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https://gitee.com/sunhf/gprMax.git
已同步 2025-08-06 20:46:52 +08:00
Merge remote-tracking branch 'origin/master'
这个提交包含在：
Craig Warren
@@ -60,7 +60,7 @@ class GeometryView(object):
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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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write_output_file(filename, G, self.type)
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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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@@ -24,11 +24,14 @@ from gprMax.materials import Material
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class Grid(object):
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"""Generic grid/mesh."""
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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.i_max = self.nx - 1
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self.j_max = self.ny - 1
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self.k_max = self.nz - 1
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self.grid = grid
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def n_edges(self):
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422
gprMax/xdmf.py
422
gprMax/xdmf.py
@@ -4,11 +4,21 @@ import h5py
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from lxml import etree
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import numpy as np
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import time
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from gprMax.grid import Grid
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class ListCounter():
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def __init__(self, npArray):
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self.array = npArray
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self.count = 0
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class Edges:
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def add(self, item):
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self.array[self.count] = item
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self.count += 1
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class EdgeLabels:
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def __init__(self, grid):
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@@ -17,33 +27,68 @@ class Edges:
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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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self.edges = np.zeros((self.total_edges, 2), np.int8)
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self.edge_counter = ListCounter(self.edges)
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def add_edge(self, in_label, i, j, k):
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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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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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edge = np.array([in_label, out_label])
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self.edge_counter.add(edge)
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class EdgeMaterials:
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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.int8)
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self.materialCounter = ListCounter(self.materials)
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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.materialCounter.add(material)
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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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self.total_coordinates = grid.n_nodes()
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self.coordinates = np.zeros((self.total_coordinates, 3), np.int8)
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self.coord_counter = ListCounter(self.coordinates)
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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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self.coord_counter.add(np.array([x, y, z]))
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def hexCellPicker(grid, i, j, k):
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"""
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class Solids:
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def __init__(self, fdtd_grid):
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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.int8)
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self.solid_counter = ListCounter(self.solids)
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def add_solid(self, i, j, k):
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self.solid_counter.add(self.fdtd_grid.solid[i][j][k])
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class SolidLabels():
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def __init__(self, label_grid):
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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.int8)
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self.label_counter = ListCounter(self.solid_labels)
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def hexCellPicker(self, 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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@@ -54,186 +99,178 @@ def hexCellPicker(grid, i, j, k):
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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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"""
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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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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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return cell
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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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solid_labels = self.hexCellPicker(self.label_grid.grid, i, j, k)
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self.label_counter.add(solid_labels)
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class SolidManager(Grid):
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def __init__(self, label_grid, fdtd_grid):
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super().__init__(label_grid.grid)
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self.solids = Solids(fdtd_grid)
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self.solid_labels = SolidLabels(label_grid)
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def createSolid(self, i, j, k):
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if i < self.i_max and j < self.j_max and k < self.k_max:
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self.solids.add_solid(i, j, k)
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self.solid_labels.add(i, j, k)
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class Materials:
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class EdgeManager(Grid):
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"""
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Class to manage the creation of edges and matching edge materials.
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"""
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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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def __init__(self, label_grid, fdtd_grid):
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super().__init__(label_grid.grid)
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self.edges = EdgeLabels(label_grid)
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self.edge_materials = EdgeMaterials(fdtd_grid)
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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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def createEdges(self, i, j, k):
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"""
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Create the relevant edges and corresponding edge materials.
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Args:
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i (int): i index of label in labels_grid
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j (int): j index of label in labels_grid
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k (int): k index of label in labels_grid
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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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"""
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edges = self.edges
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edge_materials = self.edge_materials
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i_max = self.i_max
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j_max = self.j_max
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k_max = self.k_max
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label = self.edges.grid.get(i, j, k)
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self.material_count += 1
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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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# 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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def process_grid(fdtd_grid):
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def process_grid(fdtd_grid, res):
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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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# Create a grid of labels with equal dimension to fdtd grid
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labels = np.arange(fdtd_grid.n_nodes()).reshape(fdtd_grid.nx, fdtd_grid.ny, fdtd_grid.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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solid_manager = SolidManager(label_grid, fdtd_grid)
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# Connectivity for hexhahedron grid
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solid_labels = SolidLabels(label_grid)
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if res == 'f':
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edge_manager = EdgeManager(label_grid, fdtd_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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# Iterate through the label and create relevant edges and solids.
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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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if res == 'f':
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edge_manager.createEdges(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
|
||||
solids.add_solid(i, j, k)
|
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solid_labels.add(i, j, k)
|
||||
|
||||
# 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')
|
||||
solid_manager.createSolid(i, j, k)
|
||||
|
||||
# Add the coordinates
|
||||
coordinates.add_coordinate(i, j, k)
|
||||
|
||||
return {
|
||||
data = {
|
||||
'coordinates': coordinates,
|
||||
'solids': solids,
|
||||
'solid_labels': solid_labels,
|
||||
'edges': edges,
|
||||
'edge_materials': edge_materials,
|
||||
'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
|
||||
|
||||
def write_output_file(filename, grid):
|
||||
dir(edge_manager.edge_materials)
|
||||
|
||||
data = process_grid(grid)
|
||||
return data
|
||||
|
||||
|
||||
def write_output_file(filename, grid, res):
|
||||
|
||||
data = process_grid(grid, res)
|
||||
data['filename'] = filename
|
||||
data['xml_doc'] = create_xdmf_markup(data)
|
||||
|
||||
@@ -249,14 +286,17 @@ def write_xml_doc(options):
|
||||
|
||||
def write_H5file(options):
|
||||
|
||||
f = h5py.File(options['filename'] + '.h5', "w")
|
||||
coords = f.create_group("mesh")
|
||||
coords.create_dataset('coordinates', data=options['coordinates'].coordinates)
|
||||
coords.create_dataset('connectivity', data=options['edges'].edges)
|
||||
coords.create_dataset('solid_connectivity', data=options['solid_labels'].solid_labels)
|
||||
data = f.create_group("data")
|
||||
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)
|
||||
data.create_dataset('solids', data=options['solids'].solids)
|
||||
coords.create_dataset('connectivity', data=options['edges'].edges)
|
||||
|
||||
|
||||
def create_xdmf_markup(options):
|
||||
@@ -267,36 +307,40 @@ def create_xdmf_markup(options):
|
||||
domain_el = etree.Element("Domain")
|
||||
xdmf_el.append(domain_el)
|
||||
|
||||
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
|
||||
geometry_el = etree.Element("Geometry", GeometryType="XYZ")
|
||||
grid_el.append(geometry_el)
|
||||
|
||||
# Create the origin coordinates
|
||||
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)
|
||||
|
||||
# Create the materials attribute
|
||||
attr_el = etree.Element("Attribute", Center="Cell", Name="Edge_Materials")
|
||||
grid_el.append(attr_el)
|
||||
# Check if there are edges to write
|
||||
if 'edges' in options:
|
||||
|
||||
materials_dimensions = "{} 1".format(options['edge_materials'].material_count)
|
||||
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)
|
||||
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)
|
||||
|
||||
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