Source Code for Module mvpa.tests.test_neighbor

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  5  #   See COPYING file distributed along with the PyMVPA package for the 
  6  #   copyright and license terms. 
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  9  """Unit tests for PyMVPA metrics""" 
 10   
 11   
 12  from mvpa.mappers.metric import * 
 13  from mvpa.clfs.distance import * 
 14  import unittest 
 15  import numpy as N 
 16   
 17 -class MetricTests(unittest.TestCase): 
 18      """Basic tests for metrics: neighbors etc 
 19      """ 
 20   
 21 -    def testDistances(self): 
 22          a = N.array([3,8]) 
 23          b = N.array([6,4]) 
 24          # test distances or yarik recalls unit testing ;) 
 25          self.failUnless( cartesianDistance(a, b) == 5.0 ) 
 26          self.failUnless( manhattenDistance(a, b) == 7 ) 
 27          self.failUnless( absminDistance(a, b) == 4 ) 
 28   
 29   
 30 -    def testDescreteMetric(self): 
 31          """Descrete metrics tests -- elementsizes etc""" 
 32          # who said that we will not use FSL's data 
 33          # with negative dimensions? :-) 
 34          elsize = [-2.5, 1.5] 
 35          distance = 3 
 36   
 37          # use default function 
 38          metric = DescreteMetric(elsize) 
 39   
 40          # simple check 
 41          target = N.array([ [1, 2], [2, 1], [2, 2], [2, 3], [3, 2] ]) 
 42          self.failUnless( (metric.getNeighbors([2, 2], 2.6) == target).all()) 
 43   
 44          # a bit longer one... not sure what for 
 45          for point in metric.getNeighbor([2, 2], distance): 
 46              self.failUnless( cartesianDistance(point, [2,2]) <= distance) 
 47   
 48          # use manhattenDistance function 
 49          metric = DescreteMetric(elsize, manhattenDistance) 
 50          for point in metric.getNeighbor([2, 2], distance): 
 51              self.failUnless( manhattenDistance(point, [2, 2]) <= distance) 
 52   
 53          metric.elementsize = [10, 1.5] 
 54          """We can reassign element size as a whole""" 
 55          self.failUnless((metric.elementsize == [10, 1.5]).all()) 
 56   
 57          try: 
 58              metric.elementsize[1] = 1 
 59              self.fail( 
 60                  msg="We should not be able to reassign parts of elementsize") 
 61          except RuntimeError: 
 62              pass 
 63   
 64          self.failUnless((metric.getNeighbors([2, 2], 2.6) == 
 65                           [t for t in target if t[0]==2]).all()) 
 66          """Check if new elementsize is in effect for getNeighbors""" 
 67   
 68   
 69 -    def testDescreteMetricCompatMask(self): 
 70          """Test ability to provide compatmask 
 71          """ 
 72          # let's play fMRI: 3x3x3.3 mm and 2s TR, but in NIfTI we have it 
 73          # reversed 
 74          esize = [2, 3.3, 3,  3] 
 75          # only the last three axis are spatial ones and compatible in terms 
 76          # of a meaningful distance among them. 
 77          metric = DescreteMetric(esize, compatmask=[0, 1, 1, 1]) 
 78   
 79          # neighbors in compat space will be simply propagated along remaining 
 80          # dimensions (somewhat like a backprojection from the subspace into the 
 81          # original space) 
 82          self.failUnless((metric.getNeighbors([0]*4, 1) == 
 83                          [[-1, 0, 0, 0], [0, 0, 0, 0], [1, 0, 0, 0]]).all()) 
 84          # test different radius in compat and in remaining space 
 85          # in this case usual spatial neighborhood, but no temporal 
 86          self.failUnless((metric.getNeighbors([0]*4, [0, 4, 4, 4]) == 
 87              [[0,-1,0,0],[0,0,-1,0],[0,0,0,-1],[0,0,0,0], 
 88               [0,0,0,1],[0,0,1,0],[0,1,0,0]]).all()) 
 89   
 90          # no spatial but temporal neighborhood 
 91          self.failUnless((metric.getNeighbors([0]*4, [2, 0, 0, 0]) == 
 92              [[-1,0,0,0],[0,0,0,0],[1,0,0,0]]).all()) 
 93   
 94          # check axis scaling in non-compat space 
 95          self.failUnless(len(metric.getNeighbors([0]*4, [7.9, 0, 0, 0])) == 9) 
 96   
 97          # check if we can modify compatmask and still perform fine 
 98          old_filter = metric.filter_coord.copy() 
 99          cm = metric.compatmask 
100          cm[0] = 1 
101          metric.compatmask = cm 
102          self.failUnless((metric.compatmask == [True]*4).all()) 
103          self.failUnless((metric.getNeighbors([0]*4, 3) == 
104                           [[-1,  0,  0,  0], [ 0,  0, -1,  0], [ 0,  0,  0, -1], 
105                            [ 0,  0,  0,  0], [ 0,  0,  0,  1], [ 0,  0,  1,  0], 
106                            [ 1,  0,  0,  0]]).all()) 
107          self.failUnless(N.any(old_filter != metric.filter_coord)) 
108   
109 -    def testGetNeighbors(self): 
110          """Test if generator getNeighbor and method getNeighbors 
111          return the right thing""" 
112   
113          class BM(Metric): 
114              """ Class which overrides only getNeighbor 
115              """ 
116              def getNeighbor(self): 
117                  for n in [4, 5, 6]: yield n 
118   
119          class CM(Metric): 
120              """ Class which overrides only getNeighbor 
121              """ 
122              def getNeighbors(self): 
123                  return [1, 2, 3] 
124   
125          b = BM() 
126          self.failUnless(b.getNeighbors() == [4, 5, 6]) 
127          c = CM() 
128          self.failUnless([ x for x in c.getNeighbor()] == [1, 2, 3]) 
129   
130   
131 -def suite(): 
132      """Create the suite -- pylint shut up""" 
133      return unittest.makeSuite(MetricTests) 
134   
135   
136  if __name__ == '__main__': 
137      import runner 
138