centralize functionality

processing/pre/geom_canvas.py

@@ -40,35 +40,22 @@ parser.add_option('-f','--fill',
 parser.set_defaults(offset = (0,0,0))
 
 (options, filenames) = parser.parse_args()
-
-
 if filenames == []: filenames = [None]
 
+
 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)
-  origin = geom.get_origin()
-  size   = geom.get_size()
-  old = new = geom.get_grid()
   offset = np.asarray(options.offset)
 
   if options.grid is not None:
-    new = np.maximum(1,
+      grid = np.maximum(1,
                         np.array([int(o*float(n.lower().replace('x',''))) if n.lower().endswith('x') \
-                          else int(n) for o,n in zip(old,options.grid)],dtype=int))
+                                   else int(n) for o,n in zip(geom.grid,options.grid)],dtype=int))
+  else:
+      grid = np.array(options.grid,dtype=int)
 
-  canvas = np.full(new,options.fill if options.fill is not None
+  damask.util.croak(geom.canvas(grid,np.asarray(options.offset),options.fill))
-                  else np.nanmax(geom.microstructure)+1,geom.microstructure.dtype)
-
-  l = np.clip( offset,    0,np.minimum(old  +offset,new))                                           # noqa
-  r = np.clip( offset+old,0,np.minimum(old*2+offset,new))
-  L = np.clip(-offset,    0,np.minimum(new  -offset,old))
-  R = np.clip(-offset+new,0,np.minimum(new*2-offset,old))
-  canvas[l[0]:r[0],l[1]:r[1],l[2]:r[2]] = geom.microstructure[L[0]:R[0],L[1]:R[1],L[2]:R[2]]
-
-
-  damask.util.croak(geom.update(canvas,origin=origin+offset*size/old,rescale=True))
   geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
-
   geom.to_file(sys.stdout if name is None else name,pack=False)

processing/pre/geom_renumber.py

@@ -22,8 +22,6 @@ Renumber sorted microstructure indices to 1,...,N.
 """, version=scriptID)
 
 (options, filenames) = parser.parse_args()
-
-
 if filenames == []: filenames = [None]
 
 for name in filenames:

processing/pre/geom_rotate.py

@@ -52,6 +52,7 @@ parser.add_option('-f', '--fill',
 parser.set_defaults(degrees = False)
 
 (options, filenames) = parser.parse_args()
+if filenames == []: filenames = [None]
 
 if [options.rotation,options.eulers,options.matrix,options.quaternion].count(None) < 3:
     parser.error('more than one rotation specified.')
@@ -67,32 +68,11 @@ if options.matrix is not None:
 if options.eulers is not None:
     rot = damask.Rotation.from_Eulers(np.array(options.eulers),degrees=options.degrees)
 
-eulers = rot.as_Eulers(degrees=True)
-
-
-if filenames == []: filenames = [None]
 
 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)
-  size   = geom.get_size()
+    damask.util.croak(geom.rotate(rot,options.fill))
-  grid   = geom.get_grid()
-  origin = geom.get_origin()
-  microstructure = geom.get_microstructure()
-  fill = np.nanmax(microstructure)+1 if options.fill is None else options.fill
-  dtype = float if np.isnan(fill) or int(fill) != fill or microstructure.dtype==np.float else int
-
-  # These rotations are always applied in the reference coordinate system, i.e. (z,x,z) not (z,x',z'')
-  # this seems to be ok, see https://www.cs.utexas.edu/~theshark/courses/cs354/lectures/cs354-14.pdf
-  microstructure = ndimage.rotate(microstructure,eulers[2],(0,1),order=0,
-                                  prefilter=False,output=dtype,cval=fill)            # rotation around z
-  microstructure = ndimage.rotate(microstructure,eulers[1],(1,2),order=0,
-                                  prefilter=False,output=dtype,cval=fill)            # rotation around x
-  microstructure = ndimage.rotate(microstructure,eulers[0],(0,1),order=0,
-                                  prefilter=False,output=dtype,cval=fill)            # rotation around z
-
-  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:]))
-
     geom.to_file(sys.stdout if name is None else name,pack=False)

processing/pre/geom_translate.py

@@ -40,22 +40,16 @@ parser.set_defaults(origin = (0.0,0.0,0.0),
                    )
 
 (options, filenames) = parser.parse_args()
+if filenames == []: filenames = [None]
 
 sub = list(map(int,options.substitute))
 
-
-if filenames == []: filenames = [None]
-
 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)
-
+    geom.renumber(sub[0::2],sub[1::2],origin=geom.origin+options.origin)
-  substituted = geom.get_microstructure()
+    geom.microstructure+= option.microstructure
-  for old,new in zip(sub[0::2],sub[1::2]): substituted[geom.microstructure==old] = new              # substitute microstructure indices
+    damask.util.croak(geom)
-  substituted += options.microstructure                                                             # constant shift
-
-  damask.util.croak(geom.update(substituted,origin=geom.get_origin()+options.origin))
     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

@@ -10,6 +10,7 @@ from . import VTK
 from . import util
 from . import Environment
 from . import grid_filters
+from . import Rotation
 
 
 class Geom:
@@ -581,3 +582,54 @@ class Geom:
 
         #self.add_comments('geom.py:renumber v{}'.format(version)
         return self.update(renumbered)
+
+
+    def rotate(self,R,fill=None):
+        """Rotate microstructure (pad if required)."""
+        if fill is None: fill = np.nanmax(self.microstructure) + 1
+        dtype = float if np.isnan(fill) or int(fill) != fill or self.microstructure.dtype==np.float else int
+
+        Eulers = R.as_Eulers(degrees=True)
+        # These rotations are always applied in the reference coordinate system, i.e. (z,x,z) not (z,x',z'')
+        # this seems to be ok, see https://www.cs.utexas.edu/~theshark/courses/cs354/lectures/cs354-14.pdf
+        microstructure = ndimage.rotate(self.microstructure,Eulers[2],(0,1),order=0,
+                                        prefilter=False,output=dtype,cval=fill)                     # rotation around z
+        microstructure = ndimage.rotate(microstructure,Eulers[1],(1,2),order=0,
+                                        prefilter=False,output=dtype,cval=fill)                     # rotation around x
+        microstructure = ndimage.rotate(microstructure,Eulers[0],(0,1),order=0,
+                                        prefilter=False,output=dtype,cval=fill)                     # rotation around z
+
+        origin = self.origin-(np.asarray(microstructure.shape)-self.grid)//2 * self.size/self.grid
+
+        #self.add_comments('geom.py:renumber v{}'.format(version)
+        return self.update(microstructure,origin=origin,rescale=True)
+
+
+    def canvas(self,grid=None,offset=None,fill=None):
+        """Rotate microstructure (pad if required)."""
+        if fill is None: fill = np.nanmax(self.microstructure) + 1
+        dtype = float if np.isnan(fill) or int(fill) != fill or self.microstructure.dtype==np.float else int
+
+        canvas = np.full(self.grid if grid is None else grid,
+                         fill if fill is not None else np.nanmax(self.microstructure)+1,
+                         self.microstructure.dtype)
+        if offset is None: offset = 0
+
+        l = np.clip( offset,          0,np.minimum(self.grid  +offset,grid))                        # noqa
+        r = np.clip( offset+self.grid,0,np.minimum(self.grid*2+offset,grid))
+        L = np.clip(-offset,          0,np.minimum(grid       -offset,self.grid))
+        R = np.clip(-offset+grid,     0,np.minimum(grid*2     -offset,self.grid))
+
+        canvas[l[0]:r[0],l[1]:r[1],l[2]:r[2]] = self.microstructure[L[0]:R[0],L[1]:R[1],L[2]:R[2]]
+
+        #self.add_comments('geom.py:renumber v{}'.format(version)
+        return self.update(canvas,origin=self.origin+offset*self.size/self.grid,rescale=True)
+
+
+    def substitute(self,from_microstructure,to_microstructure):
+        """Substitude microstructure indices."""
+        substituted = self.get_microstructure()
+        for from_ms,to_ms in zip(from_microstructure,to_microstructure):
+            substituted[self.microstructure==from_ms] = to_ms
+
+        return self.update(substituted)