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Use HDF5 format for voxel file rather than raw binary

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This commit is contained in:
Paul Romano 2015-09-17 12:47:20 +07:00
parent 8b67fa7a92
commit 3274cf3f6d
4 changed files with 72 additions and 55 deletions
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69
scripts/openmc-voxel-to-silovtk
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@ -1,9 +1,11 @@
#!/usr/bin/env python2
#!/usr/bin/env python
from __future__ import division, print_function
import struct
import sys
import numpy as np
import h5py
def parse_options():
"""Process command line arguments"""
@ -22,14 +24,16 @@ def parse_options():
return parsed
def main(file_, o):
print(file_)
fh = open(file_, 'rb')
header = get_header(fh)
meshparms = (header['dimension'] + header['lower_left'] +
header['upper_right'])
nx, ny, nz = meshparms[:3]
ll = header['lower_left']
def main(filename, o):
# Read data from voxel file
fh = h5py.File(filename, 'r')
dimension = fh['num_voxels'].value
width = fh['voxel_width'].value
lower_left = fh['lower_left'].value
voxel_data = fh['data'].value
nx, ny, nz = dimension
upper_right = lower_left + width*dimension
if o.vtk:
try:
@ -40,13 +44,10 @@ def main(file_, o):
'See: http://www.vtk.org/')
return
origin = [(l + w*n/2.) for n, l, w in
zip((nx, ny, nz), ll, header['width'])]
grid = vtk.vtkImageData()
grid.SetDimensions(nx+1, ny+1, nz+1)
grid.SetOrigin(*ll)
grid.SetSpacing(*header['width'])
grid.SetOrigin(*lower_left)
grid.SetSpacing(*width)
data = vtk.vtkDoubleArray()
data.SetName("id")
@ -57,8 +58,7 @@ def main(file_, o):
for y in range(ny):
for z in range(nz):
i = z*nx*ny + y*nx + x
id_ = get_int(fh)[0]
data.SetValue(i, id_)
data.SetValue(i, voxel_data[x,y,z])
grid.GetCellData().AddArray(data)
writer = vtk.vtkXMLImageDataWriter()
@ -81,44 +81,23 @@ def main(file_, o):
if not o.output.endswith(".silo"):
o.output += ".silo"
silomesh.init_silo(o.output)
silomesh.init_mesh('plot', *meshparms)
meshparams = list(map(int, dimension)) + list(map(float, lower_left)) + \
list(map(float, upper_right))
silomesh.init_mesh('plot', *meshparams)
silomesh.init_var("id")
for x in range(1, nx+1):
for x in range(nx):
sys.stdout.write(" {0}%\r".format(int(x/nx*100)))
sys.stdout.flush()
for y in range(1, ny+1):
for z in range(1, nz+1):
id_ = get_int(fh)[0]
silomesh.set_value(float(id_), x, y, z)
for y in range(ny):
for z in range(nz):
silomesh.set_value(float(voxel_data[x,y,z]),
x + 1, y + 1, z + 1)
print()
silomesh.finalize_var()
silomesh.finalize_mesh()
silomesh.finalize_silo()
def get_header(file_):
nx, ny, nz = get_int(file_, 3)
wx, wy, wz = get_double(file_, 3)
lx, ly, lz = get_double(file_, 3)
header = {'dimension': [nx, ny, nz], 'width': [wx, wy, wz],
'lower_left': [lx, ly, lz],
'upper_right': [lx+wx*nx, ly+wy*ny, lz+wz*nz]}
return header
def get_data(file_, n, typeCode, size):
return list(struct.unpack('={0}{1}'.format(n, typeCode),
file_.read(n*size)))
def get_int(file_, n=1, path=None):
return get_data(file_, n, 'i', 4)
def get_double(file_, n=1, path=None):
return get_data(file_, n, 'd', 8)
if __name__ == '__main__':
(options, args) = parse_options()
if args: