DAMASK_EICMD/processing/pre/geom_fromVPSC.py

186 lines
9.1 KiB
Python
Executable File

#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import 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 options [file[s]]', description = """
Generate geometry description and material configuration from input files used by R.A. Lebensohn.
""", version = scriptID)
parser.add_option('--column', dest='column', type='int', metavar = 'int',
help='data column to discriminate between both phases [%default]')
parser.add_option('-t','--threshold', dest='threshold', type='float', metavar = 'float',
help='threshold value for phase discrimination [%default]')
parser.add_option('--homogenization', dest='homogenization', type='int', metavar = 'int',
help='homogenization index for <microstructure> configuration [%default]')
parser.add_option('--phase', dest='phase', type='int', nargs = 2, metavar = 'int int',
help='phase indices for <microstructure> configuration %default')
parser.add_option('--crystallite', dest='crystallite', type='int', metavar = 'int',
help='crystallite index for <microstructure> configuration [%default]')
parser.add_option('--compress', dest='compress', action='store_true',
help='lump identical microstructure and texture information [%default]')
parser.add_option('-p', '--precision', dest='precision', choices=['0','1','2','3'], metavar = 'int',
help = 'euler angles decimal places for output format and compressing {0,1,2,3} [2]')
parser.set_defaults(column = 7)
parser.set_defaults(threshold = 1.0)
parser.set_defaults(homogenization = 1)
parser.set_defaults(phase = [1,2])
parser.set_defaults(crystallite = 1)
parser.set_defaults(config = False)
parser.set_defaults(compress = False)
parser.set_defaults(precision = '2')
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
outname = os.path.splitext(name)[-2]+'.geom' if name else name,
buffered = False,
labeled = False)
except: continue
damask.util.report(scriptName,name)
info = {
'grid': np.zeros(3,'i'),
'size': np.zeros(3,'d'),
'origin': np.zeros(3,'d'),
'microstructures': 0,
'homogenization': options.homogenization
}
coords = [{},{},{}]
pos = {'min':[ float("inf"), float("inf"), float("inf")],
'max':[-float("inf"),-float("inf"),-float("inf")]}
phase = []
eulerangles = []
outputAlive = True
# ------------------------------------------ process data ------------------------------------------
while outputAlive and table.data_read():
if table.data != []:
currPos = table.data[3:6]
for i in xrange(3):
coords[i][currPos[i]] = True
currPos = map(float,currPos)
for i in xrange(3):
pos['min'][i] = min(pos['min'][i],currPos[i])
pos['max'][i] = max(pos['max'][i],currPos[i])
eulerangles.append(map(math.degrees,map(float,table.data[:3])))
phase.append(options.phase[int(float(table.data[options.column-1]) > options.threshold)])
# --------------- determine size and grid ---------------------------------------------------------
info['grid'] = np.array(map(len,coords),'i')
info['size'] = info['grid']/np.maximum(np.ones(3,'d'),info['grid']-1.0)* \
np.array([pos['max'][0]-pos['min'][0],
pos['max'][1]-pos['min'][1],
pos['max'][2]-pos['min'][2]],'d')
eulerangles = np.array(eulerangles,dtype='f').reshape(info['grid'].prod(),3)
phase = np.array(phase,dtype='i').reshape(info['grid'].prod())
limits = [360,180,360]
if any([np.any(eulerangles[:,i]>=limits[i]) for i in [0,1,2]]):
file['croak'].write('Error: euler angles out of bound. Ang file might contain unidexed poins.\n')
for i,angle in enumerate(['phi1','PHI','phi2']):
for n in np.nditer(np.where(eulerangles[:,i]>=limits[i]),['zerosize_ok']):
file['croak'].write('%s in line %i (%4.2f %4.2f %4.2f)\n'
%(angle,n,eulerangles[n,0],eulerangles[n,1],eulerangles[n,2]))
continue
eulerangles=np.around(eulerangles,int(options.precision)) # round to desired precision
# ensure, that rounded euler angles are not out of bounds (modulo by limits)
for i,angle in enumerate(['phi1','PHI','phi2']):
eulerangles[:,i]%=limits[i]
# scale angles by desired precision and convert to int. create unique integer key from three euler angles by
# concatenating the string representation with leading zeros and store as integer and search unique euler angle keys.
# Texture IDs are the indices of the first occurrence, the inverse is used to construct the microstructure
# create a microstructure (texture/phase pair) for each point using unique texture IDs.
# Use longInt (64bit, i8) because the keys might be long
if options.compress:
formatString='{0:0>'+str(int(options.precision)+3)+'}'
euleranglesRadInt = (eulerangles*10**int(options.precision)).astype('int')
eulerKeys = np.array([int(''.join(map(formatString.format,euleranglesRadInt[i,:]))) \
for i in xrange(info['grid'].prod())])
devNull, texture, eulerKeys_idx = np.unique(eulerKeys, return_index = True, return_inverse=True)
msFull = np.array([[eulerKeys_idx[i],phase[i]] for i in xrange(info['grid'].prod())],'i8')
devNull,msUnique,matPoints = np.unique(msFull.view('c16'),True,True)
matPoints+=1
microstructure = np.array([msFull[i] for i in msUnique]) # pick only unique microstructures
else:
texture = np.arange(info['grid'].prod())
microstructure = np.hstack( zip(texture,phase) ).reshape(info['grid'].prod(),2) # create texture/phase pairs
formatOut = 1+int(math.log10(len(texture)))
config_header = []
formatwidth = 1+int(math.log10(len(microstructure)))
config_header += ['<microstructure>']
for i in xrange(len(microstructure)):
config_header += ['[Grain%s]'%str(i+1).zfill(formatwidth),
'crystallite\t%i'%options.crystallite,
'(constituent)\tphase %i\ttexture %i\tfraction 1.0'%(microstructure[i,1],microstructure[i,0]+1)
]
config_header += ['<texture>']
eulerFormatOut='%%%i.%if'%(int(options.precision)+4,int(options.precision))
outStringAngles='(gauss) phi1 '+eulerFormatOut+' Phi '+eulerFormatOut+' phi2 '+eulerFormatOut+' scatter 0.0 fraction 1.0'
for i in xrange(len(texture)):
config_header += ['[Texture%s]'%str(i+1).zfill(formatOut),
outStringAngles%tuple(eulerangles[texture[i],...])
]
table.labels_clear()
table.info_clear()
info['microstructures'] = len(microstructure)
#--- report ---------------------------------------------------------------------------------------
damask.util.croak('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) +
'size x y z: %s\n'%(' x '.join(map(str,info['size']))) +
'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) +
'homogenization: %i\n'%info['homogenization'] +
'microstructures: %i\n\n'%info['microstructures'])
if np.any(info['grid'] < 1):
damask.util.croak('invalid grid a b c.\n')
continue
if np.any(info['size'] <= 0.0):
damask.util.croak('invalid size x y z.\n')
continue
#--- write data -----------------------------------------------------------------------------------
table.info_append([' '.join([scriptID] + sys.argv[1:]),
"grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],),
"size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2],),
"origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],),
"microstructures\t%i"%info['microstructures'],
"homogenization\t%i"%info['homogenization'],
config_header
])
table.head_write()
if options.compress:
table.data = matPoints.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
else:
table.data = ["1 to %i\n"%(info['microstructures'])]
# ------------------------------------------ output finalization -----------------------------------
table.close()