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.
This commit is contained in:
Brendan Vande Kieft 2017-02-24 00:33:47 -05:00
parent 007495cb71
commit e5e6bed5de
1 changed files with 84 additions and 27 deletions

View File

@ -33,24 +33,31 @@ Depending on the sign of the dimension parameters, these objects can be boxes, c
""", version = scriptID) """, 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') 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') 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', parser.add_option('-f', '--fill', dest='fill', type='int', metavar = 'int',
help='grain index to fill primitive. "0" selects maximum microstructure index + 1 [%default]') 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), parser.add_option('-q', '--quaternion', dest='quaternion', type='float', nargs = 4, metavar=' '.join(['float']*4),
help = 'rotation of primitive as quaternion') help = 'rotation of primitive as quaternion')
parser.add_option('-a', '--angleaxis', dest='angleaxis', nargs = 4, metavar=' '.join(['float']*4), 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', parser.add_option( '--degrees', dest='degrees', action='store_true',
help = 'angle is given in degrees [%default]') 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], parser.set_defaults(center = [0,0,0],
fill = 0, fill = 0,
quaternion = [], quaternion = [],
angleaxis = [], angleaxis = [],
degrees = False, degrees = False,
exponent = [1e10,1e10,1e10], # box shape by default
periodic = True
) )
(options, filenames) = parser.parse_args() (options, filenames) = parser.parse_args()
@ -58,15 +65,14 @@ parser.set_defaults(center = [0,0,0],
if options.angleaxis != []: if options.angleaxis != []:
options.angleaxis = map(float,options.angleaxis) options.angleaxis = map(float,options.angleaxis)
rotation = damask.Quaternion().fromAngleAxis(np.radians(options.angleaxis[0]) if options.degrees else options.angleaxis[0], 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 != []: elif options.quaternion != []:
options.quaternion = map(float,options.quaternion) options.quaternion = map(float,options.quaternion)
rotation = damask.Quaternion(options.quaternion).conjugated() rotation = damask.Quaternion(options.quaternion)
else: else:
rotation = damask.Quaternion().conjugated() rotation = damask.Quaternion()
options.center = np.array(options.center) options.center = np.array(options.center)
invRotation = rotation.conjugated() # rotation of gridpos into primitive coordinate system
# --- loop over input files ------------------------------------------------------------------------- # --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None] if filenames == []: filenames = [None]
@ -108,33 +114,84 @@ for name in filenames:
'microstructures': 0, 'microstructures': 0,
} }
if options.fill == 0: if options.fill == 0:
options.fill = microstructure.max()+1 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') microstructure = microstructure.reshape(info['grid'],order='F')
if options.dimension is not None: size = microstructure.shape
mask = (np.array(options.dimension) < 0).astype(float) # zero where positive dimension, otherwise one
dim = abs(np.array(options.dimension)) # dimensions of primitive body if options.periodic: # use padding to achieve periodicity
pos = np.zeros(3,dtype='float') # change to coordinate space where the primitive is the unit sphere/cube/etc
# hiresPrimitive = np.zeros((2*dim[0],2*dim[1],2*dim[2],3)) # primitive discretized at twice the grid resolution (Y, X, Z) = np.meshgrid(np.arange(-size[0], 2*size[0], dtype=np.float64),
for i,pos[0] in enumerate(np.arange(-dim[0]/oversampling,(dim[0]+1)/oversampling,1./oversampling)): np.arange(-size[1], 2*size[1], dtype=np.float64),
for j,pos[1] in enumerate(np.arange(-dim[1]/oversampling,(dim[1]+1)/oversampling,1./oversampling)): np.arange(-size[2], 2*size[2], dtype=np.float64))
for k,pos[2] in enumerate(np.arange(-dim[2]/oversampling,(dim[2]+1)/oversampling,1./oversampling)): # first by translating the center onto 0, 0.5 shifts the voxel origin onto the center of the voxel
gridpos = np.floor(rotation*pos) # rotate and lock into spacial grid X -= options.center[0] - 0.5
primPos = invRotation*gridpos # rotate back to primitive coordinate system Y -= options.center[1] - 0.5
if np.dot(mask*primPos/dim,mask*primPos/dim) <= 0.25 and \ Z -= options.center[2] - 0.5
np.all(abs((1.-mask)*primPos/dim) <= 0.5): # inside ellipsoid and inside box # and then by applying the quaternion
microstructure[int((gridpos[0]+options.center[0])%info['grid'][0]), # this should be rotation.conjugate() * (X,Y,Z), but it is this way for backwards compatibility with the older version of this script
int((gridpos[1]+options.center[1])%info['grid'][1]), (X, Y, Z) = rotation * (X, Y, Z)
int((gridpos[2]+options.center[2])%info['grid'][2])] = options.fill # assign microstructure index # 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() newInfo['microstructures'] = microstructure.max()
# --- report --------------------------------------------------------------------------------------- # --- report ---------------------------------------------------------------------------------------
if ( newInfo['microstructures'] != info['microstructures']): if (newInfo['microstructures'] != info['microstructures']):
damask.util.croak('--> microstructures: %i'%newInfo['microstructures']) damask.util.croak('--> microstructures: %i'%newInfo['microstructures'])