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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
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#
# See COPYING file distributed along with the PyMVPA package for the
# copyright and license terms.
#
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"""Collection of the known atlases"""
import os
from mvpa2.atlases.base import *
from mvpa2.atlases.fsl import *
KNOWN_ATLAS_FAMILIES = {
'pymvpa': (["talairach", "talairach-dist"],
r"/usr/share/rumba/atlases/data/%(name)s_atlas.xml"),
'fsl': (["HarvardOxford-Cortical", "HarvardOxford-Subcortical",
"JHU-tracts", "Juelich", "MNI", "Thalamus"],
r"/usr/share/fsl/data/atlases/%(name)s.xml")
# XXX make use of FSLDIR
}
# map to go from the name to the path
KNOWN_ATLASES = dict(reduce(lambda x,y:x+[(yy,y[1]) for yy in y[0]],
KNOWN_ATLAS_FAMILIES.values(), []))
def Atlas(filename=None, name=None, *args, **kwargs):
"""A convinience factory for the atlases
"""
if filename is None:
if name is None:
raise ValueError, \
"Please provide either path or name of the atlas to be used"
atlaspath = KNOWN_ATLASES[name]
filename = atlaspath % ( {'name': name} )
if not os.path.exists(filename):
raise IOError, \
"File %s for atlas %s was not found" % (filename, name)
else:
if name is not None:
raise ValueError, "Provide only filename or name"
try:
# Just to guestimate what atlas that is
tempAtlas = XMLBasedAtlas(filename=filename, load_maps=False) #, *args, **kwargs)
version = tempAtlas.version
atlas_source = None
for cls in [PyMVPAAtlas, FSLAtlas]:
if cls._check_version(version):
atlas_source = cls.source
break
if atlas_source is None:
if __debug__: debug('ATL_', "Unknown atlas " + filename)
return tempAtlas
atlasTypes = {
'PyMVPA': {"Label" : LabelsAtlas,
"Reference": ReferencesAtlas},
'FSL': {"Label" : FSLLabelsAtlas,
"Probabalistic": FSLProbabilisticAtlas}
}[atlas_source]
atlasType = tempAtlas.header.type.text
if atlasTypes.has_key(atlasType):
if __debug__: debug('ATL_', "Creating %s Atlas" % atlasType)
return atlasTypes[atlasType](filename=filename, *args, **kwargs)
#return ReferencesAtlas(filename)
else:
printdebug("Unknown %s type '%s' of atlas in %s." " Known are %s" %
(atlas_source, atlasType, filename,
atlasTypes.keys()), 2)
return tempAtlas
except XMLAtlasException, e:
print "File %s is not a valid XML based atlas due to %s" \
% (filename, `e`)
raise e
if __name__ == '__main__':
from mvpa2.base import verbose
verbose.level = 10
for name in [
#'data/talairach_atlas.xml',
'/usr/share/fsl/data/atlases/HarvardOxford-Cortical.xml',
'/usr/share/fsl/data/atlases/HarvardOxford-Subcortical.xml'
]:
atlas = Atlas(name)
#print isinstance(atlas.atlas, objectify.ObjectifiedElement)
#print atlas.header.images.imagefile.get('offset')
#print atlas.label_voxel( (0, -7, 20) )
#print atlas[ 0, 0, 0 ]
print atlas[ -63, -12, 22 ]
#print atlas[ 0, -7, 20, [1,2,3] ]
#print atlas[ (0, -7, 20), 1:2 ]
#print atlas[ (0, -7, 20) ]
#print atlas[ (0, -7, 20), : ]
# print atlas.get_labels(0)
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