DAMASK_EICMD/processing/pre/geom_fromTable.py

182 lines
8.2 KiB
Python
Executable File

#!/usr/bin/env python3
import os
import sys
from optparse import OptionParser
import numpy as np
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 options [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',
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('-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 [+x +y +z]')
parser.add_option('--homogenization',
dest = 'homogenization',
type = 'int', metavar = 'int',
help = 'homogenization index to be used [%default]')
parser.set_defaults(homogenization = 1,
pos = 'pos',
)
(options,filenames) = parser.parse_args()
input = [ 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.')
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.quaternion,4,'quaternion'),
(options.microstructure,1,'microstructure'),
][np.where(input)[0][0]] # select input label that was requested
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
table = damask.ASCIItable(name = name,readonly=True)
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)
continue
table.data_readArray([options.pos] \
+ (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.phase is None:
table.data = np.column_stack((table.data,np.ones(len(table.data)))) # add single phase if no phase column given
grid,size = damask.util.coordGridAndSize(table.data[:,0:3])
coords = [np.unique(table.data[:,i]) for i in range(3)]
mincorner = np.array(list(map(min,coords)))
origin = mincorner - 0.5*size/grid # shift from cell center to corner
# ------------------------------------------ process data ------------------------------------------
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))
elif inputtype == 'quaternion':
colPhase = -1 # column of phase data comes last
index = np.lexsort((table.data[:,0],table.data[:,1],table.data[:,2])) # index of position when sorting x fast, z slow
grain = -np.ones(grid.prod(),dtype = int) # initialize empty microstructure
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
for z in range(grid[2]):
for y in range(grid[1]):
for x in range(grid[0]):
myData = table.data[index[myPos]] # read data for current grid point
myPhase = int(myData[colPhase])
o = damask.Rotation(myData[colOri:colOri+4])
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
grain += 1 # offset from starting index 0 to 1
formatwidth = 1+int(np.log10(nGrains))
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 1',
'(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)),
'(gauss)\tphi1 %g\tPhi %g\tphi2 %g'%tuple(orientation.asEulers(degrees = True)),
]
if options.axes is not None: config_header += ['axes\t{} {} {}'.format(*options.axes)]
header = [scriptID + ' ' + ' '.join(sys.argv[1:])] + config_header + ['origin x {} y {} z {}'.format(*origin)]
geom = damask.Geom(grain.reshape(grid,order='F'),size,
homogenization=options.homogenization,comments=header)
damask.util.croak(geom)
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(os.path.splitext(name)[0]+'.geom')