remove stuff

Author: Shoshana Berleant

nipype/algorithms/compcor.py

@@ -36,8 +36,6 @@ 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,
@@ -90,10 +88,6 @@ 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
@@ -108,13 +102,8 @@ def _compute_tSTD(self, M, x):
         # set bad values to x
         stdM[stdM == 0] = x
         stdM[np.isnan(stdM)] = 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 TCompCorInputSpec(CompCorInputSpec):
     # and all the fields in CompCorInputSpec
     percentile_threshold = traits.Range(low=0., high=1., value=.02,

nipype/algorithms/tests/test_compcor.py

@@ -5,7 +5,6 @@
 from ..compcor import CompCor, TCompCor, ACompCor
 
 import unittest
-import mock
 import nibabel as nb
 import numpy as np
 import os
@@ -51,14 +50,6 @@ def test_compcor(self):
         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, percentile_threshold=0.75)
         self.run_cc(ccinterface, [['-0.1535587949', '-0.4318584065'],