230 lines
11 KiB
Python
Executable File
230 lines
11 KiB
Python
Executable File
#!/usr/bin/env python2.7
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,math
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import numpy as np
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from optparse import OptionParser
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import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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identifiers = {
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'grid': ['a','b','c'],
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'size': ['x','y','z'],
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'origin': ['x','y','z'],
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}
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mappings = {
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'grid': lambda x: int(x),
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'size': lambda x: float(x),
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'origin': lambda x: float(x),
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'homogenization': lambda x: int(x),
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'microstructures': lambda x: int(x),
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}
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [geomfile(s)]', description = """
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Positions a geometric object within the (three-dimensional) canvas of a spectral geometry description.
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Depending on the sign of the dimension parameters, these objects can be boxes, cylinders, or ellipsoids.
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""", version = scriptID)
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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='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 - 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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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 = '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.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 = (20,20,20), # box shape by default
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periodic = True,
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realspace = False,
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)
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(options, filenames) = parser.parse_args()
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if options.dimension is None:
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parser.error('no dimension specified.')
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if options.angleaxis is not None:
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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])
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elif options.quaternion is not None:
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options.quaternion = map(float,options.quaternion)
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rotation = damask.Quaternion(options.quaternion)
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else:
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rotation = damask.Quaternion()
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options.center = np.array(options.center)
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options.dimension = np.array(options.dimension)
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# undo logarithmic sense of exponent and generate ellipsoids for negative dimensions (backward compatibility)
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options.exponent = np.where(np.array(options.dimension) > 0, np.power(2,options.exponent), 2)
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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: 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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# --- interpret header ----------------------------------------------------------------------------
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table.head_read()
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info,extra_header = table.head_getGeom()
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damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
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'size x y z: %s'%(' x '.join(map(str,info['size']))),
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'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
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'homogenization: %i'%info['homogenization'],
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'microstructures: %i'%info['microstructures'],
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])
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errors = []
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if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
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if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
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if errors != []:
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damask.util.croak(errors)
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table.close(dismiss = True)
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continue
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#--- read data ------------------------------------------------------------------------------------
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microstructure = table.microstructure_read(info['grid']) # read microstructure
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# --- do work ------------------------------------------------------------------------------------
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newInfo = {
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'microstructures': 0,
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}
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options.fill = microstructure.max()+1 if options.fill == 0 else options.fill
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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 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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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(-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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-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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-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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-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, 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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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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if options.periodic: # use padding to achieve periodicity
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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[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] <= 1.0, 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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# --- report ---------------------------------------------------------------------------------------
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if (newInfo['microstructures'] != info['microstructures']):
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damask.util.croak('--> microstructures: %i'%newInfo['microstructures'])
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#--- write header ---------------------------------------------------------------------------------
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table.info_clear()
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table.info_append(extra_header+[
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scriptID + ' ' + ' '.join(sys.argv[1:]),
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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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])
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table.labels_clear()
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table.head_write()
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table.output_flush()
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# --- write microstructure information ------------------------------------------------------------
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formatwidth = int(math.floor(math.log10(microstructure.max())+1))
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table.data = microstructure.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
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table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
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#--- output finalization --------------------------------------------------------------------------
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table.close()
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