DAMASK_EICMD/processing/pre/seeds_fromRandom.py

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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
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import os,sys,math,random
import numpy as np
import damask
from optparse import OptionParser,OptionGroup
from scipy import spatial
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# ------------------------------------------ aux functions ---------------------------------
def kdtree_search(cloud, queryPoints):
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"""find distances to nearest neighbor among cloud (N,d) for each of the queryPoints (n,d)"""
n = queryPoints.shape[0]
distances = np.zeros(n,dtype=float)
tree = spatial.cKDTree(cloud)
for i in xrange(n):
distances[i], index = tree.query(queryPoints[i])
return distances
# --------------------------------------------------------------------
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# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [options]', description = """
Distribute given number of points randomly within the three-dimensional cube [0.0,0.0,0.0]--[1.0,1.0,1.0].
Reports positions with random crystal orientations in seeds file format to STDOUT.
""", version = scriptID)
parser.add_option('-N', dest='N',
type = 'int', metavar = 'int',
help = 'number of seed points to distribute [%default]')
parser.add_option('-g','--grid',
dest = 'grid',
type = 'int', nargs = 3, metavar = 'int int int',
help='min a,b,c grid of hexahedral box %default')
parser.add_option('-m', '--microstructure',
dest = 'microstructure',
type = 'int', metavar='int',
help = 'first microstructure index [%default]')
parser.add_option('-r', '--rnd',
dest = 'randomSeed', type = 'int', metavar = 'int',
help = 'seed of random number generator [%default]')
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group = OptionGroup(parser, "Laguerre Tessellation Options",
"Parameters determining shape of weight distribution of seed points"
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)
group.add_option('-w', '--weights',
action = 'store_true',
dest = 'weights',
help = 'assign random weigts to seed points for Laguerre tessellation [%default]')
group.add_option('--max',
dest = 'max',
type = 'float', metavar = 'float',
help = 'max of uniform distribution for weights [%default]')
group.add_option('--mean',
dest = 'mean',
type = 'float', metavar = 'float',
help = 'mean of normal distribution for weights [%default]')
group.add_option('--sigma',
dest = 'sigma',
type = 'float', metavar = 'float',
help='standard deviation of normal distribution for weights [%default]')
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parser.add_option_group(group)
group = OptionGroup(parser, "Selective Seeding Options",
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"More uniform distribution of seed points using Mitchell\'s Best Candidate Algorithm"
)
group.add_option('-s','--selective',
action = 'store_true',
dest = 'selective',
help = 'selective picking of seed points from random seed points [%default]')
group.add_option('-f','--force',
action = 'store_true',
dest = 'force',
help = 'try selective picking despite large seed point number [%default]')
group.add_option('--distance',
dest = 'distance',
type = 'float', metavar = 'float',
help = 'minimum distance to the next neighbor [%default]')
group.add_option('--numCandidates',
dest = 'numCandidates',
type = 'int', metavar = 'int',
help = 'size of point group to select best distance from [%default]')
parser.add_option_group(group)
parser.set_defaults(randomSeed = None,
grid = (16,16,16),
N = 20,
weights = False,
max = 0.0,
mean = 0.2,
sigma = 0.05,
microstructure = 1,
selective = False,
force = False,
distance = 0.2,
numCandidates = 10,
)
(options,filenames) = parser.parse_args()
options.grid = np.array(options.grid)
gridSize = options.grid.prod()
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if options.randomSeed is None: options.randomSeed = int(os.urandom(4).encode('hex'), 16)
np.random.seed(options.randomSeed) # init random generators
random.seed(options.randomSeed)
# --- loop over output files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(outname = name,
buffered = False)
except:
continue
damask.util.report(scriptName,name)
# --- sanity checks -------------------------------------------------------------------------
remarks = []
errors = []
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if gridSize == 0:
errors.append('zero grid dimension for %s.'%(', '.join([['a','b','c'][x] for x in np.where(options.grid == 0)[0]])))
if options.N > gridSize/10.: errors.append('seed count exceeds 0.1 of grid points.')
if options.selective and 4./3.*math.pi*(options.distance/2.)**3*options.N > 0.5:
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(remarks if options.force else errors).append('maximum recommended seed point count for given distance is {}.{}'.
format(int(3./8./math.pi/(options.distance/2.)**3),'..'*options.force))
if remarks != []: damask.util.croak(remarks)
if errors != []:
damask.util.croak(errors)
sys.exit()
# --- do work ------------------------------------------------------------------------------------
grainEuler = np.random.rand(3,options.N) # create random Euler triplets
grainEuler[0,:] *= 360.0 # phi_1 is uniformly distributed
grainEuler[1,:] = np.degrees(np.arccos(2*grainEuler[1,:]-1)) # cos(Phi) is uniformly distributed
grainEuler[2,:] *= 360.0 # phi_2 is uniformly distributed
if not options.selective:
seeds = np.zeros((3,options.N),dtype='d') # seed positions array
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gridpoints = random.sample(range(gridSize),options.N) # choose first N from random permutation of grid positions
seeds[0,:] = (np.mod(gridpoints ,options.grid[0])\
+np.random.random(options.N)) /options.grid[0]
seeds[1,:] = (np.mod(gridpoints// options.grid[0] ,options.grid[1])\
+np.random.random(options.N)) /options.grid[1]
seeds[2,:] = (np.mod(gridpoints//(options.grid[1]*options.grid[0]),options.grid[2])\
+np.random.random(options.N)) /options.grid[2]
else:
seeds = np.zeros((options.N,3),dtype=float) # seed positions array
seeds[0] = np.random.random(3)*options.grid/max(options.grid)
i = 1 # start out with one given point
if i%(options.N/100.) < 1: damask.util.croak('.',False)
while i < options.N:
candidates = np.random.random(options.numCandidates*3).reshape(options.numCandidates,3)
distances = kdtree_search(seeds[:i],candidates)
best = distances.argmax()
if distances[best] > options.distance: # require minimum separation
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seeds[i] = candidates[best] # maximum separation to existing point cloud
i += 1
if i%(options.N/100.) < 1: damask.util.croak('.',False)
damask.util.croak('')
seeds = seeds.T # prepare shape for stacking
if options.weights:
if options.max > 0.0:
weights = [np.random.uniform(low = 0, high = options.max, size = options.N)]
else:
weights = [np.random.normal(loc = options.mean, scale = options.sigma, size = options.N)]
else:
weights = []
seeds = np.transpose(np.vstack(tuple([seeds,
grainEuler,
np.arange(options.microstructure,
options.microstructure + options.N),
] + weights
)))
# ------------------------------------------ assemble header ---------------------------------------
table.info_clear()
table.info_append([
scriptID + ' ' + ' '.join(sys.argv[1:]),
"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=options.grid),
"microstructures\t{}".format(options.N),
"randomSeed\t{}".format(options.randomSeed),
])
table.labels_clear()
table.labels_append( ['{dim}_{label}'.format(dim = 1+k,label = 'pos') for k in xrange(3)] +
['{dim}_{label}'.format(dim = 1+k,label = 'eulerangles') for k in xrange(3)] +
['microstructure'] +
(['weight'] if options.weights else []))
table.head_write()
table.output_flush()
# --- write seeds information ------------------------------------------------------------
table.data = seeds
table.data_writeArray()
# --- output finalization --------------------------------------------------------------------------
table.close() # close ASCII table