polishing

processing/pre/geom_clean.py

@@ -1,17 +1,20 @@
 #!/usr/bin/env python3
-# -*- coding: UTF-8 no BOM -*-
 
 import os
 import sys
-import numpy as np
-import damask
 from io import StringIO
-from scipy import ndimage
 from optparse import OptionParser
 
+from scipy import ndimage
+import numpy as np
+
+import damask
+
+
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
+
 def mostFrequent(arr):
   unique, inverse = np.unique(arr, return_inverse=True)
   return unique[np.argmax(np.bincount(inverse))]
@@ -22,11 +25,10 @@ def mostFrequent(arr):
 #--------------------------------------------------------------------------------------------------
 
 parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
-Smooth geometry by selecting most frequent microstructure index within given stencil at each location.
+Smooth microstructure by selecting most frequent index within given stencil at each location.
 
 """, version=scriptID)
 
-
 parser.add_option('-s','--stencil',
                   dest = 'stencil',
                   type = 'int', metavar = 'int',
@@ -37,8 +39,6 @@ parser.set_defaults(stencil = 3)
 (options, filenames) = parser.parse_args()
 
 
-# --- loop over input files -------------------------------------------------------------------------
-
 if filenames == []: filenames = [None]
 
 for name in filenames:
@@ -49,12 +49,12 @@ for name in filenames:
     geom = damask.Geom.from_file(virt_file)
   else:
     geom = damask.Geom.from_file(name)
-  microstructure = geom.microstructure
+  microstructure = geom.get_microstructure()
 
   microstructure = ndimage.filters.generic_filter(microstructure,mostFrequent,
                                                   size=(options.stencil,)*3).astype(microstructure.dtype)
 
-  geom.microstructure = microstructure
+  geom.set_microstructure(microstructure)
   geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:]))
   
   damask.util.croak(geom)

processing/pre/geom_renumber.py

@@ -1,28 +1,30 @@
 #!/usr/bin/env python3
-# -*- coding: UTF-8 no BOM -*-
 
 import os
 import sys
-import numpy as np
-from optparse import OptionParser
 from io import StringIO
+from optparse import OptionParser
+
+import numpy as np
+
 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 [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
-renumber sorted microstructure indices to 1,...,N.
+Renumber sorted microstructure indices to 1,...,N.
 
 """, version=scriptID)
 
 (options, filenames) = parser.parse_args()
 
-# --- loop over input files ----------------------------------------------------------------------
 
 if filenames == []: filenames = [None]
 
@@ -34,15 +36,13 @@ for name in filenames:
     geom = damask.Geom.from_file(virt_file)
   else:
     geom = damask.Geom.from_file(name)
-  microstructure = geom.microstructure
+  microstructure = geom.get_microstructure()
-
-  grainIDs = np.unique(microstructure)
-  renumbered = np.copy(microstructure)
   
-  for i, oldID in enumerate(grainIDs):
+  renumbered = np.copy(microstructure)
+  for i, oldID in enumerate(np.unique(microstructure)):
     renumbered = np.where(microstructure == oldID, i+1, renumbered)
 
-  geom.microstructure = renumbered
+  geom.set_microstructure(renumbered)
   geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:]))
   
   damask.util.croak(geom)

processing/pre/geom_rotate.py

@@ -10,15 +10,17 @@ import numpy as np
 
 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 options [geomfile(s)]', description = """
-Rotates spectral geometry description.
+Rotates and embeddeds.
 
 """, version=scriptID)
 
@@ -33,7 +35,7 @@ parser.add_option('-e', '--eulers',
 parser.add_option('-d', '--degrees',
                   dest = 'degrees',
                   action = 'store_true',
-                  help = 'Euler angles are given in degrees [%default]')
+                  help = 'Angles (Euler angles/axis angle) are given in degrees [%default]')
 parser.add_option('-m', '--matrix',
                   dest = 'matrix',
                   type = 'float', nargs = 9, metavar = ' '.join(['float']*9),
@@ -47,8 +49,7 @@ parser.add_option('-f', '--fill',
                   type = 'int', metavar = 'int',
                   help = 'background grain index, defaults to max + 1')
 
-parser.set_defaults(degrees = False,
+parser.set_defaults(degrees = False)
-                   )
 
 (options, filenames) = parser.parse_args()