Added MrPhoenixProtocol tests and bugfixes (but the code is still dodgy)

dzemanov · Jan 28, 2024 · f9ecaa5 · f9ecaa5
1 parent a936337
commit f9ecaa5
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Showing 2 changed files with 25 additions and 13 deletions.
diff --git a/bidscoin/bids.py b/bidscoin/bids.py
@@ -597,21 +597,23 @@ def get_dicomfield(tagname: str, dicomfile: Path) -> Union[str, int]:
                             value = value if (value or value==0) else Image(dicomfile).header.get(csa)
                             for csatag in tagname.split('.'):           # E.g. CSA tagname = 'SliceArray.Slice.instance_number.Position.Tra'
                                 if isinstance(value, dict):             # Final CSA header attributes in dictionary of dictionaries
-                                    print(f"{csa} tag: {csatag}")
                                     value = value.get(csatag, '')
+                                    if 'value' in value:                # Normal CSA (i.e. not MrPhoenixProtocol)
+                                        value = value['value']
                             if not isinstance(value, int):
-                                value = str(value)
+                                value = str(value if value is not None else '')
 
                     else:
 
                         for type in ('Series', 'Image'):
                             value = value if (value or value==0) else csareader.get_csa_header(dicomdata, type)['tags']
                             for csatag in tagname.split('.'):           # E.g. CSA tagname = 'SliceArray.Slice.instance_number.Position.Tra'
                                 if isinstance(value, dict):             # Final CSA header attributes in dictionary of dictionaries
-                                    print(f"{type} tag: {csatag}")
-                                    value = value.get(csatag, '')
+                                    value = value.get(csatag, {}).get('items', '')
+                                    if isinstance(value, list) and len(value) == 1:
+                                        value = value[0]
                             if not isinstance(value, int):
-                                value = str(value)
+                                value = str(value if value not in (None,[]) else '')
 
                 if not value and value != 0 and 'Modality' not in dicomdata:
                     raise ValueError(f"Missing mandatory DICOM 'Modality' field in: {dicomfile}")

diff --git a/tests/test_bids.py b/tests/test_bids.py
@@ -61,7 +61,7 @@ def test_properties(self, datasource):
         assert datasource.properties( 'filepath:.*/(.*?)_files/.*') == 'test'   # path = [..]/pydicom/data/test_files/MR_small.dcm'
         assert datasource.properties(r'filename:MR_(.*?)\.dcm')     == 'small'
         assert datasource.properties( 'filesize')                   == '9.60 kB'
-        assert datasource.properties( 'nrfiles')                    == 75
+        assert datasource.properties( 'nrfiles')                    in (75,76)  # Depends on the pydicom version
 
     def test_attributes(self, datasource, extdatasource):
         assert datasource.attributes(r'PatientName:.*\^(.*?)1') == 'MR'         # PatientName = 'CompressedSamples^MR1'
@@ -125,17 +125,27 @@ def test_get_datasource(dicomdir):
 
 def test_get_dicomfield(dcm_file_csa):
 
-    value = bids.get_dicomfield('SeriesDescription', dcm_file_csa)              # -> Standard DICOM
+    # -> Standard DICOM
+    value = bids.get_dicomfield('SeriesDescription', dcm_file_csa)
     assert value == 'CBU_DTI_64D_1A'
 
-    value = bids.get_dicomfield('PhaseGradientAmplitude', dcm_file_csa)         # -> CSA Series header
-    assert value == "{'index': 3, 'VR': 'DS', 'VM': 1, 'value': 0.0}"
+    # -> CSA Series header
+    value = bids.get_dicomfield('PhaseGradientAmplitude', dcm_file_csa)
+    assert value == '0.0'
 
-    value = bids.get_dicomfield('PhaseGradientAmplitude.index', dcm_file_csa)
-    assert value == 3
+    # -> CSA Image header
+    value = bids.get_dicomfield('B_matrix', dcm_file_csa)
+    assert value == ''
 
-    value = bids.get_dicomfield('B_matrix.index', dcm_file_csa)                 # -> CSA Image header
-    assert value == 77
+    # -> CSA MrPhoenixProtocol
+    value = bids.get_dicomfield('MrPhoenixProtocol.tProtocolName', dcm_file_csa)
+    assert value == 'CBU+AF8-DTI+AF8-64D+AF8-1A'
+
+    value = bids.get_dicomfield('MrPhoenixProtocol.sDiffusion', dcm_file_csa)
+    assert value == "{'lDiffWeightings': 2, 'alBValue': [None, 1000], 'lNoiseLevel': 40, 'lDiffDirections': 64, 'ulMode': 256}"
+
+    value = bids.get_dicomfield('MrPhoenixProtocol.sProtConsistencyInfo.tBaselineString', dcm_file_csa)
+    assert value == 'N4_VB17A_LATEST_20090307'
 
 
 @pytest.mark.parametrize('template', bcoin.list_plugins()[1])