99 lines
4.3 KiB
Python
Executable File
99 lines
4.3 KiB
Python
Executable File
#!/usr/bin/env python3
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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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from scipy import ndimage
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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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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
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Rotates original microstructure and embeddeds it into buffer material.
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""", version=scriptID)
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parser.add_option('-r', '--rotation',
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dest='rotation',
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type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
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help = 'rotation given as axis and angle')
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parser.add_option('-e', '--eulers',
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dest = 'eulers',
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type = 'float', nargs = 3, metavar = ' '.join(['float']*3),
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help = 'rotation given as Euler angles')
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parser.add_option('-d', '--degrees',
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dest = 'degrees',
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action = 'store_true',
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help = 'Euler angles/axis angle are given in degrees')
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parser.add_option('-m', '--matrix',
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dest = 'matrix',
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type = 'float', nargs = 9, metavar = ' '.join(['float']*9),
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help = 'rotation given as matrix')
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parser.add_option('-q', '--quaternion',
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dest = 'quaternion',
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type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
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help = 'rotation given as quaternion')
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parser.add_option('-f', '--fill',
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dest = 'fill',
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type = 'float', metavar = 'int',
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help = 'background microstructure index, defaults to max microstructure index + 1')
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parser.set_defaults(degrees = False)
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(options, filenames) = parser.parse_args()
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if [options.rotation,options.eulers,options.matrix,options.quaternion].count(None) < 3:
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parser.error('more than one rotation specified.')
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if [options.rotation,options.eulers,options.matrix,options.quaternion].count(None) > 3:
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parser.error('no rotation specified.')
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if options.quaternion is not None:
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rot = damask.Rotation.fromQuaternion(np.array(options.quaternion)) # we might need P=+1 here, too...
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if options.rotation is not None:
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rot = damask.Rotation.fromAxisAngle(np.array(options.rotation),degrees=options.degrees,normalise=True,P=+1)
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if options.matrix is not None:
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rot = damask.Rotation.fromMatrix(np.array(options.Matrix))
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if options.eulers is not None:
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rot = damask.Rotation.fromEulers(np.array(options.eulers),degrees=options.degrees)
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eulers = rot.asEulers(degrees=True)
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if filenames == []: filenames = [None]
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for name in filenames:
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damask.util.report(scriptName,name)
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geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
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size = geom.get_size()
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grid = geom.get_grid()
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origin = geom.get_origin()
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microstructure = geom.get_microstructure()
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fill = np.nanmax(microstructure)+1 if options.fill is None else options.fill
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dtype = float if np.isnan(fill) or int(fill) != fill or microstructure.dtype==np.float else int
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# These rotations are always applied in the reference coordinate system, i.e. (z,x,z) not (z,x',z'')
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# this seems to be ok, see https://www.cs.utexas.edu/~theshark/courses/cs354/lectures/cs354-14.pdf
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microstructure = ndimage.rotate(microstructure,eulers[2],(0,1),order=0,
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prefilter=False,output=dtype,cval=fill) # rotation around z
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microstructure = ndimage.rotate(microstructure,eulers[1],(1,2),order=0,
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prefilter=False,output=dtype,cval=fill) # rotation around x
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microstructure = ndimage.rotate(microstructure,eulers[0],(0,1),order=0,
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prefilter=False,output=dtype,cval=fill) # rotation around z
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damask.util.croak(geom.update(microstructure,origin=origin-(np.asarray(microstructure.shape)-grid)/2*size/grid,rescale=True))
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geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
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geom.to_file(sys.stdout if name is None else name)
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