DAMASK_EICMD/processing/pre/geom_fromDREAM3D.py

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#!/usr/bin/env python3
import os
import sys
from optparse import OptionParser
import h5py
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 [DREAM.3Dfile(s)]', description = """
Converts DREAM.3D file. Input can be cell data (direct pointwise takeover) or grain data (individual
grains are segmented). Requires orientation data as quaternion.
""", version = scriptID)
parser.add_option('-b','--basegroup',
dest = 'basegroup',
metavar = 'string',
help = 'name of the group in "DataContainers" containing the pointwise (and, if applicable grain average) data')
parser.add_option('-p','--pointwise',
dest = 'pointwise',
metavar = 'string',
help = 'name of the group in "DataContainers/<basegroup>" containing pointwise data [%default]')
parser.add_option('-a','--average',
dest = 'average',
metavar = 'string',
help = 'name of the group in "DataContainers</basegroup>" containing grain average data. '\
+ 'Leave empty for pointwise data')
parser.add_option('--phase',
dest = 'phase',
type = 'string',
metavar = 'string',
help = 'name of the dataset containing pointwise/average phase IDs [%default]')
parser.add_option('--microstructure',
dest = 'microstructure',
type = 'string',
metavar = 'string',
help = 'name of the dataset connecting pointwise and average data [%default]')
parser.add_option('-q', '--quaternion',
dest = 'quaternion',
type = 'string',
metavar='string',
help = 'name of the dataset containing pointwise/average orientation as quaternion [%default]')
parser.add_option('--homogenization',
dest = 'homogenization',
type = 'int', metavar = 'int',
help = 'homogenization index to be used [%default]')
parser.set_defaults(pointwise = 'CellData',
quaternion = 'Quats',
phase = 'Phases',
microstructure = 'FeatureIds',
homogenization = 1,
)
(options, filenames) = parser.parse_args()
if options.basegroup is None:
parser.error('No base group selected')
rootDir ='DataContainers'
if filenames == []: parser.error('no input file specified.')
for name in filenames:
damask.util.report(scriptName,name)
errors = []
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inFile = h5py.File(name, 'r')
group_geom = os.path.join(rootDir,options.basegroup,'_SIMPL_GEOMETRY')
try:
size = inFile[os.path.join(group_geom,'DIMENSIONS')][...] \
* inFile[os.path.join(group_geom,'SPACING')][...]
grid = inFile[os.path.join(group_geom,'DIMENSIONS')][...]
origin = inFile[os.path.join(group_geom,'ORIGIN')][...]
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except KeyError:
errors.append('Geometry data ({}) not found'.format(group_geom))
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group_pointwise = os.path.join(rootDir,options.basegroup,options.pointwise)
if options.average is None:
label = 'Point'
dataset = os.path.join(group_pointwise,options.quaternion)
try:
quats = np.reshape(inFile[dataset][...],(np.product(grid),4))
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rot = [damask.Rotation.from_quaternion(q,True,P=+1) for q in quats]
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except KeyError:
errors.append('Pointwise orientation (quaternion) data ({}) not readable'.format(dataset))
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dataset = os.path.join(group_pointwise,options.phase)
try:
phase = np.reshape(inFile[dataset][...],(np.product(grid)))
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except KeyError:
errors.append('Pointwise phase data ({}) not readable'.format(dataset))
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microstructure = np.arange(1,np.product(grid)+1,dtype=int).reshape(grid,order='F')
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else:
label = 'Grain'
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dataset = os.path.join(group_pointwise,options.microstructure)
try:
microstructure = np.transpose(inFile[dataset][...].reshape(grid[::-1]),(2,1,0)) # convert from C ordering
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except KeyError:
errors.append('Link between pointwise and grain average data ({}) not readable'.format(dataset))
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group_average = os.path.join(rootDir,options.basegroup,options.average)
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dataset = os.path.join(group_average,options.quaternion)
try:
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rot = [damask.Rotation.from_quaternion(q,True,P=+1) for q in inFile[dataset][...][1:]] # skip first entry (unindexed)
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except KeyError:
errors.append('Average orientation data ({}) not readable'.format(dataset))
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dataset = os.path.join(group_average,options.phase)
try:
phase = [i[0] for i in inFile[dataset][...]][1:] # skip first entry (unindexed)
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except KeyError:
errors.append('Average phase data ({}) not readable'.format(dataset))
if errors != []:
damask.util.croak(errors)
continue
config_header = ['<texture>']
for i in range(np.nanmax(microstructure)):
config_header += ['[{}{}]'.format(label,i+1),
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'(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 {:.2f}'.format(*rot[i].as_Eulers(degrees = True)),
]
config_header += ['<microstructure>']
for i in range(np.nanmax(microstructure)):
config_header += ['[{}{}]'.format(label,i+1),
'(constituent)\tphase {}\ttexture {}\tfraction 1.0'.format(phase[i],i+1),
]
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header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
+ config_header
geom = damask.Geom(microstructure,size,origin,
homogenization=options.homogenization,comments=header)
damask.util.croak(geom)
geom.save_ASCII(os.path.splitext(name)[0]+'.geom',compress=False)