(keys + ['SpecificCharacterSet'])
-    assert dicom_series["PatientName"] == "GivenName^FamilyName"
-    assert dicom_series["AccessionNumber"] == "987654321"
-    assert dicom_series["PatientID"] == 'Session Label'
-    assert dicom_series["StudyID"] == "PROJECT_ID"
-    assert not isinstance(dicom_series["StudyInstanceUID"], list)
-    assert isinstance(dicom_series["SOPInstanceUID"], list)
-    assert len(dicom_series["SOPInstanceUID"]) == len(list(dicom_series.contents))
+    assert dicom_series.metadata["PatientName"] == "GivenName^FamilyName"
+    assert dicom_series.metadata["AccessionNumber"] == "987654321"
+    assert dicom_series.metadata["PatientID"] == 'Session Label'
+    assert dicom_series.metadata["StudyID"] == "PROJECT_ID"
+    assert not isinstance(dicom_series.metadata["StudyInstanceUID"], list)
+    assert isinstance(dicom_series.metadata["SOPInstanceUID"], list)
+    assert len(dicom_series.metadata["SOPInstanceUID"]) == len(list(dicom_series.contents))
diff --git a/xnat_ingest/tests/test_session.py b/xnat_ingest/tests/test_session.py
@@ -46,8 +46,8 @@ def imaging_session() -> ImagingSession:
     ]
     scans = [
         ImagingScan(
-            id=str(d["SeriesNumber"]),
-            type=str(d["SeriesDescription"]),
+            id=str(d.metadata["SeriesNumber"]),
+            type=str(d.metadata["SeriesDescription"]),
             resources={"DICOM": d}) for d in dicoms]
     return ImagingSession(
         project_id="PROJECTID",