Rename layer (#368)

* rename layer

* update changelog

* update dict when renaming a layer

Author: rschwanhold

Changelog.md

@@ -14,6 +14,7 @@ For upgrade instructions, please check the respective *Breaking Changes* section
 
 ### Added
 - Added functions to `wkcuber.api.dataset.Dataset` and `wkcuber.api.layer.Layer` to set and get the view configuration. [#344](https://github.com/scalableminds/webknossos-cuber/pull/344)
+- Added option to rename a layer. [#368](https://github.com/scalableminds/webknossos-cuber/pull/368)
 
 ### Changed
 

tests/test_dataset.py

@@ -1647,3 +1647,23 @@ def test_add_copy_layer(tmp_path: Path) -> None:
 
     # Test if the changes of the properties are persisted on disk by opening it again
     assert "color" in Dataset(tmp_path / "ds").layers.keys()
+
+
+def test_rename_layer(tmp_path: Path) -> None:
+    ds = Dataset.create(tmp_path / "ds", scale=(1, 1, 1))
+    layer = ds.add_layer("color", LayerCategories.COLOR_TYPE)
+    mag = layer.add_mag(1)
+    write_data = (np.random.rand(10, 20, 30) * 255).astype(np.uint8)
+    mag.write(data=write_data)
+
+    layer.rename("color2")
+
+    assert not (tmp_path / "ds" / "color").exists()
+    assert (tmp_path / "ds" / "color2").exists()
+    assert "color2" in ds.properties.data_layers.keys()
+    assert "color2" == ds.properties.data_layers["color2"].name
+    assert "color2" in ds.layers.keys()
+    assert "color" not in ds.layers.keys()
+
+    # The "mag" object which was created before renaming the layer is still valid
+    assert np.array_equal(mag.read()[0], write_data)

wkcuber/api/layer.py

@@ -1,5 +1,6 @@
 import logging
 import math
+import os
 from argparse import Namespace
 from shutil import rmtree
 from os.path import join
@@ -254,6 +255,31 @@ def set_bounding_box_size(self, size: Tuple[int, int, int]) -> None:
     def get_bounding_box(self) -> BoundingBox:
         return self.dataset.properties.data_layers[self.name].get_bounding_box()
 
+    def rename(self, layer_name: str) -> None:
+        """
+        Renames the layer to `layer_name`. This changes the name of the directory on disk and updates the properties.
+        """
+        assert (
+            layer_name not in self.dataset.layers.keys()
+        ), f"Failed to rename layer {self.name} to {layer_name}: The new name already exists."
+        os.rename(self.dataset.path / self.name, self.dataset.path / layer_name)
+        layer_properties = self.dataset.properties.data_layers[self.name]
+        layer_properties._name = layer_name
+        del self.dataset.properties.data_layers[self.name]
+        self.dataset.properties._data_layers[layer_name] = layer_properties
+        self.dataset.properties._export_as_json()
+        del self.dataset.layers[self.name]
+        self.dataset.layers[layer_name] = self
+        self.name = layer_name
+
+        # The MagViews need to be updated
+        for mag in self._mags.values():
+            mag.path = _find_mag_path_on_disk(self.dataset.path, self.name, mag.name)
+            if mag._is_opened:
+                # Reopen handle to dataset on disk
+                mag.close()
+                mag.open()
+
     def downsample(
         self,
         from_mag: Optional[Mag] = None,