Merge remote branch 'origin/development' into cmake

.gitattributes

@@ -7,3 +7,4 @@
 *.png binary
 *.jpg binary
 *.cae binary
+installation/mods_Abaqus/abaqus_v6_windows.env -crlf

VERSION

@@ -1 +1 @@
-v2.0.0-201-gd497503
+v2.0.0-214-g6b57eec

processing/post/addEuclideanDistance.py

@@ -159,7 +159,9 @@ for name in filenames:
   if table.label_dimension(options.id) != 1: errors.append('grain identifier {} not found.'.format(options.id))
   else: idCol = table.label_index(options.id)
 
-  if remarks != []: damask.util.croak(remarks)
+  if remarks != []:
+    damask.util.croak(remarks)
+    remarks = []
   if errors  != []:
     damask.util.croak(errors)
     table.close(dismiss = True)
@@ -184,6 +186,8 @@ for name in filenames:
   N = grid.prod()
 
   if N != len(table.data): errors.append('data count {} does not match grid {}.'.format(N,'x'.join(map(str,grid))))
+  else:                   remarks.append('grid: {}x{}x{}'.format(*grid))
+  if remarks != []: damask.util.croak(remarks)
   if errors  != []:
     damask.util.croak(errors)
     table.close(dismiss = True)
@@ -194,33 +198,37 @@ for name in filenames:
   stack = [table.data]
 
   neighborhood = neighborhoods[options.neighborhood]
-  convoluted = np.empty([len(neighborhood)]+list(grid+2),'i')
+  diffToNeighbor = np.empty(list(grid+2)+[len(neighborhood)],'i')
-  microstructure = periodic_3Dpad(np.array(table.data[:,idCol].reshape(grid),'i'))
+  microstructure = periodic_3Dpad(table.data[:,idCol].astype('i').reshape(grid,order='F'))
-  
+
   for i,p in enumerate(neighborhood):
     stencil = np.zeros((3,3,3),'i')
     stencil[1,1,1] = -1
     stencil[p[0]+1,
             p[1]+1,
             p[2]+1] = 1
-    convoluted[i,:,:,:] = ndimage.convolve(microstructure,stencil)
+    diffToNeighbor[:,:,:,i] = ndimage.convolve(microstructure,stencil)                              # compare ID at each point...
+                                                                                                    # ...to every one in the specified neighborhood
+                                                                                                    # for same IDs at both locations ==> 0
   
-  distance = np.ones((len(feature_list),grid[0],grid[1],grid[2]),'d')
+  diffToNeighbor = np.sort(diffToNeighbor)                                                          # sort diff such that number of changes in diff (steps)...
-  
+                                                                                                    # ...reflects number of unique neighbors
-  convoluted = np.sort(convoluted,axis = 0)
+  uniques = np.where(diffToNeighbor[1:-1,1:-1,1:-1,0] != 0, 1,0)                                    # initialize unique value counter (exclude myself [= 0])
-  uniques = np.where(convoluted[0,1:-1,1:-1,1:-1] != 0, 1,0)                                        # initialize unique value counter (exclude myself [= 0])
 
   for i in xrange(1,len(neighborhood)):                                                             # check remaining points in neighborhood
     uniques += np.where(np.logical_and(
-                           convoluted[i,1:-1,1:-1,1:-1] != convoluted[i-1,1:-1,1:-1,1:-1],          # flip of ID difference detected?
+                         diffToNeighbor[1:-1,1:-1,1:-1,i] != 0,                                     # not myself?
-                           convoluted[i,1:-1,1:-1,1:-1] != 0),                                      # not myself?
+                         diffToNeighbor[1:-1,1:-1,1:-1,i] != diffToNeighbor[1:-1,1:-1,1:-1,i-1],
-                           1,0)                                                                     # count flip
+                         ),                                                                         # flip of ID difference detected?
+                        1,0)                                                                        # count that flip
+
+  distance = np.ones((len(feature_list),grid[0],grid[1],grid[2]),'d')
 
   for i,feature_id in enumerate(feature_list):
     distance[i,:,:,:] = np.where(uniques >= features[feature_id]['aliens'],0.0,1.0)                 # seed with 0.0 when enough unique neighbor IDs are present
     distance[i,:,:,:] = ndimage.morphology.distance_transform_edt(distance[i,:,:,:])*[options.scale]*3
 
-  distance.shape = ([len(feature_list),grid.prod(),1])
+  distance = distance.reshape([len(feature_list),grid.prod(),1],order='F')
   for i in xrange(len(feature_list)):
     stack.append(distance[i,:])
 

processing/post/sortTable.py

@@ -14,7 +14,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 # --------------------------------------------------------------------
 
 parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
-Sort rows by given column label(s).
+Sort rows by given (or all) column label(s).
 
 Examples:
 With coordinates in columns "x", "y", and "z"; sorting with x slowest and z fastest varying index: --label x,y,z.
@@ -30,25 +30,19 @@ parser.add_option('-r','--reverse',
                   action = 'store_true',
                   help   = 'sort in reverse')
 
-parser.set_defaults(key = [],
+parser.set_defaults(reverse = False,
-                    reverse = False,
                    )
 
 (options,filenames) = parser.parse_args()
 
-if options.keys is None:
-  parser.error('No sorting column(s) specified.')
-
-options.keys.reverse()                                                                              # numpy sorts with most significant column as last
 
 # --- loop over input files -------------------------------------------------------------------------
 
 if filenames == []: filenames = [None]
 
 for name in filenames:
-  try:
+  try:    table = damask.ASCIItable(name = name,
-    table = damask.ASCIItable(name = name,
+                                    buffered = False)
-                              buffered = False)
   except: continue
   damask.util.report(scriptName,name)
 
@@ -61,15 +55,16 @@ for name in filenames:
 # ------------------------------------------ process data ---------------------------------------  
 
   table.data_readArray()
+
+  keys = table.labels[::-1] if options.keys is None else options.keys[::-1]                         # numpy sorts with most significant column as last
+
   cols    = []
   remarks = []
-  for i,column in enumerate(table.label_index(options.keys)):
+  for i,column in enumerate(table.label_index(keys)):
-    if column < 0:
+    if column < 0: remarks.append('label "{}" not present...'.format(keys[i]))
-      remarks.append("label {0} not present.".format(options.keys[i]))
+    else:          cols += [table.data[:,column]]
-    else:
-      cols += [table.data[:,column]]
   if remarks != []: damask.util.croak(remarks)
-    
+  
   ind = np.lexsort(cols) if cols != [] else np.arange(table.data.shape[0])
   if options.reverse: ind = ind[::-1]