#!/usr/bin/env python
import os,sys,string,itertools,re,time,copy,operator,threading
import numpy as np
import damask
from scipy import spatial
from collections import defaultdict
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
scriptID = string.replace('$Id: addGrainID.py 2549 2013-07-10 09:13:21Z MPIE\p.eisenlohr $','\n','\\n')
scriptName = os.path.splitext(scriptID.split()[1])[0]
# -----------------------------
class backgroundMessage(threading.Thread):
# -----------------------------
def __init__(self):
threading.Thread.__init__(self)
self.message = ''
self.new_message = ''
self.counter = 0
self.symbols = ['- ', '\ ', '| ', '/ ',]
self.waittime = 0.5
def __quit__(self):
length = len(self.message) + len(self.symbols[self.counter])
sys.stderr.write(chr(8)*length + ' '*length + chr(8)*length)
sys.stderr.write('')
def run(self):
while not threading.enumerate()[0]._Thread__stopped:
time.sleep(self.waittime)
self.update_message()
self.__quit__()
def set_message(self, new_message):
self.new_message = new_message
self.print_message()
def print_message(self):
length = len(self.message) + len(self.symbols[self.counter])
sys.stderr.write(chr(8)*length + ' '*length + chr(8)*length) # delete former message
sys.stderr.write(self.symbols[self.counter] + self.new_message) # print new message
self.message = self.new_message
def update_message(self):
self.counter = (self.counter + 1)%len(self.symbols)
self.print_message()
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Add grain index based on similiarity of crystal lattice orientation.
""" + string.replace(scriptID,'\n','\\n')
)
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 = math.pi/180.0 if options.degrees else 1.0 # rescale degrees to radians
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = ['STDIN']
for name in filenames:
if not (name == 'STDIN' or os.path.exists(name)): continue
table = damask.ASCIItable(name = name, outname = name+'_tmp',
buffered = False)
table.croak('\033[1m'+scriptName+'\033[0m'+(': '+name if name != 'STDIN' else ''))
# ------------------------------------------ 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 != []: table.croak(remarks)
if errors != []:
table.croak(errors)
table.close(dismiss = True)
continue
# ------------------------------------------ assemble header ---------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
table.labels_append('grainID_{}@{}'.format(','.join(labels),options.disorientation/toRadians)) # report orientation source and disorientation in degrees
table.head_write()
# ------------------------------------------ process data ------------------------------------------
# ------------------------------------------ build KD tree -----------------------------------------
# --- start background messaging
bg = 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.Orientation(quaternion = np.array([0,0,0,1]),
symmetry = options.symmetry) # 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]) # compare against that grain's orientation
if disorientation.quaternion.w > cos_disorientation and \
disorientation.quaternion.w >= bestDisorientation.quaternion.w: # within disorientation threshold and better than current best?
matched = True
matchedID = gID # remember that grain
bestDisorientation = disorientation
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): # compare each identified orientation...
for j in xrange(i+1,len(orientations)): # ...against all others that were defined afterwards
if orientation.disorientation(orientations[j]).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(lambda x:str(x),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()
p = 0
while table.data_read(): # read next data line of ASCII table
table.data_append(1+grainID[p]) # add grain ID
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
if name != 'STDIN': os.rename(name+'_tmp',name) # overwrite old one with tmp new