completed rsfmri wf test

Author: Shoshana Berleant

nipype/workflows/rsfmri/fsl/resting.py

@@ -96,7 +96,7 @@ def create_realign_flow(name='realign'):
     return realignflow
 
 
-def create_resting_preproc(name='restpreproc'):
+def create_resting_preproc(name='restpreproc', base_dir=None):
     """Create a "resting" time series preprocessing workflow
 
     The noise removal is based on Behzadi et al. (2007)
@@ -128,7 +128,7 @@ def create_resting_preproc(name='restpreproc'):
 
     """
 
-    restpreproc = pe.Workflow(name=name)
+    restpreproc = pe.Workflow(name=name, base_dir=base_dir)
 
     # Define nodes
     inputnode = pe.Node(interface=util.IdentityInterface(fields=['func',

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

@@ -3,7 +3,7 @@
 
 from .....testing import (assert_equal, assert_true, assert_almost_equal,
                           skipif, utils)
-from .....interfaces import fsl, IdentityInterface
+from .....interfaces import fsl, IdentityInterface, utility
 from .....pipeline.engine import Node, Workflow
 
 from ..resting import create_resting_preproc
@@ -42,39 +42,61 @@ def stub_wf(*args, **kwargs):
 
 class TestResting(unittest.TestCase):
 
-    in_filenames = {}
+    in_filenames = {
+        'realigned_file': 'rsfmrifunc.nii',
+        'mask_file': 'rsfmrimask.nii'
+    }
 
     out_filenames = {
-        'noise_mask_file': '',
-        'filtered_file': ''
+        'components_file': 'restpreproc/compcor/noise_components.txt'
     }
 
+    num_noise_components = 6
+
     def setUp(self):
-        # setup
+        # setup temp folder
         self.orig_dir = os.getcwd()
         self.temp_dir = tempfile.mkdtemp()
         os.chdir(self.temp_dir)
-        self.in_filenames['realigned_file'] = utils.save_toy_nii(self.fake_data, os.path.abspath('rsfmrifunc.nii'))
+        self.in_filenames = {key: os.path.abspath(value)
+                             for key, value in self.in_filenames.items()}
+
+        # create&save input files
+        utils.save_toy_nii(self.fake_data, self.in_filenames['realigned_file'])
         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
-        self.in_filenames['noise_mask_file'] = utils.save_toy_nii(mask, os.path.abspath('rsfmrimask.nii'))
+        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()
+        wf = create_resting_preproc(base_dir=os.getcwd())
 
-        wf.inputs.inputspec.num_noise_components = 6
-        wf.get_node('slicetimer').inputs.slice_time_corrected_file = self.in_filenames['realigned_file']
-        wf.get_node('threshold').inputs.out_file = self.in_filenames['noise_mask_file']
+        wf.inputs.inputspec.num_noise_components = self.num_noise_components
+        mask_in = wf.get_node('threshold').inputs
+        mask_in.out_file = self.in_filenames['mask_file']
+        func_in = wf.get_node('slicetimer').inputs
+        func_in.slice_time_corrected_file = self.in_filenames['realigned_file']
 
         wf.run()
 
         # assert
+        expected_file = os.path.abspath(self.out_filenames['components_file'])
+        with open(expected_file, 'r') as components_file:
+            components_data = [line.split() for line in components_file]
+            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]
+            assert_equal(first_two, [['-0.5172356654', '-0.6973053243'],
+                                     ['0.2574722644', '0.1645270737'],
+                                     ['-0.0806469590', '0.5156853779'],
+                                     ['0.7187176051', '-0.3235820287'],
+                                     ['-0.3783072450', '0.3406749013']])
 
     def tearDown(self):
         os.chdir(self.orig_dir)