def test_draco():
n_points = 12
img = sphere_tissue_image(size=100, n_points=n_points)
draco = DracoMesh(img)
assert draco.point_topomesh.nb_wisps(0) == n_points + 1
draco.delaunay_adjacency_complex(surface_cleaning_criteria=[])
image_tetrahedra = np.sort(draco.image_cell_vertex.keys())
image_tetrahedra = image_tetrahedra[image_tetrahedra[:, 0] != 1]
draco_tetrahedra = np.sort([
list(draco.triangulation_topomesh.borders(3, t, 3))
for t in draco.triangulation_topomesh.wisps(3)
])
delaunay_consistency = jaccard_index(image_tetrahedra, draco_tetrahedra)
draco.adjacency_complex_optimization(n_iterations=2)
assert draco.triangulation_topomesh.nb_region_neighbors(0, 2) == n_points
image_tetrahedra = np.sort(draco.image_cell_vertex.keys())
image_tetrahedra = image_tetrahedra[image_tetrahedra[:, 0] != 1]
draco_tetrahedra = np.sort([
list(draco.triangulation_topomesh.borders(3, t, 3))
for t in draco.triangulation_topomesh.wisps(3)
])
draco_consistency = jaccard_index(image_tetrahedra, draco_tetrahedra)
# print delaunay_consistency,' -> ',draco_consistency
assert draco_consistency == 1 or (draco_consistency >= 0.9 and
draco_consistency > delaunay_consistency)
triangular = ['star', 'remeshed', 'projected', 'regular', 'flat']
image_dual_topomesh = draco.dual_reconstruction(
reconstruction_triangulation=triangular, adjacency_complex_degree=3)
image_volumes = array_dict(
nd.sum(np.ones_like(img), img, index=np.unique(img)[1:]) *
np.prod(img.voxelsize),
np.unique(img)[1:])
compute_topomesh_property(image_dual_topomesh, 'volume', 3)
draco_volumes = image_dual_topomesh.wisp_property('volume', 3)
for c in image_dual_topomesh.wisps(3):
assert np.isclose(image_volumes[c], draco_volumes[c], 0.33)
def test_draco():
n_points = 12
img = sphere_tissue_image(size=100,n_points=n_points)
draco = DracoMesh(img)
assert draco.point_topomesh.nb_wisps(0) == n_points+1
draco.delaunay_adjacency_complex(surface_cleaning_criteria = [])
image_tetrahedra = np.sort(draco.image_cell_vertex.keys())
image_tetrahedra = image_tetrahedra[image_tetrahedra[:,0] != 1]
draco_tetrahedra = np.sort([list(draco.triangulation_topomesh.borders(3,t,3)) for t in draco.triangulation_topomesh.wisps(3)])
delaunay_consistency = jaccard_index(image_tetrahedra, draco_tetrahedra)
draco.adjacency_complex_optimization(n_iterations=2)
assert draco.triangulation_topomesh.nb_region_neighbors(0,2) == n_points
image_tetrahedra = np.sort(draco.image_cell_vertex.keys())
image_tetrahedra = image_tetrahedra[image_tetrahedra[:,0] != 1]
draco_tetrahedra = np.sort([list(draco.triangulation_topomesh.borders(3,t,3)) for t in draco.triangulation_topomesh.wisps(3)])
draco_consistency = jaccard_index(image_tetrahedra, draco_tetrahedra)
# print delaunay_consistency,' -> ',draco_consistency
assert draco_consistency == 1 or (draco_consistency >= 0.9 and draco_consistency > delaunay_consistency)
triangular = ['star','remeshed','projected','regular','flat']
image_dual_topomesh = draco.dual_reconstruction(reconstruction_triangulation = triangular, adjacency_complex_degree=3)
image_volumes = array_dict(nd.sum(np.ones_like(img),img,index=np.unique(img)[1:])*np.prod(img.resolution),np.unique(img)[1:])
compute_topomesh_property(image_dual_topomesh,'volume',3)
draco_volumes = image_dual_topomesh.wisp_property('volume',3)
for c in image_dual_topomesh.wisps(3):
assert np.isclose(image_volumes[c],draco_volumes[c],0.33)
def create_CGAL_topomesh(img, mesh_fineness=1.0):
"""
"""
dirname = str(shared_data(openalea.cgal_meshing).parent.parent+'/')
start_time = time()
print "--> Input Image"
img_graph = graph_from_image(img,spatio_temporal_properties=['volume','barycenter'],ignore_cells_at_stack_margins = False,property_as_real=False)
img_labels = np.array(list(img_graph.vertices()))
img_volumes = np.array([img_graph.vertex_property('volume')[v] for v in img_graph.vertices()])
print " --> ",img_labels.shape[0]," Objects, ", img_volumes[2:].mean()," microm3 per object"
facet_distance = np.power(img_volumes[2:].mean(),1/3.)/(4.5*np.pi*mesh_fineness)
print " --> Facet Distance : ",facet_distance
print " --> Converting to 8bit"
img_neighbors = np.array([list(img_graph.neighbors(v)) for v in img_graph.vertices()])
count_labels = np.zeros(256)
img_graph.add_vertex_property('8bit_labels')
if img_labels.shape[0] < 255:
for i,v in enumerate(img_graph.vertices()):
img_graph.vertex_property('8bit_labels')[v] = i+2
else:
for v in img_graph.vertices():
possible_labels = np.array([])
select = 0
while possible_labels.size == 0:
possible_labels = set(np.arange(2,256))
possible_labels = possible_labels.difference(set(np.where(count_labels>count_labels[2:].min()+select)[0]))
#possible_labels = possible_labels.difference(set(np.where(count_labels>count_labels[2:].min()+1)[0]))
neighbor_labels = set()
for n in img_graph.neighbors(v):
try:
neighbor_label = {img_graph.vertex_property('8bit_labels')[n]}
for n2 in img_graph.neighbors(n):
if n2 != v:
try:
neighbor_label = {img_graph.vertex_property('8bit_labels')[n2]}
except KeyError:
neighbor_label = set()
pass
neighbor_labels = neighbor_labels.union(neighbor_label)
except KeyError:
neighbor_label = set()
pass
neighbor_labels = neighbor_labels.union(neighbor_label)
possible_labels = np.array(list(possible_labels.difference(neighbor_labels)),np.uint8)
if possible_labels.size == 0:
select += 1
#print neighbor_labels
new_label = possible_labels[np.random.randint(possible_labels.size)]
img_graph.vertex_property('8bit_labels')[v] = new_label
count_labels[new_label] += 1
#print v, ' -> ', new_label
new_labels = np.ones(img.max()+1,np.uint8)
new_labels[img_labels] = np.array([img_graph.vertex_property('8bit_labels')[v] for v in img_graph.vertices()],np.uint8)
if np.unique(new_labels).shape[0]<255:
label_index = np.ones(256)
label_index[np.unique(new_labels)] = np.arange(new_labels.shape[0])+1
for v in img_graph.vertices():
img_graph.vertex_property('8bit_labels')[v] = label_index[img_graph.vertex_property('8bit_labels')[v]]
new_labels = np.ones(img.max()+1,np.uint8)
#new_labels[img_labels] = np.array([img_graph.vertex_property('8bit_labels')[v] for v in img_graph.vertices()],np.uint8)
for v in img_graph.vertices():
new_labels[v] = img_graph.vertex_property('8bit_labels')[v]
mod_img = np.array(new_labels[img],np.uint8)
inrfile = dirname+"tmp/8bit_image.inr.gz"
imsave(inrfile,SpatialImage(mod_img))
end_time = time()
print "<-- Input Image [",end_time-start_time,"s]"
facet_angle = 30.0
facet_size = 40.0
edge_ratio = 4.0
cell_size = 60.0
start_time = time()
print "--> Building CGAL Mesh"
outputfile = dirname+"tmp/CGAL_output_mesh.mesh"
buildCGALMesh(inrfile,outputfile,facet_angle,facet_size,facet_distance,edge_ratio,cell_size)
end_time = time()
print "<-- Building CGAL Mesh [",end_time-start_time,"s]"
mesh = CGALMesh()
mesh.createMesh(outputfile)
start_time = time()
print "--> Re-Indexing Components"
mesh.components = np.unique(mesh.tri_subdomains)
new_mesh = CGALMesh()
new_mesh.createMesh(outputfile)
new_mesh.tri_subdomains = np.ones_like(mesh.tri_subdomains)
new_mesh.tetra_subdomains = np.ones_like(mesh.tetra_subdomains)
new_mesh.tri_subdomains[np.where(mesh.tri_subdomains == mesh.components[0])] = 1
new_mesh.tetra_subdomains[np.where(mesh.tetra_subdomains == mesh.components[0])] = 1
for c in mesh.components[1:]:
cell_labels = np.where(new_labels == c)[0]
n_cells = cell_labels.size
if n_cells > 0:
# print " --> Component ",c," -> ",n_cells," Cells"
cell_tetrahedra = mesh.tetrahedra[np.where(mesh.tetra_subdomains==c)]
#if n_cells == 1:
if False:
print " --> Component ",c," -> 1 Object (",n_cells," Cell) : ",cell_labels,"(",img_graph.vertex_property('8bit_labels')[cell_labels[0]],")"
new_mesh.tetra_subdomains[np.where(mesh.tetra_subdomains == c)] = cell_labels[0]
new_mesh.tri_subdomains[np.where(mesh.tri_subdomains == c)] = cell_labels[0]
else:
cell_tetrahedra_components = np.zeros(cell_tetrahedra.shape[0],int)
tetrahedra_component_correspondance = {}
tetra_centers = np.mean(mesh.vertices[cell_tetrahedra],axis=1)
for t, tetra in enumerate(cell_tetrahedra):
if cell_tetrahedra_components[t] == 0:
neighbour_tetrahedra = np.unique(np.append(np.where(cell_tetrahedra==tetra[0])[0],np.append(np.where(cell_tetrahedra==tetra[1])[0],np.append(np.where(cell_tetrahedra==tetra[2])[0],np.where(cell_tetrahedra==tetra[3])[0]))))
if (cell_tetrahedra_components[neighbour_tetrahedra].max()>0):
neighbour_components = cell_tetrahedra_components[neighbour_tetrahedra][np.where(cell_tetrahedra_components[neighbour_tetrahedra]>0)]
min_component = np.array([tetrahedra_component_correspondance[component] for component in neighbour_components]).min()
for component in neighbour_components:
tetrahedra_component_correspondance[tetrahedra_component_correspondance[component]] = min_component
tetrahedra_component_correspondance[component] = min_component
cell_tetrahedra_components[neighbour_tetrahedra] = min_component
else:
tetrahedra_component_correspondance[cell_tetrahedra_components.max()+1] = int(cell_tetrahedra_components.max()+1)
cell_tetrahedra_components[neighbour_tetrahedra] = int(cell_tetrahedra_components.max()+1)
for component in tetrahedra_component_correspondance:
label = component
while label != tetrahedra_component_correspondance[label]:
label = tetrahedra_component_correspondance[label]
tetrahedra_component_correspondance[component] = tetrahedra_component_correspondance[label]
component_labels = np.unique([tetrahedra_component_correspondance[component] for component in cell_tetrahedra_components])
n_objects = component_labels.size
# if n_objects != n_cells:
# print tetrahedra_component_correspondance
for component in tetrahedra_component_correspondance:
tetrahedra_component_correspondance[component] = np.where(component_labels == tetrahedra_component_correspondance[component])[0][0]
for component in tetrahedra_component_correspondance:
cell_tetrahedra_components[np.where(cell_tetrahedra_components == component)] = tetrahedra_component_correspondance[component]
tetrahedra_object_centers = np.zeros((n_objects,3))
tetrahedra_object_centers[:,0] = nd.sum(tetra_centers[:,0],cell_tetrahedra_components,index=xrange(n_objects))/nd.sum(np.ones_like(cell_tetrahedra_components),cell_tetrahedra_components,index=xrange(n_objects))
tetrahedra_object_centers[:,1] = nd.sum(tetra_centers[:,1],cell_tetrahedra_components,index=xrange(n_objects))/nd.sum(np.ones_like(cell_tetrahedra_components),cell_tetrahedra_components,index=xrange(n_objects))
tetrahedra_object_centers[:,2] = nd.sum(tetra_centers[:,2],cell_tetrahedra_components,index=xrange(n_objects))/nd.sum(np.ones_like(cell_tetrahedra_components),cell_tetrahedra_components,index=xrange(n_objects))
img_points = np.array([img_graph.vertex_property('barycenter')[v] for v in cell_labels])
tetrahedra_labels = cell_labels[vq(tetrahedra_object_centers,img_points)[0]]
# img_points = np.array([img_graph.vertex_property('barycenter')[v] for v in img_labels])
# tetrahedra_labels = img_labels[vq(tetrahedra_object_centers,img_points)[0]]
cell_triangles = mesh.triangles[np.where(mesh.tri_subdomains==c)]
cell_triangles_components = np.array([np.unique(cell_tetrahedra_components[np.where(cell_tetrahedra==tri[0])[0]])[0] for tri in cell_triangles])
print " --> Component ",c," -> ",n_objects," Objects (",n_cells," Cells) : ",tetrahedra_labels
new_mesh.tetra_subdomains[np.where(mesh.tetra_subdomains == c)] = tetrahedra_labels[cell_tetrahedra_components]
new_mesh.tri_subdomains[np.where(mesh.tri_subdomains == c)] = tetrahedra_labels[cell_triangles_components]
mesh.tri_subdomains = new_mesh.tri_subdomains
mesh.tetra_subdomains = new_mesh.tetra_subdomains
mesh.components = np.unique(mesh.tri_subdomains)
print mesh.vertices.shape[0],"Vertices, ",mesh.triangles.shape[0],"Triangles, ",mesh.tetrahedra.shape[0],"Tetrahedra, ",mesh.components.shape[0]," Components"
end_time = time()
print "<-- Re-Indexing Components [",end_time-start_time,"s]"
mesh.saveCGALfile(outputfile)
start_time = time()
print "--> Creating Topomesh"
mesh = CGALMesh()
mesh.createMesh(outputfile)
mesh.generatePropertyTopomesh()
positions = array_dict(mesh.vertex_positions.values()*np.array(img.resolution),keys=list(mesh.topo_mesh.wisps(0)))
compute_topomesh_property(mesh.topo_mesh,'barycenter',degree=0,positions=positions)
end_time = time()
print "<-- Creating Topomesh [",end_time-start_time,"s]"
return mesh.topo_mesh
figure = plt.figure(2)
figure.clf()
spider_plot(figure,np.array([dual_quality[c] for c in quality_criteria]),color1=np.array([0.3,0.6,1.]),color2=np.array([1.,0.,0.]),xlabels=quality_criteria,ytargets=0.8 * np.ones_like(quality_criteria,float),n_points=100*len(quality_criteria),linewidth=2,smooth_factor=0.0,spline_order=1)
plt.show(block=False)
raw_input()
triangular_string = ""
for t in triangular:
triangular_string += t+"_"
topomesh_filename = dirname+"/output_meshes/"+filename+"/"+filename+"_"+triangular_string+"topomesh.ply"
save_ply_property_topomesh(image_dual_topomesh,topomesh_filename,color_faces=True)
from openalea.mesh.property_topomesh_analysis import compute_topomesh_property, compute_topomesh_vertex_property_from_faces
compute_topomesh_property(image_dual_topomesh,'eccentricity',2)
compute_topomesh_vertex_property_from_faces(image_dual_topomesh,'eccentricity',weighting='uniform')
world.add(image_dual_topomesh ,'actual_dual_reconstuction')
raw_input()
# raw_file = "/Users/gcerutti/Developpement/openalea/openalea_meshing_data/share/data/nuclei_images/olli01_lti6b_150421_sam01_t000/olli01_lti6b_150421_sam01_t000_PIN.inr.gz"
# raw_img = imread(raw_file)
# raw_img = SpatialImage(np.concatenate([raw_img[:,:,35:],np.ones((raw_img.shape[0],raw_img.shape[1],5))],axis=2).astype(np.uint16),resolution=raw_img.resolution)
# world.add(raw_img,"raw_image")
from openalea.draco_stem.stem.tissue_mesh_quality import evaluate_topomesh_quality
quality_criteria=["Mesh Complexity","Triangle Area Deviation","Triangle Eccentricity","Cell Volume Error","Vertex Distance","Cell Convexity","Epidermis Cell Angle","Vertex Valence","Cell 2 Adjacency"]
draco_quality = evaluate_topomesh_quality(image_dual_topomesh,quality_criteria,image=draco.segmented_image,image_cell_vertex=draco.image_cell_vertex,image_labels=draco.image_labels,image_cell_volumes=draco.image_cell_volumes)
def optimize_topomesh(input_topomesh,omega_forces={'regularization':0.00,'laplacian':1.0,'planarization':0.27,'epidermis_planarization':0.07},omega_regularization_max=None,iterations=20,edge_flip=False,**kwargs):
"""
"""
topomesh = deepcopy(input_topomesh)
preparation_start_time = time()
# topomesh.update_wisp_property('barycenter',degree=0,values=initial_vertex_positions,keys=np.array(list(topomesh.wisps(0))))
compute_topomesh_property(topomesh,'valence',degree=0)
compute_topomesh_property(topomesh,'borders',degree=1)
compute_topomesh_property(topomesh,'vertices',degree=1)
compute_topomesh_property(topomesh,'vertices',degree=2)
compute_topomesh_property(topomesh,'vertices',degree=3)
compute_topomesh_property(topomesh,'cells',degree=2)
compute_topomesh_property(topomesh,'cells',degree=1)
compute_topomesh_property(topomesh,'cells',degree=0)
compute_topomesh_property(topomesh,'length',degree=1)
compute_topomesh_property(topomesh,'barycenter',degree=3)
compute_topomesh_property(topomesh,'barycenter',degree=2)
compute_topomesh_property(topomesh,'barycenter',degree=1)
triangular_mesh = kwargs.get('triangular_mesh',True)
if triangular_mesh:
compute_topomesh_triangle_properties(topomesh)
compute_topomesh_property(topomesh,'normal',degree=2)
compute_topomesh_property(topomesh,'angles',degree=2)
compute_topomesh_property(topomesh,'epidermis',degree=0)
compute_topomesh_property(topomesh,'epidermis',degree=1)
# compute_topomesh_property(topomesh,'epidermis',degree=3)
if omega_forces.has_key('planarization'):
start_time = time()
print "--> Computing interfaces"
for cid in topomesh.wisps(3):
for n_cid in topomesh.border_neighbors(3,cid):
if (n_cid<cid) and (not (n_cid,cid) in topomesh._interface[3].values()):
iid = topomesh._interface[3].add((n_cid,cid),None)
end_time = time()
print "<-- Computing interfaces[",end_time-start_time,"s]"
preparation_end_time = time()
print "--> Preparing topomesh [",preparation_end_time-preparation_start_time,"s]"
display = kwargs.get('display',False)
if display:
pass
optimization_start_time = time()
if omega_forces.has_key('regularization'):
if omega_regularization_max is None:
omega_regularization_max = omega_forces['regularization']
gradient_derivatives = kwargs.get("gradient_derivatives",[])
cell_vertex_motion = kwargs.get("cell_vertex_motion",False)
if cell_vertex_motion:
image_cell_vertex = deepcopy(kwargs.get("image_cell_vertex",{}))
for v in image_cell_vertex.keys():
image_cell_vertex[v] = image_cell_vertex[v]*np.array(kwargs.get("image_resolution",(1.0,1.0,1.0)))
#image_cell_vertex[v] = image_cell_vertex[v]
compute_topomesh_property(topomesh,'cells',degree=0)
vertex_cell_neighbours = topomesh.wisp_property('cells',degree=0)
epidermis_vertices = np.array(list(topomesh.wisps(0)))[np.where(topomesh.wisp_property('epidermis',degree=0).values())]
start_time = time()
print "--> Computing mesh cell vertices"
mesh_cell_vertex = {}
for v in topomesh.wisps(0):
if len(vertex_cell_neighbours[v]) == 5:
for k in xrange(5):
vertex_cell_labels = tuple([c for c in vertex_cell_neighbours[v]][:k])+tuple([c for c in vertex_cell_neighbours[v]][k+1:])
if not mesh_cell_vertex.has_key(vertex_cell_labels):
mesh_cell_vertex[vertex_cell_labels] = v
if len(vertex_cell_neighbours[v]) == 4:
vertex_cell_labels = tuple([c for c in vertex_cell_neighbours[v]])
mesh_cell_vertex[vertex_cell_labels] = v
if v in epidermis_vertices:
# and count_l1_cells(vertex_cell_neighbours[v]) == 4:
for k in xrange(4):
vertex_cell_labels = (1,) + tuple([c for c in vertex_cell_neighbours[v]][:k])+tuple([c for c in vertex_cell_neighbours[v]][k+1:])
if not mesh_cell_vertex.has_key(vertex_cell_labels):
mesh_cell_vertex[vertex_cell_labels] = v
if (len(vertex_cell_neighbours[v]) == 3) and (v in epidermis_vertices):
# and (count_l1_cells(vertex_cell_neighbours[v]) == 3):
vertex_cell_labels = (1,) + tuple([c for c in vertex_cell_neighbours[v]])
mesh_cell_vertex[vertex_cell_labels] = v
end_time = time()
print "<-- Computing mesh cell vertices [",end_time-start_time,"s]"
cell_vertex_matching = vq(np.sort(array_dict(image_cell_vertex).keys()),np.sort(array_dict(mesh_cell_vertex).keys()))
matched_image_index = np.where(cell_vertex_matching[1] == 0)[0]
matched_mesh_index = cell_vertex_matching[0][np.where(cell_vertex_matching[1] == 0)[0]]
matched_image_cell_vertex = np.array(image_cell_vertex.values())[matched_image_index]
matched_keys = np.sort(np.array(image_cell_vertex.keys()))[matched_image_index]
matched_mesh_vertices = np.array(mesh_cell_vertex.values())[cell_vertex_matching[0][np.where(cell_vertex_matching[1] == 0)[0]]]
matched_keys = np.sort(np.array(mesh_cell_vertex.keys()))[matched_mesh_index]
initial_vertex_positions = array_dict(topomesh.wisp_property('barycenter',0).values(list(topomesh.wisps(0))),list(topomesh.wisps(0)))
final_vertex_positions = array_dict()
fixed_vertex = array_dict(np.array([False for v in topomesh.wisps(0)]),np.array(list(topomesh.wisps(0))))
for i,v in enumerate(matched_mesh_vertices):
if not np.isnan(matched_image_cell_vertex[i]).any():
final_vertex_positions[v] = matched_image_cell_vertex[i]
print topomesh.wisp_property('barycenter',0)[v]," -> ",final_vertex_positions[v]
fixed_vertex[v] = True
matched_mesh_vertices = final_vertex_positions.keys()
sigma_deformation_initial = kwargs.get("sigma_deformation",np.sqrt(3)/4.)
sigma_deformation = sigma_deformation_initial*np.ones_like(np.array(list(topomesh.wisps(0))),float)
if cell_vertex_motion:
sigma_deformation[np.where(fixed_vertex.values())[0]] = 0.
iterations_per_step = kwargs.get('iterations_per_step',1)
for iteration in xrange(iterations/iterations_per_step+1):
print "_____________________________"
print ""
print " Iteration ",iteration
print "_____________________________"
start_time = time()
gaussian_sigma = kwargs.get('gaussian_sigma',10.0)
target_areas = kwargs.get('target_areas',None)
property_topomesh_vertices_deformation(topomesh,iterations=iterations_per_step,omega_forces=omega_forces,sigma_deformation=sigma_deformation,gradient_derivatives=gradient_derivatives,resolution=kwargs.get("image_resolution",(1.0,1.0,1.0)),gaussian_sigma=gaussian_sigma,target_areas=target_areas)
if cell_vertex_motion:
vertex_start_time = time()
print "--> Moving cell vertices"
if iteration <= (iterations/iterations_per_step+1)/1.:
#topomesh.update_wisp_property('barycenter',degree=0,values=((iterations/iterations_per_step+1-(iteration+1))*initial_vertex_positions.values(matched_mesh_vertices) + (iteration+1)*final_vertex_positions.values(matched_mesh_vertices))/(iterations/iterations_per_step+1),keys=matched_mesh_vertices,erase_property=False)
for v in matched_mesh_vertices:
topomesh.wisp_property('barycenter',degree=0)[v] = ((iterations/iterations_per_step+1-(iteration+1))*initial_vertex_positions[v] + (iteration+1)*final_vertex_positions[v])/(iterations/iterations_per_step+1)
vertex_end_time = time()
print "<-- Moving cell vertices [",vertex_end_time-vertex_start_time,"s]"
compute_topomesh_property(topomesh,'length',degree=1)
compute_topomesh_property(topomesh,'barycenter',degree=3)
compute_topomesh_property(topomesh,'barycenter',degree=2)
if triangular_mesh:
compute_topomesh_triangle_properties(topomesh)
compute_topomesh_property(topomesh,'normal',degree=2)
if edge_flip:
# property_topomesh_edge_flip_optimization(topomesh,omega_energies=omega_forces,simulated_annealing=True,iterations=15,display=display)
property_topomesh_edge_flip_optimization(topomesh,omega_energies=omega_forces,simulated_annealing=False,iterations=3,display=display)
compute_topomesh_property(topomesh,'length',degree=1)
compute_topomesh_property(topomesh,'barycenter',degree=3)
compute_topomesh_property(topomesh,'barycenter',degree=2)
if triangular_mesh:
compute_topomesh_triangle_properties(topomesh)
compute_topomesh_property(topomesh,'normal',degree=2)
sigma_deformation = sigma_deformation_initial*np.power(0.95,(iteration+1)*iterations_per_step)*np.ones_like(np.array(list(topomesh.wisps(0))),float)
if cell_vertex_motion:
sigma_deformation[np.where(fixed_vertex.values())[0]] = 0.
if omega_forces.has_key('regularization'):
omega_forces['regularization'] = np.minimum(omega_forces['regularization']+(omega_regularization_max*iterations_per_step)/iterations,omega_regularization_max)
if display:
pass
end_time = time()
print "_____________________________"
print ""
print " [",end_time-start_time,"s]"
#raw_input()
print "_____________________________"
optimization_end_time = time()
print "--> Optimizing Topomesh [",optimization_end_time - optimization_start_time,"s]"
return topomesh
cell_signals = dict(zip(df.Label.values[1:-4].astype(int),df.Value.values[1:-4]))
cell_flat_barycenters = deepcopy(cell_barycenters)
for c in cell_barycenters.keys():
cell_flat_barycenters[c][2] = 0.
triangles = np.array(cell_barycenters.keys())[delaunay_triangulation(np.array([cell_flat_barycenters[c] for c in cell_barycenters.keys()]))]
cell_topomesh = triangle_topomesh(triangles, cell_barycenters)
cell_topomesh.update_wisp_property('signal',0,cell_signals)
maximal_length = 15.
compute_topomesh_property(cell_topomesh,'length',1)
compute_topomesh_property(cell_topomesh,'triangles',1)
boundary_edges = np.array(map(len,cell_topomesh.wisp_property('triangles',1).values()))==1
distant_edges = cell_topomesh.wisp_property('length',1).values() > maximal_length
edges_to_remove = np.array(list(cell_topomesh.wisps(1)))[boundary_edges & distant_edges]
while len(edges_to_remove) > 0:
triangles_to_remove = np.concatenate(cell_topomesh.wisp_property('triangles',1).values(edges_to_remove))
for t in triangles_to_remove:
cell_topomesh.remove_wisp(2,t)
clean_topomesh(cell_topomesh)
compute_topomesh_property(cell_topomesh,'triangles',1)
smooth_factor=0.0,
spline_order=1)
plt.show(block=False)
raw_input()
triangular_string = ""
for t in triangular:
triangular_string += t + "_"
topomesh_filename = dirname + "/output_meshes/" + filename + "/" + filename + "_" + triangular_string + "topomesh.ply"
save_ply_property_topomesh(image_dual_topomesh,
topomesh_filename,
color_faces=True)
from openalea.mesh.property_topomesh_analysis import compute_topomesh_property, compute_topomesh_vertex_property_from_faces
compute_topomesh_property(image_dual_topomesh, 'eccentricity', 2)
compute_topomesh_vertex_property_from_faces(image_dual_topomesh,
'eccentricity',
weighting='uniform')
world.add(image_dual_topomesh, 'actual_dual_reconstuction')
raw_input()
# raw_file = "/Users/gcerutti/Developpement/openalea/openalea_meshing_data/share/data/nuclei_images/olli01_lti6b_150421_sam01_t000/olli01_lti6b_150421_sam01_t000_PIN.inr.gz"
# raw_img = imread(raw_file)
# raw_img = SpatialImage(np.concatenate([raw_img[:,:,35:],np.ones((raw_img.shape[0],raw_img.shape[1],5))],axis=2).astype(np.uint16),voxelsize=raw_img.voxelsize)
# world.add(raw_img,"raw_image")
from openalea.draco_stem.stem.tissue_mesh_quality import evaluate_topomesh_quality
quality_criteria = [
"Mesh Complexity", "Triangle Area Deviation", "Triangle Eccentricity",
def optimize_topomesh(input_topomesh,omega_forces={'regularization':0.00,'laplacian':1.0,'planarization':0.27,'epidermis_planarization':0.07},omega_regularization_max=None,iterations=20,edge_flip=False,**kwargs):
"""
"""
topomesh = deepcopy(input_topomesh)
preparation_start_time = time()
# topomesh.update_wisp_property('barycenter',degree=0,values=initial_vertex_positions,keys=np.array(list(topomesh.wisps(0))))
compute_topomesh_property(topomesh,'valence',degree=0)
compute_topomesh_property(topomesh,'borders',degree=1)
compute_topomesh_property(topomesh,'vertices',degree=1)
compute_topomesh_property(topomesh,'vertices',degree=2)
compute_topomesh_property(topomesh,'vertices',degree=3)
compute_topomesh_property(topomesh,'cells',degree=2)
compute_topomesh_property(topomesh,'cells',degree=1)
compute_topomesh_property(topomesh,'cells',degree=0)
compute_topomesh_property(topomesh,'length',degree=1)
compute_topomesh_property(topomesh,'barycenter',degree=3)
compute_topomesh_property(topomesh,'barycenter',degree=2)
compute_topomesh_property(topomesh,'barycenter',degree=1)
triangular_mesh = kwargs.get('triangular_mesh',True)
if triangular_mesh:
compute_topomesh_triangle_properties(topomesh)
compute_topomesh_property(topomesh,'normal',degree=2)
compute_topomesh_property(topomesh,'angles',degree=2)
compute_topomesh_property(topomesh,'epidermis',degree=0)
compute_topomesh_property(topomesh,'epidermis',degree=1)
# compute_topomesh_property(topomesh,'epidermis',degree=3)
if omega_forces.has_key('planarization'):
start_time = time()
print "--> Computing interfaces"
for cid in topomesh.wisps(3):
for n_cid in topomesh.border_neighbors(3,cid):
if (n_cid<cid) and (not (n_cid,cid) in topomesh._interface[3].values()):
iid = topomesh._interface[3].add((n_cid,cid),None)
end_time = time()
print "<-- Computing interfaces[",end_time-start_time,"s]"
preparation_end_time = time()
print "--> Preparing topomesh [",preparation_end_time-preparation_start_time,"s]"
display = kwargs.get('display',False)
if display:
pass
optimization_start_time = time()
if omega_forces.has_key('regularization'):
if omega_regularization_max is None:
omega_regularization_max = omega_forces['regularization']
gradient_derivatives = kwargs.get("gradient_derivatives",[])
cell_vertex_motion = kwargs.get("cell_vertex_motion",False)
if cell_vertex_motion:
image_cell_vertex = deepcopy(kwargs.get("image_cell_vertex",{}))
for v in image_cell_vertex.keys():
image_cell_vertex[v] = image_cell_vertex[v]*np.array(kwargs.get("image_voxelsize",(1.0,1.0,1.0)))
#image_cell_vertex[v] = image_cell_vertex[v]
compute_topomesh_property(topomesh,'cells',degree=0)
vertex_cell_neighbours = topomesh.wisp_property('cells',degree=0)
epidermis_vertices = np.array(list(topomesh.wisps(0)))[np.where(topomesh.wisp_property('epidermis',degree=0).values())]
start_time = time()
print "--> Computing mesh cell vertices"
mesh_cell_vertex = {}
for v in topomesh.wisps(0):
if len(vertex_cell_neighbours[v]) == 5:
for k in xrange(5):
vertex_cell_labels = tuple([c for c in vertex_cell_neighbours[v]][:k])+tuple([c for c in vertex_cell_neighbours[v]][k+1:])
if not mesh_cell_vertex.has_key(vertex_cell_labels):
mesh_cell_vertex[vertex_cell_labels] = v
if len(vertex_cell_neighbours[v]) == 4:
vertex_cell_labels = tuple([c for c in vertex_cell_neighbours[v]])
mesh_cell_vertex[vertex_cell_labels] = v
if v in epidermis_vertices:
# and count_l1_cells(vertex_cell_neighbours[v]) == 4:
for k in xrange(4):
vertex_cell_labels = (1,) + tuple([c for c in vertex_cell_neighbours[v]][:k])+tuple([c for c in vertex_cell_neighbours[v]][k+1:])
if not mesh_cell_vertex.has_key(vertex_cell_labels):
mesh_cell_vertex[vertex_cell_labels] = v
if (len(vertex_cell_neighbours[v]) == 3) and (v in epidermis_vertices):
# and (count_l1_cells(vertex_cell_neighbours[v]) == 3):
vertex_cell_labels = (1,) + tuple([c for c in vertex_cell_neighbours[v]])
mesh_cell_vertex[vertex_cell_labels] = v
end_time = time()
print "<-- Computing mesh cell vertices [",end_time-start_time,"s]"
cell_vertex_matching = vq(np.sort(array_dict(image_cell_vertex).keys()),np.sort(array_dict(mesh_cell_vertex).keys()))
matched_image_index = np.where(cell_vertex_matching[1] == 0)[0]
matched_mesh_index = cell_vertex_matching[0][np.where(cell_vertex_matching[1] == 0)[0]]
matched_image_cell_vertex = np.array(image_cell_vertex.values())[matched_image_index]
matched_keys = np.sort(np.array(image_cell_vertex.keys()))[matched_image_index]
matched_mesh_vertices = np.array(mesh_cell_vertex.values())[cell_vertex_matching[0][np.where(cell_vertex_matching[1] == 0)[0]]]
matched_keys = np.sort(np.array(mesh_cell_vertex.keys()))[matched_mesh_index]
initial_vertex_positions = array_dict(topomesh.wisp_property('barycenter',0).values(list(topomesh.wisps(0))),list(topomesh.wisps(0)))
final_vertex_positions = array_dict()
fixed_vertex = array_dict(np.array([False for v in topomesh.wisps(0)]),np.array(list(topomesh.wisps(0))))
for i,v in enumerate(matched_mesh_vertices):
if not np.isnan(matched_image_cell_vertex[i]).any():
final_vertex_positions[v] = matched_image_cell_vertex[i]
# print topomesh.wisp_property('barycenter',0)[v]," -> ",final_vertex_positions[v]
fixed_vertex[v] = True
matched_mesh_vertices = final_vertex_positions.keys()
sigma_deformation_initial = kwargs.get("sigma_deformation",np.sqrt(3)/4.)
sigma_deformation = sigma_deformation_initial*np.ones_like(np.array(list(topomesh.wisps(0))),float)
if cell_vertex_motion:
sigma_deformation[np.where(fixed_vertex.values())[0]] = 0.
iterations_per_step = kwargs.get('iterations_per_step',1)
for iteration in xrange(iterations/iterations_per_step+1):
print "_____________________________"
print ""
print " Iteration ",iteration
print "_____________________________"
start_time = time()
gaussian_sigma = kwargs.get('gaussian_sigma',10.0)
target_areas = kwargs.get('target_areas',None)
property_topomesh_vertices_deformation(topomesh,iterations=iterations_per_step,omega_forces=omega_forces,sigma_deformation=sigma_deformation,gradient_derivatives=gradient_derivatives,voxelsize=kwargs.get("image_voxelsize",(1.0,1.0,1.0)),gaussian_sigma=gaussian_sigma,target_areas=target_areas)
if cell_vertex_motion:
vertex_start_time = time()
print "--> Moving cell vertices"
if iteration <= (iterations/iterations_per_step+1)/1.:
#topomesh.update_wisp_property('barycenter',degree=0,values=((iterations/iterations_per_step+1-(iteration+1))*initial_vertex_positions.values(matched_mesh_vertices) + (iteration+1)*final_vertex_positions.values(matched_mesh_vertices))/(iterations/iterations_per_step+1),keys=matched_mesh_vertices,erase_property=False)
for v in matched_mesh_vertices:
topomesh.wisp_property('barycenter',degree=0)[v] = ((iterations/iterations_per_step+1-(iteration+1))*initial_vertex_positions[v] + (iteration+1)*final_vertex_positions[v])/(iterations/iterations_per_step+1)
vertex_end_time = time()
print "<-- Moving cell vertices [",vertex_end_time-vertex_start_time,"s]"
compute_topomesh_property(topomesh,'length',degree=1)
compute_topomesh_property(topomesh,'barycenter',degree=3)
compute_topomesh_property(topomesh,'barycenter',degree=2)
if triangular_mesh:
compute_topomesh_triangle_properties(topomesh)
compute_topomesh_property(topomesh,'normal',degree=2)
if edge_flip:
# property_topomesh_edge_flip_optimization(topomesh,omega_energies=omega_forces,simulated_annealing=True,iterations=15,display=display)
property_topomesh_edge_flip_optimization(topomesh,omega_energies=omega_forces,simulated_annealing=False,iterations=3,display=display)
compute_topomesh_property(topomesh,'length',degree=1)
compute_topomesh_property(topomesh,'barycenter',degree=3)
compute_topomesh_property(topomesh,'barycenter',degree=2)
if triangular_mesh:
compute_topomesh_triangle_properties(topomesh)
compute_topomesh_property(topomesh,'normal',degree=2)
sigma_deformation = sigma_deformation_initial*np.power(0.95,(iteration+1)*iterations_per_step)*np.ones_like(np.array(list(topomesh.wisps(0))),float)
if cell_vertex_motion:
sigma_deformation[np.where(fixed_vertex.values())[0]] = 0.
if omega_forces.has_key('regularization'):
omega_forces['regularization'] = np.minimum(omega_forces['regularization']+(omega_regularization_max*iterations_per_step)/iterations,omega_regularization_max)
if display:
pass
end_time = time()
print "_____________________________"
print ""
print " [",end_time-start_time,"s]"
#raw_input()
print "_____________________________"
optimization_end_time = time()
print "--> Optimizing Topomesh [",optimization_end_time - optimization_start_time,"s]"
return topomesh