negated option from "voxelspace" to "realspace".

introduced logarithmic sense of curvature exponents, additional polishing
This commit is contained in:
Philip Eisenlohr 2017-08-03 12:08:51 -04:00
parent 67ad20a1c7
commit 84a3885af8
1 changed files with 45 additions and 45 deletions

View File

@ -36,8 +36,9 @@ parser.add_option('-c', '--center', dest='center', type='float', nargs = 3,
parser.add_option('-d', '--dimension', dest='dimension', type='float', nargs = 3, metavar=' '.join(['float']*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), 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 \ help='i,j,k exponents for axes - 0 gives octahedron (|x|^(2^0) + |y|^(2^0) + |z|^(2^0) < 1), \
octahedron (|x| + |y| + |z| < 1). Large values produce boxes, 0 - 1 is concave. ') 1 gives a sphere (|x|^(2^1) + |y|^(2^1) + |z|^(2^1) < 1), \
large values produce boxes, negative turns 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),
@ -48,15 +49,14 @@ 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', parser.add_option( '--nonperiodic', dest='periodic', action='store_false',
help = 'wrap around edges [%default]') help = 'wrap around edges [%default]')
parser.add_option( '--voxelspace', dest='voxelspace', action='store_true', parser.add_option( '--realspace', dest='realspace', action='store_true',
help = '-c and -d are given in (0 to grid) coordinates instead of (origin to origin+size) \ help = '-c and -d span [origin,origin+size] instead of [0,grid] coordinates')
coordinates [%default]')
parser.set_defaults(center = (.0,.0,.0), parser.set_defaults(center = (.0,.0,.0),
fill = 0, fill = 0,
degrees = False, degrees = False,
exponent = (1e10,1e10,1e10), # box shape by default exponent = (1e10,1e10,1e10), # box shape by default
periodic = True, periodic = True,
voxelspace = False realspace = False,
) )
(options, filenames) = parser.parse_args() (options, filenames) = parser.parse_args()
@ -74,14 +74,15 @@ else:
options.center = np.array(options.center) options.center = np.array(options.center)
options.dimension = np.array(options.dimension) options.dimension = np.array(options.dimension)
options.exponent = np.power(2,options.exponent) # undo logarithmic sense of exponent
# --- loop over input files ------------------------------------------------------------------------- # --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None] if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
try: try: table = damask.ASCIItable(name = name,
table = damask.ASCIItable(name = name, buffered = False,
buffered = False, labeled = False) labeled = False)
except: continue except: continue
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
@ -115,45 +116,44 @@ for name in filenames:
'microstructures': 0, 'microstructures': 0,
} }
if options.fill == 0: options.fill = microstructure.max()+1 if options.fill == 0 else options.fill
options.fill = microstructure.max()+1
# If we have a negative dimension, make it an ellipsoid for backwards compatibility # 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) 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')
# coordinates given in real space (default) vs voxel space # coordinates given in real space (default) vs voxel space
if not options.voxelspace: if options.realspace:
options.center += info['origin'] options.center -= info['origin']
options.center *= np.array(info['grid']) / np.array(info['size']) options.center *= np.array(info['grid']) / np.array(info['size'])
options.dimension *= np.array(info['grid']) / np.array(info['size']) options.dimension *= np.array(info['grid']) / np.array(info['size'])
size = microstructure.shape grid = microstructure.shape
# change to coordinate space where the primitive is the unit sphere/cube/etc # change to coordinate space where the primitive is the unit sphere/cube/etc
if options.periodic: # use padding to achieve periodicity if options.periodic: # use padding to achieve periodicity
(X, Y, Z) = np.meshgrid(np.arange(-size[0]/2, (3*size[0])/2, dtype=np.float32), # 50% padding on each side (X, Y, Z) = np.meshgrid(np.arange(-grid[0]/2, (3*grid[0])/2, dtype=np.float32), # 50% padding on each side
np.arange(-size[1]/2, (3*size[1])/2, dtype=np.float32), np.arange(-grid[1]/2, (3*grid[1])/2, dtype=np.float32),
np.arange(-size[2]/2, (3*size[2])/2, dtype=np.float32), np.arange(-grid[2]/2, (3*grid[2])/2, dtype=np.float32),
indexing='ij') indexing='ij')
# Padding handling # Padding handling
X = np.roll(np.roll(np.roll(X, X = np.roll(np.roll(np.roll(X,
-size[0]/2, axis=0), -grid[0]/2, axis=0),
-size[1]/2, axis=1), -grid[1]/2, axis=1),
-size[2]/2, axis=2) -grid[2]/2, axis=2)
Y = np.roll(np.roll(np.roll(Y, Y = np.roll(np.roll(np.roll(Y,
-size[0]/2, axis=0), -grid[0]/2, axis=0),
-size[1]/2, axis=1), -grid[1]/2, axis=1),
-size[2]/2, axis=2) -grid[2]/2, axis=2)
Z = np.roll(np.roll(np.roll(Z, Z = np.roll(np.roll(np.roll(Z,
-size[0]/2, axis=0), -grid[0]/2, axis=0),
-size[1]/2, axis=1), -grid[1]/2, axis=1),
-size[2]/2, axis=2) -grid[2]/2, axis=2)
else: # nonperiodic, much lighter on resources else: # nonperiodic, much lighter on resources
# change to coordinate space where the primitive is the unit sphere/cube/etc # change to coordinate space where the primitive is the unit sphere/cube/etc
(X, Y, Z) = np.meshgrid(np.arange(0, size[0], dtype=np.float32), (X, Y, Z) = np.meshgrid(np.arange(0, grid[0], dtype=np.float32),
np.arange(0, size[1], dtype=np.float32), np.arange(0, grid[1], dtype=np.float32),
np.arange(0, size[2], dtype=np.float32), np.arange(0, grid[2], dtype=np.float32),
indexing='ij') indexing='ij')
# first by translating the center onto 0, 0.5 shifts the voxel origin onto the center of the voxel # first by translating the center onto 0, 0.5 shifts the voxel origin onto the center of the voxel
@ -174,27 +174,27 @@ for name in filenames:
np.seterr(over='ignore', under='ignore') np.seterr(over='ignore', under='ignore')
if options.periodic: # use padding to achieve periodicity if options.periodic: # use padding to achieve periodicity
inside = np.zeros(size, dtype=bool) inside = np.zeros(grid, dtype=bool)
for i in range(2): for i in range(2):
for j in range(2): for j in range(2):
for k in range(2): for k in range(2):
inside = inside | ( # Most of this is handling the padding inside = inside | ( # Most of this is handling the padding
np.abs(X[size[0] * i : size[0] * (i+1), np.abs(X[grid[0] * i : grid[0] * (i+1),
size[1] * j : size[1] * (j+1), grid[1] * j : grid[1] * (j+1),
size[2] * k : size[2] * (k+1)])**options.exponent[0] + grid[2] * k : grid[2] * (k+1)])**options.exponent[0] +
np.abs(Y[size[0] * i : size[0] * (i+1), np.abs(Y[grid[0] * i : grid[0] * (i+1),
size[1] * j : size[1] * (j+1), grid[1] * j : grid[1] * (j+1),
size[2] * k : size[2] * (k+1)])**options.exponent[1] + grid[2] * k : grid[2] * (k+1)])**options.exponent[1] +
np.abs(Z[size[0] * i : size[0] * (i+1), np.abs(Z[grid[0] * i : grid[0] * (i+1),
size[1] * j : size[1] * (j+1), grid[1] * j : grid[1] * (j+1),
size[2] * k : size[2] * (k+1)])**options.exponent[2] < 1) grid[2] * k : grid[2] * (k+1)])**options.exponent[2] <= 1.0)
microstructure = np.where(inside, options.fill, microstructure) microstructure = np.where(inside, options.fill, microstructure)
else: # nonperiodic, much lighter on resources else: # nonperiodic, much lighter on resources
microstructure = np.where(np.abs(X)**options.exponent[0] + microstructure = np.where(np.abs(X)**options.exponent[0] +
np.abs(Y)**options.exponent[1] + np.abs(Y)**options.exponent[1] +
np.abs(Z)**options.exponent[2] < 1, options.fill, microstructure) np.abs(Z)**options.exponent[2] <= 1.0, options.fill, microstructure)
np.seterr(**old_settings) # Reset warnings to old state np.seterr(**old_settings) # Reset warnings to old state
newInfo['microstructures'] = microstructure.max() newInfo['microstructures'] = microstructure.max()
@ -209,11 +209,11 @@ for name in filenames:
table.info_clear() table.info_clear()
table.info_append([ table.info_append([
scriptID + ' ' + ' '.join(sys.argv[1:]), scriptID + ' ' + ' '.join(sys.argv[1:]),
"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=info['grid']), "grid\ta {}\tb {}\tc {}".format(*info['grid']),
"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['size']), "size\tx {}\ty {}\tz {}".format(*info['size']),
"origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']), "origin\tx {}\ty {}\tz {}".format(*info['origin']),
"homogenization\t{homog}".format(homog=info['homogenization']), "homogenization\t{}".format(info['homogenization']),
"microstructures\t{microstructures}".format(microstructures=newInfo['microstructures']), "microstructures\t{}".format(newInfo['microstructures']),
extra_header extra_header
]) ])
table.labels_clear() table.labels_clear()