def mesh_contour_with_files(input_mesh,
input_labels,
output_mesh=None,
output_labels=None):
""" TODO: use nibabel here """
#from gifti import loadImage, saveImage, GiftiDataArray, GiftiImage
#from gifti import GiftiImage_fromarray, GiftiImage_fromTriangles
#from gifti import GiftiIntentCode, GiftiEncoding
labels = loadImage(input_labels).arrays[0].data.astype(int)
cor, triangles = loadImage(input_mesh).arrays
contour_cor, contour_tri = mesh_contour(cor.data,
triangles.data.astype(int), labels)
k = GiftiImage_fromarray(contour_cor)
k.arrays[0].intentString = "NIFTI_INTENT_POINTSET"
k.addDataArray_fromarray(contour_tri,
GiftiIntentCode.NIFTI_INTENT_TRIANGLE)
for a in k.arrays:
a.encoding = GiftiEncoding.GIFTI_ENCODING_ASCII
if output_mesh is None:
output_mesh = non_existent_file(add_suffix(input_mesh, '_contour'))
logger.info('saving to %s', output_mesh)
k.save(output_mesh)
def extract_sub_mesh_with_files(input_mesh, center_node, radius,
output_mesh=None):
from nibabel import gifti
from nibabel.gifti import GiftiImage, GiftiDataArray
from pyhrf.tools.io import read_mesh
cor, tri, coord_sys = read_mesh(input_mesh)
sub_cor, sub_tri = extract_sub_mesh(cor, tri, center_node, radius)
#nimg = GiftiImage_fromTriangles(sub_cor, sub_tri)
nimg = GiftiImage()
intent = 'NIFTI_INTENT_POINTSET'
nimg.add_gifti_data_array(GiftiDataArray.from_array(sub_cor,intent))
intent = 'NIFTI_INTENT_TRIANGLE'
nimg.add_gifti_data_array(GiftiDataArray.from_array(sub_tri,intent))
if output_mesh is None:
output_mesh = non_existent_file(add_suffix(input_mesh, '_sub'))
pyhrf.verbose(1, 'Saving extracted mesh to %s' %output_mesh)
gifti.write(nimg, output_mesh)
return sub_cor, sub_tri, coord_sys
def mesh_contour_with_files(input_mesh, input_labels, output_mesh=None, output_labels=None):
""" TODO: use nibabel here """
# from gifti import loadImage, saveImage, GiftiDataArray, GiftiImage
# from gifti import GiftiImage_fromarray, GiftiImage_fromTriangles
# from gifti import GiftiIntentCode, GiftiEncoding
labels = loadImage(input_labels).arrays[0].data.astype(int)
cor, triangles = loadImage(input_mesh).arrays
contour_cor, contour_tri = mesh_contour(cor.data, triangles.data.astype(int), labels)
k = GiftiImage_fromarray(contour_cor)
k.arrays[0].intentString = "NIFTI_INTENT_POINTSET"
k.addDataArray_fromarray(contour_tri, GiftiIntentCode.NIFTI_INTENT_TRIANGLE)
for a in k.arrays:
a.encoding = GiftiEncoding.GIFTI_ENCODING_ASCII
if output_mesh is None:
output_mesh = non_existent_file(add_suffix(input_mesh, "_contour"))
logger.info("saving to %s", output_mesh)
k.save(output_mesh)
def mesh_contour_with_files(input_mesh, input_labels, output_mesh=None,
output_labels=None):
from gifti import loadImage, saveImage, GiftiDataArray, GiftiImage
from gifti import GiftiImage_fromarray, GiftiImage_fromTriangles
from gifti import GiftiIntentCode, GiftiEncoding
labels = loadImage(input_labels).arrays[0].data.astype(int)
cor, triangles = loadImage(input_mesh).arrays
contour_cor, contour_tri = mesh_contour(cor.data, triangles.data.astype(int),
labels)
k = GiftiImage_fromarray(contour_cor)
k.arrays[0].intentString = "NIFTI_INTENT_POINTSET"
k.addDataArray_fromarray(contour_tri, GiftiIntentCode.NIFTI_INTENT_TRIANGLE)
for a in k.arrays:
a.encoding = GiftiEncoding.GIFTI_ENCODING_ASCII
if output_mesh is None:
output_mesh = non_existent_file(add_suffix(input_mesh, '_contour'))
pyhrf.verbose(1, 'saving to %s' %output_mesh)
k.save(output_mesh)
def extract_sub_mesh_with_files(input_mesh,
center_node,
radius,
output_mesh=None):
from nibabel import gifti
from nibabel.gifti import GiftiImage, GiftiDataArray
from pyhrf.tools._io import read_mesh
cor, tri, coord_sys = read_mesh(input_mesh)
sub_cor, sub_tri = extract_sub_mesh(cor, tri, center_node, radius)
#nimg = GiftiImage_fromTriangles(sub_cor, sub_tri)
nimg = GiftiImage()
intent = 'NIFTI_INTENT_POINTSET'
nimg.add_gifti_data_array(GiftiDataArray.from_array(sub_cor, intent))
intent = 'NIFTI_INTENT_TRIANGLE'
nimg.add_gifti_data_array(GiftiDataArray.from_array(sub_tri, intent))
if output_mesh is None:
output_mesh = non_existent_file(add_suffix(input_mesh, '_sub'))
logger.info('Saving extracted mesh to %s', output_mesh)
gifti.write(nimg, output_mesh)
return sub_cor, sub_tri, coord_sys
