def _make_root(self, rootpath):
"""
Creates a root mesh by merging the mesh corresponding to each neuron,
then saves it as an obj file at rootpath
"""
raise NotImplementedError(
"Create root method not supported yet, sorry")
print(f"Creating root mesh for atlas {self.atlas_name}")
temp_scene = Scene(
atlas=Celegans,
add_root=False,
display_inset=False,
atlas_kwargs=dict(data_folder=self.data_folder),
)
temp_scene.add_neurons(self.neurons_names)
temp_scene.render(interactive=False)
temp_scene.close()
root = merge(*temp_scene.actors["neurons"]).clean().cap()
# root = mesh2Volume(root, spacing=(0.02, 0.02, 0.02)).isosurface()
points = Points(root.points()).smoothMLS2D(f=0.8).clean(tol=0.005)
root = recoSurface(points, dims=100, radius=0.2)
# Save
write(root, rootpath)
del temp_scene
return root
def make_root_mesh(self):
if self.structures is None:
return
obj_path = os.path.join(self.meshes_folder, "root.vtk")
if os.path.isfile(obj_path):
return
# Get the mesh for each brain region to create root
meshes = [
self._get_structure_mesh(reg) for reg in self.region_acronyms
]
root = merge(meshes)
write(root, obj_path)
def write_neuron_to_cache(self, neuron_name, neuron, _params):
# Write params to file
save_yaml(self.get_cache_params_filename(neuron_name), _params)
# Write neurons to file
file_names = self.get_cache_filenames(neuron_name)
if isinstance(neuron, Mesh):
write(neuron, [f for f in file_names if f.endswith("soma.obj")][0])
else:
if not isinstance(neuron, dict):
raise ValueError(
f"Invalid neuron argument passed while caching: {neuron}")
for key, actor in neuron.items():
if key == "whole_neuron":
fname = [f for f in file_names if f.endswith(f"{key}.obj")]
write(actor, fname[0])
else:
# Get a single actor for each neuron component.
# If there's no data for the component create an empty actor
if not isinstance(actor, Mesh):
if isinstance(actor, (list, tuple)):
if len(actor) == 1:
actor = actor[0]
elif not actor or actor is None:
actor = Mesh()
else:
try:
actor = merge(actor)
except:
raise ValueError(
f"{key} actor should be a mesh or a list of 1 mesh not {actor}"
)
if actor is None:
actor = Mesh()
# Save to file
fname = [f for f in file_names if f.endswith(f"{key}.obj")]
if fname:
write(actor, fname[0])
else:
raise ValueError(
f"No filename found for {key}. Filenames {file_names}"
)
A_S = torch.from_numpy(A_S).to(device, dtype=torch.float)
A_L = torch.from_numpy(A_L).to(device, dtype=torch.float)
tensor_prob_output = model(X, A_S, A_L).to(device,
dtype=torch.float)
patch_prob_output = tensor_prob_output.cpu().numpy()
for i_label in range(num_classes):
predicted_labels_d[np.argmax(patch_prob_output[0, :], axis=-1)
== i_label] = i_label
# output downsampled predicted labels
mesh2 = mesh_d.clone()
mesh2.addCellArray(predicted_labels_d, 'Label')
vedo.write(
mesh2,
os.path.join(output_path,
'{}_d_predicted.vtp'.format(i_sample[:-4])))
# refinement
print('\tRefining by pygco...')
round_factor = 100
patch_prob_output[patch_prob_output < 1.0e-6] = 1.0e-6
# unaries
unaries = -round_factor * np.log10(patch_prob_output)
unaries = unaries.astype(np.int32)
unaries = unaries.reshape(-1, num_classes)
# parawise
pairwise = (1 - np.eye(num_classes, dtype=np.int32))
def vtk_plot(vtk_dir, output_dir):
vtk_obj = load(vtk_dir)
write(objct=vtk_obj, fileoutput=output_dir + "/vtk_obj.vti")
A_L = torch.from_numpy(A_L).to(device, dtype=torch.float)
tensor_prob_output = model(X, A_S, A_L).to(device,
dtype=torch.float)
patch_prob_output = tensor_prob_output.cpu().numpy()
for i_label in range(num_classes):
predicted_labels[np.argmax(patch_prob_output[0, :], axis=-1) ==
i_label] = i_label
# output predicted labels
mesh2 = mesh.clone()
mesh2.addCellArray(predicted_labels, 'Label')
vedo.write(
mesh2,
os.path.join(test_path,
'Sample_{}_predicted.vtp'.format(i_sample)),
binary=True)
# convert predict result and label to one-hot maps
tensor_predicted_labels = torch.from_numpy(predicted_labels)
tensor_test_labels = torch.from_numpy(labels)
tensor_predicted_labels = tensor_predicted_labels.long()
tensor_test_labels = tensor_test_labels.long()
one_hot_predicted_labels = nn.functional.one_hot(
tensor_predicted_labels[:, 0], num_classes=num_classes)
one_hot_labels = nn.functional.one_hot(tensor_test_labels[:, 0],
num_classes=num_classes)
# calculate DSC
i_dsc = DSC(one_hot_predicted_labels, one_hot_labels)