fixed systematic drift of grain structure along -[1,1,1]
correction of periodic Gauss kernel extension, inclusion of ndimage.gaussian_filter alternative (same runtime as FFT), proper output handling of grids <3D
This commit is contained in:
Philip Eisenlohr
parent
40de6910b8
commit
cb95f3b244
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@ -22,32 +22,46 @@ The final geometry is assembled by selecting at each voxel that grain index for
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""", version = scriptID)
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parser.add_option('-d', '--distance', dest='d', type='int', metavar='int',
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help='diffusion distance in voxels [%default]')
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parser.add_option('-N', '--smooth', dest='N', type='int', metavar='int',
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help='N for curvature flow [%default]')
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parser.add_option('-r', '--renumber', dest='renumber', action='store_true',
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help='renumber microstructure indices from 1...N [%default]')
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parser.add_option('-i', '--immutable', action='extend', dest='immutable', metavar = '<int LIST>',
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help='list of immutable microstructures')
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parser.add_option('-d', '--distance',
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dest = 'd',
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type = 'float', metavar = 'float',
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help = 'diffusion distance in voxels [%default]')
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parser.add_option('-N', '--iterations',
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dest = 'N',
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type = 'int', metavar = 'int',
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help = 'curvature flow iterations [%default]')
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parser.add_option('-i', '--immutable',
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action = 'extend', dest = 'immutable', metavar = '<int LIST>',
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help = 'list of immutable microstructure indices')
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parser.add_option('-r', '--renumber',
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dest = 'renumber', action='store_true',
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help = 'output consecutive microstructure indices')
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parser.add_option('--ndimage',
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dest = 'ndimage', action='store_true',
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help = 'use ndimage.gaussian_filter in lieu of explicit FFT')
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parser.set_defaults(d = 1)
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parser.set_defaults(N = 1)
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parser.set_defaults(renumber = False)
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parser.set_defaults(immutable = [])
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parser.set_defaults(d = 1,
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N = 1,
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immutable = [],
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renumber = False,
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ndimage = False,
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)
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(options, filenames) = parser.parse_args()
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options.immutable = map(int,options.immutable)
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# --- loop over input files -------------------------------------------------------------------------
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getInterfaceEnergy = lambda A,B: (A*B != 0)*(A != B)*1.0 # 1.0 if A & B are distinct & nonzero, 0.0 otherwise
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struc = ndimage.generate_binary_structure(3,1) # 3D von Neumann neighborhood
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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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@ -56,12 +70,12 @@ for name in filenames:
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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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damask.util.croak(['grid a b c: {}'.format(' x '.join(map(str,info['grid']))),
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'size x y z: {}'.format(' x '.join(map(str,info['size']))),
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'origin x y z: {}'.format(' : '.join(map(str,info['origin']))),
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'homogenization: {}'.format(info['homogenization']),
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'microstructures: {}'.format(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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@ -71,39 +85,35 @@ for name in filenames:
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table.close(dismiss = True)
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continue
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# --- read data ------------------------------------------------------------------------------------
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microstructure = np.tile(np.array(table.microstructure_read(info['grid']),'i').reshape(info['grid'],order='F'),
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np.where(info['grid'] == 1, 2,1)) # make one copy along dimensions with grid == 1
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# --- read data -----------------------------------------------------------------------------------
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microstructure = np.tile(table.microstructure_read(info['grid']).reshape(info['grid'],order='F'),
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np.where(info['grid'] == 1, 2,1)) # make one copy along dimensions with grid == 1
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grid = np.array(microstructure.shape)
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#--- initialize support data -----------------------------------------------------------------------
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# --- initialize support data ---------------------------------------------------------------------
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# store a copy the initial microstructure to find locations of immutable indices
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microstructure_original = np.copy(microstructure)
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X,Y,Z = np.mgrid[0:grid[0],0:grid[1],0:grid[2]]
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if not options.ndimage:
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X,Y,Z = np.mgrid[0:grid[0],0:grid[1],0:grid[2]]
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# Calculates gaussian weights for simulating 3d diffusion
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gauss = np.exp(-(X*X + Y*Y + Z*Z)/(2.0*options.d*options.d))/math.pow(2.0*np.pi*options.d*options.d,1.5)
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gauss[:,:,grid[2]/2::] = gauss[:,:,int(round(grid[2]/2.))-1::-1] # trying to cope with uneven (odd) grid size
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gauss[:,grid[1]/2::,:] = gauss[:,int(round(grid[1]/2.))-1::-1,:]
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gauss[grid[0]/2::,:,:] = gauss[int(round(grid[0]/2.))-1::-1,:,:]
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gauss = np.fft.rfftn(gauss)
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getInterfaceEnergy = lambda A,B: (A*B != 0)*(A != B)*1.0 # 1.0 if A & B are distinct & nonzero, 0.0 otherwise
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struc = ndimage.generate_binary_structure(3,1) # 3D von Neumann neighborhood
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# Calculates gaussian weights for simulating 3d diffusion
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gauss = np.exp(-(X*X + Y*Y + Z*Z)/(2.0*options.d*options.d)) \
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/math.pow(2.0*np.pi*options.d*options.d,(3.0 - np.count_nonzero(info['grid'] == 1))/2.)
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gauss[:,:,:grid[2]/2:-1] = gauss[:,:,1:(grid[2]+1)/2] # trying to cope with uneven (odd) grid size
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gauss[:,:grid[1]/2:-1,:] = gauss[:,1:(grid[1]+1)/2,:]
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gauss[:grid[0]/2:-1,:,:] = gauss[1:(grid[0]+1)/2,:,:]
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gauss = np.fft.rfftn(gauss)
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for smoothIter in range(options.N):
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periodic_microstructure = np.tile(microstructure,(3,3,3))[grid[0]/2:-grid[0]/2,
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grid[1]/2:-grid[1]/2,
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grid[2]/2:-grid[2]/2] # periodically extend the microstructure
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interfaceEnergy = np.zeros(microstructure.shape)
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for i in (-1,0,1):
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for j in (-1,0,1):
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for k in (-1,0,1):
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# assign interfacial energy to all voxels that have a differing neighbor (in Moore neighborhood)
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# assign interfacial energy to all voxels that have a differing neighbor (in Moore neighborhood)
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interfaceEnergy = np.maximum(interfaceEnergy,
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getInterfaceEnergy(microstructure,np.roll(np.roll(np.roll(
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microstructure,i,axis=0), j,axis=1), k,axis=2)))
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@ -112,44 +122,65 @@ for name in filenames:
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periodic_interfaceEnergy = np.tile(interfaceEnergy,(3,3,3))[grid[0]/2:-grid[0]/2,
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grid[1]/2:-grid[1]/2,
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grid[2]/2:-grid[2]/2]
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# transform bulk volume (i.e. where interfacial energy is zero)
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# transform bulk volume (i.e. where interfacial energy remained zero), store index of closest boundary voxel
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index = ndimage.morphology.distance_transform_edt(periodic_interfaceEnergy == 0.,
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return_distances = False,
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return_indices = True)
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# want array index of nearest voxel on periodically extended boundary
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periodic_bulkEnergy = periodic_interfaceEnergy[index[0],
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index[1],
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index[2]].reshape(2*grid) # fill bulk with energy of nearest interface
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diffusedEnergy = np.fft.irfftn(np.fft.rfftn(
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np.where(
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ndimage.morphology.binary_dilation(interfaceEnergy > 0.,
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structure = struc,
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iterations = options.d/2 + 1), # fat boundary | PE: why 2d-1? I would argue for d/2 + 1
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periodic_bulkEnergy[grid[0]/2:-grid[0]/2, # retain filled energy on fat boundary...
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grid[1]/2:-grid[1]/2,
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grid[2]/2:-grid[2]/2], # ...and zero everywhere else
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0.))*gauss)
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periodic_diffusedEnergy = np.tile(diffusedEnergy,(3,3,3))[grid[0]/2:-grid[0]/2,
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grid[1]/2:-grid[1]/2,
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grid[2]/2:-grid[2]/2] # periodically extend the smoothed bulk energy
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# transform voxels close to interface region | question PE: what motivates 1/2 (could be any small number, or)?
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index = ndimage.morphology.distance_transform_edt(periodic_diffusedEnergy >= 0.5,
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index[2]].reshape(2*grid) # fill bulk with energy of nearest interface
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if options.ndimage:
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periodic_diffusedEnergy = ndimage.gaussian_filter(
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np.where(ndimage.morphology.binary_dilation(periodic_interfaceEnergy > 0.,
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structure = struc,
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iterations = int(round(options.d*2.)), # fat boundary
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),
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periodic_bulkEnergy, # ...and zero everywhere else
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0.),
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sigma = options.d)
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else:
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diffusedEnergy = np.fft.irfftn(np.fft.rfftn(
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np.where(
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ndimage.morphology.binary_dilation(interfaceEnergy > 0.,
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structure = struc,
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iterations = int(round(options.d*2.))),# fat boundary
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periodic_bulkEnergy[grid[0]/2:-grid[0]/2, # retain filled energy on fat boundary...
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grid[1]/2:-grid[1]/2,
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grid[2]/2:-grid[2]/2], # ...and zero everywhere else
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0.))*gauss)
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periodic_diffusedEnergy = np.tile(diffusedEnergy,(3,3,3))[grid[0]/2:-grid[0]/2,
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grid[1]/2:-grid[1]/2,
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grid[2]/2:-grid[2]/2] # periodically extend the smoothed bulk energy
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# transform voxels close to interface region
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index = ndimage.morphology.distance_transform_edt(periodic_diffusedEnergy >= 0.5*np.amax(periodic_diffusedEnergy),
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return_distances = False,
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return_indices = True) # want index of closest bulk grain
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return_indices = True) # want index of closest bulk grain
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periodic_microstructure = np.tile(microstructure,(3,3,3))[grid[0]/2:-grid[0]/2,
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grid[1]/2:-grid[1]/2,
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grid[2]/2:-grid[2]/2] # periodically extend the microstructure
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microstructure = periodic_microstructure[index[0],
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index[1],
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index[2]].reshape(2*grid)[grid[0]/2:-grid[0]/2,
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grid[1]/2:-grid[1]/2,
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grid[2]/2:-grid[2]/2] # extent grains into interface region
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grid[2]/2:-grid[2]/2] # extent grains into interface region
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immutable = np.zeros(microstructure.shape, dtype=bool)
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# find locations where immutable microstructures have been or are now
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for micro in options.immutable:
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immutable += np.logical_or(microstructure == micro, microstructure_original == micro)
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# undo any changes involving immutable microstructures
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microstructure = np.where(immutable, microstructure_original,microstructure)
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immutable += np.logical_or(microstructure == micro, microstructure_original == micro)
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# --- renumber to sequence 1...Ngrains if requested ------------------------------------------------
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# undo any changes involving immutable microstructures
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microstructure = np.where(immutable, microstructure_original,microstructure)
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# --- renumber to sequence 1...Ngrains if requested -----------------------------------------------
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# http://stackoverflow.com/questions/10741346/np-frequency-counts-for-unique-values-in-an-array
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if options.renumber:
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@ -162,13 +193,14 @@ for name in filenames:
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newInfo = {'microstructures': 0,}
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newInfo['microstructures'] = microstructure.max()
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# --- report ---------------------------------------------------------------------------------------
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# --- report --------------------------------------------------------------------------------------
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remarks = []
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if (newInfo['microstructures'] != info['microstructures']): remarks.append('--> microstructures: %i'%newInfo['microstructures'])
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if newInfo['microstructures'] != info['microstructures']:
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remarks.append('--> microstructures: {}'.format(newInfo['microstructures']))
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if remarks != []: damask.util.croak(remarks)
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# --- write header ---------------------------------------------------------------------------------
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# --- write header --------------------------------------------------------------------------------
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table.labels_clear()
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table.info_clear()
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@ -185,8 +217,11 @@ for name in filenames:
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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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table.data = microstructure[::1 if info['grid'][0]>1 else 2,
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::1 if info['grid'][1]>1 else 2,
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::1 if info['grid'][2]>1 else 2,].\
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reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
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table.data_writeArray('%{}i'.format(formatwidth),delimiter = ' ')
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# --- output finalization --------------------------------------------------------------------------
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