Add support for .txt files exported by older versions of jMRUI (#133)

* Add support for .txt files exported by older versions of jMRUI Expanded 'signal' regular expression to include syntax from earlier jMRUI versions (namely, 'Signal number: ' rather than 'Signal') * Add test case * Update changelog --------- Co-authored-by: wtclarke <[email protected]>
wtclarke · Mar 26, 2024 · 306c039 · 306c039
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,7 +2,8 @@ This document contains the Spec2nii release history in reverse chronological ord
 
 0.7.4 (WIP)
 ---------------------------------
-- Refinements and improvements to the GE SVS pipeline from Mark Mikkelsen
+- Refinements and improvements to the GE SVS pipeline from Mark Mikkelsen.
+- Add support for older jMRUI text formats which have a slightly different syntax. With thanks to Donnie Cameron.
 
 0.7.3 (Tuesday 12th March 2024)
 -------------------------------

diff --git a/spec2nii/jmrui.py b/spec2nii/jmrui.py
@@ -246,7 +246,7 @@ def readjMRUItxt(filename):
         Header information
 
     """
-    signalRe = re.compile(r'Signal (\d{1,}) out of (\d{1,}) in file')
+    signalRe = re.compile(r'Signal (?:number: |)(\d{1,}) out of (\d{1,}) in file')
     headerRe = re.compile(r'(\w*):(.*)')
     header = {}
     data   = []

diff --git a/tests/spec2nii_test_data b/tests/spec2nii_test_data
diff --git a/tests/test_jmrui.py b/tests/test_jmrui.py
@@ -16,7 +16,8 @@
 testdata = {'fida_single': file_path / 'spec2nii_test_data/jmrui/metab_jmrui.txt',
             'txt_multi': file_path / 'spec2nii_test_data/jmrui/basis_woTMS.txt',
             'mrui_single': file_path / 'spec2nii_test_data/jmrui/press2.mrui',
-            'mrui_multi': file_path / 'spec2nii_test_data/jmrui/ALLSIG.mrui'}
+            'mrui_multi': file_path / 'spec2nii_test_data/jmrui/ALLSIG.mrui',
+            'txt_old': file_path / 'spec2nii_test_data/jmrui/P31rest_proc_jmrui.txt'}
 
 
 @pytest.fixture
@@ -106,3 +107,22 @@ def test_jmrui_multi_mrui(affine_file, tmp_path):
     assert converted.shape == (1, 1, 1, 2048, 28)
     assert np.iscomplexobj(converted.dataobj)
     assert np.allclose(np.loadtxt(affine_file), converted.affine)
+
+
+def test_jmrui_old(affine_file, tmp_path):
+    """Test the 'jmrui' txt old format with different # signal syntax.
+    Namely, 'Signal number: ' rather than 'Signal')
+    """
+    # Run spec2nii on text
+    subprocess.call(['spec2nii', 'jmrui',
+                     '-f', 'txt_old',
+                     '-o', str(tmp_path),
+                     '-a', affine_file,
+                     '-j', testdata['txt_old']])
+
+    # Load the new nifti file
+    converted = nib.load(tmp_path / 'txt_old.nii.gz')
+
+    assert converted.shape == (1, 1, 1, 2048)
+    assert np.iscomplexobj(converted.dataobj)
+    assert np.allclose(np.loadtxt(affine_file), converted.affine)