mesh-cardiology / AV /code /1.mesh_data.py

加密主动脉管道的网格

d07e4ac over 1 year ago

4.31 kB

raw_fiber_file = "../ibamr/fibers.txt.gz"
raw_sheet_file = ""
raw_mesh_file = "../ibamr/mesh.xda.gz"
output_path = "../mesh/"
temp_path = "../trash/"

cell_types = []
cell_markers = []
cell_nodes = []
mesh_vertices = []

# Open file    
import gzip
file_handler  =  gzip.open(raw_mesh_file, "rt")

for i in range(16):
    line = file_handler.readline()
    print(line)

line = file_handler.readline()
num_cells = int(line.split('\t')[0])
for i in range(num_cells):
    line = file_handler.readline().split(" ")
    cell_types.append(int(line[0]))
    cell_markers.append(int(line[1]))
    local_cell_nodes = []
    for j in range(2, len(line)-1):
        local_cell_nodes.append(int(line[j]))
    cell_nodes.append(local_cell_nodes)

# 节点数量
for i in range(58319):
    line = file_handler.readline()
    line = line.split(" ")
    mesh_vertices.append([float(line[0]), float(line[1]), float(line[2])])

file_handler.close()

num_tets = 0
for i in range(num_cells):
    if cell_types[i] == 8 :
        num_tets += 1

from fenics import *
mesh = Mesh()
editor = MeshEditor()
editor.open(mesh,"tetrahedron",3,3)
editor.init_vertices(len(mesh_vertices))
editor.init_cells(num_tets)

for i in range(len(mesh_vertices)):
    node = Point(mesh_vertices[i][0], mesh_vertices[i][1], mesh_vertices[i][2])
    editor.add_vertex(i, node)

elements = []
j = 0
for i in range(num_cells):
    if cell_types[i] == 8 :
        element = [cell_nodes[i][0], cell_nodes[i][1], cell_nodes[i][2], cell_nodes[i][3]]
        elements.append(element)
        editor.add_cell(j,element)
        # print(i,j)
        j+=1



nodes = []
for i in range(len(elements)):
    element = elements[i]
    nodes.append(mesh_vertices[element[0]])
    nodes.append(mesh_vertices[element[1]])
    nodes.append(mesh_vertices[element[2]])
    nodes.append(mesh_vertices[element[3]])


editor.close()

xdmf = XDMFFile(output_path+"mesh.xdmf")
xdmf.write(mesh)
xdmf.close()

# fibers = []
# file_handler  =  open(raw_fiber_file, "r")
# while True:
#     line = file_handler.readline()
#     if line == '':
#         break
#     else :
#         line  = line.split("\n")[0].split("\t")
#         fiber = [float(line[1]), float(line[2]), float(line[3])]
#         fibers.append(fiber)


# file_handler.close()




materials_remarked = MeshFunction("size_t", mesh, 3, 4)

for i in range(num_tets):
    materials_remarked[i] = cell_markers[i]

File(output_path + "materials_remarked.xml") << materials_remarked
# File(temp_path + "materials_remarked.pvd") << materials_remarked

bdry_remarked = MeshFunction("size_t", mesh, 2, 2)
File(output_path + "boundaries_remarked.xml") << bdry_remarked

# f0 = MeshFunction("double", mesh, 3, 0.0)
# f1 = MeshFunction("double", mesh, 3, 0.0)
# f2 = MeshFunction("double", mesh, 3, 0.0)

# for i in range(f1.size()):
#     f0[i] = fibers[i][0]
#     f1[i] = fibers[i][0]
#     f2[i] = fibers[i][0]

# class F1(UserExpression):
#     def __init__(self, mesh, f0, f1, f2, *arg, **kwargs):
#         super().__init__(*arg, **kwargs)
#         self.mesh = mesh
#         self.f0 = f0
#         self.f1 = f1
#         self.f2 = f2
#     def eval_cell(self, values, x, cell):
#         values[0] = f0[cell.index]
#         values[1] = f1[cell.index]
#         values[2] = f2[cell.index]
#     def value_shape(self):
#         return (3,)

# V = VectorFunctionSpace(mesh, 'DG', 2)
# e1 = F1(mesh, f0, f1, f2, degree=2)
# u1 = interpolate(e1, V)
# f1 = Function(V)
# File("fibers.pvd") << f1
# xdmf = XDMFFile("mesh.xdmf")
# xdmf.write(f1)
# xdmf.close()
# File("mesh.pvd") << mesh

# TODO : I can generate tube mesh with mshr.
# mesh_2 = Mesh()
# editor.open(mesh_2, "hexahedron", 3, 3)
# editor.init_vertices(len(mesh_vertices))
# editor.init_cells(num_cells - num_tets)
#
# for i in range(len(mesh_vertices)):
#     node = Point(mesh_vertices[i][0], mesh_vertices[i][1], mesh_vertices[i][2])
#     editor.add_vertex(i, node)
#
# j = 0
# for i in range(num_cells):
#     if cell_types[i] is 10 :
#         element = [cell_nodes[i][0], cell_nodes[i][1], cell_nodes[i][2], cell_nodes[i][3], cell_nodes[i][4], cell_nodes[i][5], cell_nodes[i][6], cell_nodes[i][7]]
#         editor.add_cell(j,element)
#         j+=1
#
#
# editor.close()
#
# xdmf = XDMFFile("mesh_2.xdmf")
# xdmf.write(mesh_2)
# xdmf.close()


	raw_fiber_file = "../ibamr/fibers.txt.gz"
	raw_sheet_file = ""
	raw_mesh_file = "../ibamr/mesh.xda.gz"
	output_path = "../mesh/"
	temp_path = "../trash/"

	cell_types = []
	cell_markers = []
	cell_nodes = []
	mesh_vertices = []

	# Open file
	import gzip
	file_handler = gzip.open(raw_mesh_file, "rt")

	for i in range(16):
	line = file_handler.readline()
	print(line)

	line = file_handler.readline()
	num_cells = int(line.split('\t')[0])
	for i in range(num_cells):
	line = file_handler.readline().split(" ")
	cell_types.append(int(line[0]))
	cell_markers.append(int(line[1]))
	local_cell_nodes = []
	for j in range(2, len(line)-1):
	local_cell_nodes.append(int(line[j]))
	cell_nodes.append(local_cell_nodes)

	# 节点数量
	for i in range(58319):
	line = file_handler.readline()
	line = line.split(" ")
	mesh_vertices.append([float(line[0]), float(line[1]), float(line[2])])

	file_handler.close()

	num_tets = 0
	for i in range(num_cells):
	if cell_types[i] == 8 :
	num_tets += 1

	from fenics import *
	mesh = Mesh()
	editor = MeshEditor()
	editor.open(mesh,"tetrahedron",3,3)
	editor.init_vertices(len(mesh_vertices))
	editor.init_cells(num_tets)

	for i in range(len(mesh_vertices)):
	node = Point(mesh_vertices[i][0], mesh_vertices[i][1], mesh_vertices[i][2])
	editor.add_vertex(i, node)

	elements = []
	j = 0
	for i in range(num_cells):
	if cell_types[i] == 8 :
	element = [cell_nodes[i][0], cell_nodes[i][1], cell_nodes[i][2], cell_nodes[i][3]]
	elements.append(element)
	editor.add_cell(j,element)
	# print(i,j)
	j+=1



	nodes = []
	for i in range(len(elements)):
	element = elements[i]
	nodes.append(mesh_vertices[element[0]])
	nodes.append(mesh_vertices[element[1]])
	nodes.append(mesh_vertices[element[2]])
	nodes.append(mesh_vertices[element[3]])


	editor.close()

	xdmf = XDMFFile(output_path+"mesh.xdmf")
	xdmf.write(mesh)
	xdmf.close()

	# fibers = []
	# file_handler = open(raw_fiber_file, "r")
	# while True:
	# line = file_handler.readline()
	# if line == '':
	# break
	# else :
	# line = line.split("\n")[0].split("\t")
	# fiber = [float(line[1]), float(line[2]), float(line[3])]
	# fibers.append(fiber)


	# file_handler.close()




	materials_remarked = MeshFunction("size_t", mesh, 3, 4)

	for i in range(num_tets):
	materials_remarked[i] = cell_markers[i]

	File(output_path + "materials_remarked.xml") << materials_remarked
	# File(temp_path + "materials_remarked.pvd") << materials_remarked

	bdry_remarked = MeshFunction("size_t", mesh, 2, 2)
	File(output_path + "boundaries_remarked.xml") << bdry_remarked

	# f0 = MeshFunction("double", mesh, 3, 0.0)
	# f1 = MeshFunction("double", mesh, 3, 0.0)
	# f2 = MeshFunction("double", mesh, 3, 0.0)

	# for i in range(f1.size()):
	# f0[i] = fibers[i][0]
	# f1[i] = fibers[i][0]
	# f2[i] = fibers[i][0]

	# class F1(UserExpression):
	# def __init__(self, mesh, f0, f1, f2, arg, *kwargs):
	# super().__init__(arg, *kwargs)
	# self.mesh = mesh
	# self.f0 = f0
	# self.f1 = f1
	# self.f2 = f2
	# def eval_cell(self, values, x, cell):
	# values[0] = f0[cell.index]
	# values[1] = f1[cell.index]
	# values[2] = f2[cell.index]
	# def value_shape(self):
	# return (3,)

	# V = VectorFunctionSpace(mesh, 'DG', 2)
	# e1 = F1(mesh, f0, f1, f2, degree=2)
	# u1 = interpolate(e1, V)
	# f1 = Function(V)
	# File("fibers.pvd") << f1
	# xdmf = XDMFFile("mesh.xdmf")
	# xdmf.write(f1)
	# xdmf.close()
	# File("mesh.pvd") << mesh

	# TODO : I can generate tube mesh with mshr.
	# mesh_2 = Mesh()
	# editor.open(mesh_2, "hexahedron", 3, 3)
	# editor.init_vertices(len(mesh_vertices))
	# editor.init_cells(num_cells - num_tets)
	#
	# for i in range(len(mesh_vertices)):
	# node = Point(mesh_vertices[i][0], mesh_vertices[i][1], mesh_vertices[i][2])
	# editor.add_vertex(i, node)
	#
	# j = 0
	# for i in range(num_cells):
	# if cell_types[i] is 10 :
	# element = [cell_nodes[i][0], cell_nodes[i][1], cell_nodes[i][2], cell_nodes[i][3], cell_nodes[i][4], cell_nodes[i][5], cell_nodes[i][6], cell_nodes[i][7]]
	# editor.add_cell(j,element)
	# j+=1
	#
	#
	# editor.close()
	#
	# xdmf = XDMFFile("mesh_2.xdmf")
	# xdmf.write(mesh_2)
	# xdmf.close()