136 lines
5.2 KiB
Python
Executable File
136 lines
5.2 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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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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Inserts a primitive geometric object at a given position.
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These objects can be boxes, cylinders, or ellipsoids.
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""", version = scriptID)
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parser.add_option('-c', '--center',
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dest='center',
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type='float', nargs = 3, metavar=' '.join(['float']*3),
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help='a,b,c origin of primitive %default')
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parser.add_option('-d', '--dimension',
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dest='dimension',
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type='float', nargs = 3, metavar=' '.join(['float']*3),
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help='a,b,c extension of hexahedral box')
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parser.add_option('-e', '--exponent',
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dest='exponent',
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type='float', nargs = 3, metavar=' '.join(['float']*3),
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help='i,j,k exponents for axes: '+
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'0 gives octahedron (|x|^(2^0) + |y|^(2^0) + |z|^(2^0) < 1), '+
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'1 gives a sphere (|x|^(2^1) + |y|^(2^1) + |z|^(2^1) < 1), '+
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'large values produce boxes, negative turn concave.')
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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='microstructure index to fill primitive, defaults to max microstructure index + 1')
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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 of primitive as quaternion')
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parser.add_option('-a', '--angleaxis',
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dest='angleaxis',
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type=float, nargs = 4, metavar=' '.join(['float']*4),
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help = 'axis and angle to rotate primitive')
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parser.add_option( '--degrees',
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dest='degrees',
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action='store_true',
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help = 'angle is given in degrees')
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parser.add_option( '--nonperiodic',
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dest='periodic',
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action='store_false',
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help = 'wrap around edges')
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parser.add_option( '--realspace',
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dest='realspace',
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action='store_true',
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help = '-c and -d span [origin,origin+size] instead of [0,grid] coordinates')
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parser.add_option( '--invert',
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dest='inside',
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action='store_false',
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help = 'invert the volume filled by the primitive (inside/outside)')
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parser.set_defaults(center = (.0,.0,.0),
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degrees = False,
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exponent = (20,20,20), # box shape by default
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periodic = True,
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realspace = False,
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inside = True,
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)
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(options, filenames) = parser.parse_args()
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if options.dimension is None:
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parser.error('no dimension specified.')
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if [options.angleaxis,options.quaternion].count(None) == 0:
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parser.error('more than one rotation specified.')
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if options.angleaxis is not None:
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rotation = damask.Rotation.fromAxisAngle(np.array(options.angleaxis),options.degrees,normalise=True)
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elif options.quaternion is not None:
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rotation = damask.Rotation.fromQuaternion(options.quaternion)
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else:
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rotation = damask.Rotation()
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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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grid = geom.get_grid()
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size = geom.get_size()
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# scale to box of size [1.0,1.0,1.0]
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if options.realspace:
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center = (np.array(options.center) - geom.get_origin())/size
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r = np.array(options.dimension)/size/2.0
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else:
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center = (np.array(options.center) + 0.5)/grid
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r = np.array(options.dimension)/grid/2.0
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if np.any(center<0.0) or np.any(center>=1.0): print('error')
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offset = np.ones(3)*0.5 if options.periodic else center
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mask = np.full(grid,False)
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# High exponents can cause underflow & overflow - okay here, just compare to 1, so +infinity and 0 are fine
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np.seterr(over='ignore', under='ignore')
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e = 2.0**np.array(options.exponent)
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for x in range(grid[0]):
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for y in range(grid[1]):
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for z in range(grid[2]):
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coords = np.array([x+0.5,y+0.5,z+0.5])/grid
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mask[x,y,z] = np.sum(np.abs((rotation*(coords-offset))/r)**e) < 1
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if options.periodic:
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shift = ((offset-center)*grid).astype(int)
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mask = np.roll(mask,shift,(0,1,2))
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if options.inside: mask = np.logical_not(mask)
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fill = np.nanmax(geom.microstructure)+1 if options.fill is None else options.fill
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damask.util.croak(geom.update(np.where(mask,geom.microstructure,fill)))
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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,pack=False)
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