Merge branch 'load-DREAM3d-improvements' into 'development'

Load dream3d improvements

See merge request damask/DAMASK!821

python/damask/_configmaterial.py

@@ -106,15 +106,12 @@ class ConfigMaterial(Config):
         Load DREAM.3D (HDF5) file.
 
         Data in DREAM.3D files can be stored per cell ('CellData')
-        and/or per grain ('Grain Data'). Per default, cell-wise data
+        and/or per grain ('Grain Data'). Per default, i.e. if
-        is assumed.
+        'grain_data' is None, cell-wise data is assumed.
-
-        damask.Grid.load_DREAM3D allows to get the corresponding geometry
-        for the grid solver.
 
         Parameters
         ----------
-        fname : str
+        fname : str or pathlib.Path
             Filename of the DREAM.3D (HDF5) file.
         grain_data : str
             Name of the group (folder) containing grain-wise data. Defaults
@@ -140,36 +137,43 @@ class ConfigMaterial(Config):
             and grain- or cell-wise data. Defaults to None, in which case
             it is set as the path that contains _SIMPL_GEOMETRY/SPACING.
 
-        Notes
-        -----
-        Homogenization and phase entries are emtpy and need to be defined separately.
-
         Returns
         -------
         loaded : damask.ConfigMaterial
             Material configuration from file.
 
+        Notes
+        -----
+        damask.Grid.load_DREAM3D gives the corresponding geometry for
+        the grid solver.
+
+        For cell-wise data, only unique combinations of
+        orientation and phase are considered.
+
+        Homogenization and phase entries are emtpy and need to be
+        defined separately.
+
         """
-        b = util.DREAM3D_base_group(fname) if base_group is None else base_group
+        with h5py.File(fname, 'r') as f:
-        c = util.DREAM3D_cell_data_group(fname) if cell_data is None else cell_data
+            b = util.DREAM3D_base_group(f) if base_group is None else base_group
-        f = h5py.File(fname,'r')
+            c = util.DREAM3D_cell_data_group(f) if cell_data is None else cell_data
 
-        if grain_data is None:
+            if grain_data is None:
-            phase = f['/'.join([b,c,phases])][()].flatten()
+                phase = f['/'.join([b,c,phases])][()].flatten()
-            O = Rotation.from_Euler_angles(f['/'.join([b,c,Euler_angles])]).as_quaternion().reshape(-1,4) # noqa
+                O = Rotation.from_Euler_angles(f['/'.join([b,c,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.unique(np.hstack([O,phase.reshape(-1,1)]),return_index=True,axis=0)
-            idx = np.sort(idx)
+                idx = np.sort(idx)
-        else:
+            else:
-            phase = f['/'.join([b,grain_data,phases])][()]
+                phase = f['/'.join([b,grain_data,phases])][()]
-            O = Rotation.from_Euler_angles(f['/'.join([b,grain_data,Euler_angles])]).as_quaternion() # noqa
+                O = Rotation.from_Euler_angles(f['/'.join([b,grain_data,Euler_angles])]).as_quaternion() # noqa
-            idx = np.arange(phase.size)
+                idx = np.arange(phase.size)
 
-        if cell_ensemble_data is not None and phase_names is not None:
+            if cell_ensemble_data is not None and phase_names is not None:
-            try:
+                try:
-                names = np.array([s.decode() for s in f['/'.join([b,cell_ensemble_data,phase_names])]])
+                    names = np.array([s.decode() for s in f['/'.join([b,cell_ensemble_data,phase_names])]])
-                phase = names[phase]
+                    phase = names[phase]
-            except KeyError:
+                except KeyError:
-                pass
+                    pass
 
 
         base_config = ConfigMaterial({'phase':{k if isinstance(k,int) else str(k): None for k in np.unique(phase)},

python/damask/_grid.py

@@ -358,14 +358,14 @@ class Grid:
         """
         Load DREAM.3D (HDF5) file.
 
-        Data in DREAM.3D files can be stored per cell ('CellData') and/or
+        Data in DREAM.3D files can be stored per cell ('CellData')
-        per grain ('Grain Data'). Per default, cell-wise data is assumed.
+        and/or per grain ('Grain Data'). Per default, i.e. if
+        'feature_IDs' is None, cell-wise data is assumed.
 
-        damask.ConfigMaterial.load_DREAM3D gives the corresponding material definition.
 
         Parameters
         ----------
-        fname : str or or pathlib.Path
+        fname : str or pathlib.Path
             Filename of the DREAM.3D (HDF5) file.
         feature_IDs : str, optional
             Name of the dataset containing the mapping between cells and
@@ -392,23 +392,31 @@ class Grid:
         loaded : damask.Grid
             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.
+
         """
-        b = util.DREAM3D_base_group(fname)      if base_group is None else base_group
+        with h5py.File(fname, 'r') as f:
-        c = util.DREAM3D_cell_data_group(fname) if cell_data  is None else cell_data
+            b = util.DREAM3D_base_group(f) if base_group is None else base_group
-        f = h5py.File(fname, 'r')
+            c = util.DREAM3D_cell_data_group(f) if cell_data is None else cell_data
 
-        cells  = f['/'.join([b,'_SIMPL_GEOMETRY','DIMENSIONS'])][()]
+            cells  = f['/'.join([b,'_SIMPL_GEOMETRY','DIMENSIONS'])][()]
-        size   = f['/'.join([b,'_SIMPL_GEOMETRY','SPACING'])] * cells
+            size   = f['/'.join([b,'_SIMPL_GEOMETRY','SPACING'])] * cells
-        origin = f['/'.join([b,'_SIMPL_GEOMETRY','ORIGIN'])][()]
+            origin = f['/'.join([b,'_SIMPL_GEOMETRY','ORIGIN'])][()]
 
-        if feature_IDs is None:
+            if feature_IDs is None:
-            phase = f['/'.join([b,c,phases])][()].reshape(-1,1)
+                phase = f['/'.join([b,c,phases])][()].reshape(-1,1)
-            O = Rotation.from_Euler_angles(f['/'.join([b,c,Euler_angles])]).as_quaternion().reshape(-1,4) # noqa
+                O = Rotation.from_Euler_angles(f['/'.join([b,c,Euler_angles])]).as_quaternion().reshape(-1,4) # noqa
-            unique,unique_inverse = np.unique(np.hstack([O,phase]),return_inverse=True,axis=0)
+                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 \
+                ma = np.arange(cells.prod()) if len(unique) == cells.prod() else \
-                 np.arange(unique.size)[np.argsort(pd.unique(unique_inverse))][unique_inverse]
+                     np.arange(unique.size)[np.argsort(pd.unique(unique_inverse))][unique_inverse]
-        else:
+            else:
-            ma = f['/'.join([b,c,feature_IDs])][()].flatten()
+                ma = f['/'.join([b,c,feature_IDs])][()].flatten()
 
         return Grid(material = ma.reshape(cells,order='F'),
                     size     = size,

python/damask/util.py

@@ -698,7 +698,7 @@ def pass_on(keyword: str,
         return wrapper
     return decorator
 
-def DREAM3D_base_group(fname: _Union[str, _Path]) -> str:
+def DREAM3D_base_group(fname: _Union[str, _Path, _h5py.File]) -> str:
     """
     Determine the base group of a DREAM.3D file.
 
@@ -707,7 +707,7 @@ def DREAM3D_base_group(fname: _Union[str, _Path]) -> str:
 
     Parameters
     ----------
-    fname : str or pathlib.Path
+    fname : str, pathlib.Path, or _h5py.File
         Filename of the DREAM.3D (HDF5) file.
 
     Returns
@@ -716,15 +716,19 @@ def DREAM3D_base_group(fname: _Union[str, _Path]) -> str:
         Path to the base group.
 
     """
-    with _h5py.File(_Path(fname).expanduser(),'r') as f:
+    def get_base_group(f: _h5py.File) -> str:
         base_group = f.visit(lambda path: path.rsplit('/',2)[0] if '_SIMPL_GEOMETRY/SPACING' in path else None)
+        if base_group is None:
+            raise ValueError(f'could not determine base group in file "{fname}"')
+        return base_group
 
-    if base_group is None:
+    if isinstance(fname,_h5py.File):
-        raise ValueError(f'could not determine base group in file "{fname}"')
+        return get_base_group(fname)
 
-    return base_group
+    with _h5py.File(_Path(fname).expanduser(),'r') as f:
+        return get_base_group(f)
 
-def DREAM3D_cell_data_group(fname: _Union[str, _Path]) -> str:
+def DREAM3D_cell_data_group(fname: _Union[str, _Path, _h5py.File]) -> str:
     """
     Determine the cell data group of a DREAM.3D file.
 
@@ -734,7 +738,7 @@ def DREAM3D_cell_data_group(fname: _Union[str, _Path]) -> str:
 
     Parameters
     ----------
-    fname : str or pathlib.Path
+    fname : str, pathlib.Path, or h5py.File
         Filename of the DREAM.3D (HDF5) file.
 
     Returns
@@ -743,17 +747,21 @@ def DREAM3D_cell_data_group(fname: _Union[str, _Path]) -> str:
         Path to the cell data group.
 
     """
-    base_group = DREAM3D_base_group(fname)
+    def get_cell_data_group(f: _h5py.File) -> str:
-    with _h5py.File(_Path(fname).expanduser(),'r') as f:
+        base_group = DREAM3D_base_group(f)
         cells = tuple(f['/'.join([base_group,'_SIMPL_GEOMETRY','DIMENSIONS'])][()][::-1])
         cell_data_group = f[base_group].visititems(lambda path,obj: path.split('/')[0] \
                                                    if isinstance(obj,_h5py._hl.dataset.Dataset) and _np.shape(obj)[:-1] == cells \
                                                    else None)
+        if cell_data_group is None:
+            raise ValueError(f'could not determine cell-data group in file "{fname}/{base_group}"')
+        return cell_data_group
 
-    if cell_data_group is None:
+    if isinstance(fname,_h5py.File):
-        raise ValueError(f'could not determine cell-data group in file "{fname}/{base_group}"')
+        return get_cell_data_group(fname)
 
-    return cell_data_group
+    with _h5py.File(_Path(fname).expanduser(),'r') as f:
+        return get_cell_data_group(f)
 
 
 def Bravais_to_Miller(*,

python/tests/test_util.py

@@ -146,21 +146,25 @@ class TestUtil:
         assert 'DAMASK' in style('DAMASK')
 
     @pytest.mark.parametrize('complete',[True,False])
-    def test_D3D_base_group(self,tmp_path,complete):
+    @pytest.mark.parametrize('fhandle',[True,False])
+    def test_D3D_base_group(self,tmp_path,complete,fhandle):
         base_group = ''.join(random.choices('DAMASK', k=10))
         with h5py.File(tmp_path/'base_group.dream3d','w') as f:
             f.create_group('/'.join((base_group,'_SIMPL_GEOMETRY')))
             if complete:
                 f['/'.join((base_group,'_SIMPL_GEOMETRY'))].create_dataset('SPACING',data=np.ones(3))
 
+        fname = tmp_path/'base_group.dream3d'
+        if fhandle: fname = h5py.File(fname)
         if complete:
-            assert base_group == util.DREAM3D_base_group(tmp_path/'base_group.dream3d')
+            assert base_group == util.DREAM3D_base_group(fname)
         else:
             with pytest.raises(ValueError):
-                util.DREAM3D_base_group(tmp_path/'base_group.dream3d')
+                util.DREAM3D_base_group(fname)
 
     @pytest.mark.parametrize('complete',[True,False])
-    def test_D3D_cell_data_group(self,tmp_path,complete):
+    @pytest.mark.parametrize('fhandle',[True,False])
+    def test_D3D_cell_data_group(self,tmp_path,complete,fhandle):
         base_group = ''.join(random.choices('DAMASK', k=10))
         cell_data_group = ''.join(random.choices('KULeuven', k=10))
         cells = np.random.randint(1,50,3)
@@ -172,11 +176,13 @@ class TestUtil:
             if complete:
                 f['/'.join((base_group,cell_data_group))].create_dataset('data',shape=np.append(cells,1))
 
+        fname = tmp_path/'cell_data_group.dream3d'
+        if fhandle: fname = h5py.File(fname)
         if complete:
-            assert cell_data_group == util.DREAM3D_cell_data_group(tmp_path/'cell_data_group.dream3d')
+            assert cell_data_group == util.DREAM3D_cell_data_group(fname)
         else:
             with pytest.raises(ValueError):
-                util.DREAM3D_cell_data_group(tmp_path/'cell_data_group.dream3d')
+                util.DREAM3D_cell_data_group(fname)
 
 
     @pytest.mark.parametrize('full,reduced',[({},                           {}),