bunch of new scripts:
gwyddion_filter tries to smoothen out Gwyddion data sets. vtk_fromGwyddion produces vtk mesh from Gwyddion data set. geom_addPrimitive allows to add box, cylinder, or ellipsoidal blobs to geom file.
This commit is contained in:
Philip Eisenlohr
parent
24e9bdb523
commit
943349fdbb
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@ -36,6 +36,7 @@ bin_link = { \
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'geom_fromMinimalSurface.py',
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'geom_fromMinimalSurface.py',
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'geom_fromVoronoiTessellation.py',
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'geom_fromVoronoiTessellation.py',
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'geom_fromOsteonGeometry.py',
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'geom_fromOsteonGeometry.py',
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'geom_addPrimitive.py',
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'geom_canvas.py',
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'geom_canvas.py',
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'geom_check.py',
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'geom_check.py',
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'geom_rescale.py',
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'geom_rescale.py',
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@ -91,6 +92,10 @@ bin_link = { \
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'vtk_voxelcloud.py',
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'vtk_voxelcloud.py',
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'vtk_addVoxelcloudData.py',
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'vtk_addVoxelcloudData.py',
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],
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],
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'misc' : [
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'gwyddion_filter.py',
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'vtk_fromGwyddion.py',
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],
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}
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}
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for dir in bin_link:
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for dir in bin_link:
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@ -0,0 +1,83 @@
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#!/usr/bin/env python
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import os,sys,string,re,numpy,scipy.ndimage,scipy.signal,vtk
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import damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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scriptID = '$Id$'
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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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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 = numpy.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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numpy.savetxt(os.path.splitext(file)[0]+filters+os.path.splitext(file)[1],elevation,header='\n'.join(header))
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@ -0,0 +1,116 @@
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#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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import os,sys,string,re,numpy,scipy.ndimage,scipy.signal,vtk
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import damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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scriptID = '$Id$'
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scriptName = scriptID.split()[1]
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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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#--------------------------------------------------------------------------------------------------
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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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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 = numpy.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 numpy.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 numpy.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(numpy.prod(elevation.shape));
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for i,z in enumerate(numpy.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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@ -0,0 +1,217 @@
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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,math,numpy
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import damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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scriptID = '$Id$'
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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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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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synonyms = {
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'grid': ['resolution'],
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'size': ['dimension'],
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}
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identifiers = {
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'grid': ['a','b','c'],
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'size': ['x','y','z'],
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'origin': ['x','y','z'],
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}
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mappings = {
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'grid': lambda x: int(x),
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'size': lambda x: float(x),
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'origin': lambda x: float(x),
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'homogenization': lambda x: int(x),
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'microstructures': lambda x: int(x),
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}
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parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
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Changes the (three-dimensional) canvas of a spectral geometry description.
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""" + string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-o', '--origin', dest='origin', type='int', nargs = 3, metavar='int int int', \
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help='a,b,c origin of primitive %default')
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parser.add_option('-d', '--dimension', dest='dimension', type='int', nargs = 3, metavar='int int int', \
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help='a,b,c extension of hexahedral box; negative values are diameters')
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parser.add_option('-f', '--fill', dest='fill', type='int', metavar = 'int', \
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help='grain index to fill primitive. "0" selects maximum microstructure index + 1 [%default]')
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parser.set_defaults(origin = [0,0,0],
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fill = 0,
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)
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(options, filenames) = parser.parse_args()
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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',
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'input':sys.stdin,
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'output':sys.stdout,
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'croak':sys.stderr,
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})
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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,
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'input':open(name),
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'output':open(name+'_tmp','w'),
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'croak':sys.stdout,
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})
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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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theTable = damask.ASCIItable(file['input'],file['output'],labels = False)
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theTable.head_read()
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#--- interpret header ----------------------------------------------------------------------------
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info = {
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'grid': numpy.zeros(3,'i'),
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'size': numpy.zeros(3,'d'),
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'origin': numpy.zeros(3,'d'),
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'homogenization': 0,
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'microstructures': 0,
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}
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newInfo = {
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'grid': numpy.zeros(3,'i'),
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'origin': numpy.zeros(3,'d'),
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'microstructures': 0,
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}
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extra_header = []
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for header in theTable.info:
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headitems = map(str.lower,header.split())
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if len(headitems) == 0: continue # skip blank lines
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for synonym,alternatives in synonyms.iteritems():
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if headitems[0] in alternatives: headitems[0] = synonym
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if headitems[0] in mappings.keys():
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if headitems[0] in identifiers.keys():
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for i in xrange(len(identifiers[headitems[0]])):
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info[headitems[0]][i] = \
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mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
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else:
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info[headitems[0]] = mappings[headitems[0]](headitems[1])
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else:
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extra_header.append(header)
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file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
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'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
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'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
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'homogenization: %i\n'%info['homogenization'] + \
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'microstructures: %i\n'%info['microstructures'])
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if numpy.any(info['grid'] < 1):
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file['croak'].write('invalid grid a b c.\n')
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continue
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if numpy.any(info['size'] <= 0.0):
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file['croak'].write('invalid size x y z.\n')
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continue
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#--- read data ------------------------------------------------------------------------------------
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microstructure = numpy.zeros(info['grid'].prod(),'i') # initialize as flat array
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|
i = 0
|
||||||
|
|
||||||
|
while theTable.data_read():
|
||||||
|
items = theTable.data
|
||||||
|
if len(items) > 2:
|
||||||
|
if items[1].lower() == 'of': items = [int(items[2])]*int(items[0])
|
||||||
|
elif items[1].lower() == 'to': items = xrange(int(items[0]),1+int(items[2]))
|
||||||
|
else: items = map(int,items)
|
||||||
|
else: items = map(int,items)
|
||||||
|
|
||||||
|
s = len(items)
|
||||||
|
microstructure[i:i+s] = items
|
||||||
|
i += s
|
||||||
|
|
||||||
|
#--- do work ------------------------------------------------------------------------------------
|
||||||
|
|
||||||
|
if options.fill == 0:
|
||||||
|
options.fill = microstructure.max()+1
|
||||||
|
|
||||||
|
microstructure = microstructure.reshape(info['grid'],order='F')
|
||||||
|
|
||||||
|
if options.dimension != None:
|
||||||
|
mask = (numpy.array(options.dimension) < 0).astype(float)
|
||||||
|
dim = abs(numpy.array(options.dimension))
|
||||||
|
scale = 2.0/dim
|
||||||
|
d = numpy.zeros(3,dtype='float')
|
||||||
|
|
||||||
|
d[0] = (1.-dim[0])/2.0
|
||||||
|
for x in xrange(int(math.ceil(options.origin[0]-dim[0]/2.)),
|
||||||
|
int(math.ceil(options.origin[0]+dim[0]/2.))):
|
||||||
|
i = x%info['grid'][0]
|
||||||
|
d[1] = (1.-dim[1])/2.0
|
||||||
|
|
||||||
|
for y in xrange(int(math.ceil(options.origin[1]-dim[1]/2.)),
|
||||||
|
int(math.ceil(options.origin[1]+dim[1]/2.))):
|
||||||
|
j = y%info['grid'][1]
|
||||||
|
d[2] = (1.-dim[2])/2.0
|
||||||
|
|
||||||
|
for z in xrange(int(math.ceil(options.origin[2]-dim[2]/2.)),
|
||||||
|
int(math.ceil(options.origin[2]+dim[2]/2.))):
|
||||||
|
k = z%info['grid'][2]
|
||||||
|
|
||||||
|
if numpy.dot(d*scale*mask,d*scale*mask) <= 1.0:
|
||||||
|
microstructure[i,j,k] = options.fill
|
||||||
|
|
||||||
|
d[2] += 1.
|
||||||
|
d[1] += 1.
|
||||||
|
d[0] += 1.
|
||||||
|
|
||||||
|
newInfo['microstructures'] = microstructure.max()
|
||||||
|
|
||||||
|
|
||||||
|
#--- report ---------------------------------------------------------------------------------------
|
||||||
|
if (newInfo['microstructures'] != info['microstructures']):
|
||||||
|
file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures'])
|
||||||
|
|
||||||
|
#--- write header ---------------------------------------------------------------------------------
|
||||||
|
theTable.labels_clear()
|
||||||
|
theTable.info_clear()
|
||||||
|
theTable.info_append(extra_header+[
|
||||||
|
scriptID + ' ' + ' '.join(sys.argv[1:]),
|
||||||
|
"grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],),
|
||||||
|
"size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2],),
|
||||||
|
"origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],),
|
||||||
|
"homogenization\t%i"%info['homogenization'],
|
||||||
|
"microstructures\t%i"%(newInfo['microstructures']),
|
||||||
|
])
|
||||||
|
theTable.head_write()
|
||||||
|
theTable.output_flush()
|
||||||
|
|
||||||
|
# --- write microstructure information ------------------------------------------------------------
|
||||||
|
formatwidth = int(math.floor(math.log10(microstructure.max())+1))
|
||||||
|
theTable.data = microstructure.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
|
||||||
|
theTable.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
|
||||||
|
|
||||||
|
#--- output finalization --------------------------------------------------------------------------
|
||||||
|
if file['name'] != 'STDIN':
|
||||||
|
file['input'].close()
|
||||||
|
file['output'].close()
|
||||||
|
os.rename(file['name']+'_tmp',file['name'])
|
||||||
Loading…
Reference in New Issue