some more changes improving the post processing scripts
This commit is contained in:
Martin Diehl
parent
1707f7d367
commit
e5dc9e79cc
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@ -274,7 +274,7 @@ parser.add_option('-v', '--vector', action='extend', dest='vector', type='string
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help='list of vectors to visualize', metavar = '<string LIST>')
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parser.add_option('-t', '--tensor', action='extend', dest='tensor', type='string', \
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help='list of tensors to visualize', metavar = '<string LIST>')
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parser.add_option('-d', '--deformation', dest='defgrad', type='string', \
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parser.add_option('-d', '--deformation', dest='defgrad', action='store', type='string', \
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help='heading of deformation gradient columns [%default]', metavar = 'string')
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parser.add_option('--reference', dest='undeformed', action='store_true',\
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help='map results to reference (undeformed) configuration [%default]')
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@ -290,15 +290,15 @@ parser.add_option('--points', dest='output_points', action='store_true', \
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help='produce VTK points file [%default]')
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parser.add_option('--nopoints', dest='output_points', action='store_false', \
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help='omit VTK points file')
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parser.add_option('--separator', dest='separator', type='string', \
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parser.add_option('--separator', dest='separator', action='store', type='string', \
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help='data separator (t(ab), n(ewline), s(pace)) [%default]', metavar = 'string')
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parser.add_option('--scaling', dest='scaling', action='extend', type='string', \
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help='scaling of fluctuation', metavar = '<float LIST>')
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parser.add_option('-u', '--unitlength', dest='unitlength', type='float', \
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parser.add_option('-u', '--unitlength', dest='unitlength', action='store', type='float', \
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help='set unit length for 2D model [%default]', metavar = 'float')
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parser.add_option('--filenodalcoords', dest='filenodalcoords', type='string', \
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parser.add_option('--filenodalcoords', dest='filenodalcoords', action='store', type='string', \
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help='ASCII table containing nodal coords', metavar = 'string')
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parser.add_option('--labelnodalcoords', dest='labelnodalcoords', type='string', nargs=3, \
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parser.add_option('--labelnodalcoords', dest='labelnodalcoords', action='store', type='string', nargs=3, \
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help='labels of nodal coords in ASCII table %default', metavar = 'string string string')
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parser.add_option('-l', '--linear', dest='linearreconstruction', action='store_true',\
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help='use linear reconstruction of geometry [%default]')
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@ -21,9 +21,9 @@ deformation gradient and first Piola--Kirchhoff stress.
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""", version = string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-f','--defgrad', dest='defgrad', type='string', metavar='string', \
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parser.add_option('-f','--defgrad', dest='defgrad', action='store', type='string', metavar='string', \
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help='heading of columns containing deformation gradient [%default]')
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parser.add_option('-p','--stress', dest='stress', type='string', metavar='string', \
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parser.add_option('-p','--stress', dest='stress', action='store', type='string', metavar='string', \
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help='heading of columns containing first Piola--Kirchhoff stress [%default]')
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parser.set_defaults(defgrad = 'f')
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parser.set_defaults(stress = 'p')
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@ -24,9 +24,9 @@ parser.add_option('--no-shape','-s', dest='noShape', action='store_false', \
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help='do not calcuate shape mismatch [%default]')
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parser.add_option('--no-volume','-v', dest='noVolume', action='store_false', \
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help='do not calculate volume mismatch [%default]')
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parser.add_option('-c','--coordinates', dest='coords', type='string', metavar='string', \
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parser.add_option('-c','--coordinates', dest='coords', action='store', type='string', metavar='string', \
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help='column heading for coordinates [%default]')
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parser.add_option('-f','--deformation', dest='defgrad', type='string', metavar='string ', \
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parser.add_option('-f','--deformation', dest='defgrad', action='store', type='string', metavar='string ', \
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help='column heading for coordinates [%defgrad]')
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parser.set_defaults(noVolume = False)
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parser.set_defaults(noShape = False)
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@ -22,7 +22,7 @@ Deals with both vector- and tensor-valued fields.
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""", version = string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-c','--coordinates', dest='coords', type='string', metavar='string', \
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parser.add_option('-c','--coordinates', dest='coords', action='store', type='string', metavar='string', \
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help='column heading for coordinates [%default]')
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parser.add_option('-v','--vector', dest='vector', action='extend', type='string', metavar='<string LIST>', \
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help='heading of columns containing vector field values')
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@ -21,9 +21,9 @@ Operates on periodic ordered three-dimensional data sets.
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""", version = string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-c','--coordinates', dest='coords', type='string', metavar='string', \
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parser.add_option('-c','--coordinates', dest='coords', action='store', type='string', metavar='string', \
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help='column heading for coordinates [%default]')
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parser.add_option('-d','--defgrad', dest='defgrad', type='string', metavar='string', \
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parser.add_option('-d','--defgrad', dest='defgrad', action='store', type='string', metavar='string', \
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help='heading of columns containing tensor field values')
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parser.add_option('-l', '--linear', dest='linearreconstruction', action='store_true',\
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help='use linear reconstruction of geometry [%default]')
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@ -27,7 +27,7 @@ parser.add_option('--fdm', dest='accuracy', action='extend', type='
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help='degree of central difference accuracy (%s)'%(','.join(accuracyChoices)))
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parser.add_option('--fft', dest='fft', action='store_true', \
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help='calculate divergence in Fourier space')
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parser.add_option('-c','--coordinates', dest='coords', type='string', metavar = 'string', \
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parser.add_option('-c','--coordinates', dest='coords', action='store', type='string', metavar = 'string', \
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help='column heading for coordinates [%default]')
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parser.add_option('-v','--vector', dest='vector', action='extend', type='string', metavar='<string LIST>', \
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help='heading of columns containing vector field values')
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@ -1,39 +1,25 @@
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,re,sys,math,numpy,string,damask
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import os,re,sys,math,string
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import numpy as np
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from optparse import OptionParser
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from scipy import ndimage
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from optparse import OptionParser, Option
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# -----------------------------
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class extendableOption(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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import damask
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scriptID = '$Id$'
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scriptName = scriptID.split()[1]
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def periodic_3Dpad(array, rimdim=(1,1,1)):
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rimdim = numpy.array(rimdim,'i')
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size = numpy.array(array.shape,'i')
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padded = numpy.empty(size+2*rimdim,array.dtype)
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rimdim = np.array(rimdim,'i')
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size = np.array(array.shape,'i')
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padded = np.empty(size+2*rimdim,array.dtype)
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padded[rimdim[0]:rimdim[0]+size[0],
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rimdim[1]:rimdim[1]+size[1],
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rimdim[2]:rimdim[2]+size[2]] = array
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p = numpy.zeros(3,'i')
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p = np.zeros(3,'i')
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for side in xrange(3):
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for p[(side+2)%3] in xrange(padded.shape[(side+2)%3]):
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for p[(side+1)%3] in xrange(padded.shape[(side+1)%3]):
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@ -56,7 +42,7 @@ features = [ \
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]
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neighborhoods = {
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'neumann':numpy.array([
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'neumann':np.array([
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[-1, 0, 0],
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[ 1, 0, 0],
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[ 0,-1, 0],
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@ -64,7 +50,7 @@ neighborhoods = {
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[ 0, 0,-1],
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[ 0, 0, 1],
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]),
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'moore':numpy.array([
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'moore':np.array([
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[-1,-1,-1],
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[ 0,-1,-1],
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[ 1,-1,-1],
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@ -95,22 +81,22 @@ neighborhoods = {
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])
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}
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parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Add column(s) containing Euclidean distance to grain structural features:
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boundaries, triple lines, and quadruple points.
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""" + string.replace('$Id$','\n','\\n')
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""", version = string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-i','--identifier', dest='id', action='store', type='string', \
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help='heading of column containing grain identifier [%default]', \
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metavar='<label>')
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parser.add_option('-t','--type', dest='type', action='extend', type='string', \
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parser.add_option('-c','--coordinates', dest='coords', action='store', type='string', metavar='string', \
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help='column heading for coordinates [%default]')
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parser.add_option('-i','--identifier', dest='id', action='store', type='string', metavar = 'string', \
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help='heading of column containing grain identifier [%default]')
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parser.add_option('-t','--type', dest='type', action='extend', type='string', metavar='<string LIST>', \
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help='feature type (%s)'%(', '.join(map(lambda x:', '.join(x['names']),features))))
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parser.add_option('-n','--neighborhood', dest='neigborhood', action='store', type='string', \
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help='type of neighborhood (%s)'%(', '.join(neighborhoods.keys())), \
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metavar='<int>')
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parser.add_option('-n','--neighborhood',dest='neigborhood', action='store', type='string', metavar='int', \
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help='type of neighborhood (%s)'%(', '.join(neighborhoods.keys())))
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parser.set_defaults(coords = 'ip')
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parser.set_defaults(type = [])
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parser.set_defaults(id = 'texture')
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parser.set_defaults(neighborhood = 'neumann')
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@ -126,60 +112,61 @@ for i,feature in enumerate(features):
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for name in feature['names']:
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for type in options.type:
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if name.startswith(type):
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feature_list.append(i) # remember valid features
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feature_list.append(i) # remember valid features
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break
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# ------------------------------------------ setup file handles ---------------------------------------
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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', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr})
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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, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
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# ------------------------------------------ loop over input files ---------------------------------------
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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, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
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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(file['name']+'\n')
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file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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table.info_append(string.replace('$Id$','\n','\\n') + \
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'\t' + ' '.join(sys.argv[1:]))
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table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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table.info_append(string.replace(scriptID,'\n','\\n') + '\t' + ' '.join(sys.argv[1:]))
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# ------------------------------------------ assemble header ---------------------------------------
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# --------------- figure out position of labels and coordinates ------------------------------------
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try:
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locationCol = table.labels.index('%s.x'%options.coords) # columns containing location data
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except ValueError:
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file['croak'].write('no coordinate data found...\n'%key)
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continue
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if options.id not in table.labels:
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file['croak'].write('column %s not found...\n'%options.id)
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continue
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# ------------------------------------------ assemble header ---------------------------------------
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for feature in feature_list:
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table.labels_append('ED_%s(%s)'%(features[feature]['names'][0],options.id)) # extend ASCII header with new labels
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table.labels_append('ED_%s(%s)'%(features[feature]['names'][0],options.id)) # extend ASCII header with new labels
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table.head_write()
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# ------------------------------------------ process data ---------------------------------------
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table.data_readArray(['ip.x','ip.y','ip.z',options.id])
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table.data_readArray([options.coords+'.x',options.coords+'.y',options.coords+'.z',options.id])
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grid = [{},{},{}]
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for i in xrange(len(table.data)):
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for j in xrange(3):
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grid[j][str(table.data[i,j])] = True
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resolution = numpy.array(map(len,grid),'i')
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resolution = np.array(map(len,grid),'i')
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unitlength = 0.0
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for i,r in enumerate(resolution):
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if r > 1: unitlength = max(unitlength,(max(map(float,grid[i].keys()))-min(map(float,grid[i].keys())))/(r-1.0))
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neighborhood = neighborhoods[options.neighborhood]
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convoluted = numpy.empty([len(neighborhood)]+list(resolution+2),'i')
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microstructure = periodic_3Dpad(numpy.array(table.data[:,3].reshape(resolution),'i'))
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convoluted = np.empty([len(neighborhood)]+list(resolution+2),'i')
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microstructure = periodic_3Dpad(np.array(table.data[:,3].reshape(resolution),'i'))
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for i,p in enumerate(neighborhood):
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stencil = numpy.zeros((3,3,3),'i')
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stencil = np.zeros((3,3,3),'i')
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stencil[1,1,1] = -1
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stencil[p[0]+1,
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p[1]+1,
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@ -187,36 +174,34 @@ for file in files:
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convoluted[i,:,:,:] = ndimage.convolve(microstructure,stencil)
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distance = numpy.ones((len(feature_list),resolution[0],resolution[1],resolution[2]),'d')
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distance = np.ones((len(feature_list),resolution[0],resolution[1],resolution[2]),'d')
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convoluted = numpy.sort(convoluted,axis=0)
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uniques = numpy.zeros(resolution)
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check = numpy.empty(resolution)
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check[:,:,:] = numpy.nan
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convoluted = np.sort(convoluted,axis=0)
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uniques = np.zeros(resolution)
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check = np.empty(resolution)
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check[:,:,:] = np.nan
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for i in xrange(len(neighborhood)):
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uniques += numpy.where(convoluted[i,1:-1,1:-1,1:-1] == check,0,1)
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uniques += np.where(convoluted[i,1:-1,1:-1,1:-1] == check,0,1)
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check = convoluted[i,1:-1,1:-1,1:-1]
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for i,feature_id in enumerate(feature_list):
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distance[i,:,:,:] = numpy.where(uniques > features[feature_id]['aliens'],0.0,1.0)
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distance[i,:,:,:] = np.where(uniques > features[feature_id]['aliens'],0.0,1.0)
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for i in xrange(len(feature_list)):
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distance[i,:,:,:] = ndimage.morphology.distance_transform_edt(distance[i,:,:,:])*[unitlength]*3
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distance.shape = (len(feature_list),resolution.prod())
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# ------------------------------------------ process data ---------------------------------------
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table.data_rewind()
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l = 0
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while table.data_read():
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for i in xrange(len(feature_list)):
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table.data_append(distance[i,l]) # add all distance fields
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table.data_write() # output processed line
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table.data_append(distance[i,l]) # add all distance fields
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outputAlive = table.data_write() # output processed line
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l += 1
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# ------------------------------------------ output result ---------------------------------------
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outputAlive and table.output_flush() # just in case of buffered ASCII table
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table.output_flush() # just in case of buffered ASCII table
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if file['name'] != 'STDIN':
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file['input'].close() # close input ASCII table
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file['output'].close() # close output ASCII table
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os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
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file['input'].close() # close input ASCII table (works for stdin)
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file['output'].close() # close output ASCII table (works for stdout)
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os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
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@ -1,56 +1,43 @@
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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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import os,re,sys,math,string
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import numpy as np
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from collections import defaultdict
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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from optparse import OptionParser
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import damask
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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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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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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:
|
||||
Option.take_action(self, action, dest, opt, value, values, parser)
|
||||
|
||||
|
||||
parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
Add RGB color value corresponding to TSL-OIM scheme for inverse pole figures.
|
||||
""" + string.replace(scriptID,'\n','\\n')
|
||||
|
||||
""", version = string.replace(scriptID,'\n','\\n')
|
||||
)
|
||||
|
||||
parser.add_option('-p', '--pole', dest='pole', type='float', nargs=3, metavar='X Y Z',
|
||||
help = 'lab frame direction for inverse pole figure %default')
|
||||
parser.add_option('-s', '--symmetry', dest='symmetry', type='string',
|
||||
help = 'crystal symmetry [%default]')
|
||||
parser.add_option('-e', '--eulers', dest='eulers', type='string', metavar='LABEL',
|
||||
help = 'Euler angles label')
|
||||
parser.add_option('-d', '--degrees', dest='degrees', action='store_true',
|
||||
help = 'Euler angles are given in degrees [%default]')
|
||||
parser.add_option('-m', '--matrix', dest='matrix', type='string', metavar='LABEL',
|
||||
help = 'orientation matrix label')
|
||||
parser.add_option('-a', dest='a', type='string', metavar='LABEL',
|
||||
help = 'crystal frame a vector label')
|
||||
parser.add_option('-b', dest='b', type='string', metavar='LABEL',
|
||||
help = 'crystal frame b vector label')
|
||||
parser.add_option('-c', dest='c', type='string', metavar='LABEL',
|
||||
help = 'crystal frame c vector label')
|
||||
parser.add_option('-p', '--pole', dest='pole', type='float', nargs=3, metavar='X Y Z',
|
||||
help = 'lab frame direction for inverse pole figure %default')
|
||||
parser.add_option('-s', '--symmetry', dest='symmetry', type='string',
|
||||
help = 'crystal symmetry [%default]')
|
||||
parser.add_option('-e', '--eulers', dest='eulers', type='string', metavar='LABEL',
|
||||
help = 'Euler angles label')
|
||||
parser.add_option('-d', '--degrees', dest='degrees', action='store_true',
|
||||
help = 'Euler angles are given in degrees [%default]')
|
||||
parser.add_option('-m', '--matrix', dest='matrix', type='string', metavar='LABEL',
|
||||
help = 'orientation matrix label')
|
||||
parser.add_option('-a', dest='a', type='string', metavar='LABEL',
|
||||
help = 'crystal frame a vector label')
|
||||
parser.add_option('-b', dest='b', type='string', metavar='LABEL',
|
||||
help = 'crystal frame b vector label')
|
||||
parser.add_option('-c', dest='c', type='string', metavar='LABEL',
|
||||
help = 'crystal frame c vector label')
|
||||
parser.add_option('-q', '--quaternion', dest='quaternion', type='string', metavar='LABEL',
|
||||
help = 'quaternion label')
|
||||
help = 'quaternion label')
|
||||
|
||||
parser.set_defaults(pole = [0.0,0.0,1.0])
|
||||
parser.set_defaults(symmetry = 'cubic')
|
||||
|
|
@ -75,8 +62,8 @@ if options.matrix != None: datainfo['tensor']['label'] += [options.matrix];
|
|||
if options.quaternion != None: datainfo['quaternion']['label'] += [options.quaternion]; input = 'quaternion'
|
||||
|
||||
toRadians = math.pi/180.0 if options.degrees else 1.0 # rescale degrees to radians
|
||||
pole = numpy.array(options.pole)
|
||||
pole /= numpy.linalg.norm(pole)
|
||||
pole = np.array(options.pole)
|
||||
pole /= np.linalg.norm(pole)
|
||||
|
||||
# ------------------------------------------ setup file handles ---------------------------------------
|
||||
|
||||
|
|
@ -124,15 +111,15 @@ for file in files:
|
|||
while table.data_read(): # read next data line of ASCII table
|
||||
|
||||
if input == 'eulers':
|
||||
o = damask.Orientation(Eulers=toRadians*numpy.array(map(float,table.data[column['vector'][options.eulers]:\
|
||||
o = damask.Orientation(Eulers=toRadians*np.array(map(float,table.data[column['vector'][options.eulers]:\
|
||||
column['vector'][options.eulers]+datainfo['vector']['len']])),
|
||||
symmetry=options.symmetry).reduced()
|
||||
elif input == 'matrix':
|
||||
o = damask.Orientation(matrix=numpy.array([map(float,table.data[column['tensor'][options.matrix]:\
|
||||
o = damask.Orientation(matrix=np.array([map(float,table.data[column['tensor'][options.matrix]:\
|
||||
column['tensor'][options.matrix]+datainfo['tensor']['len']])]),
|
||||
symmetry=options.symmetry).reduced()
|
||||
elif input == 'frame':
|
||||
o = damask.Orientation(matrix=numpy.array([map(float,table.data[column['vector'][options.a]:\
|
||||
o = damask.Orientation(matrix=np.array([map(float,table.data[column['vector'][options.a]:\
|
||||
column['vector'][options.a]+datainfo['vector']['len']] + \
|
||||
table.data[column['vector'][options.b]:\
|
||||
column['vector'][options.b]+datainfo['vector']['len']] + \
|
||||
|
|
@ -141,19 +128,17 @@ for file in files:
|
|||
)]).reshape(3,3),
|
||||
symmetry=options.symmetry).reduced()
|
||||
elif input == 'quaternion':
|
||||
o = damask.Orientation(quaternion=numpy.array(map(float,table.data[column['quaternion'][options.quaternion]:\
|
||||
o = damask.Orientation(quaternion=np.array(map(float,table.data[column['quaternion'][options.quaternion]:\
|
||||
column['quaternion'][options.quaternion]+datainfo['quaternion']['len']])),
|
||||
symmetry=options.symmetry).reduced()
|
||||
|
||||
table.data_append(o.IPFcolor(pole))
|
||||
|
||||
table.data_write() # output processed line
|
||||
outputAlive = table.data_write() # output processed line
|
||||
|
||||
# ------------------------------------------ output result ---------------------------------------
|
||||
outputAlive and table.output_flush() # just in case of buffered ASCII table
|
||||
|
||||
table.output_flush() # just in case of buffered ASCII table
|
||||
|
||||
file['input'].close() # close input ASCII table (works for stdin)
|
||||
file['output'].close() # close output ASCII table (works for stdout)
|
||||
if file['name'] != 'STDIN':
|
||||
file['input'].close() # close input ASCII table
|
||||
file['output'].close() # close output ASCII table
|
||||
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
|
||||
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
|
||||
|
|
|
|||
Loading…
Reference in New Issue