using geom class

- dropped the use of the material class as it does not allow to have
empty phase and crystallite. The material.config class needs a severe
refurbishing (no crystallite, use orderedDict instead of hand written
solution, drop of texture components). Probably best solution is to
postpone this until we have a yaml/json reader for Fortran.
This commit is contained in:
Martin Diehl 2019-05-30 13:30:38 +02:00
parent 7d07a3752f
commit 8380071564
1 changed files with 59 additions and 88 deletions

View File

@ -1,11 +1,15 @@
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,h5py
import numpy as np
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])
@ -14,40 +18,50 @@ 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.
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',
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',
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',
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',
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',
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',
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',
crystallite = 1,
homogenization = 1,
)
(options, filenames) = parser.parse_args()
@ -57,59 +71,51 @@ if options.basegroup is None:
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')][...]
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')][...]
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'])
label = 'Point'
dataset = os.path.join(group_pointwise,options.quaternion)
try:
quats = np.reshape(inFile[dataset][...],(N_microstructure,4))
texture = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in quats]
quats = np.reshape(inFile[dataset][...],(np.product(grid),4))
rot = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in quats]
except:
errors.append('Pointwise orientation (quaternion) data ({}) not readable'.format(dataset))
dataset = os.path.join(group_pointwise,options.phase)
try:
phase = np.reshape(inFile[dataset][...],(N_microstructure))
phase = np.reshape(inFile[dataset][...],(np.product(grid)))
except:
errors.append('Pointwise phase data ({}) not readable'.format(dataset))
microstructure = np.arange(1,np.product(grid)+1,dtype=int).reshape(grid,order='F')
else:
label = 'grain'
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)
microstructure = np.transpose(inFile[dataset][...].reshape(grid[::-1]),(2,1,0)) # convert from C ordering
except:
errors.append('Link between pointwise and grain average data ({}) not readable'.format(dataset))
@ -117,7 +123,7 @@ for name in filenames:
dataset = os.path.join(group_average,options.quaternion)
try:
texture = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in inFile[dataset][...][1:]] # skip first entry (unindexed)
rot = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in inFile[dataset][...][1:]] # skip first entry (unindexed)
except:
errors.append('Average orientation data ({}) not readable'.format(dataset))
@ -129,60 +135,25 @@ for name in filenames:
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
config_header = ['<microstructure>']
for i in range(np.nanmax(microstructure)):
config_header += ['[{}{}]'.format(label,i+1),
'crystallite 1',
'(constituent)\tphase {}\ttexture {}\tfraction 1.0'.format(phase[i],i+1),
]
mat = damask.Material()
mat.verbose = False
config_header += ['<texture>']
for i in range(np.nanmax(microstructure)):
config_header += ['[{}{}]'.format(label,i+1),
'(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 {:.2f}'.format(*rot[i].asEulers(degrees = True)),
]
# dummy <homogenization>
h = damask.config.material.Homogenization()
mat.add_section('Homogenization','none',h)
info['homogenization'] = 1
header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
+ config_header
geom = damask.Geom(microstructure,size,origin,
homogenization=options.homogenization,comments=header)
damask.util.croak(geom)
# <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()
geom.to_file(os.path.splitext(name)[0]+'.geom')