Source Code for Module mvpa.tests.test_atlases

 1  #emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*- 
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 4  # 
 5  #   See COPYING file distributed along with the PyMVPA package for the 
 6  #   copyright and license terms. 
 7  # 
 8  ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ## 
 9  """Unit tests for PyMVPA atlases""" 
10   
11  import unittest 
12   
13  from mvpa.base import externals, warning 
14  if externals.exists('nifti', raiseException=True): 
15      from mvpa.atlases import * 
16  else: 
17      raise RuntimeError, "Don't run me if no nifti is present" 
18   
19 -class AtlasesTests(unittest.TestCase): 
20      """Basic tests for support of atlases such as the ones 
21      shipped with FSL 
22      """ 
23 -    def testTransformations(self): 
24          """TODO""" 
25          pass 
26   
27 -    def testAtlases(self): 
28          """Basic testing of atlases""" 
29   
30          tested = 0 
31          for name in KNOWN_ATLASES.keys(): 
32              #filename = KNOWN_ATLASES[name] % {'name': name} 
33              try: 
34                  atlas = Atlas(name=name) 
35                  tested += 1 
36              except IOError: 
37                  # so we just don't have it 
38                  continue 
39              #print isinstance(atlas.atlas, objectify.ObjectifiedElement) 
40              #print atlas.header.images.imagefile.get('offset') 
41              #print atlas.labelVoxel( (0, -7, 20) ) 
42              #print atlas[ 0, 0, 0 ] 
43              coord = (-63, -12, 22) 
44   
45              # Atlas must have at least 1 level and that one must 
46              # have some labels 
47              self.failUnless(len(atlas.levels_dict[0].labels) > 0) 
48   
49              for res in [ atlas[coord], 
50                           atlas.labelPoint(coord) ]: 
51                  self.failUnless(res.get('coord_queried', None) == coord, 
52                                  '%s: Comparison failed. Got %s and %s' 
53                                  % (name, res.get('coord_queried', None), coord)) 
54                  self.failUnless('labels' in res) 
55                  # all atlases so far are based on voxels 
56                  self.failUnless('voxel_queried' in res) 
57   
58              # test explicit level specification via slice, although bogus here 
59              # XXX levels in queries should be deprecated -- too much of 
60              # performance hit 
61              res0 = atlas[coord, range(atlas.Nlevels)] 
62              self.failUnless(res0 == res) 
63   
64              #print atlas[ 0, -7, 20, [1,2,3] ] 
65              #print atlas[ (0, -7, 20), 1:2 ] 
66              #print atlas[ (0, -7, 20) ] 
67              #print atlas[ (0, -7, 20), : ] 
68              #   print atlas.getLabels(0) 
69          if not tested: 
70              warning("No atlases were found -- thus no testing was done") 
71   
72 -def suite(): 
73      return unittest.makeSuite(AtlasesTests) 
74   
75   
76  if __name__ == '__main__': 
77      import runner 
78