Merge branch 'geom_from_xx' into development
This commit is contained in:
Sharan Roongta
commit
8ab405e5d8
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@ -8,6 +8,7 @@
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*.jpg binary
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*.hdf5 binary
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*.pdf binary
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*.dream3d binary
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|
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# ignore files from MSC.Marc in language statistics
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installation/mods_MarcMentat/20*/* linguist-vendored
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|
|
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|
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@ -1,12 +1,8 @@
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#!/usr/bin/env python3
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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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@ -64,88 +60,12 @@ parser.set_defaults(pointwise = 'CellData',
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if options.basegroup is None:
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parser.error('No base group selected')
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rootDir ='DataContainers'
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if filenames == []: parser.error('no input file specified.')
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for name in filenames:
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damask.util.report(scriptName,name)
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damask.util.report(scriptName,name)
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errors = []
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geom = damask.Geom.load_DREAM3D(name,options.basegroup,options.pointwise)
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damask.util.croak(geom)
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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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size = inFile[os.path.join(group_geom,'DIMENSIONS')][...] \
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* inFile[os.path.join(group_geom,'SPACING')][...]
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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 KeyError:
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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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dataset = os.path.join(group_pointwise,options.quaternion)
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try:
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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:
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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][...],(np.product(grid)))
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except KeyError:
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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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dataset = os.path.join(group_pointwise,options.microstructure)
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try:
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microstructure = np.transpose(inFile[dataset][...].reshape(grid[::-1]),(2,1,0)) # convert from C ordering
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except KeyError:
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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)
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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:
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errors.append('Average orientation data ({}) not readable'.format(dataset))
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dataset = os.path.join(group_average,options.phase)
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try:
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phase = [i[0] for i in inFile[dataset][...]][1:] # skip first entry (unindexed)
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except KeyError:
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errors.append('Average phase data ({}) not readable'.format(dataset))
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if errors != []:
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damask.util.croak(errors)
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continue
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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].as_Eulers(degrees = True)),
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]
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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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'(constituent)\tphase {}\ttexture {}\tfraction 1.0'.format(phase[i],i+1),
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]
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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,comments=header)
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damask.util.croak(geom)
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geom.save_ASCII(os.path.splitext(name)[0]+'.geom',compress=False)
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geom.save_ASCII(os.path.splitext(name)[0]+'.geom',compress=False)
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@ -2,11 +2,8 @@
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import os
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import sys
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from io import StringIO
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from optparse import OptionParser
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import numpy as np
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import damask
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@ -40,64 +37,21 @@ parser.add_option('-q', '--quaternion',
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dest = 'quaternion',
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type = 'string', metavar='string',
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help = 'quaternion label')
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parser.add_option('--axes',
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dest = 'axes',
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type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
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help = 'orientation coordinate frame in terms of position coordinate frame [+x +y +z]')
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parser.set_defaults(pos = 'pos',
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)
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parser.set_defaults(pos= 'pos')
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|
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(options,filenames) = parser.parse_args()
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if filenames == []: filenames = [None]
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if np.sum([options.quaternion is not None,
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options.microstructure is not None]) != 1:
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parser.error('need either microstructure or quaternion (and optionally phase) as input.')
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if options.microstructure is not None and options.phase is not None:
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parser.error('need either microstructure or phase (and mandatory quaternion) as input.')
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if options.axes is not None and not set(options.axes).issubset(set(['x','+x','-x','y','+y','-y','z','+z','-z'])):
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parser.error('invalid axes {} {} {}.'.format(*options.axes))
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for name in filenames:
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damask.util.report(scriptName,name)
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table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
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table.sort_by(['{}_{}'.format(i,options.pos) for i in range(3,0,-1)]) # x fast, y slow
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grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
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labels = []
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for l in [options.quaternion,options.phase,options.microstructure]:
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if l is not None: labels.append(l)
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config_header = table.comments
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if options.microstructure:
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microstructure = table.get(options.microstructure).reshape(grid,order='F')
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elif options.quaternion:
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q = table.get(options.quaternion)
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phase = table.get(options.phase).astype(int) if options.phase else \
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np.ones((table.data.shape[0],1),dtype=int)
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unique,unique_inverse = np.unique(np.hstack((q,phase)),return_inverse=True,axis=0)
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microstructure = unique_inverse.reshape(grid,order='F') + 1
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config_header = ['<texture>']
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for i,data in enumerate(unique):
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ori = damask.Rotation(data[0:4])
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config_header += ['[Grain{}]'.format(i+1),
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'(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 {:.2f}'.format(*ori.as_Eulers(degrees = True)),
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]
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if options.axes is not None: config_header += ['axes\t{} {} {}'.format(*options.axes)]
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|
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config_header += ['<microstructure>']
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for i,data in enumerate(unique):
|
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config_header += ['[Grain{}]'.format(i+1),
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'(constituent)\tphase {}\ttexture {}\tfraction 1.0'.format(int(data[4]),i+1),
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]
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|
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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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comments=header)
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t = damask.Table.load(name)
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geom = damask.Geom.from_table(t,options.pos,labels)
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damask.util.croak(geom)
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geom.save_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',compress=False)
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|
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@ -10,21 +10,21 @@ with open(_Path(__file__).parent/_Path('VERSION')) as _f:
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# make classes directly accessible as damask.Class
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from ._environment import Environment as _ # noqa
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environment = _()
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from ._table import Table # noqa
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from ._vtk import VTK # noqa
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from ._colormap import Colormap # noqa
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from ._rotation import Rotation # noqa
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from ._lattice import Symmetry, Lattice# noqa
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from ._orientation import Orientation # noqa
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from ._result import Result # noqa
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from ._geom import Geom # noqa
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from ._config import Config # noqa
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from ._configmaterial import ConfigMaterial # noqa
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from . import solver # noqa
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from . import util # noqa
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from . import seeds # noqa
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from . import grid_filters # noqa
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from . import mechanics # noqa
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from . import solver # noqa
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from . import grid_filters # noqa
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from ._lattice import Symmetry, Lattice# noqa
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from ._table import Table # noqa
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from ._rotation import Rotation # noqa
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from ._vtk import VTK # noqa
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from ._colormap import Colormap # noqa
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from ._orientation import Orientation # noqa
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from ._config import Config # noqa
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from ._configmaterial import ConfigMaterial # noqa
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from ._geom import Geom # noqa
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from ._result import Result # noqa
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|
|
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@ -2,6 +2,7 @@ import copy
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import numpy as np
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from . import grid_filters
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from . import Config
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from . import Lattice
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from . import Rotation
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@ -17,12 +18,73 @@ class ConfigMaterial(Config):
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----------
|
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fname : file, str, or pathlib.Path, optional
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Filename or file for writing. Defaults to 'material.yaml'.
|
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**kwargs : dict
|
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**kwargs
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||||
Keyword arguments parsed to yaml.dump.
|
||||
|
||||
"""
|
||||
super().save(fname,**kwargs)
|
||||
|
||||
|
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@staticmethod
|
||||
def from_table(table,coordinates=None,constituents={},**kwargs):
|
||||
"""
|
||||
Load from an ASCII table.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
table : damask.Table
|
||||
Table that contains material information.
|
||||
coordinates : str, optional
|
||||
Label of spatial coordiates. Used for sorting and performing a
|
||||
sanity check. Default to None, in which case no sorting or checking is
|
||||
peformed.
|
||||
constituents : dict, optional
|
||||
Entries for 'constituents'. The key is the name and the value specifies
|
||||
the label of the data column in the table
|
||||
**kwargs
|
||||
Keyword arguments where the key is the name and the value specifies
|
||||
the label of the data column in the table
|
||||
|
||||
Examples
|
||||
--------
|
||||
>>> import damask
|
||||
>>> import damask.ConfigMaterial as cm
|
||||
>>> t = damask.Table.load('small.txt')
|
||||
>>> t
|
||||
pos pos pos qu qu qu qu phase homog
|
||||
0 0 0 0 0.19 0.8 0.24 -0.51 Aluminum SX
|
||||
1 1 0 0 0.8 0.19 0.24 -0.51 Steel SX
|
||||
>>> cm.from_table(t,'pos',{'O':'qu','phase':'phase'},homogenization='homog')
|
||||
material:
|
||||
- constituents:
|
||||
- O: [0.19, 0.8, 0.24, -0.51]
|
||||
fraction: 1.0
|
||||
phase: Aluminum
|
||||
homogenization: SX
|
||||
- constituents:
|
||||
- O: [0.8, 0.19, 0.24, -0.51]
|
||||
fraction: 1.0
|
||||
phase: Steel
|
||||
homogenization: SX
|
||||
|
||||
"""
|
||||
if coordinates is not None:
|
||||
t = table.sort_by([f'{i}_{coordinates}' for i in range(3,0,-1)])
|
||||
grid_filters.coord0_check(t.get(coordinates))
|
||||
else:
|
||||
t = table
|
||||
|
||||
constituents_ = {k:t.get(v) for k,v in constituents.items()}
|
||||
kwargs_ = {k:t.get(v) for k,v in kwargs.items()}
|
||||
|
||||
_,idx = np.unique(np.hstack(list({**constituents_,**kwargs_}.values())),return_index=True,axis=0)
|
||||
|
||||
constituents_ = {k:v[idx].squeeze() for k,v in constituents_.items()}
|
||||
kwargs_ = {k:v[idx].squeeze() for k,v in kwargs_.items()}
|
||||
|
||||
return ConfigMaterial().material_add(constituents_,**kwargs_)
|
||||
|
||||
|
||||
@property
|
||||
def is_complete(self):
|
||||
"""Check for completeness."""
|
||||
|
|
@ -62,10 +124,10 @@ class ConfigMaterial(Config):
|
|||
print(f'No lattice specified in phase {k}')
|
||||
ok = False
|
||||
|
||||
#for k,v in self['homogenization'].items():
|
||||
# if 'N_constituents' not in v:
|
||||
# print(f'No. of constituents not specified in homogenization {k}'}
|
||||
# ok = False
|
||||
for k,v in self['homogenization'].items():
|
||||
if 'N_constituents' not in v:
|
||||
print(f'No. of constituents not specified in homogenization {k}')
|
||||
ok = False
|
||||
|
||||
if phase - set(self['phase']):
|
||||
print(f'Phase(s) {phase-set(self["phase"])} missing')
|
||||
|
|
@ -158,3 +220,80 @@ class ConfigMaterial(Config):
|
|||
except KeyError:
|
||||
continue
|
||||
return dup
|
||||
|
||||
|
||||
def material_add(self,constituents,**kwargs):
|
||||
"""
|
||||
Add material entries.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
constituents : dict
|
||||
Entries for 'constituents'. The key is the name and the value specifies
|
||||
the label of the data column in the table
|
||||
**kwargs
|
||||
Keyword arguments where the key is the name and the value specifies
|
||||
the label of the data column in the table
|
||||
|
||||
Examples
|
||||
--------
|
||||
>>> import damask
|
||||
>>> m = damask.ConfigMaterial()
|
||||
>>> O = damask.Rotation.from_random(3).as_quaternion()
|
||||
>>> phase = ['Aluminum','Steel','Aluminum']
|
||||
>>> m.material_add(constituents={'phase':phase,'O':O},homogenization='SX')
|
||||
material:
|
||||
- constituents:
|
||||
- O: [0.577764, -0.146299, -0.617669, 0.513010]
|
||||
fraction: 1.0
|
||||
phase: Aluminum
|
||||
homogenization: SX
|
||||
- constituents:
|
||||
- O: [0.184176, 0.340305, 0.737247, 0.553840]
|
||||
fraction: 1.0
|
||||
phase: Steel
|
||||
homogenization: SX
|
||||
- constituents:
|
||||
- O: [0.0886257, -0.144848, 0.615674, -0.769487]
|
||||
fraction: 1.0
|
||||
phase: Aluminum
|
||||
homogenization: SX
|
||||
|
||||
"""
|
||||
c = [{'constituents':u} for u in ConfigMaterial._constituents(**constituents)]
|
||||
for k,v in kwargs.items():
|
||||
if hasattr(v,'__len__') and not isinstance(v,str):
|
||||
if len(v) != len(c):
|
||||
raise ValueError('len mismatch 1')
|
||||
for i,vv in enumerate(v):
|
||||
c[i][k] = [w.item() for w in vv] if isinstance(vv,np.ndarray) else vv.item()
|
||||
else:
|
||||
for i in range(len(c)):
|
||||
c[i][k] = v
|
||||
dup = copy.deepcopy(self)
|
||||
if 'material' not in dup: dup['material'] = []
|
||||
dup['material'] +=c
|
||||
|
||||
return dup
|
||||
|
||||
|
||||
@staticmethod
|
||||
def _constituents(N=1,**kwargs):
|
||||
"""Construct list of constituents."""
|
||||
for v in kwargs.values():
|
||||
if hasattr(v,'__len__') and not isinstance(v,str): N_material = len(v)
|
||||
|
||||
if N == 1:
|
||||
m = [[{'fraction':1.0}] for _ in range(N_material)]
|
||||
for k,v in kwargs.items():
|
||||
if hasattr(v,'__len__') and not isinstance(v,str):
|
||||
if len(v) != N_material:
|
||||
raise ValueError('len mismatch 2')
|
||||
for i,vv in enumerate(np.array(v)):
|
||||
m[i][0][k] = [w.item() for w in vv] if isinstance(vv,np.ndarray) else vv.item()
|
||||
else:
|
||||
for i in range(N_material):
|
||||
m[i][0][k] = v
|
||||
return m
|
||||
else:
|
||||
raise NotImplementedError
|
||||
|
|
|
|||
|
|
@ -1,15 +1,17 @@
|
|||
import copy
|
||||
import multiprocessing as mp
|
||||
from functools import partial
|
||||
from os import path
|
||||
|
||||
import numpy as np
|
||||
import h5py
|
||||
from scipy import ndimage,spatial
|
||||
|
||||
from . import environment
|
||||
from . import Rotation
|
||||
from . import VTK
|
||||
from . import util
|
||||
from . import grid_filters
|
||||
from . import Rotation
|
||||
|
||||
|
||||
class Geom:
|
||||
|
|
@ -207,6 +209,68 @@ class Geom:
|
|||
return Geom(material.reshape(grid,order='F'),size,origin,comments)
|
||||
|
||||
|
||||
|
||||
@staticmethod
|
||||
def load_DREAM3D(fname,base_group,point_data=None,material='FeatureIds'):
|
||||
"""
|
||||
Load a DREAM.3D file.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
fname : str
|
||||
Filename of the DREAM.3D file
|
||||
base_group : str
|
||||
Name of the group (folder) below 'DataContainers'. For example
|
||||
'SyntheticVolumeDataContainer'.
|
||||
point_data : str, optional
|
||||
Name of the group (folder) containing the point wise material data,
|
||||
for example 'CellData'. Defaults to None, in which case points consecutively numbered.
|
||||
material : str, optional
|
||||
Name of the dataset containing the material ID. Defaults to
|
||||
'FeatureIds'.
|
||||
|
||||
"""
|
||||
root_dir ='DataContainers'
|
||||
f = h5py.File(fname, 'r')
|
||||
g = path.join(root_dir,base_group,'_SIMPL_GEOMETRY')
|
||||
size = f[path.join(g,'DIMENSIONS')][()] * f[path.join(g,'SPACING')][()]
|
||||
grid = f[path.join(g,'DIMENSIONS')][()]
|
||||
origin = f[path.join(g,'ORIGIN')][()]
|
||||
group_pointwise = path.join(root_dir,base_group,point_data)
|
||||
|
||||
ma = np.arange(1,np.product(grid)+1,dtype=int) if point_data is None else \
|
||||
np.reshape(f[path.join(group_pointwise,material)],grid.prod())
|
||||
|
||||
return Geom(ma.reshape(grid,order='F'),size,origin,util.execution_stamp('Geom','load_DREAM3D'))
|
||||
|
||||
|
||||
@staticmethod
|
||||
def from_table(table,coordinates,labels):
|
||||
"""
|
||||
Load an ASCII table.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
table : damask.Table
|
||||
Table that contains material information.
|
||||
coordinates : str
|
||||
Label of the column containing the spatial coordinates.
|
||||
labels : str or list of str
|
||||
Label(s) of the columns containing the material definition.
|
||||
Each unique combintation of values results in a material.
|
||||
|
||||
"""
|
||||
t = table.sort_by([f'{i}_{coordinates}' for i in range(3,0,-1)])
|
||||
|
||||
grid,size,origin = grid_filters.cell_coord0_gridSizeOrigin(t.get(coordinates))
|
||||
|
||||
labels_ = [labels] if isinstance(labels,str) else labels
|
||||
_,unique_inverse = np.unique(np.hstack([t.get(l) for l in labels_]),return_inverse=True,axis=0)
|
||||
ma = unique_inverse.reshape(grid,order='F') + 1
|
||||
|
||||
return Geom(ma,size,origin,util.execution_stamp('Geom','from_table'))
|
||||
|
||||
|
||||
@staticmethod
|
||||
def _find_closest_seed(seeds, weights, point):
|
||||
return np.argmin(np.sum((np.broadcast_to(point,(len(seeds),3))-seeds)**2,axis=1) - weights)
|
||||
|
|
@ -353,7 +417,7 @@ class Geom:
|
|||
Number of periods per unit cell. Defaults to 1.
|
||||
materials : (int, int), optional
|
||||
Material IDs. Defaults to (1,2).
|
||||
|
||||
|
||||
Notes
|
||||
-----
|
||||
The following triply-periodic minimal surfaces are implemented:
|
||||
|
|
@ -399,7 +463,7 @@ class Geom:
|
|||
|
||||
def save(self,fname,compress=True):
|
||||
"""
|
||||
Generates vtk rectilinear grid.
|
||||
Store as vtk rectilinear grid.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
|
|
@ -536,7 +600,7 @@ class Geom:
|
|||
coords_rot = R.broadcast_to(tuple(self.grid))@coords
|
||||
|
||||
with np.errstate(all='ignore'):
|
||||
mask = np.where(np.sum(np.power(coords_rot/r,2.0**exponent),axis=-1) > 1.0,True,False)
|
||||
mask = np.sum(np.power(coords_rot/r,2.0**np.array(exponent)),axis=-1) > 1.0
|
||||
|
||||
if periodic: # translate back to center
|
||||
mask = np.roll(mask,((c-np.ones(3)*.5)*self.grid).astype(int),(0,1,2))
|
||||
|
|
|
|||
|
|
@ -33,6 +33,10 @@ class Table:
|
|||
"""Brief overview."""
|
||||
return util.srepr(self.comments)+'\n'+self.data.__repr__()
|
||||
|
||||
def __len__(self):
|
||||
"""Number of rows."""
|
||||
return len(self.data)
|
||||
|
||||
def __copy__(self):
|
||||
"""Copy Table."""
|
||||
return copy.deepcopy(self)
|
||||
|
|
|
|||
|
|
@ -1,8 +1,10 @@
|
|||
homogenization:
|
||||
SX:
|
||||
N_constituents: 2
|
||||
mech: {type: none}
|
||||
Taylor:
|
||||
mech: {N_constituents: 2, type: isostrain}
|
||||
N_constituents: 2
|
||||
mech: {type: isostrain}
|
||||
|
||||
material:
|
||||
- constituents:
|
||||
|
|
|
|||
Loading…
Reference in New Issue