# 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()
# is continuous and the arms are removed in all z-layers
model_trunk[61, 97:99, 253] = np.array([42, 42])
model_trunk = AustinWoman.remove_arms(model_trunk)
trunk_mask = {
'x': range(0, model_trunk.shape[0]),
'y': range(0, model_trunk.shape[1]),
'z': range(z_start, z_end)
}
outer_shape_trunk = txt_data.calculate_outer_shape(model_trunk)
AustinWoman.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 = AustinWoman.create_3d_model(model_type='trunk', patch_size=(30, 30))
AustinWoman.models['trunk'].surface_3d = surface
surface = AustinWoman.models['trunk'].surface_3d
AustinWoman.models['trunk'].endpoints = []
for (i, s) in enumerate(surface):
AustinWoman.models['trunk'].endpoints.append(
Coordinate(np.array(s['centroid'])))
# save the model
AustinWoman.save_model()
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))
surf.set_edgecolor('k')
ax.add_collection3d(surf)
ax.plot(np.array([centroid[0]]), np.array([centroid[1]]), np.array([centroid[2]]), '.')
ax.set_zlim(800, 1500)
ax.set_aspect('equal', 'box')
plt.show()
# save the model
AustinMan.save_model()
outer_shape=outer_shape,
tissue_mapping=tissue_mapping)
# Calculate the trunk model
start_slice = int(177)
end_slice = int(290)
(model_trunk, trunk_mask) = AVW_Data.calculate_trunk_model(Katja,
'complete',
z_start=start_slice,
z_end=end_slice)
outer_shape_trunk = AVW_Data.calculate_outer_shape(model_trunk)
Katja.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 = Katja.create_3d_model(model_type='trunk', patch_size=(30, 30))
Katja.models['trunk'].surface_3d = surface
Katja.models['trunk'].endpoints = []
for (i, s) in enumerate(surface):
Katja.models['trunk'].endpoints.append(Coordinate(np.array(s['centroid'])))
Katja.save_model()
outer_shape=outer_shape,
tissue_mapping=tissue_mapping)
# Calculate the trunk model 30:81
start_slice = int(177)
end_slice = int(290)
(model_trunk, trunk_mask) = AVW_Data.calculate_trunk_model(Irene,
'complete',
z_start=start_slice,
z_end=end_slice)
outer_shape_trunk = AVW_Data.calculate_outer_shape(model_trunk)
Irene.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 = Irene.create_3d_model(model_type='trunk', patch_size=(30, 30))
Irene.models['trunk'].surface_3d = surface
Irene.models['trunk'].endpoints = []
for (i, s) in enumerate(surface):
Irene.models['trunk'].endpoints.append(Coordinate(np.array(s['centroid'])))
Irene.save_model()
short_name='complete',
name='The \'original\' model converted to our TissueProperties.',
model=Helga.models['original'].data,
outer_shape=outer_shape,
tissue_mapping=tissue_mapping)
# Calculate the trunk model
(model_trunk, trunk_mask) = AVW_Data.calculate_trunk_model(Helga,
'complete',
z_start=30,
z_end=81)
outer_shape_trunk = AVW_Data.calculate_outer_shape(model_trunk)
Helga.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 = Helga.create_3d_model(model_type='trunk', patch_size=(30, 30))
Helga.models['trunk'].surface_3d = surface
Helga.models['trunk'].endpoints = []
for (i, s) in enumerate(surface):
Helga.models['trunk'].endpoints.append(Coordinate(np.array(s['centroid'])))
Helga.save_model()
outer_shape=outer_shape,
tissue_mapping=tissue_mapping)
# Calculate the trunk model
start_slice = int(0)
end_slice = int(110)
(model_trunk, trunk_mask) = AVW_Data.calculate_trunk_model(Frank,
'complete',
z_start=start_slice,
z_end=end_slice)
outer_shape_trunk = AVW_Data.calculate_outer_shape(model_trunk)
Frank.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 = Frank.create_3d_model(model_type='trunk', patch_size=(30, 30))
Frank.models['trunk'].surface_3d = surface
Frank.models['trunk'].endpoints = []
for (i, s) in enumerate(surface):
Frank.models['trunk'].endpoints.append(Coordinate(np.array(s['centroid'])))
Frank.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()