enable extra_regressors (needed by rsfmri_surface_vol...)

Author: Shoshana Berleant

nipype/algorithms/compcor.py

@@ -23,6 +23,8 @@ class CompCorInputSpec(BaseInterfaceInputSpec):
                                    'pre-component extraction')
     regress_poly_degree = traits.Range(low=1, default=1, usedefault=True,
                                        desc='the degree polynomial to use')
+    extra_regressors = File(exists=True, mandatory=False,
+                            desc='additional regressors to add')
 
 class CompCorOutputSpec(TraitedSpec):
     components_file = File(exists=True,
@@ -75,6 +77,10 @@ def _run_interface(self, runtime):
         # principal components using a singular value decomposition."
         u, _, _ = linalg.svd(M, full_matrices=False)
         components = u[:, :self.inputs.num_components]
+        if self.inputs.extra_regressors:
+            components = self._add_extras(components,
+                                          self.inputs.extra_regressors)
+
         components_file = os.path.join(os.getcwd(), self.inputs.components_file)
         np.savetxt(components_file, components, fmt="%.10f")
         return runtime
@@ -92,6 +98,10 @@ def _compute_tSTD(self, M, x):
         stdM[np.isinf(stdM)] = x
         return stdM
 
+    def _add_extras(self, components, extra_regressors):
+            regressors = np.genfromtxt(self.inputs.extra_regressors)
+            return np.hstack((components, regressors))
+
 class TCompCor(CompCor):
 
     def _run_interface(self, runtime):

nipype/algorithms/tests/test_compcor.py

@@ -27,31 +27,38 @@ def setUp(self):
         noise = np.fromfunction(self.fake_noise_fun, self.fake_data.shape)
         self.realigned_file = utils.save_toy_nii(self.fake_data + noise,
                                                  self.filenames['functionalnii'])
-
-    def test_compcor(self):
         mask = np.ones(self.fake_data.shape[:3])
         mask[0,0,0] = 0
         mask[0,0,1] = 0
-        mask_file = utils.save_toy_nii(mask, self.filenames['masknii'])
+        self.mask_file = utils.save_toy_nii(mask, self.filenames['masknii'])
 
+    def test_compcor(self):
         expected_components = [['-0.1989607212', '-0.5753813646'],
                                ['0.5692369697', '0.5674945949'],
                                ['-0.6662573243', '0.4675843432'],
                                ['0.4206466244', '-0.3361270124'],
                                ['-0.1246655485', '-0.1235705610']]
 
         ccresult = self.run_cc(CompCor(realigned_file=self.realigned_file,
-                                       mask_file=mask_file),
+                                       mask_file=self.mask_file),
                                expected_components)
 
         accresult = self.run_cc(ACompCor(realigned_file=self.realigned_file,
-                                         mask_file=mask_file,
+                                         mask_file=self.mask_file,
                                          components_file='acc_components_file'),
                                 expected_components)
 
         assert_equal(os.path.getsize(ccresult.outputs.components_file),
                      os.path.getsize(accresult.outputs.components_file))
 
+    @mock.patch('nipype.algorithms.compcor.CompCor._add_extras')
+    def test_compcor_with_extra_regressors(self, mock_add_extras):
+        regressors_file ='regress.txt'
+        open(regressors_file, 'a').close() # make sure file exists
+        CompCor(realigned_file=self.realigned_file, mask_file=self.mask_file,
+                extra_regressors=regressors_file).run()
+        assert_true(mock_add_extras.called)
+
     def test_tcompcor(self):
         ccinterface = TCompCor(realigned_file=self.realigned_file)
         self.run_cc(ccinterface, [['-0.2846272268'], ['0.7115680670'],