def __init__(self, distance=0, reference_level=None, *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 mvpa2.atlases.warehouse import Atlas
self.__referenceAtlas = Atlas(filename=reuse_absolute_path(
self._filename, referenceAtlasName))
if self.__referenceAtlas.space != self.space or \
self.__referenceAtlas.space_flavor != self.space_flavor:
raise XMLAtlasException(
"Reference and original atlases should be in the same space")
self.__referenceLevel = None # pylint shut up
if reference_level is not None:
self.set_reference_level(reference_level)
self.set_distance(distance)
def __init__(self, distance=0, reference_level=None, *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 mvpa2.atlases.warehouse import Atlas
self.__referenceAtlas = Atlas(
filename=reuse_absolute_path(self._filename, referenceAtlasName))
if self.__referenceAtlas.space != self.space or \
self.__referenceAtlas.space_flavor != self.space_flavor:
raise XMLAtlasException(
"Reference and original atlases should be in the same space")
self.__referenceLevel = None # pylint shut up
if reference_level is not None:
self.set_reference_level(reference_level)
self.set_distance(distance)
def _load_images(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 = np.array( (0, 0, 0) )
if imagefile.attrib.has_key('offset'):
self._origin = np.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 = reuse_absolute_path(self._filename, imagefilename)
try:
self._image = None
for ext in ['', '.nii.gz']:
try:
self._image = nb.load(imagefilename + ext)
break
except Exception, e:
pass
if self._image is None:
raise e
def _load_images(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 = np.array((0, 0, 0))
if imagefile.attrib.has_key('offset'):
self._origin = np.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 = reuse_absolute_path(self._filename, imagefilename)
try:
self._image = None
for ext in ['', '.nii.gz']:
try:
self._image = nb.load(imagefilename + ext)
break
except Exception, e:
pass
if self._image is None:
raise e
def _load_images(self):
resolution = self._resolution
header = self.header
images = header.images
# Load present images
# XXX might be refactored to avoid duplication of
# effort with PyMVPAAtlas
ni_image = None
resolutions = []
if self._force_image_file is None:
imagefile_candidates = [
reuse_absolute_path(self._filename, i.imagefile.text, force=True)
for i in images]
else:
imagefile_candidates = [self._force_image_file]
for imagefilename in imagefile_candidates:
try:
if not os.path.exists(imagefilename):
# try with extension if filename doesn't exist
imagefilename += '.nii.gz'
ni_image_ = nb.load(imagefilename)
except RuntimeError as e:
raise RuntimeError(" Cannot open file " + imagefilename)
resolution_ = ni_image_.header.get_zooms()[0]
if resolution is None:
# select this one if the best
if ni_image is None or \
resolution_ < ni_image.header.get_zooms()[0]:
ni_image = ni_image_
self._image_file = imagefilename
else:
if resolution_ == resolution:
ni_image = ni_image_
self._image_file = imagefilename
break
else:
resolutions += [resolution_]
# TODO: also make use of summaryimagefile may be?
if ni_image is None:
msg = "Could not find an appropriate atlas among %d atlases." \
% len(imagefile_candidates)
if resolution is not None:
msg += " Atlases had resolutions %s" % \
(resolutions,)
raise RuntimeError(msg)
if __debug__:
debug('ATL__', "Loading atlas data from %s" % self._image_file)
self._image = ni_image
self._resolution = ni_image.header.get_zooms()[0]
self._origin = np.abs(ni_image.header.get_qform()[:3,3]) # XXX
self._data = self._image.get_data()
if len(self._data.shape) == 4:
# want to have volume axis first
self._data = np.rollaxis(self._data, -1)
def _load_images(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 = np.array((0, 0, 0))
if 'offset' in imagefile.attrib:
self._origin = np.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 = reuse_absolute_path(self._filename, imagefilename)
try:
self._image = None
for ext in ['', '.nii.gz']:
try:
self._image = nb.load(imagefilename + ext)
break
except Exception as e:
pass
if self._image is None:
raise e
except RuntimeError as e:
raise RuntimeError(" Cannot open file %s due to %s" %
(imagefilename, e))
self._data = self._image.get_data()
# we get the data as x,y,z[,t] but we want to have the time axis first
# if any
if len(self._data.shape) == 4:
self._data = np.rollaxis(self._data, -1)
# 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)
def _load_images(self):
resolution = self._resolution
header = self.header
images = header.images
# Load present images
# XXX might be refactored to avoid duplication of
# effort with PyMVPAAtlas
ni_image = None
resolutions = []
if self._force_image_file is None:
imagefile_candidates = [
reuse_absolute_path(self._filename,
i.imagefile.text,
force=True) for i in images
]
else:
imagefile_candidates = [self._force_image_file]
for imagefilename in imagefile_candidates:
try:
if not os.path.exists(imagefilename):
# try with extension if filename doesn't exist
imagefilename += '.nii.gz'
ni_image_ = nb.load(imagefilename)
except RuntimeError, e:
raise RuntimeError, " Cannot open file " + imagefilename
resolution_ = ni_image_.get_header().get_zooms()[0]
if resolution is None:
# select this one if the best
if ni_image is None or \
resolution_ < ni_image.get_header().get_zooms()[0]:
ni_image = ni_image_
self._image_file = imagefilename
else:
if resolution_ == resolution:
ni_image = ni_image_
self._image_file = imagefilename
break
else:
resolutions += [resolution_]
def _load_images(self):
resolution = self._resolution
header = self.header
images = header.images
# Load present images
# XXX might be refactored to avoid duplication of
# effort with PyMVPAAtlas
ni_image = None
resolutions = []
if self._force_image_file is None:
imagefile_candidates = [
reuse_absolute_path(self._filename, i.imagefile.text, force=True)
for i in images]
else:
imagefile_candidates = [self._force_image_file]
for imagefilename in imagefile_candidates:
try:
if not os.path.exists(imagefilename):
# try with extension if filename doesn't exist
imagefilename += '.nii.gz'
ni_image_ = nb.load(imagefilename)
except RuntimeError, e:
raise RuntimeError, " Cannot open file " + imagefilename
resolution_ = ni_image_.get_header().get_zooms()[0]
if resolution is None:
# select this one if the best
if ni_image is None or \
resolution_ < ni_image.get_header().get_zooms()[0]:
ni_image = ni_image_
self._image_file = imagefilename
else:
if resolution_ == resolution:
ni_image = ni_image_
self._image_file = imagefilename
break
else:
resolutions += [resolution_]
