DAMASK_EICMD/processing/pre/geom_fromTable.py

355 lines
19 KiB
Python
Raw Normal View History

2018-11-15 21:10:54 +05:30
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
2018-07-20 07:20:07 +05:30
import os,sys,math,time
import scipy.spatial, numpy as np
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [ASCIItable(s)]', description = """
Generate geometry description and material configuration from position, phase, and orientation (or microstructure) data.
""", version = scriptID)
parser.add_option('--coordinates',
dest = 'pos',
type = 'string', metavar = 'string',
2017-05-29 14:02:22 +05:30
help = 'coordinates label (%default)')
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.add_option('--verbose',
dest = 'verbose', action = 'store_true',
help = 'output extra info')
parser.set_defaults(symmetry = [damask.Symmetry.lattices[-1]],
tolerance = 0.0,
degrees = False,
homogenization = 1,
crystallite = 1,
2015-12-03 04:43:10 +05:30
verbose = False,
2017-05-29 14:02:22 +05:30
pos = 'pos',
)
(options,filenames) = parser.parse_args()
2016-03-02 17:13:09 +05:30
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,
options.microstructure is not None,
]
if np.sum(input) != 1:
parser.error('need either microstructure label or exactly one orientation input format.')
2016-03-02 17:13:09 +05:30
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'),
(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 -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
2015-08-13 02:58:07 +05:30
table = damask.ASCIItable(name = name,
outname = os.path.splitext(name)[-2]+'.geom' if name else name,
buffered = False)
except: continue
damask.util.report(scriptName,name)
# ------------------------------------------ read head ---------------------------------------
table.head_read() # read ASCII header info
# ------------------------------------------ sanity checks ---------------------------------------
coordDim = table.label_dimension(options.pos)
errors = []
if not 3 >= coordDim >= 2:
errors.append('coordinates "{}" need to have two or three dimensions.'.format(options.pos))
if not np.all(table.label_dimension(label) == dim):
errors.append('input "{}" needs to have dimension {}.'.format(label,dim))
if options.phase and table.label_dimension(options.phase) != 1:
errors.append('phase column "{}" is not scalar.'.format(options.phase))
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
table.data_readArray([options.pos] \
2018-07-20 04:09:50 +05:30
+ (label if isinstance(label, list) else [label]) \
+ ([options.phase] if options.phase else []))
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...')
2016-03-02 17:13:09 +05:30
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 ---------------------------------------------------------
2016-10-25 00:46:29 +05:30
coords = [np.unique(table.data[:,i]) for i in range(3)]
2018-07-20 04:09:50 +05:30
mincorner = np.array(list(map(min,coords)))
maxcorner = np.array(list(map(max,coords)))
grid = np.array(list(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)
2016-03-02 17:13:09 +05:30
size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 set 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 != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
# ------------------------------------------ process data ------------------------------------------
2016-03-02 17:13:09 +05:30
colOri = table.label_index(label)+(3-coordDim) # column(s) of orientation data followed by 3 coordinates
if inputtype == 'microstructure':
grain = table.data[:,colOri]
nGrains = len(np.unique(grain))
else:
if options.verbose: bg = damask.util.backgroundMessage(); bg.start() # start background messaging
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
2016-03-02 17:13:09 +05:30
orientations = [] # orientations
multiplicity = [] # orientation multiplicity (number of group members)
phases = [] # phase info
nGrains = 0 # counter for detected grains
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...')
2016-10-25 00:46:29 +05:30
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])
2016-03-02 17:13:09 +05:30
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).transpose(),
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)
2015-09-11 21:08:03 +05:30
cos_disorientations = -np.ones(1,dtype='f') # 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
2016-03-02 17:13:09 +05:30
# filter neighbors: skip myself, anyone further ahead (cannot yet have a grain ID), and other phases
neighbors = neighbors[(neighbors < myPos) & \
2016-03-02 17:13:09 +05:30
(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.w \
for grainID in grains]) # store disorientation per grainID
2016-03-02 17:13:09 +05:30
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?
2016-03-02 17:13:09 +05:30
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.w \
for grainID in grains]) # store disorientation per grainID
2016-03-02 17:13:09 +05:30
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
myPos += 1
if options.verbose:
bg.stop()
bg.join()
2015-12-03 04:43:10 +05:30
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
# --- generate header ----------------------------------------------------------------------------
info = {
'grid': grid,
'size': size,
'origin': origin,
'microstructures': nGrains,
'homogenization': options.homogenization,
}
damask.util.croak(['grid a b c: {}'.format(' x '.join(map(str,info['grid']))),
'size x y z: {}'.format(' x '.join(map(str,info['size']))),
'origin x y z: {}'.format(' : '.join(map(str,info['origin']))),
'homogenization: {}'.format(info['homogenization']),
'microstructures: {}'.format(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,orientation in enumerate(orientations):
config_header += ['[Grain%s]'%(str(i+1).zfill(formatwidth)),
2016-03-02 17:13:09 +05:30
'axes\t%s %s %s'%tuple(options.axes) if options.axes is not None else '',
'(gauss)\tphi1 %g\tPhi %g\tphi2 %g\tscatter 0.0\tfraction 1.0'%tuple(orientation.asEulers(degrees = True)),
]
table.labels_clear()
table.info_clear()
table.info_append([scriptID + ' ' + ' '.join(sys.argv[1:])])
table.head_putGeom(info)
table.info_append(config_header)
table.head_write()
# --- write microstructure information ------------------------------------------------------------
table.data = grain.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
#--- output finalization --------------------------------------------------------------------------
table.close()