你已经派生过 gprMax
镜像自地址
https://gitee.com/sunhf/gprMax.git
已同步 2025-08-06 04:26:52 +08:00
Removed XDMF work from master branch.
这个提交包含在：
Craig Warren
@@ -8,7 +8,6 @@ dependencies:
|
||||
- cython
|
||||
- h5py
|
||||
- jupyter
|
||||
- lxml
|
||||
- matplotlib
|
||||
- numpy
|
||||
- psutil
|
||||
|
||||
374
gprMax/xdmf.py
374
gprMax/xdmf.py
@@ -1,374 +0,0 @@
|
||||
import copy
|
||||
|
||||
import h5py
|
||||
from lxml import etree
|
||||
import numpy as np
|
||||
|
||||
from gprMax.grid import Grid
|
||||
|
||||
|
||||
class ListCounter():
|
||||
|
||||
def __init__(self, npArray):
|
||||
self.array = npArray
|
||||
self.count = 0
|
||||
|
||||
def add(self, item):
|
||||
self.array[self.count] = item
|
||||
self.count += 1
|
||||
|
||||
|
||||
class EdgeLabels:
|
||||
|
||||
def __init__(self, grid):
|
||||
"""
|
||||
Class to define some connectivity of for an n x l x m
|
||||
grid
|
||||
"""
|
||||
self.total_edges = grid.n_edges()
|
||||
self.grid = grid
|
||||
self.edges = np.zeros((self.total_edges, 2), np.int8)
|
||||
self.edge_counter = ListCounter(self.edges)
|
||||
|
||||
def add_edge(self, in_label, i, j, k):
|
||||
"""
|
||||
Adds the the edge specified by in_node and the i,j,k position of the outnode
|
||||
"""
|
||||
out_label = self.grid.get(i, j, k)
|
||||
edge = np.array([in_label, out_label])
|
||||
self.edge_counter.add(edge)
|
||||
|
||||
|
||||
class EdgeMaterials:
|
||||
|
||||
def __init__(self, fdtd_grid):
|
||||
self.fdtd_grid = fdtd_grid
|
||||
self.n_edges = fdtd_grid.n_edges()
|
||||
self.materials = np.zeros((self.n_edges), np.int8)
|
||||
self.materialCounter = ListCounter(self.materials)
|
||||
|
||||
# direction x->0 y->1 z->2
|
||||
def add_material(self, i, j, k, direction):
|
||||
|
||||
material = self.fdtd_grid.ID[direction, i, j, k]
|
||||
self.materialCounter.add(material)
|
||||
|
||||
|
||||
class Coordinates:
|
||||
|
||||
def __init__(self, grid):
|
||||
self.total_coordinates = grid.n_nodes()
|
||||
self.coordinates = np.zeros((self.total_coordinates, 3), np.int8)
|
||||
self.coord_counter = ListCounter(self.coordinates)
|
||||
|
||||
def add_coordinate(self, x, y, z):
|
||||
self.coord_counter.add(np.array([x, y, z]))
|
||||
|
||||
|
||||
class Solids:
|
||||
|
||||
def __init__(self, fdtd_grid):
|
||||
self.fdtd_grid = fdtd_grid
|
||||
self.total_solids = fdtd_grid.n_cells()
|
||||
self.solids = np.zeros((self.total_solids), np.int8)
|
||||
self.solid_counter = ListCounter(self.solids)
|
||||
|
||||
def add_solid(self, i, j, k):
|
||||
|
||||
self.solid_counter.add(self.fdtd_grid.solid[i][j][k])
|
||||
|
||||
|
||||
class SolidLabels():
|
||||
|
||||
def __init__(self, label_grid):
|
||||
self.label_grid = label_grid
|
||||
self.total_solids = label_grid.n_cells()
|
||||
self.solid_labels = np.zeros((self.total_solids, 8), np.int8)
|
||||
self.label_counter = ListCounter(self.solid_labels)
|
||||
|
||||
def hexCellPicker(self, grid, i, j, k):
|
||||
"""
|
||||
This is the ordering of nodes in the hexahedron cell.
|
||||
|
||||
7 --------- 6
|
||||
/ /|
|
||||
4 --------- 5 2
|
||||
| 3 | /
|
||||
| / |/
|
||||
0 --------- 1
|
||||
|
||||
0 1 2 3 4 5 6 7
|
||||
"""
|
||||
|
||||
cell = [
|
||||
grid[i][j][k],
|
||||
# 1
|
||||
grid[i + 1][j][k],
|
||||
# 2
|
||||
grid[i + 1][j + 1][k],
|
||||
# 3
|
||||
grid[i][j + 1][k],
|
||||
# 4
|
||||
grid[i][j][k + 1],
|
||||
# 5
|
||||
grid[i + 1][j][k + 1],
|
||||
# 6
|
||||
grid[i + 1][j + 1][k + 1],
|
||||
# 7
|
||||
grid[i][j + 1][k + 1]
|
||||
]
|
||||
|
||||
return cell
|
||||
|
||||
def add(self, i, j, k):
|
||||
|
||||
solid_labels = self.hexCellPicker(self.label_grid.grid, i, j, k)
|
||||
self.label_counter.add(solid_labels)
|
||||
|
||||
|
||||
class SolidManager(Grid):
|
||||
|
||||
def __init__(self, label_grid, fdtd_grid):
|
||||
|
||||
super().__init__(label_grid.grid)
|
||||
self.solids = Solids(fdtd_grid)
|
||||
self.solid_labels = SolidLabels(label_grid)
|
||||
|
||||
def createSolid(self, i, j, k):
|
||||
if i < self.i_max and j < self.j_max and k < self.k_max:
|
||||
self.solids.add_solid(i, j, k)
|
||||
self.solid_labels.add(i, j, k)
|
||||
|
||||
|
||||
class EdgeManager(Grid):
|
||||
"""
|
||||
Class to manage the creation of edges and matching edge materials.
|
||||
"""
|
||||
|
||||
def __init__(self, label_grid, fdtd_grid):
|
||||
super().__init__(label_grid.grid)
|
||||
self.edges = EdgeLabels(label_grid)
|
||||
self.edge_materials = EdgeMaterials(fdtd_grid)
|
||||
|
||||
def createEdges(self, i, j, k):
|
||||
"""
|
||||
Create the relevant edges and corresponding edge materials.
|
||||
Args:
|
||||
i (int): i index of label in labels_grid
|
||||
j (int): j index of label in labels_grid
|
||||
k (int): k index of label in labels_grid
|
||||
|
||||
"""
|
||||
edges = self.edges
|
||||
edge_materials = self.edge_materials
|
||||
i_max = self.i_max
|
||||
j_max = self.j_max
|
||||
k_max = self.k_max
|
||||
label = self.edges.grid.get(i, j, k)
|
||||
|
||||
# Each vertex can have varying numbers of edges
|
||||
|
||||
# Type 1 vertex
|
||||
if i < i_max and j < j_max and k < k_max:
|
||||
edges.add_edge(label, i + 1, j, k)
|
||||
edges.add_edge(label, i, j + 1, k)
|
||||
edges.add_edge(label, i, j, k + 1)
|
||||
|
||||
edge_materials.add_material(i, j, k, 0)
|
||||
edge_materials.add_material(i, j, k, 1)
|
||||
edge_materials.add_material(i, j, k, 2)
|
||||
|
||||
# Only this node can support a cell
|
||||
|
||||
# Type 2 vertex
|
||||
elif i < i_max and j == j_max and k == k_max:
|
||||
edges.add_edge(label, i + 1, j, k)
|
||||
edge_materials.add_material(i, j, k, 0)
|
||||
|
||||
# Type 7 vertex
|
||||
elif i < i_max and j == j_max and k < k_max:
|
||||
edges.add_edge(label, i + 1, j, k)
|
||||
edges.add_edge(label, i, j, k + 1)
|
||||
edge_materials.add_material(i, j, k, 0)
|
||||
edge_materials.add_material(i, j, k, 2)
|
||||
|
||||
# Type 6 vertex
|
||||
elif i == i_max and j == j_max and k < k_max:
|
||||
edges.add_edge(label, i, j, k + 1)
|
||||
edge_materials.add_material(i, j, k, 2)
|
||||
|
||||
# Type 5 vertex
|
||||
elif i == i_max and j < j_max and k < k_max:
|
||||
edges.add_edge(label, i, j, k + 1)
|
||||
edges.add_edge(label, i, j + 1, k)
|
||||
edge_materials.add_material(i, j, k, 2)
|
||||
edge_materials.add_material(i, j, k, 1)
|
||||
|
||||
# Type 4 vertex
|
||||
elif i == i_max and j < j_max and k == k_max:
|
||||
edges.add_edge(label, i, j + 1, k)
|
||||
edge_materials.add_material(i, j, k, 1)
|
||||
|
||||
# Type 8 vertex
|
||||
elif i < i_max and j < j_max and k == k_max:
|
||||
edges.add_edge(label, i, j + 1, k)
|
||||
edges.add_edge(label, i + 1, j, k)
|
||||
edge_materials.add_material(i, j, k, 1)
|
||||
edge_materials.add_material(i, j, k, 0)
|
||||
|
||||
# Type 3 vertex
|
||||
# Has no new connectivity
|
||||
elif i == i_max and j == j_max and k == k_max:
|
||||
pass
|
||||
else:
|
||||
print('oh no')
|
||||
|
||||
|
||||
def process_grid(fdtd_grid, res):
|
||||
|
||||
# Create a grid of labels with equal dimension to fdtd grid
|
||||
labels = np.arange(fdtd_grid.n_nodes()).reshape(fdtd_grid.nx, fdtd_grid.ny, fdtd_grid.nz)
|
||||
|
||||
label_grid = Grid(labels)
|
||||
|
||||
# Define coordinates for each node
|
||||
coordinates = Coordinates(fdtd_grid)
|
||||
|
||||
solid_manager = SolidManager(label_grid, fdtd_grid)
|
||||
|
||||
if res == 'f':
|
||||
edge_manager = EdgeManager(label_grid, fdtd_grid)
|
||||
|
||||
# Iterate through the label and create relevant edges and solids.
|
||||
|
||||
for i, ix in enumerate(labels):
|
||||
for j, jx in enumerate(ix):
|
||||
for k, kx in enumerate(jx):
|
||||
|
||||
if res == 'f':
|
||||
edge_manager.createEdges(i, j, k)
|
||||
|
||||
solid_manager.createSolid(i, j, k)
|
||||
|
||||
# Add the coordinates
|
||||
coordinates.add_coordinate(i, j, k)
|
||||
|
||||
data = {
|
||||
'coordinates': coordinates,
|
||||
'solids': solid_manager.solids,
|
||||
'solid_labels': solid_manager.solid_labels,
|
||||
}
|
||||
|
||||
if res == 'f':
|
||||
data['edges'] = edge_manager.edges
|
||||
data['edge_materials'] = edge_manager.edge_materials
|
||||
|
||||
dir(edge_manager.edge_materials)
|
||||
|
||||
return data
|
||||
|
||||
|
||||
def write_output_file(filename, grid, res):
|
||||
|
||||
data = process_grid(grid, res)
|
||||
data['filename'] = filename
|
||||
data['xml_doc'] = create_xdmf_markup(data)
|
||||
|
||||
write_H5file(data)
|
||||
write_xml_doc(data)
|
||||
|
||||
|
||||
def write_xml_doc(options):
|
||||
# write xml to file
|
||||
with open(options['filename'] + '.xdmf', 'wb') as xdmf_f:
|
||||
xdmf_f.write(options['xml_doc'])
|
||||
|
||||
|
||||
def write_H5file(options):
|
||||
|
||||
f = h5py.File(options['filename'] + '.h5', "w")
|
||||
coords = f.create_group("mesh")
|
||||
data = f.create_group("data")
|
||||
|
||||
coords.create_dataset('coordinates', data=options['coordinates'].coordinates)
|
||||
coords.create_dataset('solid_connectivity', data=options['solid_labels'].solid_labels)
|
||||
data.create_dataset('solids', data=options['solids'].solids)
|
||||
|
||||
if 'edges' in options:
|
||||
data.create_dataset('materials', data=options['edge_materials'].materials)
|
||||
coords.create_dataset('connectivity', data=options['edges'].edges)
|
||||
|
||||
|
||||
def create_xdmf_markup(options):
|
||||
|
||||
# Write the XDMF markup for edge style grid
|
||||
xdmf_el = etree.Element("Xdmf", Version="2.0")
|
||||
|
||||
domain_el = etree.Element("Domain")
|
||||
xdmf_el.append(domain_el)
|
||||
|
||||
geometry_el = etree.Element("Geometry", GeometryType="XYZ")
|
||||
coordinates_dimensions = "{} 3".format(options['coordinates'].total_coordinates)
|
||||
origin_el = etree.Element("DataItem", Dimensions=coordinates_dimensions, NumberType="Float", Precision="8", Format="HDF")
|
||||
origin_el.text = "{}:/mesh/coordinates".format(options['filename'] + '.h5')
|
||||
geometry_el.append(origin_el)
|
||||
|
||||
# Check if there are edges to write
|
||||
if 'edges' in options:
|
||||
|
||||
grid_el = etree.Element("Grid", Name="Edges", GridType="Uniform")
|
||||
domain_el.append(grid_el)
|
||||
|
||||
# Create the grid node
|
||||
topology_el = etree.Element("Topology", TopologyType="Polyline", NumberOfElements=str(options['edges'].total_edges))
|
||||
grid_el.append(topology_el)
|
||||
|
||||
topology_dimensions = "{} 2".format(options['edges'].total_edges)
|
||||
top_data_el = etree.Element("DataItem", Dimensions=topology_dimensions, NumberType="Float", Precision="8", Format="HDF")
|
||||
top_data_el.text = "{}:/mesh/connectivity".format(options['filename'] + '.h5')
|
||||
topology_el.append(top_data_el)
|
||||
|
||||
# Create the Geometry node
|
||||
grid_el.append(copy.deepcopy(geometry_el))
|
||||
|
||||
# Create the origin coordinates
|
||||
|
||||
# Create the materials attribute
|
||||
attr_el = etree.Element("Attribute", Center="Cell", Name="Edge_Materials")
|
||||
grid_el.append(attr_el)
|
||||
|
||||
materials_dimensions = "{} 1".format(options['edge_materials'].materials.size)
|
||||
materials_el = etree.Element("DataItem", Dimensions=materials_dimensions, NumberType="Float", Precision="8", Format="HDF")
|
||||
materials_el.text = "{}:/data/materials".format(options['filename'] + '.h5')
|
||||
attr_el.append(materials_el)
|
||||
|
||||
v_grid_el = etree.Element("Grid", Name="Voxel", GridType="Uniform")
|
||||
domain_el.append(v_grid_el)
|
||||
|
||||
n_solids = str(options['solids'].solids.size)
|
||||
v_topology_el = etree.Element("Topology", TopologyType="Hexahedron", NumberOfElements=str(options['solids'].solids.size))
|
||||
v_grid_el.append(v_topology_el)
|
||||
|
||||
solid_label_d = "{} {}".format(n_solids, 8)
|
||||
solid_labels_el = etree.Element("DataItem", Dimensions=solid_label_d, Format="HDF")
|
||||
solid_labels_el.text = "{}:/mesh/solid_connectivity".format(options['filename'] + '.h5')
|
||||
v_topology_el.append(solid_labels_el)
|
||||
|
||||
# Same geometry as edges
|
||||
v_grid_el.append(copy.deepcopy(geometry_el))
|
||||
|
||||
v_attr = etree.Element("Attribute", Name="Voxel_Materials", Center="Cell")
|
||||
v_grid_el.append(v_attr)
|
||||
|
||||
d4 = etree.Element("DataItem", Format="HDF", NumberType="Float", Precision="4", Dimensions=str(options['solids'].solids.size))
|
||||
d4.text = "{}:/data/solids".format(options['filename'] + '.h5')
|
||||
v_attr.append(d4)
|
||||
|
||||
# Define a doctype - useful for parsers
|
||||
doc_type = '<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>'
|
||||
|
||||
# Serialize elements
|
||||
xml_doc = etree.tostring(xdmf_el, xml_declaration=True,
|
||||
encoding="utf-8", doctype=doc_type, pretty_print=True)
|
||||
|
||||
return xml_doc
|
||||
在新工单中引用
屏蔽一个用户