added geomCrop to crop a box out of a geom file

processing/pre/spectral_geomCrop.py

@@ -0,0 +1,152 @@
+#!/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('-r', '--resolution', dest='resolution', type='int', nargs = 3, \
+                  help='a,b,c resolution of cropped box')
+parser.add_option('-o', '--offset', dest='offset', type='int', nargs = 3, \
+                  help='a,b,c offset of cropped box')
+parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \
+                  help='output geom file with two-dimensional data arrangement')
+
+parser.set_defaults(resolution = [0,0,0])
+parser.set_defaults(offset = [0,0,0])
+parser.set_defaults(twoD = False)
+
+(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()
+  if 0 in options.resolution:  
+    for header in headers:
+      headitems = header.split()
+      if headitems[0] == 'resolution':         # located resolution entry
+        for i in xrange(3):
+          options.resolution[i] = mappings['resolution'](headitems[headitems.index(identifiers['resolution'][i])+1])
+
+  resolution = [0,0,0]
+  dimension = [0.0,0.0,0.0]
+  new_header = []
+  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])
+      header = "resolution\ta %i\tb %i\tc %i\n"%(options.resolution[0],options.resolution[1],options.resolution[2],)
+    if headitems[0] == 'dimension':          # located dimension entry
+      for i in xrange(3):
+        dimension[i] = mappings['dimension'](headitems[headitems.index(identifiers['dimension'][i])+1])
+      header = "dimension\tx %f\ty %f\tz %f\n"%(dimension[0]/resolution[0]*options.resolution[0],
+                                              dimension[1]/resolution[1]*options.resolution[1],
+                                              dimension[2]/resolution[2]*options.resolution[2],)
+    
+    new_header.append(header)
+    
+  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())))
+  
+
+            
+# ------------------------------------------ assemble header ---------------------------------------  
+
+  output = ''.join(new_header)
+
+# ------------------------------------- regenerate texture information ----------------------------------  
+
+  for z in xrange(options.offset[2],options.offset[2]+options.resolution[2]):
+    for y in xrange(options.offset[1],options.offset[1]+options.resolution[1]):
+      output += {True:' ',False:'\n'}[options.twoD].join(map(lambda x: ('%%%ii'%formatwidth)%x, microstructure[options.offset[0]:options.offset[0]+options.resolution[0],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'])
+    

processing/setup/setup_processing.py

@@ -63,6 +63,8 @@ bin_link = { \
                 'mentat_spectralBox.py',
                 'patchFromReconstructedBoundaries.py',
                 'spectral_geomCheck.py',
+                'spectral_geomScale.py',
+                'spectral_geomCrop.py',
                 'spectral_minimalSurface.py',
                 'spectral_vicinityOffset.py',
                 'voronoi_randomSeeding.exe',
@@ -83,7 +85,6 @@ bin_link = { \
                 'postResults.py',
                 'spectral_iterationCount.py',
                 'spectral_convergence.py',
-                'spectral_scaleGeom.py',
                 ],
             }