functionality for geom generation in python lib
This commit is contained in:
Martin Diehl
parent
bdfbd2c62e
commit
952ad4f8fe
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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 +37,20 @@ 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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(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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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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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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geom = damask.Geom.load_table(name,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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@ -1,15 +1,18 @@
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import copy
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import multiprocessing as mp
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from functools import partial
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from os import path
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import numpy as np
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import h5py
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from scipy import ndimage,spatial
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from . import environment
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from . import Rotation
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from . import VTK
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from . import util
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from . import grid_filters
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from . import Table
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from . import Rotation
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class Geom:
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@ -353,7 +356,7 @@ class Geom:
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Number of periods per unit cell. Defaults to 1.
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materials : (int, int), optional
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Material IDs. Defaults to (1,2).
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Notes
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-----
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The following triply-periodic minimal surfaces are implemented:
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@ -397,6 +400,35 @@ class Geom:
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)
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@staticmethod
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def load_DREAM3D(fname,base_group,point_data=None,material='FeatureIds'):
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root_dir ='DataContainers'
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f = h5py.File(fname, 'r')
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g = path.join(root_dir,base_group,'_SIMPL_GEOMETRY')
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size = f[path.join(g,'DIMENSIONS')][()] * f[path.join(g,'SPACING')][()]
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grid = f[path.join(g,'DIMENSIONS')][()]
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origin = f[path.join(g,'ORIGIN')][()]
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group_pointwise = path.join(root_dir,base_group,point_data)
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ma = np.arange(1,np.product(grid)+1,dtype=int) if point_data is None else \
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np.reshape(f[path.join(group_pointwise,material)],grid.prod())
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return Geom(ma.reshape(grid,order='F'),size,origin,util.execution_stamp('Geom','from_DREAM3D'))
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@staticmethod
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def load_table(fname,coordinates,labels):
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table = Table.load(fname).sort_by([f'{i}_{coordinates}' for i in range(3,0,-1)])
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grid,size,origin = grid_filters.cell_coord0_gridSizeOrigin(table.get(coordinates))
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labels_ = [labels] if isinstance(labels,str) else labels
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_,unique_inverse = np.unique(np.hstack([table.get(l) for l in labels_]),return_inverse=True,axis=0)
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ma = unique_inverse.reshape(grid,order='F') + 1
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return Geom(ma,size,origin,util.execution_stamp('Geom','from_table'))
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def save(self,fname,compress=True):
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"""
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Generates vtk rectilinear grid.
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@ -536,7 +568,7 @@ class Geom:
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coords_rot = R.broadcast_to(tuple(self.grid))@coords
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with np.errstate(all='ignore'):
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mask = np.where(np.sum(np.power(coords_rot/r,2.0**exponent),axis=-1) > 1.0,True,False)
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mask = np.sum(np.power(coords_rot/r,2.0**np.array(exponent)),axis=-1) > 1.0
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if periodic: # translate back to center
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mask = np.roll(mask,((c-np.ones(3)*.5)*self.grid).astype(int),(0,1,2))
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