diff --git a/processing/pre/geom_fromTable.py b/processing/pre/geom_fromTable.py index e1157d325..f06f0e3d0 100755 --- a/processing/pre/geom_fromTable.py +++ b/processing/pre/geom_fromTable.py @@ -32,34 +32,6 @@ parser.add_option('--microstructure', dest = 'microstructure', type = 'string', metavar = 'string', help = 'microstructure label') -parser.add_option('-t', '--tolerance', - dest = 'tolerance', - type = 'float', metavar = 'float', - help = 'angular tolerance for orientation squashing [%default]') -parser.add_option('-e', '--eulers', - dest = 'eulers', - type = 'string', metavar = 'string', - help = 'Euler angles label') -parser.add_option('-d', '--degrees', - dest = 'degrees', - action = 'store_true', - help = 'all angles are in degrees') -parser.add_option('-m', '--matrix', - dest = 'matrix', - type = 'string', metavar = 'string', - help = 'orientation matrix label') -parser.add_option('-a', - dest='a', - type = 'string', metavar = 'string', - help = 'crystal frame a vector label') -parser.add_option('-b', - dest='b', - type = 'string', metavar = 'string', - help = 'crystal frame b vector label') -parser.add_option('-c', - dest = 'c', - type = 'string', metavar='string', - help = 'crystal frame c vector label') parser.add_option('-q', '--quaternion', dest = 'quaternion', type = 'string', metavar='string', @@ -68,10 +40,7 @@ parser.add_option('--axes', dest = 'axes', type = 'string', nargs = 3, metavar = ' '.join(['string']*3), help = 'orientation coordinate frame in terms of position coordinate frame [same]') -parser.add_option('-s', '--symmetry', - dest = 'symmetry', - action = 'extend', metavar = '', - help = 'crystal symmetry of each phase %default {{{}}} '.format(', '.join(damask.Symmetry.lattices[1:]))) + parser.add_option('--homogenization', dest = 'homogenization', type = 'int', metavar = 'int', @@ -80,9 +49,7 @@ parser.add_option('--crystallite', dest = 'crystallite', type = 'int', metavar = 'int', help = 'crystallite index to be used [%default]') -parser.add_option('--verbose', - dest = 'verbose', action = 'store_true', - help = 'output extra info') + parser.set_defaults(symmetry = [damask.Symmetry.lattices[-1]], tolerance = 0.0, @@ -95,12 +62,7 @@ parser.set_defaults(symmetry = [damask.Symmetry.lattices[-1]], (options,filenames) = parser.parse_args() -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, +input = [ options.quaternion is not None, options.microstructure is not None, ] @@ -109,14 +71,9 @@ if np.sum(input) != 1: 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.eulers,3,'eulers'), - ([options.a,options.b,options.c],[3,3,3],'frame'), - (options.matrix,9,'matrix'), - (options.quaternion,4,'quaternion'), +(label,dim,inputtype) = [(options.quaternion,4,'quaternion'), (options.microstructure,1,'microstructure'), ][np.where(input)[0][0]] # select input label that was requested -toRadians = math.pi/180.0 if options.degrees else 1.0 # rescale all angles to radians -threshold = np.cos(options.tolerance/2.*toRadians) # cosine of (half of) tolerance angle # --- loop over input files ------------------------------------------------------------------------- @@ -157,10 +114,8 @@ for name in filenames: 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.verbose: damask.util.croak('extending to 3D...') 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 - if options.verbose: damask.util.croak('adding dummy phase info...') # --------------- figure out size and grid --------------------------------------------------------- @@ -196,17 +151,10 @@ for name in filenames: grain = table.data[:,colOri] nGrains = len(np.unique(grain)) - else: - - if options.verbose: bg = damask.util.backgroundMessage(); bg.start() # start background messaging + elif inputtype == 'quaternion': colPhase = -1 # column of phase data comes last - if options.verbose: bg.set_message('sorting positions...') index = np.lexsort((table.data[:,0],table.data[:,1],table.data[:,2])) # index of position when sorting x fast, z slow - if options.verbose: bg.set_message('building KD tree...') - KDTree = scipy.spatial.KDTree((table.data[index,:3]-mincorner) / delta) # build KDTree with dX = dY = dZ = 1 and origin 0,0,0 - - statistics = {'global': 0, 'local': 0} grain = -np.ones(N,dtype = 'int32') # initialize empty microstructure orientations = [] # orientations multiplicity = [] # orientation multiplicity (number of group members) @@ -215,87 +163,26 @@ for name in filenames: existingGrains = np.arange(nGrains) myPos = 0 # position (in list) of current grid point - tick = time.clock() - if options.verbose: bg.set_message('assigning grain IDs...') for z in range(grid[2]): for y in range(grid[1]): for x in range(grid[0]): - if (myPos+1)%(N/500.) < 1: - time_delta = (time.clock()-tick) * (N - myPos) / myPos - if options.verbose: bg.set_message('(%02i:%02i:%02i) processing point %i of %i (grain count %i)...' - %(time_delta//3600,time_delta%3600//60,time_delta%60,myPos,N,nGrains)) + myData = table.data[index[myPos]] # read data for current grid point myPhase = int(myData[colPhase]) - mySym = options.symmetry[min(myPhase,len(options.symmetry))-1] # take last specified option for all with higher index - - if inputtype == 'eulers': - o = damask.Orientation(Eulers = myData[colOri:colOri+3]*toRadians, - symmetry = mySym) - elif inputtype == 'matrix': - o = damask.Orientation(matrix = myData[colOri:colOri+9].reshape(3,3), - symmetry = mySym) - elif inputtype == 'frame': - o = damask.Orientation(matrix = np.hstack((myData[colOri[0]:colOri[0]+3], - myData[colOri[1]:colOri[1]+3], - myData[colOri[2]:colOri[2]+3], - )).reshape(3,3), - symmetry = mySym) - elif inputtype == 'quaternion': - o = damask.Orientation(quaternion = myData[colOri:colOri+4], - symmetry = mySym) + + o = damask.Rotation(myData[colOri:colOri+4]) - cos_disorientations = -np.ones(1,dtype=float) # largest possible disorientation - closest_grain = -1 # invalid neighbor - - if options.tolerance > 0.0: # only try to compress orientations if asked to - neighbors = np.array(KDTree.query_ball_point([x,y,z], 3)) # point indices within radius -# filter neighbors: skip myself, anyone further ahead (cannot yet have a grain ID), and other phases - neighbors = neighbors[(neighbors < myPos) & \ - (table.data[index[neighbors],colPhase] == myPhase)] - grains = np.unique(grain[neighbors]) # unique grain IDs among valid neighbors - - if len(grains) > 0: # check immediate neighborhood first - cos_disorientations = np.array([o.disorientation(orientations[grainID], - SST = False)[0].quaternion.q \ - for grainID in grains]) # store disorientation per grainID - closest_grain = np.argmax(cos_disorientations) # grain among grains with closest orientation to myself - match = 'local' - - if cos_disorientations[closest_grain] < threshold: # orientation not close enough? - grains = existingGrains[np.atleast_1d( (np.array(phases) == myPhase ) & \ - (np.in1d(existingGrains,grains,invert=True)))] # other already identified grains (of my phase) - - if len(grains) > 0: - cos_disorientations = np.array([o.disorientation(orientations[grainID], - SST = False)[0].quaternion.q \ - for grainID in grains]) # store disorientation per grainID - closest_grain = np.argmax(cos_disorientations) # grain among grains with closest orientation to myself - match = 'global' - - if cos_disorientations[closest_grain] >= threshold: # orientation now close enough? - grainID = grains[closest_grain] - grain[myPos] = grainID # assign myself to that grain ... - orientations[grainID] = damask.Orientation.average([orientations[grainID],o], - [multiplicity[grainID],1]) # update average orientation of best matching grain - multiplicity[grainID] += 1 - statistics[match] += 1 - else: - 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 + 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 - if options.verbose: - bg.stop() - bg.join() - damask.util.croak("{} seconds total.\n{} local and {} global matches.".\ - format(time.clock()-tick,statistics['local'],statistics['global'])) grain += 1 # offset from starting index 0 to 1