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已同步 2025-08-07 04:56:51 +08:00
hdf5 xdmf support
这个提交包含在：
jasminium
@@ -19,6 +19,7 @@
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import sys
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import numpy as np
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from struct import pack
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from gprMax.xdmf import write_output_file
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from gprMax.utilities import round_value
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@@ -55,6 +56,10 @@ class GeometryView:
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self.filename = filename
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self.type = type
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def write_xdmf(self, modelrun, numbermodelruns, G):
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filename = self.filename[:-4]
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write_output_file(filename, G)
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def write_vtk(self, modelrun, numbermodelruns, G):
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"""Writes the geometry information to a VTK file. Either ImageData (.vti) for a per-cell geometry view, or PolygonalData (.vtp) for a per-cell-edge geometry view.
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@@ -348,6 +348,7 @@ def run_model(args, modelrun, numbermodelruns, inputfile, usernamespace):
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tgeostart = perf_counter()
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for geometryview in G.geometryviews:
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geometryview.write_vtk(modelrun, numbermodelruns, G)
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geometryview.write_xdmf(modelrun, numbermodelruns, G)
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tgeoend = perf_counter()
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print('\nGeometry file(s) written in [HH:MM:SS]: {}'.format(datetime.timedelta(seconds=int(tgeoend - tgeostart))))
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@@ -22,8 +22,31 @@ import matplotlib.pyplot as plt
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from gprMax.constants import c, floattype, complextype
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from gprMax.materials import Material
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class Grid():
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class FDTDGrid:
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def __init__(self, grid):
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self.nx = grid.shape[0]
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self.ny = grid.shape[1]
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self.nz = grid.shape[2]
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self.grid = grid
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def n_edges(self):
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l = self.nx
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m = self.ny
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n = self.nz
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e = (l * m * (n - 1)) + (m * n * (l - 1)) + (l * n * (m - 1))
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return e
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def n_nodes(self):
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return self.nx * self.ny * self.nz
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def n_cells(self):
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return (self.nx - 1) * (self.ny - 1) * (self.nz - 1)
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def get(self, i, j, k):
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return self.grid[i, j, k]
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class FDTDGrid(Grid):
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"""Holds attributes associated with the entire grid. A convenient way for accessing regularly used parameters."""
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def __init__(self):
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361
gprMax/xdmf.py
普通文件
361
gprMax/xdmf.py
普通文件
@@ -0,0 +1,361 @@
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import numpy as np
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import h5py
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from lxml import etree
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from gprMax.grid import Grid
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import copy
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class Edges:
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def __init__(self, grid):
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"""
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Class to define some connectivity of for an n x l x m
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grid
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"""
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self.total_edges = grid.n_edges()
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self.edges = np.zeros((self.total_edges, 2), np.float32)
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self.edge_count = 0
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self.grid = grid
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"""
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Adds the the edge specified by in_node and the i,j,k position of the outnode
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"""
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def add_edge(self, in_label, i, j, k):
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out_label = self.grid.get(i, j, k)
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self.edges[self.edge_count] = np.array([in_label, out_label])
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self.edge_count += 1
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class Coordinates:
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def __init__(self, grid):
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self.total_coordinates = grid.nx * grid.ny * grid.nz
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self.coordinate_count = 0
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self.coordinates = np.zeros((self.total_coordinates, 3), np.float32)
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def add_coordinate(self, x, y, z):
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self.coordinates[self.coordinate_count] = np.array([x, y, z])
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self.coordinate_count += 1
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def hexCellPicker(grid, i, j, k):
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"""
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This is the ordering of nodes in the hexahedron cell.
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7 --------- 6
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/ /|
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4 --------- 5 2
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| 3 | /
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| / |/
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0 --------- 1
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0 1 2 3 4 5 6 7
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"""
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cell = [
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grid[i][j][k],
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# 1
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grid[i + 1][j][k],
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# 2
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grid[i + 1][j + 1][k],
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# 3
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grid[i][j + 1][k],
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# 4
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grid[i][j][k + 1],
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# 5
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grid[i + 1][j][k + 1],
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# 6
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grid[i + 1][j + 1][k + 1],
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# 7
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grid[i][j + 1][k + 1]
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]
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return cell
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class Solids:
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def __init__(self, fdtd_grid):
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self.count = 0
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self.fdtd_grid = fdtd_grid
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self.total_solids = fdtd_grid.n_cells()
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self.solids = np.zeros((self.total_solids), np.float32)
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def add_solid(self, i, j, k):
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self.solids[self.count] = self.fdtd_grid.solid[i][j][k]
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self.count += 1
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class SolidLabels():
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def __init__(self, label_grid):
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self.count = 0
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self.label_grid = label_grid
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self.total_solids = label_grid.n_cells()
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self.solid_labels = np.zeros((self.total_solids, 8), np.float32)
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def add(self, i, j, k):
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solid_labels = hexCellPicker(self.label_grid.grid, i, j, k)
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self.solid_labels[self.count] = solid_labels
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self.count += 1
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class Materials:
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def __init__(self, fdtd_grid):
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self.fdtd_grid = fdtd_grid
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self.n_edges = fdtd_grid.n_edges()
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self.materials = np.zeros((self.n_edges), np.float32)
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self.material_count = 0
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# direction x->0 y->1 z->2
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def add_material(self, i, j, k, direction):
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material = self.fdtd_grid.ID[direction, i, j, k]
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self.materials[self.material_count] = material
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self.material_count += 1
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def process_grid(fdtd_grid):
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# Dimensions of the problem domain.
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nx = fdtd_grid.nx
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ny = fdtd_grid.ny
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nz = fdtd_grid.nz
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# label each node in the space
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labels = np.arange(nx * ny * nz).reshape(nx, ny, nz)
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label_grid = Grid(labels)
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# Edges define the connectivity of the grid.
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edges = Edges(label_grid)
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# Material for each edge
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edge_materials = Materials(fdtd_grid)
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# Define coordinates for each node
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coordinates = Coordinates(fdtd_grid)
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# Material for each solid
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solids = Solids(fdtd_grid)
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# Connectivity for hexhahedron grid
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solid_labels = SolidLabels(label_grid)
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i_max = nx - 1
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j_max = ny - 1
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k_max = nz - 1
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for i, ix in enumerate(labels):
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for j, jx in enumerate(ix):
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for k, kx in enumerate(jx):
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label = labels[i][j][k]
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# Each vertex can have varying numbers of edges
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# Type 1 vertex
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if i < i_max and j < j_max and k < k_max:
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edges.add_edge(label, i + 1, j, k)
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edges.add_edge(label, i, j + 1, k)
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edges.add_edge(label, i, j, k + 1)
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edge_materials.add_material(i, j, k, 0)
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edge_materials.add_material(i, j, k, 1)
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edge_materials.add_material(i, j, k, 2)
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# Only this node can support a cell
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solids.add_solid(i, j, k)
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solid_labels.add(i, j, k)
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# Type 2 vertex
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elif i < i_max and j == j_max and k == k_max:
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edges.add_edge(label, i + 1, j, k)
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edge_materials.add_material(i, j, k, 0)
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# Type 7 vertex
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elif i < i_max and j == j_max and k < k_max:
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edges.add_edge(label, i + 1, j, k)
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edges.add_edge(label, i, j, k + 1)
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edge_materials.add_material(i, j, k, 0)
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edge_materials.add_material(i, j, k, 2)
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# Type 6 vertex
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elif i == i_max and j == j_max and k < k_max:
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edges.add_edge(label, i, j, k + 1)
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edge_materials.add_material(i, j, k, 2)
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# Type 5 vertex
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elif i == i_max and j < j_max and k < k_max:
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edges.add_edge(label, i, j, k + 1)
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edges.add_edge(label, i, j + 1, k)
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edge_materials.add_material(i, j, k, 2)
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edge_materials.add_material(i, j, k, 1)
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# Type 4 vertex
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elif i == i_max and j < j_max and k == k_max:
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edges.add_edge(label, i, j + 1, k)
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edge_materials.add_material(i, j, k, 1)
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# Type 8 vertex
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elif i < i_max and j < j_max and k == k_max:
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edges.add_edge(label, i, j + 1, k)
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edges.add_edge(label, i + 1, j, k)
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edge_materials.add_material(i, j, k, 1)
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edge_materials.add_material(i, j, k, 0)
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# Type 3 vertex
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# Has no new connectivity
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elif i == i_max and j == j_max and k == k_max:
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pass
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else:
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print('oh no')
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# Add the coordinates
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coordinates.add_coordinate(i, j, k)
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#x = np.arange(fdtd_grid.nx)
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#y = np.arange(fdtd_grid.ny)
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#z = np.arange(fdtd_grid.nz)
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return {
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'coordinates': coordinates,
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'solids': solids,
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'solid_labels': solid_labels,
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'edges': edges,
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'edge_materials': edge_materials,
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#'x': x,
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#'y': y,
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#'z': z
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}
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def write_output_file(filename, grid):
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data = process_grid(grid)
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data['filename'] = filename
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data['xml_doc'] = create_xdmf_markup(data)
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write_H5file(data)
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write_xml_doc(data)
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def write_xml_doc(options):
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#write xml to file
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with open(options['filename'] + '.xdmf', 'wb') as xdmf_f:
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xdmf_f.write(options['xml_doc'])
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def write_H5file(options):
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f = h5py.File(options['filename'] + '.h5', "w")
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coords = f.create_group("mesh")
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coords.create_dataset('coordinates', data=options['coordinates'].coordinates)
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coords.create_dataset('connectivity', data=options['edges'].edges)
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coords.create_dataset('solid_connectivity', data=options['solid_labels'].solid_labels)
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#coords.create_dataset('x', data=options['x'])
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#coords.create_dataset('y', data=options['y'])
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#coords.create_dataset('z', data=options['z'])
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data = f.create_group("data")
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data.create_dataset('materials', data=options['edge_materials'].materials)
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data.create_dataset('solids', data=options['solids'].solids)
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def create_xdmf_markup(options):
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# Write the XDMF markup for edge style grid
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xdmf_el = etree.Element("Xdmf", Version="2.0")
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domain_el = etree.Element("Domain")
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xdmf_el.append(domain_el)
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grid_el = etree.Element("Grid", Name="Edges", GridType="Uniform")
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domain_el.append(grid_el)
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# Create the grid node
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topology_el = etree.Element("Topology", TopologyType="Polyline", NumberOfElements=str(options['edges'].total_edges))
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grid_el.append(topology_el)
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topology_dimensions = "{} 2".format(options['edges'].total_edges)
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top_data_el = etree.Element("DataItem", Dimensions=topology_dimensions, NumberType="Float", Precision="8", Format="HDF")
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top_data_el.text = "{}:/mesh/connectivity".format(options['filename'] + '.h5')
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topology_el.append(top_data_el)
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# Create the Geometry node
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geometry_el = etree.Element("Geometry", GeometryType="XYZ")
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grid_el.append(geometry_el)
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# Create the origin coordinates
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coordinates_dimensions = "{} 3".format(options['coordinates'].total_coordinates)
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origin_el = etree.Element("DataItem", Dimensions=coordinates_dimensions, NumberType="Float", Precision="8", Format="HDF")
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origin_el.text = "{}:/mesh/coordinates".format(options['filename'] + '.h5')
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geometry_el.append(origin_el)
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# Create the materials attribute
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attr_el = etree.Element("Attribute", Center="Cell", Name="Edge_Materials")
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grid_el.append(attr_el)
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materials_dimensions = "{} 1".format(options['edge_materials'].material_count)
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materials_el = etree.Element("DataItem", Dimensions=materials_dimensions, NumberType="Float", Precision="8", Format="HDF")
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materials_el.text = "{}:/data/materials".format(options['filename'] + '.h5')
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attr_el.append(materials_el)
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"""
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# VOXEL style markup
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v_grid_el = etree.Element("Grid", Name="Voxel", GridType="Uniform")
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domain_el.append(v_grid_el)
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noe = "{} {} {}".format(options['x'].size, options['y'].size, options['y'].size)
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v_topology_el = etree.Element("Topology", TopologyType="3DRectMesh", NumberOfElements=noe)
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v_grid_el.append(v_topology_el)
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v_geometry = etree.Element("Geometry", GeometryType="VXVYVZ")
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v_grid_el.append(v_geometry)
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d1 = etree.Element("DataItem", Dimensions=str(options['x'].size), NumberType="Float", Precision="4", Format="HDF")
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d1.text = "{}:/mesh/x".format(options['filename'] + '.h5')
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v_geometry.append(d1)
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d2 = etree.Element("DataItem", Dimensions=str(options['y'].size), NumberType="Float", Precision="4", Format="HDF")
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d2.text = "{}:/mesh/y".format(options['filename'] + '.h5')
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v_geometry.append(d2)
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d3 = etree.Element("DataItem", Dimensions=str(options['z'].size), NumberType="Float", Precision="4", Format="HDF")
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d3.text = "{}:/mesh/z".format(options['filename'] + '.h5')
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v_geometry.append(d3)
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v_attr = etree.Element("Attribute", Name="material-blocks", Center="Cell")
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v_grid_el.append(v_attr)
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d4 = etree.Element("DataItem", Format="HDF", NumberType="Float", Precision="4", Dimensions=str(options['solids'].solids.size))
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d4.text = "{}:/data/solids".format(options['filename'] + '.h5')
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v_attr.append(d4)
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"""
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v_grid_el = etree.Element("Grid", Name="Voxel", GridType="Uniform")
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domain_el.append(v_grid_el)
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n_solids = str(options['solids'].solids.size)
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v_topology_el = etree.Element("Topology", TopologyType="Hexahedron", NumberOfElements=str(options['solids'].solids.size))
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v_grid_el.append(v_topology_el)
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solid_label_d = "{} {}".format(n_solids, 8)
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solid_labels_el = etree.Element("DataItem", Dimensions=solid_label_d, Format="HDF")
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solid_labels_el.text = "{}:/mesh/solid_connectivity".format(options['filename'] + '.h5')
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v_topology_el.append(solid_labels_el)
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# Same geometry as edges
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v_grid_el.append(copy.deepcopy(geometry_el))
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v_attr = etree.Element("Attribute", Name="Voxel_Materials", Center="Cell")
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v_grid_el.append(v_attr)
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d4 = etree.Element("DataItem", Format="HDF", NumberType="Float", Precision="4", Dimensions=str(options['solids'].solids.size))
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d4.text = "{}:/data/solids".format(options['filename'] + '.h5')
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v_attr.append(d4)
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# Define a doctype - useful for parsers
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doc_type = '<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>'
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# Serialize elements
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xml_doc = etree.tostring(xdmf_el, xml_declaration=True,
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encoding="utf-8", doctype=doc_type, pretty_print=True)
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return xml_doc
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|
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