Missed a PSD in ge_read_pfile.py - adding in for hbcd2 (#145)

* Missed a PSD in ge_read_pfile.py - adding in for hbcd2

* Add test for HBCD ge data.

* Update changelog

---------

Co-authored-by: wtclarke <[email protected]>

CHANGELOG.md

@@ -1,5 +1,9 @@
 This document contains the Spec2nii release history in reverse chronological order.
 
+0.8.3 (Tuesday 9th August 2024)
+-------------------------------
+- Fix for multiple GE HBCD sequence names (again).
+
 0.8.2 (Tuesday 9th July 2024)
 -------------------------------
 - Fix for multiple GE HBCD sequence names.

spec2nii/GE/ge_read_pfile.py

@@ -206,7 +206,9 @@ def get_mapper(self):
                     'jpress',            # wtc - added for J-edited data.
                     'jpress_ac',         # ARC - added for Bergen jpress patch
                     'gaba',              # wtc - added for Nottingham MEGA-PRESS sequence
-                    'hbcd',              # ATG - added HBCD - reuse GABA mapper
+                    'hbcd',              # ATG - added HBCD  - reuse GABA mapper
+                    'hbcd1',             # ATG - added HBCD1 - reuse GABA mapper
+                    'hbcd2',             # ATG - added HBCD2 - reuse GABA mapper
                     'probe-p-mega_rml',  # MM - added for Calgary MEGA-PRESS sequence
                     'repress7'           # MM - added for old CUBRIC data
                 ):

tests/test_ge_pfile.py

@@ -12,7 +12,7 @@
 
 from .io_for_tests import read_nifti_mrs
 from .io_for_tests import read_nifti_mrs_with_hdr
-
+from nifti_mrs.nifti_mrs import NIFTI_MRS
 
 # Data paths
 ge_path = Path(__file__).parent / 'spec2nii_test_data' / 'ge'
@@ -32,6 +32,9 @@
 mm_press_noid = ge_path / 'pFiles' / 'PRESS' / 'sub-01_ses-01_acq-press_svs_noID.7'
 mm_slaser = ge_path / 'pFiles' / 'sLASER' / 'sub-01_ses-01_acq-slaser_svs_noID.7'
 
+# HBCD / ISTHMUS datasets
+hbcd2_path = ge_path / 'pFiles' / 'hbcd' / 'P31744.7'
+
 
 def test_svs(tmp_path):
 
@@ -322,3 +325,33 @@ def test_mm_slaser(tmp_path):
     assert img_ref.shape[:5] == (1, 1, 1, 4096, 32)
     assert not hdr_ext_ref['WaterSuppressed']
     assert hdr_ext_ref['dim_5'] == 'DIM_COIL'
+
+
+def test_hbcd_isthmus(tmp_path):
+    subprocess.run([
+        'spec2nii', 'ge',
+        '-f', 'hbcd',
+        '-o', tmp_path,
+        '-j',
+        hbcd2_path])
+
+    assert (tmp_path / 'hbcd_edited.nii.gz').is_file()
+    assert (tmp_path / 'hbcd_ref_edited.nii.gz').is_file()
+    assert (tmp_path / 'hbcd_ref_short_te.nii.gz').is_file()
+    assert (tmp_path / 'hbcd_short_te.nii.gz').is_file()
+
+    img = NIFTI_MRS(tmp_path / 'hbcd_edited.nii.gz')
+    assert img.shape == (1, 1, 1, 2048, 56, 8, 4)
+    assert img.dim_tags == ['DIM_DYN', 'DIM_COIL', 'DIM_EDIT']
+
+    img = NIFTI_MRS(tmp_path / 'hbcd_ref_edited.nii.gz')
+    assert img.shape == (1, 1, 1, 2048, 4, 8)
+    assert img.dim_tags == ['DIM_DYN', 'DIM_COIL', None]
+
+    img = NIFTI_MRS(tmp_path / 'hbcd_ref_short_te.nii.gz')
+    assert img.shape == (1, 1, 1, 2048, 4, 8)
+    assert img.dim_tags == ['DIM_DYN', 'DIM_COIL', None]
+
+    img = NIFTI_MRS(tmp_path / 'hbcd_short_te.nii.gz')
+    assert img.shape == (1, 1, 1, 2048, 32, 8)
+    assert img.dim_tags == ['DIM_DYN', 'DIM_COIL', None]