migrating shell scripts to library

processing/pre/geom_vicinityOffset.py

@@ -5,7 +5,6 @@ import sys
 from io import StringIO
 from optparse import OptionParser
 
-from scipy import ndimage
 import numpy as np
 
 import damask
@@ -15,18 +14,6 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
 
-def taintedNeighborhood(stencil,trigger=[],size=1):
-
-  me = stencil[stencil.shape[0]//2]
-  if len(trigger) == 0:
-    return np.any(stencil != me)
-  if me in trigger:
-    trigger = set(trigger)
-    trigger.remove(me)
-    trigger = list(trigger)
-  return np.any(np.in1d(stencil,np.array(trigger)))
-
-
 #--------------------------------------------------------------------------------------------------
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
@@ -67,19 +54,12 @@ options.trigger = np.array(options.trigger, dtype=int)
 if filenames == []: filenames = [None]
 
 for name in filenames:
-  damask.util.report(scriptName,name)
+    damask.util.report(scriptName,name)
 
-  geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
 
-  offset = np.nanmax(geom.microstructure) if options.offset is None else options.offset
+    damask.util.croak(geom.vicinity_offset(options.vicinity,options.offset,options.trigger,
+                                           True if options.mode is 'wrap' else False))
+    geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
 
-  damask.util.croak(geom.update(np.where(ndimage.filters.generic_filter(
+    geom.to_file(sys.stdout if name is None else name,pack=False)
-                                           geom.microstructure,
-                                           taintedNeighborhood,
-                                           size=1+2*options.vicinity,mode=options.mode,
-                                           extra_arguments=(),
-                                           extra_keywords={"trigger":options.trigger,"size":1+2*options.vicinity}),
-                                           geom.microstructure + offset,geom.microstructure)))
-  geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
-
-  geom.to_file(sys.stdout if name is None else name,pack=False)

python/damask/_geom.py

@@ -278,7 +278,7 @@ class Geom:
         Parameters
         ----------
         fname : str or file handle
-            geometry file to read.
+            Geometry file to read.
 
         """
         try:
@@ -345,15 +345,15 @@ class Geom:
         Parameters
         ----------
         grid : numpy.ndarray of shape (3)
-            number of grid points in x,y,z direction.
+            Number of grid points in x,y,z direction.
         size : list or numpy.ndarray of shape (3)
-            physical size of the microstructure in meter.
+            Physical size of the microstructure in meter.
         seeds : numpy.ndarray of shape (:,3)
-            position of the seed points in meter. All points need to lay within the box.
+            Position of the seed points in meter. All points need to lay within the box.
         weights : numpy.ndarray of shape (seeds.shape[0])
-            weights of the seeds. Setting all weights to 1.0 gives a standard Voronoi tessellation.
+            Weights of the seeds. Setting all weights to 1.0 gives a standard Voronoi tessellation.
         periodic : Boolean, optional
-            perform a periodic tessellation. Defaults to True.
+            Perform a periodic tessellation. Defaults to True.
 
         """
         if periodic:
@@ -391,13 +391,13 @@ class Geom:
         Parameters
         ----------
         grid : numpy.ndarray of shape (3)
-            number of grid points in x,y,z direction.
+            Number of grid points in x,y,z direction.
         size : list or numpy.ndarray of shape (3)
-            physical size of the microstructure in meter.
+            Physical size of the microstructure in meter.
         seeds : numpy.ndarray of shape (:,3)
-            position of the seed points in meter. All points need to lay within the box.
+            Position of the seed points in meter. All points need to lay within the box.
         periodic : Boolean, optional
-            perform a periodic tessellation. Defaults to True.
+            Perform a periodic tessellation. Defaults to True.
 
         """
         coords = grid_filters.cell_coord0(grid,size).reshape(-1,3)
@@ -415,9 +415,9 @@ class Geom:
         Parameters
         ----------
         fname : str or file handle
-            geometry file to write.
+            Geometry file to write.
         pack : bool, optional
-            compress geometry with 'x of y' and 'a to b'.
+            Compress geometry with 'x of y' and 'a to b'.
 
         """
         header = self.get_header()
@@ -481,7 +481,7 @@ class Geom:
         Parameters
         ----------
         fname : str, optional
-            vtk file to write. If no file is given, a string is returned.
+            Vtk file to write. If no file is given, a string is returned.
 
         """
         v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin)
@@ -508,9 +508,9 @@ class Geom:
         Parameters
         ----------
         directions : iterable containing str
-            direction(s) along which the microstructure is mirrored. Valid entries are 'x', 'y', 'z'.
+            Direction(s) along which the microstructure is mirrored. Valid entries are 'x', 'y', 'z'.
         reflect : bool, optional
-            reflect (include) outermost layers.
+            Reflect (include) outermost layers.
 
         """
         valid = {'x','y','z'}
@@ -540,7 +540,7 @@ class Geom:
         Parameters
         ----------
         grid : numpy.ndarray of shape (3)
-            number of grid points in x,y,z direction.
+            Number of grid points in x,y,z direction.
 
         """
         #ToDo: self.add_comments('geom.py:scale v{}'.format(version)
@@ -563,7 +563,7 @@ class Geom:
         Parameters
         ----------
         stencil : int, optional
-            size of smoothing stencil.
+            Size of smoothing stencil.
 
         """
         def mostFrequent(arr):
@@ -596,9 +596,9 @@ class Geom:
         Parameters
         ----------
         R : damask.Rotation
-            rotation to apply to the microstructure.
+            Rotation to apply to the microstructure.
         fill : int or float, optional
-            microstructure index to fill the corners. Defaults to microstructure.max() + 1.
+            Microstructure index to fill the corners. Defaults to microstructure.max() + 1.
 
         """
         if fill is None: fill = np.nanmax(self.microstructure) + 1
@@ -631,11 +631,11 @@ class Geom:
         Parameters
         ----------
         grid : numpy.ndarray of shape (3)
-            number of grid points in x,y,z direction.
+            Number of grid points in x,y,z direction.
         offset : numpy.ndarray of shape (3)
-            offset (measured in grid points) from old to new microstructue[0,0,0].
+            Offset (measured in grid points) from old to new microstructure[0,0,0].
         fill : int or float, optional
-            microstructure index to fill the corners. Defaults to microstructure.max() + 1.
+            Microstructure index to fill the corners. Defaults to microstructure.max() + 1.
 
         """
         if fill is None: fill = np.nanmax(self.microstructure) + 1
@@ -658,14 +658,14 @@ class Geom:
 
     def substitute(self,from_microstructure,to_microstructure):
         """
-        Substitude microstructure indices.
+        Substitute microstructure indices.
 
         Parameters
         ----------
         from_microstructure : iterable of ints
-            microstructure indices to be substituted.
+            Microstructure indices to be substituted.
         to_microstructure : iterable of ints
-            new microstructure indices.
+            New microstructure indices.
 
         """
         substituted = self.get_microstructure()
@@ -674,3 +674,50 @@ class Geom:
 
         #ToDo: self.add_comments('geom.py:substitute v{}'.format(version)
         return self.update(substituted)
+
+
+    def vicinity_offset(self,vicinity=1,offset=None,trigger=[],periodic=True):
+        """
+        Offset microstructure index of points in the vicinity of xxx.
+
+        Different from themselves (or listed as triggers) within a given (cubic) vicinity,
+        i.e. within the region close to a grain/phase boundary.
+        ToDo: use include/exclude as in seeds.from_geom
+
+        Parameters
+        ----------
+        vicinity : int, optional
+            Voxel distance checked for presence of other microstructure.
+            Defaults to 1.
+        offset : int, optional
+            Offset (positive or negative) to tag microstructure indices,
+            defaults to microstructure.max() + 1.
+        trigger : list of ints, optional
+            List of microstructure indices triggering a change.
+            Defaults to [], meaning that different neigboors trigger a change.
+        periodic : Boolean, optional
+            Assume geometry to be periodic. Defaults to True.
+
+        """
+        def tainted_neighborhood(stencil,trigger):
+
+            me = stencil[stencil.shape[0]//2]
+            if len(trigger) == 0:
+                return np.any(stencil != me)
+            if me in trigger:
+                trigger = set(trigger)
+                trigger.remove(me)
+                trigger = list(trigger)
+            return np.any(np.in1d(stencil,np.array(trigger)))
+
+        offset_ = np.nanmax(self.microstructure) if offset is None else offset
+        mask = ndimage.filters.generic_filter(self.microstructure,
+                                              tainted_neighborhood,
+                                              size=1+2*vicinity,
+                                              mode=('wrap' if periodic else 'nearest'),
+                                              extra_keywords={'trigger':trigger})
+        microstructure = np.ma.MaskedArray(self.microstructure + offset_, np.logical_not(mask))
+
+        #ToDo: self.add_comments('geom.py:vicinity_offset v{}'.format(version)
+        return self.update(microstructure)
+

python/tests/test_Geom.py

@@ -77,9 +77,19 @@ class TestGeom:
         with pytest.raises(ValueError):
             default.update(default.microstructure[1:,1:,1:],size=np.ones(2))
 
-    def test_invalid_microstructure(self,default):
+    def test_invalid_origin(self,default):
         with pytest.raises(ValueError):
-            default.update(default.microstructure[1])
+            default.update(default.microstructure[1:,1:,1:],origin=np.ones(4))
+
+    def test_invalid_microstructure_size(self,default):
+        microstructure=np.ones((3,3))
+        with pytest.raises(ValueError):
+            default.update(microstructure)
+
+    def test_invalid_microstructure_type(self,default):
+        microstructure=np.random.randint(1,300,(3,4,5))==1
+        with pytest.raises(TypeError):
+            default.update(microstructure)
 
     def test_invalid_homogenization(self,default):
         with pytest.raises(TypeError):
@@ -172,6 +182,33 @@ class TestGeom:
         e = default.grid
         assert np.all(modified.microstructure[:e[0],:e[1],:e[2]] == default.microstructure)
     
+    @pytest.mark.parametrize('trigger',[[1],[]])
+    def test_vicinity_offset(self,trigger):
+        offset = np.random.randint(2,4)
+        vicinity = np.random.randint(2,4)
+        
+        g=np.random.randint(28,40,(3))
+        m=np.ones(g,'i')
+        x=(g*np.random.permutation(np.array([.5,1,1]))).astype('i')
+        m[slice(0,x[0]),slice(0,x[1]),slice(0,x[2])]=2
+        m2=copy.deepcopy(m)
+        for i in [0,1,2]:
+            m2[(np.roll(m,+vicinity,i)-m)!=0] +=offset
+            m2[(np.roll(m,-vicinity,i)-m)!=0] +=offset
+        if len(trigger) > 0:
+            m2[m==1]=1
+        
+        geom = Geom(m,np.random.rand(3))
+        geom.vicinity_offset(vicinity,offset,trigger=trigger)
+        
+        assert np.all(m2==geom.microstructure)
+
+    @pytest.mark.parametrize('periodic',[True,False])
+    def test_vicinity_offset_invariant(self,default,periodic):
+        old = default.get_microstructure()
+        default.vicinity_offset(trigger=[old.max()+1,old.min()-1])  
+        assert np.all(old==default.microstructure)
+    
     @pytest.mark.parametrize('periodic',[True,False])
     def test_tessellation_approaches(self,periodic):
         grid   = np.random.randint(10,20,3)