Validated svs rda orientations.

CHANGELOG.md

@@ -1,5 +1,10 @@
 This document contains the Spec2nii release history in reverse chronological order.
 
+0.7.3 (WIP)
+-----------
+- Siemens .rda format now had corrected and validated orientations (tested on VE11 baseline).
+-
+
 0.7.2 (Thursday 7th December 2023)
 ----------------------------------
 - SpectralWidth now added to header extension automatically to match bids specification.

spec2nii/Siemens/rda.py

@@ -91,9 +91,9 @@ def convert_rda(rda_path, fname_out, verbose):
         ' Please contribute test data if you can!')
 
     imagePositionPatient = np.asarray([
-        _locale_float(hdr['PositionVector[0]']),
-        _locale_float(hdr['PositionVector[1]']),
-        _locale_float(hdr['PositionVector[2]'])])
+        _locale_float(hdr['VOIPositionSag']),
+        _locale_float(hdr['VOIPositionCor']),
+        _locale_float(hdr['VOIPositionTra'])])
 
     imageOrientationPatient = np.asarray([
         [_locale_float(hdr['RowVector[0]']), _locale_float(hdr['ColumnVector[0]'])],
@@ -137,13 +137,14 @@ def extractRdaMetadata(hdr):
         hdr['Nucleus'])
 
     # Standard defined metadata
-    def set_standard_def(nifti_mrs_key, location, key, cast=None):
-        if key in location\
-                and location[key] is not None:
+    def set_standard_def(nifti_mrs_key, key, cast=None):
+        if key in hdr\
+                and hdr[key] is not None\
+                and hdr[key]:
             if cast is not None:
-                obj.set_standard_def(nifti_mrs_key, cast(location[key]))
+                obj.set_standard_def(nifti_mrs_key, cast(hdr[key]))
             else:
-                obj.set_standard_def(nifti_mrs_key, location[key])
+                obj.set_standard_def(nifti_mrs_key, hdr[key])
 
     # # 5.1 MRS specific Tags
     # 'EchoTime'
@@ -180,22 +181,22 @@ def set_standard_def(nifti_mrs_key, location, key, cast=None):
 
     # # 5.3 Sequence information
     # 'SequenceName'
-    obj.set_standard_def('SequenceName', hdr['SequenceName'])
+    set_standard_def('SequenceName', 'SequenceName')
     # 'ProtocolName'
-    obj.set_standard_def('ProtocolName', hdr['ProtocolName'])
+    set_standard_def('ProtocolName', 'ProtocolName')
     # # 5.4 Sequence information
     # 'PatientPosition'
-    obj.set_standard_def('PatientPosition', hdr['PatientPosition'])
+    set_standard_def('PatientPosition', 'PatientPosition')
     # 'PatientName'
-    obj.set_standard_def('PatientName', hdr['PatientName'])
+    set_standard_def('PatientName', 'PatientName')
     # 'PatientID'
-    obj.set_standard_def('PatientID', hdr['PatientID'])
+    set_standard_def('PatientID', 'PatientID')
     # 'PatientWeight'
-    obj.set_standard_def('PatientWeight', _locale_float(hdr['PatientWeight']))
+    set_standard_def('PatientWeight', 'PatientWeight', cast=_locale_float)
     # 'PatientDoB'
-    obj.set_standard_def('PatientDoB', hdr['PatientBirthDate'])
+    set_standard_def('PatientDoB', 'PatientBirthDate')
     # 'PatientSex'
-    obj.set_standard_def('PatientSex', hdr['PatientSex'])
+    set_standard_def('PatientSex', 'PatientSex')
 
     # # 5.5 Provenance and conversion metadata
     obj.set_standard_def('ConversionMethod', f'spec2nii v{spec2nii_ver}')

tests/test_siemens_rda.py

@@ -20,6 +20,50 @@
 
 latin1_encoding = siemens_path / 'rda' / 'latin1.rda'
 
+ve_path = siemens_path / 'VEData' / 'rda'
+paired_ve_data = {
+    'svs_se_c_t15_s10_r10': 'svs_se_c>t15>s10_R10_12_1',
+    'svs_se_iso_tra_sat': 'svs_se_iso_tra_sat_13_1',
+    'svs_se_s_c10_t5_r10': 'svs_se_s>c10>t5_R10_11_1',
+    'svs_se_t_c15_s10_r10': 'svs_se_t>c15>s10_R10_10_1'}
+
+
+def test_ve_against_dicom(tmp_path):
+    for rda_file in ve_path.glob("svs_se*.rda"):
+        print(rda_file.stem)
+        dcm_dir = rda_file.parent.parent / 'DICOM' / paired_ve_data[rda_file.stem]
+
+        subprocess.run([
+            'spec2nii', 'rda',
+            '-f', rda_file.stem + '_rda',
+            '-o', tmp_path,
+            '-j', rda_file])
+
+        subprocess.run([
+            'spec2nii', 'dicom',
+            '-f', rda_file.stem + '_dcm',
+            '-o', tmp_path,
+            '-j', dcm_dir])
+
+        rda_out = tmp_path / (rda_file.stem + '_rda.nii.gz')
+        dcm_out = tmp_path / (rda_file.stem + '_dcm.nii.gz')
+        assert rda_out.exists()
+        assert dcm_out.exists()
+
+        dcm = read_nifti_mrs(dcm_out)
+        rda = read_nifti_mrs(rda_out)
+        assert dcm.shape == rda.shape
+        assert np.allclose(dcm.get_fdata(dtype=complex), rda.get_fdata(dtype=complex))
+        assert np.allclose(dcm.get_sform(), rda.get_sform())
+
+        hdr_ext_codes = dcm.header.extensions.get_codes()
+        hdr_ext_dcm = json.loads(dcm.header.extensions[hdr_ext_codes.index(44)].get_content())
+        hdr_ext_codes = rda.header.extensions.get_codes()
+        hdr_ext_rda = json.loads(rda.header.extensions[hdr_ext_codes.index(44)].get_content())
+
+        for key in ['SpectrometerFrequency', 'ResonantNucleus', 'EchoTime', 'RepetitionTime']:
+            assert hdr_ext_dcm[key] == hdr_ext_rda[key]
+
 
 def test_xa20_svs(tmp_path):