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]
synonyms = {
'grid': ['resolution'],
'size': ['dimension'],
}
identifiers = {
'grid': ['a','b','c'],
'size': ['x','y','z'],
'origin': ['x','y','z'],
}
mappings = {
'grid': lambda x: int(x),
'size': lambda x: float(x),
'origin': lambda x: float(x),
'microstructures': lambda x: int(x),
}
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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='pos', 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')
parser.set_defaults(pos = 'pos')
parser.set_defaults(origin = (0.0,0.0,0.0))
parser.set_defaults(geom = False)
(options, filenames) = parser.parse_args()
if options.size == None and not options.geom:
parser.error('no size sprecified.')
datainfo = { # list of requested labels per datatype
'vector': {'len':3,
'label':[]},
}
if options.pos != None: datainfo['vector']['label'] += [options.pos]
# ------------------------------------------ setup file handles ---------------------------------------
files = []
for name in filenames:
if os.path.exists(name):
files.append({'name':name, 'input':open(name), 'output':os.path.splitext(name)[0]+'.vtu', 'croak':sys.stderr})
#--- loop over input files ------------------------------------------------------------------------
for file in files:
if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
table = damask.ASCIItable(file['input'],file['croak'],False) # make unbuffered ASCII_table
table.head_read() # read ASCII header info
#--- interpret header ----------------------------------------------------------------------------
info = {
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'grid': np.zeros(3,'i'),
'size': np.zeros(3,'d'),
'origin': np.zeros(3,'d'),
'homogenization': 0,
'microstructures': 0,
}
if options.geom:
for header in table.info:
headitems = map(str.lower,header.split())
if len(headitems) == 0: continue
for synonym,alternatives in synonyms.iteritems():
if headitems[0] in alternatives: headitems[0] = synonym
if headitems[0] in mappings.keys():
if headitems[0] in identifiers.keys():
for i in xrange(len(identifiers[headitems[0]])):
info[headitems[0]][i] = \
mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
else:
info[headitems[0]] = mappings[headitems[0]](headitems[1])
file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
'homogenization: %i\n'%info['homogenization'] + \
'microstructures: %i\n'%info['microstructures'])
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if np.any(info['grid'] < 1):
file['croak'].write('invalid grid a b c.\n')
continue
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if np.any(info['size'] <= 0.0):
file['croak'].write('invalid size x y z.\n')
continue
else:
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info['size'] = np.ones(3)
info['grid'] = info['size'] / options.size
info['origin'] = options.origin
# --------------- figure out columns to process
active = {}
column = {}
head = []
for datatype,infos in datainfo.items():
for label in infos['label']:
foundIt = False
for key in ['1_'+label,label]:
if key in table.labels:
foundIt = True
if datatype not in active: active[datatype] = []
if datatype not in column: column[datatype] = {}
active[datatype].append(label)
column[datatype][label] = table.labels.index(key) # remember columns of requested data
if not foundIt:
file['croak'].write('column %s not found...\n'%label)
break
# ------------------------------------------ process data ---------------------------------------
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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],
])
Points = vtk.vtkPoints()
Hex = vtk.vtkHexahedron()
uGrid = vtk.vtkUnstructuredGrid()
table.data_readArray(range(column['vector'][options.pos],\
column['vector'][options.pos]+datainfo['vector']['len']))
table.data[:,0:3] *= info['size']
table.data[:,0:3] += info['origin']
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# minD = np.array(options.size,dtype=float)
# for i in xrange(3):
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# coords = np.unique(table.data[:,i])
# minD[i] = coords[-1]-coords[0]
# for j in xrange(len(coords)-1):
# d = coords[j+1]-coords[j]
# if d < minD[i]:
# minD[i] = d
for p in table.data:
for i,h in enumerate(hexPoints):
id = Points.InsertNextPoint(p+h*info['size']/info['grid']/2.)
Hex.GetPointIds().SetId(i,id)
uGrid.InsertNextCell(Hex.GetCellType(), Hex.GetPointIds())
uGrid.SetPoints(Points)
# ------------------------------------------ output result ---------------------------------------
writer = vtk.vtkXMLUnstructuredGridWriter()
writer.SetDataModeToBinary()
writer.SetCompressorTypeToZLib()
writer.SetFileName(file['output'])
if vtk.VTK_MAJOR_VERSION <= 5:
writer.SetInput(uGrid)
else:
writer.SetInputData(uGrid)
writer.Write()
table.input_close() # close input ASCII table