Merge pull request #220 from DominikaZ/csa-header

Add CSA header support using nibabel or dicom-parser

bidscoin/bids.py

@@ -22,6 +22,7 @@
 from pathlib import Path
 from typing import List, Set, Tuple, Union
 from nibabel.parrec import parse_PAR_header
+from nibabel.nicom import csareader
 from pydicom import dcmread, fileset, datadict
 from importlib.util import find_spec
 if find_spec('bidscoin') is None:
@@ -581,7 +582,7 @@ def get_dicomfield(tagname: str, dicomfile: Path) -> Union[str, int]:
                 try:                                                    # Try Pydicom's hexadecimal tag number first
                     value = eval(f"dicomdata[{tagname}].value")         # NB: This may generate e.g. UserWarning: Invalid value 'filepath' used with the 'in' operator: must be an element tag as a 2-tuple or int, or an element keyword
                 except (NameError, KeyError, SyntaxError):
-                    value = dicomdata.get(tagname) if tagname in dicomdata else ''  # Then try and see if it is an attribute name. NB: Do not use dicomdata.get(tagname, '') to avoid using its class attributes (e.g. 'filename')
+                    value = dicomdata.get(tagname,'') if tagname in dicomdata else ''  # Then try and see if it is an attribute name. NB: Do not use dicomdata.get(tagname, '') to avoid using its class attributes (e.g. 'filename')
 
                 # Try a recursive search
                 if not value and value != 0:
@@ -590,7 +591,35 @@ def get_dicomfield(tagname: str, dicomfile: Path) -> Union[str, int]:
                             value = elem.value
                             break
 
-                if not value and value!=0 and 'Modality' not in dicomdata:
+                # Try reading the Siemens CSA header. For V* versions the CSA header tag is (0029,1020), for XA versions (0021,1019). TODO: see if dicom_parser is supporting this
+                if not value and value != 0 and is_dicomfile_siemens(dicomfile):
+
+                    if find_spec('dicom_parser'):
+                        from dicom_parser import Image
+
+                        for csa in ('CSASeriesHeaderInfo', 'CSAImageHeaderInfo'):
+                            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
+                                    value = value.get(csatag, '')
+                                    if 'value' in value:                # Normal CSA (i.e. not MrPhoenixProtocol)
+                                        value = value['value']
+                            if value != 0:
+                                value = str(value or '')
+
+                    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('.'):           # NB: Currently MrPhoenixProtocol is not supported
+                                if isinstance(value, dict):             # Final CSA header attributes in dictionary of dictionaries
+                                    value = value.get(csatag, {}).get('items', '')
+                                    if isinstance(value, list) and len(value) == 1:
+                                        value = value[0]
+                            if value != 0:
+                                value = str(value or '')
+
+                if not value and value != 0 and 'Modality' not in dicomdata:
                     raise ValueError(f"Missing mandatory DICOM 'Modality' field in: {dicomfile}")
 
                 # XA-30 enhanced DICOM hack: Catch missing EchoNumbers from ice-dims
@@ -605,11 +634,7 @@ def get_dicomfield(tagname: str, dicomfile: Path) -> Union[str, int]:
 
             except Exception as dicomerror:
                 LOGGER.warning(f"Could not read {tagname} from {dicomfile}\n{dicomerror}")
-                try:
-                    value = parse_x_protocol(tagname, dicomfile)
-                except Exception as dicomerror:
-                    LOGGER.warning(f'Could not parse {tagname} from {dicomfile}\n{dicomerror}')
-                    value = ''
+                value = ''
 
     # Cast the dicom data type to int or str (i.e. to something that yaml.dump can handle)
     if isinstance(value, int):

pyproject.toml

@@ -37,10 +37,11 @@ dependencies     = ['pandas',
 dcm2niix2bids    = ['dcm2niix']
 spec2nii2bids    = ['spec2nii >= 0.6.1']
 deface           = ['pydeface']
+siemens          = ['dicom-parser']
 # pet2bids         = ['pypet2bids >= 1.0.12']
 # phys2bidscoin    = ['bioread >= 1.0.5', 'pymatreader >= 0.0.24', 'phys2bids >= 2.0.0, < 3.0.0']
-all              = ['bidscoin[dcm2niix2bids,spec2nii2bids,deface]']    # + pet2bids + phys2bidscoin
-dev              = ['bidscoin[spec2nii2bids,deface]', 'tox', 'pytest', 'jsonschema', 'sphinx-rtd-theme', 'myst-parser'] # + pet2bids + phys2bidscoin
+all              = ['bidscoin[dcm2niix2bids,spec2nii2bids,deface,siemens]']    # + pet2bids + phys2bidscoin
+dev              = ['bidscoin[spec2nii2bids,deface,siemens]', 'tox', 'pytest', 'jsonschema', 'sphinx-rtd-theme', 'myst-parser'] # + pet2bids + phys2bidscoin
 
 [project.urls]
 documentation    = 'https://bidscoin.readthedocs.io'

tests/test_bids.py

@@ -18,6 +18,11 @@ def dcm_file():
     return Path(get_testdata_file('MR_small.dcm'))
 
 
+@pytest.fixture(scope='module')
+def dcm_file_csa():
+    return Path(data_path)/'1.dcm'
+
+
 @pytest.fixture(scope='module')
 def dicomdir():
     return Path(get_testdata_file('DICOMDIR'))
@@ -56,7 +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')                    == 76
+        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'
@@ -118,6 +123,34 @@ def test_get_datasource(dicomdir):
     assert datasource.dataformat == 'DICOM'
 
 
+def test_get_dicomfield(dcm_file_csa):
+
+    # -> Standard DICOM
+    value = bids.get_dicomfield('SeriesDescription', dcm_file_csa)
+    assert value == 'CBU_DTI_64D_1A'
+
+    # -> CSA Series header
+    value = bids.get_dicomfield('PhaseGradientAmplitude', dcm_file_csa)
+    assert value == '0.0'
+
+    # -> CSA Image header
+    value = bids.get_dicomfield('ImaCoilString', dcm_file_csa)
+    assert value == 'T:HEA;HEP'
+
+    value = bids.get_dicomfield('B_matrix', dcm_file_csa)
+    assert value == ''
+
+    # -> 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])
 def test_load_check_template(template):