direct translation from DREAM.3D to DAMASK geom
needs test
This commit is contained in:
Martin Diehl
parent
95be7ef938
commit
0d7fd587e3
|
|
@ -0,0 +1,189 @@
|
|||
#!/usr/bin/env python3
|
||||
# -*- coding: UTF-8 no BOM -*-
|
||||
|
||||
import os,sys,h5py
|
||||
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 [dream3dfile[s]]', description = """
|
||||
Convert DREAM3D file to geometry file. This can be done from cell data (direct pointwise takeover) or
|
||||
from 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" that contains all the data')
|
||||
parser.add_option('-p','--pointwise',
|
||||
dest = 'pointwise', metavar = 'string',
|
||||
help = 'name of the group in "DataContainers/<basegroup>" that contains pointwise data [%default]')
|
||||
parser.add_option('-a','--average',
|
||||
dest = 'average', metavar = 'string',
|
||||
help = 'name of the group in "DataContainers</basegroup>" that contains 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.set_defaults(pointwise = 'CellData',
|
||||
quaternion = 'Quats',
|
||||
phase = 'Phases',
|
||||
microstructure = 'FeatureIds',
|
||||
crystallite = 1,
|
||||
)
|
||||
|
||||
(options, filenames) = parser.parse_args()
|
||||
|
||||
if options.basegroup is None:
|
||||
parser.error('No base group selected')
|
||||
|
||||
rootDir ='DataContainers'
|
||||
|
||||
# --- loop over input files -------------------------------------------------------------------------
|
||||
|
||||
if filenames == []: parser.error('no input file specified.')
|
||||
|
||||
for name in filenames:
|
||||
try:
|
||||
table = damask.ASCIItable(outname = os.path.splitext(name)[0]+'.geom',
|
||||
buffered = False, labeled=False,
|
||||
)
|
||||
except: continue
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
errors = []
|
||||
|
||||
info = {}
|
||||
ori = []
|
||||
inFile = h5py.File(name, 'r')
|
||||
group_geom = os.path.join(rootDir,options.basegroup,'_SIMPL_GEOMETRY')
|
||||
try:
|
||||
info['size'] = inFile[os.path.join(group_geom,'DIMENSIONS')][...] \
|
||||
* inFile[os.path.join(group_geom,'SPACING')][...]
|
||||
info['grid'] = inFile[os.path.join(group_geom,'DIMENSIONS')][...]
|
||||
info['origin'] = inFile[os.path.join(group_geom,'ORIGIN')][...]
|
||||
except:
|
||||
errors.append('Geometry data ({}) not found'.format(group_geom))
|
||||
|
||||
|
||||
group_pointwise = os.path.join(rootDir,options.basegroup,options.pointwise)
|
||||
if options.average is None:
|
||||
label = 'point'
|
||||
N_microstructure = np.product(info['grid'])
|
||||
|
||||
dataset = os.path.join(group_pointwise,options.quaternion)
|
||||
try:
|
||||
quats = np.reshape(inFile[dataset][...],(N_microstructure,3))
|
||||
except:
|
||||
errors.append('Pointwise orientation data ({}) not found'.format(dataset))
|
||||
|
||||
texture = [damask.Rotation.fromQuaternion(q,P=+1) for q in quats]
|
||||
|
||||
dataset = os.path.join(group_pointwise,options.phase)
|
||||
try:
|
||||
phase = np.reshape(inFile[dataset][...],(N_microstructure))
|
||||
except:
|
||||
errors.append('Pointwise phase data ({}) not found'.format(dataset))
|
||||
|
||||
|
||||
else:
|
||||
label = 'grain'
|
||||
|
||||
dataset = os.path.join(group_pointwise,options.microstructure)
|
||||
try:
|
||||
microstructure = np.reshape(inFile[dataset][...],(np.product(info['grid'])))
|
||||
N_microstructure = np.max(microstructure)
|
||||
except:
|
||||
errors.append('Link between pointwise and grain average data ({}) not found'.format(dataset))
|
||||
|
||||
group_average = os.path.join(rootDir,options.basegroup,options.average)
|
||||
|
||||
dataset = os.path.join(group_average,options.quaternion)
|
||||
try:
|
||||
texture = [damask.Rotation.fromQuaternion(q,P=+1) for q in inFile[dataset][...][1:]] # skip first entry (unindexed)
|
||||
except:
|
||||
errors.append('Average orientation data ({}) not found'.format(dataset))
|
||||
|
||||
dataset = os.path.join(group_average,options.phase)
|
||||
try:
|
||||
phase = [i[0] for i in inFile[dataset][...]][1:] # skip first entry (unindexed)
|
||||
except:
|
||||
errors.append('Average phase data ({}) not found'.format(dataset))
|
||||
|
||||
if errors != []:
|
||||
damask.util.croak(errors)
|
||||
table.close(dismiss = True)
|
||||
continue
|
||||
|
||||
|
||||
mat = damask.Material()
|
||||
mat.verbose = False
|
||||
|
||||
# dummy <homogenization>
|
||||
h = damask.config.material.Homogenization()
|
||||
mat.add_section('Homogenization','none',h)
|
||||
info['homogenization'] = 1
|
||||
|
||||
# <crystallite> placeholder (same for all microstructures at the moment)
|
||||
c = damask.config.material.Crystallite()
|
||||
mat.add_section('Crystallite','tbd',c)
|
||||
|
||||
# <phase> placeholders
|
||||
for i in range(np.max(phase)):
|
||||
p = damask.config.material.Phase()
|
||||
mat.add_section('phase','phase{}-tbd'.format(i+1),p)
|
||||
|
||||
# <texture>
|
||||
for i,o in enumerate(texture):
|
||||
t = damask.config.material.Texture()
|
||||
t.add_component('gauss',{'eulers':o.asEulers(degrees=True)})
|
||||
mat.add_section(part='texture', section='{}{}'.format(label,i+1),initialData=t)
|
||||
|
||||
# <microstructure>
|
||||
for i in range(N_microstructure):
|
||||
m = damask.config.material.Microstructure()
|
||||
mat.add_section('microstructure','{}{}'.format(label,i+1),m)
|
||||
mat.add_microstructure('{}{}'.format(label,i+1),
|
||||
{'phase': 'phase{}-tbd'.format(phase[i]),
|
||||
'texture':'{}{}'.format(label,i+1),
|
||||
'crystallite':'tbd',
|
||||
'fraction':1
|
||||
})
|
||||
|
||||
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']),
|
||||
str(mat).split('\n')
|
||||
])
|
||||
table.head_write()
|
||||
|
||||
if options.average is None:
|
||||
table.data = [1, 'to', format(N_microstructure)]
|
||||
table.data_write()
|
||||
else:
|
||||
table.data = microstructure.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
|
||||
table.data_writeArray()
|
||||
|
||||
|
||||
table.close()
|
||||
|
|
@ -39,7 +39,7 @@ parser.add_option('-q', '--quaternion',
|
|||
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]')
|
||||
help = 'orientation coordinate frame in terms of position coordinate frame [+x +y +z]')
|
||||
|
||||
parser.add_option('--homogenization',
|
||||
dest = 'homogenization',
|
||||
|
|
@ -51,8 +51,7 @@ parser.add_option('--crystallite',
|
|||
help = 'crystallite index to be used [%default]')
|
||||
|
||||
|
||||
parser.set_defaults(symmetry = [damask.Symmetry.lattices[-1]],
|
||||
homogenization = 1,
|
||||
parser.set_defaults(homogenization = 1,
|
||||
crystallite = 1,
|
||||
pos = 'pos',
|
||||
)
|
||||
|
|
|
|||
Loading…
Reference in New Issue