avoid repeated opening of files

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',[({},                           {}),