dataset.add_symlink_layer handles Layer argument (#389)

* add_symlink_layer can now handle a Layer argument

* update changelog

* use path api

* Update Changelog.md

Co-authored-by: R Schwanhold <[email protected]>

Co-authored-by: R Schwanhold <[email protected]>

Author: valentin-pinkau

Changelog.md

@@ -12,6 +12,7 @@ For upgrade instructions, please check the respective *Breaking Changes* section
 ### Breaking Changes in Config & CLI
 
 ### Added
+- `dataset.add_symlink_layer` and `dataset.add_copy_layer` can now handle `Layer` arguments as well. The parameter `foreign_layer_path` was renamed to `foreign_layer`. [#389](https://github.com/scalableminds/webknossos-cuber/pull/389)
 
 ### Changed
 - Bump scipy to `1.6.0` and `scikit-image` to `0.18.0` while keeping `numpy` to under `1.20.0` [#372](https://github.com/scalableminds/webknossos-cuber/pull/372/files)

wkcuber/api/dataset.py

@@ -409,16 +409,22 @@ def delete_layer(self, layer_name: str) -> None:
         rmtree(join(self.path, layer_name))
 
     def add_symlink_layer(
-        self, foreign_layer_path: Union[str, Path], make_relative: bool = False
+        self, foreign_layer: Union[str, Path, Layer], make_relative: bool = False
     ) -> Layer:
         """
-        Creates a symlink to the data at `foreign_layer_path` which belongs to another dataset.
+        Creates a symlink to the data at `foreign_layer` which belongs to another dataset.
         The relevant information from the `datasource-properties.json` of the other dataset is copied to this dataset.
         Note: If the other dataset modifies its bounding box afterwards, the change does not affect this properties
         (or vice versa).
         If make_relative is True, the symlink is made relative to the current dataset path.
         """
-        foreign_layer_path = Path(os.path.abspath(foreign_layer_path))
+
+        if isinstance(foreign_layer, Layer):
+            foreign_layer_path = foreign_layer.path
+        else:
+            foreign_layer_path = Path(foreign_layer).absolute()
+
+        foreign_layer_path = foreign_layer_path.resolve()
         layer_name = foreign_layer_path.name
         if layer_name in self.layers.keys():
             raise IndexError(
@@ -451,13 +457,18 @@ def add_symlink_layer(
             self.get_layer(layer_name)._setup_mag(resolution.mag.to_layer_name())
         return self.layers[layer_name]
 
-    def add_copy_layer(self, foreign_layer_path: Union[str, Path]) -> Layer:
+    def add_copy_layer(self, foreign_layer: Union[str, Path, Layer]) -> Layer:
         """
-        Copies the data at `foreign_layer_path` which belongs to another dataset to the current dataset.
+        Copies the data at `foreign_layer` which belongs to another dataset to the current dataset.
         Additionally, the relevant information from the `datasource-properties.json` of the other dataset are copied too.
         """
 
-        foreign_layer_path = Path(os.path.abspath(foreign_layer_path))
+        if isinstance(foreign_layer, Layer):
+            foreign_layer_path = foreign_layer.path
+        else:
+            foreign_layer_path = Path(foreign_layer)
+
+        foreign_layer_path = foreign_layer_path.resolve()
         layer_name = foreign_layer_path.name
         if layer_name in self.layers.keys():
             raise IndexError(

wkcuber/api/layer.py

@@ -86,8 +86,11 @@ def __init__(
         self.num_channels = num_channels
         self._mags: Dict[Mag, MagView] = {}
 
-        full_path = join(dataset.path, name)
-        makedirs(full_path, exist_ok=True)
+        makedirs(self.path, exist_ok=True)
+
+    @property
+    def path(self) -> Path:
+        return Path(join(self.dataset.path, self.name))
 
     @property
     def mags(self) -> Dict[Mag, MagView]: