migrating shell scripts to python class

processing/pre/geom_clean.py

@@ -15,11 +15,6 @@ 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))]
-
-
 #--------------------------------------------------------------------------------------------------
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
@@ -46,9 +41,8 @@ for name in filenames:
 
   geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
 
-  damask.util.croak(geom.update(ndimage.filters.generic_filter(
-                                  geom.microstructure,mostFrequent,
-                                  size=(options.stencil,)*3).astype(geom.microstructure.dtype)))
+  damask.util.croak(geom.clean(options.stencil))
+
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
   if name is None:

processing/pre/geom_mirror.py

@@ -38,16 +38,6 @@ parser.set_defaults(reflect = False)
 
 (options, filenames) = parser.parse_args()
 
-if options.directions is None:
-  parser.error('no direction given.')
-
-if not set(options.directions).issubset(validDirections):
-  invalidDirections = [str(e) for e in set(options.directions).difference(validDirections)]
-  parser.error('invalid directions {}. '.format(*invalidDirections))
-
-limits = [None,None] if options.reflect else [-2,0]
-
-
 if filenames == []: filenames = [None]
 
 for name in filenames:
@@ -55,15 +45,7 @@ for name in filenames:
 
   geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
 
-  microstructure = geom.get_microstructure()
-  if 'z' in options.directions:
-    microstructure = np.concatenate([microstructure,microstructure[:,:,limits[0]:limits[1]:-1]],2)
-  if 'y' in options.directions:
-    microstructure = np.concatenate([microstructure,microstructure[:,limits[0]:limits[1]:-1,:]],1)
-  if 'x' in options.directions:
-    microstructure = np.concatenate([microstructure,microstructure[limits[0]:limits[1]:-1,:,:]],0)
-
-  damask.util.croak(geom.update(microstructure,rescale=True))
+  damask.util.croak(geom.mirror(options.directions,options.reflect))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
   if name is None:

python/damask/geom.py

@@ -2,6 +2,7 @@ import os
 from io import StringIO
 
 import numpy as np
+from scipy import ndimage
 import vtk
 from vtk.util import numpy_support
 
@@ -385,3 +386,51 @@ class Geom():
         self.to_file(f)
         f.seek(0)
         return ''.join(f.readlines())
+
+
+    def mirror(self,directions,reflect=False):
+        """
+        Mirror microstructure along given directions.
+        Parameters
+        ----------
+        directions : iterable containing str
+            direction(s) along which the microstructure is mirrored. Valid entries are 'x', 'y', 'z'.
+        reflect : bool, optional
+            reflect (include) outermost layers.
+        """
+        valid = {'x','y','z'}
+        if not all(isinstance(d, str) for d in directions):
+            raise TypeError('Directions are not of type str.')
+        elif not set(directions).issubset(valid):
+            raise ValueError('Invalid direction specified {}'.format(*set(directions).difference(valid)))
+
+        limits = [None,None] if reflect else [-2,0]
+        ms = self.get_microstructure()
+
+        if 'z' in directions:
+            ms = np.concatenate([ms,ms[:,:,limits[0]:limits[1]:-1]],2)
+        if 'y' in directions:
+            ms = np.concatenate([ms,ms[:,limits[0]:limits[1]:-1,:]],1)
+        if 'x' in directions:
+            ms = np.concatenate([ms,ms[limits[0]:limits[1]:-1,:,:]],0)
+     
+        return self.update(ms,rescale=True)
+        #self.add_comments('tbd')
+
+
+    def clean(self,stencil=3):
+        """
+        Smooth microstructure by selecting most frequent index within given stencil at each location.
+        Parameters
+        ----------
+        stencil : int, optional
+            size of smoothing stencil.
+        """
+        def mostFrequent(arr):
+            unique, inverse = np.unique(arr, return_inverse=True)
+            return unique[np.argmax(np.bincount(inverse))]
+
+        return self.update(ndimage.filters.generic_filter(self.microstructure,
+                                                          mostFrequent,
+                                                          size=(stencil,)*3).astype(self.microstructure.dtype))
+        #self.add_comments('tbd')