script for adding data from HDF5 to vtk file
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#!/usr/bin/env python2.7
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# -*- coding: UTF-8 no BOM -*-
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import os
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import vtk
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import damask
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from vtk.util import numpy_support
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from optparse import OptionParser
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName, damask.version])
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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msg = "Add scalars, vectors, and/or an RGB tuple from"
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msg += "an HDF5 to existing VTK rectilinear grid (.vtr/.vtk)."
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parser = OptionParser(option_class=damask.extendableOption,
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usage='%prog options [file[s]]',
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description=msg,
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version=scriptID)
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parser.add_option('--vtk',
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dest='vtk',
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type='string', metavar='string',
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help='VTK file name')
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parser.add_option('--inplace',
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dest='inplace',
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action='store_true',
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help='modify VTK file in-place')
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parser.add_option('-r', '--render',
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dest='render',
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action='store_true',
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help='open output in VTK render window')
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parser.add_option('-d', '--data',
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dest='data',
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action='extend', metavar='<string LIST>',
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help='scalar/vector value(s) label(s)')
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parser.add_option('-t', '--tensor',
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dest='tensor',
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action='extend', metavar='<string LIST>',
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help='tensor (3x3) value label(s)')
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parser.add_option('-c', '--color',
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dest='color',
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action='extend', metavar='<string LIST>',
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help='RGB color tuple label')
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parser.add_option('-m',
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'--mode',
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dest='mode',
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metavar='string',
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type='choice', choices=['cell', 'point'],
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help='cell-centered or point-centered coordinates')
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parser.set_defaults(data=[],
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tensor=[],
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color=[],
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mode='cell',
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inplace=False,
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render=False)
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(options, filenames) = parser.parse_args()
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# ----- Legacy VTK format support ----- #
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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.GetRectilinearGridOutput()
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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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# ----- Summary output (Sanity Check) ----- #
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msg = '{}: {} points and {} cells...'.format(options.vtk,
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Npoints,
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Ncells)
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damask.util.croak(msg)
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# ----- Read HDF5 file ----- #
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# NOTE:
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# --> It is possible in the future we are trying to add data
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# from different increment into the same VTK file, but
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# this feature is not supported for the moment.
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# --> Let it fail, if the HDF5 is invalid, python interpretor
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# --> should be able to catch this error.
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h5f = damask.H5Table(filenames[0], new_file=False)
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# ----- Process data ----- #
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featureToAdd = {'data': options.data,
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'tensor': options.tensor,
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'color': options.color}
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VTKarray = {} # store all vtkData in dict, then ship them to file
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for dataType in featureToAdd.keys():
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featureNames = featureToAdd[dataType]
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for featureName in featureNames:
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VTKtype = vtk.VTK_DOUBLE
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VTKdata = h5f.get_data(featureName)
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if dataType == 'color':
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VTKtype = vtk.VTK_UNSIGNED_CHAR
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VTKdata = (VTKdata*255).astype(int)
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elif dataType == 'tensor':
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# Force symmetries tensor type data
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VTKdata[:, 1] = VTKdata[:, 3] = 0.5*(VTKdata[:, 1]+VTKdata[:, 3])
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VTKdata[:, 2] = VTKdata[:, 6] = 0.5*(VTKdata[:, 2]+VTKdata[:, 6])
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VTKdata[:, 5] = VTKdata[:, 7] = 0.5*(VTKdata[:, 5]+VTKdata[:, 7])
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# use vtk build-in numpy support to add data (much faster)
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# NOTE:
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# --> deep copy is necessary here, otherwise memory leak could occur
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VTKarray[featureName] = numpy_support.numpy_to_vtk(num_array=VTKdata,
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deep=True,
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array_type=VTKtype)
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VTKarray[featureName].SetName(featureName)
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# ----- ship data to vtkGrid ----- #
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mode = options.mode
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damask.util.croak('{} mode...'.format(mode))
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# NOTE:
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# --> For unknown reason, Paraview only recognize one
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# tensor attributes per cell, thus it would be safe
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# to only add one attributes as tensor.
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for dataType in featureToAdd.keys():
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featureNames = featureToAdd[dataType]
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for featureName in featureNames:
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if dataType == 'color':
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if mode == 'cell':
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rGrid.GetCellData().SetScalars(VTKarray[featureName])
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elif mode == 'point':
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rGrid.GetPointData().SetScalars(VTKarray[featureName])
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elif dataType == 'tensor':
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if mode == 'cell':
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rGrid.GetCellData().SetTensors(VTKarray[featureName])
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elif mode == 'point':
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rGrid.GetPointData().SetTensors(VTKarray[featureName])
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else:
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if mode == 'cell':
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rGrid.GetCellData().AddArray(VTKarray[featureName])
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elif mode == 'point':
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rGrid.GetPointData().AddArray(VTKarray[featureName])
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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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# ----- write Grid to VTK file ----- #
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writer = vtk.vtkXMLRectilinearGridWriter()
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writer.SetDataModeToBinary()
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writer.SetCompressorTypeToZLib()
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vtkFileN = os.path.splitext(options.vtk)[0]
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vtkExtsn = '.vtr' if options.inplace else '_added.vtr'
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writer.SetFileName(vtkFileN+vtkExtsn)
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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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# ----- render results from script ----- #
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if options.render:
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mapper = vtk.vtkDataSetMapper()
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mapper.SetInputData(rGrid)
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actor = vtk.vtkActor()
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actor.SetMapper(mapper)
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# Create the graphics structure. The renderer renders into the
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# render window. The render window interactor captures mouse events
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# and will perform appropriate camera or actor manipulation
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# depending on the nature of the events.
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ren = vtk.vtkRenderer()
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renWin = vtk.vtkRenderWindow()
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renWin.AddRenderer(ren)
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ren.AddActor(actor)
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ren.SetBackground(1, 1, 1)
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renWin.SetSize(200, 200)
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iren = vtk.vtkRenderWindowInteractor()
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iren.SetRenderWindow(renWin)
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iren.Initialize()
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renWin.Render()
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iren.Start()
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