/usr/share/pyshared/mvpa/atlases/base.py is in python-mvpa 0.4.8-1.
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#
# See COPYING file distributed along with the PyMVPA package for the
# copyright and license terms.
#
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"""Base classes for Anatomy atlases support
TODOs:
======
* major optimization. Now code is sloppy and slow -- plenty of checks etc
Module Organization
===================
mvpa.atlases.base module contains support for various atlases
.. packagetree::
:style: UML
:group Base: BaseAtlas XMLBasedAtlas Label Level LabelsLevel
:group Talairach: PyMVPAAtlas LabelsAtlas ReferencesAtlas
:group Exceptions: XMLAtlasException
"""
from mvpa.base import externals
if externals.exists('lxml', raiseException=True):
from lxml import etree, objectify
from mvpa.base.dochelpers import enhancedDocString
import os, re
import numpy as N
from numpy.linalg import norm
from mvpa.atlases.transformation import SpaceTransformation, Linear
from mvpa.misc.support import reuseAbsolutePath
if externals.exists('nifti', raiseException=True):
from nifti import NiftiImage
from mvpa.base import warning
if __debug__:
from mvpa.base import debug
def checkRange(coord, range):
"""
Check if coordinates are within range (0,0,0) - (range)
Return True on success
"""
# TODO: optimize
if len(coord) != len(range):
raise ValueError("Provided coordinate %s and given range %s" % \
(`coord`, `range`) + \
" have different dimensionality"
)
for c,r in zip(coord, range):
if c<0 or c>=r:
return False
return True
class BaseAtlas(object):
"""Base class for the atlases.
"""
def __init__ (self):
"""
Create an atlas object based on the... XXX
"""
self.__name = "blank" # XXX use or remove
class XMLAtlasException(Exception):
""" Exception to be thrown if smth goes wrong dealing with XML based atlas
"""
def __init__(self, msg=""):
self.__msg = msg
def __repr__(self):
return self.__msg
class XMLBasedAtlas(BaseAtlas):
def __init__(self, filename=None,
resolution=None, image_file=None,
query_voxel=False,
coordT=None, levels=None):
"""
:Parameters:
filename : string
Filename for the xml definition of the atlas
resolution : None or float
Some atlases link to multiple images at different
resolutions. if None -- best resolution is selected
using 0th dimension resolution
image_file : None or str
If None, overrides filename for the used imagefile, so
it could load a custom (re-registered) atlas maps
query_voxel : bool
By default [x,y,z] assumes coordinates in space, but if
query_voxel is True, they are assumed to be voxel coordinates
coordT
Optional transformation to apply first
levels : None or slice or list of int
What levels by default to operate on
"""
BaseAtlas.__init__(self)
self.__version = None
self.__type = None # XXX use or remove
self._image_file = None
self.__atlas = None
self._filename = filename
self._resolution = resolution
self._force_image_file = image_file
self.query_voxel = query_voxel
self.levels = levels
if filename:
self.loadAtlas(filename)
# common sanity checks
if not self._checkVersion(self.version):
raise IOError("Version %s is not recognized to be native to class %s" % \
(self.version, self.__name__))
if not set(['header', 'data']) == set([i.tag for i in self.getchildren()]):
raise IOError("No header or data were defined in %s" % filename)
header = self.header
headerChildrenTags = XMLBasedAtlas._children_tags(header)
if not ('images' in headerChildrenTags) or \
not ('imagefile' in XMLBasedAtlas._children_tags(header.images)):
raise XMLAtlasException("Atlas requires image/imagefile header fields")
# Load and post-process images
self._image = None
self._loadImages()
if self._image is not None:
self._extent = N.abs(N.asanyarray(self._image.extent[0:3]))
self._voxdim = N.asanyarray(self._image.voxdim)
self.relativeToOrigin = True
# Assign transformation to get into voxel coordinates,
# spaceT will be set accordingly
self.setCoordT(coordT)
self._loadData()
def _checkRange(self, c):
""" check and adjust the voxel coordinates"""
# check range
# list(c) for consistent appearance... some times c might be ndarray
if __debug__: debug('ATL__', "Querying for voxel %s" % `list(c)`)
if not checkRange(c, self.extent):
msg = "Coordinates %s are not within the extent %s." \
"Reset to (0,0,0)" % ( `c`, `self.extent` )
if __debug__: debug('ATL_', msg)
# assume that voxel [0,0,0] is blank
c = [0]*3;
return c
@staticmethod
def _checkVersion(version):
"""To be overriden in the derived classes. By default anything is good"""
return True
def _loadImages(self):
"""To be overriden in the derived classes. By default does nothing"""
pass
def _loadData(self):
"""To be overriden in the derived classes. By default does nothing"""
pass
def loadAtlas(self, filename):
if __debug__: debug('ATL_', "Loading atlas definition xml file " + filename)
# Create objectify parser first
parser = etree.XMLParser(remove_blank_text=True)
lookup = objectify.ObjectifyElementClassLookup()
parser.setElementClassLookup(lookup)
try:
self.__atlas = etree.parse(filename, parser).getroot()
except IOError:
raise XMLAtlasException("Failed to load XML file %s" % filename)
@property
def version(self):
if not self.__atlas is None \
and ("version" in self.__atlas.attrib.keys()):
return self.__atlas.get("version")
else:
return None
@staticmethod
def _compare_lists(checkitems, neededitems):
raise RuntimeError, "DEPRECATED _compare_lists"
checkitems.sort()
neededitems.sort()
return (checkitems == neededitems)
@staticmethod
def _children_tags(root):
return [i.tag for i in root.getchildren()]
def __getattr__(self, attr):
"""
Lazy way to provide access to the definitions in the atlas
"""
if not self.__atlas is None:
return getattr(self.__atlas, attr)
else:
raise XMLAtlasException("Atlas in " + self.__name__ + " was not read yet")
def setCoordT(self, coordT):
"""Set coordT transformation.
spaceT needs to be adjusted since we glob those two
transformations together
"""
self._coordT = coordT # lets store for debugging etc
if self._image is not None:
# Combine with the image's qform
coordT = Linear(N.linalg.inv(self._image.qform),
previous=coordT)
self._spaceT = SpaceTransformation(
previous=coordT, toRealSpace=False
)
def labelPoint(self, coord, levels=None):
"""Return labels for the given spatial point at specified levels
Function takes care about first transforming the point into
the voxel space
:Parameters:
coord : tuple
Coordinates of the point (xyz)
levels : None or list of int
At what levels to return the results
"""
coord_ = N.asarray(coord) # or we would alter what should be constant
#if not isinstance(coord, N.numpy):
#c = self.getVolumeCoordinate(coord)
#c = self.spaceT.toVoxelSpace(coord_)
#if self.coordT:
# coord_t = self.coordT[coord_]
#else:
# coord_t = coord_
c = self.spaceT(coord_)
result = self.labelVoxel(c, levels)
result['coord_queried'] = coord
#result['coord_trans'] = coord_t
result['voxel_atlas'] = c
return result
def levelsListing(self):
lkeys = range(self.Nlevels)
return '\n'.join(['%d: ' % k + str(self._levels_dict[k])
for k in lkeys])
def _getLevels(self, levels=None):
"""Helper to provide list of levels to operate on
Depends on given `levels` as well as self.levels
"""
if levels is None:
levels = [ i for i in xrange(self.Nlevels) ]
elif (isinstance(levels, slice)):
# levels are given as a range
if levels.step: step = levels.step
else: step = 1
if levels.start: start = levels.start
else: start = 0
if levels.stop: stop = levels.stop
else: stop = self.Nlevels
levels = [ i for i in xrange(start, stop, step) ]
elif isinstance(levels, list) or isinstance(levels, tuple):
# levels given as list
levels = list(levels)
elif isinstance(levels, int):
levels = [ levels ]
else:
raise TypeError('Given levels "%s" are of unsupported type' % `levels`)
# test given values
levels_dict = self.levels_dict
for level in levels:
if not level in levels_dict:
raise ValueError, \
"Levels %s is not known (out of range?). Known levels are:\n%s" \
% (level, self.levelsListing())
return levels
def __getitem__(self, index):
"""
Accessing the elements via simple indexing. Examples:
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), : ]
"""
if len(index) in [2, 4]:
levels_slice = index[-1]
else:
if self.levels is None:
levels_slice = slice(None,None,None)
else:
levels_slice = self.levels
levels = self._getLevels(levels=levels_slice)
if len(index) in [3, 4]:
# we got coordinates 1 by 1 + may be a level
coord = index[0:3]
elif len(index) in [1, 2]:
coord = index[0]
if isinstance(coord, list) or isinstance(coord, tuple):
if len(coord) != 3:
raise TypeError("Given coordinates must be in 3D")
else:
raise TypeError("Given coordinates must be a list or a tuple")
else:
raise TypeError("Unknown shape of parameters `%s`" % `index`)
if self.query_voxel:
return self.labelVoxel(coord, levels)
else:
return self.labelPoint(coord, levels)
# REDO in some sane fashion so referenceatlas returns levels for the base
def _getLevelsDict(self):
return self._getLevelsDict_virtual()
def _getLevelsDict_virtual(self):
return self._levels_dict
levels_dict = property(fget=_getLevelsDict)
origin = property(fget=lambda self:self._origin)
extent = property(fget=lambda self:self._extent)
voxdim = property(fget=lambda self:self._voxdim)
spaceT = property(fget=lambda self:self._spaceT)
coordT = property(fget=lambda self:self._spaceT,
fset=setCoordT)
class Label(object):
"""Represents a label. Just to bring all relevant information together
"""
def __init__ (self, text, abbr=None, coord=(None, None,None),
count=0, index=0):
"""
:Parameters:
text : basestring
fullname of the label
abbr : basestring
abbreviated name (optional)
coord : tuple of float
coordinates (optional)
count : int
count of those labels in the atlas (optional)
"""
self.__text = text.strip()
if abbr is not None:
abbr = abbr.strip()
self.__abbr = abbr
self.__coord = coord
self.__count = count
self.__index = int(index)
@property
def index(self):
return self.__index
def __repr__(self):
return "Label(%s%s, coord=(%s, %s, %s), count=%s, index=%s)" % \
((self.__text,
(', abbr=%s' % repr(self.__abbr), '')[int(self.__abbr is None)])
+ tuple(self.__coord) + (self.__count, self.__index))
def __str__(self):
return self.__text
@staticmethod
def generateFromXML(Elabel):
kwargs = {}
if Elabel.attrib.has_key('x'):
kwargs['coord'] = ( Elabel.attrib.get('x'),
Elabel.attrib.get('y'),
Elabel.attrib.get('z') )
for l in ('count', 'abbr', 'index'):
if Elabel.attrib.has_key(l):
kwargs[l] = Elabel.attrib.get(l)
return Label(Elabel.text.strip(), **kwargs)
@property
def count(self): return self.__count
@property
def coord(self): return self.__coord
@property
def text(self): return self.__text
@property
def abbr(self):
"""Returns abbreviated version if such is available
"""
if self.__abbr in [None, ""]:
return self.__text
else:
return self.__abbr
class Level(object):
"""Represents a level. Just to bring all relevant information together
"""
def __init__ (self, description):
self.description = description
self._type = "Base"
def __repr__(self):
return "%s Level: %s" % \
(self.levelType, self.description)
def __str__(self):
return self.description
@staticmethod
def generateFromXML(Elevel, levelType=None):
"""
Simple factory of levels
"""
if levelType is None:
if not Elevel.attrib.has_key("type"):
raise XMLAtlasException("Level must have type specified. Level: " + `Elevel`)
levelType = Elevel.get("type")
levelTypes = { 'label': LabelsLevel,
'reference': ReferencesLevel }
if levelTypes.has_key(levelType):
return levelTypes[levelType].generateFromXML(Elevel)
else:
raise XMLAtlasException("Unknown level type " + levelType)
levelType = property(lambda self: self._type)
class LabelsLevel(Level):
"""Level of labels.
XXX extend
"""
def __init__ (self, description, index=None, labels=[]):
Level.__init__(self, description)
self.__index = index
self.__labels = labels
self._type = "Labels"
def __repr__(self):
return Level.__repr__(self) + " [%d] " % \
(self.__index)
@staticmethod
def generateFromXML(Elevel, levelIndex=[0]):
# XXX this is just for label type of level. For distance we need to ...
# we need to assure the right indexing
index = 0
if Elevel.attrib.has_key("index"):
index = int(Elevel.get("index"))
maxindex = max([int(i.get('index')) \
for i in Elevel.label[:]])
labels = [ None for i in xrange(maxindex+1) ]
for label in Elevel.label[:]:
labels[ int(label.get('index')) ] = Label.generateFromXML(label)
levelIndex[0] = max(levelIndex[0], index) + 1 # assign next one
return LabelsLevel(Elevel.get('description'),
index,
labels)
@property
def index(self): return self.__index
@property
def labels(self): return self.__labels
def __getitem__(self, index):
return self.__labels[index]
def find(self, target, unique=True):
"""Return labels descr of which matches the string
:Parameters:
target : str or re._pattern_type
Substring in abbreviation to be searched for, or compiled
regular expression to be searched or matched if anchored.
unique : bool
If True, raise exception if none or more than 1 was found. Return
just a single item if found (not list).
"""
if isinstance(target, re._pattern_type):
res = [l for l in self.__labels if target.search(l.abbr)]
else:
res = [l for l in self.__labels if target in l.abbr]
if unique:
if len(res) != 1:
raise ValueError, "Got %d matches whenever just 1 was " \
"looked for (target was %s)." % (len(res), target)
return res[0]
else:
return res
class ReferencesLevel(Level):
"""Level which carries reference points
"""
def __init__ (self, description, indexes=[]):
Level.__init__(self, description)
self.__indexes = indexes
self._type = "References"
@staticmethod
def generateFromXML(Elevel):
# XXX should probably do the same for the others?
requiredAttrs = ['x', 'y', 'z', 'type', 'description']
if not set(requiredAttrs) == set(Elevel.attrib.keys()):
raise XMLAtlasException("ReferencesLevel has to have " +
"following attributes defined " +
`requiredAttrs`)
indexes = ( int(Elevel.get("x")), int(Elevel.get("y")),
int(Elevel.get("z")) )
return ReferencesLevel(Elevel.get('description'),
indexes)
@property
def indexes(self): return self.__indexes
class PyMVPAAtlas(XMLBasedAtlas):
"""Base class for PyMVPA atlases, such as LabelsAtlas and ReferenceAtlas
"""
source = 'PyMVPA'
def __init__(self, *args, **kwargs):
XMLBasedAtlas.__init__(self, *args, **kwargs)
# sanity checks
header = self.header
headerChildrenTags = XMLBasedAtlas._children_tags(header)
if not ('space' in headerChildrenTags) or \
not ('space-flavor' in headerChildrenTags):
raise XMLAtlasException("PyMVPA Atlas requires specification of" +
" the space in which atlas resides")
self.__space = header.space.text
self.__spaceFlavor = header['space-flavor'].text
__doc__ = enhancedDocString('PyMVPAAtlas', locals(), XMLBasedAtlas)
def _loadImages(self):
# shortcut
imagefile = self.header.images.imagefile
#self.Nlevels = len(self._levels_by_id)
# Set offset if defined in XML file
# XXX: should just take one from the qoffset... now that one is
# defined... this origin might be misleading actually
self._origin = N.array( (0, 0, 0) )
if imagefile.attrib.has_key('offset'):
self._origin = N.array( [int(x) for x in
imagefile.get('offset').split(',')] )
# Load the image file which has labels
if self._force_image_file is not None:
imagefilename = self._force_image_file
else:
imagefilename = imagefile.text
imagefilename = reuseAbsolutePath(self._filename, imagefilename)
try:
self._image = NiftiImage(imagefilename)
except RuntimeError, e:
raise RuntimeError, " Cannot open file %s due to %s" % (imagefilename, e)
self._data = self._image.data
# remove bogus dimensions on top of 4th
if len(self._data.shape[0:-4]) > 0:
bogus_dims = self._data.shape[0:-4]
if max(bogus_dims)>1:
raise RuntimeError, "Atlas %s has more than 4 of non-singular" \
"dimensions" % imagefilename
new_shape = self._data.shape[-4:]
self._data.reshape(new_shape)
#if self._image.extent[3] != self.Nlevels:
# raise XMLAtlasException("Atlas %s has %d levels defined whenever %s has %d volumes" % \
# ( filename, self.Nlevels, imagefilename, self._image.extent[3] ))
def _loadData(self):
# Load levels
self._levels_dict = {}
# preprocess labels for different levels
self._Nlevels = 0
index_incr = 0
for index, child in enumerate(self.data.getchildren()):
if child.tag == 'level':
level = Level.generateFromXML(child)
self._levels_dict[level.description] = level
if hasattr(level, 'index'):
index = level.index
else:
# to avoid collision if some levels do
# have indexes
while index_incr in self._levels_dict:
index_incr += 1
index, index_incr = index_incr, index_incr+1
self._levels_dict[index] = level
else:
raise XMLAtlasException(
"Unknown child '%s' within data" % child.tag)
self._Nlevels += 1
def _getNLevelsVirtual(self):
return self._Nlevels
def _getNLevels(self):
return self._getNLevelsVirtual()
@staticmethod
def _checkVersion(version):
# For compatibility lets support "RUMBA" atlases
return version.startswith("pymvpa-") or version.startswith("rumba-")
space = property(fget=lambda self:self.__space)
spaceFlavor = property(fget=lambda self:self.__spaceFlavor)
Nlevels = property(fget=_getNLevels)
class LabelsAtlas(PyMVPAAtlas):
"""
Atlas which provides labels for the given coordinate
"""
def labelVoxel(self, c, levels=None):
"""
Return labels for the given voxel at specified levels specified by index
"""
levels = self._getLevels(levels=levels)
result = {'voxel_queried' : c}
# check range
c = self._checkRange(c)
resultLevels = []
for level in levels:
if self._levels_dict.has_key(level):
level_ = self._levels_dict[ level ]
else:
raise IndexError(
"Unknown index or description for level %d" % level)
resultIndex = int(self._data[ level_.index, \
c[2], c[1], c[0] ])
resultLevels += [ {'index': level_.index,
'id': level_.description,
'label' : level_[ resultIndex ]} ]
result['labels'] = resultLevels
return result
__doc__ = enhancedDocString('LabelsAtlas', locals(), PyMVPAAtlas)
class ReferencesAtlas(PyMVPAAtlas):
"""
Atlas which provides references to the other atlases.
Example: the atlas which has references to the closest points
(closest Gray, etc) in another atlas.
"""
def __init__(self, distance=0, *args, **kwargs):
"""Initialize `ReferencesAtlas`
"""
PyMVPAAtlas.__init__(self, *args, **kwargs)
# sanity checks
if not ('reference-atlas' in XMLBasedAtlas._children_tags(self.header)):
raise XMLAtlasException(
"ReferencesAtlas must refer to a some other atlas")
referenceAtlasName = self.header["reference-atlas"].text
# uff -- another evil import but we better use the factory method
from mvpa.atlases.warehouse import Atlas
self.__referenceAtlas = Atlas(filename=reuseAbsolutePath(
self._filename, referenceAtlasName))
if self.__referenceAtlas.space != self.space or \
self.__referenceAtlas.spaceFlavor != self.spaceFlavor:
raise XMLAtlasException(
"Reference and original atlases should be in the same space")
self.__referenceLevel = None
self.setDistance(distance)
__doc__ = enhancedDocString('ReferencesAtlas', locals(), PyMVPAAtlas)
# number of levels must be of the referenced atlas due to
# handling of that in __getitem__
#Nlevels = property(fget=lambda self:self.__referenceAtlas.Nlevels)
def _getNLevelsVirtual(self):
return self.__referenceAtlas.Nlevels
def setReferenceLevel(self, level):
"""
Set the level which will be queried
"""
if self._levels_dict.has_key(level):
self.__referenceLevel = self._levels_dict[level]
else:
raise IndexError("Unknown reference level " + `level` +
". Known are " + `self._levels_dict.keys()`)
def labelVoxel(self, c, levels = None):
if self.__referenceLevel is None:
warning("You did not provide what level to use "
"for reference. Assigning 0th level -- '%s'"
% (self._levels_dict[0],))
self.setReferenceLevel(0)
# return self.__referenceAtlas.labelVoxel(c, levels)
c = self._checkRange(c)
# obtain coordinates of the closest voxel
cref = self._data[ self.__referenceLevel.indexes, c[2], c[1], c[0] ]
dist = norm( (cref - c) * self.voxdim )
if __debug__:
debug('ATL__', "Closest referenced point for %s is "
"%s at distance %3.2f" % (`c`, `cref`, dist))
if (self.distance - dist) >= 1e-3: # neglect everything smaller
result = self.__referenceAtlas.labelVoxel(cref, levels)
result['voxel_referenced'] = c
result['distance'] = dist
else:
result = self.__referenceAtlas.labelVoxel(c, levels)
if __debug__:
debug('ATL__', "Closest referenced point is "
"further than desired distance %.2f" % self.distance)
result['voxel_referenced'] = None
result['distance'] = 0
return result
def levelsListing(self):
return self.__referenceAtlas.levelsListing()
def _getLevelsDict_virtual(self):
return self.__referenceAtlas.levels_dict
def setDistance(self, distance):
"""
Set desired maximal distance for the reference
"""
if distance < 0:
raise ValueError("Distance should not be negative. "
" Thus '%f' is not a legal value" % distance)
if __debug__:
debug('ATL__',
"Setting maximal distance for queries to be %d" % distance)
self.__distance = distance
distance = property(fget=lambda self:self.__distance, fset=setDistance)
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