Fix bug in mrs_tools split.

fsl_mrs/scripts/mrs_tools

@@ -256,7 +256,7 @@ def split(args):
     split_name = args.file.with_suffix('').with_suffix('').name
 
     # 2. Merge the files
-    if args.index:
+    if args.index is not None:
         split_1, split_2 = nmrs_tools.split(to_split, args.dim, args.index)
     elif args.indices:
         split_1, split_2 = nmrs_tools.split(to_split, args.dim, args.indices)

fsl_mrs/tests/test_scripts_mrs_tools.py

@@ -7,6 +7,7 @@ Copyright Will Clarke, University of Oxford, 2021'''
 # Imports
 import subprocess
 from pathlib import Path
+import nibabel as nib
 
 # Files
 testsPath = Path(__file__).parent
@@ -99,6 +100,10 @@ def test_split(tmp_path):
 
     assert (tmp_path / 'split_file_1.nii.gz').exists()
     assert (tmp_path / 'split_file_2.nii.gz').exists()
+    f1 = nib.load(tmp_path / 'split_file_1.nii.gz')
+    f2 = nib.load(tmp_path / 'split_file_2.nii.gz')
+    assert f1.shape[5] == 32
+    assert f2.shape[5] == 32
 
     subprocess.check_call(['mrs_tools', 'split',
                            '--dim', 'DIM_DYN',
@@ -108,15 +113,24 @@ def test_split(tmp_path):
 
     assert (tmp_path / 'metab_raw_1.nii.gz').exists()
     assert (tmp_path / 'metab_raw_2.nii.gz').exists()
+    f1 = nib.load(tmp_path / 'metab_raw_1.nii.gz')
+    f2 = nib.load(tmp_path / 'metab_raw_2.nii.gz')
+    assert f1.shape[5] == 32
+    assert f2.shape[5] == 32
 
     subprocess.check_call(['mrs_tools', 'split',
                            '--dim', 'DIM_DYN',
                            '--indices', '31', '34', '40',
+                           '--filename', 'indicies_select',
                            '--output', str(tmp_path),
                            '--file', str(test_data_split)])
 
-    assert (tmp_path / 'metab_raw_1.nii.gz').exists()
-    assert (tmp_path / 'metab_raw_2.nii.gz').exists()
+    assert (tmp_path / 'indicies_select_1.nii.gz').exists()
+    assert (tmp_path / 'indicies_select_2.nii.gz').exists()
+    f1 = nib.load(tmp_path / 'indicies_select_1.nii.gz')
+    f2 = nib.load(tmp_path / 'indicies_select_2.nii.gz')
+    assert f1.shape[5] == 61
+    assert f2.shape[5] == 3
 
 
 # Test reorder option

fsl_mrs/utils/nifti_mrs_tools/split_merge.py

@@ -53,7 +53,7 @@ def split(nmrs, dimension, index_or_indicies):
     # Construct indexing
     if isinstance(index_or_indicies, int):
         if index_or_indicies < 0\
-                or index_or_indicies >= nmrs.shape[dim_index]:
+                or (index_or_indicies + 1) >= nmrs.shape[dim_index]:
             raise ValueError('index_or_indicies must be between 0 and N-1,'
                              f' where N is the size of the specified dimension ({nmrs.shape[dim_index]}).')
         index = np.arange(index_or_indicies + 1, nmrs.shape[dim_index])