negated option from "voxelspace" to "realspace".
introduced logarithmic sense of curvature exponents, additional polishing
This commit is contained in:
Philip Eisenlohr
parent
67ad20a1c7
commit
84a3885af8
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@ -36,8 +36,9 @@ parser.add_option('-c', '--center', dest='center', type='float', nargs = 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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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 turns 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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@ -48,15 +49,14 @@ 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.add_option( '--voxelspace', dest='voxelspace', action='store_true',
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help = '-c and -d are given in (0 to grid) coordinates instead of (origin to origin+size) \
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coordinates [%default]')
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parser.add_option( '--realspace', dest='realspace', 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.set_defaults(center = (.0,.0,.0),
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fill = 0,
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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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voxelspace = False
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realspace = False,
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)
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(options, filenames) = parser.parse_args()
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@ -74,14 +74,15 @@ else:
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options.center = np.array(options.center)
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options.dimension = np.array(options.dimension)
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options.exponent = np.power(2,options.exponent) # undo logarithmic sense of exponent
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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for name in filenames:
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try:
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table = damask.ASCIItable(name = name,
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buffered = False, labeled = False)
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try: table = damask.ASCIItable(name = name,
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buffered = False,
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labeled = False)
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except: continue
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damask.util.report(scriptName,name)
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@ -115,45 +116,44 @@ 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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options.fill = microstructure.max()+1 if options.fill == 0 else options.fill
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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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# coordinates given in real space (default) vs voxel space
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if not options.voxelspace:
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options.center += info['origin']
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if options.realspace:
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options.center -= info['origin']
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options.center *= np.array(info['grid']) / np.array(info['size'])
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options.dimension *= np.array(info['grid']) / np.array(info['size'])
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size = microstructure.shape
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grid = microstructure.shape
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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(-size[0]/2, (3*size[0])/2, dtype=np.float32), # 50% padding on each side
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np.arange(-size[1]/2, (3*size[1])/2, dtype=np.float32),
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np.arange(-size[2]/2, (3*size[2])/2, dtype=np.float32),
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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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-size[0]/2, axis=0),
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-size[1]/2, axis=1),
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-size[2]/2, axis=2)
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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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-size[0]/2, axis=0),
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-size[1]/2, axis=1),
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-size[2]/2, axis=2)
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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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-size[0]/2, axis=0),
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-size[1]/2, axis=1),
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-size[2]/2, axis=2)
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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, size[0], dtype=np.float32),
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np.arange(0, size[1], dtype=np.float32),
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np.arange(0, size[2], dtype=np.float32),
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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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@ -174,27 +174,27 @@ for name in filenames:
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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(size, dtype=bool)
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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[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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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, options.fill, microstructure)
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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, options.fill, microstructure)
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np.abs(Z)**options.exponent[2] <= 1.0, 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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@ -209,11 +209,11 @@ for name in filenames:
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table.info_clear()
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table.info_append([
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scriptID + ' ' + ' '.join(sys.argv[1:]),
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"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=info['grid']),
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"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['size']),
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"origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']),
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"homogenization\t{homog}".format(homog=info['homogenization']),
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"microstructures\t{microstructures}".format(microstructures=newInfo['microstructures']),
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"grid\ta {}\tb {}\tc {}".format(*info['grid']),
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"size\tx {}\ty {}\tz {}".format(*info['size']),
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"origin\tx {}\ty {}\tz {}".format(*info['origin']),
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"homogenization\t{}".format(info['homogenization']),
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"microstructures\t{}".format(newInfo['microstructures']),
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extra_header
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])
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table.labels_clear()
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