use abs paths; +appropriate way to test this

Author: Shoshana Berleant

nipype/interfaces/nilearn.py

@@ -74,6 +74,7 @@ class SignalExtraction(BaseInterface):
     '''
     input_spec = SignalExtractionInputSpec
     output_spec = SignalExtractionOutputSpec
+    _results = {}
 
     def _run_interface(self, runtime):
         maskers = self._process_inputs()
@@ -86,7 +87,8 @@ def _run_interface(self, runtime):
         output = np.vstack((self.inputs.class_labels, region_signals.astype(str)))
 
         # save output
-        np.savetxt(os.path.abspath(self.inputs.out_file), output, fmt=b'%s', delimiter='\t')
+        self._results['out_file'] = os.path.abspath(self.inputs.out_file)
+        np.savetxt(self._results['out_file'], output, fmt=b'%s', delimiter='\t')
         return runtime
 
     def _process_inputs(self):
@@ -137,6 +139,4 @@ def _4d(self, array, affine):
         return nb.Nifti1Image(array[:, :, :, np.newaxis], affine)
 
     def _list_outputs(self):
-        outputs = self._outputs().get()
-        outputs['out_file'] = self.inputs.out_file
-        return outputs
+        return self._results

nipype/interfaces/tests/test_nilearn.py

@@ -10,6 +10,7 @@
 from ...testing import (assert_equal, utils, assert_almost_equal, raises,
                         skipif)
 from .. import nilearn as iface
+from ...pipeline import engine as pe
 
 no_nilearn = True
 try:
@@ -110,6 +111,22 @@ def test_signal_extr_shared(self):
         # run & assert
         self._test_4d_label(wanted, self.fake_4d_label_data)
 
+    @skipif(no_nilearn)
+    def test_signal_extr_traits_valid(self):
+        ''' Test a node using the SignalExtraction interface.
+        Unlike interface.run(), node.run() checks the traits
+        '''
+        # run
+        node = pe.Node(iface.SignalExtraction(in_file=os.path.abspath(self.filenames['in_file']),
+                                              label_files=os.path.abspath(self.filenames['label_files']),
+                                              class_labels=self.labels,
+                                              incl_shared_variance=False),
+                       name='SignalExtraction')
+        node.run()
+
+        # assert
+        # just checking that it passes trait validations
+
     def _test_4d_label(self, wanted, fake_labels, include_global=False, incl_shared_variance=True):
         # set up
         utils.save_toy_nii(fake_labels, self.filenames['4d_label_file'])