factor out deleting temp files

Author: Shoshana Berleant

nipype/algorithms/tests/test_compcor.py

@@ -14,21 +14,21 @@
 class TestCompCor(unittest.TestCase):
     ''' Note: Tests currently do a poor job of testing functionality '''
 
-    functionalnii = 'compcorfunc.nii'
-    masknii = 'compcormask.nii'
-    components_file = None
+    filenames = {'functionalnii': 'compcorfunc.nii',
+                 'masknii': 'compcormask.nii',
+                 'components_file': None}
 
     def setUp(self):
         # setup
         noise = np.fromfunction(self.fake_noise_fun, self.fake_data.shape)
         self.realigned_file = utils.save_toy_nii(self.fake_data + noise,
-                                                 self.functionalnii)
+                                                 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.masknii)
+        mask_file = utils.save_toy_nii(mask, self.filenames['masknii'])
 
         ccresult = self.run_cc(CompCor(realigned_file=self.realigned_file,
                                mask_file=mask_file))
@@ -58,13 +58,7 @@ def run_cc(self, ccinterface):
         return ccresult
 
     def tearDown(self):
-        # remove temporary nifti files
-        try:
-            os.remove(self.functionalnii)
-            os.remove(self.components_file)
-            os.remove(self.masknii)
-        except (OSError, TypeError) as e:
-            print(e)
+        utils.remove_nii(self.filenames.values())
 
     def fake_noise_fun(self, i, j, l, m):
         return m*i + l - j

nipype/algorithms/tests/test_tsnr.py

@@ -16,11 +16,20 @@ class TestTSNR(unittest.TestCase):
     in_file = InputMultiPath(File(exists=True), mandatory=True,
     regress_poly = traits.Range(low=1, desc='Remove polynomials')
     '''
-    in_file_name = 'tsnrinfile.nii'
+
+    filenames = {
+        'in_file': 'tsnrinfile.nii',
+
+        # default output file names
+        'detrended_file': '/home/ubuntu/nipype/detrend.nii.gz',
+        'mean_file':  '/home/ubuntu/nipype/mean.nii.gz',
+        'stddev_file': '/home/ubuntu/nipype/stdev.nii.gz',
+        'tsnr_file': '/home/ubuntu/nipype/tsnr.nii.gz'
+    }
 
     def setUp(self):
         # setup
-        utils.save_toy_nii(self.fake_data, self.in_file_name)
+        utils.save_toy_nii(self.fake_data, self.filenames['in_file'])
 
     def test_tsnr(self):
         # setup
@@ -30,11 +39,7 @@ def test_tsnr(self):
         # cleanup
 
     def tearDown(self):
-        # remove temporary nifti files
-        try:
-            os.remove(self.in_file_name)
-        except (OSError, TypeError) as e:
-            print(e)
+        utils.remove_nii(self.filenames.values())
 
     fake_data = np.array([[[[2, 4, 3, 9, 1],
                             [3, 6, 4, 7, 4]],

nipype/testing/utils.py

@@ -106,3 +106,11 @@ def save_toy_nii(ndarray, filename):
     toy = nb.Nifti1Image(ndarray, np.eye(4))
     nb.nifti1.save(toy, filename)
     return filename
+
+def remove_nii(filenames):
+    ''' remove temporary nifti files'''
+    for filename in filenames:
+        try:
+            os.remove(filename)
+        except (OSError, TypeError) as e:
+            print(e)