DAMASK_EICMD/processing/misc/vtk_fromGwyddion.py

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#!/usr/bin/env python2.7
# -*- coding: UTF-8 no BOM -*-
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import os,string,vtk
import numpy as np
import damask
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from optparse import OptionParser
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
scalingFactor = { \
'm': {
'm': 1e0,
'mm': 1e-3,
'µm': 1e-6,
},
'mm': {
'm': 1e+3,
'mm': 1e0,
'µm': 1e-3,
},
'µm': {
'm': 1e+6,
'mm': 1e+3,
'µm': 1e0,
},
}
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Produce VTK rectilinear grid from Gwyddion dataset exported as text.
""" + string.replace(scriptID,'\n','\\n')
)
parser.add_option('-s', '--scaling', dest='scaling', type='float',
help = 'scaling factor for elevation data [auto]')
parser.set_defaults(scaling = 0.0)
(options, filenames) = parser.parse_args()
# ------------------------------------------ read Gwyddion data ---------------------------------------
for file in filenames:
with open(file,'r') as f:
for line in f:
pieces = line.split()
if pieces[0] != '#': break
if len(pieces) < 2: continue
if pieces[1] == 'Width:':
width = float(pieces[2])
lateralunit = pieces[3]
if pieces[1] == 'Height:':
height = float(pieces[2])
lateralunit = pieces[3]
if pieces[1] == 'Value' and pieces[2] == 'units:':
elevationunit = pieces[3]
if options.scaling == 0.0:
options.scaling = scalingFactor[lateralunit][elevationunit]
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elevation = np.loadtxt(file)*options.scaling
grid = vtk.vtkRectilinearGrid()
grid.SetDimensions(elevation.shape[1],elevation.shape[0],1)
xCoords = vtk.vtkDoubleArray()
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for x in np.arange(0.0,width,width/elevation.shape[1],'d'):
xCoords.InsertNextValue(x)
yCoords = vtk.vtkDoubleArray()
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for y in np.arange(0.0,height,height/elevation.shape[0],'d'):
yCoords.InsertNextValue(y)
zCoords = vtk.vtkDoubleArray()
zCoords.InsertNextValue(0.0)
grid.SetXCoordinates(xCoords)
grid.SetYCoordinates(yCoords)
grid.SetZCoordinates(zCoords)
vector = vtk.vtkFloatArray()
vector.SetName("elevation");
vector.SetNumberOfComponents(3);
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vector.SetNumberOfTuples(np.prod(elevation.shape));
for i,z in enumerate(np.ravel(elevation)):
vector.SetTuple3(i,0,0,z)
grid.GetPointData().AddArray(vector)
writer = vtk.vtkXMLRectilinearGridWriter()
writer.SetDataModeToBinary()
writer.SetCompressorTypeToZLib()
writer.SetFileName(os.path.splitext(file)[0]+'.vtr')
if vtk.VTK_MAJOR_VERSION <= 5:
writer.SetInput(grid)
else:
writer.SetInputData(grid)
writer.Write()