238 lines
12 KiB
Python
Executable File
238 lines
12 KiB
Python
Executable File
#!/usr/bin/env python
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import os,sys,time,copy
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import numpy as np
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import damask
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from optparse import OptionParser
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from scipy import spatial
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Add grain index based on similiarity of crystal lattice orientation.
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""", version = scriptID)
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parser.add_option('-r', '--radius',
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dest = 'radius',
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type = 'float', metavar = 'float',
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help = 'search radius')
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parser.add_option('-d', '--disorientation',
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dest = 'disorientation',
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type = 'float', metavar = 'float',
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help = 'disorientation threshold in degrees [%default]')
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parser.add_option('-s', '--symmetry',
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dest = 'symmetry',
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type = 'string', metavar = 'string',
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help = 'crystal symmetry [%default]')
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parser.add_option('-e', '--eulers',
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dest = 'eulers',
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type = 'string', metavar = 'string',
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help = 'Euler angles')
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parser.add_option( '--degrees',
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dest = 'degrees',
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action = 'store_true',
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help = 'Euler angles are given in degrees [%default]')
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parser.add_option('-m', '--matrix',
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dest = 'matrix',
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type = 'string', metavar = 'string',
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help = 'orientation matrix')
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parser.add_option('-a',
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dest = 'a',
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type = 'string', metavar = 'string',
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help = 'crystal frame a vector')
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parser.add_option('-b',
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dest = 'b',
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type = 'string', metavar = 'string',
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help = 'crystal frame b vector')
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parser.add_option('-c',
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dest = 'c',
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type = 'string', metavar = 'string',
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help = 'crystal frame c vector')
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parser.add_option('-q', '--quaternion',
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dest = 'quaternion',
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type = 'string', metavar = 'string',
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help = 'quaternion')
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parser.add_option('-p', '--position',
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dest = 'coords',
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type = 'string', metavar = 'string',
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help = 'spatial position of voxel [%default]')
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parser.set_defaults(disorientation = 5,
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symmetry = 'cubic',
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coords = 'pos',
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degrees = False,
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)
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(options, filenames) = parser.parse_args()
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if options.radius is None:
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parser.error('no radius specified.')
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input = [options.eulers is not None,
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options.a is not None and \
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options.b is not None and \
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options.c is not None,
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options.matrix is not None,
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options.quaternion is not None,
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]
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if np.sum(input) != 1: parser.error('needs exactly one input format.')
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(label,dim,inputtype) = [(options.eulers,3,'eulers'),
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([options.a,options.b,options.c],[3,3,3],'frame'),
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(options.matrix,9,'matrix'),
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(options.quaternion,4,'quaternion'),
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][np.where(input)[0][0]] # select input label that was requested
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toRadians = np.pi/180.0 if options.degrees else 1.0 # rescale degrees to radians
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cos_disorientation = np.cos(np.radians(options.disorientation/2.)) # cos of half the disorientation angle
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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for name in filenames:
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try: table = damask.ASCIItable(name = name,
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buffered = False)
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except: continue
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damask.util.report(scriptName,name)
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# ------------------------------------------ read header -------------------------------------------
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table.head_read()
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# ------------------------------------------ sanity checks -----------------------------------------
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errors = []
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remarks = []
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if not 3 >= table.label_dimension(options.coords) >= 1:
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errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.coords))
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if not np.all(table.label_dimension(label) == dim):
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errors.append('input {} does not have dimension {}.'.format(label,dim))
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else: column = table.label_index(label)
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if remarks != []: damask.util.croak(remarks)
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if errors != []:
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damask.util.croak(errors)
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table.close(dismiss = True)
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continue
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# ------------------------------------------ assemble header ---------------------------------------
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table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
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table.labels_append('grainID_{}@{:g}'.format('+'.join(label)
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if isinstance(label, (list,tuple))
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else label,
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options.disorientation)) # report orientation source and disorientation
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table.head_write()
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# ------------------------------------------ process data ------------------------------------------
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# ------------------------------------------ build KD tree -----------------------------------------
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# --- start background messaging
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bg = damask.util.backgroundMessage()
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bg.start()
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bg.set_message('reading positions...')
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table.data_readArray(options.coords) # read position vectors
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grainID = -np.ones(len(table.data),dtype=int)
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start = tick = time.clock()
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bg.set_message('building KD tree...')
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kdtree = spatial.KDTree(copy.deepcopy(table.data))
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# ------------------------------------------ assign grain IDs --------------------------------------
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tick = time.clock()
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orientations = [] # quaternions found for grain
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memberCounts = [] # number of voxels in grain
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p = 0 # point counter
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g = 0 # grain counter
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matchedID = -1
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lastDistance = np.dot(kdtree.data[-1]-kdtree.data[0],kdtree.data[-1]-kdtree.data[0]) # (arbitrarily) use diagonal of cloud
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table.data_rewind()
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while table.data_read(): # read next data line of ASCII table
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if p > 0 and p % 1000 == 0:
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time_delta = (time.clock()-tick) * (len(grainID) - p) / p
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bg.set_message('(%02i:%02i:%02i) processing point %i of %i (grain count %i)...'\
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%(time_delta//3600,time_delta%3600//60,time_delta%60,p,len(grainID),np.count_nonzero(memberCounts)))
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if inputtype == 'eulers':
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o = damask.Orientation(Eulers = np.array(map(float,table.data[column:column+3]))*toRadians,
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symmetry = options.symmetry).reduced()
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elif inputtype == 'matrix':
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o = damask.Orientation(matrix = np.array(map(float,table.data[column:column+9])).reshape(3,3).transpose(),
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symmetry = options.symmetry).reduced()
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elif inputtype == 'frame':
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o = damask.Orientation(matrix = np.array(map(float,table.data[column[0]:column[0]+3] + \
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table.data[column[1]:column[1]+3] + \
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table.data[column[2]:column[2]+3])).reshape(3,3),
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symmetry = options.symmetry).reduced()
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elif inputtype == 'quaternion':
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o = damask.Orientation(quaternion = np.array(map(float,table.data[column:column+4])),
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symmetry = options.symmetry).reduced()
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matched = False
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alreadyChecked = {}
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candidates = []
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bestDisorientation = damask.Quaternion([0,0,0,1]) # initialize to 180 deg rotation as worst case
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for i in kdtree.query_ball_point(kdtree.data[p],options.radius): # check all neighboring points
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gID = grainID[i]
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if gID != -1 and gID not in alreadyChecked: # indexed point belonging to a grain not yet tested?
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alreadyChecked[gID] = True # remember not to check again
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disorientation = o.disorientation(orientations[gID],SST = False)[0] # compare against other orientation
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if disorientation.quaternion.w > cos_disorientation: # within threshold ...
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candidates.append(gID) # remember as potential candidate
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if disorientation.quaternion.w >= bestDisorientation.w: # ... and better than current best?
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matched = True
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matchedID = gID # remember that grain
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bestDisorientation = disorientation.quaternion
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if matched: # did match existing grain
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memberCounts[matchedID] += 1
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if len(candidates) > 1: # ambiguity in grain identification?
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largestGrain = sorted(candidates,key=lambda x:memberCounts[x])[-1] # find largest among potential candidate grains
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matchedID = largestGrain
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for c in [c for c in candidates if c != largestGrain]: # loop over smaller candidates
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memberCounts[largestGrain] += memberCounts[c] # reassign member count of smaller to largest
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memberCounts[c] = 0
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grainID = np.where(np.in1d(grainID,candidates), largestGrain, grainID) # relabel grid points of smaller candidates as largest one
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else: # no match -> new grain found
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orientations += [o] # initialize with current orientation
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memberCounts += [1] # start new membership counter
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matchedID = g
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g += 1 # increment grain counter
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grainID[p] = matchedID # remember grain index assigned to point
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p += 1 # increment point
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grainIDs = np.where(np.array(memberCounts) > 0)[0] # identify "live" grain identifiers
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packingMap = dict(zip(list(grainIDs),range(len(grainIDs)))) # map to condense into consecutive IDs
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table.data_rewind()
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outputAlive = True
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p = 0
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while outputAlive and table.data_read(): # read next data line of ASCII table
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table.data_append(1+packingMap[grainID[p]]) # add (condensed) grain ID
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outputAlive = table.data_write() # output processed line
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p += 1
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bg.set_message('done after {} seconds'.format(time.clock()-start))
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# ------------------------------------------ output finalization -----------------------------------
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table.close() # close ASCII tables
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