From 30d38436c7c875aa7589bd410703f102dbabe960 Mon Sep 17 00:00:00 2001 From: Pratheek Shanthraj Date: Thu, 29 Mar 2012 16:41:23 +0000 Subject: [PATCH] switched voronoi seeding to python --- processing/pre/voronoi_randomSeeding.f90 | 93 ------------------------ processing/pre/voronoi_randomSeeding.py | 89 +++++++++++++++++++++++ processing/setup/setup_processing.py | 3 +- 3 files changed, 90 insertions(+), 95 deletions(-) delete mode 100644 processing/pre/voronoi_randomSeeding.f90 create mode 100755 processing/pre/voronoi_randomSeeding.py diff --git a/processing/pre/voronoi_randomSeeding.f90 b/processing/pre/voronoi_randomSeeding.f90 deleted file mode 100644 index fb9815567..000000000 --- a/processing/pre/voronoi_randomSeeding.f90 +++ /dev/null @@ -1,93 +0,0 @@ -!prec.f90 407 2009-08-31 15:09:15Z MPIE\f.roters -!############################################################## - MODULE prec -!############################################################## - - implicit none - -! *** Precision of real and integer variables *** - integer, parameter :: pReal = selected_real_kind(15,300) ! 15 significant digits, up to 1e+-300 - integer, parameter :: pInt = selected_int_kind(9) ! up to +- 1e9 - integer, parameter :: pLongInt = 8 ! should be 64bit - - END MODULE prec - -program voronoi - use prec, only: pReal, pInt - implicit none - - logical, dimension(:), allocatable :: seedmap - character(len=1024) filename - integer(pInt), dimension(3) :: seedcoord - integer(pInt), dimension(:), allocatable :: rndInit - integer(pInt) a, b, c, N_Seeds, seedpoint, i, randomSeed, rndSize - real(pReal), dimension(:,:), allocatable :: grainEuler, seeds - real(pReal), parameter :: pi = 3.14159265358979323846264338327950288419716939937510_pReal - - print*, '******************************************************************************' - print*, ' Voronoi description file' - print*, '******************************************************************************' - print*, '$Id$' - print*, '' - print*, 'generates:' - print*, ' * description file "_OUTPUT_.seeds":' - print*, '' - write(*, '(A)', advance = 'NO') 'output seed filename: ' - read(*, *), filename - write(*, '(A)', advance = 'NO') 'seed of random number generator: ' - read(*, *), randomSeed; randomSeed = max(0_pInt,randomSeed) - write(*, '(A)', advance = 'NO') 'number of grains: ' - read(*, *), N_Seeds - write(*, '(A)', advance = 'NO') 'min. Fourier points in x: ' - read(*, *), a - write(*, '(A)', advance = 'NO') 'min. Fourier points in y: ' - read(*, *), b - write(*, '(A)', advance = 'NO') 'min. Fourier points in z: ' - read(*, *), c - - allocate (seedmap(a*b*c)); seedmap = .false. ! logical to store information which position is occupied by a voronoi seed - allocate (seeds(N_Seeds,3)) - allocate (grainEuler(N_Seeds,3)) - - call random_seed(size=rndSize) - allocate(rndInit(rndSize)) - rndInit = randomSeed - call random_seed(put=rndInit) - call random_seed(get=rndInit) - - do i=1, N_Seeds - call random_number(grainEuler(i,1)) - call random_number(grainEuler(i,2)) - call random_number(grainEuler(i,3)) - grainEuler(i,1) = (grainEuler(i,1))*360.0 - grainEuler(i,2) = acos(2.0_pReal*(grainEuler(i,2))-1.0_pReal)*180.0/pi - grainEuler(i,3) = grainEuler(i,3)*360.0 - enddo - -!generate random position of seeds for voronoi tessellation - i = 1 - do while (i <= N_Seeds) - call random_number(seeds(i,1)); seedcoord(1) = min(a,int(seeds(i,1)*a)+1_pInt)-1_pInt - call random_number(seeds(i,2)); seedcoord(2) = min(b,int(seeds(i,2)*b)+1_pInt)-1_pInt - call random_number(seeds(i,3)); seedcoord(3) = min(c,int(seeds(i,3)*c)+1_pInt)-1_pInt - seedpoint = seedcoord(1) + seedcoord(2)*a + seedcoord(3)*a*b - if (.not. seedmap(seedpoint+1)) then - seedmap(seedpoint+1) = .true. - i = i + 1 - end if - end do - -! write description file with orientation and position of each seed - open(21, file = trim(filename)//('.seeds')) - write(21, '(i1,a1,a6)') 4,achar(9),'header' - write(21, '(A, I8, A, I8, A, I8)') 'resolution a ', a, ' b ', b, ' c ', c - write(21, '(A, I8)') 'grains', N_Seeds - write(21, '(A, I8)') 'random seed ',rndInit(1) - write(21,'(6(a,a1))') 'x',achar(9),'y',achar(9),'z',achar(9),'phi1',achar(9),'Phi',achar(9),'phi2',achar(9) - do i = 1, n_Seeds - write(21, '(6(F10.6,a1))'),seeds(i,1), achar(9), seeds(i,2), achar(9), seeds(i,3), achar(9), & - grainEuler(i,1),achar(9), grainEuler(i,2),achar(9), grainEuler(i,3),achar(9) - end do - close(21) - deallocate (rndInit) -end program voronoi diff --git a/processing/pre/voronoi_randomSeeding.py b/processing/pre/voronoi_randomSeeding.py new file mode 100755 index 000000000..572051de2 --- /dev/null +++ b/processing/pre/voronoi_randomSeeding.py @@ -0,0 +1,89 @@ +#!/usr/bin/env python +# -*- coding: UTF-8 no BOM -*- + +import os,sys,string,re,math,numpy,random +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 ------------------------------- + +identifiers = { + 'resolution': ['a','b','c'], + 'dimension': ['x','y','z'], + } +mappings = { + 'resolution': lambda x: int(x), + 'dimension': lambda x: float(x), + } + + +parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """ +Offset microstructure index for points which see a microstructure different from themselves within a given (cubic) vicinity, +i.e. within the region close to a grain/phase boundary. +""" + string.replace('$Id: spectral_geomCheck 994 2011-09-05 13:38:10Z MPIE\p.eisenlohr $','\n','\\n') +) + +parser.add_option('-f', '--file', dest='filename', type="string", \ + help='output seed file name') +parser.add_option('-s', '--seed', dest='randomSeed', type='int', \ + help='seed of random number generator') +parser.add_option('-n', '--ngrains', dest='N_Seeds', type='int', \ + help='seed of random number generator') +parser.add_option('-r','--res', dest='res', type='int', nargs=3, \ + help='Min Fourier points in x, y, z') + +parser.set_defaults(filename = 'seeds') +parser.set_defaults(randomSeed = 0) + +(options, filenames) = parser.parse_args() + +if options.N_Seeds > options.res[0]*options.res[1]*options.res[2]: + print 'Warning: Number of grains exceeds min resolution' + options.N_Seeds = options.res[0]*options.res[1]*options.res[2] + +seeds = numpy.zeros((3,options.N_Seeds),float) +numpy.random.seed(options.randomSeed) + +grainEuler=numpy.random.rand(3,options.N_Seeds) +grainEuler[0,:] = 360*grainEuler[0,:] +grainEuler[1,:] = numpy.arccos(2*grainEuler[1,:]-1)*180/math.pi +grainEuler[2,:] = 360*grainEuler[2,:] + +seedpoint = numpy.random.permutation(options.res[0]*options.res[1]*options.res[2])[:options.N_Seeds] +seeds[0,:]=numpy.mod(seedpoint,options.res[0])/options.res[0]+1 +seeds[1,:]=numpy.mod((seedpoint-seeds[0,:])/options.res[0],options.res[1])+1 +seeds[2,:]=(seedpoint-seeds[0,:]-options.res[1]*seeds[1,:])/(options.res[0]*options.res[1])+1 +seeds[0,:]=(seeds[0,:]+numpy.random.rand(1,options.N_Seeds)-0.5)/options.res[0] +seeds[1,:]=(seeds[1,:]+numpy.random.rand(1,options.N_Seeds)-0.5)/options.res[1] +seeds[2,:]=(seeds[2,:]+numpy.random.rand(1,options.N_Seeds)-0.5)/options.res[2] + +f = open(options.filename+'.seeds', 'w') + +f.write("{0:1d} {1:6s}\n".format(4,'header')) +f.write("{0:s} {1:8d} {2:s} {3:8d} {4:s} {5:8d}\n".format('resolution a',options.res[0],'b',options.res[1],'c',options.res[2])) +f.write("{0:s} {1:8d}\n".format('grains',options.N_Seeds)) +f.write("{0:s} {1:8d}\n".format('random seed',options.randomSeed)) +f.write("x y z phi1 Phi phi2\n") +f.close() +f=file(options.filename+'.seeds','a') +numpy.savetxt(f,numpy.transpose(numpy.concatenate((seeds,grainEuler),axis=0)),fmt='%10.6f',delimiter=' ') +f.close() diff --git a/processing/setup/setup_processing.py b/processing/setup/setup_processing.py index 4a4659ab5..e03fad476 100755 --- a/processing/setup/setup_processing.py +++ b/processing/setup/setup_processing.py @@ -85,7 +85,7 @@ bin_link = { \ 'spectral_geomCrop.py', 'spectral_minimalSurface.py', 'spectral_vicinityOffset.py', - 'voronoi_randomSeeding.exe', + 'voronoi_randomSeeding.py', 'voronoi_tessellation.exe', ], 'post' : [ @@ -113,7 +113,6 @@ bin_link = { \ compile = { \ 'pre' : [ - 'voronoi_randomSeeding.f90', 'voronoi_tessellation.f90', ], 'post' : [