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Changing zyx ordering of voxel files to xyz and updating the voxel-to-vtk script. Adding check for version number in the script to avoid incorrect conversion of older voxel files.

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Patrick Shriwise 2019-02-27 17:11:16 -06:00
parent 16fac7cc07
commit 14f9d04ad7
2 changed files with 28 additions and 15 deletions
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15
scripts/openmc-voxel-to-vtk
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@ -8,6 +8,9 @@ import numpy as np
import h5py
import vtk
_min_version = (0,10,0)
def main():
# Process command line arguments
parser = ArgumentParser()
@ -18,6 +21,17 @@ def main():
# Read data from voxel file
fh = h5py.File(args.voxel_file, 'r')
# check version
version = tuple(fh.attrs['openmc_version'])
if version < _min_version:
old_version = ".".join(map(str,version))
min_version = ".".join(map(str,_min_version))
err_msg = "This voxel file was generated using OpenMC " \
"version {}. Please re-generate using "\
"version {} or higher.".format(old_version, min_version)
raise ValueError(err_msg)
dimension = fh.attrs['num_voxels']
width = fh.attrs['voxel_width']
lower_left = fh.attrs['lower_left']
@ -34,7 +48,6 @@ def main():
# and flatten to 1-D array
print("Reading and translating data...")
h5data = fh['data'][...]
h5data = h5data.T.copy()
data = vtk.vtkIntArray()
data.SetName("id")

28
src/plot.cpp
View file

@ -884,9 +884,9 @@ void create_voxel(Plot pl)
// Create dataset for voxel data -- note that the dimensions are reversed
// since we want the order in the file to be z, y, x
hsize_t dims[3];
dims[0] = pl.pixels_[0];
dims[0] = pl.pixels_[2];
dims[1] = pl.pixels_[1];
dims[2] = pl.pixels_[2];
dims[2] = pl.pixels_[0];
hid_t dspace, dset, memspace;
voxel_init(file_id, &(dims[0]), &dspace, &dset, &memspace);
@ -895,33 +895,33 @@ void create_voxel(Plot pl)
ll[1] = ll[1] + vox[1] / 2.;
ll[2] = ll[2] + vox[2] / 2.;
int data[pl.pixels_[1]][pl.pixels_[2]];
int data[pl.pixels_[1]][pl.pixels_[0]];
ProgressBar pb;
RGBColor rgb;
int id;
for (int x = 0; x < pl.pixels_[0]; x++) {
pb.set_value(100.*(double)x/(double)(pl.pixels_[0]-1));
for (int z = 0; z < pl.pixels_[2]; z++) {
pb.set_value(100.*(double)z/(double)(pl.pixels_[2]-1));
for (int y = 0; y < pl.pixels_[1]; y++) {
for (int z = 0; z < pl.pixels_[2]; z++) {
for (int x = 0; x < pl.pixels_[0]; x++) {
// get voxel color
position_rgb(p, pl, rgb, id);
// write to plot data
data[y][z] = id;
// advance particle in z direction
p.coord[0].xyz[2] = p.coord[0].xyz[2] + vox[2];
data[y][x] = id;
// advance particle in x direction
p.coord[0].xyz[0] = p.coord[0].xyz[0] + vox[0];
}
// advance particle in y direction
p.coord[0].xyz[1] = p.coord[0].xyz[1] + vox[1];
p.coord[0].xyz[2] = ll[2];
p.coord[0].xyz[0] = ll[0];
}
// advance particle in x direction
p.coord[0].xyz[0] = p.coord[0].xyz[0] + vox[0];
// advance particle in z direction
p.coord[0].xyz[2] = p.coord[0].xyz[2] + vox[2];
p.coord[0].xyz[1] = ll[1];
p.coord[0].xyz[2] = ll[2];
p.coord[0].xyz[0] = ll[0];
// Write to HDF5 dataset
voxel_write_slice(x, dspace, dset, memspace, &(data[0]));
voxel_write_slice(z, dspace, dset, memspace, &(data[0]));
}
voxel_finalize(dspace, dset, memspace);