produce VTK unstructured grid with voxels around all points given in an ASCIItable.
This commit is contained in:
Philip Eisenlohr
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#!/usr/bin/env python
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import os,sys,string,re,numpy,vtk
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import damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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scriptID = '$Id: vtk_pointcloud.py 2748 2013-11-26 20:24:40Z MPIE\p.eisenlohr $'
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scriptName = scriptID.split()[1]
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#--------------------------------------------------------------------------------------------------
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class extendedOption(Option):
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#--------------------------------------------------------------------------------------------------
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# used for definition of new option parser action 'extend', which enables to take multiple option arguments
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# taken from online tutorial http://docs.python.org/library/optparse.html
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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
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Create hexahedral voxels around points in an ASCIItable.
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""" + string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-p', '--positions', dest='pos', type='string',
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help = 'coordinate label')
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parser.add_option('-s', '--size', dest='size', type='float', nargs=3,
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help = 'x,y,z size of voxel')
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parser.set_defaults(pos = 'pos')
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(options, filenames) = parser.parse_args()
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if options.size == None:
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parser.error('no size sprecified.')
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datainfo = { # list of requested labels per datatype
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'vector': {'len':3,
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'label':[]},
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}
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if options.pos != None: datainfo['vector']['label'] += [options.pos]
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# ------------------------------------------ setup file handles ---------------------------------------
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files = []
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for name in filenames:
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if os.path.exists(name):
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files.append({'name':name, 'input':open(name), 'output':os.path.splitext(name)[0]+'.vtu', 'croak':sys.stderr})
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#--- loop over input files ------------------------------------------------------------------------
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for file in files:
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if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
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table = damask.ASCIItable(file['input'],file['croak'],False) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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# --------------- figure out columns to process
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active = {}
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column = {}
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head = []
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for datatype,info in datainfo.items():
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for label in info['label']:
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foundIt = False
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for key in ['1_'+label,label]:
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if key in table.labels:
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foundIt = True
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if datatype not in active: active[datatype] = []
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if datatype not in column: column[datatype] = {}
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active[datatype].append(label)
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column[datatype][label] = table.labels.index(key) # remember columns of requested data
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if not foundIt:
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file['croak'].write('column %s not found...\n'%label)
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break
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# ------------------------------------------ process data ---------------------------------------
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hexPoints = numpy.array([[-1,-1,-1],
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[ 1,-1,-1],
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[ 1, 1,-1],
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[-1, 1,-1],
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[-1,-1, 1],
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[ 1,-1, 1],
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[ 1, 1, 1],
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[-1, 1, 1],
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])
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Points = vtk.vtkPoints()
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Hex = vtk.vtkHexahedron()
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uGrid = vtk.vtkUnstructuredGrid()
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table.data_readArray(range(column['vector'][options.pos],\
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column['vector'][options.pos]+datainfo['vector']['len']))
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minD = numpy.array(options.size,dtype=float)
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# for i in xrange(3):
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# coords = numpy.unique(table.data[:,i])
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# minD[i] = coords[-1]-coords[0]
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# for j in xrange(len(coords)-1):
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# d = coords[j+1]-coords[j]
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# if d < minD[i]:
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# minD[i] = d
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for p in table.data:
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for i,h in enumerate(hexPoints):
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id = Points.InsertNextPoint(p+h*minD/2.)
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Hex.GetPointIds().SetId(i,id)
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uGrid.InsertNextCell(Hex.GetCellType(), Hex.GetPointIds())
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uGrid.SetPoints(Points)
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# ------------------------------------------ output result ---------------------------------------
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writer = vtk.vtkXMLUnstructuredGridWriter()
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writer.SetDataModeToBinary()
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writer.SetCompressorTypeToZLib()
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writer.SetFileName(file['output'])
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if vtk.VTK_MAJOR_VERSION <= 5:
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writer.SetInput(uGrid)
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else:
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writer.SetInputData(uGrid)
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writer.Write()
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file['input'].close() # close input ASCII table
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