improving import from DREAM.3D

- no duplicated entries even for non-segmented data
- using phase labels from file
- material.yaml: Dummy homogenization and phase
- tests to ensure correct order and match between Grid and
  ConfigMaterial

python/damask/_configmaterial.py

@@ -1,4 +1,4 @@
-from os import path
+import os.path
 
 import numpy as np
 import h5py
@@ -98,7 +98,10 @@ class ConfigMaterial(Config):
 
 
     @staticmethod
-    def load_DREAM3D(fname,data_group,ori_data,phase_id,phase_name,base_group=None):
+    def load_DREAM3D(fname,
+                     grain_data=None,cell_data='CellData',cell_ensemble_data='CellEnsembleData',
+                     phases='Phases',Euler_angles='EulerAngles',phase_names='PhaseName',
+                     base_group=None):
         """
         Load material data from DREAM3D file.
 
@@ -107,70 +110,33 @@ class ConfigMaterial(Config):
         Parameters
         ----------
         fname : str
-            path to the DREAM3D file.
+            Filename of the DREAM.3D (HDF5) file.
         base_group : str
-            Name of the group (folder) below 'DataContainers',
+            Path to the group (folder) that contains the geometry (_SIMPL_GEOMETRY),
-            for example 'SyntheticVolumeDataContainer'.
+            and, optionally, the cell data. Defaults to None, in which case
-        data_group : str
+            it is set as the path that contains _SIMPL_GEOMETRY/SPACING.
-            Name of the group (folder) having relevant data for conversion,
-            for example 'Grain Data' or 'CellData'.
-        ori_data : str
-            Name of the dataset having orientation data (working with Euler Angles in dream3D file),
-            For example 'EulerAngles'.
-        phase_id : str
-            Name of the dataset containing phase IDs for each grain,
-            for example 'Phases'.
-        phase_name : list
-            List with name of the phases.
-
-        Examples
-        --------
-        for grain based data with single phase
-        >>> import damask
-        >>> import damask.ConfigMaterial as cm
-        >>> cm.load_from_Dream3D('20grains16x16x16.dream3D','SyntheticVolumeDataContainer', 'Grain Data',
-        ...                      'EulerAngles','Phases',['Ferrite'])
-
-        for point based data with single phase
-        >>> import damask
-        >>> import damask.ConfigMaterial as cm
-        >>> cm.load_from_Dream3D('20grains16x16x16.dream3D','SyntheticVolumeDataContainer', 'CellData',
-        ...                       'EulerAngles','Phases',['Ferrite'])
-
-        for grain based data with dual phase
-        >>> import damask
-        >>> import damask.ConfigMaterial as cm
-        >>> cm.load_from_Dream3D('20grains16x16x16.dream3D','SyntheticVolumeDataContainer', 'Grain Data',
-        ...                       'EulerAngles','Phases',['Ferrite','Martensite'])
-
-        for point based data with dual phase
-        >>> import damask
-        >>> import damask.ConfigMaterial as cm
-        >>> cm.load_from_Dream3D('20grains16x16x16.dream3D','SyntheticVolumeDataContainer', 'CellData',
-        ...                       'EulerAngles','Phases',['Ferrite','Martensite'])
 
         """
         b = util.DREAM3D_base_group(fname) if base_group is None else base_group
-        hdf = h5py.File(fname,'r')
+        f = h5py.File(fname,'r')
 
-        orientation_path = path.join(b,data_group,ori_data)
+        if grain_data is None:
-        if hdf[orientation_path].attrs['TupleDimensions'].shape == (3,):
+            phase = f[os.path.join(b,cell_data,phases)][()].flatten()
-           grain_orientations = np.array(hdf[orientation_path]).reshape(-1,3,order='F')
+            O = Rotation.from_Euler_angles(f[os.path.join(b,cell_data,Euler_angles)]).as_quaternion().reshape(-1,4) # noqa
+            _,idx = np.unique(np.hstack([O,phase.reshape(-1,1)]),return_index=True,axis=0)
+            idx = np.sort(idx)
         else:
-           grain_orientations = np.array(hdf[orientation_path])[1:]
+            phase = f[os.path.join(b,grain_data,phases)][()]
+            O = Rotation.from_Euler_angles(f[os.path.join(b,grain_data,Euler_angles)]).as_quaternion() # noqa
+            idx = np.arange(phase.size)
 
-        grain_quats = Rotation.from_Euler_angles(grain_orientations).as_quaternion()
+        if cell_ensemble_data is not None:
+            names = np.array([s.decode() for s in f[os.path.join(b,cell_ensemble_data,phase_names)]])
+            phase = names[phase]
 
-        phase_path  = path.join(b,data_group,phase_id)
+        material = {k:np.atleast_1d(v[idx].squeeze()) for k,v in zip(['O','phase'],[O,phase])}
-        if hdf[phase_path].attrs['TupleDimensions'].shape == (3,):
+        return ConfigMaterial({'phase':{k if isinstance(k,int) else str(k):'tbd' for k in np.unique(phase)},
-           grain_phase = np.array(hdf[phase_path]).reshape(-1,order='F')
+                               'homogenization':{'direct':{'N_constituents':1}}}).material_add(**material)
-        else:
-           grain_phase = np.array(hdf[phase_path])[1:]
-
-        grain_phase = grain_phase.reshape(len(grain_phase),)
-        phase_name_list = [phase_name[i - 1] for i in grain_phase]
-
-        return ConfigMaterial().material_add(phase=phase_name_list, O = grain_quats)                # noqa
 
 
     @property

python/damask/_grid.py

@@ -256,14 +256,17 @@ class Grid:
 
 
     @staticmethod
-    def load_DREAM3D(fname,cell_data=None,material='FeatureIds',base_group=None):
+    def load_DREAM3D(fname,
+                     feature_IDs=None,cell_data='CellData',
+                     phases='Phases',Euler_angles='EulerAngles',
+                     base_group=None):
         """
         Load from DREAM.3D file.
 
         Parameters
         ----------
         fname : str
-            Filename of the DREAM.3D file
+            Filename of the DREAM.3D (HDF5) file.
         cell_data : str, optional
             Name of the group (folder) containing the pointwise material data,
             for example 'CellData'. Defaults to None, in which case points are consecutively numbered.
@@ -279,11 +282,17 @@ class Grid:
         b = util.DREAM3D_base_group(fname) if base_group is None else base_group
         f = h5py.File(fname, 'r')
         cells  = f[os.path.join(b,'_SIMPL_GEOMETRY','DIMENSIONS')][()]
-        size   = f[os.path.join(b,'_SIMPL_GEOMETRY','SPACING')][()] * cells
+        size   = f[os.path.join(b,'_SIMPL_GEOMETRY','SPACING')] * cells
         origin = f[os.path.join(b,'_SIMPL_GEOMETRY','ORIGIN')][()]
 
-        ma = np.arange(cells.prod(),dtype=int) if cell_data is None else \
+        if feature_IDs is None:
-             np.reshape(f[os.path.join(b,cell_data,material)],cells.prod())
+            phase = f[os.path.join(b,cell_data,phases)][()].reshape(-1,1)
+            O = Rotation.from_Euler_angles(f[os.path.join(b,cell_data,Euler_angles)]).as_quaternion().reshape(-1,4) # noqa
+            unique,unique_inverse = np.unique(np.hstack([O,phase]),return_inverse=True,axis=0)
+            ma = np.arange(cells.prod()) if len(unique) == cells.prod() else \
+                 np.arange(unique.size)[np.argsort(pd.unique(unique_inverse))][unique_inverse]
+        else:
+            ma = f[os.path.join(b,cell_data,feature_IDs)][()].flatten()
 
         return Grid(ma.reshape(cells,order='F'),size,origin,util.execution_stamp('Grid','load_DREAM3D'))
 

python/tests/test_ConfigMaterial.py

@@ -6,6 +6,7 @@ import numpy as np
 from damask import ConfigMaterial
 from damask import Table
 from damask import Rotation
+from damask import Grid
 
 @pytest.fixture
 def ref_path(ref_path_base):
@@ -108,3 +109,24 @@ class TestConfigMaterial:
         m = ConfigMaterial().material_add(**kw)
         assert len(m['material']) == N
         assert len(m['material'][0]['constituents']) == n
+
+
+    @pytest.mark.parametrize('cell_ensemble_data',[None,'CellEnsembleData'])
+    def test_load_DREAM3D(self,ref_path,cell_ensemble_data):
+        grain_c = ConfigMaterial.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d','Grain Data',
+                  cell_ensemble_data = cell_ensemble_data)
+        point_c = ConfigMaterial.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d',
+                  cell_ensemble_data = cell_ensemble_data)
+
+        assert point_c.is_valid and grain_c.is_valid
+        assert len(point_c['material'])+1 == len(grain_c['material'])
+
+        grain_m = Grid.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d','FeatureIds').material.flatten()
+        point_m = Grid.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d').material.flatten()
+
+        for i in np.unique(point_m):
+            j = int(grain_m[(point_m==i).nonzero()[0][0]])
+            assert np.allclose(point_c['material'][i]['constituents'][0]['O'],
+                               grain_c['material'][j]['constituents'][0]['O'])
+            assert point_c['material'][i]['constituents'][0]['phase'] == \
+                   grain_c['material'][j]['constituents'][0]['phase']

python/tests/test_Grid.py

@@ -420,12 +420,22 @@ class TestGrid:
         t = Table(np.column_stack((coords.reshape(-1,3,order='F'),grid.material.flatten(order='F'))),{'c':3,'m':1})
         assert grid_equal(grid.sort().renumber(),Grid.from_table(t,'c',['m']))
 
+
     @pytest.mark.parametrize('periodic',[True,False])
     @pytest.mark.parametrize('direction',['x','y','z',['x','y'],'zy','xz',['x','y','z']])
     def test_get_grain_boundaries(self,update,ref_path,periodic,direction):
-        grid=Grid.load(ref_path/'get_grain_boundaries_8g12x15x20.vtr')
+        grid = Grid.load(ref_path/'get_grain_boundaries_8g12x15x20.vtr')
-        current=grid.get_grain_boundaries(periodic,direction)
+        current = grid.get_grain_boundaries(periodic,direction)
         if update:
             current.save(ref_path/f'get_grain_boundaries_8g12x15x20_{direction}_{periodic}.vtu',parallel=False)
-        reference=VTK.load(ref_path/f'get_grain_boundaries_8g12x15x20_{"".join(direction)}_{periodic}.vtu')
+        reference = VTK.load(ref_path/f'get_grain_boundaries_8g12x15x20_{"".join(direction)}_{periodic}.vtu')
         assert current.__repr__() == reference.__repr__()
+
+
+    def test_load_DREAM3D(self,ref_path):
+        grain = Grid.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d','FeatureIds')
+        point = Grid.load_DREAM3D(ref_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()