BF: Correct Universal editing sequence HERMES conditions and tests fo…

…r XA50 twix and RDA (#130)

* Fix issues in un tested lines of the universal editing special case

* Fix issue in mgs_svs_ed special casing. Add xa50 test data.

CHANGELOG.md

@@ -4,6 +4,8 @@ This document contains the Spec2nii release history in reverse chronological ord
 -----------
 - Siemens .rda format now had corrected and validated orientations (tested on VE11 baseline).
 - Siemens .rda format now handles MRSI/CSI data and matches DICOM output. Validated on VE11 baseline data.
+- Fixes in Siemens Twix special case for universal editing sequence (HERMES conditions).
+- Added handling of custom Bruker sequences `mt_sLASER`, `mt_MEGA_sLASER_V35` and `cl_STELASER_PA360_b`.
 
 0.7.2 (Thursday 7th December 2023)
 ----------------------------------

spec2nii/Siemens/twix_special_case.py

@@ -142,24 +142,24 @@ def mgs_svs_ed_twix(twixObj, reord_data, meta_obj, dim_tags):
             "OFF": {"PulseOffset": edit_pulse_off, "PulseDuration": pulse_length}}
     elif seq_mode == 1.0:
         # HERMES GABA GSH (3 edit, 1 ctrl condition)
-        edit_cases = 3
+        edit_cases = 4
         dim_info = "HERMES j-difference editing, GABA GSH, four conditions"
         dim_header = {"EditCondition": ["A", "B", "C", "D"]}
         edit_pulse_val = {
             "A": {"PulseOffset": edit_pulse_1, "PulseDuration": 0.02},
-            "B": {"PulseOffset": None, "PulseDuration": None},
-            "C": {"PulseOffset": edit_pulse_off, "PulseDuration": 0.02},
-            "D": {"PulseOffset": [edit_pulse_1, edit_pulse_off], "PulseDuration": 0.02}}
+            "B": {"PulseOffset": edit_pulse_off, "PulseDuration": 0.02},
+            "C": {"PulseOffset": edit_pulse_2, "PulseDuration": 0.02},
+            "D": {"PulseOffset": [edit_pulse_1, edit_pulse_2], "PulseDuration": 0.02}}
     elif seq_mode == 2.0:
         # HERMES GABA GSH EtOH (3 edit, 1 ctrl condition)
         edit_cases = 4
         dim_info = "HERMES j-difference editing, GABA GSH EtOH, four conditions"
         dim_header = {"EditCondition": ["A", "B", "C", "D"]}
         edit_pulse_val = {
-            "A": {"PulseOffset": [edit_pulse_1, edit_pulse_2], "PulseDuration": 0.02},
-            "B": {"PulseOffset": [edit_pulse_3, edit_pulse_2], "PulseDuration": None},
-            "C": {"PulseOffset": [edit_pulse_1, edit_pulse_3], "PulseDuration": 0.02},
-            "D": {"PulseOffset": None, "PulseDuration": None}}
+            "A": {"PulseOffset": [edit_pulse_1, edit_pulse_3], "PulseDuration": 0.02},
+            "B": {"PulseOffset": edit_pulse_off, "PulseDuration": 0.02},
+            "C": {"PulseOffset": [edit_pulse_2, edit_pulse_3], "PulseDuration": 0.02},
+            "D": {"PulseOffset": [edit_pulse_1, edit_pulse_2], "PulseDuration": 0.02}}
     elif seq_mode == 3.0:
         # HERCULES (4 edit conditions)
         edit_cases = 4
@@ -170,16 +170,17 @@ def mgs_svs_ed_twix(twixObj, reord_data, meta_obj, dim_tags):
             "B": {"PulseOffset": [edit_pulse_off, edit_pulse_2], "PulseDuration": 0.02},
             "C": {"PulseOffset": edit_pulse_1, "PulseDuration": 0.02},
             "D": {"PulseOffset": edit_pulse_off, "PulseDuration": 0.02}}
-    elif seq_mode == 3.0:
+    elif seq_mode == 4.0:
+        # This is possibly only a condition for smm_svs_herc as not present in VE11c version.
         # HERMES GABA LAC (3 edit 1 ctrl conditions)
         edit_cases = 4
         dim_info = "HERMES j-difference editing, GABA LAC, four conditions"
         dim_header = {"EditCondition": ["A", "B", "C", "D"]}
         edit_pulse_val = {
             "A": {"PulseOffset": edit_pulse_1, "PulseDuration": 0.02},
-            "B": {"PulseOffset": None, "PulseDuration": None},
-            "C": {"PulseOffset": edit_pulse_off, "PulseDuration": 0.02},
-            "D": {"PulseOffset": [edit_pulse_1, edit_pulse_off], "PulseDuration": 0.02}}
+            "B": {"PulseOffset": edit_pulse_off, "PulseDuration": 0.02},
+            "C": {"PulseOffset": edit_pulse_2, "PulseDuration": 0.02},
+            "D": {"PulseOffset": [edit_pulse_1, edit_pulse_2], "PulseDuration": 0.02}}
     else:
         raise ValueError('Unknown sequence mode in mgs_svs_ed sequence.')
 

tests/test_siemens_rda.py

@@ -17,6 +17,7 @@
 
 xa20_svs_path = siemens_path / 'XAData' / 'XA20/rda/spct_002.MR.MRI-LAB Test_Dir.5.1.114540.rda'
 xa31_locale_svs_path = siemens_path / 'XAData' / 'XA31/rda/locale_XA31.rda'
+xa50_path = siemens_path / 'XAData' / 'XA50' / 'Phantom_20240129.MR.10.1.155227.rda'
 
 latin1_encoding = siemens_path / 'rda' / 'latin1.rda'
 
@@ -147,6 +148,25 @@ def test_xa31_locale_svs(tmp_path):
     assert np.iscomplexobj(img_t.dataobj)
 
 
+def test_xa50_svs(tmp_path):
+
+    subprocess.run([
+        'spec2nii', 'rda',
+        '-f', 'xa50_svs',
+        '-o', tmp_path,
+        '-j', xa50_path])
+
+    img_t = read_nifti_mrs(tmp_path / 'xa50_svs.nii.gz')
+
+    hdr_ext_codes = img_t.header.extensions.get_codes()
+    hdr_ext = json.loads(img_t.header.extensions[hdr_ext_codes.index(44)].get_content())
+
+    hdr_ext['ResonantNucleus'] = ['1H', ]
+
+    assert img_t.shape == (1, 1, 1, 2048)
+    assert np.iscomplexobj(img_t.dataobj)
+
+
 def test_latin_encoding(tmp_path):
 
     subprocess.check_call(['spec2nii', 'rda',

tests/test_twix.py → tests/test_siemens_twix.py

@@ -23,6 +23,7 @@
 # Special cased data
 hercules_ve = siemens_path / 'HERCULES' / 'Siemens_TIEMO_HERC.dat'
 hercules_xa30 = siemens_path / 'HERCULES' / 'meas_MID02595_FID60346_HERC.dat'
+hermes_xa50 = siemens_path / 'XAData' / 'XA50' / 'smm_svs_herc_v2_hermes.dat'
 
 
 def test_VB(tmp_path):
@@ -202,6 +203,27 @@ def test_XA_HERCULES(tmp_path):
     assert hdr_ext['dim_7'] == 'DIM_DYN'
 
 
+def test_XA_HERMES(tmp_path):
+
+    subprocess.check_call(['spec2nii', 'twix',
+                           '-e', 'image',
+                           '-f', 'hermes_xa',
+                           '-o', tmp_path,
+                           '-j', str(hermes_xa50)])
+
+    img_t = read_nifti_mrs(tmp_path / 'hermes_xa.nii.gz')
+
+    hdr_ext_codes = img_t.header.extensions.get_codes()
+    hdr_ext = json.loads(img_t.header.extensions[hdr_ext_codes.index(44)].get_content())
+
+    assert img_t.shape == (1, 1, 1, 4096, 42, 4, 80)
+    assert np.iscomplexobj(img_t.dataobj)
+
+    assert hdr_ext['dim_5'] == 'DIM_COIL'
+    assert hdr_ext['dim_6'] == 'DIM_EDIT'
+    assert hdr_ext['dim_7'] == 'DIM_DYN'
+
+
 def test_twix_mrsi_orientation(tmp_path):
     '''Test that the (empty) mrsi has information matching the twix equivalent.'''