DAMASK_EICMD/processing/pre/geom_rotate.py

100 lines
4.0 KiB
Python
Executable File

#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os
import sys
import numpy as np
import damask
from io import StringIO
from scipy import ndimage
from optparse import OptionParser
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
Rotates spectral geometry description.
""", version=scriptID)
parser.add_option('-r', '--rotation',
dest='rotation',
type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
help = 'rotation given as angle and axis')
parser.add_option('-e', '--eulers',
dest = 'eulers',
type = 'float', nargs = 3, metavar = ' '.join(['float']*3),
help = 'rotation given as Euler angles')
parser.add_option('-d', '--degrees',
dest = 'degrees',
action = 'store_true',
help = 'Euler angles are given in degrees [%default]')
parser.add_option('-m', '--matrix',
dest = 'matrix',
type = 'float', nargs = 9, metavar = ' '.join(['float']*9),
help = 'rotation given as matrix')
parser.add_option('-q', '--quaternion',
dest = 'quaternion',
type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
help = 'rotation given as quaternion')
parser.add_option('-f', '--fill',
dest = 'fill',
type = 'int', metavar = 'int',
help = 'background grain index, defaults to max + 1')
parser.set_defaults(degrees = False,
)
(options, filenames) = parser.parse_args()
if sum(x is not None for x in [options.rotation,options.eulers,options.matrix,options.quaternion]) != 1:
parser.error('not exactly one rotation specified...')
if options.quaternion is not None:
eulers = damask.Rotation.fromQuaternion(np.array(options.quaternion)).asEulers(degrees=True)
if options.rotation is not None:
eulers = damask.Rotation.fromAxisAngle(np.array(options.rotation,degrees=True)).asEulers(degrees=True)
if options.matrix is not None:
eulers = damask.Rotation.fromMatrix(np.array(options.Matrix)).asEulers(degrees=True)
if options.eulers is not None:
eulers = damask.Rotation.fromEulers(np.array(options.eulers),degrees=True).asEulers(degrees=True)
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
if name is None:
virt_file = StringIO(''.join(sys.stdin.read()))
geom = damask.Geom.from_file(virt_file)
else:
geom = damask.Geom.from_file(name)
damask.util.report(scriptName,name)
microstructure = geom.microstructure
spacing = geom.get_size()/geom.get_grid()
newGrainID = options.fill if options.fill is not None else np.nanmax(microstructure)+1
microstructure = ndimage.rotate(microstructure,eulers[2],(0,1),order=0,
prefilter=False,output=microstructure.dtype,cval=newGrainID) # rotation around Z
microstructure = ndimage.rotate(microstructure,eulers[1],(1,2),order=0,
prefilter=False,output=microstructure.dtype,cval=newGrainID) # rotation around X
microstructure = ndimage.rotate(microstructure,eulers[0],(0,1),order=0,
prefilter=False,output=microstructure.dtype,cval=newGrainID) # rotation around Z
geom.microstructure = microstructure
geom.set_size(microstructure.shape*spacing)
geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:]))
damask.util.croak('\n'.join(geom.info()))
if name is None:
sys.stdout.write(str(geom))
else:
geom.to_file(name)