gaussian filter (wrapper no ndimage)

PRIVATE

@@ -1 +1 @@
-Subproject commit 19a53f6229603aeafb2466b58679a1cd04fc0142
+Subproject commit 596ec41a5117c5f2a09356ffeee8cd8ce9a149d7

processing/post/addGaussian.py

@@ -0,0 +1,137 @@
+#!/usr/bin/env python2.7
+# -*- coding: UTF-8 no BOM -*-
+
+import os,sys
+import numpy as np
+from optparse import OptionParser
+from scipy import ndimage
+import damask
+
+scriptName = os.path.splitext(os.path.basename(__file__))[0]
+scriptID   = ' '.join([scriptName,damask.version])
+
+
+# --------------------------------------------------------------------
+#                                MAIN
+# --------------------------------------------------------------------
+
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [ASCIItable(s)]', description = """
+Add column(s) containing gradient of requested column(s).
+Operates on periodic ordered three-dimensional data sets.
+Deals with both vector- and scalar fields.
+
+""", version = scriptID)
+
+parser.add_option('-p','--pos','--periodiccellcenter',
+                  dest = 'pos',
+                  type = 'string', metavar = 'string',
+                  help = 'label of coordinates [%default]')
+parser.add_option('-s','--scalar',
+                  dest = 'scalar',
+                  action = 'extend', metavar = '<string LIST>',
+                  help = 'label(s) of scalar field values')
+parser.add_option('-o','--order',
+                  dest = 'order',
+                  type = int,
+                  metavar = 'int',
+                  help = 'order of the filter')
+parser.add_option('--sigma',
+                  dest = 'sigma',
+                  type = float,
+                  metavar = 'float',
+                  help = 'standard deviation')
+parser.add_option('--periodic',
+                  dest = 'periodic',
+                  action = 'store_true',
+                  help = 'assume periodic grain structure'
+                 )
+
+
+
+parser.set_defaults(pos = 'pos',
+                    order = 0,
+                    sigma = 1,
+                    periodic = False
+                   )
+
+(options,filenames) = parser.parse_args()
+
+if options.scalar is None:
+  parser.error('no data column specified.')
+
+# --- loop over input files ------------------------------------------------------------------------
+
+if filenames == []: filenames = [None]
+
+for name in filenames:
+  try:    table = damask.ASCIItable(name = name,buffered = False)
+  except: continue
+  damask.util.report(scriptName,name)
+
+# ------------------------------------------ read header ------------------------------------------
+
+  table.head_read()
+
+# ------------------------------------------ sanity checks ----------------------------------------
+
+  items = {
+            'scalar': {'dim': 1, 'shape': [1], 'labels':options.scalar, 'active':[], 'column': []},
+          }
+  errors  = []
+  remarks = []
+  column = {}
+  
+  if table.label_dimension(options.pos) != 3: errors.append('coordinates {} are not a vector.'.format(options.pos))
+  else: colCoord = table.label_index(options.pos)
+
+  for type, data in items.iteritems():
+    for what in (data['labels'] if data['labels'] is not None else []):
+      dim = table.label_dimension(what)
+      if dim != data['dim']: remarks.append('column {} is not a {}.'.format(what,type))
+      else:
+        items[type]['active'].append(what)
+        items[type]['column'].append(table.label_index(what))
+
+  if remarks != []: damask.util.croak(remarks)
+  if errors  != []:
+    damask.util.croak(errors)
+    table.close(dismiss = True)
+    continue
+
+# ------------------------------------------ assemble header --------------------------------------
+
+  table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
+  for type, data in items.iteritems():
+    for label in data['active']:
+      table.labels_append(['Gauss{}({})'.format(options.sigma,label)])                              # extend ASCII header with new labels
+  table.head_write()
+
+# --------------- figure out size and grid ---------------------------------------------------------
+
+  table.data_readArray()
+
+  coords = [np.unique(table.data[:,colCoord+i]) for i in range(3)]
+  mincorner = np.array(map(min,coords))
+  maxcorner = np.array(map(max,coords))
+  grid   = np.array(map(len,coords),'i')
+  size   = grid/np.maximum(np.ones(3,'d'), grid-1.0) * (maxcorner-mincorner)                        # size from edge to edge = dim * n/(n-1) 
+  size   = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1]))                             # spacing for grid==1 equal to smallest among other ones
+
+# ------------------------------------------ process value field -----------------------------------
+
+  stack = [table.data]
+  for type, data in items.iteritems():
+    for i,label in enumerate(data['active']):
+      stack.append(ndimage.filters.gaussian_filter(table.data[:,data['column'][i]],
+                                                   options.sigma,options.order,
+                                                   mode = 'wrap' if options.periodic else 'nearest'
+                                                   ).reshape([table.data.shape[0],1])
+                   )
+
+# ------------------------------------------ output result -----------------------------------------
+  if len(stack) > 1: table.data = np.hstack(tuple(stack))
+  table.data_writeArray('%.12g')
+
+# ------------------------------------------ output finalization -----------------------------------
+
+  table.close()                                                                                     # close input ASCII table (works for stdin)

processing/pre/geom_fromTable.py

@@ -23,7 +23,7 @@ Generate geometry description and material configuration from position, phase, a
 parser.add_option('--coordinates',
                   dest = 'pos',
                   type = 'string', metavar = 'string',
-                  help = 'coordinates label')
+                  help = 'coordinates label (%default)')
 parser.add_option('--phase',
                   dest = 'phase',
                   type = 'string', metavar = 'string',
@@ -90,6 +90,7 @@ parser.set_defaults(symmetry       = [damask.Symmetry.lattices[-1]],
                     homogenization = 1,
                     crystallite    = 1,
                     verbose        = False,
+                    pos            = 'pos',
                    )
 
 (options,filenames) = parser.parse_args()