add global signal test

Author: Shoshana Berleant

nipype/algorithms/tests/test_stats.py

@@ -42,7 +42,7 @@ def test_signal_extraction(self):
                                label_files=self.filenames['label_files'],
                                class_labels=self.labels).run()
         # assert
-        self.assert_expected_output(self.base_wanted)
+        self.assert_expected_output(self.labels, self.base_wanted)
 
 
     @skipif(no_nilearn)
@@ -65,6 +65,25 @@ def test_signal_extraction_4d(self):
                              [5.19565217391, -3.66304347826, -1.51630434783],
                              [-12.0, 3., 0.5]], self.fake_4d_label_data)
 
+    @skipif(True)
+    @skipif(no_nilearn)
+    def test_signal_extraction_include_global(self):
+        # wanted
+        wanted_global = [[3./8], [-3./8], [1./8], [-7./8], [-9./8]]
+        for i, vals in enumerate(self.base_wanted):
+            wanted_global[i].extend(vals)
+        wanted_labels = ['global']
+        wanted_labels.extend(self.labels)
+
+        # run
+        stats.SignalExtraction(in_file=self.filenames['in_file'],
+                               label_files=self.filenames['label_files'],
+                               class_labels=self.labels,
+                               include_global=True).run()
+
+        # assert
+        self.assert_expected_output(wanted_labels, wanted_global)
+
     def _test_4d_label(self, wanted, fake_labels):
         # setup
         utils.save_toy_nii(fake_labels, self.filenames['4d_label_file'])
@@ -74,19 +93,19 @@ def _test_4d_label(self, wanted, fake_labels):
                                label_files=self.filenames['4d_label_file'],
                                class_labels=self.labels).run()
 
-        self.assert_expected_output(wanted)
+        self.assert_expected_output(self.labels, wanted)
 
-    def assert_expected_output(self, wanted):
+    def assert_expected_output(self, labels, wanted):
         with open(self.filenames['out_file'], 'r') as output:
             got = [line.split() for line in output]
             labels_got = got.pop(0) # remove header
-            assert_equal(labels_got, self.labels)
+            assert_equal(labels_got, labels)
             assert_equal(len(got), self.fake_fmri_data.shape[3],
                          'num rows and num volumes')
             # convert from string to float
             got = [[float(num) for num in row] for row in got]
             for i, time in enumerate(got):
-                assert_equal(len(self.labels), len(time))
+                assert_equal(len(labels), len(time))
                 for j, segment in enumerate(time):
                     assert_almost_equal(segment, wanted[i][j], decimal=1)