DAMASK_EICMD/processing/post/vtk_voxelcloud.py

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#!/usr/bin/env python
import os,sys,string,re,numpy,vtk
import damask
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
scriptID = '$Id: vtk_pointcloud.py 2748 2013-11-26 20:24:40Z MPIE\p.eisenlohr $'
scriptName = scriptID.split()[1]
#--------------------------------------------------------------------------------------------------
class extendedOption(Option):
#--------------------------------------------------------------------------------------------------
# used for definition of new option parser action 'extend', which enables to take multiple option arguments
# taken from online tutorial http://docs.python.org/library/optparse.html
ACTIONS = Option.ACTIONS + ("extend",)
STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
def take_action(self, action, dest, opt, value, values, parser):
if action == "extend":
lvalue = value.split(",")
values.ensure_value(dest, []).extend(lvalue)
else:
Option.take_action(self, action, dest, opt, value, values, parser)
parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
Create hexahedral voxels around points in an ASCIItable.
""" + string.replace(scriptID,'\n','\\n')
)
parser.add_option('-p', '--positions', dest='pos', type='string',
help = 'coordinate label')
parser.add_option('-s', '--size', dest='size', type='float', nargs=3,
help = 'x,y,z size of voxel')
parser.set_defaults(pos = 'pos')
(options, filenames) = parser.parse_args()
if options.size == None:
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
# --------------- figure out columns to process
active = {}
column = {}
head = []
for datatype,info in datainfo.items():
for label in info['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 ---------------------------------------
hexPoints = numpy.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']))
minD = numpy.array(options.size,dtype=float)
# for i in xrange(3):
# coords = numpy.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*minD/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()
file['input'].close() # close input ASCII table