Source Code for Module mvpa.tests.test_searchlight

  1  # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 
  2  # vi: set ft=python sts=4 ts=4 sw=4 et: 
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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 searchlight algorithm""" 
 10   
 11  from mvpa.base import externals 
 12  from mvpa.datasets.masked import MaskedDataset 
 13  from mvpa.measures.searchlight import Searchlight 
 14  from mvpa.datasets.splitters import NFoldSplitter 
 15  from mvpa.algorithms.cvtranserror import CrossValidatedTransferError 
 16  from mvpa.clfs.transerror import TransferError 
 17   
 18  from tests_warehouse import * 
 19  from tests_warehouse_clfs import * 
 20   
 21 -class SearchlightTests(unittest.TestCase): 
 22   
 23 -    def setUp(self): 
 24          self.dataset = datasets['3dlarge'] 
 25   
 26   
 27 -    def testSearchlight(self): 
 28          # compute N-1 cross-validation for each sphere 
 29          transerror = TransferError(sample_clf_lin) 
 30          cv = CrossValidatedTransferError( 
 31                  transerror, 
 32                  NFoldSplitter(cvtype=1)) 
 33          # contruct radius 1 searchlight 
 34          sl = Searchlight(cv, radius=1.0, transformer=N.array, 
 35                           enable_states=['spheresizes', 'raw_results']) 
 36   
 37          # run searchlight 
 38          results = sl(self.dataset) 
 39   
 40          # check for correct number of spheres 
 41          self.failUnless(len(results) == 106) 
 42   
 43          # verify if we can map correctly back 
 44          results_ospace = self.dataset.mapper.reverse(results) 
 45   
 46          # check for chance-level performance across all spheres 
 47          self.failUnless(0.4 < results.mean() < 0.6) 
 48   
 49          # check resonable sphere sizes 
 50          self.failUnless(len(sl.spheresizes) == 106) 
 51          self.failUnless(max(sl.spheresizes) == 7) 
 52          self.failUnless(min(sl.spheresizes) == 4) 
 53   
 54          # check base-class state 
 55          self.failUnlessEqual(len(sl.raw_results), 106) 
 56   
 57   
 58 -    def testPartialSearchlightWithFullReport(self): 
 59          # compute N-1 cross-validation for each sphere 
 60          transerror = TransferError(sample_clf_lin) 
 61          cv = CrossValidatedTransferError( 
 62                  transerror, 
 63                  NFoldSplitter(cvtype=1), 
 64                  combiner=N.array) 
 65          # contruct radius 1 searchlight 
 66          sl = Searchlight(cv, radius=1.0, transformer=N.array, 
 67                           center_ids=[3,50]) 
 68   
 69          # run searchlight 
 70          results = sl(self.dataset) 
 71   
 72          # only two spheres but error for all CV-folds 
 73          self.failUnlessEqual(results.shape, (2, len(self.dataset.uniquechunks))) 
 74   
 75   
 76 -    def testChiSquareSearchlight(self): 
 77          # only do partial to save time 
 78          if not externals.exists('scipy'): 
 79              return 
 80   
 81          from mvpa.misc.stats import chisquare 
 82   
 83          transerror = TransferError(sample_clf_lin) 
 84          cv = CrossValidatedTransferError( 
 85                  transerror, 
 86                  NFoldSplitter(cvtype=1), 
 87                  enable_states=['confusion']) 
 88   
 89   
 90          def getconfusion(data): 
 91              cv(data) 
 92              return chisquare(cv.confusion.matrix)[0] 
 93   
 94          # contruct radius 1 searchlight 
 95          sl = Searchlight(getconfusion, radius=1.0, 
 96                           center_ids=[3,50]) 
 97   
 98          # run searchlight 
 99          results = sl(self.dataset) 
100   
101          self.failUnless(len(results) == 2) 
102   
103   
104   
105 -def suite(): 
106      return unittest.makeSuite(SearchlightTests) 
107   
108   
109  if __name__ == '__main__': 
110      import runner 
111