def close_file(self, left_hemi_file, right_hemi_file, left_curvature_output_file, right_curvature_output_file):
'''
'''
m = numpy.ctypeslib.as_array(self.__matrix.get_obj())
m = m.reshape(self.__shape)
#here
lh_vertices, lh_faces = nibabel.freesurfer.read_geometry( left_hemi_file )
rh_vertices, rh_faces = nibabel.freesurfer.read_geometry( right_hemi_file )
sum_vector = numpy.sum( m, axis=0 )
import sys, os
sys.path.append(os.path.join( os.path.dirname( __file__ ),'../'))
from utility import Utility
# write curvature files
Utility.write_freesurfer_curvature( left_curvature_output_file, sum_vector[0:len( lh_vertices )] )
Utility.write_freesurfer_curvature( right_curvature_output_file, sum_vector[len( lh_vertices ):] ) # here we start with the offset
# end here
print 'crv written!!! FTW!'
numpy.save( self.__matrix_file, m)
print 'stored matrix'
def create_curvature_files( matrix_file, left_hemi_file, right_hemi_file, left_curvature_output_file, right_curvature_output_file, manual=False ):
'''
'''
# load the surfaces to compute the offsets correctly
# as a reminder: the offset for the right hemisphere is the number of vertices in the left hemisphere
# else-wise the vertex indices for right would start at 0 again
lh_vertices, lh_faces = nibabel.freesurfer.read_geometry( left_hemi_file )
rh_vertices, rh_faces = nibabel.freesurfer.read_geometry( right_hemi_file )
# load the connectivity matrix
#m = numpy.loadtxt( matrix_file, dtype=numpy.uint16 )
m = numpy.load(matrix_file)
sum_vector = numpy.sum( m, axis=0 )
# write curvature files
Utility.write_freesurfer_curvature( left_curvature_output_file, sum_vector[0:len( lh_vertices )] )
Utility.write_freesurfer_curvature( right_curvature_output_file, sum_vector[len( lh_vertices ):] ) # here we start with the offset
