192 lines
8.1 KiB
Python
Executable File
192 lines
8.1 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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Depending on the sign of the dimension parameters, 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 - 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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options.center = np.array(options.center)
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options.dimension = np.array(options.dimension)
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# undo logarithmic sense of exponent and generate ellipsoids for negative dimensions (backward compatibility)
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options.exponent = np.where(np.array(options.dimension) > 0, np.power(2,options.exponent), 2)
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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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origin = geom.get_origin()
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microstructure = geom.get_microstructure()
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# coordinates given in real space, not (default) voxel space
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if options.realspace:
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options.center -= origin
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options.center *= grid / size
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options.dimension *= grid / size
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# change to coordinate space where the primitive is the unit sphere/cube/etc
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if options.periodic: # use padding to achieve periodicity
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(X, Y, Z) = np.meshgrid(np.arange(-grid[0]/2, (3*grid[0])/2, dtype=np.float32), # 50% padding on each side
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np.arange(-grid[1]/2, (3*grid[1])/2, dtype=np.float32),
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np.arange(-grid[2]/2, (3*grid[2])/2, dtype=np.float32),
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indexing='ij')
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# Padding handling
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X = np.roll(np.roll(np.roll(X,
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-grid[0]//2, axis=0),
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-grid[1]//2, axis=1),
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-grid[2]//2, axis=2)
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Y = np.roll(np.roll(np.roll(Y,
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-grid[0]//2, axis=0),
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-grid[1]//2, axis=1),
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-grid[2]//2, axis=2)
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Z = np.roll(np.roll(np.roll(Z,
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-grid[0]//2, axis=0),
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-grid[1]//2, axis=1),
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-grid[2]//2, axis=2)
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else: # nonperiodic, much lighter on resources
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# change to coordinate space where the primitive is the unit sphere/cube/etc
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(X, Y, Z) = np.meshgrid(np.arange(0, grid[0], dtype=np.float32),
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np.arange(0, grid[1], dtype=np.float32),
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np.arange(0, grid[2], dtype=np.float32),
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indexing='ij')
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# first by translating the center onto 0, 0.5 shifts the voxel origin onto the center of the voxel
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X -= options.center[0] - 0.5
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Y -= options.center[1] - 0.5
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Z -= options.center[2] - 0.5
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# and then by applying the rotation
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(X, Y, Z) = rotation * (X, Y, Z)
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# and finally by scaling (we don't worry about options.dimension being negative, np.abs occurs on the microstructure = np.where... line)
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X /= options.dimension[0] * 0.5
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Y /= options.dimension[1] * 0.5
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Z /= options.dimension[2] * 0.5
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fill = np.nanmax(microstructure)+1 if options.fill is None else options.fill
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# High exponents can cause underflow & overflow - loss of precision is okay here, we just compare it to 1, so +infinity and 0 are fine
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old_settings = np.seterr()
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np.seterr(over='ignore', under='ignore')
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if options.periodic: # use padding to achieve periodicity
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inside = np.zeros(grid, dtype=bool)
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for i in range(2):
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for j in range(2):
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for k in range(2):
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inside = inside | ( # Most of this is handling the padding
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np.abs(X[grid[0] * i : grid[0] * (i+1),
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grid[1] * j : grid[1] * (j+1),
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grid[2] * k : grid[2] * (k+1)])**options.exponent[0] +
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np.abs(Y[grid[0] * i : grid[0] * (i+1),
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grid[1] * j : grid[1] * (j+1),
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grid[2] * k : grid[2] * (k+1)])**options.exponent[1] +
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np.abs(Z[grid[0] * i : grid[0] * (i+1),
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grid[1] * j : grid[1] * (j+1),
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grid[2] * k : grid[2] * (k+1)])**options.exponent[2] <= 1.0)
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microstructure = np.where(inside,
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fill if options.inside else microstructure,
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microstructure if options.inside else fill)
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else: # nonperiodic, much lighter on resources
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microstructure = np.where(np.abs(X)**options.exponent[0] +
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np.abs(Y)**options.exponent[1] +
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np.abs(Z)**options.exponent[2] <= 1.0,
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fill if options.inside else microstructure,
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microstructure if options.inside else fill)
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damask.util.croak(geom.update(microstructure))
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geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
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if name is None:
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sys.stdout.write(str(geom.show()))
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else:
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geom.to_file(name)
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