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
parent
7d07a3752f
commit
8380071564
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@ -1,11 +1,15 @@
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#!/usr/bin/env python3
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,h5py
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import numpy as np
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import os
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import sys
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from optparse import OptionParser
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import h5py
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import numpy as np
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import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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@ -14,40 +18,50 @@ scriptID = ' '.join([scriptName,damask.version])
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# MAIN
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#--------------------------------------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog [dream3dfile[s]]', description = """
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Convert DREAM3D file to geometry file. This can be done from cell data (direct pointwise takeover) or
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from grain data (individual grains are segmented). Requires orientation data as quaternion.
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [DREAM.3Dfile(s)]', description = """
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Converts DREAM.3D file. Input can be cell data (direct pointwise takeover) or grain data (individual
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grains are segmented). Requires orientation data as quaternion.
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""", version = scriptID)
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parser.add_option('-b','--basegroup',
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dest = 'basegroup', metavar = 'string',
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dest = 'basegroup',
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metavar = 'string',
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help = 'name of the group in "DataContainers" containing the pointwise (and, if applicable grain average) data')
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parser.add_option('-p','--pointwise',
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dest = 'pointwise', metavar = 'string',
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dest = 'pointwise',
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metavar = 'string',
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help = 'name of the group in "DataContainers/<basegroup>" containing pointwise data [%default]')
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parser.add_option('-a','--average',
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dest = 'average', metavar = 'string',
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dest = 'average',
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metavar = 'string',
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help = 'name of the group in "DataContainers</basegroup>" containing grain average data. '\
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+ 'Leave empty for pointwise data')
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parser.add_option('--phase',
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dest = 'phase',
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type = 'string', metavar = 'string',
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type = 'string',
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metavar = 'string',
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help = 'name of the dataset containing pointwise/average phase IDs [%default]')
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parser.add_option('--microstructure',
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dest = 'microstructure',
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type = 'string', metavar = 'string',
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type = 'string',
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metavar = 'string',
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help = 'name of the dataset connecting pointwise and average data [%default]')
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parser.add_option('-q', '--quaternion',
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dest = 'quaternion',
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type = 'string', metavar='string',
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type = 'string',
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metavar='string',
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help = 'name of the dataset containing pointwise/average orientation as quaternion [%default]')
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parser.add_option('--homogenization',
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dest = 'homogenization',
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type = 'int', metavar = 'int',
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help = 'homogenization index to be used [%default]')
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parser.set_defaults(pointwise = 'CellData',
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quaternion = 'Quats',
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phase = 'Phases',
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microstructure = 'FeatureIds',
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crystallite = 1,
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homogenization = 1,
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)
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(options, filenames) = parser.parse_args()
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@ -57,59 +71,51 @@ if options.basegroup is None:
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rootDir ='DataContainers'
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: parser.error('no input file specified.')
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for name in filenames:
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try:
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table = damask.ASCIItable(outname = os.path.splitext(name)[0]+'.geom',
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buffered = False, labeled=False,
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)
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except: continue
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damask.util.report(scriptName,name)
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errors = []
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info = {}
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ori = []
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inFile = h5py.File(name, 'r')
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group_geom = os.path.join(rootDir,options.basegroup,'_SIMPL_GEOMETRY')
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try:
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info['size'] = inFile[os.path.join(group_geom,'DIMENSIONS')][...] \
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size = inFile[os.path.join(group_geom,'DIMENSIONS')][...] \
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* inFile[os.path.join(group_geom,'SPACING')][...]
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info['grid'] = inFile[os.path.join(group_geom,'DIMENSIONS')][...]
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info['origin'] = inFile[os.path.join(group_geom,'ORIGIN')][...]
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grid = inFile[os.path.join(group_geom,'DIMENSIONS')][...]
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origin = inFile[os.path.join(group_geom,'ORIGIN')][...]
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except:
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errors.append('Geometry data ({}) not found'.format(group_geom))
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group_pointwise = os.path.join(rootDir,options.basegroup,options.pointwise)
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if options.average is None:
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label = 'point'
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N_microstructure = np.product(info['grid'])
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label = 'Point'
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dataset = os.path.join(group_pointwise,options.quaternion)
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try:
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quats = np.reshape(inFile[dataset][...],(N_microstructure,4))
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texture = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in quats]
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quats = np.reshape(inFile[dataset][...],(np.product(grid),4))
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rot = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in quats]
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except:
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errors.append('Pointwise orientation (quaternion) data ({}) not readable'.format(dataset))
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dataset = os.path.join(group_pointwise,options.phase)
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try:
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phase = np.reshape(inFile[dataset][...],(N_microstructure))
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phase = np.reshape(inFile[dataset][...],(np.product(grid)))
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except:
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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:
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label = 'grain'
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label = 'Grain'
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dataset = os.path.join(group_pointwise,options.microstructure)
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try:
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microstructure = np.reshape(inFile[dataset][...],(np.product(info['grid'])))
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N_microstructure = np.max(microstructure)
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microstructure = np.transpose(inFile[dataset][...].reshape(grid[::-1]),(2,1,0)) # convert from C ordering
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except:
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errors.append('Link between pointwise and grain average data ({}) not readable'.format(dataset))
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@ -117,7 +123,7 @@ for name in filenames:
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dataset = os.path.join(group_average,options.quaternion)
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try:
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texture = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in inFile[dataset][...][1:]] # skip first entry (unindexed)
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rot = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in inFile[dataset][...][1:]] # skip first entry (unindexed)
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except:
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errors.append('Average orientation data ({}) not readable'.format(dataset))
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@ -129,60 +135,25 @@ for name in filenames:
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if errors != []:
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damask.util.croak(errors)
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table.close(dismiss = True)
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continue
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config_header = ['<microstructure>']
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for i in range(np.nanmax(microstructure)):
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config_header += ['[{}{}]'.format(label,i+1),
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'crystallite 1',
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'(constituent)\tphase {}\ttexture {}\tfraction 1.0'.format(phase[i],i+1),
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]
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mat = damask.Material()
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mat.verbose = False
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config_header += ['<texture>']
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for i in range(np.nanmax(microstructure)):
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config_header += ['[{}{}]'.format(label,i+1),
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'(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 {:.2f}'.format(*rot[i].asEulers(degrees = True)),
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]
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# dummy <homogenization>
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h = damask.config.material.Homogenization()
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mat.add_section('Homogenization','none',h)
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info['homogenization'] = 1
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header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
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+ config_header
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geom = damask.Geom(microstructure,size,origin,
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homogenization=options.homogenization,comments=header)
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damask.util.croak(geom)
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# <crystallite> placeholder (same for all microstructures at the moment)
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c = damask.config.material.Crystallite()
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mat.add_section('Crystallite','tbd',c)
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# <phase> placeholders
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for i in range(np.max(phase)):
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p = damask.config.material.Phase()
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mat.add_section('phase','phase{}-tbd'.format(i+1),p)
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# <texture>
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for i,o in enumerate(texture):
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t = damask.config.material.Texture()
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t.add_component('gauss',{'eulers':o.asEulers(degrees=True)})
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mat.add_section(part='texture', section='{}{}'.format(label,i+1),initialData=t)
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# <microstructure>
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for i in range(N_microstructure):
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m = damask.config.material.Microstructure()
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mat.add_section('microstructure','{}{}'.format(label,i+1),m)
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mat.add_microstructure('{}{}'.format(label,i+1),
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{'phase': 'phase{}-tbd'.format(phase[i]),
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'texture':'{}{}'.format(label,i+1),
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'crystallite':'tbd',
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'fraction':1
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})
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table.info_append([
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scriptID + ' ' + ' '.join(sys.argv[1:]),
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"grid\ta {}\tb {}\tc {}".format(*info['grid']),
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"size\tx {}\ty {}\tz {}".format(*info['size']),
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"origin\tx {}\ty {}\tz {}".format(*info['origin']),
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"homogenization\t{}".format(info['homogenization']),
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str(mat).split('\n')
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])
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table.head_write()
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if options.average is None:
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table.data = [1, 'to', format(N_microstructure)]
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table.data_write()
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else:
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table.data = microstructure.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
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table.data_writeArray()
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table.close()
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geom.to_file(os.path.splitext(name)[0]+'.geom')
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