#!/usr/bin/python # -*- coding: UTF-8 no BOM -*- import threading,time,os,subprocess,shlex,string,sys,random import numpy as np from optparse import OptionParser from operator import mul from cStringIO import StringIO import damask scriptID = string.replace('$Id$','\n','\\n') scriptName = os.path.splitext(scriptID.split()[1])[0] mismatch = None currentSeedsName = None def execute(cmd,streamIn=None,dir='./'): ''' executes a command in given directory and returns stdout and stderr for optional stdin ''' initialPath=os.getcwd() os.chdir(dir) process = subprocess.Popen(shlex.split(cmd),stdout=subprocess.PIPE,stderr = subprocess.PIPE,stdin=subprocess.PIPE) if streamIn != None: out,error = process.communicate(streamIn.read()) else: out,error = process.communicate() os.chdir(initialPath) return out,error #--------------------------------------------------------------------------------------------------- class myThread (threading.Thread): #--------------------------------------------------------------------------------------------------- ''' perturbes seed in seed file, performes Voronoi tessellation, evaluates, and updates best match ''' def __init__(self, threadID): threading.Thread.__init__(self) self.threadID = threadID def run(self): global bestSeedsUpdate global bestSeedsVFile global nMicrostructures global delta global points global target global match global baseFile global maxSeeds s.acquire() bestMatch = match s.release() random.seed(options.randomSeed+self.threadID) # initializes to given seeds knownSeedsUpdate = bestSeedsUpdate -1.0 # trigger update of local best seeds (time when the best seed file was found known to thread) randReset = True # aquire new direction myBestSeedsVFile = StringIO() # in-memory file to store local copy of best seeds file perturbedSeedsVFile = StringIO() # in-memory file for perturbed best seeds file perturbedGeomVFile = StringIO() # in-memory file for tessellated geom file #--- still not matching desired bin class ---------------------------------------------------------- while bestMatch < options.threshold: s.acquire() # accessing global data, ensure only one thread does it per time if bestSeedsUpdate > knownSeedsUpdate: # if a newer best seed file exist, read it into a virtual file knownSeedsUpdate = bestSeedsUpdate bestSeedsVFile.reset() myBestSeedsVFile.close() myBestSeedsVFile = StringIO() i=0 for line in bestSeedsVFile: myBestSeedsVFile.write(line) s.release() if randReset: # new direction because current one led to worse fit randReset = False NmoveGrains = random.randrange(1,maxSeeds) selectedMs = [] direction = [] for i in xrange(NmoveGrains): selectedMs.append(random.randrange(1,nMicrostructures)) direction.append(np.array(((random.random()-0.5)*delta[0], (random.random()-0.5)*delta[1], (random.random()-0.5)*delta[2]))) perturbedSeedsVFile.close() # reset virtual file perturbedSeedsVFile = StringIO() myBestSeedsVFile.reset() perturbedSeedsTable = damask.ASCIItable(myBestSeedsVFile,perturbedSeedsVFile,labeled=True) # read current best fitting seed file and to perturbed seed file perturbedSeedsTable.head_read() perturbedSeedsTable.head_write() outputAlive=True ms = 1 while outputAlive and perturbedSeedsTable.data_read(): # perturbe selected microstructure if ms in selectedMs: direction+=direction newCoords=np.array(tuple(map(float,perturbedSeedsTable.data[0:3]))+direction[i]) newCoords=np.where(newCoords>=1.0,newCoords-1.0,newCoords) # ensure that the seeds remain in the box (move one side out, other side in) newCoords=np.where(newCoords <0.0,newCoords+1.0,newCoords) perturbedSeedsTable.data[0:3]=[format(f, '8.6f') for f in newCoords] ms+=1 perturbedSeedsTable.data_write() #--- do tesselation with perturbed seed file ---------------------------------------------------------- perturbedGeomVFile.close() perturbedGeomVFile = StringIO() perturbedSeedsVFile.reset() perturbedGeomVFile.write(execute('geom_fromVoronoiTessellation '+ ' -g '+' '.join(map(str, options.grid)),streamIn=perturbedSeedsVFile)[0]) perturbedGeomVFile.reset() #--- evaluate current seeds file ---------------------------------------------------------------------- perturbedGeomTable = damask.ASCIItable(perturbedGeomVFile,labeled=False,readonly=True) perturbedGeomTable.head_read() for i in perturbedGeomTable.info: if i.startswith('microstructures'): myNmicrostructures = int(i.split('\t')[1]) perturbedGeomTable.data_readArray() perturbedGeomTable.output_flush() currentData=np.bincount(perturbedGeomTable.data.astype(int).ravel())[1:]/points currentError=[] currentHist=[] for i in xrange(nMicrostructures): # calculate the deviation in all bins per histogram currentHist.append(np.histogram(currentData,bins=target[i]['bins'])[0]) currentError.append(np.sqrt(np.square(np.array(target[i]['histogram']-currentHist[i])).sum())) if currentError[0]>0.0: # as long as not all grains are within the range of the target, use the deviation to left and right as error currentError[0] *=((target[0]['bins'][0]-np.min(currentData))**2.0+ (target[0]['bins'][1]-np.max(currentData))**2.0)**0.5 # norm of deviations by number of usual bin deviation s.acquire() # do the evaluation serially bestMatch = match #--- count bin classes with no mismatch ---------------------------------------------------------------------- myMatch=0 for i in xrange(nMicrostructures): if currentError[i] > 0.0: break myMatch = i+1 if myNmicrostructures == nMicrostructures: for i in xrange(min(nMicrostructures,myMatch+options.bins)): if currentError[i] > target[i]['error']: # worse fitting, next try randReset = True break elif currentError[i] < target[i]['error']: # better fit bestSeedsUpdate = time.time() # save time of better fit print 'Thread %i: Better match (%i bins, %6.4f --> %6.4f)'%(self.threadID,i+1,target[i]['error'],currentError[i]) print ' target: ',target[i]['histogram'] print ' best: ',currentHist[i] currentSeedsName = baseFile+'_'+str(bestSeedsUpdate).replace('.','-') # name of new seed file (use time as unique identifier) perturbedSeedsVFile.reset() bestSeedsVFile.close() bestSeedsVFile = StringIO() sys.stdout.flush() with open(currentSeedsName+'.seeds','w') as currentSeedsFile: # write to new file for line in perturbedSeedsVFile: currentSeedsFile.write(line) bestSeedsVFile.write(line) for j in xrange(nMicrostructures): # save new errors for all bins target[j]['error'] = currentError[j] if myMatch > match: # one or more new bins have no deviation print 'Stage %i cleared'%(myMatch) match=myMatch sys.stdout.flush() break if i == min(nMicrostructures,myMatch+options.bins)-1: # same quality as before (for the considered bins): take it to keep on moving bestSeedsUpdate = time.time() perturbedSeedsVFile.reset() bestSeedsVFile.close() bestSeedsVFile = StringIO() for line in perturbedSeedsVFile: bestSeedsVFile.write(line) for j in xrange(nMicrostructures): target[j]['error'] = currentError[j] randReset = True else: #--- not all grains are tessellated print 'Thread %i: Microstructure mismatch (%i microstructures mapped)'%(self.threadID,myNmicrostructures) randReset = True s.release() # -------------------------------------------------------------------- # MAIN # -------------------------------------------------------------------- parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """ Monte Carlo simulation to produce seed file that gives same size distribution like given geometry file. """, version = scriptID) parser.add_option('-s','--seeds', dest='seedFile', metavar='string', help='name of the intial seed file. If not found, a new one is created [%default]') parser.add_option('-g','--grid', dest='grid', type='int', nargs=3, metavar='int int int', help='a,b,c grid of hexahedral box [%default]') parser.add_option('-t','--threads', dest='threads', type='int', metavar='int', help='number of parallel executions [%default]') parser.add_option('-r', '--rnd', dest='randomSeed', type='int', metavar='int', help='seed of random number generator [%default]') parser.add_option('--target', dest='target', metavar='string', help='name of the geom file with target distribution [%default]') parser.add_option('--tolerance', dest='threshold', type='int', metavar='int', help='stopping criterion (bin number) [%default]') parser.add_option('--scale', dest='scale',type='float', metavar='float', help='maximum moving distance of perturbed seed in pixel [%default]') parser.add_option('--bins', dest='bins', type='int', metavar='int', help='bins to sort beyond current best fit [%default]') parser.add_option('--maxseeds', dest='maxseeds', type='int', metavar='int', help='maximum number of seeds to move simulateneously [number of seeds]') parser.set_defaults(seedFile = 'seeds') parser.set_defaults(grid = (64,64,64)) parser.set_defaults(threads = 2) parser.set_defaults(randomSeed = None) parser.set_defaults(target = 'geom') parser.set_defaults(threshold = 20) parser.set_defaults(bins = 15) parser.set_defaults(scale = 1.0) parser.set_defaults(maxseeds = 0) options = parser.parse_args()[0] if options.randomSeed == None: options.randomSeed = int(os.urandom(4).encode('hex'), 16) print 'random seed', options.randomSeed delta = (options.scale/options.grid[0],options.scale/options.grid[1],options.scale/options.grid[2]) baseFile=os.path.splitext(os.path.basename(options.seedFile))[0] points = float(reduce(mul,options.grid)) # ----------- calculate target distribution and bin edges targetGeomFile = os.path.splitext(os.path.basename(options.target))[0]+'.geom' targetGeomTable = damask.ASCIItable(targetGeomFile,labeled=False,readonly=True) targetGeomTable.head_read() for i in targetGeomTable.info: if i.startswith('microstructures'): nMicrostructures = int(i.split()[1]) if i.startswith('grid'): targetPoints = int(np.array(map(float,i.split()[2:7:2])).prod()) targetGeomTable.data_readArray() targetVolFrac = np.bincount(targetGeomTable.data.astype(int).ravel())[1:nMicrostructures+1]/targetPoints target=[] for i in xrange(1,nMicrostructures+1): targetHist,targetBins = np.histogram(targetVolFrac,bins=i) #bin boundaries target.append({'histogram':targetHist,'bins':targetBins}) # ----------- create initial seed file or open existing one bestSeedsVFile = StringIO() if os.path.isfile(os.path.splitext(options.seedFile)[0]+'.seeds'): with open(os.path.splitext(options.seedFile)[0]+'.seeds') as initialSeedFile: for line in initialSeedFile: bestSeedsVFile.write(line) else: bestSeedsVFile.write(execute('seeds_fromRandom'+\ ' -g '+' '.join(map(str, options.grid))+\ ' -r %i'%options.randomSeed+\ ' -N '+str(nMicrostructures))[0]) bestSeedsUpdate = time.time() # ----------- tessellate initial seed file to get and evaluate geom file bestSeedsVFile.reset() initialGeomVFile = StringIO() initialGeomVFile.write(execute('geom_fromVoronoiTessellation '+ ' -g '+' '.join(map(str, options.grid)),bestSeedsVFile)[0]) initialGeomVFile.reset() initialGeomTable = damask.ASCIItable(initialGeomVFile,labeled=False,readonly=True) initialGeomTable.head_read() for i in initialGeomTable.info: if i.startswith('microstructures'): initialMicrostructures = int(i.split('\t')[1]) if initialMicrostructures != nMicrostructures: print 'error. Microstructure count mismatch' initialGeomTable.data_readArray() initialData = np.bincount(initialGeomTable.data.astype(int).ravel())[1:]/points for i in xrange(nMicrostructures): initialHist = np.histogram(initialData,bins=target[i]['bins'])[0] target[i]['error']=np.sqrt(np.square(np.array(target[i]['histogram']-initialHist)).sum()) # as long as not all grain sizes are within the range, the error is the deviation to left and right if target[0]['error'] > 0.0: target[0]['error'] *=((target[0]['bins'][0]-np.min(initialData))**2.0+ (target[0]['bins'][1]-np.max(initialData))**2.0)**0.5 match=0 for i in xrange(nMicrostructures): if target[i]['error'] > 0.0: break match = i+1 if options.maxseeds < 1: maxSeeds = initialMicrostructures else: maxSeeds = options.maxseeds if match >0: print 'Stage %i cleared'%match sys.stdout.flush() initialGeomVFile.close() # start mulithreaded monte carlo simulation threads=[] s=threading.Semaphore(1) for i in range(options.threads): threads.append(myThread(i)) threads[i].start() for i in range(options.threads): threads[i].join()