script to add scalar data and/or RGB color tuples to rectilinear VTK file (*.vtr)
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Philip Eisenlohr
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923adbc2d3
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,string,re,numpy,vtk
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import damask
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from collections import defaultdict
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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scriptID = '$Id: vtk_addVoxelcloudData.py 3064 2014-04-03 01:00:00Z 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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Add scalar and RGB tuples from ASCIItable to existing VTK voxel grid (.vtr).
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""" + string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-v', '--vtk', dest='vtk', type='string',
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help = 'VTK file name')
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parser.add_option('-s', '--scalar', dest='scalar', action='extend',
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help = 'scalar values')
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parser.add_option('-c', '--color', dest='color', action='extend',
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help = 'RGB color tuples')
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parser.set_defaults(scalar = [])
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parser.set_defaults(color = [])
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(options, filenames) = parser.parse_args()
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datainfo = { # list of requested labels per datatype
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'scalar': {'len':1,
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'label':[]},
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'color': {'len':3,
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'label':[]},
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}
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if options.vtk == None or not os.path.exists(options.vtk):
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parser.error('VTK file does not exist')
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if os.path.splitext(options.vtk)[1] == '.vtr':
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reader = vtk.vtkXMLRectilinearGridReader()
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reader.SetFileName(options.vtk)
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reader.Update()
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rGrid = reader.GetOutput()
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elif os.path.splitext(options.vtk)[1] == '.vtk':
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reader = vtk.vtkGenericDataObjectReader()
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reader.SetFileName(options.vtk)
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reader.Update()
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rGrid = reader.GetRectiliearGridOutput()
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else:
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parser.error('unsupported VTK file type extension')
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Npoints = rGrid.GetNumberOfPoints()
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Ncells = rGrid.GetNumberOfCells()
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#if Npoints != Ncells or Npoints != Nvertices:
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# parser.error('Number of points, cells, and vertices in VTK differ from each other'); sys.exit()
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if options.scalar != None: datainfo['scalar']['label'] += options.scalar
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if options.color != None: datainfo['color']['label'] += options.color
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# ------------------------------------------ setup file handles ---------------------------------------
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files = []
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if filenames == []:
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files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr})
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else:
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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':sys.stderr, '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['output'],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 = defaultdict(list)
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column = defaultdict(dict)
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array = defaultdict(dict)
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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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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 datatype == 'scalar':
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array[datatype][label] = vtk.vtkDoubleArray()
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array[datatype][label].SetNumberOfComponents(1)
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array[datatype][label].SetName(label)
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elif datatype == 'color':
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array[datatype][label] = vtk.vtkUnsignedCharArray()
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array[datatype][label].SetNumberOfComponents(3)
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array[datatype][label].SetName(label)
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if not foundIt:
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file['croak'].write('column %s not found...\n'%label)
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# ------------------------------------------ process data ---------------------------------------
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while table.data_read(): # read next data line of ASCII table
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for datatype,labels in active.items(): # loop over scalar,color
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for label in labels: # loop over all requested items
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theData = table.data[column[datatype][label]:\
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column[datatype][label]+datainfo[datatype]['len']] # read strings
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if datatype == 'color':
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theData = map(lambda x: int(255.*float(x)),theData)
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array[datatype][label].InsertNextTuple3(theData[0],theData[1],theData[2],)
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elif datatype == 'scalar':
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array[datatype][label].InsertNextValue(float(theData[0]))
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file['input'].close() # close input ASCII table
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# ------------------------------------------ add data ---------------------------------------
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for datatype,labels in active.items(): # loop over scalar,color
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if datatype == 'color':
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# Polydata.GetPointData().SetScalars(array[datatype][labels[0]])
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rGrid.GetCellData().SetScalars(array[datatype][labels[0]])
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for label in labels: # loop over all requested items
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# Polydata.GetPointData().AddArray(array[datatype][label])
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rGrid.GetCellData().AddArray(array[datatype][label])
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rGrid.Modified()
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if vtk.VTK_MAJOR_VERSION <= 5:
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rGrid.Update()
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# ------------------------------------------ output result ---------------------------------------
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writer = vtk.vtkXMLRectilinearGridWriter()
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writer.SetDataModeToBinary()
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writer.SetCompressorTypeToZLib()
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writer.SetFileName(os.path.splitext(options.vtk)[0]+'_added.vtr')
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if vtk.VTK_MAJOR_VERSION <= 5:
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writer.SetInput(rGrid)
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else:
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writer.SetInputData(rGrid)
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writer.Write()
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