#!/usr/bin/env python2.7
# -*- coding: UTF-8 no BOM -*-
import os,sys,time,copy
import numpy as np
import damask
from optparse import OptionParser
from scipy import spatial
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(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 in degrees [%default]')
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 = 'label of 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 = 'label of orientation matrix')
parser.add_option('-a',
dest = 'a',
type = 'string', metavar = 'string',
help = 'label of crystal frame a vector')
parser.add_option('-b',
dest = 'b',
type = 'string', metavar = 'string',
help = 'label of crystal frame b vector')
parser.add_option('-c',
dest = 'c',
type = 'string', metavar = 'string',
help = 'label of crystal frame c vector')
parser.add_option('-q',
'--quaternion',
dest = 'quaternion',
type = 'string', metavar = 'string',
help = 'label of quaternion')
parser.add_option('-p',
'--pos', '--position',
dest = 'pos',
type = 'string', metavar = 'string',
help = 'label of coordinates [%default]')
parser.set_defaults(disorientation = 5,
symmetry = 'cubic',
pos = 'pos',
degrees = False,
)
(options, filenames) = parser.parse_args()
if options.radius is None:
parser.error('no radius specified.')
input = [options.eulers is not None,
options.a is not None and \
options.b is not None and \
options.c is not None,
options.matrix is not None,
options.quaternion is not 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(np.radians(options.disorientation/2.)) # cos of half the disorientation angle
# --- 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 not 3 >= table.label_dimension(options.pos) >= 1:
errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.pos))
if not np.all(table.label_dimension(label) == dim):
errors.append('input "{}" does not have 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_{}@{:g}'.format('+'.join(label)
if isinstance(label, (list,tuple))
else label,
options.disorientation)) # report orientation source and disorientation
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.pos) # 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),np.count_nonzero(memberCounts)))
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
alreadyChecked = {}
candidates = []
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: # 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 other orientation
if disorientation.quaternion.w > cos_disorientation: # within threshold ...
candidates.append(gID) # remember as potential candidate
if disorientation.quaternion.w >= bestDisorientation.w: # ... and better than current best?
matched = True
matchedID = gID # remember that grain
bestDisorientation = disorientation.quaternion
if matched: # did match existing grain
memberCounts[matchedID] += 1
if len(candidates) > 1: # ambiguity in grain identification?
largestGrain = sorted(candidates,key=lambda x:memberCounts[x])[-1] # find largest among potential candidate grains
matchedID = largestGrain
for c in [c for c in candidates if c != largestGrain]: # loop over smaller candidates
memberCounts[largestGrain] += memberCounts[c] # reassign member count of smaller to largest
memberCounts[c] = 0
grainID = np.where(np.in1d(grainID,candidates), largestGrain, grainID) # relabel grid points of smaller candidates as largest one
else: # no match -> new grain found
orientations += [o] # initialize with current orientation
memberCounts += [1] # start new membership counter
matchedID = g
g += 1 # increment grain counter
grainID[p] = matchedID # remember grain index assigned to point
p += 1 # increment point
grainIDs = np.where(np.array(memberCounts) > 0)[0] # identify "live" grain identifiers
packingMap = dict(zip(list(grainIDs),range(len(grainIDs)))) # map to condense into consecutive IDs
table.data_rewind()
outputAlive = True
p = 0
while outputAlive and table.data_read(): # read next data line of ASCII table
table.data_append(1+packingMap[grainID[p]]) # add (condensed) 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