old python2.7 scripts with only a loose connection to DAMASK
if needed, simply take them from an old release version
This commit is contained in:
Martin Diehl
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dc9aca5710
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#!/usr/bin/env python2.7
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# -*- coding: UTF-8 no BOM -*-
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import os,string,scipy
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import numpy as np
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import damask
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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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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Apply filter(s) to Gwyddion data.
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""" + string.replace(scriptID,'\n','\\n')
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)
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for option in ['opening',
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'closing',
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'erosion',
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'dilation',
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'average',
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'median',
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]:
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parser.add_option('-%s'%option[0], '--%s'%option, dest=option, type='int',
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help = 'stencil size for %s filter'%option)
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parser.set_default(option, 0)
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(options, filenames) = parser.parse_args()
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# ------------------------------------------ read Gwyddion data ---------------------------------------
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for file in filenames:
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filters = ''
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header = []
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with open(file,'r') as f:
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for line in f:
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pieces = line.split()
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if pieces[0] != '#': break
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if pieces[1] == 'Width:': width = float(pieces[2])
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if pieces[1] == 'Height:': height = float(pieces[2])
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header.append(line.lstrip('#').strip())
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elevation = np.loadtxt(file)#*1e6
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if options.opening > 0:
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elevation = scipy.ndimage.morphology.grey_opening(elevation,options.opening)
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filters += '_opening%i'%options.opening
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if options.closing > 0:
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elevation = scipy.ndimage.morphology.grey_closing(elevation,options.closing)
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filters += '_closing%i'%options.closing
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if options.erosion > 0:
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elevation = scipy.ndimage.morphology.grey_erosion(elevation,options.erosion)
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filters += '_erosion%i'%options.erosion
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if options.dilation > 0:
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elevation = scipy.ndimage.morphology.grey_dilation(elevation,options.dilation)
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filters += '_dilation%i'%options.dilation
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if options.average > 0:
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elevation = scipy.ndimage.filters.uniform_filter(elevation,options.average)
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filters += '_avg%i'%options.average
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if options.median > 0:
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elevation = scipy.ndimage.filters.median_filter(elevation,options.median)
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filters += '_median%i'%options.median
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np.savetxt(os.path.splitext(file)[0]+filters+os.path.splitext(file)[1],elevation,header='\n'.join(header))
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@ -1,98 +0,0 @@
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#!/usr/bin/env python2.7
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# -*- coding: UTF-8 no BOM -*-
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import os,string,vtk
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import numpy as np
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import damask
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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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scalingFactor = { \
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'm': {
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'm': 1e0,
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'mm': 1e-3,
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'µm': 1e-6,
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},
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'mm': {
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'm': 1e+3,
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'mm': 1e0,
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'µm': 1e-3,
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},
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'µm': {
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'm': 1e+6,
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'mm': 1e+3,
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'µm': 1e0,
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},
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}
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Produce VTK rectilinear grid from Gwyddion dataset exported as text.
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""" + string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-s', '--scaling', dest='scaling', type='float',
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help = 'scaling factor for elevation data [auto]')
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parser.set_defaults(scaling = 0.0)
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(options, filenames) = parser.parse_args()
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# ------------------------------------------ read Gwyddion data ---------------------------------------
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for file in filenames:
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with open(file,'r') as f:
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for line in f:
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pieces = line.split()
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if pieces[0] != '#': break
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if len(pieces) < 2: continue
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if pieces[1] == 'Width:':
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width = float(pieces[2])
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lateralunit = pieces[3]
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if pieces[1] == 'Height:':
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height = float(pieces[2])
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lateralunit = pieces[3]
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if pieces[1] == 'Value' and pieces[2] == 'units:':
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elevationunit = pieces[3]
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if options.scaling == 0.0:
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options.scaling = scalingFactor[lateralunit][elevationunit]
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elevation = np.loadtxt(file)*options.scaling
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grid = vtk.vtkRectilinearGrid()
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grid.SetDimensions(elevation.shape[1],elevation.shape[0],1)
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xCoords = vtk.vtkDoubleArray()
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for x in np.arange(0.0,width,width/elevation.shape[1],'d'):
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xCoords.InsertNextValue(x)
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yCoords = vtk.vtkDoubleArray()
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for y in np.arange(0.0,height,height/elevation.shape[0],'d'):
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yCoords.InsertNextValue(y)
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zCoords = vtk.vtkDoubleArray()
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zCoords.InsertNextValue(0.0)
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grid.SetXCoordinates(xCoords)
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grid.SetYCoordinates(yCoords)
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grid.SetZCoordinates(zCoords)
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vector = vtk.vtkFloatArray()
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vector.SetName("elevation");
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vector.SetNumberOfComponents(3);
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vector.SetNumberOfTuples(np.prod(elevation.shape));
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for i,z in enumerate(np.ravel(elevation)):
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vector.SetTuple3(i,0,0,z)
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grid.GetPointData().AddArray(vector)
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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(file)[0]+'.vtr')
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if vtk.VTK_MAJOR_VERSION <= 5:
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writer.SetInput(grid)
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else:
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writer.SetInputData(grid)
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writer.Write()
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