Source Code for Module mvpa.atlases.warehouse

  1  # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 
  2  # vi: set ft=python sts=4 ts=4 sw=4 et: 
  3  ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ## 
  4  # 
  5  #   See COPYING file distributed along with the PyMVPA package for the 
  6  #   copyright and license terms. 
  7  # 
  8  ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ## 
  9  """Collection of the known atlases""" 
 10   
 11  import os 
 12   
 13  from mvpa.atlases.base import * 
 14  from mvpa.atlases.fsl import * 
 15   
 16   
 17  KNOWN_ATLAS_FAMILIES = { 
 18      'pymvpa': (["talairach", "talairach-dist"], 
 19                 r"/usr/share/rumba/atlases/data/%(name)s_atlas.xml"), 
 20      'fsl': (["HarvardOxford-Cortical", "HarvardOxford-Subcortical", 
 21               "JHU-tracts", "Juelich", "MNI", "Thalamus"], 
 22              r"/usr/share/fsl/data/atlases/%(name)s.xml") 
 23      # XXX make use of FSLDIR 
 24      } 
 25   
 26  # map to go from the name to the path 
 27  KNOWN_ATLASES = dict(reduce(lambda x,y:x+[(yy,y[1]) for yy in y[0]], 
 28                               KNOWN_ATLAS_FAMILIES.values(), [])) 
 29   
 30   
 31 -def Atlas(filename=None, name=None, *args, **kwargs): 
 32      """A convinience factory for the atlases 
 33      """ 
 34      if filename is None: 
 35          if name is None: 
 36              raise ValueError, \ 
 37                    "Please provide either path or name of the atlas to be used" 
 38          atlaspath = KNOWN_ATLASES[name] 
 39          filename = atlaspath % ( {'name': name} ) 
 40          if not os.path.exists(filename): 
 41              raise IOError, \ 
 42                    "File %s for atlas %s was not found" % (filename, name) 
 43      else: 
 44          if name is not None: 
 45              raise ValueError, "Provide only filename or name" 
 46   
 47      try: 
 48          tempAtlas = XMLBasedAtlas(filename=filename, *args, **kwargs) 
 49          version = tempAtlas.version 
 50          atlas_source = None 
 51          for cls in [PyMVPAAtlas, FSLAtlas]: 
 52              if cls._checkVersion(version): 
 53                  atlas_source = cls.source 
 54                  break 
 55          if atlas_source is None: 
 56              if __debug__: debug('ATL_', "Unknown atlas " + filename) 
 57              return tempAtlas 
 58   
 59          atlasTypes = { 
 60              'PyMVPA': {"Label" : LabelsAtlas, 
 61                         "Reference": ReferencesAtlas}, 
 62              'FSL': {"Label" : FSLLabelsAtlas, 
 63                      "Probabalistic": FSLProbabilisticAtlas} 
 64              }[atlas_source] 
 65          atlasType = tempAtlas.header.type.text 
 66          if atlasTypes.has_key(atlasType): 
 67              if __debug__: debug('ATL_', "Creating %s Atlas" % atlasType) 
 68              return atlasTypes[atlasType](filename=filename, *args, **kwargs) 
 69              #return ReferencesAtlas(filename) 
 70          else: 
 71              printdebug("Unknown %s type '%s' of atlas in %s." " Known are %s" % 
 72                         (atlas_source, atlasType, filename, 
 73                          atlasTypes.keys()), 2) 
 74              return tempAtlas 
 75      except XMLAtlasException, e: 
 76          print "File %s is not a valid XML based atlas due to %s" \ 
 77                % (filename, `e`) 
 78          raise e 
 79   
 80   
 81  if __name__ == '__main__': 
 82      from mvpa.base import verbose 
 83      verbose.level = 10 
 84      for name in [ 
 85          #'data/talairach_atlas.xml', 
 86          '/usr/share/fsl/data/atlases/HarvardOxford-Cortical.xml', 
 87          '/usr/share/fsl/data/atlases/HarvardOxford-Subcortical.xml' 
 88          ]: 
 89          atlas = Atlas(name) 
 90          #print isinstance(atlas.atlas, objectify.ObjectifiedElement) 
 91          #print atlas.header.images.imagefile.get('offset') 
 92          #print atlas.labelVoxel( (0, -7, 20) ) 
 93          #print atlas[ 0, 0, 0 ] 
 94          print atlas[ -63, -12, 22 ] 
 95          #print atlas[ 0, -7, 20, [1,2,3] ] 
 96          #print atlas[ (0, -7, 20), 1:2 ] 
 97          #print atlas[ (0, -7, 20) ] 
 98          #print atlas[ (0, -7, 20), : ] 
 99          #   print atlas.getLabels(0) 
100