BF: Improvements in Philips tag handling.

CHANGELOG.md

@@ -1,9 +1,10 @@
 This document contains the Spec2nii release history in reverse chronological order.
 
-0.7.2 (WIP)
----------------------------------
+0.7.2 (Thursday 7th December 2023)
+----------------------------------
 - SpectralWidth now added to header extension automatically to match bids specification.
 - NIfTI-MRS V0.8 now generated.
+- Better handling of philips spar/sdat tags and singleton dimensions.
 
 0.7.1 (Tuesday 7th November 2023)
 ---------------------------------

spec2nii/Philips/philips.py

@@ -12,6 +12,8 @@
 from spec2nii.nifti_orientation import NIFTIOrient, calc_affine
 from spec2nii import __version__ as spec2nii_ver
 
+default_tag_order = ['DIM_DYN', 'DIM_EDIT', 'DIM_USER_0']
+
 
 def read_sdat_spar_pair(sdat_file, spar_file, shape=None, tags=None, fileout=None, special=None):
     """Read and convert SPAR/SDAT pairs from Philips scanners
@@ -55,9 +57,19 @@ def read_sdat_spar_pair(sdat_file, spar_file, shape=None, tags=None, fileout=Non
     meta = spar_to_nmrs_hdrext(spar_params)
     meta.set_standard_def('OriginalFile', [sdat_file.name])
 
-    for idx, tag in enumerate(tags):
+    # Sort dimension tags
+    # First ensure user defined tags has length of 3.
+    while len(tags) < 3:
+        tags.append(None)
+
+    # Set user defined tags, or the default if the dimension exists
+    # and is larger than 1
+    for idx, (tag, default) in enumerate(zip(tags, default_tag_order)):
+        npdim = idx + 4
         if tag is not None:
             meta.set_dim_info(idx, tag)
+        elif data.ndim > npdim and data.shape[npdim] > 1:
+            meta.set_dim_info(idx, default)
 
     # Orientation
     if spar_params["volume_selection_enable"] == "yes":

spec2nii/spec2nii.py

@@ -108,8 +108,10 @@ def add_common_parameters(subparser):
             "-t", "--tags",
             type=str,
             nargs='+',
-            default=["DIM_DYN", None, None],
-            help="Specify NIfTI MRS tags used for higher (5th-7th) dimensions.")
+            default=[None, None, None],
+            help="Specify NIfTI MRS tags used for higher (5th-7th) dimensions. "
+                 "Defaults to DIM_DYN if more than one spectrum is present. "
+                 "Can be used to create singleton higher dimensions.")
         parser_philips.add_argument(
             "-s", "--shape",
             type=int,

tests/test_philips_sdat_spar.py

@@ -11,12 +11,16 @@
 import numpy as np
 
 from .io_for_tests import read_nifti_mrs
+from nifti_mrs.nifti_mrs import NIFTI_MRS
 
 # Data paths
 philips_path = Path(__file__).parent / 'spec2nii_test_data' / 'philips'
 svs_path_sdat = philips_path / 'P1' / 'SV_PRESS_sh_6_2_raw_act.SDAT'
 svs_path_spar = philips_path / 'P1' / 'SV_PRESS_sh_6_2_raw_act.SPAR'
 
+svs_ma_path_sdat = philips_path / 'spar_multi_avg' / 'multi_avg.sdat'
+svs_ma_path_spar = philips_path / 'spar_multi_avg' / 'multi_avg.spar'
+
 svs_edit_path_sdat = philips_path / 'HERCULES_spar_sdat' / 'HERCULES_Example_noID.sdat'
 svs_edit_path_spar = philips_path / 'HERCULES_spar_sdat' / 'HERCULES_Example_noID.spar'
 
@@ -50,6 +54,66 @@ def test_svs(tmp_path):
     assert hdr_ext['OriginalFile'][0] == svs_path_sdat.name
     assert hdr_ext['SoftwareVersions'] == '5.5.2 ; .5.2 ;'
 
+    # Check no hanging singleton dimension
+    nmrs_obj = NIFTI_MRS(tmp_path / 'svs.nii.gz')
+    assert nmrs_obj.shape == (1, 1, 1, 2048)
+
+    subprocess.check_call([
+        'spec2nii', 'philips',
+        '-t', 'DIM_DYN',
+        '-f', 'svs_singleton',
+        '-o', tmp_path,
+        '-j',
+        str(svs_path_sdat),
+        str(svs_path_spar)])
+
+    img_t = read_nifti_mrs(tmp_path / 'svs_singleton.nii.gz')
+    assert img_t.shape == (1, 1, 1, 2048)
+
+    nmrs_obj = NIFTI_MRS(tmp_path / 'svs_singleton.nii.gz')
+    assert nmrs_obj.shape == (1, 1, 1, 2048, 1)
+
+    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 hdr_ext['dim_5'] == 'DIM_DYN'
+
+
+def test_multiavg_svs(tmp_path):
+
+    subprocess.check_call(['spec2nii', 'philips',
+                           '-f', 'svs',
+                           '-o', tmp_path,
+                           '-j',
+                           str(svs_ma_path_sdat),
+                           str(svs_ma_path_spar)])
+
+    img_t = read_nifti_mrs(tmp_path / 'svs.nii.gz')
+
+    assert img_t.shape == (1, 1, 1, 2048, 10)
+    assert np.iscomplexobj(img_t.dataobj)
+
+    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 hdr_ext['dim_5'] == 'DIM_DYN'
+
+    # Check override tags
+    subprocess.check_call([
+        'spec2nii', 'philips',
+        '-t', 'DIM_USER_0',
+        '-f', 'svs_2',
+        '-o', tmp_path,
+        '-j',
+        str(svs_ma_path_sdat),
+        str(svs_ma_path_spar)])
+
+    img_t = read_nifti_mrs(tmp_path / 'svs_2.nii.gz')
+    assert img_t.shape == (1, 1, 1, 2048, 10)
+
+    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 hdr_ext['dim_5'] == 'DIM_USER_0'
+
 
 def test_svs_edit(tmp_path):