#!/usr/bin/env python3 # -*- coding: UTF-8 no BOM -*- import os,sys,math import numpy as np from optparse import OptionParser 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 option(s) [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.add_option('--crystallite', dest = 'crystallite', type = 'int', metavar = 'int', help = 'crystallite index to be used [%default]') parser.set_defaults(homogenization = 1, crystallite = 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 # --- loop over input files ------------------------------------------------------------------------- if filenames == []: filenames = [None] for name in filenames: try: table = damask.ASCIItable(name = name, outname = os.path.splitext(name)[-2]+'.geom' if name else name, buffered = False) except: continue damask.util.report(scriptName,name) # ------------------------------------------ read head --------------------------------------- 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) table.close(dismiss = True) 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 # --------------- figure out size and grid --------------------------------------------------------- coords = [np.unique(table.data[:,i]) for i in range(3)] mincorner = np.array(list(map(min,coords))) maxcorner = np.array(list(map(max,coords))) grid = np.array(list(map(len,coords)),'i') size = grid/np.maximum(np.ones(3,'d'), grid-1.0) * (maxcorner-mincorner) # size from edge to edge = dim * n/(n-1) size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 set to smallest among other spacings delta = size/np.maximum(np.ones(3,'d'), grid) origin = mincorner - 0.5*delta # shift from cell center to corner N = grid.prod() if N != len(table.data): errors.append('data count {} does not match grid {}.'.format(len(table.data),' x '.join(map(repr,grid)))) if np.any(np.abs(np.log10((coords[0][1:]-coords[0][:-1])/delta[0])) > 0.01) \ or np.any(np.abs(np.log10((coords[1][1:]-coords[1][:-1])/delta[1])) > 0.01) \ or np.any(np.abs(np.log10((coords[2][1:]-coords[2][:-1])/delta[2])) > 0.01): errors.append('regular grid spacing {} violated.'.format(' x '.join(map(repr,delta)))) if errors != []: damask.util.croak(errors) table.close(dismiss = True) continue # ------------------------------------------ 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(N,dtype = 'int32') # 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 # --- generate header ---------------------------------------------------------------------------- info = { 'grid': grid, 'size': size, 'origin': origin, 'microstructures': nGrains, 'homogenization': options.homogenization, } damask.util.report_geom(info) # --- write header --------------------------------------------------------------------------------- formatwidth = 1+int(math.log10(info['microstructures'])) if inputtype == 'microstructure': config_header = [] else: config_header = [''] for i,phase in enumerate(phases): config_header += ['[Grain%s]'%(str(i+1).zfill(formatwidth)), 'crystallite %i'%options.crystallite, '(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)), 'axes\t%s %s %s'%tuple(options.axes) if options.axes is not None else '', '(gauss)\tphi1 %g\tPhi %g\tphi2 %g\tscatter 0.0\tfraction 1.0'%tuple(orientation.asEulers(degrees = True)), ] table.labels_clear() table.info_clear() table.info_append([scriptID + ' ' + ' '.join(sys.argv[1:])]) table.head_putGeom(info) table.info_append(config_header) table.head_write() # --- write microstructure information ------------------------------------------------------------ table.data = grain.reshape(info['grid'][1]*info['grid'][2],info['grid'][0]) table.data_writeArray('%{}i'.format(formatwidth),delimiter=' ') #--- output finalization -------------------------------------------------------------------------- table.close()