Merge branch 'improved-load_DREAM3D-test' into 'development'

more thorough check

See merge request damask/DAMASK!936

Author: dmentock

python/damask/_configmaterial.py

@@ -106,11 +106,20 @@ def load_DREAM3D(fname: str,
 
         Notes
         -----
-        damask.GeomGrid.load_DREAM3D gives the corresponding geometry for
-        the grid solver.
-
-        For cell-wise data, only unique combinations of
-        orientation and phase are considered.
+        A grain-wise material configuration is based on segmented data from
+        the DREAM.3D file. This data is typically available when the microstructure
+        was synthetically created. In cell-wise representations, cells having the
+        same orientation and phase are grouped. Since synthetically created
+        microstructures have typically no in-grain scatter, cell-wise grids
+        can appear to be segmented.
+
+        damask.GeomGrid.load_DREAM3D creates the corresponding grid-based
+        geometry definition. Since the numbering of materials in cell-wise
+        and grain-wise grids is different, it is imperative to use the same
+        mode for both load_DREAM3D functions. That means, if the "grain_data"
+        argument is used for this function, the correct grid configuration
+        is only obtained if the "feature_IDs" argument is used when calling
+        damask.GeomGrid.load_DREAM3D.
 
         Homogenization and phase entries are emtpy and need to be
         defined separately.

python/damask/_geomgrid.py

@@ -212,7 +212,7 @@ def _load(fname: Union[str, Path], label: str) -> 'GeomGrid':
         Returns
         -------
         loaded : damask.GeomGrid
-            GeomGrid-based geometry from file.
+            Grid-based geometry from file.
 
         """
         v = VTK.load(fname if str(fname).endswith('.vti') else str(fname)+'.vti')
@@ -241,7 +241,7 @@ def load(fname: Union[str, Path]) -> 'GeomGrid':
         Returns
         -------
         loaded : damask.GeomGrid
-            GeomGrid-based geometry from file.
+            Grid-based geometry from file.
 
         """
         return GeomGrid._load(fname,'material')
@@ -261,7 +261,7 @@ def load_SPPARKS(fname: Union[str, Path]) -> 'GeomGrid':
         Returns
         -------
         loaded : damask.GeomGrid
-            GeomGrid-based geometry from file.
+            Grid-based geometry from file.
 
         Notes
         -----
@@ -289,7 +289,7 @@ def load_ASCII(fname)-> 'GeomGrid':
         Returns
         -------
         loaded : damask.GeomGrid
-            GeomGrid-based geometry from file.
+            Grid-based geometry from file.
 
         """
         warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.0.0', DeprecationWarning,2)
@@ -362,7 +362,7 @@ def load_Neper(fname: Union[str, Path]) -> 'GeomGrid':
         Returns
         -------
         loaded : damask.GeomGrid
-            GeomGrid-based geometry from file.
+            Grid-based geometry from file.
 
         Notes
         -----
@@ -437,15 +437,24 @@ def load_DREAM3D(fname: Union[str, Path],
         Returns
         -------
         loaded : damask.GeomGrid
-            GeomGrid-based geometry from file.
+            Grid-based geometry from file.
 
         Notes
         -----
-        damask.ConfigMaterial.load_DREAM3D gives the corresponding
-        material definition.
-
-        For cell-wise data, only unique combinations of
-        orientation and phase are considered.
+        A grain-wise geometry definition is based on segmented data from the
+        DREAM.3D file. This data is typically available when the microstructure
+        was synthetically created. In cell-wise representations, cells having
+        the same orientation and phase are grouped. Since synthetically created
+        microstructures have typically no in-grain scatter, cell-wise grids
+        can appear to be segmented.
+
+        damask.ConfigMaterial.load_DREAM3D creates the corresponding
+        material definition. Since the numbering of materials in cell-wise
+        and grain-wise grids is different, it is imperative to use the same
+        mode for both load_DREAM3D functions. That means, if the "feature_IDs"
+        argument is used for this function, the correct material configuration
+        is only obtained if the "grain_data" argument is used when calling
+        damask.ConfigMaterial.load_DREAM3D.
 
         """
         with h5py.File(fname, 'r') as f:
@@ -493,7 +502,7 @@ def from_table(table: Table,
         Returns
         -------
         new : damask.GeomGrid
-            GeomGrid-based geometry from values in table.
+            Grid-based geometry from values in table.
 
         """
         cells,size,origin = grid_filters.cellsSizeOrigin_coordinates0_point(table.get(coordinates))
@@ -548,7 +557,7 @@ def from_Laguerre_tessellation(cells: IntSequence,
         Returns
         -------
         new : damask.GeomGrid
-            GeomGrid-based geometry from tessellation.
+            Grid-based geometry from tessellation.
 
         """
         weights_p: FloatSequence
@@ -604,7 +613,7 @@ def from_Voronoi_tessellation(cells: IntSequence,
         Returns
         -------
         new : damask.GeomGrid
-            GeomGrid-based geometry from tessellation.
+            Grid-based geometry from tessellation.
 
         """
         coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
@@ -691,7 +700,7 @@ def from_minimal_surface(cells: IntSequence,
         Returns
         -------
         new : damask.GeomGrid
-            GeomGrid-based geometry from definition of minimal surface.
+            Grid-based geometry from definition of minimal surface.
 
         Notes
         -----

python/tests/test_GeomGrid.py

@@ -9,6 +9,7 @@
 from damask import Table
 from damask import Rotation
 from damask import Colormap
+from damask import ConfigMaterial
 from damask import util
 from damask import seeds
 from damask import grid_filters
@@ -491,12 +492,24 @@ def test_get_grain_boundaries_invalid(self,default,directions):
             default.get_grain_boundaries(directions=directions)
 
     def test_load_DREAM3D(self,res_path):
-        grain = GeomGrid.load_DREAM3D(res_path/'2phase_irregularGrid.dream3d','FeatureIds')
-        point = GeomGrid.load_DREAM3D(res_path/'2phase_irregularGrid.dream3d')
-
-        assert np.allclose(grain.origin,point.origin) and \
-               np.allclose(grain.size,point.size) and \
-               (grain.sort().material == point.material+1).all()
+        """
+        For synthetic microstructures (no in-grain scatter), check that:
+        1) the sorted and renumbered grain-wise representation is equivalent to the cell-wise representation.
+        2) the same orientations are assigned to each cell for the grain-wise and cell-wise approaches.
+        """
+        # grain-wise data (using existing DREAM.3D segmentation)
+        grid_grain = GeomGrid.load_DREAM3D(res_path/'2phase_irregularGrid.dream3d','FeatureIds')
+        material_grain = ConfigMaterial.load_DREAM3D(res_path/'2phase_irregularGrid.dream3d','Grain Data')
+        O_grain = np.array([material['constituents'][0]['O'] for material in material_grain['material']])
+        # cell-wise data (clustering identical orientation-phase combinations)
+        grid_cell = GeomGrid.load_DREAM3D(res_path/'2phase_irregularGrid.dream3d')
+        material_cell = ConfigMaterial.load_DREAM3D(res_path/'2phase_irregularGrid.dream3d')
+        O_cell = np.array([material['constituents'][0]['O'] for material in material_cell['material']])
+
+        assert np.allclose(grid_grain.origin,grid_cell.origin) and \
+               np.allclose(grid_grain.size,grid_cell.size) and \
+               np.allclose(O_grain[grid_grain.material],O_cell[grid_cell.material]) and \
+               (grid_grain.renumber().sort().material == grid_cell.material).all()
 
     def test_load_DREAM3D_reference(self,res_path,update):
         current   = GeomGrid.load_DREAM3D(res_path/'measured.dream3d')