DAMASK_EICMD/processing/post/vtk_voxelcloud.py

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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
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import os,sys,string,re,vtk
import numpy as np
from optparse import OptionParser
import damask
scriptID = '$Id$'
scriptName = os.path.splitext(scriptID.split()[1])[0]
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# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Create hexahedral voxels around points in an ASCIItable.
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""", version = scriptID)
parser.add_option('-p', '--positions',
dest = 'position',
type = 'string', metavar = 'string',
help = 'coordinate label [%default]')
parser.add_option('-s', '--size',
dest = 'size',
type = 'float', nargs = 3, metavar = 'float float float',
help = 'x,y,z size of voxel')
parser.add_option('-o', '--origin',
dest = 'origin',
type = 'float', nargs = 3, metavar = 'float float float',
help = 'x,y,z origin of coordinate system')
parser.add_option('-g', '--geom',
dest = 'geom', action='store_true',
help = 'derive geometry from geom-file header information [%default]')
parser.set_defaults(position = 'pos',
origin = (0.0,0.0,0.0),
geom = False,
)
(options, filenames) = parser.parse_args()
if options.size == None and not options.geom:
parser.error('no size specified.')
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
buffered = False, readonly = True)
except: continue
table.croak(damask.util.emph(scriptName)+(': '+name if name else ''))
# --- interpret header ----------------------------------------------------------------------------
table.head_read()
if options.geom:
info,extra_header = table.head_getGeom()
table.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
'size x y z: %s'%(' x '.join(map(str,info['size']))),
'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
'homogenization: %i'%info['homogenization'],
'microstructures: %i'%info['microstructures'],
])
else:
info = {}
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info['size'] = np.ones(3)
info['grid'] = info['size'] / options.size
info['origin'] = options.origin
errors = []
if table.label_dimension(options.position) != 3: errors.append('columns "{}" have dimension {}'.format(options.position,
table.label_dimension(options.position)))
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
if errors != []:
table.croak(errors)
table.close(dismiss = True)
continue
# ------------------------------------------ process data ---------------------------------------
table.data_readArray(options.position)
table.data[:,0:3] *= info['size']
table.data[:,0:3] += info['origin']
hexPoints = np.array([[-1,-1,-1],
[ 1,-1,-1],
[ 1, 1,-1],
[-1, 1,-1],
[-1,-1, 1],
[ 1,-1, 1],
[ 1, 1, 1],
[-1, 1, 1],
])
halfDelta = 0.5*info['size']/info['grid']
Points = vtk.vtkPoints()
Hex = vtk.vtkHexahedron()
uGrid = vtk.vtkUnstructuredGrid()
for p in table.data:
for i,h in enumerate(hexPoints):
id = Points.InsertNextPoint(p+h*halfDelta)
Hex.GetPointIds().SetId(i,id)
uGrid.InsertNextCell(Hex.GetCellType(), Hex.GetPointIds())
uGrid.SetPoints(Points)
# ------------------------------------------ output result ---------------------------------------
if name:
(dir,filename) = os.path.split(name)
writer = vtk.vtkXMLUnstructuredGridWriter()
writer.SetDataModeToBinary()
writer.SetCompressorTypeToZLib()
writer.SetFileName(os.path.join(dir,os.path.splitext(filename)[0]+'_{}'.format(options.position) \
+'.'+writer.GetDefaultFileExtension()))
if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(uGrid)
else: writer.SetInputData(uGrid)
writer.Write()
else:
writer = vtk.vtkUnstructuredGridWriter()
writer.WriteToOutputStringOn()
writer.SetFileTypeToASCII()
writer.SetHeader('# powered by '+scriptID)
if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(uGrid)
else: writer.SetInputData(uGrid)
writer.Write()
sys.stdout.write(writer.GetOutputString()[0:writer.GetOutputStringLength()])
table.close() # close input ASCII table