first draft of a constraint voronoi tessellation to match grain distribution
This commit is contained in:
Martin Diehl
parent
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#!/usr/bin/python
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# -*- coding: UTF-8 no BOM -*-
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import threading,time,os,subprocess,shlex,string,sys,random
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import numpy as np
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from optparse import OptionParser
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from operator import mul
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from cStringIO import StringIO
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import damask
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scriptID = '$Id: yieldSurface.py 3390 2014-08-18 20:09:09Z MPIE\m.diehl $'
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scriptName = scriptID.split()[1]
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mismatch = None
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currentSeedsName = None
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def execute(cmd,streamIn=None,dir='./'):
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initialPath=os.getcwd()
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os.chdir(dir)
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process = subprocess.Popen(shlex.split(cmd),stdout=subprocess.PIPE,stderr = subprocess.PIPE,stdin=subprocess.PIPE)
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if streamIn != None:
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out,error = process.communicate(streamIn.read())
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else:
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out,error = process.communicate()
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os.chdir(initialPath)
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return out,error
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#---------------------------------------------------------------------------------------------------
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class myThread (threading.Thread):
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#---------------------------------------------------------------------------------------------------
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'''
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Runner class
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'''
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def __init__(self, threadID):
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threading.Thread.__init__(self)
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self.threadID = threadID
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def run(self):
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global mismatch
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global bestSeedsUpdate
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global bestSeedsVFile
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global nMicrostructures
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global delta
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global points
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global target
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global match
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global baseFile
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s.acquire()
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myMatch = match
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s.release()
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random.seed(options.randomSeed+self.threadID)
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knownSeedsUpdate = bestSeedsUpdate -1.0
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randReset = True
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myBestSeedsVFile = StringIO()
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perturbedSeedsVFile = StringIO()
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perturbedGeomVFile = StringIO()
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while not match:
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# if a better seed file exist, read it into a virtual file
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s.acquire()
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if bestSeedsUpdate > knownSeedsUpdate:
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print 'Thread %i: '%self.threadID+'Reading new best seeds from', bestSeedsUpdate
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knownSeedsUpdate = bestSeedsUpdate
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bestSeedsVFile.reset()
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myBestSeedsVFile.close()
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myBestSeedsVFile = StringIO()
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i=0
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for line in bestSeedsVFile:
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myBestSeedsVFile.write(line)
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s.release()
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# new direction if current one is not good
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if randReset:
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selectedMs = random.randrange(1,nMicrostructures)
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direction = np.array(((random.random()-0.5)*delta[0],
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(random.random()-0.5)*delta[1],
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(random.random()-0.5)*delta[2]))
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randReset = False
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# set virtual file pointer to the beginning
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perturbedSeedsVFile.close()
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perturbedSeedsVFile = StringIO()
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myBestSeedsVFile.reset()
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# perturbe current best fitting seed file (virtual file lastSeedsVFile)
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perturbedSeedsTable = damask.ASCIItable(myBestSeedsVFile,
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perturbedSeedsVFile,
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labels=True)
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perturbedSeedsTable.head_read() # read ASCII header info
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perturbedSeedsTable.head_write()
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outputAlive=True
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ms = 1
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while outputAlive and perturbedSeedsTable.data_read():
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if ms == selectedMs:
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direction+=direction
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newCoords=np.array(tuple(map(float,perturbedSeedsTable.data[0:3]))+direction)
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np.where(newCoords>=1.0,newCoords-1.0,newCoords)
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np.where(newCoords <1.0,newCoords+1.0,newCoords)
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#print ms,perturbedSeedsTable.data[0:3],'-->',[format(f, '8.6f') for f in newCoords]
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perturbedSeedsTable.data[0:3]=[format(f, '8.6f') for f in newCoords]
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ms+=1
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perturbedSeedsTable.data_write()
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# do tesselation with perturbed seed file and evaluate geometry
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perturbedGeomVFile.close()
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perturbedGeomVFile = StringIO()
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perturbedSeedsVFile.reset()
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perturbedGeomVFile.write(execute('geom_fromVoronoiTessellation '+
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' -g '+' '.join(map(str, options.grid)),streamIn=perturbedSeedsVFile)[0])
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perturbedGeomVFile.reset()
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perturbedGeomTable = damask.ASCIItable(perturbedGeomVFile,labels=False)
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perturbedGeomTable.head_read()
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for i in perturbedGeomTable.info:
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if i.startswith('microstructures'): myNmicrostructures = int(i.split('\t')[1])
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perturbedGeomTable.data_readArray()
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perturbedGeomTable.output_flush()
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currentData=np.bincount(perturbedGeomTable.data.astype(int).ravel())[1:]/points
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currentError=[]
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currentHist=[]
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for i in xrange(nMicrostructures):
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currentHist.append(np.histogram(currentData,bins=target[i]['bins'])[0])
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currentError.append(np.sqrt(np.square(np.array(target[i]['histogram']-currentHist[i])).sum()))
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s.acquire()
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myMatch = match
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print 'Thread %i: finished tessellation (%i microstructures)'%(self.threadID, myNmicrostructures)
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if currentError[nMicrostructures-1] == 0.0:
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print 'finished'
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match = True
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if match: return
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if myNmicrostructures != nMicrostructures:
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print 'microstructure mismatch %i'%myNmicrostructures
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randReset = True
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else:
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for i in xrange(nMicrostructures):
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ratio = target[i]['error']/currentError[i]
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if currentError[i] > target[i]['error']:
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print '%i decreased quality to %8.6f'%(i+2,ratio)
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print 'target',target[i]['histogram']
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print 'current',currentHist[i]
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randReset = True
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break
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elif currentError[i] < target[i]['error']:
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bestSeedsUpdate = time.time()
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print '%i increased quality to %8.6f'%(i+2,ratio)
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print 'target',target[i]['histogram']
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print 'current',currentHist[i]
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print 'Thread', self.threadID, 'new best fit. time,', bestSeedsUpdate
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currentSeedsName = baseFile+'_'+str(bestSeedsUpdate).replace('.','-')
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perturbedSeedsVFile.reset()
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bestSeedsVFile.close()
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bestSeedsVFile = StringIO()
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with open(currentSeedsName+'.seeds','w') as currentSeedsFile:
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for line in perturbedSeedsVFile:
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currentSeedsFile.write(line)
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bestSeedsVFile.write(line)
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for j in xrange(nMicrostructures):
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target[j]['error'] = currentError[j]
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break
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if i == nMicrostructures-1: print 'continue along trajectory '
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s.release()
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Monte Carlo simulation to produce seed file that gives same size distribution like given geometry file.
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""", version=string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-s','--seeds', dest='seedFile', metavar='string',
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help='name of the intial seed file. If not found, a new one is created [%default]')
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parser.add_option('-g','--grid', dest='grid', type='int', nargs=3, metavar='int int int',
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help='a,b,c grid of hexahedral box [%default]')
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parser.add_option('-t','--threads', dest='threads', type='int', metavar='int',
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help='number of parallel executions [%default]')
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parser.add_option('-r', '--rnd', dest='randomSeed', type='int', metavar='int',
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help='seed of random number generator [%default]')
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parser.add_option('--target', dest='target', metavar='string',
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help='name of the geom file with target distribution [%default]')
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parser.add_option('--tolerance', dest='threshold', type='float', metavar='float',
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help='stopping criterion [%default]')
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parser.add_option('--scale', dest='scale',type='float', metavar='float',
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help='maximum moving distance of perturbed seed in pixel [%default]')
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parser.set_defaults(seedFile = 'seeds')
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parser.set_defaults(grid = (64,64,64))
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parser.set_defaults(threads = 2)
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parser.set_defaults(randomSeed = None)
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parser.set_defaults(target = 'geom')
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parser.set_defaults(threshold = 1.0)
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parser.set_defaults(scale = 1.0)
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options = parser.parse_args()[0]
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if options.randomSeed == None:
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options.randomSeed = int(os.urandom(4).encode('hex'), 16)
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print 'random seed', options.randomSeed
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delta = (options.scale/options.grid[0],options.scale/options.grid[1],options.scale/options.grid[2])
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baseFile=os.path.splitext(os.path.basename(options.seedFile))[0]
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points = float(reduce(mul,options.grid))
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# ----------- calculate target distribution and bin edges
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targetGeomVFile=StringIO()
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with open(os.path.splitext(os.path.basename(options.target))[0]+'.geom') as targetGeomFile:
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targetGeomTable = damask.ASCIItable(targetGeomFile,targetGeomVFile,labels=False)
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targetGeomTable.head_read()
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targetGeomTable.head_write()
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for i in targetGeomTable.info:
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if i.startswith('microstructures'): nMicrostructures = int(i.split()[1])
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if i.startswith('grid'): targetPoints = float(int(i.split()[2])*\
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int(i.split()[4])*\
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int(i.split()[6]))
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targetGeomTable.data_readArray()
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targetGeomTable.data_writeArray()
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targetData = np.bincount(targetGeomTable.data.astype(int).ravel())[1:nMicrostructures]/targetPoints
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target=[]
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for i in xrange(1,nMicrostructures+1):
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targetHist,targetBins = np.histogram(targetData,bins=i)
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target.append({'histogram':targetHist,'bins':targetBins})
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targetGeomVFile.close()
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# ----------- create initial seed file or open existing one
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bestSeedsVFile = StringIO()
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if os.path.isfile(os.path.splitext(options.seedFile)[0]+'.seeds'):
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with open(os.path.splitext(options.seedFile)[0]+'.seeds') as initialSeedFile:
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for line in initialSeedFile: bestSeedsVFile.write(line)
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else:
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bestSeedsVFile.write(execute('seeds_fromRandom'+\
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' -g '+' '.join(map(str, options.grid))+\
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' -r %i'%options.randomSeed+\
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' -N '+str(nMicrostructures))[0])
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bestSeedsUpdate = time.time()
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# ----------- tessellate initial seed file to get and evaluate geom file
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bestSeedsVFile.reset()
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initialGeomVFile = StringIO()
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initialGeomVFile.write(execute('geom_fromVoronoiTessellation '+
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' -g '+' '.join(map(str, options.grid)),bestSeedsVFile)[0])
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initialGeomVFile.reset()
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initialGeomTable = damask.ASCIItable(initialGeomVFile,labels=False)
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initialGeomTable.head_read()
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for i in initialGeomTable.info:
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if i.startswith('microstructures'): initialMicrostructures = int(i.split('\t')[1])
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if initialMicrostructures != nMicrostructures: print 'error. Microstructure count mismatch'
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initialGeomTable.data_readArray()
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initialData = np.bincount(initialGeomTable.data.astype(int).ravel())[1:]/points
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for i in xrange(nMicrostructures):
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initialHist = np.histogram(initialData,bins=target[i]['bins'])[0]
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target[i]['error']=np.sqrt(np.square(np.array(target[i]['histogram']-initialHist)).sum())
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print target[i]['histogram']
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print initialHist
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print target[i]['error'],'\n-----------------------------------'
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match = target[nMicrostructures-1]==0.0
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initialGeomVFile.close()
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# strart mulithreaded monte carlo simulation
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threads=[]
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s=threading.Semaphore(1)
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for i in range(options.threads):
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threads.append(myThread(i))
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threads[i].start()
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for i in range(options.threads):
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threads[i].join()
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