fix: squeeze image with np.squeeze / change input name for consistency

nipreps · Apr 8, 2020 · 9446d47 · 9446d47
1 parent 03ebb6d
commit 9446d47
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Showing 2 changed files with 12 additions and 6 deletions.
diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
@@ -94,7 +94,7 @@ def _run_interface(self, runtime):
 
 class _FourToThreeInputSpec(BaseInterfaceInputSpec):
     in_file = File(exists=True, mandatory=True, desc='input 4d image')
-    accept_3D = traits.Bool(False, usedefault=True, desc='do not fail if a 3D volume is passed in')
+    allow_3D = traits.Bool(False, usedefault=True, desc='do not fail if a 3D volume is passed in')
 
 
 class _FourToThreeOutputSpec(TraitedSpec):
@@ -110,17 +110,22 @@ class SplitSeries(SimpleInterface):
 
     def _run_interface(self, runtime):
         filenii = nb.squeeze_image(nb.load(self.inputs.in_file))
+        filenii = filenii.__class__(
+            np.squeeze(filenii.dataobj), filenii.affine, filenii.header
+        )
         ndim = filenii.dataobj.ndim
         if ndim != 4:
-            if self.inputs.accept_3D and ndim == 3:
+            if self.inputs.allow_3D and ndim == 3:
                 out_file = str(
                     Path(fname_presuffix(self.inputs.in_file, suffix=f"_idx-000")).absolute()
                 )
                 self._results['out_files'] = out_file
                 filenii.to_filename(out_file)
                 return runtime
             raise RuntimeError(
-                f"Input image image is {ndim}D ({'x'.join(['%d' % s for s in filenii.shape])}).")
+                f"Input image <{self.inputs.in_file}> is {ndim}D "
+                f"({'x'.join(['%d' % s for s in filenii.shape])})."
+            )
 
         files_3d = nb.four_to_three(filenii)
         self._results['out_files'] = []

diff --git a/niworkflows/interfaces/tests/test_nibabel.py b/niworkflows/interfaces/tests/test_nibabel.py
@@ -91,7 +91,7 @@ def test_SplitSeries(tmp_path):
     with pytest.raises(RuntimeError):
         SplitSeries(in_file=str(in_file)).run()
 
-    split = SplitSeries(in_file=str(in_file), accept_3D=True).run()
+    split = SplitSeries(in_file=str(in_file), allow_3D=True).run()
     assert isinstance(split.outputs.out_files, str)
 
     # Test the 3D
@@ -102,7 +102,7 @@ def test_SplitSeries(tmp_path):
     with pytest.raises(RuntimeError):
         SplitSeries(in_file=str(in_file)).run()
 
-    split = SplitSeries(in_file=str(in_file), accept_3D=True).run()
+    split = SplitSeries(in_file=str(in_file), allow_3D=True).run()
     assert isinstance(split.outputs.out_files, str)
 
     # Test the 5D
@@ -114,7 +114,7 @@ def test_SplitSeries(tmp_path):
         SplitSeries(in_file=str(in_file)).run()
 
     with pytest.raises(RuntimeError):
-        SplitSeries(in_file=str(in_file), accept_3D=True).run()
+        SplitSeries(in_file=str(in_file), allow_3D=True).run()
 
     # Test splitting ANTs warpfields
     data = np.ones((20, 20, 20, 1, 3), dtype=float)
@@ -124,6 +124,7 @@ def test_SplitSeries(tmp_path):
     split = SplitSeries(in_file=str(in_file)).run()
     assert len(split.outputs.out_files) == 3
 
+
 def test_MergeSeries(tmp_path):
     """Test 3-to-4 NIfTI concatenation interface."""
     os.chdir(str(tmp_path))