added script to convert data used by R.A. Lebensohn to spectral solver (geom, material.config) format

processing/pre/geom_fromAng.py

@@ -34,17 +34,17 @@ Dual phases can be discriminated based on threshold value in a given data column
 
 
 parser.add_option('--column',          dest='column', type='int', \
-                                       help='data column to separate phase 1 and 2 [%default]')
+                                       help='data column to discriminate phase 1 from 2 [%default]')
-parser.add_option('-f','--threshold',  dest='threshold', type='float', \
+parser.add_option('-t','--threshold',  dest='threshold', type='float', \
-                                       help='threshold value to discriminate phase 1 from 2')
+                                       help='threshold value to discriminate phase 1 from 2 [%default]')
 parser.add_option('--homogenization', dest='homogenization', type='int', \
-                                      help='homogenization index to be used')
+                                      help='homogenization index to be used [%default]')
 parser.add_option('--phase', dest='phase', type='int', nargs = 2, \
                              help='two phase indices to be used %default')
 parser.add_option('--crystallite', dest='crystallite', type='int', \
-                             help='crystallite index to be used')
+                             help='crystallite index to be used [%default]')
 parser.add_option('-c', '--configuration', dest='config', action='store_true', \
-                                           help='output material configuration')
+                                           help='output material configuration [%default]')
 
 parser.set_defaults(column = 1)
 parser.set_defaults(threshold = 0.0)

processing/pre/geom_fromVPSC.py

@@ -0,0 +1,125 @@
+#!/usr/bin/env python
+
+import os,sys,math,string,numpy
+from optparse import OptionParser, Option
+
+# -----------------------------
+class extendableOption(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
+# --------------------------------------------------------------------
+
+parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
+Generate geometry description and material configuration from input files used by R.A. Lebensohn
+""" + string.replace('$Id$','\n','\\n')
+)
+
+
+parser.add_option('--column',          dest='column', type='int', \
+                                       help='data column to discriminate phase 1 from 2 [%default]')
+parser.add_option('-t','--treshold',   dest='threshold', type='float', \
+                                       help='threshold value to discriminate phase 1 from 2 [%default]')
+parser.add_option('--homogenization', dest='homogenization', type='int', \
+                                      help='homogenization index to be used [%default]')
+parser.add_option('--phase', dest='phase', type='int', nargs = 2, \
+    help='two phase indices to be used %default')
+parser.add_option('--crystallite', dest='crystallite', type='int', \
+                             help='crystallite index to be used [%default]')
+parser.add_option('-c', '--configuration', dest='config', action='store_true', \
+                                           help='output material configuration [%default]')
+
+parser.set_defaults(column = 7)
+parser.set_defaults(threshold = 1.0)
+parser.set_defaults(homogenization = 1)
+parser.set_defaults(phase          = [1,2])
+parser.set_defaults(crystallite    = 1)
+parser.set_defaults(config = False)
+
+(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')
+
+  point          = 0
+  geomdim        = [0.0,0.0,0.0]
+  needInfo       = [True,True,True]
+  resolution     = [0,0,0]
+  microstructure = ['<microstructure>']
+  texture        = ['<texture>']
+
+  for line in file['input']:
+    if line.strip():
+      point += 1
+      words = line.split()
+      if options.config:                                                # write configuration (line by line)
+        me = str(point)
+        microstructure += ['[Grain%s]\n'%me + \
+                           'crystallite\t%i\n'%options.crystallite + \
+                           '(constituent)\tphase %s\ttexture %s\tfraction 1.0\n'%(options.phase[{True:0,False:1}[float(words[options.column-1])<options.threshold]],me)
+                          ]
+        texture +=        ['[Grain%s]\n'%me + \
+                           '(gauss)\tphi1 %s\tPhi %s\tphi2 %s\tscatter 0.0\tfraction 1.0\n'%tuple(words[:3])
+                          ]
+      else:
+        currPos = map(float,words[3:6])
+        for i in xrange(3):
+          if currPos[i] > geomdim[i]: 
+            geomdim[i] = currPos[i]
+            resolution[i]+=1
+  
+  if options.config:
+    file['output'].write('\n'.join(microstructure) + \
+                         '\n'.join(texture))
+  else:
+    file['output'].write("4 header\n" + \
+                         "resolution\ta %i\tb %i\tc %i\n"%tuple(resolution) + \
+                         "dimension\tx %g\ty %g\tz %g\n"%tuple(geomdim) + \
+                         "origin\tx 0\ty 0\tz 0\n" + \
+                         "homogenization %i\n"%options.homogenization + \
+                         "1 to %i\n"%(resolution[0]*resolution[1]*resolution[2]))
+
+  # ------------------------------------------ output finalization ---------------------------------------  
+
+  if file['name'] != 'STDIN':
+    file['output'].close()
+    os.rename(file['name']+'_tmp',os.path.splitext(file['name'])[0] + \
+                                  {True: '_material.config',
+                                   False:'.geom'}[options.config])

processing/setup/symLink_Processing.py

@@ -18,6 +18,7 @@ bin_link = { \
                 'patchFromReconstructedBoundaries.py',
                 'randomSeeding.py',
                 'geom_fromAng.py',
+                'geom_fromVPSC.py',
                 'geom_fromMinimalSurface.py',
                 'geom_fromVoronoiTessellation.py',
                 'geom_Osteon.py',