fix up test (e.g. pep8)

Author: Shoshana Berleant

nipype/workflows/rsfmri/fsl/tests/test_resting.py

@@ -1,23 +1,21 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 
-from .....testing import (assert_equal, assert_true, assert_almost_equal,
-                          skipif, utils)
-from .....interfaces import fsl, IdentityInterface, utility
-from .....pipeline.engine import Node, Workflow
-
-from ..resting import create_resting_preproc
-
 import unittest
-import mock
-from mock import MagicMock
-import nibabel as nb
-import numpy as np
 import os
 import tempfile
 import shutil
 
-all_fields = ['func', 'in_file', 'slice_time_corrected_file', 'stddev_file',
+import mock
+import numpy as np
+
+from .....testing import (assert_equal, assert_true, utils)
+from .....interfaces import IdentityInterface
+from .....pipeline.engine import Node, Workflow
+
+from ..resting import create_resting_preproc
+
+ALL_FIELDS = ['func', 'in_file', 'slice_time_corrected_file', 'stddev_file',
               'out_stat', 'thresh', 'num_noise_components', 'detrended_file',
               'design_file', 'highpass_sigma', 'lowpass_sigma', 'out_file',
               'noise_mask_file', 'filtered_file']
@@ -29,16 +27,16 @@ def stub_node_factory(*args, **kwargs):
     if name == 'compcor':
         return Node(*args, **kwargs)
     else: # replace with an IdentityInterface
-        return Node(IdentityInterface(fields=all_fields),
+        return Node(IdentityInterface(fields=ALL_FIELDS),
                     name=name)
 
 def stub_wf(*args, **kwargs):
-    wf = Workflow(name='realigner')
+    wflow = Workflow(name='realigner')
     inputnode = Node(IdentityInterface(fields=['func']), name='inputspec')
     outputnode = Node(interface=IdentityInterface(fields=['realigned_file']),
                       name='outputspec')
-    wf.connect(inputnode, 'func', outputnode, 'realigned_file')
-    return wf
+    wflow.connect(inputnode, 'func', outputnode, 'realigned_file')
+    return wflow
 
 class TestResting(unittest.TestCase):
 
@@ -66,23 +64,23 @@ def setUp(self):
         mask = np.zeros(self.fake_data.shape[:3])
         for i in range(mask.shape[0]):
             for j in range(mask.shape[1]):
-                if i==j:
-                    mask[i,j] = 1
+                if i == j:
+                    mask[i, j] = 1
         utils.save_toy_nii(mask, self.in_filenames['mask_file'])
 
     @mock.patch('nipype.workflows.rsfmri.fsl.resting.create_realign_flow',
                 side_effect=stub_wf)
     @mock.patch('nipype.pipeline.engine.Node', side_effect=stub_node_factory)
-    def test_create_resting_preproc(self, mock_Node, mock_realign_wf):
-        wf = create_resting_preproc(base_dir=os.getcwd())
+    def test_create_resting_preproc(self, mock_node, mock_realign_wf):
+        wflow = create_resting_preproc(base_dir=os.getcwd())
 
-        wf.inputs.inputspec.num_noise_components = self.num_noise_components
-        mask_in = wf.get_node('threshold').inputs
+        wflow.inputs.inputspec.num_noise_components = self.num_noise_components
+        mask_in = wflow.get_node('threshold').inputs
         mask_in.out_file = self.in_filenames['mask_file']
-        func_in = wf.get_node('slicetimer').inputs
+        func_in = wflow.get_node('slicetimer').inputs
         func_in.slice_time_corrected_file = self.in_filenames['realigned_file']
 
-        wf.run()
+        wflow.run()
 
         # assert
         expected_file = os.path.abspath(self.out_filenames['components_file'])
@@ -91,7 +89,7 @@ def test_create_resting_preproc(self, mock_Node, mock_realign_wf):
             num_got_components = len(components_data)
             assert_true(num_got_components == self.num_noise_components
                         or num_got_components == self.fake_data.shape[3])
-            first_two = [row[:2] for row in components_data]
+            first_two = [row[:2] for row in components_data[1:]]
             assert_equal(first_two, [['-0.5172356654', '-0.6973053243'],
                                      ['0.2574722644', '0.1645270737'],
                                      ['-0.0806469590', '0.5156853779'],