more logical encapsulation

- getting data out of VTK is a functionality of the VTK class. Need to
  discuss whether the VTK class should also provide grid and size (works
  only for rectilinear grid, so hiding VTK type is not possible
  anymore), but the current situation requires the Geom class to rely on
  'internals' of the VTK class
- header is specific to *.geom format, not to Geom objects.

python/damask/_geom.py

@@ -7,7 +7,6 @@ from functools import partial
 
 import numpy as np
 from scipy import ndimage,spatial
-from vtk.util.numpy_support import vtk_to_numpy as vtk_to_np
 
 from . import environment
 from . import Rotation
@@ -271,16 +270,6 @@ class Geom:
         return self.comments[:]
 
 
-    def get_header(self):
-        """Return the full header (grid, size, origin, homogenization, comments)."""
-        header =  [f'{len(self.comments)+4} header'] + self.comments
-        header.append('grid   a {} b {} c {}'.format(*self.get_grid()))
-        header.append('size   x {} y {} z {}'.format(*self.get_size()))
-        header.append('origin x {} y {} z {}'.format(*self.get_origin()))
-        header.append(f'homogenization {self.get_homogenization()}')
-        return header
-
-
     @staticmethod
     def from_file(fname):
         """
@@ -356,19 +345,12 @@ class Geom:
             Valid extension is .vtr, it will be appended if not given.
 
         """
-        g = VTK.from_file(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr').geom
+        v = VTK.from_file(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
-        grid = np.array(g.GetDimensions())-1
+        grid = np.array(v.geom.GetDimensions())-1
-        bbox = np.array(g.GetBounds()).reshape(3,2).T
+        bbox = np.array(v.geom.GetBounds()).reshape(3,2).T
         size = bbox[1] - bbox[0]
 
-        celldata = g.GetCellData()
+        return Geom(v.get('materialpoint').reshape(grid,order='F'),size,bbox[0])
-        for a in range(celldata.GetNumberOfArrays()):
-            if celldata.GetArrayName(a) == 'materialpoint':
-                materialpoint = vtk_to_np(celldata.GetArray(a))
-                return Geom(materialpoint.reshape(grid,order='F'),size,bbox[0])
-
-        raise ValueError(f'"materialpoint" array not found in {fname}')
-
 
 
     @staticmethod
@@ -417,7 +399,7 @@ class Geom:
         else:
             microstructure = microstructure.reshape(grid)
 
-        creator = util.edit_info('damask.Result.'+inspect.stack()[0][3])
+        creator = util.edit_info('damask.Geom.'+inspect.stack()[0][3])
         return Geom(microstructure+1,size,homogenization=1,comments=creator)
 
 
@@ -442,7 +424,7 @@ class Geom:
         KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
         devNull,microstructure = KDTree.query(coords)
 
-        creator = util.edit_info('damask.Result.'+inspect.stack()[0][3])
+        creator = util.edit_info('damask.Geom.'+inspect.stack()[0][3])
         return Geom(microstructure.reshape(grid)+1,size,homogenization=1,comments=creator)
 
 
@@ -458,8 +440,13 @@ class Geom:
             Compress geometry with 'x of y' and 'a to b'.
 
         """
-        header = self.get_header()
+        header =  [f'{len(self.comments)+4} header'] + self.comments
-        grid   = self.get_grid()
+        header.append('grid   a {} b {} c {}'.format(*self.get_grid()))
+        header.append('size   x {} y {} z {}'.format(*self.get_size()))
+        header.append('origin x {} y {} z {}'.format(*self.get_origin()))
+        header.append(f'homogenization {self.get_homogenization()}')
+
+        grid = self.get_grid()
 
         if pack is None:
             plain = grid.prod()/self.N_microstructure < 250
@@ -490,7 +477,7 @@ class Geom:
                     reps += 1
                 else:
                     if   compressType is None:
-                        f.write('\n'.join(self.get_header())+'\n')
+                        f.write('\n'.join(header)+'\n')
                     elif compressType == '.':
                         f.write(f'{former}\n')
                     elif compressType == 'to':
@@ -589,7 +576,7 @@ class Geom:
         fill_ = np.full_like(self.microstructure,np.nanmax(self.microstructure)+1 if fill is None else fill)
         ms = np.ma.MaskedArray(fill_,np.logical_not(mask) if inverse else mask)
 
-        self.add_comments(util.edit_info('damask.Result.'+inspect.stack()[0][3]))
+        self.add_comments(util.edit_info('damask.Geom.'+inspect.stack()[0][3]))
         return self.update(ms)
 
 
@@ -620,7 +607,7 @@ class Geom:
         if 'x' in directions:
             ms = np.concatenate([ms,ms[limits[0]:limits[1]:-1,:,:]],0)
 
-        self.add_comments(util.edit_info('damask.Result.'+inspect.stack()[0][3]))
+        self.add_comments(util.edit_info('damask.Geom.'+inspect.stack()[0][3]))
         return self.update(ms,rescale=True)
 
 
@@ -636,7 +623,7 @@ class Geom:
             Assume geometry to be periodic. Defaults to True.
 
         """
-        self.add_comments(util.edit_info('damask.Result.'+inspect.stack()[0][3]))
+        self.add_comments(util.edit_info('damask.Geom.'+inspect.stack()[0][3]))
         return self.update(
                            ndimage.interpolation.zoom(
                                                       self.microstructure,
@@ -671,7 +658,7 @@ class Geom:
             else:
                 return me
 
-        self.add_comments(util.edit_info('damask.Result.'+inspect.stack()[0][3]))
+        self.add_comments(util.edit_info('damask.Geom.'+inspect.stack()[0][3]))
         return self.update(ndimage.filters.generic_filter(
                                                           self.microstructure,
                                                           mostFrequent,
@@ -688,7 +675,7 @@ class Geom:
         for i, oldID in enumerate(np.unique(self.microstructure)):
             renumbered = np.where(self.microstructure == oldID, i+1, renumbered)
 
-        self.add_comments(util.edit_info('damask.Result.'+inspect.stack()[0][3]))
+        self.add_comments(util.edit_info('damask.Geom.'+inspect.stack()[0][3]))
         return self.update(renumbered)
 
 
@@ -723,7 +710,7 @@ class Geom:
 
         origin = self.origin-(np.asarray(microstructure_in.shape)-self.grid)*.5 * self.size/self.grid
 
-        self.add_comments(util.edit_info('damask.Result.'+inspect.stack()[0][3]))
+        self.add_comments(util.edit_info('damask.Geom.'+inspect.stack()[0][3]))
         return self.update(microstructure_in,origin=origin,rescale=True)
 
 
@@ -756,7 +743,7 @@ class Geom:
 
         canvas[ll[0]:ur[0],ll[1]:ur[1],ll[2]:ur[2]] = self.microstructure[LL[0]:UR[0],LL[1]:UR[1],LL[2]:UR[2]]
 
-        self.add_comments(util.edit_info('damask.Result.'+inspect.stack()[0][3]))
+        self.add_comments(util.edit_info('damask.Geom.'+inspect.stack()[0][3]))
         return self.update(canvas,origin=self.origin+offset*self.size/self.grid,rescale=True)
 
 
@@ -776,7 +763,7 @@ class Geom:
         for from_ms,to_ms in zip(from_microstructure,to_microstructure):
             substituted[self.microstructure==from_ms] = to_ms
 
-        self.add_comments(util.edit_info('damask.Result.'+inspect.stack()[0][3]))
+        self.add_comments(util.edit_info('damask.Geom.'+inspect.stack()[0][3]))
         return self.update(substituted)
 
 
@@ -822,5 +809,5 @@ class Geom:
                                               extra_keywords={'trigger':trigger})
         microstructure = np.ma.MaskedArray(self.microstructure + offset_, np.logical_not(mask))
 
-        self.add_comments(util.edit_info('damask.Result.'+inspect.stack()[0][3]))
+        self.add_comments(util.edit_info('damask.Geom.'+inspect.stack()[0][3]))
         return self.update(microstructure)