def test_copy_modif_texture(self):
test_textureA = texture.TextureND()
darrayA = np.zeros((4, 1))
test_textureA.update_darray(darrayA)
test_textureB = test_textureA.copy()
test_textureB.darray[0][0] = 1
assert not (test_textureA.darray == test_textureB.darray).all()
def load_texture(gifti_file):
"""
load gifti_file and create a TextureND object (multidimensional)
:param gifti_file: str, path to the gifti file on the disk
:return: the corresponding TextureND object
"""
# read the gifti usinng nibabel
nb_texture = nb.gifti.read(gifti_file)
# concatenate all the data arrays in a single numpy array
cat_darrays = [
nb_texture.darrays[i].data for i in range(len(nb_texture.darrays))
]
return texture.TextureND(darray=np.array(cat_darrays),
metadata=nb_texture.meta.metadata)
def test_z_score_texture(self):
darrayA = np.array([
[5, 3, 2],
[7, 2, 1],
[4, 7, 4],
])
outA = np.array([
[3, 3, 3],
[2, 2, 1],
[4, 4, 4],
])
test_textureA = texture.TextureND()
test_textureA.update_darray(darrayA)
test_textureA.z_score_filtering(1)
assert test_textureA.darray.all() == outA.all()
def main(arguments):
if len(arguments)==3:
meshN = arguments[1]
texN = arguments[2]
mesh = sio.load_mesh(meshN)
maxCurv = maxAbsCurvature(mesh)
# visb_sc = splt.visbrain_plot(mesh=mesh, tex=maxCurv,
# caption='max absolute curvature',
# cblabel='max absolute curvature')
# visb_sc.preview()
sio.write_texture(stex.TextureND(darray=maxCurv), texN)
else:
print('Usage:')
print('python computeMaxCurvature.py mesh curvTex')
def test_update_darray():
test_texture = texture.TextureND()
darray = np.zeros((4, 1))
test_texture.update_darray(darray)
assert test_texture.shape == darray.shape
def test_copy_texture(self):
test_textureA = texture.TextureND()
darray = np.zeros((4, 1))
test_textureA.update_darray(darray)
test_textureB = test_textureA.copy()
assert (test_textureA.darray == test_textureB.darray).all()
import numpy as np
from slam import texture
from slam import io as sio
if __name__ == '__main__':
tex = sio.load_texture('data/example_texture.gii')
print(tex)
print(tex.metadata)
print(tex.shape)
print(tex.dtype)
print(tex.min())
print(tex.max())
darray = np.zeros((2, 3))
tex2 = texture.TextureND(darray=darray)
print(tex2.metadata)
print(tex2)
print(tex2.shape)
print(tex2.dtype)
print(tex2.min())
print(tex2.max())
sio.write_texture(tex2, 'test.gii')
tex_files = list()
for subject_mesh_file in subjects_mesh_files:
filename_split = subject_mesh_file.split('/')
subj = filename_split[6]
filename = filename_split[-1]
side = filename[0]
print(subj + ' ' + side)
curv = os.path.join(
output_folder, subj + '.' + side + 'h.white_curv_' +
curv_type + '_NN_FSsphere.ico7.gii')
if not os.path.exists(curv):
mesh_files.append(subject_mesh_file)
tex_files.append(curv)
print('nb of meshes to be processed: ' + str(len(mesh_files)))
#mesh_files_i = mesh_files[:2]
#tex_files_i = tex_files[:2]
for mesh_file, tex_file in zip(mesh_files, tex_files):
print('remeshing for ' + tex_file)
file_tex_in = tex_file[:-21] + '.gii'
print(file_tex_in)
source_tex = sio.load_texture(file_tex_in)
source_spherical_mesh = sio.load_mesh(mesh_file)
interpolated_tex = \
srem.spherical_interpolation_nearest_neigbhor(source_spherical_mesh, target_spherical_mesh, source_tex.darray)
#splt.pyglet_plot(target_spherical_mesh, interpolated_tex, -1, 1)
output_texture = stex.TextureND(darray=interpolated_tex)
sio.write_texture(output_texture, tex_file)
