switched voronoi seeding to python

processing/pre/voronoi_randomSeeding.f90

@@ -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

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()

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' : [