getting rid of shell scripts

processing/pre/geom_canvas.py

@@ -71,7 +71,4 @@ for name in filenames:
   damask.util.croak(geom.update(canvas,origin=origin+offset*size/old,rescale=True))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else name)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_clean.py

@@ -37,9 +37,6 @@ for name in filenames:
   damask.util.report(scriptName,name)
 
   geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
-
   damask.util.croak(geom.clean(options.stencil))
-
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
-
   geom.to_file(sys.stdout if name is None else name)

processing/pre/geom_mirror.py

@@ -42,8 +42,6 @@ for name in filenames:
   damask.util.report(scriptName,name)
 
   geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
-
   damask.util.croak(geom.mirror(options.directions,options.reflect))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
-
   geom.to_file(sys.stdout if name is None else name)

processing/pre/geom_renumber.py

@@ -32,15 +32,6 @@ for name in filenames:
   damask.util.report(scriptName,name)
 
   geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
-
+  damask.util.croak(self.renumber)
-  renumbered = np.empty(geom.get_grid(),dtype=geom.microstructure.dtype)
-  for i, oldID in enumerate(np.unique(geom.microstructure)):
-    renumbered = np.where(geom.microstructure == oldID, i+1, renumbered)
-
-  damask.util.croak(geom.update(renumbered))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
-
+  geom.to_file(sys.stdout if name is None else name)
-  if name is None:
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_rescale.py

@@ -56,8 +56,6 @@ for name in filenames:
                   else float(n) for o,n in zip(size,options.size)],dtype=float)
 
   geom.scale(new_grid)
-  damask.util.croak(geom.update(microstructure = None,
+  damask.util.croak(geom.update(microstructure = None,size = new_size))
-                                size = new_size))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
-
   geom.to_file(sys.stdout if name is None else name)

processing/pre/geom_rotate.py

@@ -95,7 +95,4 @@ for name in filenames:
   damask.util.croak(geom.update(microstructure,origin=origin-(np.asarray(microstructure.shape)-grid)/2*size/grid,rescale=True))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else name)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

processing/pre/geom_vicinityOffset.py

@@ -82,7 +82,4 @@ for name in filenames:
                                            geom.microstructure + offset,geom.microstructure)))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  if name is None:
+  geom.to_file(sys.stdout if name is None else name)
-    sys.stdout.write(str(geom.show()))
-  else:
-    geom.to_file(name)

python/damask/geom.py

@@ -504,7 +504,20 @@ class Geom():
             unique, inverse = np.unique(arr, return_inverse=True)
             return unique[np.argmax(np.bincount(inverse))]
 
-        return self.update(ndimage.filters.generic_filter(self.microstructure,
+        return self.update(ndimage.filters.generic_filter(
+                                                          self.microstructure,
                                                           mostFrequent,
-                                                          size=(stencil,)*3).astype(self.microstructure.dtype))
+                                                          size=(stencil,)*3
+                                                         ).astype(self.microstructure.dtype)
+                          )
+        #self.add_comments('tbd')
+
+
+    def renumber(self):
+        """Renumber sorted microstructure indices to 1,...,N."""
+        renumbered = np.empty(self.get_grid(),dtype=self.microstructure.dtype)
+        for i, oldID in enumerate(np.unique(self.microstructure)):
+          renumbered = np.where(self.microstructure == oldID, i+1, renumbered)
+
+        return self.update(renumbered))
         #self.add_comments('tbd')