added option '--renumber' to geom_rescale and geom_grainGrowth to renumber microstructures from 1 to N (without gaps), off by default.

added metavar information to some scripts

processing/pre/OIMang_hex2cub.py

@@ -34,7 +34,7 @@ Converts ang files (EBSD Data) from hexagonal grid to a pixel grid
 """ + string.replace(scriptID,'\n','\\n')
 )
 
-parser.add_option('-x', dest='columnX', action='store', type='int', \
+parser.add_option('-x', dest='columnX', action='store', type='int', metavar='int', \
                         help='column containing x coordinates [%default]')
 
 parser.set_defaults(columnX = 3)

processing/pre/geom_grainGrowth.py

@@ -61,9 +61,12 @@ parser.add_option('-d', '--distance', dest='d', type='int', metavar='int', \
                   help='diffusion distance in voxels [%default]')
 parser.add_option('-N', '--smooth', dest='N', type='int', metavar='int', \
                  help='N for curvature flow [%default]')
+parser.add_option('-r', '--renumber', dest='renumber', action='store_true', \
+                  help='renumber microstructure indices from 1...N [%default]')
 
 parser.set_defaults(d = 1)
 parser.set_defaults(N = 1)
+parser.set_defaults(renumber = False)
 (options, filenames) = parser.parse_args()
 
 
@@ -192,7 +195,15 @@ for file in files:
     index = ndimage.morphology.distance_transform_edt(boundary >= 0.5,return_distances=False,return_indices=True)
     microstructure = microstructure[index[0].flatten(),index[1].flatten(),index[2].flatten()].reshape(microstructure.shape)
 
- # --- assemble header -----------------------------------------------------------------------------
+# --- renumber to sequence 1...Ngrains if requested ------------------------------------------------
+#  http://stackoverflow.com/questions/10741346/numpy-frequency-counts-for-unique-values-in-an-array  
+  if options.renumber:
+    newID=0
+    for microstructureID,count in enumerate(numpy.bincount(microstructure.reshape(info['grid'].prod()))):
+      if count != 0:
+        newID+=1
+        microstructure=numpy.where(microstructure==microstructureID,newID,microstructure).reshape(microstructure.shape)
+# --- assemble header -----------------------------------------------------------------------------
   newInfo['microstructures'] = microstructure[0:info['grid'][0],0:info['grid'][1],0:info['grid'][2]].max()
 
 #--- report ---------------------------------------------------------------------------------------

processing/pre/geom_rescale.py

@@ -57,7 +57,10 @@ parser.add_option('-g', '--grid', dest='grid', type='string', nargs = 3, metavar
                   help='a,b,c grid of hexahedral box [unchanged]')
 parser.add_option('-s', '--size', dest='size', type='string', nargs = 3, metavar = 'string string string', \
                   help='x,y,z size of hexahedral box [unchanged]')
+parser.add_option('-r', '--renumber', dest='renumber', action='store_true', \
+                  help='renumber microstructure indices from 1...N [%default]')
 
+parser.set_defaults(renumber = False)
 parser.set_defaults(grid = ['0','0','0'])
 parser.set_defaults(size  = ['0.0','0.0','0.0'])
 
@@ -169,6 +172,14 @@ for file in files:
                    numpy.repeat(microstructure,multiplicity[0], axis=0),
                                                multiplicity[1], axis=1),
                                                multiplicity[2], axis=2)
+# --- renumber to sequence 1...Ngrains if requested ------------------------------------------------
+#  http://stackoverflow.com/questions/10741346/numpy-frequency-counts-for-unique-values-in-an-array  
+  if options.renumber:
+    newID=0
+    for microstructureID,count in enumerate(numpy.bincount(microstructure.reshape(info['grid'].prod()))):
+      if count != 0:
+        newID+=1
+        microstructure=numpy.where(microstructure==microstructureID,newID,microstructure).reshape(microstructure.shape)
 
   newInfo['microstructures'] = microstructure.max()
 

processing/pre/seeds_check.py

@@ -53,9 +53,9 @@ Produce VTK point mesh from seeds file
 """ + string.replace(scriptID,'\n','\\n')
 )
 
-parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, \
+parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, metavar='int int int', \
                   help='a,b,c grid of hexahedral box [from seeds file]')
-parser.add_option('-s', '--size', dest='size', type='float', nargs = 3, \
+parser.add_option('-s', '--size', dest='size', type='float', nargs = 3, metavar='float float float',\
                   help='x,y,z size of hexahedral box [1.0 along largest grid point number]')
 
 parser.set_defaults(grid = [0,0,0])

processing/pre/seeds_fromRandom.py

@@ -43,11 +43,11 @@ Reports positions with random crystal orientations in seeds file format to STDOU
 """ + string.replace(scriptID,'\n','\\n')
 )
 
-parser.add_option('-N', dest='N', type='int', \
+parser.add_option('-N', dest='N', type='int', metavar='int', \
                   help='number of seed points to distribute [%default]')
-parser.add_option('-g','--grid', dest='grid', type='int', nargs=3, \
+parser.add_option('-g','--grid', dest='grid', type='int', nargs=3, metavar='int int int', \
                   help='min a,b,c grid of hexahedral box %default')
-parser.add_option('-r', '--rnd', dest='randomSeed', type='int', \
+parser.add_option('-r', '--rnd', dest='randomSeed', type='int', metavar='int', \
                   help='seed of random number generator [%default]')
 
 parser.set_defaults(randomSeed = 0)