diff --git a/processing/pre/geom_stretchInterfaces.py b/processing/pre/geom_stretchInterfaces.py new file mode 100755 index 000000000..59407a33d --- /dev/null +++ b/processing/pre/geom_stretchInterfaces.py @@ -0,0 +1,219 @@ +#!/usr/bin/env python +# -*- coding: UTF-8 no BOM -*- + +import os,sys,string,re,math,numpy +from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP + +#-------------------------------------------------------------------------------------------------- +class extendedOption(Option): +#-------------------------------------------------------------------------------------------------- +# used for definition of new option parser action 'extend', which enables to take multiple option arguments +# taken from online tutorial http://docs.python.org/library/optparse.html + + ACTIONS = Option.ACTIONS + ("extend",) + STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",) + TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",) + ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",) + + def take_action(self, action, dest, opt, value, values, parser): + if action == "extend": + lvalue = value.split(",") + values.ensure_value(dest, []).extend(lvalue) + else: + Option.take_action(self, action, dest, opt, value, values, parser) + + +#-------------------------------------------------------------------------------------------------- +# MAIN +#-------------------------------------------------------------------------------------------------- +neighborhood = numpy.array([ [-1,-1,-1], + [ 0,-1,-1], + [ 1,-1,-1], + [-1, 0,-1], + [ 0, 0,-1], + [ 1, 0,-1], + [-1, 1,-1], + [ 0, 1,-1], + [ 1, 1,-1], + [-1,-1, 0], + [ 0,-1, 0], + [ 1,-1, 0], + [-1, 0, 0], + [ 0, 0, 0], + [ 1, 0, 0], + [-1, 1, 0], + [ 0, 1, 0], + [ 1, 1, 0], + [-1,-1, 1], + [ 0,-1, 1], + [ 1,-1, 1], + [-1, 0, 1], + [ 0, 0, 1], + [ 1, 0, 1], + [-1, 1, 1], + [ 0, 1, 1], + [ 1, 1, 1], + ],'i') + +identifiers = { + 'grid': ['a','b','c'], + 'size': ['x','y','z'], + 'origin': ['x','y','z'], + } +mappings = { + 'grid': lambda x: int(x), + 'size': lambda x: float(x), + 'origin': lambda x: float(x), + 'homogenization': lambda x: int(x), + } + +parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """ +Smoothens out interface roughness. +""" + string.replace('$Id$','\n','\\n') +) + +parser.add_option('-N', '--iterations', dest='N', type='int', \ + help='number of iterations to apply smoothing [%default]') +parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \ + help='output geom file with two-dimensional data arrangement [%default]') + +parser.set_defaults(twoD = False) +parser.set_defaults(N = 1) + +(options, filenames) = parser.parse_args() + +#--- setup file handles -------------------------------------------------------------------------- +files = [] +if filenames == []: + files.append({'name':'STDIN', + 'input':sys.stdin, + 'output':sys.stdout, + 'croak':sys.stderr, + }) +else: + for name in filenames: + if os.path.exists(name): + files.append({'name':name, + 'input':open(name), + 'output':open(name+'_tmp','w'), + 'croak':sys.stdout, + }) + +#--- loop over input files ------------------------------------------------------------------------ +for file in files: + if file['name'] != 'STDIN': file['croak'].write(file['name']+'\n') + + firstline = file['input'].readline() + m = re.search('(\d+)\s*head', firstline.lower()) + if m: + headerlines = int(m.group(1)) + headers = [file['input'].readline() for i in range(headerlines)] + else: + headerlines = 1 + headers = firstline + + content = file['input'].readlines() + file['input'].close() + +#--- interprete header ---------------------------------------------------------------------------- + info = { + 'grid': numpy.zeros(3,'i'), + 'size': numpy.zeros(3,'d'), + 'origin': numpy.zeros(3,'d'), + 'microstructures': 0, + 'homogenization': 0, + } + + new_header = [] + for header in headers: + headitems = map(str.lower,header.split()) + if headitems[0] == 'resolution': headitems[0] = 'grid' + if headitems[0] == 'dimension': headitems[0] = 'size' + if headitems[0] in mappings.keys(): + if headitems[0] in identifiers.keys(): + for i in xrange(len(identifiers[headitems[0]])): + info[headitems[0]][i] = \ + mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1]) + else: + info[headitems[0]] = mappings[headitems[0]](headitems[1]) + + file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \ + 'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \ + 'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \ + 'homogenization: %i\n'%info['homogenization'] + \ + 'microstructures: %i\n'%info['microstructures']) + + if numpy.any(info['grid'] < 1): + file['croak'].write('invalid grid a b c.\n') + sys.exit() + if numpy.any(info['size'] <= 0.0): + file['croak'].write('invalid size x y z.\n') + sys.exit() + +#--- read data ------------------------------------------------------------------------------------ + microstructure = numpy.zeros(info['grid'],'i') + i = 0 + for line in content: + for item in map(int,line.split()): + microstructure[i%info['grid'][0], + (i/info['grid'][0])%info['grid'][1], + i/info['grid'][0] /info['grid'][1]] = item + i += 1 + + for i in range(options.N): + active = [] + for z in xrange(info['grid'][2]): + for y in xrange(info['grid'][1]): + for x in xrange(info['grid'][0]): + me = microstructure[x,y,z] + others = me*numpy.ones(1+len(neighborhood),'i') + hot = False + o = 0 + + for offset in neighborhood: + otherX = (x+offset[0])%info['grid'][0] + otherY = (y+offset[1])%info['grid'][1] + otherZ = (z+offset[2])%info['grid'][2] + other = microstructure[otherX,otherY,otherZ] + o += 1 + others[o] = other + if other != me: + hot = True + + + if hot: + active.insert(0,numpy.array([x,y,z,0,0],'i')) # remember current position, best candidate, and best change + # append might be not a good idea in linked lists. try to put at the start, not end! + for o in xrange(len(others)): + howMany = numpy.array(others[1:] == others[o],'i').sum() # count number of particular others in neighborhood + if active[0][3] < howMany: + active[0][3:5] = [howMany,others[o]] + + for spot in active: + microstructure[spot[0],spot[1],spot[2]] = spot[4] + + formatwidth = int(math.floor(math.log10(microstructure.max())+1)) + + +# --- assemble header ----------------------------------------------------------------------------- + new_header.append('$Id$\n') + new_header.append("grid\ta %i\tb %i\tc %i\n"%( + info['grid'][0],info['grid'][1],info['grid'][2])) + new_header.append("size\tx %f\ty %f\tz %f\n"%( + info['size'][0],info['size'][1],info['size'][2])) + new_header.append("origin\tx %f\ty %f\tz %f\n"%( + info['origin'][0],info['origin'][1],info['origin'][2])) + new_header.append("homogenization\t%i\n"%info['homogenization']) + new_header.append("microstructures\t%i\n"%info['microstructures']) + file['output'].write('%i\theader\n'%(len(new_header))+''.join(new_header)) + +# --- write microstructure information ------------------------------------------------------------ + for z in xrange(info['grid'][2]): + for y in xrange(info['grid'][1]): + file['output'].write({True:' ',False:'\n'}[options.twoD].join(map(lambda x: \ + ('%%%ii'%formatwidth)%x, microstructure[:,y,z])) + '\n') + +#--- output finalization -------------------------------------------------------------------------- + if file['name'] != 'STDIN': + file['output'].close() + os.rename(file['name']+'_tmp',file['name']) diff --git a/processing/setup/symLink_Processing.py b/processing/setup/symLink_Processing.py index 63476a8b5..831ba437e 100755 --- a/processing/setup/symLink_Processing.py +++ b/processing/setup/symLink_Processing.py @@ -19,6 +19,7 @@ bin_link = { \ 'randomSeeding.py', 'geom_fromAng.py', 'geom_fromVPSC.py', + 'geom_fromEuclideanDistance.py' 'geom_fromMinimalSurface.py', 'geom_fromVoronoiTessellation.py', 'geom_fromOsteonGeometry.py', @@ -29,7 +30,7 @@ bin_link = { \ 'geom_unpack.py', 'geom_translate.py', 'geom_vicinityOffset.py', - 'geom_fromEuclideanDistance.py' + 'geom_stretchInterfaces.py', ], 'post' : [ '3Dvisualize.py',