fix: added few bugfixes and regression tests

Author: oesteban

niworkflows/interfaces/nibabel.py

@@ -1,6 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Nibabel-based interfaces."""
+from pathlib import Path
 import numpy as np
 import nibabel as nb
 from nipype import logging
@@ -98,12 +99,11 @@ class _FourToThreeInputSpec(BaseInterfaceInputSpec):
 
 class _FourToThreeOutputSpec(TraitedSpec):
     out_files = OutputMultiObject(File(exists=True),
-                                     desc='output list of 3d images')
+                                  desc='output list of 3d images')
 
 
 class SplitSeries(SimpleInterface):
-    """Split a 4D dataset along the last dimension
-    into a series of 3D volumes."""
+    """Split a 4D dataset along the last dimension into a series of 3D volumes."""
 
     input_spec = _FourToThreeInputSpec
     output_spec = _FourToThreeOutputSpec
@@ -119,7 +119,8 @@ def _run_interface(self, runtime):
                 self._results['out_files'] = out_file
                 filenii.to_filename(out_file)
                 return runtime
-            raise RuntimeError(f"Input image image is {ndim}D.")
+            raise RuntimeError(
+                f"Input image image is {ndim}D ({'x'.join(['%d' % s for s in filenii.shape])}).")
 
         files_3d = nb.four_to_three(filenii)
         self._results['out_files'] = []
@@ -137,7 +138,8 @@ def _run_interface(self, runtime):
 class _MergeSeriesInputSpec(BaseInterfaceInputSpec):
     in_files = InputMultiObject(File(exists=True, mandatory=True,
                                      desc='input list of 3d images'))
-    allow_4D = traits.Bool(True, usedefault=True, desc='whether 4D images are allowed to be concatenated')
+    allow_4D = traits.Bool(True, usedefault=True,
+                           desc='whether 4D images are allowed to be concatenated')
 
 
 class _MergeSeriesOutputSpec(TraitedSpec):
@@ -153,15 +155,18 @@ class MergeSeries(SimpleInterface):
     def _run_interface(self, runtime):
         nii_list = []
         for f in self.inputs.in_files:
-            filenii = nb.load(f)
-            filenii = nb.squeeze_image(filenii)
-            if filenii.dataobj.ndim == 3:
+            filenii = nb.squeeze_image(nb.load(f))
+            ndim = filenii.dataobj.ndim
+            if ndim == 3:
                 nii_list.append(filenii)
-            elif self.inputs.allow_4D and filenii.dataobj.ndim == 4:
+                continue
+            elif self.inputs.allow_4D and ndim == 4:
                 nii_list += nb.four_to_three(filenii)
+                continue
             else:
                 raise ValueError("Input image has an incorrect number of dimensions"
-                                 f" ({filenii.dataobj.ndim}).")
+                                 f" ({ndim}).")
+
         img_4d = nb.concat_images(nii_list)
         out_file = fname_presuffix(self.inputs.in_files[0], suffix="_merged")
         img_4d.to_filename(out_file)

niworkflows/interfaces/tests/test_nibabel.py

@@ -4,7 +4,7 @@
 import nibabel as nb
 import pytest
 
-from ..nibabel import Binarize, ApplyMask
+from ..nibabel import Binarize, ApplyMask, SplitSeries, MergeSeries
 
 
 def test_Binarize(tmp_path):
@@ -69,3 +69,79 @@ def test_ApplyMask(tmp_path):
         ApplyMask(in_file=str(in_file), in_mask=str(in_mask), threshold=0.4).run()
     with pytest.raises(ValueError):
         ApplyMask(in_file=str(in_file4d), in_mask=str(in_mask), threshold=0.4).run()
+
+
+def test_SplitSeries(tmp_path):
+    """Test 4-to-3 NIfTI split interface."""
+    os.chdir(str(tmp_path))
+
+    # Test the 4D
+    data = np.ones((20, 20, 20, 15), dtype=float)
+    in_file = tmp_path / 'input4D.nii.gz'
+    nb.Nifti1Image(data, np.eye(4), None).to_filename(str(in_file))
+
+    split = SplitSeries(in_file=str(in_file)).run()
+    assert len(split.outputs.out_files) == 15
+
+    # Test the 3D
+    data = np.ones((20, 20, 20), dtype=float)
+    in_file = tmp_path / 'input3D.nii.gz'
+    nb.Nifti1Image(data, np.eye(4), None).to_filename(str(in_file))
+
+    with pytest.raises(RuntimeError):
+        SplitSeries(in_file=str(in_file)).run()
+
+    split = SplitSeries(in_file=str(in_file), accept_3D=True).run()
+    assert isinstance(split.outputs.out_files, str)
+
+    # Test the 3D
+    data = np.ones((20, 20, 20, 1), dtype=float)
+    in_file = tmp_path / 'input3D.nii.gz'
+    nb.Nifti1Image(data, np.eye(4), None).to_filename(str(in_file))
+
+    with pytest.raises(RuntimeError):
+        SplitSeries(in_file=str(in_file)).run()
+
+    split = SplitSeries(in_file=str(in_file), accept_3D=True).run()
+    assert isinstance(split.outputs.out_files, str)
+
+    # Test the 5D
+    data = np.ones((20, 20, 20, 2, 2), dtype=float)
+    in_file = tmp_path / 'input5D.nii.gz'
+    nb.Nifti1Image(data, np.eye(4), None).to_filename(str(in_file))
+
+    with pytest.raises(RuntimeError):
+        SplitSeries(in_file=str(in_file)).run()
+
+    with pytest.raises(RuntimeError):
+        SplitSeries(in_file=str(in_file), accept_3D=True).run()
+
+    # Test splitting ANTs warpfields
+    data = np.ones((20, 20, 20, 1, 3), dtype=float)
+    in_file = tmp_path / 'warpfield.nii.gz'
+    nb.Nifti1Image(data, np.eye(4), None).to_filename(str(in_file))
+
+    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))
+
+    data = np.ones((20, 20, 20), dtype=float)
+    in_file = tmp_path / 'input3D.nii.gz'
+    nb.Nifti1Image(data, np.eye(4), None).to_filename(str(in_file))
+
+    merge = MergeSeries(in_files=[str(in_file)] * 5).run()
+    assert nb.load(merge.outputs.out_file).dataobj.shape == (20, 20, 20, 5)
+
+    in_4D = tmp_path / 'input4D.nii.gz'
+    nb.Nifti1Image(
+        np.ones((20, 20, 20, 4), dtype=float), np.eye(4), None
+    ).to_filename(str(in_4D))
+
+    merge = MergeSeries(in_files=[str(in_file)] + [str(in_4D)]).run()
+    assert nb.load(merge.outputs.out_file).dataobj.shape == (20, 20, 20, 5)
+
+    with pytest.raises(ValueError):
+        MergeSeries(in_files=[str(in_file)] + [str(in_4D)], allow_4D=False).run()