#!/usr/bin/env python3 import os import sys from optparse import OptionParser import numpy as np import damask scriptName = os.path.splitext(os.path.basename(__file__))[0] scriptID = ' '.join([scriptName,damask.version]) # -------------------------------------------------------------------- # MAIN # -------------------------------------------------------------------- parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """ Generate geometry description and material configuration from position, phase, and orientation (or microstructure) data. """, version = scriptID) parser.add_option('--coordinates', dest = 'pos', type = 'string', metavar = 'string', help = 'coordinates label (%default)') parser.add_option('--phase', dest = 'phase', type = 'string', metavar = 'string', help = 'phase label') parser.add_option('--microstructure', dest = 'microstructure', type = 'string', metavar = 'string', help = 'microstructure label') parser.add_option('-q', '--quaternion', dest = 'quaternion', type = 'string', metavar='string', help = 'quaternion label') parser.add_option('--axes', dest = 'axes', type = 'string', nargs = 3, metavar = ' '.join(['string']*3), help = 'orientation coordinate frame in terms of position coordinate frame [+x +y +z]') parser.add_option('--homogenization', dest = 'homogenization', type = 'int', metavar = 'int', help = 'homogenization index to be used [%default]') parser.set_defaults(homogenization = 1, pos = 'pos', ) (options,filenames) = parser.parse_args() input = [ options.quaternion is not None, options.microstructure is not None, ] if np.sum(input) != 1: parser.error('need either microstructure label or exactly one orientation input format.') if options.axes is not None and not set(options.axes).issubset(set(['x','+x','-x','y','+y','-y','z','+z','-z'])): parser.error('invalid axes {} {} {}.'.format(*options.axes)) (label,dim,inputtype) = [(options.quaternion,4,'quaternion'), (options.microstructure,1,'microstructure'), ][np.where(input)[0][0]] # select input label that was requested if filenames == []: filenames = [None] for name in filenames: damask.util.report(scriptName,name) table = damask.ASCIItable(name = name,readonly=True) table.head_read() # read ASCII header info # ------------------------------------------ sanity checks --------------------------------------- coordDim = table.label_dimension(options.pos) errors = [] if not 3 >= coordDim >= 2: errors.append('coordinates "{}" need to have two or three dimensions.'.format(options.pos)) if not np.all(table.label_dimension(label) == dim): errors.append('input "{}" needs to have dimension {}.'.format(label,dim)) if options.phase and table.label_dimension(options.phase) != 1: errors.append('phase column "{}" is not scalar.'.format(options.phase)) if errors != []: damask.util.croak(errors) continue table.data_readArray([options.pos] \ + (label if isinstance(label, list) else [label]) \ + ([options.phase] if options.phase else [])) if coordDim == 2: table.data = np.insert(table.data,2,np.zeros(len(table.data)),axis=1) # add zero z coordinate for two-dimensional input if options.phase is None: table.data = np.column_stack((table.data,np.ones(len(table.data)))) # add single phase if no phase column given grid,size = damask.util.coordGridAndSize(table.data[:,0:3]) coords = [np.unique(table.data[:,i]) for i in range(3)] mincorner = np.array(list(map(min,coords))) origin = mincorner - 0.5*size/grid # shift from cell center to corner # ------------------------------------------ process data ------------------------------------------ colOri = table.label_index(label)+(3-coordDim) # column(s) of orientation data followed by 3 coordinates if inputtype == 'microstructure': grain = table.data[:,colOri] nGrains = len(np.unique(grain)) elif inputtype == 'quaternion': colPhase = -1 # column of phase data comes last index = np.lexsort((table.data[:,0],table.data[:,1],table.data[:,2])) # index of position when sorting x fast, z slow grain = -np.ones(grid.prod(),dtype = int) # initialize empty microstructure orientations = [] # orientations multiplicity = [] # orientation multiplicity (number of group members) phases = [] # phase info nGrains = 0 # counter for detected grains existingGrains = np.arange(nGrains) myPos = 0 # position (in list) of current grid point for z in range(grid[2]): for y in range(grid[1]): for x in range(grid[0]): myData = table.data[index[myPos]] # read data for current grid point myPhase = int(myData[colPhase]) o = damask.Rotation(myData[colOri:colOri+4]) grain[myPos] = nGrains # assign new grain to me ... nGrains += 1 # ... and update counter orientations.append(o) # store new orientation for future comparison multiplicity.append(1) # having single occurrence so far phases.append(myPhase) # store phase info for future reporting existingGrains = np.arange(nGrains) # update list of existing grains myPos += 1 grain += 1 # offset from starting index 0 to 1 formatwidth = 1+int(np.log10(nGrains)) if inputtype == 'microstructure': config_header = [] else: config_header = [''] for i,phase in enumerate(phases): config_header += ['[Grain%s]'%(str(i+1).zfill(formatwidth)), 'crystallite 1', '(constituent)\tphase %i\ttexture %s\tfraction 1.0'%(phase,str(i+1).rjust(formatwidth)), ] config_header += [''] for i,orientation in enumerate(orientations): config_header += ['[Grain%s]'%(str(i+1).zfill(formatwidth)), '(gauss)\tphi1 %g\tPhi %g\tphi2 %g'%tuple(orientation.asEulers(degrees = True)), ] if options.axes is not None: config_header += ['axes\t{} {} {}'.format(*options.axes)] header = [scriptID + ' ' + ' '.join(sys.argv[1:])] + config_header + ['origin x {} y {} z {}'.format(*origin)] geom = damask.Geom(grain.reshape(grid,order='F'),size,options.homogenization,comments=header) damask.util.croak(geom) if name is None: sys.stdout.write(str(geom.show())) else: geom.to_file(os.path.splitext(name)[0]+'.geom')