diff --git a/processing/pre/geom_grainGrowth.py b/processing/pre/geom_grainGrowth.py index b6c1953c4..9b354762c 100755 --- a/processing/pre/geom_grainGrowth.py +++ b/processing/pre/geom_grainGrowth.py @@ -22,32 +22,46 @@ The final geometry is assembled by selecting at each voxel that grain index for """, version = scriptID) -parser.add_option('-d', '--distance', dest='d', type='int', metavar='int', - help='diffusion distance in voxels [%default]') -parser.add_option('-N', '--smooth', dest='N', type='int', metavar='int', - help='N for curvature flow [%default]') -parser.add_option('-r', '--renumber', dest='renumber', action='store_true', - help='renumber microstructure indices from 1...N [%default]') -parser.add_option('-i', '--immutable', action='extend', dest='immutable', metavar = '', - help='list of immutable microstructures') +parser.add_option('-d', '--distance', + dest = 'd', + type = 'float', metavar = 'float', + help = 'diffusion distance in voxels [%default]') +parser.add_option('-N', '--iterations', + dest = 'N', + type = 'int', metavar = 'int', + help = 'curvature flow iterations [%default]') +parser.add_option('-i', '--immutable', + action = 'extend', dest = 'immutable', metavar = '', + help = 'list of immutable microstructure indices') +parser.add_option('-r', '--renumber', + dest = 'renumber', action='store_true', + help = 'output consecutive microstructure indices') +parser.add_option('--ndimage', + dest = 'ndimage', action='store_true', + help = 'use ndimage.gaussian_filter in lieu of explicit FFT') -parser.set_defaults(d = 1) -parser.set_defaults(N = 1) -parser.set_defaults(renumber = False) -parser.set_defaults(immutable = []) +parser.set_defaults(d = 1, + N = 1, + immutable = [], + renumber = False, + ndimage = False, + ) (options, filenames) = parser.parse_args() options.immutable = map(int,options.immutable) -# --- loop over input files ------------------------------------------------------------------------- +getInterfaceEnergy = lambda A,B: (A*B != 0)*(A != B)*1.0 # 1.0 if A & B are distinct & nonzero, 0.0 otherwise +struc = ndimage.generate_binary_structure(3,1) # 3D von Neumann neighborhood + +# --- loop over input files ----------------------------------------------------------------------- if filenames == []: filenames = [None] for name in filenames: - try: - table = damask.ASCIItable(name = name, - buffered = False, labeled = False) + try: table = damask.ASCIItable(name = name, + buffered = False, + labeled = False) except: continue damask.util.report(scriptName,name) @@ -56,12 +70,12 @@ for name in filenames: table.head_read() info,extra_header = table.head_getGeom() - damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))), - 'size x y z: %s'%(' x '.join(map(str,info['size']))), - 'origin x y z: %s'%(' : '.join(map(str,info['origin']))), - 'homogenization: %i'%info['homogenization'], - 'microstructures: %i'%info['microstructures'], - ]) + damask.util.croak(['grid a b c: {}'.format(' x '.join(map(str,info['grid']))), + 'size x y z: {}'.format(' x '.join(map(str,info['size']))), + 'origin x y z: {}'.format(' : '.join(map(str,info['origin']))), + 'homogenization: {}'.format(info['homogenization']), + 'microstructures: {}'.format(info['microstructures']), + ]) errors = [] if np.any(info['grid'] < 1): errors.append('invalid grid a b c.') @@ -71,39 +85,35 @@ for name in filenames: table.close(dismiss = True) continue -# --- read data ------------------------------------------------------------------------------------ - microstructure = np.tile(np.array(table.microstructure_read(info['grid']),'i').reshape(info['grid'],order='F'), - np.where(info['grid'] == 1, 2,1)) # make one copy along dimensions with grid == 1 +# --- read data ----------------------------------------------------------------------------------- + microstructure = np.tile(table.microstructure_read(info['grid']).reshape(info['grid'],order='F'), + np.where(info['grid'] == 1, 2,1)) # make one copy along dimensions with grid == 1 grid = np.array(microstructure.shape) -#--- initialize support data ----------------------------------------------------------------------- - +# --- initialize support data --------------------------------------------------------------------- # store a copy the initial microstructure to find locations of immutable indices microstructure_original = np.copy(microstructure) - X,Y,Z = np.mgrid[0:grid[0],0:grid[1],0:grid[2]] + if not options.ndimage: + X,Y,Z = np.mgrid[0:grid[0],0:grid[1],0:grid[2]] - # Calculates gaussian weights for simulating 3d diffusion - 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) - gauss[:,:,grid[2]/2::] = gauss[:,:,int(round(grid[2]/2.))-1::-1] # trying to cope with uneven (odd) grid size - gauss[:,grid[1]/2::,:] = gauss[:,int(round(grid[1]/2.))-1::-1,:] - gauss[grid[0]/2::,:,:] = gauss[int(round(grid[0]/2.))-1::-1,:,:] - gauss = np.fft.rfftn(gauss) - - getInterfaceEnergy = lambda A,B: (A*B != 0)*(A != B)*1.0 # 1.0 if A & B are distinct & nonzero, 0.0 otherwise - struc = ndimage.generate_binary_structure(3,1) # 3D von Neumann neighborhood + # Calculates gaussian weights for simulating 3d diffusion + 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,(3.0 - np.count_nonzero(info['grid'] == 1))/2.) + + gauss[:,:,:grid[2]/2:-1] = gauss[:,:,1:(grid[2]+1)/2] # trying to cope with uneven (odd) grid size + gauss[:,:grid[1]/2:-1,:] = gauss[:,1:(grid[1]+1)/2,:] + gauss[:grid[0]/2:-1,:,:] = gauss[1:(grid[0]+1)/2,:,:] + gauss = np.fft.rfftn(gauss) for smoothIter in range(options.N): - periodic_microstructure = np.tile(microstructure,(3,3,3))[grid[0]/2:-grid[0]/2, - grid[1]/2:-grid[1]/2, - grid[2]/2:-grid[2]/2] # periodically extend the microstructure interfaceEnergy = np.zeros(microstructure.shape) for i in (-1,0,1): for j in (-1,0,1): for k in (-1,0,1): - # assign interfacial energy to all voxels that have a differing neighbor (in Moore neighborhood) + # assign interfacial energy to all voxels that have a differing neighbor (in Moore neighborhood) interfaceEnergy = np.maximum(interfaceEnergy, getInterfaceEnergy(microstructure,np.roll(np.roll(np.roll( microstructure,i,axis=0), j,axis=1), k,axis=2))) @@ -112,44 +122,65 @@ for name in filenames: periodic_interfaceEnergy = np.tile(interfaceEnergy,(3,3,3))[grid[0]/2:-grid[0]/2, grid[1]/2:-grid[1]/2, grid[2]/2:-grid[2]/2] - # transform bulk volume (i.e. where interfacial energy is zero) + + # transform bulk volume (i.e. where interfacial energy remained zero), store index of closest boundary voxel index = ndimage.morphology.distance_transform_edt(periodic_interfaceEnergy == 0., return_distances = False, return_indices = True) + # want array index of nearest voxel on periodically extended boundary periodic_bulkEnergy = periodic_interfaceEnergy[index[0], index[1], - index[2]].reshape(2*grid) # fill bulk with energy of nearest interface - diffusedEnergy = np.fft.irfftn(np.fft.rfftn( - np.where( - ndimage.morphology.binary_dilation(interfaceEnergy > 0., - structure = struc, - iterations = options.d/2 + 1), # fat boundary | PE: why 2d-1? I would argue for d/2 + 1 - periodic_bulkEnergy[grid[0]/2:-grid[0]/2, # retain filled energy on fat boundary... - grid[1]/2:-grid[1]/2, - grid[2]/2:-grid[2]/2], # ...and zero everywhere else - 0.))*gauss) - periodic_diffusedEnergy = np.tile(diffusedEnergy,(3,3,3))[grid[0]/2:-grid[0]/2, - grid[1]/2:-grid[1]/2, - grid[2]/2:-grid[2]/2] # periodically extend the smoothed bulk energy - # transform voxels close to interface region | question PE: what motivates 1/2 (could be any small number, or)? - index = ndimage.morphology.distance_transform_edt(periodic_diffusedEnergy >= 0.5, + index[2]].reshape(2*grid) # fill bulk with energy of nearest interface + if options.ndimage: + periodic_diffusedEnergy = ndimage.gaussian_filter( + np.where(ndimage.morphology.binary_dilation(periodic_interfaceEnergy > 0., + structure = struc, + iterations = int(round(options.d*2.)), # fat boundary + ), + periodic_bulkEnergy, # ...and zero everywhere else + 0.), + sigma = options.d) + else: + diffusedEnergy = np.fft.irfftn(np.fft.rfftn( + np.where( + ndimage.morphology.binary_dilation(interfaceEnergy > 0., + structure = struc, + iterations = int(round(options.d*2.))),# fat boundary + periodic_bulkEnergy[grid[0]/2:-grid[0]/2, # retain filled energy on fat boundary... + grid[1]/2:-grid[1]/2, + grid[2]/2:-grid[2]/2], # ...and zero everywhere else + 0.))*gauss) + + periodic_diffusedEnergy = np.tile(diffusedEnergy,(3,3,3))[grid[0]/2:-grid[0]/2, + grid[1]/2:-grid[1]/2, + grid[2]/2:-grid[2]/2] # periodically extend the smoothed bulk energy + + + # transform voxels close to interface region + index = ndimage.morphology.distance_transform_edt(periodic_diffusedEnergy >= 0.5*np.amax(periodic_diffusedEnergy), return_distances = False, - return_indices = True) # want index of closest bulk grain + return_indices = True) # want index of closest bulk grain + + periodic_microstructure = np.tile(microstructure,(3,3,3))[grid[0]/2:-grid[0]/2, + grid[1]/2:-grid[1]/2, + grid[2]/2:-grid[2]/2] # periodically extend the microstructure + microstructure = periodic_microstructure[index[0], index[1], index[2]].reshape(2*grid)[grid[0]/2:-grid[0]/2, grid[1]/2:-grid[1]/2, - grid[2]/2:-grid[2]/2] # extent grains into interface region + grid[2]/2:-grid[2]/2] # extent grains into interface region immutable = np.zeros(microstructure.shape, dtype=bool) # find locations where immutable microstructures have been or are now for micro in options.immutable: - immutable += np.logical_or(microstructure == micro, microstructure_original == micro) - # undo any changes involving immutable microstructures - microstructure = np.where(immutable, microstructure_original,microstructure) + immutable += np.logical_or(microstructure == micro, microstructure_original == micro) -# --- renumber to sequence 1...Ngrains if requested ------------------------------------------------ + # undo any changes involving immutable microstructures + microstructure = np.where(immutable, microstructure_original,microstructure) + +# --- renumber to sequence 1...Ngrains if requested ----------------------------------------------- # http://stackoverflow.com/questions/10741346/np-frequency-counts-for-unique-values-in-an-array if options.renumber: @@ -162,13 +193,14 @@ for name in filenames: newInfo = {'microstructures': 0,} newInfo['microstructures'] = microstructure.max() -# --- report --------------------------------------------------------------------------------------- +# --- report -------------------------------------------------------------------------------------- remarks = [] - if (newInfo['microstructures'] != info['microstructures']): remarks.append('--> microstructures: %i'%newInfo['microstructures']) + if newInfo['microstructures'] != info['microstructures']: + remarks.append('--> microstructures: {}'.format(newInfo['microstructures'])) if remarks != []: damask.util.croak(remarks) -# --- write header --------------------------------------------------------------------------------- +# --- write header -------------------------------------------------------------------------------- table.labels_clear() table.info_clear() @@ -185,8 +217,11 @@ for name in filenames: # --- write microstructure information ------------------------------------------------------------ formatwidth = int(math.floor(math.log10(microstructure.max())+1)) - table.data = microstructure.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose() - table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ') + table.data = microstructure[::1 if info['grid'][0]>1 else 2, + ::1 if info['grid'][1]>1 else 2, + ::1 if info['grid'][2]>1 else 2,].\ + reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose() + table.data_writeArray('%{}i'.format(formatwidth),delimiter = ' ') # --- output finalization --------------------------------------------------------------------------