Improve performance and generalize primitive shape
- Behavior is mostly unchanged, but the primitive may be shifted by a voxel when compared to the previous version, which had rounding issues near the edge of the primitive. - exponent flag specifies the exponents that satisfy the equation x^e1 + y^e2 + z^e3 < 1. (1,1,1) gives an octahedron, (2,2,2) a sphere, and large values (1e10, 1e10, 1e10) gives a hexahedral box for any reasonable resolution. Mixing the two can produce a cylinder, (1e10, 2, 2) gives one with rotational symmetry about the x-axis.
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Brendan Vande Kieft
parent
007495cb71
commit
e5e6bed5de
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@ -33,24 +33,31 @@ Depending on the sign of the dimension parameters, these objects can be boxes, c
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""", version = scriptID)
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parser.add_option('-c', '--center', dest='center', type='int', nargs = 3, metavar=' '.join(['int']*3),
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parser.add_option('-c', '--center', dest='center', 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', dest='dimension', type='int', nargs = 3, metavar=' '.join(['int']*3),
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parser.add_option('-d', '--dimension', dest='dimension', type='float', nargs = 3, metavar=' '.join(['float']*3),
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help='a,b,c extension of hexahedral box; negative values are diameters')
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parser.add_option('-e', '--exponent', dest='exponent', type='float', nargs = 3, metavar=' '.join(['float']*3),
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help='i,j,k exponents for axes - 2 gives a sphere (x^2 + y^2 + z^2 < 1), 1 makes \
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octahedron (|x| + |y| + |z| < 1). Large values produce boxes, 0 - 1 is concave. ')
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parser.add_option('-f', '--fill', dest='fill', type='int', metavar = 'int',
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help='grain index to fill primitive. "0" selects maximum microstructure index + 1 [%default]')
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parser.add_option('-q', '--quaternion', dest='quaternion', 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', dest='angleaxis', nargs = 4, metavar=' '.join(['float']*4),
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help = 'rotation of primitive as angle and axis')
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help = 'angle,x,y,z clockwise rotation of primitive about axis by angle')
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parser.add_option( '--degrees', dest='degrees', action='store_true',
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help = 'angle is given in degrees [%default]')
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parser.add_option( '--nonperiodic', dest='periodic', action='store_false',
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help = 'wrap around edges [%default]')
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parser.set_defaults(center = [0,0,0],
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fill = 0,
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quaternion = [],
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angleaxis = [],
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degrees = False,
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exponent = [1e10,1e10,1e10], # box shape by default
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periodic = True
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)
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(options, filenames) = parser.parse_args()
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@ -58,15 +65,14 @@ parser.set_defaults(center = [0,0,0],
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if options.angleaxis != []:
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options.angleaxis = map(float,options.angleaxis)
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rotation = damask.Quaternion().fromAngleAxis(np.radians(options.angleaxis[0]) if options.degrees else options.angleaxis[0],
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options.angleaxis[1:4]).conjugated()
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options.angleaxis[1:4])
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elif options.quaternion != []:
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options.quaternion = map(float,options.quaternion)
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rotation = damask.Quaternion(options.quaternion).conjugated()
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rotation = damask.Quaternion(options.quaternion)
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else:
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rotation = damask.Quaternion().conjugated()
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rotation = damask.Quaternion()
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options.center = np.array(options.center)
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invRotation = rotation.conjugated() # rotation of gridpos into primitive coordinate system
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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@ -108,33 +114,84 @@ for name in filenames:
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'microstructures': 0,
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}
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if options.fill == 0:
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options.fill = microstructure.max()+1
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# If we have a negative dimension, make it an ellipsoid for backwards compatibility
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options.exponent = np.where(np.array(options.dimension) > 0, options.exponent, 2)
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microstructure = microstructure.reshape(info['grid'],order='F')
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if options.dimension is not None:
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mask = (np.array(options.dimension) < 0).astype(float) # zero where positive dimension, otherwise one
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dim = abs(np.array(options.dimension)) # dimensions of primitive body
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pos = np.zeros(3,dtype='float')
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# hiresPrimitive = np.zeros((2*dim[0],2*dim[1],2*dim[2],3)) # primitive discretized at twice the grid resolution
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for i,pos[0] in enumerate(np.arange(-dim[0]/oversampling,(dim[0]+1)/oversampling,1./oversampling)):
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for j,pos[1] in enumerate(np.arange(-dim[1]/oversampling,(dim[1]+1)/oversampling,1./oversampling)):
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for k,pos[2] in enumerate(np.arange(-dim[2]/oversampling,(dim[2]+1)/oversampling,1./oversampling)):
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gridpos = np.floor(rotation*pos) # rotate and lock into spacial grid
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primPos = invRotation*gridpos # rotate back to primitive coordinate system
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if np.dot(mask*primPos/dim,mask*primPos/dim) <= 0.25 and \
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np.all(abs((1.-mask)*primPos/dim) <= 0.5): # inside ellipsoid and inside box
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microstructure[int((gridpos[0]+options.center[0])%info['grid'][0]),
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int((gridpos[1]+options.center[1])%info['grid'][1]),
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int((gridpos[2]+options.center[2])%info['grid'][2])] = options.fill # assign microstructure index
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size = microstructure.shape
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if options.periodic: # use padding to achieve periodicity
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# change to coordinate space where the primitive is the unit sphere/cube/etc
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(Y, X, Z) = np.meshgrid(np.arange(-size[0], 2*size[0], dtype=np.float64),
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np.arange(-size[1], 2*size[1], dtype=np.float64),
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np.arange(-size[2], 2*size[2], dtype=np.float64))
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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 quaternion
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# this should be rotation.conjugate() * (X,Y,Z), but it is this way for backwards compatibility with the older version of this script
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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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# 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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inside = np.zeros(size, dtype=bool)
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for i in range(3):
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for j in range(3):
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for k in range(3):
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inside = inside | ( # Most of this is handling the padding
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np.abs(X[size[0] * i : size[0] * (i+1),
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size[1] * j : size[1] * (j+1),
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size[2] * k : size[2] * (k+1)])**options.exponent[0] +
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np.abs(Y[size[0] * i : size[0] * (i+1),
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size[1] * j : size[1] * (j+1),
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size[2] * k : size[2] * (k+1)])**options.exponent[1] +
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np.abs(Z[size[0] * i : size[0] * (i+1),
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size[1] * j : size[1] * (j+1),
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size[2] * k : size[2] * (k+1)])**options.exponent[2] < 1)
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microstructure = np.where(inside, options.fill, microstructure)
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np.seterr(**old_settings) # Reset warnings to old state
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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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(Y, X, Z) = np.meshgrid(np.arange(0, size[0], dtype=np.float64),
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np.arange(0, size[1], dtype=np.float64),
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np.arange(0, size[2], dtype=np.float64))
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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 quaternion (the implementation of quat. does q*v*q.conj)
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# this should be rotation.conjugate() * (X,Y,Z), but it is this way for backwards compatibility with the older version of this script
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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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# 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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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, options.fill, microstructure)
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np.seterr(**old_settings) # Reset warnings to old state
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newInfo['microstructures'] = microstructure.max()
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# --- report ---------------------------------------------------------------------------------------
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if ( newInfo['microstructures'] != info['microstructures']):
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if (newInfo['microstructures'] != info['microstructures']):
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damask.util.croak('--> microstructures: %i'%newInfo['microstructures'])
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