#!/usr/bin/env python import os,sys,string,time,copy import numpy as np import damask from optparse import OptionParser from scipy import spatial from collections import defaultdict scriptID = string.replace('$Id$','\n','\\n') scriptName = os.path.splitext(scriptID.split()[1])[0] parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """ Add grain index based on similiarity of crystal lattice orientation. """, version = scriptID) parser.add_option('-r', '--radius', dest = 'radius', type = 'float', metavar = 'float', help = 'search radius') parser.add_option('-d', '--disorientation', dest = 'disorientation', type = 'float', metavar = 'float', help = 'disorientation threshold per grain [%default] (degrees)') parser.add_option('-s', '--symmetry', dest = 'symmetry', type = 'string', metavar = 'string', help = 'crystal symmetry [%default]') parser.add_option('-e', '--eulers', dest = 'eulers', type = 'string', metavar = 'string', help = 'Euler angles') parser.add_option( '--degrees', dest = 'degrees', action = 'store_true', help = 'Euler angles are given in degrees [%default]') parser.add_option('-m', '--matrix', dest = 'matrix', type = 'string', metavar = 'string', help = 'orientation matrix') parser.add_option('-a', dest = 'a', type = 'string', metavar = 'string', help = 'crystal frame a vector') parser.add_option('-b', dest = 'b', type = 'string', metavar = 'string', help = 'crystal frame b vector') parser.add_option('-c', dest = 'c', type = 'string', metavar = 'string', help = 'crystal frame c vector') parser.add_option('-q', '--quaternion', dest = 'quaternion', type = 'string', metavar = 'string', help = 'quaternion') parser.add_option('-p', '--position', dest = 'coords', type = 'string', metavar = 'string', help = 'spatial position of voxel [%default]') parser.set_defaults(symmetry = 'cubic', coords = 'pos', degrees = False, ) (options, filenames) = parser.parse_args() if options.radius == None: parser.error('no radius specified.') input = [options.eulers != None, options.a != None and \ options.b != None and \ options.c != None, options.matrix != None, options.quaternion != None, ] if np.sum(input) != 1: parser.error('needs exactly one input format.') (label,dim,inputtype) = [(options.eulers,3,'eulers'), ([options.a,options.b,options.c],[3,3,3],'frame'), (options.matrix,9,'matrix'), (options.quaternion,4,'quaternion'), ][np.where(input)[0][0]] # select input label that was requested toRadians = np.pi/180.0 if options.degrees else 1.0 # rescale degrees to radians cos_disorientation = np.cos(options.disorientation/2.*toRadians) # --- loop over input files ------------------------------------------------------------------------- if filenames == []: filenames = [None] for name in filenames: try: table = damask.ASCIItable(name = name, buffered = False) except: continue damask.util.report(scriptName,name) # ------------------------------------------ read header ------------------------------------------- table.head_read() # ------------------------------------------ sanity checks ----------------------------------------- errors = [] remarks = [] if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords)) if not np.all(table.label_dimension(label) == dim): errors.append('input {} has wrong dimension {}.'.format(label,dim)) else: column = table.label_index(label) if remarks != []: damask.util.croak(remarks) if errors != []: damask.util.croak(errors) table.close(dismiss = True) continue # ------------------------------------------ assemble header --------------------------------------- table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:])) table.labels_append('grainID_{}@{}'.format(label, options.disorientation if options.degrees else np.degrees(options.disorientation))) # report orientation source and disorientation in degrees table.head_write() # ------------------------------------------ process data ------------------------------------------ # ------------------------------------------ build KD tree ----------------------------------------- # --- start background messaging bg = damask.util.backgroundMessage() bg.start() bg.set_message('reading positions...') table.data_readArray(options.coords) # read position vectors grainID = -np.ones(len(table.data),dtype=int) start = tick = time.clock() bg.set_message('building KD tree...') kdtree = spatial.KDTree(copy.deepcopy(table.data)) # ------------------------------------------ assign grain IDs -------------------------------------- tick = time.clock() orientations = [] # quaternions found for grain memberCounts = [] # number of voxels in grain p = 0 # point counter g = 0 # grain counter matchedID = -1 lastDistance = np.dot(kdtree.data[-1]-kdtree.data[0],kdtree.data[-1]-kdtree.data[0]) # (arbitrarily) use diagonal of cloud table.data_rewind() while table.data_read(): # read next data line of ASCII table if p > 0 and p % 1000 == 0: time_delta = (time.clock()-tick) * (len(grainID) - p) / p bg.set_message('(%02i:%02i:%02i) processing point %i of %i (grain count %i)...'%(time_delta//3600,time_delta%3600//60,time_delta%60,p,len(grainID),len(orientations))) if inputtype == 'eulers': o = damask.Orientation(Eulers = np.array(map(float,table.data[column:column+3]))*toRadians, symmetry = options.symmetry).reduced() elif inputtype == 'matrix': o = damask.Orientation(matrix = np.array(map(float,table.data[column:column+9])).reshape(3,3).transpose(), symmetry = options.symmetry).reduced() elif inputtype == 'frame': o = damask.Orientation(matrix = np.array(map(float,table.data[column[0]:column[0]+3] + \ table.data[column[1]:column[1]+3] + \ table.data[column[2]:column[2]+3])).reshape(3,3), symmetry = options.symmetry).reduced() elif inputtype == 'quaternion': o = damask.Orientation(quaternion = np.array(map(float,table.data[column:column+4])), symmetry = options.symmetry).reduced() matched = False # check against last matched needs to be really picky. best would be to exclude jumps across the poke (checking distance between last and me?) # when walking through neighborhood first check whether grainID of that point has already been tested, if yes, skip! if matchedID != -1: # has matched before? matched = (o.quaternion.conjugated() * orientations[matchedID].quaternion).w > cos_disorientation if not matched: alreadyChecked = {} bestDisorientation = damask.Quaternion([0,0,0,1]) # initialize to 180 deg rotation as worst case for i in kdtree.query_ball_point(kdtree.data[p],options.radius): # check all neighboring points gID = grainID[i] if gID != -1 and gID not in alreadyChecked: # an already indexed point belonging to a grain not yet tested? alreadyChecked[gID] = True # remember not to check again disorientation = o.disorientation(orientations[gID],SST = False)[0] # compare against that grain's orientation (and skip requirement of axis within SST) if disorientation.quaternion.w > cos_disorientation and \ disorientation.quaternion.w >= bestDisorientation.w: # within disorientation threshold and better than current best? matched = True matchedID = gID # remember that grain bestDisorientation = disorientation.quaternion if not matched: # no match -> new grain found memberCounts += [1] # start new membership counter orientations += [o] # initialize with current orientation matchedID = g g += 1 # increment grain counter else: # did match existing grain memberCounts[matchedID] += 1 grainID[p] = matchedID # remember grain index assigned to point p += 1 # increment point bg.set_message('identifying similar orientations among {} grains...'.format(len(orientations))) memberCounts = np.array(memberCounts) similarOrientations = [[] for i in xrange(len(orientations))] for i,orientation in enumerate(orientations[:-1]): # compare each identified orientation... for j in xrange(i+1,len(orientations)): # ...against all others that were defined afterwards if orientation.disorientation(orientations[j],SST = False)[0].quaternion.w > cos_disorientation: # similar orientations in both grainIDs? similarOrientations[i].append(j) # remember in upper triangle... similarOrientations[j].append(i) # ...and lower triangle of matrix if similarOrientations[i] != []: bg.set_message('grainID {} is as: {}'.format(i,' '.join(map(str,similarOrientations[i])))) stillShifting = True while stillShifting: stillShifting = False tick = time.clock() for p,gID in enumerate(grainID): # walk through all points if p > 0 and p % 1000 == 0: time_delta = (time.clock()-tick) * (len(grainID) - p) / p bg.set_message('(%02i:%02i:%02i) shifting ID of point %i out of %i (grain count %i)...'%(time_delta//3600,time_delta%3600//60,time_delta%60,p,len(grainID),len(orientations))) if similarOrientations[gID] != []: # orientation of my grainID is similar to someone else? similarNeighbors = defaultdict(int) # dict holding frequency of neighboring grainIDs that share my orientation (freq info not used...) for i in kdtree.query_ball_point(kdtree.data[p],options.radius): # check all neighboring points if grainID[i] in similarOrientations[gID]: # neighboring point shares my orientation? similarNeighbors[grainID[i]] += 1 # remember its grainID if similarNeighbors != {}: # found similar orientation(s) in neighborhood candidates = np.array([gID]+similarNeighbors.keys()) # possible replacement grainIDs for me grainID[p] = candidates[np.argsort(memberCounts[candidates])[-1]] # adopt ID that is most frequent in overall dataset memberCounts[gID] -= 1 # my former ID loses one fellow memberCounts[grainID[p]] += 1 # my new ID gains one fellow bg.set_message('{}:{} --> {}'.format(p,gID,grainID[p])) # report switch of grainID stillShifting = True table.data_rewind() outputAlive = True p = 0 while outputAlive and table.data_read(): # read next data line of ASCII table table.data_append(1+grainID[p]) # add grain ID outputAlive = table.data_write() # output processed line p += 1 bg.set_message('done after {} seconds'.format(time.clock()-start)) # ------------------------------------------ output finalization ----------------------------------- table.close() # close ASCII tables