DAMASK_EICMD/processing/misc/vtk_fromGwyddion.py

117 lines
3.9 KiB
Python
Executable File

#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os,sys,string,re,numpy,scipy.ndimage,scipy.signal,vtk
import damask
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
scriptID = '$Id$'
scriptName = scriptID.split()[1]
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,
},
}
#--------------------------------------------------------------------------------------------------
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 = """
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]
elevation = numpy.loadtxt(file)*options.scaling
grid = vtk.vtkRectilinearGrid()
grid.SetDimensions(elevation.shape[1],elevation.shape[0],1)
xCoords = vtk.vtkDoubleArray()
for x in numpy.arange(0.0,width,width/elevation.shape[1],'d'):
xCoords.InsertNextValue(x)
yCoords = vtk.vtkDoubleArray()
for y in numpy.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);
vector.SetNumberOfTuples(numpy.prod(elevation.shape));
for i,z in enumerate(numpy.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()