Smooth geometry by selecting most frequent microstructure index within given stencil at each location.

processing/pre/geom_clean.py

@@ -0,0 +1,98 @@
+#!/usr/bin/env python
+# -*- coding: UTF-8 no BOM -*-
+
+import os,sys,string,math
+import numpy as np
+import damask
+from scipy import ndimage
+from optparse import OptionParser
+from collections import defaultdict
+
+scriptID   = string.replace('$Id: geom_rotate.py 4627 2015-11-14 09:47:18Z MPIE\m.diehl $','\n','\\n')
+scriptName = os.path.splitext(scriptID.split()[1])[0]
+
+def mostFrequent(arr):
+  d = defaultdict(int)
+  for i in arr: d[i] += 1
+  return sorted(d.iteritems(), key=lambda x: x[1], reverse=True)[0][0]                              # return value of most frequent microstructure
+
+
+#--------------------------------------------------------------------------------------------------
+#                                MAIN
+#--------------------------------------------------------------------------------------------------
+
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+Smooth geometry by selecting most frequent microstructure index within given stencil at each location.
+
+""", version=scriptID)
+
+
+parser.add_option('-s','--stencil',
+                  dest = 'stencil',
+                  type = 'int', metavar = 'int',
+                  help = 'size of smoothing stencil [%default]')
+
+parser.set_defaults(stencil = 3,
+                   )
+
+(options, filenames) = parser.parse_args()
+
+
+# --- loop over input files -------------------------------------------------------------------------
+
+if filenames == []: filenames = [None]
+
+for name in filenames:
+  try:
+    table = damask.ASCIItable(name = name,
+                              buffered = False,
+                              labeled = False)
+  except: continue
+  damask.util.report(scriptName,name)
+
+# --- interpret header ----------------------------------------------------------------------------
+
+  table.head_read()
+  info,extra_header = table.head_getGeom()
+
+  damask.util.croak(['grid     a b c:  {}'.format(' x '.join(map(str,info['grid']))),
+                     'size     x y z:  {}'.format(' x '.join(map(str,info['size']))),
+                     'origin   x y z:  {}'.format(' : '.join(map(str,info['origin']))),
+                     'homogenization:  {}'.format(info['homogenization']),
+                     'microstructures: {}'.format(info['microstructures']),
+                    ])
+
+  errors = []
+  if np.any(info['grid'] < 1):    errors.append('invalid grid a b c.')
+  if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
+  if errors != []:
+    damask.util.croak(errors)
+    table.close(dismiss = True)
+    continue
+
+# --- read data ------------------------------------------------------------------------------------
+
+  microstructure = table.microstructure_read(info['grid']).reshape(info['grid'],order='F')                    # read microstructure
+
+# --- do work ------------------------------------------------------------------------------------
+
+  microstructure = ndimage.filters.generic_filter(microstructure,mostFrequent,size=(options.stencil,options.stencil,options.stencil))
+
+# --- write header ---------------------------------------------------------------------------------
+
+  table.info_clear()
+  table.info_append([scriptID + ' ' + ' '.join(sys.argv[1:]),])
+  table.head_putGeom(info)
+  table.info_append([extra_header])
+  table.labels_clear()
+  table.head_write()
+
+# --- write microstructure information ------------------------------------------------------------
+
+  formatwidth = int(math.floor(math.log10(microstructure.max())+1))
+  table.data = microstructure.reshape((info['grid'][0],np.prod(info['grid'][1:])),order='F').transpose()
+  table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
+
+# --- output finalization --------------------------------------------------------------------------
+
+  table.close()                                                                                     # close ASCII table