alter a spectral geom file such that any voxel that sees within a given vicinity a different microstructure than itself gets offset by a given value. this allows to identify/isolate grain boundary regions...

processing/pre/spectral_vicinityOffset

@@ -0,0 +1,154 @@
+#!/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 -------------------------------
+
+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('-v', '--vicinity', dest='vicinity', type='int', \
+                  help='voxel distance checked for presence of other microstructure')
+parser.add_option('-o', '--offset', dest='offset', type='int', \
+                  help='integer offset for tagged microstructure')
+
+parser.set_defaults(vicinity = 1)
+
+(options, filenames) = parser.parse_args()
+
+# ------------------------------------------ setup file handles ---------------------------------------  
+
+files = []
+if filenames == []:
+  files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout})
+else:
+  for name in filenames:
+    if os.path.exists(name):
+      files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w')})
+
+# ------------------------------------------ loop over input files ---------------------------------------  
+
+for file in files:
+  if file['name'] != 'STDIN': print file['name']
+
+  #  get labels by either read the first row, or - if keyword header is present - the last line of the header
+
+  firstline = file['input'].readline()
+  m = re.search('(\d+)\s*head', firstline.lower())
+  if m:
+    headerlines = int(m.group(1))
+    headers  = [firstline]+[file['input'].readline() for i in range(headerlines)]
+  else:
+    headerlines = 1
+    headers = firstline
+
+  content = file['input'].readlines()
+  file['input'].close()
+
+  resolution = [0,0,0]
+  dimension = [0.0,0.0,0.0]
+  for header in headers:
+    headitems = header.split()
+    if headitems[0] == 'resolution':         # located resolution entry
+      for i in xrange(3):
+        resolution[i] = mappings['resolution'](headitems[headitems.index(identifiers['resolution'][i])+1])
+    if headitems[0] == 'dimension':          # located dimension entry
+      for i in xrange(3):
+        dimension[i] = mappings['dimension'](headitems[headitems.index(identifiers['dimension'][i])+1])
+
+  if resolution == [0,0,0]:
+    print 'no resolution info found.'
+    sys.exit(1)
+  if dimension == [0.0,0.0,0.0]:
+    print 'no dimension info found.'
+    sys.exit(1)
+
+  if file['name'] != 'STDIN':
+    print 'resolution: %s'%(' x '.join(map(str,resolution)))
+    print 'dimension:  %s'%(' x '.join(map(str,dimension)))
+    
+  microstructure = numpy.zeros(resolution,'i')
+  i = 0
+  for line in content:  
+    for item in map(int,line.split()):
+      microstructure[i%resolution[0],(i/resolution[0])%resolution[1],i/resolution[0]/resolution[1]] = item
+      i += 1
+  
+  formatwidth = int(math.floor(math.log10(microstructure.max())))
+  
+  for x in xrange(resolution[0]):
+    for y in xrange(resolution[1]):
+      for z in xrange(resolution[2]):
+
+        me = microstructure[x,y,z]
+        breaker = False
+        
+        for dx in xrange(-options.vicinity,options.vicinity+1):
+          for dy in xrange(-options.vicinity,options.vicinity+1):
+            for dz in xrange(-options.vicinity,options.vicinity+1):
+
+              they = microstructure[(x+dx)%resolution[0],(y+dy)%resolution[1],(z+dz)%resolution[2]]
+              if they != me and they != me+options.offset:                    # located alien microstructure in vicinity
+                microstructure[x,y,z] += options.offset                       # tag myself as close to aliens!
+                breaker = True
+                break
+
+            if breaker: break
+
+          if breaker: break
+
+            
+# ------------------------------------------ assemble header ---------------------------------------  
+
+  output = ''.join(headers)
+
+# ------------------------------------- regenerate texture information ----------------------------------  
+
+  for z in xrange(resolution[2]):
+    for y in xrange(resolution[2]):
+      output += ' '.join(map(lambda x: ('%%%ii'%formatwidth)%x, microstructure[:,y,z])) + '\n'
+    
+    output += '\n'
+    
+# ------------------------------------------ output result ---------------------------------------  
+
+  file['output'].write(output)
+
+  if file['name'] != 'STDIN':
+    file['output'].close
+    os.rename(file['name']+'_tmp',file['name'])