Add diff to basis tool script.

fsl_mrs/scripts/basis_tools

@@ -101,6 +101,23 @@ def main():
                              help='Output location, can overwrite.')
     scaleparser.set_defaults(func=rescale)
 
+    # Differenceing (add/subtract)
+    diffparser = sp.add_parser(
+        'diff',
+        help='Form difference basis sepctra from two basis spectra.')
+    diffparser.add_argument('file1', type=Path,
+                            help='Basis file one')
+    diffparser.add_argument('file2', type=Path,
+                            help='Basis file two, if subtract file 2 is subtracted from file 1.')
+    diffparser.add_argument('output', type=Path,
+                            help='Output fsl formatted folder, will be created if needed.')
+    diffparser.add_argument('--add_or_sub', type=str,
+                            default='sub',
+                            help="'add' or 'sub'")
+    diffparser.add_argument('--ignore_missing', action="store_true",
+                            help='Ignore missing basis sets in one basis.')
+    diffparser.set_defaults(func=diff)
+
     # Parse command-line arguments
     args = p.parse_args()
 
@@ -188,5 +205,26 @@ def rescale(args):
     basis.save(args.output, overwrite=True)
 
 
+def diff(args):
+    from fsl_mrs.utils import basis_tools
+    from fsl_mrs.utils.mrs_io import read_basis
+
+    basis1 = read_basis(args.file1)
+    basis2 = read_basis(args.file2)
+
+    if args.ignore_missing:
+        missing_action = 'ignore'
+    else:
+        missing_action = 'raise'
+
+    new = basis_tools.difference_basis_sets(
+        basis1,
+        basis2,
+        add_or_subtract=args.add_or_sub,
+        missing_metabs=missing_action)
+
+    new.save(args.output)
+
+
 if __name__ == '__main__':
     main()

fsl_mrs/tests/test_scripts_basis_tools.py

@@ -17,6 +17,8 @@ jmrui = testsPath / 'testdata/mrs_io/basisset_JMRUI'
 lcm = testsPath / 'testdata/mrs_io/basisset_LCModel.BASIS'
 fsl = testsPath / 'testdata/mrs_io/basisset_FSL'
 mac = testsPath / 'testdata/basis_tools/macSeed.json'
+diff1 = testsPath / 'testdata/basis_tools/low_res_off'
+diff2 = testsPath / 'testdata/basis_tools/low_res_on'
 
 
 def test_info():
@@ -87,3 +89,16 @@ def test_rescale(tmp_path):
 
     assert out_loc.is_dir()
     assert (out_loc / 'NAA.json').is_file()
+
+
+def test_diff(tmp_path):
+    out_loc = tmp_path / 'test_basis'
+
+    subprocess.check_call(['basis_tools', 'diff',
+                           '--add_or_sub', 'sub',
+                           str(diff1),
+                           str(diff2),
+                           str(out_loc)])
+
+    assert out_loc.is_dir()
+    assert (out_loc / 'NAA.json').is_file()