changing _format_arg in WarpImageMultiTransform and adding simple tests (mostly copy of doctests)

Author: djarecka

nipype/interfaces/ants/resampling.py

@@ -86,7 +86,7 @@ def _format_arg(self, opt, spec, val):
                         isdefined(self.inputs.invert_affine):
                     affine_counter += 1
                     if affine_counter in self.inputs.invert_affine:
-                        series += ['-i'],
+                        series += ['-i']
                 series += [transformation]
             return ' '.join(series)
         return super(WarpTimeSeriesImageMultiTransform, self)._format_arg(opt, spec, val)
@@ -195,7 +195,7 @@ def _format_arg(self, opt, spec, val):
                         isdefined(self.inputs.invert_affine):
                     affine_counter += 1
                     if affine_counter in self.inputs.invert_affine:
-                        series += '-i',
+                        series += ['-i']
                 series += [transformation]
             return ' '.join(series)
         return super(WarpImageMultiTransform, self)._format_arg(opt, spec, val)

nipype/interfaces/ants/tests/test_resampling.py

@@ -0,0 +1,93 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:                                                                                                                 
+
+from nipype.interfaces.ants import WarpImageMultiTransform, WarpTimeSeriesImageMultiTransform
+import os
+import pytest, pdb
+
+
+@pytest.fixture()
+def change_dir(request):
+   orig_dir = os.getcwd()
+   filepath = os.path.dirname( os.path.realpath( __file__ ) )
+   datadir = os.path.realpath(os.path.join(filepath, '../../../testing/data'))
+   os.chdir(datadir)
+
+   def move2orig():
+      os.chdir(orig_dir)
+
+   request.addfinalizer(move2orig)
+
+
+
+def test_WarpImageMultiTransform(change_dir):
+   wimt = WarpImageMultiTransform()
+   wimt.inputs.input_image = 'diffusion_weighted.nii'
+   wimt.inputs.reference_image = 'functional.nii'
+   wimt.inputs.transformation_series = ['func2anat_coreg_Affine.txt','func2anat_InverseWarp.nii.gz', \
+                                           'dwi2anat_Warp.nii.gz','dwi2anat_coreg_Affine.txt']
+   assert wimt.cmdline == 'WarpImageMultiTransform 3 diffusion_weighted.nii diffusion_weighted_wimt.nii -R functional.nii \
+func2anat_coreg_Affine.txt func2anat_InverseWarp.nii.gz dwi2anat_Warp.nii.gz dwi2anat_coreg_Affine.txt'
+
+
+def test_WarpImageMultiTransform_invaffine_1(change_dir):
+   wimt = WarpImageMultiTransform() 
+   wimt.inputs.input_image = 'diffusion_weighted.nii'
+   wimt.inputs.reference_image = 'functional.nii'
+   wimt.inputs.transformation_series = ['func2anat_coreg_Affine.txt','func2anat_InverseWarp.nii.gz', \
+                                           'dwi2anat_Warp.nii.gz','dwi2anat_coreg_Affine.txt']  
+   wimt.inputs.invert_affine = [1]
+   assert wimt.cmdline == 'WarpImageMultiTransform 3 diffusion_weighted.nii diffusion_weighted_wimt.nii -R functional.nii \
+-i func2anat_coreg_Affine.txt func2anat_InverseWarp.nii.gz dwi2anat_Warp.nii.gz dwi2anat_coreg_Affine.txt'
+
+
+def test_WarpImageMultiTransform_invaffine_2(change_dir):
+   wimt = WarpImageMultiTransform()
+   wimt.inputs.input_image = 'diffusion_weighted.nii'
+   wimt.inputs.reference_image = 'functional.nii'
+   wimt.inputs.transformation_series = ['func2anat_coreg_Affine.txt','func2anat_InverseWarp.nii.gz', \
+                                           'dwi2anat_Warp.nii.gz','dwi2anat_coreg_Affine.txt']
+   wimt.inputs.invert_affine = [2]
+   assert wimt.cmdline == 'WarpImageMultiTransform 3 diffusion_weighted.nii diffusion_weighted_wimt.nii -R functional.nii func2anat_coreg_Affine.txt func2anat_InverseWarp.nii.gz dwi2anat_Warp.nii.gz -i dwi2anat_coreg_Affine.txt'
+
+
+@pytest.mark.xfail(reason="dj: should it fail?")
+def test_WarpImageMultiTransform_invaffine_wrong(change_dir):
+   wimt = WarpImageMultiTransform()
+   wimt.inputs.input_image = 'diffusion_weighted.nii'
+   wimt.inputs.reference_image = 'functional.nii'
+   wimt.inputs.transformation_series = ['func2anat_coreg_Affine.txt','func2anat_InverseWarp.nii.gz', \
+                                           'dwi2anat_Warp.nii.gz','dwi2anat_coreg_Affine.txt']
+   wimt.inputs.invert_affine = [3]
+   with pytest.raises(Exception):
+      assert wimt.cmdline
+
+
+def test_WarpTimeSeriesImageMultiTransform(change_dir):
+   wtsimt = WarpTimeSeriesImageMultiTransform()                                                        
+   wtsimt.inputs.input_image = 'resting.nii'                                                           
+   wtsimt.inputs.reference_image = 'ants_deformed.nii.gz'                                              
+   wtsimt.inputs.transformation_series = ['ants_Warp.nii.gz','ants_Affine.txt']
+   assert wtsimt.cmdline == 'WarpTimeSeriesImageMultiTransform 4 resting.nii resting_wtsimt.nii \
+-R ants_deformed.nii.gz ants_Warp.nii.gz ants_Affine.txt'                                                                                            
+
+
+def test_WarpTimeSeriesImageMultiTransform_invaffine(change_dir):
+   wtsimt = WarpTimeSeriesImageMultiTransform()
+   wtsimt.inputs.input_image = 'resting.nii'
+   wtsimt.inputs.reference_image = 'ants_deformed.nii.gz'
+   wtsimt.inputs.transformation_series = ['ants_Warp.nii.gz','ants_Affine.txt']
+   wtsimt.inputs.invert_affine = [1]
+   assert wtsimt.cmdline == 'WarpTimeSeriesImageMultiTransform 4 resting.nii resting_wtsimt.nii \
+-R ants_deformed.nii.gz ants_Warp.nii.gz -i ants_Affine.txt'
+
+
+@pytest.mark.xfail(reason="dj: should it fail?")
+def test_WarpTimeSeriesImageMultiTransform_invaffine_wrong(change_dir):
+   wtsimt = WarpTimeSeriesImageMultiTransform()
+   wtsimt.inputs.input_image = 'resting.nii'
+   wtsimt.inputs.reference_image = 'ants_deformed.nii.gz'
+   wtsimt.inputs.transformation_series = ['ants_Warp.nii.gz','ants_Affine.txt']
+   wtsimt.inputs.invert_affine = [0]
+   with pytest.raises(Exception):
+      wtsimt.cmdline