Merge pull request #821 from bp/hdf5_overwrite

whole array overwrite method in Model

resqpy/model/_hdf5.py

@@ -286,6 +286,14 @@ def _h5_overwrite_array_slice(model, h5_key_pair, slice_tuple, array_slice):
     dset[slice_tuple] = array_slice
 
 
+def _h5_overwrite_array(model, h5_key_pair, array):
+    """Overwrites (updates) the whole of an hdf5 array."""
+
+    h5_root = _h5_access(model, h5_key_pair[0], mode = 'a')
+    dset = h5_root[h5_key_pair[1]]
+    dset[...] = array
+
+
 def h5_clear_filename_cache(model):
     """Clears the cached filenames associated with all ext uuids."""
 

resqpy/model/_model.py

@@ -1475,6 +1475,21 @@ def h5_overwrite_array_slice(self, h5_key_pair, slice_tuple, array_slice):
 
         return m_h._h5_overwrite_array_slice(self, h5_key_pair, slice_tuple, array_slice)
 
+    def h5_overwrite_array(self, h5_key_pair, array):
+        """Overwrites (updates) the whole of an hdf5 array.
+
+        arguments:
+           h5_key_pair (uuid, string): the uuid of the hdf5 ext part and the hdf5 internal path to the
+              required hdf5 array
+           array (numpy array of shape to match existing hdf5 dataset): the data to write
+
+        notes:
+           this method naively updates an hdf5 array without using mpi to look after parallel updates;
+           metadata (such as uuid or property min, max values) is not modified in any way by the method
+        """
+
+        return m_h._h5_overwrite_array(self, h5_key_pair, array)
+
     def h5_clear_filename_cache(self):
         """Clears the cached filenames associated with all ext uuids."""
 

tests/unit_tests/model/test_model.py

@@ -741,6 +741,31 @@ def test_h5_array_element(example_model_with_properties):
     assert zone == 2
 
 
+def test_h5_overwrite_array(example_model_with_properties):
+    model = example_model_with_properties
+    zone_root = model.root(obj_type = 'DiscreteProperty', title = 'Zone')
+    assert zone_root is not None
+    key_pair = model.h5_uuid_and_path_for_node(rqet.find_nested_tags(zone_root, ['PatchOfValues', 'Values']))
+    assert key_pair is not None and all([x is not None for x in key_pair])
+    # check full array is expected size and shape
+    shape, dtype = model.h5_array_shape_and_type(key_pair)
+    assert shape == (3, 5, 5)
+    newzone = np.arange(3 * 5 * 5, dtype = int).reshape(shape)
+    model.h5_overwrite_array(key_pair, newzone)
+    model = rq.Model(model.epc_file)
+    zone_root = model.root(obj_type = 'DiscreteProperty', title = 'Zone')
+    assert zone_root is not None
+    key_pair = model.h5_uuid_and_path_for_node(rqet.find_nested_tags(zone_root, ['PatchOfValues', 'Values']))
+    model.h5_array_element(key_pair, cache_array = True, object = model, array_attribute = 'zone_reload')
+    assert model.zone_reload.shape == (3, 5, 5)
+    assert np.all(model.zone_reload == np.arange(3 * 5 * 5, dtype = int).reshape(shape))
+    slice_tuple = (slice(1), slice(2, 5), slice(1, 3))
+    model.h5_overwrite_array_slice(key_pair, slice_tuple, 0)
+    model.h5_array_element(key_pair, cache_array = True, object = model, array_attribute = 'zone_reloaded_again')
+    assert np.count_nonzero(model.zone_reloaded_again == model.zone_reload) == 69
+    assert np.min(model.zone_reloaded_again) == 0
+
+
 def add_grids(model, crs, add_lengths):
     grid_a = grr.RegularGrid(model,
                              extent_kji = (2, 2, 2),