functionality for geom generation in python lib

This commit is contained in:
Martin Diehl 2020-10-08 18:33:40 +02:00
parent bdfbd2c62e
commit 952ad4f8fe
3 changed files with 44 additions and 139 deletions

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@ -1,12 +1,8 @@
#!/usr/bin/env python3 #!/usr/bin/env python3
import os import os
import sys
from optparse import OptionParser from optparse import OptionParser
import h5py
import numpy as np
import damask import damask
@ -64,88 +60,12 @@ parser.set_defaults(pointwise = 'CellData',
if options.basegroup is None: if options.basegroup is None:
parser.error('No base group selected') parser.error('No base group selected')
rootDir ='DataContainers'
if filenames == []: parser.error('no input file specified.') if filenames == []: parser.error('no input file specified.')
for name in filenames: for name in filenames:
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
errors = [] geom = damask.Geom.load_DREAM3D(name,options.basegroup,options.pointwise)
inFile = h5py.File(name, 'r')
group_geom = os.path.join(rootDir,options.basegroup,'_SIMPL_GEOMETRY')
try:
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 KeyError:
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'
dataset = os.path.join(group_pointwise,options.quaternion)
try:
quats = np.reshape(inFile[dataset][...],(np.product(grid),4))
rot = [damask.Rotation.from_quaternion(q,True,P=+1) for q in quats]
except KeyError:
errors.append('Pointwise orientation (quaternion) data ({}) not readable'.format(dataset))
dataset = os.path.join(group_pointwise,options.phase)
try:
phase = np.reshape(inFile[dataset][...],(np.product(grid)))
except KeyError:
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'
dataset = os.path.join(group_pointwise,options.microstructure)
try:
microstructure = np.transpose(inFile[dataset][...].reshape(grid[::-1]),(2,1,0)) # convert from C ordering
except KeyError:
errors.append('Link between pointwise and grain average data ({}) not readable'.format(dataset))
group_average = os.path.join(rootDir,options.basegroup,options.average)
dataset = os.path.join(group_average,options.quaternion)
try:
rot = [damask.Rotation.from_quaternion(q,True,P=+1) for q in inFile[dataset][...][1:]] # skip first entry (unindexed)
except KeyError:
errors.append('Average orientation data ({}) not readable'.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 KeyError:
errors.append('Average phase data ({}) not readable'.format(dataset))
if errors != []:
damask.util.croak(errors)
continue
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].as_Eulers(degrees = True)),
]
config_header += ['<microstructure>']
for i in range(np.nanmax(microstructure)):
config_header += ['[{}{}]'.format(label,i+1),
'(constituent)\tphase {}\ttexture {}\tfraction 1.0'.format(phase[i],i+1),
]
header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
+ config_header
geom = damask.Geom(microstructure,size,origin,comments=header)
damask.util.croak(geom) damask.util.croak(geom)
geom.save_ASCII(os.path.splitext(name)[0]+'.geom',compress=False) geom.save_ASCII(os.path.splitext(name)[0]+'.geom',compress=False)

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@ -2,11 +2,8 @@
import os import os
import sys import sys
from io import StringIO
from optparse import OptionParser from optparse import OptionParser
import numpy as np
import damask import damask
@ -40,64 +37,20 @@ parser.add_option('-q', '--quaternion',
dest = 'quaternion', dest = 'quaternion',
type = 'string', metavar='string', type = 'string', metavar='string',
help = 'quaternion label') help = 'quaternion label')
parser.add_option('--axes',
dest = 'axes',
type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
help = 'orientation coordinate frame in terms of position coordinate frame [+x +y +z]')
parser.set_defaults(pos= 'pos')
parser.set_defaults(pos = 'pos',
)
(options,filenames) = parser.parse_args() (options,filenames) = parser.parse_args()
if filenames == []: filenames = [None] if filenames == []: filenames = [None]
if np.sum([options.quaternion is not None,
options.microstructure is not None]) != 1:
parser.error('need either microstructure or quaternion (and optionally phase) as input.')
if options.microstructure is not None and options.phase is not None:
parser.error('need either microstructure or phase (and mandatory quaternion) as input.')
if options.axes is not None and not set(options.axes).issubset(set(['x','+x','-x','y','+y','-y','z','+z','-z'])):
parser.error('invalid axes {} {} {}.'.format(*options.axes))
for name in filenames: for name in filenames:
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name) labels = []
table.sort_by(['{}_{}'.format(i,options.pos) for i in range(3,0,-1)]) # x fast, y slow for l in [options.quaternion,options.phase,options.microstructure]:
grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos)) if l is not None: labels.append(l)
config_header = table.comments geom = damask.Geom.load_table(name,options.pos,labels)
if options.microstructure:
microstructure = table.get(options.microstructure).reshape(grid,order='F')
elif options.quaternion:
q = table.get(options.quaternion)
phase = table.get(options.phase).astype(int) if options.phase else \
np.ones((table.data.shape[0],1),dtype=int)
unique,unique_inverse = np.unique(np.hstack((q,phase)),return_inverse=True,axis=0)
microstructure = unique_inverse.reshape(grid,order='F') + 1
config_header = ['<texture>']
for i,data in enumerate(unique):
ori = damask.Rotation(data[0:4])
config_header += ['[Grain{}]'.format(i+1),
'(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 {:.2f}'.format(*ori.as_Eulers(degrees = True)),
]
if options.axes is not None: config_header += ['axes\t{} {} {}'.format(*options.axes)]
config_header += ['<microstructure>']
for i,data in enumerate(unique):
config_header += ['[Grain{}]'.format(i+1),
'(constituent)\tphase {}\ttexture {}\tfraction 1.0'.format(int(data[4]),i+1),
]
header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
+ config_header
geom = damask.Geom(microstructure,size,origin,
comments=header)
damask.util.croak(geom) damask.util.croak(geom)
geom.save_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',compress=False) 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 @@
import copy import copy
import multiprocessing as mp import multiprocessing as mp
from functools import partial from functools import partial
from os import path
import numpy as np import numpy as np
import h5py
from scipy import ndimage,spatial from scipy import ndimage,spatial
from . import environment from . import environment
from . import Rotation
from . import VTK from . import VTK
from . import util from . import util
from . import grid_filters from . import grid_filters
from . import Table
from . import Rotation
class Geom: class Geom:
@ -397,6 +400,35 @@ class Geom:
) )
@staticmethod
def load_DREAM3D(fname,base_group,point_data=None,material='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','from_DREAM3D'))
@staticmethod
def load_table(fname,coordinates,labels):
table = Table.load(fname).sort_by([f'{i}_{coordinates}' for i in range(3,0,-1)])
grid,size,origin = grid_filters.cell_coord0_gridSizeOrigin(table.get(coordinates))
labels_ = [labels] if isinstance(labels,str) else labels
_,unique_inverse = np.unique(np.hstack([table.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'))
def save(self,fname,compress=True): def save(self,fname,compress=True):
""" """
Generates vtk rectilinear grid. Generates vtk rectilinear grid.
@ -536,7 +568,7 @@ class Geom:
coords_rot = R.broadcast_to(tuple(self.grid))@coords coords_rot = R.broadcast_to(tuple(self.grid))@coords
with np.errstate(all='ignore'): 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 if periodic: # translate back to center
mask = np.roll(mask,((c-np.ones(3)*.5)*self.grid).astype(int),(0,1,2)) mask = np.roll(mask,((c-np.ones(3)*.5)*self.grid).astype(int),(0,1,2))