DAMASK_EICMD/processing/pre/geom_fromTable.py

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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,re,string,math
import scipy.spatial, numpy as np
from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Generate geometry description and material configuration from position, phase, and orientation (or microstructure) data.
""", version = scriptID)
parser.add_option('--coordinates',
dest = 'coordinates',
type = 'string', metavar = 'string',
help = 'coordinates label')
parser.add_option('--phase',
dest = 'phase',
type = 'string', metavar = 'string',
help = 'phase label')
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 = 'angles are given in degrees [%default]')
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',
help = 'quaternion label')
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 = '<string LIST>',
help = 'crystal symmetry %default {{{}}} '.format(', '.join(damask.Symmetry.lattices[1:])))
parser.add_option('--homogenization',
dest = 'homogenization',
type = 'int', metavar = 'int',
help = 'homogenization index to be used [%default]')
parser.add_option('--crystallite',
dest = 'crystallite',
type = 'int', metavar = 'int',
help = 'crystallite index to be used [%default]')
parser.set_defaults(symmetry = [damask.Symmetry.lattices[-1]],
tolerance = 0.0,
degrees = False,
homogenization = 1,
crystallite = 1,
)
(options,filenames) = parser.parse_args()
input = [options.eulers != None,
options.a != None and \
options.b != None and \
options.c != None,
options.matrix != None,
options.quaternion != None,
options.microstructure != None,
]
if np.sum(input) != 1:
parser.error('need either microstructure label or exactly one orientation input format.')
if options.axes != 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'),
(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 degrees to radians
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
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table = damask.ASCIItable(name = name,
outname = os.path.splitext(name)[0]+'.geom' if name else name,
buffered = False)
except: continue
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table.croak(damask.util.emph(scriptName)+(': '+name if name else ''))
# ------------------------------------------ read head ---------------------------------------
table.head_read() # read ASCII header info
# ------------------------------------------ sanity checks ---------------------------------------
coordDim = table.label_dimension(options.coordinates)
errors = []
if not 3 >= coordDim >= 2:
errors.append('coordinates {} need to have two or three dimensions.'.format(options.coordinates))
if not np.all(table.label_dimension(label) == dim):
errors.append('input {} needs to have dimension {}.'.format(label,dim))
if options.phase != None and table.label_dimension(options.phase) != 1:
errors.append('phase column {} is not scalar.'.format(options.phase))
if errors != []:
table.croak(errors)
table.close(dismiss = True)
continue
table.data_readArray([options.coordinates,label]+([] if options.phase == None else [options.phase]))
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.phase == None:
table.data = np.column_stack((table.data,np.ones(len(table.data)))) # add single phase if no phase column given
# --------------- figure out size and grid ---------------------------------------------------------
coords = [np.unique(table.data[:,i]) for i in xrange(3)]
mincorner = np.array(map(min,coords))
maxcorner = np.array(map(max,coords))
grid = np.array(map(len,coords),'i')
size = grid/np.maximum(np.ones(3,'d'), grid-1.0) * (maxcorner-mincorner) # size from edge to edge = dim * n/(n-1)
size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 equal to smallest among other spacings
delta = size/np.maximum(np.ones(3,'d'), grid)
origin = mincorner - 0.5*delta # shift from cell center to corner
N = grid.prod()
if N != len(table.data):
errors.append('data count {} does not match grid {}.'.format(len(table.data),' x '.join(map(repr,grid))))
if np.any(np.abs(np.log10((coords[0][1:]-coords[0][:-1])/delta[0])) > 0.01) \
or np.any(np.abs(np.log10((coords[1][1:]-coords[1][:-1])/delta[1])) > 0.01) \
or np.any(np.abs(np.log10((coords[2][1:]-coords[2][:-1])/delta[2])) > 0.01):
errors.append('regular grid spacing {} violated.'.format(' x '.join(map(repr,delta))))
if errors != []:
table.croak(errors)
table.close(dismiss = True)
continue
# ------------------------------------------ process data ------------------------------------------
colOri = table.label_index(label)+(3-coordDim) # column(s) of orientation data (following 3 or 2 coordinates that were expanded to 3!)
if inputtype == 'microstructure':
microstructure = table.data[:,colOri]
nGrains = len(np.unique(microstructure))
else:
colPhase = colOri + np.sum(dim) # column of phase data comes after orientation
index = np.lexsort((table.data[:,0],table.data[:,1],table.data[:,2])) # index of rank when sorting x fast, z slow
rank = np.argsort(index) # rank of index
KDTree = scipy.spatial.KDTree((table.data[:,:3]-mincorner) / delta) # build KDTree with dX = dY = dZ = 1 and origin 0,0,0
microstructure = np.zeros(N,dtype = 'uint32') # initialize empty microstructure
symQuats = [] # empty list of sym equiv orientations
phases = [] # empty list of phase info
nGrains = 0 # counter for detected grains
myRank = 0 # rank of current grid point
for z in xrange(grid[2]):
for y in xrange(grid[1]):
for x in xrange(grid[0]):
if (myRank+1)%(N/100.) < 1: table.croak('.',False)
myData = table.data[index[myRank]]
mySym = options.symmetry[min(int(myData[colPhase]),len(options.symmetry))-1] # select symmetry from option (take last specified option for all with higher index)
if inputtype == 'eulers':
o = damask.Orientation(Eulers = myData[colOri:colOri+3]*toRadians,
symmetry = mySym).reduced()
elif inputtype == 'matrix':
o = damask.Orientation(matrix = myData[colOri:colOri+9].reshape(3,3).transpose(),
symmetry = mySym).reduced()
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).reduced()
elif inputtype == 'quaternion':
o = damask.Orientation(quaternion = myData[colOri:colOri+4],
symmetry = mySym).reduced()
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oInv = o.quaternion.conjugated()
neighbors = KDTree.query_ball_point([x,y,z], 3) # search points within radius
breaker = False
for n in neighbors: # check each neighbor
if myRank <= rank[n] or table.data[n,colPhase] != myData[colPhase]: continue # skip myself, anyone further ahead (cannot yet have a grain ID), and other phases
for symQ in symQuats[microstructure[rank[n]]-1]:
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if (symQ*oInv).asAngleAxis(degrees = options.degrees)[0] <= options.tolerance: # found existing orientation resembling me
microstructure[myRank] = microstructure[rank[n]]
breaker = True; break
if breaker: break
if microstructure[myRank] == 0: # no other orientation resembled me
nGrains += 1 # make new grain ...
microstructure[myRank] = nGrains # ... and assign to me
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symQuats.append(o.symmetry.equivalentQuaternions(o.quaternion)) # store all symmetrically equivalent orientations for future comparison
phases.append(myData[colPhase]) # store phase info for future reporting
myRank += 1
table.croak('')
# --- generate header ----------------------------------------------------------------------------
info = {
'grid': grid,
'size': size,
'origin': origin,
'microstructures': nGrains,
'homogenization': options.homogenization,
}
table.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
'size x y z: %s'%(' x '.join(map(str,info['size']))),
'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
'homogenization: %i'%info['homogenization'],
'microstructures: %i'%info['microstructures'],
])
# --- write header ---------------------------------------------------------------------------------
formatwidth = 1+int(math.log10(info['microstructures']))
if inputtype == 'microstructure':
config_header = []
else:
config_header = ['<microstructure>']
for i,phase in enumerate(phases):
config_header += ['[Grain%s]'%(str(i+1).zfill(formatwidth)),
'crystallite %i'%options.crystallite,
'(constituent)\tphase %i\ttexture %s\tfraction 1.0'%(phase,str(i+1).rjust(formatwidth)),
]
config_header += ['<texture>']
for i,quats in enumerate(symQuats):
config_header += ['[Grain%s]'%(str(i+1).zfill(formatwidth)),
'axes\t%s %s %s'%tuple(options.axes) if options.axes != None else '',
'(gauss)\tphi1 %g\tPhi %g\tphi2 %g\tscatter 0.0\tfraction 1.0'%tuple(np.degrees(quats[0].asEulers())),
]
table.labels_clear()
table.info_clear()
table.info_append([
scriptID + ' ' + ' '.join(sys.argv[1:]),
"grid\ta {}\tb {}\tc {}".format(*info['grid']),
"size\tx {}\ty {}\tz {}".format(*info['size']),
"origin\tx {}\ty {}\tz {}".format(*info['origin']),
"homogenization\t{}".format(info['homogenization']),
"microstructures\t{}".format(info['microstructures']),
config_header,
])
table.head_write()
# --- write microstructure information ------------------------------------------------------------
table.data = microstructure.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
#--- output finalization --------------------------------------------------------------------------
table.close()