Novel script to generate geometry description and material configuration from position, phase, and orientation data in an ASCIItable.
Can deal with phase-specific lattice symmetry, condenses orientations within a given angular threshold, and might be used in lieu of geom_fromANG when replacing the ANG header.
This commit is contained in:
Philip Eisenlohr
parent
9b1f16e99e
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,re,string,math
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import scipy.spatial, numpy as np
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from optparse import OptionParser
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import damask
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scriptID = string.replace('$Id$','\n','\\n')
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scriptName = os.path.splitext(scriptID.split()[1])[0]
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# --------------------------------------------------------------------
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# MAIN
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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=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Generate geometry description and material configuration from position, phase, and orientation data.
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""", version = scriptID)
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parser.add_option('--coordinates', dest='coordinates', type='string', metavar='string',
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help='coordinates label')
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parser.add_option('--phase', dest='phase', type='string', metavar='string',
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help='phase label')
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parser.add_option('-e', '--eulers', dest='eulers', metavar='string',
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help = 'Euler angles label')
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parser.add_option('-d', '--degrees', dest='degrees', action='store_true',
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help = 'angles are given in degrees [%default]')
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parser.add_option('-m', '--matrix', dest='matrix', metavar='string',
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help = 'orientation matrix label')
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parser.add_option('-a', dest='a', metavar='string',
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help = 'crystal frame a vector label')
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parser.add_option('-b', dest='b', metavar='string',
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help = 'crystal frame b vector label')
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parser.add_option('-c', dest='c', metavar='string',
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help = 'crystal frame c vector label')
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parser.add_option('-q', '--quaternion', dest='quaternion', metavar='string',
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help = 'quaternion label')
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parser.add_option( '--axes', dest='axes', nargs=3, metavar=' '.join(['string']*3),
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help = 'orientation coordinate frame in terms of position coordinate frame [same]')
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parser.add_option('-s', '--symmetry', dest='symmetry', action='extend',
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metavar='<string LIST>',
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help = 'crystal symmetry [%s] {%s} '%(damask.Symmetry.lattices[-1],
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', '.join(damask.Symmetry.lattices[1:])))
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parser.add_option('-t', '--tolerance', dest='tolerance', type='float', metavar='float',
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help = 'angular tolerance for orientation squashing [%default]')
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parser.add_option('--homogenization', dest='homogenization', type='int', metavar='int',
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help='homogenization index to be used [%default]')
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parser.add_option('--crystallite', dest='crystallite', type='int', metavar='int',
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help='crystallite index to be used [%default]')
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parser.set_defaults(symmetry = [],
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tolerance = 0.0,
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degrees = False,
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homogenization = 1,
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crystallite = 1,
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)
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(options,filenames) = parser.parse_args()
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input = [options.eulers != None,
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options.a != None and \
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options.b != None and \
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options.c != None,
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options.matrix != None,
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options.quaternion != None,
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]
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if np.sum(input) != 1: parser.error('needs exactly one orientation input format...')
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if options.axes != None and not set(options.axes).issubset(set(['x','+x','-x','y','+y','-y','z','+z','-z'])):
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parser.error('invalid axes %s %s %s'%tuple(options.axes))
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(label,dim,inputtype) = [(options.eulers,3,'eulers'),
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([options.a,options.b,options.c],[3,3,3],'frame'),
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(options.matrix,9,'matrix'),
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(options.quaternion,4,'quaternion'),
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][np.where(input)[0][0]] # select input label that was requested
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toRadians = math.pi/180.0 if options.degrees else 1.0 # rescale degrees to radians
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options.tolerance *= toRadians # angular tolerance in radians
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []:
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filenames = ['STDIN']
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for name in filenames:
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if name == 'STDIN':
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file = {'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr}
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file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
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else:
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if not os.path.exists(name): continue
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file = {'name':name,
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'input':open(name),
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'output':open(name + '_tmp','w'),
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'croak':sys.stderr}
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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'],buffered=False) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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errors = []
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if table.label_dimension(options.coordinates) != 2:
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errors.append('coordinates %s need to have two dimensions...'%options.coordinates)
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if not np.all(table.label_dimension(label) == dim):
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errors.append('orientation %s needs to have dimension %i...\n'%(label,dim))
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if options.phase != None and table.label_dimension(options.phase) != 1:
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errors.append('phase column %s is not scalar...'%options.phase)
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if errors == []:
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table.data_readArray([options.coordinates,label]+([] if options.phase == None else [options.phase]))
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if options.phase == None:
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table.data = np.column_stack((table.data,np.ones(len(table.data)))) # add single phase if no phase column given
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coordsX = np.unique(table.data[:,0])
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coordsY = np.unique(table.data[:,1])
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nX = len(coordsX)
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nY = len(coordsY)
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dX = (coordsX[-1]-coordsX[0])/(nX-1)
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dY = (coordsY[-1]-coordsY[0])/(nY-1)
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if nX*nY != len(table.data) \
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or np.any(np.abs(np.log10((coordsX[1:]-coordsX[:-1])/dX)) > 0.01) \
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or np.any(np.abs(np.log10((coordsY[1:]-coordsY[:-1])/dY)) > 0.01):
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errors.append('data is not on square grid...')
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if errors != []:
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file['croak'].write('\n'.join(errors)+'\n')
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table.close(dismiss = True)
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continue
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# ------------------------------------------ process data ------------------------------------------
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colOri = table.label_index(label) # column(s) of orientation data
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colPhase = colOri + np.sum(dim) # column of phase data comes after orientation
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index = np.lexsort((table.data[:,0],table.data[:,1])) # index of rank when sorting x fast, y slow
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rank = np.argsort(index) # rank of index
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KDTree = scipy.spatial.KDTree((table.data[:,:2]-np.array([coordsX[0],coordsY[0]])) \
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/ np.array([dX,dY])) # build KDTree with dX = dY = 1
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microstructure = np.zeros(nX*nY,dtype='uint32') # initialize empty microstructure
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symQuats = [] # empty list of sym equiv orientations
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phases = [] # empty list of phase info
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nGrains = 0 # counter for detected grains
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myRank = 0 # rank of current grid point
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for y in xrange(nY):
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for x in xrange(nX):
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if (myRank+1)%max(1,nX*nY/100) == 0:
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file['croak'].write('.')
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myData = table.data[index[myRank]]
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mySym = options.symmetry[min(int(myData[colPhase]),len(options.symmetry))-1] # select symmetry from option (take last specified option for all with higher index)
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if inputtype == 'eulers':
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o = damask.Orientation(Eulers=toRadians*\
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np.array(map(float,myData[colOri:colOri+3])),
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symmetry=mySym).reduced()
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elif inputtype == 'matrix':
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o = damask.Orientation(matrix=\
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np.array([map(float,myData[colOri:colOri+9])]).reshape(3,3).transpose(),
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symmetry=mySym).reduced()
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elif inputtype == 'frame':
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o = damask.Orientation(matrix=\
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np.array([map(float,myData[colOri[0]:colOri[0]+3] + \
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myData[colOri[1]:colOri[1]+3] + \
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myData[colOri[2]:colOri[2]+3]
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)]).reshape(3,3),
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symmetry=mySym).reduced()
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elif inputtype == 'quaternion':
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o = damask.Orientation(quaternion=\
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np.array(map(float,myData[colOri:colOri+4])),
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symmetry=mySym).reduced()
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oInv = o.quaternion.conjugated()
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neighbors = KDTree.query_ball_point([x,y], 3) # search points within radius
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breaker = False
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for n in neighbors: # check each neighbor
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if myRank <= rank[n] or table.data[n,colPhase] != myData[colPhase]: continue # skip myself, anyone further ahead (cannot yet have a grain ID), and other phases
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for q in symQuats[microstructure[rank[n]]-1]:
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if abs((q*oInv).asAngleAxis()[0]) <= options.tolerance: # found existing orientation resembling me
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microstructure[myRank] = microstructure[rank[n]]
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breaker = True; break
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if breaker: break
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if microstructure[myRank] == 0: # no other orientation resembled me
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nGrains += 1
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microstructure[myRank] = nGrains
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symQuats.append(o.equivalentQuaternions()) # store all symmetrically equivalent orientations for future comparison
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phases.append(myData[colPhase]) # store phase info for future reporting
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myRank += 1
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file['croak'].write('\n')
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#--- generate header ----------------------------------------------------------------------------
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info = {
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'grid': np.array([nX,nY,1]),
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'size': np.array([coordsX[-1]-coordsX[0],
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coordsY[-1]-coordsY[0],
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min((coordsX[-1]-coordsX[0])/nX,
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(coordsY[-1]-coordsY[0])/nY,
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)
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]),
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'origin': np.array([coordsX[0],coordsY[0],0.0]),
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'microstructures': nGrains,
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'homogenization': options.homogenization,
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}
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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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#--- write header ---------------------------------------------------------------------------------
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formatwidth = 1+int(math.log10(info['microstructures']))
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config_header = ['<microstructure>']
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for i,phase in enumerate(phases):
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config_header += ['[Grain%s]'%(str(i+1).zfill(formatwidth)),
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'crystallite %i'%options.crystallite,
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'(constituent)\tphase %i\ttexture %s\tfraction 1.0'%(phase,str(i+1).rjust(formatwidth)),
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]
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config_header += ['<texture>']
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for i,quats in enumerate(symQuats):
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config_header += ['[Grain%s]'%(str(i+1).zfill(formatwidth)),
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'axes\t%s %s %s'%tuple(options.axes) if options.axes != None else '',
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'(gauss)\tphi1 %g\tPhi %g\tphi2 %g\tscatter 0.0\tfraction 1.0'%tuple(np.degrees(quats[0].asEulers())),
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]
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table.labels_clear()
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table.info_clear()
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table.info_append([
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scriptID + ' ' + ' '.join(sys.argv[1:]),
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"grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],),
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"size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2],),
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"origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],),
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"homogenization\t%i"%info['homogenization'],
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"microstructures\t%i"%(info['microstructures']),
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config_header,
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])
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table.head_write()
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# --- write microstructure information ------------------------------------------------------------
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table.data = microstructure.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
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table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
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#--- output finalization --------------------------------------------------------------------------
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table.close()
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if file['name'] != 'STDIN':
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os.rename(file['name']+'_tmp',
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os.path.splitext(file['name'])[0] + '.geom')
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