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镜像自地址 https://gitee.com/sunhf/gprMax.git 已同步 2025-08-08 07:24:19 +08:00
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Tidied up geometry file writing.

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这个提交包含在：
Craig Warren
2022-01-05 16:36:54 +00:00
父节点 81bcf48dc5
当前提交 6f77535870
共有 2 个文件被更改，包括 91 次插入 和 59 次删除
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27
gprMax/cython/geometry_outputs.pyx
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@@ -20,14 +20,15 @@ import numpy as np
cimport numpy as np
cpdef write_lines(int nx, int ny, int nz, int dx, int dy, int dz,
np.uint32_t[:, :, :, :] ID):
cpdef write_lines(float xs, float ys, float zs, int nx, int ny, int nz,
float dx, float dy, float dz, np.uint32_t[:, :, :, :] ID):
"""This function generates arrays with to be written as lines (cell edges)
to a VTK file.
Args:
xs, ys, zs (float): Starting coordinates of geometry view in metres
nx, ny, nz (int): Size of the volume in cells
dx, dy, dz (int): Spatial discretisation of geometry view in cells
dx, dy, dz (float): Spatial discretisation of geometry view in metres
ID (nparray): Sampled ID array according to geometry view spatial
discretisation
@@ -64,11 +65,11 @@ cpdef write_lines(int nx, int ny, int nz, int dx, int dy, int dz,
# Material ID of line
lines[lc] = ID[0][i, j, k]
# Set the starting point position of the edge
x[pc], y[pc], z[pc] = i * dx, j * dy, k * dz
x[pc], y[pc], z[pc] = i, j, k
# Next point
pc += 1
# Set the end point position of the edge
x[pc], y[pc], z[pc] = (i + 1) * dx, j * dy, k * dz
x[pc], y[pc], z[pc] = (i + 1), j, k
# Next point
pc += 1
# Next line
@@ -76,18 +77,26 @@ cpdef write_lines(int nx, int ny, int nz, int dx, int dy, int dz,
# y-direction cell edge
lines[lc] = ID[1, i, j, k]
x[pc], y[pc], z[pc] = i * dx, j * dy, k * dz
x[pc], y[pc], z[pc] = i, j, k
pc += 1
x[pc], y[pc], z[pc] = i * dx, (j + 1) * dy, k * dz
x[pc], y[pc], z[pc] = i, (j + 1), k
pc += 1
lc += 1
# z-direction cell edge
lines[lc] = ID[2, i, j, k]
x[pc], y[pc], z[pc] = i * dx, j * dy, k * dz
x[pc], y[pc], z[pc] = i, j, k
pc += 1
x[pc], y[pc], z[pc] = i * dx, j * dy, (k + 1) * dz
x[pc], y[pc], z[pc] = i, j, (k + 1)
pc += 1
lc += 1
x *= dx
y *= dy
z *= dz
x += xs
y += ys
z += zs
return x, y, z, lines

123
gprMax/geometry_outputs.py
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@@ -30,8 +30,8 @@ from pathlib import Path
import h5py
import numpy as np
from evtk.hl import linesToVTK, rectilinearToVTK
from evtk.vtk import VtkGroup, VtkRectilinearGrid, VtkUnstructuredGrid
from evtk.hl import imageToVTK, linesToVTK
from evtk.vtk import VtkGroup, VtkImageData, VtkUnstructuredGrid
from tqdm import tqdm
import gprMax.config as config
@@ -59,7 +59,7 @@ def write_vtk_pvd(gvs):
# Add filenames of all GeometryViews to group
for gv in gvs:
sim_time = 0
pvd.addFile(str(gv.filename.name) + gv.vtkfiletype.ext, sim_time,
pvd.addFile(str(gv.filename) + gv.vtkfiletype.ext, sim_time,
group = "", part = "0")
pvd.save()
@@ -76,13 +76,13 @@ def save_geometry_views(gvs):
logger.info('')
for i, gv in enumerate(gvs):
gv.set_filename()
gvsample = gv.sample()
pbar = tqdm(total=gvsample.nbytes, unit='byte', unit_scale=True,
vtk_data = gv.prep_vtk()
pbar = tqdm(total=vtk_data['nbytes'], unit='byte', unit_scale=True,
desc=f'Writing geometry view file {i + 1}/{len(gvs)}, {gv.filename.name}{gv.vtkfiletype.ext}',
ncols=get_terminal_width() - 1, file=sys.stdout,
disable=not config.sim_config.general['progressbars'])
gv.write_vtk(gvsample)
pbar.update(gvsample.nbytes)
gv.write_vtk(vtk_data)
pbar.update(vtk_data['nbytes'])
pbar.close()
# Write a Paraview data file (.pvd) if there is more than one GeometryView
@@ -133,8 +133,14 @@ class GeometryViewLines(GeometryView):
super().__init__(*args)
self.vtkfiletype = VtkUnstructuredGrid
def sample(self):
"""Sample ID array according to geometry view spatial discretisation."""
def prep_vtk(self):
"""Prepare data for writing to VTK file.
Returns:
vtk_data (dict): coordinates, data, and comments for VTK file
"""
# Sample ID array according to geometry view spatial discretisation
# Only create a new array if subsampling is required
if (self.grid.ID.shape != (self.xf, self.yf, self.zf) or
(self.dx, self.dy, self.dz) != (1, 1, 1) or
@@ -147,18 +153,13 @@ class GeometryViewLines(GeometryView):
# This array is contiguous by design
ID = self.grid.ID
return ID
def write_vtk(self, ID):
"""Writes the geometry information to a VTK file.
Args:
ID (array): sampled ID array at the user specified region and
discretisation.
"""
x, y, z, lines = write_lines(self.nx, self.ny, self.nz,
self.dx, self.dy, self.dz, ID)
x, y, z, lines = write_lines((self.xs * self.grid.dx),
(self.ys * self.grid.dy),
(self.zs * self.grid.dz),
self.nx, self.ny, self.nz,
(self.dx * self.grid.dx),
(self.dy * self.grid.dy),
(self.dz * self.grid.dz), ID)
# Write information about any PMLs, sources, receivers
comments = Comments(self.grid, self)
@@ -167,8 +168,28 @@ class GeometryViewLines(GeometryView):
info = comments.get_gprmax_info()
comments = json.dumps(info)
linesToVTK(str(self.filename), x, y, z, cellData={"Material": lines},
comments=[comments])
# Number of bytes of data to be written to file
offsets_size = np.arange(start = 2, step = 2, stop = len(x) + 1,
dtype = 'int32').nbytes
connect_size = len(x) * np.dtype('int32').itemsize
cell_type_size = len(x) * np.dtype('uint8').itemsize
nbytes = (x.nbytes + y.nbytes + z.nbytes + lines.nbytes + offsets_size
+ connect_size + cell_type_size)
vtk_data = {'x': x, 'y': y, 'z': z, 'data': lines, 'comments': comments, 'nbytes': nbytes}
return vtk_data
def write_vtk(self, vtk_data):
"""Write geometry information to a VTK file.
Args:
vtk_data (dict): coordinates, data, and comments for VTK file
"""
# Write the VTK file .vtu
linesToVTK(str(self.filename), vtk_data['x'], vtk_data['y'], vtk_data['z'], cellData={"Material": vtk_data['data']},
comments=[vtk_data['comments']])
class GeometryViewVoxels(GeometryView):
@@ -176,11 +197,16 @@ class GeometryViewVoxels(GeometryView):
def __init__(self, *args):
super().__init__(*args)
self.vtkfiletype = VtkRectilinearGrid
self.vtkfiletype = VtkImageData
def sample(self):
"""Sample solid array according to geometry view spatial discretisation."""
def prep_vtk(self):
"""Prepare data for writing to VTK file.
Returns:
vtk_data (dict): data and comments for VTK file
"""
# Sample solid array according to geometry view spatial discretisation
# Only create a new array if subsampling is required
if (self.grid.solid.shape != (self.xf, self.yf, self.zf) or
(self.dx, self.dy, self.dz) != (1, 1, 1) or
@@ -193,35 +219,32 @@ class GeometryViewVoxels(GeometryView):
# This array is contiguous by design
solid = self.grid.solid
return solid
def get_coordinates(self, solid):
# (length is number of vertices in each direction) * (size of each block [m]) + (starting offset)
x = np.arange(0, solid.shape[0] + 1) * (self.grid.dx * self.dx) + (self.xs * self.grid.dx)
y = np.arange(0, solid.shape[1] + 1) * (self.grid.dy * self.dy) + (self.ys * self.grid.dy)
z = np.arange(0, solid.shape[2] + 1) * (self.grid.dz * self.dz) + (self.zs * self.grid.dz)
return x, y, z
def write_vtk(self, solid):
"""Writes the geometry information to a VTK file.
Args:
solid (array): sampled solid array at the user specified region and
discretisation.
"""
# coordinates of vertices (rectilinear)
x, y, z = self.get_coordinates(solid)
# Get information about pml, sources, receivers
comments = Comments(self.grid, self)
info = comments.get_gprmax_info()
comments = json.dumps(info)
# Write the VTK file .vtr
rectilinearToVTK(str(self.filename), x, y, z, cellData={"Material": solid},
comments=[comments])
vtk_data = {'data': solid, 'comments': comments, 'nbytes': solid.nbytes}
return vtk_data
def write_vtk(self, vtk_data):
"""Write geometry information to a VTK file.
Args:
vtk_data (dict): data and comments for VTK file
"""
# Write the VTK file .vti
imageToVTK(str(self.filename),
origin=((self.xs * self.grid.dx),
(self.ys * self.grid.dy),
(self.zs * self.grid.dz)),
spacing=((self.dx * self.grid.dx),
(self.dy * self.grid.dy),
(self.dz * self.grid.dz)),
cellData={"Material": vtk_data['data']},
comments=[vtk_data['comments']])
class GeometryViewSubgridVoxels(GeometryViewVoxels):