Add tests

Author: oesteban

nipype/algorithms/metrics.py

@@ -339,7 +339,8 @@ def _run_interface(self, runtime):
 
         self._labels = labels
         self._ove_rois = results
-        self._vol_rois = np.abs(np.array(volumes1) - np.array(volumes2))
+        self._vol_rois = ((np.array(volumes1) - np.array(volumes2)) /
+                          np.array(volumes1))
 
         self._dice = round(np.sum(weights*results['dice']), 5)
         self._jaccard = round(np.sum(weights*results['jaccard']), 5)

nipype/algorithms/tests/test_normalize_tpms.py

@@ -2,11 +2,6 @@
 # -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-#
-# @Author: oesteban - code@oscaresteban.es
-# @Date:   2014-05-28 17:57:20
-# @Last Modified by:   oesteban
-# @Last Modified time: 2014-05-29 13:43:09
 
 import os
 from shutil import rmtree

nipype/algorithms/tests/test_overlap.py

@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+
+import os
+from shutil import rmtree
+from tempfile import mkdtemp
+
+from nipype.testing import (assert_equal, assert_raises,
+                            assert_almost_equal, example_data)
+
+import numpy as np
+import nibabel as nb
+
+
+def test_overlap():
+    from nipype.algorithms.metrics import Overlap
+
+    def check_close(val1, val2):
+        import numpy.testing as npt
+        return npt.assert_almost_equal(val1, val2, decimal=3)
+
+    tempdir = mkdtemp()
+    in1 = example_data('segmentation0.nii.gz')
+    in2 = example_data('segmentation1.nii.gz')
+
+    os.chdir(tempdir)
+    overlap = Overlap()
+    overlap.inputs.volume1 = in1
+    overlap.inputs.volume2 = in1
+    res = overlap.run()
+    yield check_close, res.outputs.jaccard, 1.0
+    overlap = Overlap()
+    overlap.inputs.volume1 = in1
+    overlap.inputs.volume2 = in2
+    res = overlap.run()
+
+    yield check_close, res.outputs.jaccard, 0.99705
+
+    overlap = Overlap()
+    overlap.inputs.volume1 = in1
+    overlap.inputs.volume2 = in2
+    overlap.inputs.vol_units = 'mm'
+    res = overlap.run()
+
+    yield check_close, res.outputs.jaccard, 0.99705
+    yield (check_close, res.outputs.roi_voldiff,
+           np.array([0.0063086, -0.0025506, 0.0]))
+
+    rmtree(tempdir)