"""
# remove the arms, this function makes a copy of the model array. Hence, the tissue indices have been converted to
# our tissue names and it is not necessary to store the tissue_mapping for this model.
(model_trunk, trunk_mask) = txt_data.calculate_trunk_model(AustinMan, model_type='complete', z_start=480, z_end=821)
outer_shape_trunk = txt_data.calculate_outer_shape(model_trunk)
AustinMan.add_voxel_data(short_name='trunk',
name="The trunk of the 'complete' model. Arms have been removed using "
"VoxelModel.remove_arms().",
outer_shape=outer_shape_trunk,
model=model_trunk,
mask=trunk_mask,
tissue_mapping=None)
# create the 3D surface of the voxel model
surface = AustinMan.create_3d_model(model_type='trunk', patch_size=(30, 30))
AustinMan.models['trunk'].surface_3d = surface
AustinMan.models['trunk'].endpoints = []
for (i, s) in enumerate(surface):
AustinMan.models['trunk'].endpoints.append(Coordinate(np.array(s['centroid'])))
# plot all the patches
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
# plot the surface:
for s in AustinMan.models['trunk'].surface_3d:
verts = s['verts']
centroid = s['centroid']
surf = Poly3DCollection(verts)
surf.set_facecolor((0, 0, 0, 0.7))
# Calculate the trunk model
start_slice = int(96)
end_slice = int(141)
(model_trunk, trunk_mask) = AVW_Data.calculate_trunk_model(Donna,
'complete',
z_start=start_slice,
z_end=end_slice)
outer_shape_trunk = AVW_Data.calculate_outer_shape(model_trunk)
Donna.add_voxel_data(
short_name='trunk',
name="The trunk of the 'complete' model. Arms have been removed using "
"VoxelModel.remove_arms().",
outer_shape=outer_shape_trunk,
model=model_trunk,
mask=trunk_mask,
tissue_mapping=None)
# Calculate the 3D surface of Donna
surface = Donna.create_3d_model(model_type='trunk', patch_size=(30, 30))
Donna.models['trunk'].surface_3d = surface
Donna.models['trunk'].endpoints = []
for (i, s) in enumerate(surface):
Donna.models['trunk'].endpoints.append(Coordinate(np.array(
s['centroid']))) #
Donna.save_model()
tissue_names=tissue_name_orig)
VisibleHuman.add_voxel_data(short_name='complete',
name='The \'original\' model converted to our TissueProperties.',
model=VisibleHuman.models['original'].data,
outer_shape=outer_shape,
tissue_mapping=tissue_mapping)
# calculate the trunk model
# the slice z_end will not be included in the final model
(model_trunk, trunk_mask) = AVW_Data.calculate_trunk_model(VisibleHuman, model_type='complete', z_start=75, z_end=196)
outer_shape_trunk = AVW_Data.calculate_outer_shape(model_trunk)
VisibleHuman.add_voxel_data(short_name='trunk',
name="The trunk of the 'complete' model. Arms have been removed using "
"VoxelModel.remove_arms().",
outer_shape=outer_shape_trunk,
model=model_trunk,
mask=trunk_mask,
tissue_mapping=None)
surface = VisibleHuman.create_3d_model(model_type='trunk', patch_size=(30, 30))
VisibleHuman.models['trunk'].surface_3d = surface
VisibleHuman.models['trunk'].endpoints = []
for (i, s) in enumerate(surface):
VisibleHuman.models['trunk'].endpoints.append(Coordinate(np.array(s['centroid'])))
VisibleHuman.save_model()