From c4c27860b27e74716e6c560777cded10d36b3959 Mon Sep 17 00:00:00 2001 From: Philip Eisenlohr Date: Wed, 7 Nov 2012 16:52:10 +0000 Subject: [PATCH] renamed script updated to recent standard in io processing introduced "primitive" bicontinuous structure in addition to "diamond" and "gyroid" --- processing/pre/geom_fromMinimalSurface.py | 105 ++++++++++++++++++ .../pre/spectral_geomFromMinimalSurface.py | 75 ------------- processing/setup/setup_processing.py | 6 +- 3 files changed, 108 insertions(+), 78 deletions(-) create mode 100755 processing/pre/geom_fromMinimalSurface.py delete mode 100755 processing/pre/spectral_geomFromMinimalSurface.py diff --git a/processing/pre/geom_fromMinimalSurface.py b/processing/pre/geom_fromMinimalSurface.py new file mode 100755 index 000000000..075da81c5 --- /dev/null +++ b/processing/pre/geom_fromMinimalSurface.py @@ -0,0 +1,105 @@ +#!/usr/bin/env python +# -*- coding: UTF-8 no BOM -*- + +import os,sys,string,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 ------------------------------- + + +minimal_surfaces = ['primitive','gyroid','diamond',] + +surface = { + 'primitive': lambda x,y,z: math.cos(x)+math.cos(y)+math.cos(z), + 'gyroid': lambda x,y,z: math.sin(x)*math.cos(y)+math.sin(y)*math.cos(z)+math.cos(x)*math.sin(z), + 'diamond': lambda x,y,z: math.cos(x-y)*math.cos(z)+math.sin(x+y)*math.sin(z), + } + + +parser = OptionParser(option_class=extendedOption, usage='%prog', description = """ +Generate a geometry file of a bicontinuous structure of given type. +""" + string.replace('$Id: spectral_geomCheck 994 2011-09-05 13:38:10Z MPIE\p.eisenlohr $','\n','\\n') +) + +parser.add_option('-t','--type', dest='type', type='string', \ + help='type of minimal surface (%s)'%(','.join(minimal_surfaces))) +parser.add_option('-f','--threshold', dest='threshold', type='float', \ + help='threshold value defining minimal surface') +parser.add_option('-r', '--resolution', dest='resolution', type='int', nargs=3, \ + help='a,b,c resolution of periodic box') +parser.add_option('-d', '--dimension', dest='dimension', type='float', nargs=3, \ + help='x,y,z dimension of periodic box') +parser.add_option('-p', '--periods', dest='periods', type='int', \ + help='number of repetitions of unit cell') +parser.add_option('--homogenization', dest='homogenization', type='int', \ + help='homogenization index to be used') +parser.add_option('--phase', dest='phase', type='int', nargs = 2, \ + help='two phase indices to be used %default') +parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \ + help='output geom file with two-dimensional data arrangement') + +parser.set_defaults(type = minimal_surfaces[0]) +parser.set_defaults(threshold = 0.0) +parser.set_defaults(periods = 1) +parser.set_defaults(resolution = numpy.array([16,16,16])) +parser.set_defaults(dimension = numpy.array([1.0,1.0,1.0])) +parser.set_defaults(homogenization = 1) +parser.set_defaults(phase = [1,2]) +parser.set_defaults(twoD = False) + +(options, args) = parser.parse_args() + +# ------------------------------------------ setup file handles --------------------------------------- + +file = {'name':'STDIN', + 'input':sys.stdin, + 'output':sys.stdout, + 'croak':sys.stderr, + } + +if numpy.any(options.resolution < 1): + file['croak'].write('invalid resolution...\n') + sys.exit() + +if numpy.any(options.dimension < 0.0): + file['croak'].write('invalid dimension...\n') + sys.exit() + + +file['output'].write("4 header\n" + \ + "resolution\ta %i\tb %i\tc %i\n"%(options.resolution[0],options.resolution[1],options.resolution[2],) + \ + "dimension\tx %g\ty %g\tz %g\n"%(options.dimension[0],options.dimension[1],options.dimension[2],) + \ + "origin\tx 0\ty 0\tz 0\n" + \ + "homogenization %i\n"%options.homogenization + ) + +for z in xrange(options.resolution[2]): + Z = options.periods*2.0*math.pi*(z+0.5)/options.resolution[2] + for y in xrange(options.resolution[1]): + Y = options.periods*2.0*math.pi*(y+0.5)/options.resolution[1] + for x in xrange(options.resolution[0]): + X = options.periods*2.0*math.pi*(x+0.5)/options.resolution[0] + file['output'].write(\ + str({True:options.phase[0],False:options.phase[1]}[options.threshold > surface[options.type](X,Y,Z)]) + \ + {True:' ',False:'\n'}[options.twoD] ) + file['output'].write({True:'\n',False:''}[options.twoD]) diff --git a/processing/pre/spectral_geomFromMinimalSurface.py b/processing/pre/spectral_geomFromMinimalSurface.py deleted file mode 100755 index 16436aff6..000000000 --- a/processing/pre/spectral_geomFromMinimalSurface.py +++ /dev/null @@ -1,75 +0,0 @@ -#!/usr/bin/env python -# -*- coding: UTF-8 no BOM -*- - -import os,sys,string,math -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 ------------------------------- - - -minimal_surfaces = ['gyroid','d'] - -surface = { - 'gyroid': lambda x,y,z: math.sin(x)*math.cos(y)+math.sin(y)*math.cos(z)+math.cos(x)*math.sin(z), - 'd': lambda x,y,z: math.cos(z)*math.sin(x+y)+math.sin(z)*math.cos(x-y), - } - - -parser = OptionParser(option_class=extendedOption, usage='%prog', description = """ -Produce VTK point file from geom data -""" + string.replace('$Id: spectral_geomCheck 994 2011-09-05 13:38:10Z MPIE\p.eisenlohr $','\n','\\n') -) - -parser.add_option('-t', '--type', dest='type', type='string', \ - help='type of minimal surface [%s]'%(','.join(minimal_surfaces))) -parser.add_option('-c', '--threshold', dest='threshold', type='float', \ - help='threshold value defining minimal surface') -parser.add_option('-p', '--periods', dest='periods', type='int', \ - help='number of repetitions of unit cell') -parser.add_option('-r', '--resolution', dest='resolution', type='int', nargs=3, \ - help='resolution in x, y, and z') -parser.add_option('-d', '--dimension', dest='dimension', type='float', nargs=3, \ - help='physical dimension in x, y, and z') - -parser.set_defaults(type = 'gyroid') -parser.set_defaults(threshold = 0.5) -parser.set_defaults(periods = 1) -parser.set_defaults(resolution = [8,8,8]) -parser.set_defaults(dimension = [1.0,1.0,1.0]) - -(options, args) = parser.parse_args() - -print "3 header" -print "resolution\ta %i\tb %i\tc %i"%(options.resolution[0],options.resolution[1],options.resolution[2],) -print "dimension\tx %g\ty %g\tz %g"%(options.dimension[0],options.dimension[1],options.dimension[2],) -print "homogenization 1" - -for z in range(options.resolution[2]): - for y in range(options.resolution[1]): - for x in range(options.resolution[0]): - print {True:'1',False:'2'}\ - [options.threshold > - surface[options.type](options.periods*2.0*math.pi*x/options.resolution[0], - options.periods*2.0*math.pi*y/options.resolution[1], - options.periods*2.0*math.pi*z/options.resolution[2], - )] diff --git a/processing/setup/setup_processing.py b/processing/setup/setup_processing.py index 2f1d1cd67..af1038bb9 100755 --- a/processing/setup/setup_processing.py +++ b/processing/setup/setup_processing.py @@ -83,16 +83,16 @@ bin_link = { \ 'OIMang_hex2cub.py', 'patchFromReconstructedBoundaries.py', 'spectral_geomFromAng.py', - 'spectral_geomFromMinimalSurface.py', + 'randomSeeding.py', + 'geom_fromMinimalSurface.py', + 'geom_fromVoronoiTessellation.py', 'geom_canvas.py', 'geom_check.py', - 'geom_fromVoronoiTessellation.py', 'geom_rescale.py', 'geom_pack.py', 'geom_unpack.py', 'geom_translate.py', 'geom_vicinityOffset.py', - 'randomSeeding.py', ], 'post' : [ '3Dvisualize.py',