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DAMASK_EICMD
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added immutable option

This commit is contained in:
Pratheek Shanthraj 2014-06-05 17:18:52 +00:00
parent 4d3b09030c
commit 522efaac92
1 changed files with 22 additions and 6 deletions
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28
processing/pre/geom_grainGrowth.py
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@ -63,10 +63,13 @@ 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', type='string', \
help='immutable microstructures')
parser.set_defaults(d = 1)
parser.set_defaults(N = 1)
parser.set_defaults(renumber = False)
parser.set_defaults(immutable = [0])
(options, filenames) = parser.parse_args()
@ -172,6 +175,7 @@ for file in files:
interfacialEnergy = lambda A,B: (A*B != 0)*(A != B)*1.0
struc = ndimage.generate_binary_structure(3,1)
microstructure_original = numpy.copy(microstructure)
for smoothIter in xrange(options.N):
boundary = numpy.zeros(microstructure.shape)
for i in range(3):
@ -179,13 +183,20 @@ for file in files:
for k in range(3):
boundary = numpy.maximum(boundary,
interfacialEnergy(microstructure,numpy.roll(numpy.roll(numpy.roll(
microstructure,i-1,axis=0),j-1,axis=1),k-1,axis=2)))
index = ndimage.morphology.distance_transform_edt(boundary == 0.,return_distances = False,return_indices = True)
boundary = numpy.fft.irfftn(numpy.fft.rfftn(numpy.where(ndimage.morphology.binary_dilation(boundary != 0.,
microstructure,i-1,axis=0),j-1,axis=1),k-1,axis=2)))
boundaryExt = numpy.tile(boundary,(3,3,3))
boundaryExt = boundaryExt[(expandedGrid[0])/2:-(expandedGrid[0])/2,
(expandedGrid[1])/2:-(expandedGrid[1])/2,
(expandedGrid[2])/2:-(expandedGrid[2])/2]
index = ndimage.morphology.distance_transform_edt(boundaryExt == 0.,return_distances = False,return_indices = True) # array index of nearest voxel on periodically extended boundary
boundaryExt = boundaryExt[index[0].flatten(),index[1].flatten(),index[2].flatten()].reshape(boundaryExt.shape) # fill bulk with energy of nearest interface
boundary = numpy.fft.irfftn(numpy.fft.rfftn(numpy.where(ndimage.morphology.binary_dilation(boundary > 0.,
structure = struc,
iterations = 2*options.d-1),
boundary[index[0].flatten(),index[1].flatten(),index[2].flatten()].reshape(microstructure.shape),
0.))*gauss)
iterations = 2*options.d-1), # fat boundary
boundaryExt[(expandedGrid[0])/2:-(expandedGrid[0])/2, # retain filled energy on fat boundary
(expandedGrid[1])/2:-(expandedGrid[1])/2,
(expandedGrid[2])/2:-(expandedGrid[2])/2],
0.))*gauss) # zero everywhere else
boundaryExt = numpy.tile(boundary,(3,3,3))
boundaryExt = boundaryExt[(expandedGrid[0])/2:-(expandedGrid[0])/2,
(expandedGrid[1])/2:-(expandedGrid[1])/2,
@ -199,6 +210,11 @@ for file in files:
microstructure = microstructureExt[(expandedGrid[0])/2:-(expandedGrid[0])/2,
(expandedGrid[1])/2:-(expandedGrid[1])/2,
(expandedGrid[2])/2:-(expandedGrid[2])/2]
immutable = numpy.zeros(microstructure.shape, dtype=bool)
for micro in options.immutable:
immutable = numpy.logical_or(immutable, numpy.logical_or(microstructure == int(micro), microstructure_original == int(micro)))
microstructure = numpy.where(immutable, microstructure_original,microstructure)
# --- renumber to sequence 1...Ngrains if requested ------------------------------------------------
# http://stackoverflow.com/questions/10741346/numpy-frequency-counts-for-unique-values-in-an-array