diff --git a/processing/pre/geom_addPrimitive.py b/processing/pre/geom_addPrimitive.py index 8d934368f..18a73c4e3 100755 --- a/processing/pre/geom_addPrimitive.py +++ b/processing/pre/geom_addPrimitive.py @@ -33,24 +33,31 @@ Depending on the sign of the dimension parameters, these objects can be boxes, c """, version = scriptID) -parser.add_option('-c', '--center', dest='center', type='int', nargs = 3, metavar=' '.join(['int']*3), +parser.add_option('-c', '--center', dest='center', type='float', nargs = 3, metavar=' '.join(['float']*3), help='a,b,c origin of primitive %default') -parser.add_option('-d', '--dimension', dest='dimension', type='int', nargs = 3, metavar=' '.join(['int']*3), +parser.add_option('-d', '--dimension', dest='dimension', type='float', nargs = 3, metavar=' '.join(['float']*3), help='a,b,c extension of hexahedral box; negative values are diameters') +parser.add_option('-e', '--exponent', dest='exponent', type='float', nargs = 3, metavar=' '.join(['float']*3), + help='i,j,k exponents for axes - 2 gives a sphere (x^2 + y^2 + z^2 < 1), 1 makes \ +octahedron (|x| + |y| + |z| < 1). Large values produce boxes, 0 - 1 is concave. ') parser.add_option('-f', '--fill', dest='fill', type='int', metavar = 'int', help='grain index to fill primitive. "0" selects maximum microstructure index + 1 [%default]') parser.add_option('-q', '--quaternion', dest='quaternion', type='float', nargs = 4, metavar=' '.join(['float']*4), help = 'rotation of primitive as quaternion') parser.add_option('-a', '--angleaxis', dest='angleaxis', nargs = 4, metavar=' '.join(['float']*4), - help = 'rotation of primitive as angle and axis') + help = 'angle,x,y,z clockwise rotation of primitive about axis by angle') parser.add_option( '--degrees', dest='degrees', action='store_true', help = 'angle is given in degrees [%default]') +parser.add_option( '--nonperiodic', dest='periodic', action='store_false', + help = 'wrap around edges [%default]') parser.set_defaults(center = [0,0,0], fill = 0, quaternion = [], angleaxis = [], degrees = False, + exponent = [1e10,1e10,1e10], # box shape by default + periodic = True ) (options, filenames) = parser.parse_args() @@ -58,15 +65,14 @@ parser.set_defaults(center = [0,0,0], if options.angleaxis != []: options.angleaxis = map(float,options.angleaxis) rotation = damask.Quaternion().fromAngleAxis(np.radians(options.angleaxis[0]) if options.degrees else options.angleaxis[0], - options.angleaxis[1:4]).conjugated() + options.angleaxis[1:4]) elif options.quaternion != []: options.quaternion = map(float,options.quaternion) - rotation = damask.Quaternion(options.quaternion).conjugated() + rotation = damask.Quaternion(options.quaternion) else: - rotation = damask.Quaternion().conjugated() + rotation = damask.Quaternion() options.center = np.array(options.center) -invRotation = rotation.conjugated() # rotation of gridpos into primitive coordinate system # --- loop over input files ------------------------------------------------------------------------- if filenames == []: filenames = [None] @@ -108,33 +114,84 @@ for name in filenames: 'microstructures': 0, } - if options.fill == 0: options.fill = microstructure.max()+1 - + + # If we have a negative dimension, make it an ellipsoid for backwards compatibility + options.exponent = np.where(np.array(options.dimension) > 0, options.exponent, 2) + microstructure = microstructure.reshape(info['grid'],order='F') - - if options.dimension is not None: - mask = (np.array(options.dimension) < 0).astype(float) # zero where positive dimension, otherwise one - dim = abs(np.array(options.dimension)) # dimensions of primitive body - pos = np.zeros(3,dtype='float') -# hiresPrimitive = np.zeros((2*dim[0],2*dim[1],2*dim[2],3)) # primitive discretized at twice the grid resolution - for i,pos[0] in enumerate(np.arange(-dim[0]/oversampling,(dim[0]+1)/oversampling,1./oversampling)): - for j,pos[1] in enumerate(np.arange(-dim[1]/oversampling,(dim[1]+1)/oversampling,1./oversampling)): - for k,pos[2] in enumerate(np.arange(-dim[2]/oversampling,(dim[2]+1)/oversampling,1./oversampling)): - gridpos = np.floor(rotation*pos) # rotate and lock into spacial grid - primPos = invRotation*gridpos # rotate back to primitive coordinate system - if np.dot(mask*primPos/dim,mask*primPos/dim) <= 0.25 and \ - np.all(abs((1.-mask)*primPos/dim) <= 0.5): # inside ellipsoid and inside box - microstructure[int((gridpos[0]+options.center[0])%info['grid'][0]), - int((gridpos[1]+options.center[1])%info['grid'][1]), - int((gridpos[2]+options.center[2])%info['grid'][2])] = options.fill # assign microstructure index + + size = microstructure.shape + + if options.periodic: # use padding to achieve periodicity + # change to coordinate space where the primitive is the unit sphere/cube/etc + (Y, X, Z) = np.meshgrid(np.arange(-size[0], 2*size[0], dtype=np.float64), + np.arange(-size[1], 2*size[1], dtype=np.float64), + np.arange(-size[2], 2*size[2], dtype=np.float64)) + # first by translating the center onto 0, 0.5 shifts the voxel origin onto the center of the voxel + X -= options.center[0] - 0.5 + Y -= options.center[1] - 0.5 + Z -= options.center[2] - 0.5 + # and then by applying the quaternion + # this should be rotation.conjugate() * (X,Y,Z), but it is this way for backwards compatibility with the older version of this script + (X, Y, Z) = rotation * (X, Y, Z) + # and finally by scaling (we don't worry about options.dimension being negative, np.abs occurs on the microstructure = np.where... line) + X /= options.dimension[0] * 0.5 + Y /= options.dimension[1] * 0.5 + Z /= options.dimension[2] * 0.5 + + # High exponents can cause underflow & overflow - loss of precision is okay here, we just compare it to 1, so +infinity and 0 are fine + old_settings = np.seterr() + np.seterr(over='ignore', under='ignore') + + inside = np.zeros(size, dtype=bool) + for i in range(3): + for j in range(3): + for k in range(3): + inside = inside | ( # Most of this is handling the padding + np.abs(X[size[0] * i : size[0] * (i+1), + size[1] * j : size[1] * (j+1), + size[2] * k : size[2] * (k+1)])**options.exponent[0] + + np.abs(Y[size[0] * i : size[0] * (i+1), + size[1] * j : size[1] * (j+1), + size[2] * k : size[2] * (k+1)])**options.exponent[1] + + np.abs(Z[size[0] * i : size[0] * (i+1), + size[1] * j : size[1] * (j+1), + size[2] * k : size[2] * (k+1)])**options.exponent[2] < 1) + + microstructure = np.where(inside, options.fill, microstructure) + np.seterr(**old_settings) # Reset warnings to old state + + else: # nonperiodic, much lighter on resources + # change to coordinate space where the primitive is the unit sphere/cube/etc + (Y, X, Z) = np.meshgrid(np.arange(0, size[0], dtype=np.float64), + np.arange(0, size[1], dtype=np.float64), + np.arange(0, size[2], dtype=np.float64)) + # first by translating the center onto 0, 0.5 shifts the voxel origin onto the center of the voxel + X -= options.center[0] - 0.5 + Y -= options.center[1] - 0.5 + Z -= options.center[2] - 0.5 + # and then by applying the quaternion (the implementation of quat. does q*v*q.conj) + # this should be rotation.conjugate() * (X,Y,Z), but it is this way for backwards compatibility with the older version of this script + (X, Y, Z) = rotation * (X, Y, Z) + # and finally by scaling (we don't worry about options.dimension being negative, np.abs occurs on the microstructure = np.where... line) + X /= options.dimension[0] * 0.5 + Y /= options.dimension[1] * 0.5 + Z /= options.dimension[2] * 0.5 + + # High exponents can cause underflow & overflow - loss of precision is okay here, we just compare it to 1, so +infinity and 0 are fine + old_settings = np.seterr() + np.seterr(over='ignore', under='ignore') + microstructure = np.where(np.abs(X)**options.exponent[0] + + np.abs(Y)**options.exponent[1] + + np.abs(Z)**options.exponent[2] < 1, options.fill, microstructure) + np.seterr(**old_settings) # Reset warnings to old state newInfo['microstructures'] = microstructure.max() - # --- report --------------------------------------------------------------------------------------- - if ( newInfo['microstructures'] != info['microstructures']): + if (newInfo['microstructures'] != info['microstructures']): damask.util.croak('--> microstructures: %i'%newInfo['microstructures'])