def process_surface(self, surface_node, nsprefix):
""" Processing of the surface node
Parameters
----------
surface_node: the lxml node
The XML node network-surface from the meta.xml file
nsprefix: String
The Name Space Prefix for clean iterating
Returns
-------
tmpsurfacecontainer: `ISurfaceContainer` instance to add to the network
"""
from surface_container import SurfaceContainer
# create surface
tmpsurfacecontainer = SurfaceContainer(name = surface_node.attrib['name'], \
src = surface_node.attrib['src'])
tmpsurfacecontainer.set(_lxml_node = surface_node, _lxml_node_prefix = nsprefix, \
is_atlas = False)
# adding label information to the surface container
labelidentification = ''
l_cnt = 0
for tmplabels in surface_node.iterchildren():
if tmplabels.tag == (nsprefix + 'surface-label'):
l_cnt = l_cnt + 1
if l_cnt > 2:
logger.error(
'There are multiple label for one surface container! Please check your meta.xml'
)
continue
lattr = tmplabels.attrib
if lattr.has_key('labelid'):
labelidentification = lattr['labelid']
if lattr.has_key('src'):
tmpsurfacecontainer._add_label(labelid = labelidentification,\
src = lattr['src'])
return tmpsurfacecontainer
def process_atlas(self, surface_node, nsprefix):
""" Processing of the surface node for atlases
Parameters
----------
surface_node: the lxml node
The XML node network-surface from the meta.xml file
nsprefix: String
The Name Space Prefix for clean iterating
Returns
-------
tmpsurfacecontainer: `ISurfaceContainer` instance to add to the network
"""
from surface_container import SurfaceContainer
if not cmp(surface_node.attrib['addatlas'], 'template_atlas_homo_sapiens_01'):
logger.debug('Load the H**o sapiens Template Atlas 01 ...')
from cviewer.resources.atlases.library import get_template_atlas, get_template_atlas_label
atlaspathtofile = get_template_atlas(atlastype = 'homo_sapiens_01')
if os.path.isfile(atlaspathtofile):
logger.debug('Valid Freesurfer Atlas file. Add it as SurfaceContainer...')
tmpsurfacecontaineratlas = SurfaceContainer(name = 'Freesurfer Atlas', \
src = atlaspathtofile)
tmpsurfacecontaineratlas.set(_lxml_node = surface_node, _lxml_node_prefix = nsprefix, \
is_atlas = True)
# add the freesurfer label file
labelidentification = ''
nolabelid = False
l_cnt = 0
for tmplabels in surface_node.iterchildren():
if tmplabels.tag == (nsprefix+'surface-label'):
l_cnt = l_cnt + 1
if l_cnt > 2:
logger.error('There are multiple label for one surface container! Please check your meta.xml')
nolabelid = True
continue
lattr = tmplabels.attrib
if lattr.has_key('labelid'):
labelidentification = lattr['labelid']
if not nolabelid:
logger.debug('Using LabelID: %s' % labelidentification)
labelfile = get_template_atlas_label(atlastype = 'homo_sapiens_01')
tmpsurfacecontaineratlas._add_label(labelid = labelidentification, \
src = labelfile)
return tmpsurfacecontaineratlas
else:
logger.error('No valid labelid is given in the meta.xml file')
else:
logger.debug('No valid file. Freesurfer Atlas not loaded.')
