testing skeleton for tsnr

Author: Shoshana Berleant

nipype/algorithms/tests/test_tsnr.py

@@ -1,86 +1,49 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 import nipype
-from nipype.testing import assert_equal, assert_true, assert_false, skipif
-from nipype.algorithms.compcor import CompCor, TCompCor, ACompCor
+from nipype.testing import assert_equal, assert_true, skipif, utils
+from nipype.algorithms.misc import TSNR
 
 import unittest
 import mock
 import nibabel as nb
 import numpy as np
 import os
 
-class TestCompCor(unittest.TestCase):
+class TestTSNR(unittest.TestCase):
     ''' Note: Tests currently do a poor job of testing functionality '''
-
-    functionalnii = 'compcorfunc.nii'
-    masknii = 'compcormask.nii'
-    components_file = None
+    '''
+    in_file = InputMultiPath(File(exists=True), mandatory=True,
+    regress_poly = traits.Range(low=1, desc='Remove polynomials')
+    '''
+    in_file_name = 'tsnrinfile.nii'
 
     def setUp(self):
         # setup
-        noise = np.fromfunction(self.fake_noise_fun, self.fake_data.shape)
-        self.realigned_file = self.make_toy(self.fake_data + noise,
-                                            self.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 = self.make_toy(mask, self.masknii)
-
-        ccresult = self.run_cc(CompCor(realigned_file=self.realigned_file,
-                               mask_file=mask_file))
-
-        accresult = self.run_cc(ACompCor(realigned_file=self.realigned_file,
-                             mask_file=mask_file,
-                             components_file='acc_components_file'))
-
-        assert_equal(os.path.getsize(ccresult.outputs.components_file),
-                     os.path.getsize(accresult.outputs.components_file))
-
-    def test_tcompcor(self):
-        ccinterface = TCompCor(realigned_file=self.realigned_file)
-        self.run_cc(ccinterface)
+        utils.save_toy_nii(self.fake_data, self.in_file_name)
 
-    def run_cc(self, ccinterface):
+    def test_tsnr(self):
+        # setup
         # run
-        ccresult = ccinterface.run()
-
+        tsnrresult = TSNR(in_file=self.in_file_name, regress_poly=1)
         # assert
-        expected_file = ccinterface._list_outputs()['components_file']
-        assert_equal(ccresult.outputs.components_file, expected_file)
-        assert_true(os.path.exists(expected_file))
-        assert_true(os.path.getsize(expected_file) > 0)
-        assert_equal(ccinterface.inputs.num_components, 6)
-
-        return ccresult
+        # cleanup
 
     def tearDown(self):
         # remove temporary nifti files
         try:
-            os.remove(self.functionalnii)
-            os.remove(self.components_file)
-            os.remove(self.masknii)
+            os.remove(self.in_file_name)
         except (OSError, TypeError) as e:
             print(e)
 
-    def make_toy(self, ndarray, filename):
-        toy = nb.Nifti1Image(ndarray, np.eye(4))
-        nb.nifti1.save(toy, filename)
-        return filename
-
-    def fake_noise_fun(self, i, j, l, m):
-        return m*i + l - j
-
-    fake_data = np.array([[[[8, 5, 3, 8, 0],
-                            [6, 7, 4, 7, 1]],
+    fake_data = np.array([[[[2, 4, 3, 9, 1],
+                            [3, 6, 4, 7, 4]],
 
-                           [[7, 9, 1, 6, 5],
-                            [0, 7, 4, 7, 7]]],
+                           [[8, 3, 4, 6, 2],
+                            [4, 0, 4, 4, 2]]],
 
-                          [[[2, 4, 5, 7, 0],
-                            [1, 7, 0, 5, 4]],
+                          [[[9, 7, 5, 5, 7],
+                            [7, 8, 4, 8, 4]],
 
-                           [[7, 3, 9, 0, 4],
-                            [9, 4, 1, 5, 0]]]])
+                           [[0, 4, 7, 1, 7],
+                            [6, 8, 8, 8, 7]]]])