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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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Started adding method for writing HDF5 snapshot files as option to VTK

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Craig Warren
2020-11-23 10:15:03 +00:00
父节点 abb391283f
当前提交 ded9a457f3
共有 1 个文件被更改，包括 68 次插入 和 37 次删除
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105
gprMax/snapshots.py
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@@ -19,9 +19,12 @@
import sys import sys
from struct import pack from struct import pack
import gprMax.config as config import h5py
import numpy as np import numpy as np
import gprMax.config as config
from ._version import __version__
from .cython.snapshots import calculate_snapshot_fields from .cython.snapshots import calculate_snapshot_fields
from .utilities import round_value from .utilities import round_value
@@ -91,12 +94,12 @@ class Snapshot:
Hzslice = np.ascontiguousarray(G.Hz[self.sx, self.sy, self.sz]) Hzslice = np.ascontiguousarray(G.Hz[self.sx, self.sy, self.sz])
# Create arrays to hold the field data for snapshot # Create arrays to hold the field data for snapshot
Exsnap = np.zeros((self.nx, self.ny, self.nz), dtype=config.sim_config.dtypes['float_or_double']) self.Exsnap = np.zeros((self.nx, self.ny, self.nz), dtype=config.sim_config.dtypes['float_or_double'])
Eysnap = np.zeros((self.nx, self.ny, self.nz), dtype=config.sim_config.dtypes['float_or_double']) self.Eysnap = np.zeros((self.nx, self.ny, self.nz), dtype=config.sim_config.dtypes['float_or_double'])
Ezsnap = np.zeros((self.nx, self.ny, self.nz), dtype=config.sim_config.dtypes['float_or_double']) self.Ezsnap = np.zeros((self.nx, self.ny, self.nz), dtype=config.sim_config.dtypes['float_or_double'])
Hxsnap = np.zeros((self.nx, self.ny, self.nz), dtype=config.sim_config.dtypes['float_or_double']) self.Hxsnap = np.zeros((self.nx, self.ny, self.nz), dtype=config.sim_config.dtypes['float_or_double'])
Hysnap = np.zeros((self.nx, self.ny, self.nz), dtype=config.sim_config.dtypes['float_or_double']) self.Hysnap = np.zeros((self.nx, self.ny, self.nz), dtype=config.sim_config.dtypes['float_or_double'])
Hzsnap = np.zeros((self.nx, self.ny, self.nz), dtype=config.sim_config.dtypes['float_or_double']) self.Hzsnap = np.zeros((self.nx, self.ny, self.nz), dtype=config.sim_config.dtypes['float_or_double'])
# Calculate field values at points (comes from averaging field components in cells) # Calculate field values at points (comes from averaging field components in cells)
calculate_snapshot_fields( calculate_snapshot_fields(
@@ -109,19 +112,15 @@ class Snapshot:
Hxslice, Hxslice,
Hyslice, Hyslice,
Hzslice, Hzslice,
Exsnap, self.Exsnap,
Eysnap, self.Eysnap,
Ezsnap, self.Ezsnap,
Hxsnap, self.Hxsnap,
Hysnap, self.Hysnap,
Hzsnap) self.Hzsnap)
# Convert to format for Paraview
self.electric = np.stack((Exsnap, Eysnap, Ezsnap)).reshape(-1, order='F')
self.magnetic = np.stack((Hxsnap, Hysnap, Hzsnap)).reshape(-1, order='F')
def write_vtk_imagedata(self, pbar, G): def write_vtk_imagedata(self, pbar, G):
"""Write snapshot data to a VTK ImageData (.vti) file. """Write snapshot file in VTK ImageData (.vti) format.
N.B. No Python 3 support for VTK at time of writing (03/2015) N.B. No Python 3 support for VTK at time of writing (03/2015)
@@ -133,41 +132,73 @@ class Snapshot:
hfield_offset = (3 * np.dtype(config.sim_config.dtypes['float_or_double']).itemsize hfield_offset = (3 * np.dtype(config.sim_config.dtypes['float_or_double']).itemsize
* self.ncells + np.dtype(np.uint32).itemsize) * self.ncells + np.dtype(np.uint32).itemsize)
self.filehandle = open(self.filename, 'wb') f = open(self.filename, 'wb')
self.filehandle.write('<?xml version="1.0"?>\n'.encode('utf-8')) f.write('<?xml version="1.0"?>\n'.encode('utf-8'))
self.filehandle.write(f'<VTKFile type="ImageData" version="1.0" byte_order="{config.sim_config.vtk_byteorder}">\n'.encode('utf-8')) f.write(f'<VTKFile type="ImageData" version="1.0" byte_order="{config.sim_config.vtk_byteorder}">\n'.encode('utf-8'))
self.filehandle.write(f'<ImageData WholeExtent="{self.xs} {round_value(self.xf / self.dx)} {self.ys} {round_value(self.yf / self.dy)} {self.zs} {round_value(self.zf / self.dz)}" Origin="0 0 0" Spacing="{self.dx * G.dx:.3} {self.dy * G.dy:.3} {self.dz * G.dz:.3}">\n'.encode('utf-8')) f.write(f'<ImageData WholeExtent="{self.xs} {round_value(self.xf / self.dx)} {self.ys} {round_value(self.yf / self.dy)} {self.zs} {round_value(self.zf / self.dz)}" Origin="0 0 0" Spacing="{self.dx * G.dx:.3} {self.dy * G.dy:.3} {self.dz * G.dz:.3}">\n'.encode('utf-8'))
self.filehandle.write(f'<Piece Extent="{self.xs} {round_value(self.xf / self.dx)} {self.ys} {round_value(self.yf / self.dy)} {self.zs} {round_value(self.zf / self.dz)}">\n'.encode('utf-8')) f.write(f'<Piece Extent="{self.xs} {round_value(self.xf / self.dx)} {self.ys} {round_value(self.yf / self.dy)} {self.zs} {round_value(self.zf / self.dz)}">\n'.encode('utf-8'))
if self.fieldoutputs['electric'] and self.fieldoutputs['magnetic']: if self.fieldoutputs['electric'] and self.fieldoutputs['magnetic']:
self.filehandle.write('<CellData Vectors="E-field H-field">\n'.encode('utf-8')) f.write('<CellData Vectors="E-field H-field">\n'.encode('utf-8'))
self.filehandle.write(f"""<DataArray type="{config.sim_config.dtypes['vtk_float']}" Name="E-field" NumberOfComponents="3" format="appended" offset="0" />\n""".encode('utf-8')) f.write(f"""<DataArray type="{config.sim_config.dtypes['vtk_float']}" Name="E-field" NumberOfComponents="3" format="appended" offset="0" />\n""".encode('utf-8'))
self.filehandle.write(f"""<DataArray type="{config.sim_config.dtypes['vtk_float']}" Name="H-field" NumberOfComponents="3" format="appended" offset="{hfield_offset}" />\n""".encode('utf-8')) f.write(f"""<DataArray type="{config.sim_config.dtypes['vtk_float']}" Name="H-field" NumberOfComponents="3" format="appended" offset="{hfield_offset}" />\n""".encode('utf-8'))
elif self.fieldoutputs['electric']: elif self.fieldoutputs['electric']:
self.filehandle.write('<CellData Vectors="E-field">\n'.encode('utf-8')) f.write('<CellData Vectors="E-field">\n'.encode('utf-8'))
self.filehandle.write(f"""<DataArray type="{config.sim_config.dtypes['vtk_float']}" Name="E-field" NumberOfComponents="3" format="appended" offset="0" />\n""".encode('utf-8')) f.write(f"""<DataArray type="{config.sim_config.dtypes['vtk_float']}" Name="E-field" NumberOfComponents="3" format="appended" offset="0" />\n""".encode('utf-8'))
elif self.fieldoutputs['magnetic']: elif self.fieldoutputs['magnetic']:
self.filehandle.write('<CellData Vectors="H-field">\n'.encode('utf-8')) f.write('<CellData Vectors="H-field">\n'.encode('utf-8'))
self.filehandle.write(f"""<DataArray type="{config.sim_config.dtypes['vtk_float']}" Name="H-field" NumberOfComponents="3" format="appended" offset="0" />\n""".encode('utf-8')) f.write(f"""<DataArray type="{config.sim_config.dtypes['vtk_float']}" Name="H-field" NumberOfComponents="3" format="appended" offset="0" />\n""".encode('utf-8'))
self.filehandle.write('</CellData>\n</Piece>\n</ImageData>\n<AppendedData encoding="raw">\n_'.encode('utf-8')) f.write('</CellData>\n</Piece>\n</ImageData>\n<AppendedData encoding="raw">\n_'.encode('utf-8'))
if self.fieldoutputs['electric']: if self.fieldoutputs['electric']:
# Write number of bytes of appended data as UInt32 # Write number of bytes of appended data as UInt32
self.filehandle.write(pack('I', self.datasizefield)) f.write(pack('I', self.datasizefield))
pbar.update(n=4) pbar.update(n=4)
self.electric.tofile(self.filehandle) # Convert to format for Paraview
electric = np.stack((self.Exsnap, self.Eysnap, self.Ezsnap)).reshape(-1, order='F')
electric.tofile(f)
pbar.update(n=self.datasizefield) pbar.update(n=self.datasizefield)
if self.fieldoutputs['magnetic']: if self.fieldoutputs['magnetic']:
# Write number of bytes of appended data as UInt32 # Write number of bytes of appended data as UInt32
self.filehandle.write(pack('I', self.datasizefield)) f.write(pack('I', self.datasizefield))
pbar.update(n=4) pbar.update(n=4)
self.magnetic.tofile(self.filehandle) magnetic = np.stack((self.Hxsnap, self.Hysnap, self.Hzsnap)).reshape(-1, order='F')
magnetic.tofile(f)
pbar.update(n=self.datasizefield) pbar.update(n=self.datasizefield)
self.filehandle.write('\n</AppendedData>\n</VTKFile>'.encode('utf-8')) f.write('\n</AppendedData>\n</VTKFile>'.encode('utf-8'))
self.filehandle.close() f.close()
def write_hdf5(self, pbar, G):
"""Write snapshot file in HDF5 (.h5) format.
Args:
pbar (class): Progress bar class instance.
G (FDTDGrid): Parameters describing a grid in a model.
"""
f = h5py.File(self.filename, 'w')
f.attrs['gprMax'] = __version__
f.attrs['Title'] = G.title
f.attrs['nx_ny_nz'] = (self.nx, self.ny, self.nz)
f.attrs['dx_dy_dz'] = (self.dx * G.dx, self.dy * G.dy, self.dz * G.dz)
f.attrs['time'] = self.time * G.dt
if self.fieldoutputs['electric']:
f['Ex'] = self.Exsnap
f['Ey'] = self.Eysnap
f['Ez'] = self.Ezsnap
pbar.update(n=self.datasizefield)
if self.fieldoutputs['magnetic']:
f['Hx'] = self.Hxsnap
f['Hy'] = self.Hysnap
f['Hz'] = self.Hzsnap
pbar.update(n=self.datasizefield)
f.close()
def htod_snapshot_array(G): def htod_snapshot_array(G):