extract DataFormat into separate file

webknossos/webknossos/dataset/__init__.py

@@ -9,7 +9,7 @@
 Each dataset consists of one or more layers (webknossos.dataset.layer.Layer), which themselves can comprise multiple magnifications (webknossos.dataset.mag_view.MagView).
 """
 
-from ._array import DataFormat
+from .data_format import DataFormat
 from .dataset import Dataset, RemoteDataset
 from .layer import Layer, SegmentationLayer
 from .layer_categories import COLOR_CATEGORY, SEGMENTATION_CATEGORY, LayerCategoryType

webknossos/webknossos/dataset/_array.py

@@ -3,7 +3,6 @@
 from abc import ABC, abstractmethod
 from contextlib import contextmanager
 from dataclasses import dataclass
-from enum import Enum
 from os.path import relpath
 from pathlib import Path
 from typing import TYPE_CHECKING, Any, Dict, Iterator, List, Optional, Type, Union
@@ -15,10 +14,10 @@
 from upath import UPath
 from zarr.storage import FSStore
 
-from webknossos.dataset.defaults import WK_USE_ZARRITA
-
 from ..geometry import BoundingBox, Vec3Int, Vec3IntLike
 from ..utils import warn_deprecated
+from .data_format import DataFormat
+from .defaults import WK_USE_ZARRITA
 
 if TYPE_CHECKING:
     import zarrita
@@ -55,15 +54,6 @@ class ArrayException(Exception):
     pass
 
 
-class DataFormat(Enum):
-    WKW = "wkw"
-    Zarr = "zarr"
-    Zarr3 = "zarr3"
-
-    def __str__(self) -> str:
-        return self.value
-
-
 @dataclass
 class ArrayInfo:
     data_format: DataFormat

webknossos/webknossos/dataset/data_format.py

@@ -0,0 +1,10 @@
+from enum import Enum
+
+
+class DataFormat(Enum):
+    WKW = "wkw"
+    Zarr = "zarr"
+    Zarr3 = "zarr3"
+
+    def __str__(self) -> str:
+        return self.value

webknossos/webknossos/dataset/dataset.py

@@ -36,7 +36,8 @@
 from upath import UPath
 
 from ..geometry.vec3_int import Vec3Int, Vec3IntLike
-from ._array import ArrayException, ArrayInfo, BaseArray, DataFormat
+from ._array import ArrayException, ArrayInfo, BaseArray
+from .data_format import DataFormat
 from .defaults import (
     DEFAULT_BIT_DEPTH,
     DEFAULT_CHUNK_SHAPE,

webknossos/webknossos/dataset/defaults.py

@@ -1,7 +1,7 @@
 from os import environ
 
 from ..geometry import Vec3Int
-from ._array import DataFormat
+from .data_format import DataFormat
 
 WK_USE_ZARRITA = environ.get("WK_USE_ZARRITA") is not None
 DEFAULT_WKW_FILE_LEN = 32

webknossos/webknossos/dataset/layer.py

@@ -17,7 +17,7 @@
 from webknossos.dataset.view import View, _copy_job
 from webknossos.geometry import BoundingBox, Mag, Vec3Int, Vec3IntLike
 
-from ._array import ArrayException, BaseArray, DataFormat
+from ._array import ArrayException, BaseArray
 from ._downsampling_utils import (
     calculate_default_coarsest_mag,
     calculate_mags_to_downsample,
@@ -27,6 +27,7 @@
     parse_interpolation_mode,
 )
 from ._upsampling_utils import upsample_cube_job
+from .data_format import DataFormat
 from .layer_categories import COLOR_CATEGORY, SEGMENTATION_CATEGORY, LayerCategoryType
 from .properties import (
     LayerProperties,

webknossos/webknossos/dataset/ome_metadata.py

@@ -1,15 +1,19 @@
 import json
-from typing import Any, Dict
+from typing import TYPE_CHECKING, Any, Dict
 
 import numpy as np
 
-from ._array import DataFormat
-from .dataset import Dataset
+from .data_format import DataFormat
 from .defaults import ZARR_JSON_FILE_NAME, ZATTRS_FILE_NAME, ZGROUP_FILE_NAME
-from .layer import Layer
 
+if TYPE_CHECKING:
+    from .dataset import Dataset
+    from .layer import Layer
 
-def get_ome_0_4_multiscale_metadata(dataset: Dataset, layer: Layer) -> Dict[str, Any]:
+
+def get_ome_0_4_multiscale_metadata(
+    dataset: "Dataset", layer: "Layer"
+) -> Dict[str, Any]:
     return {
         "version": "0.4",
         "axes": [
@@ -46,7 +50,9 @@ def get_ome_0_4_multiscale_metadata(dataset: Dataset, layer: Layer) -> Dict[str,
     }
 
 
-def get_ome_zarr3_multiscale_metadata(dataset: Dataset, layer: Layer) -> Dict[str, Any]:
+def get_ome_zarr3_multiscale_metadata(
+    dataset: "Dataset", layer: "Layer"
+) -> Dict[str, Any]:
     return {
         "coordinateSystems": [
             {
@@ -79,8 +85,8 @@ def get_ome_zarr3_multiscale_metadata(dataset: Dataset, layer: Layer) -> Dict[st
                         "type": "scale",
                         "scale": [1.0]
                         + (np.array(dataset.voxel_size) * mag.mag.to_np()).tolist(),
-                        "input": mag.path.name,
-                        "output": "example",
+                        "input": f"/{mag.path.name}",
+                        "output": f"/{layer.name}",
                     }
                 ],
             }
@@ -89,7 +95,7 @@ def get_ome_zarr3_multiscale_metadata(dataset: Dataset, layer: Layer) -> Dict[st
     }
 
 
-def write_ome_0_4_metadata(dataset: Dataset) -> None:
+def write_ome_0_4_metadata(dataset: "Dataset") -> None:
     zgroup_content = {"zarr_format": "2"}
     with (dataset.path / ZGROUP_FILE_NAME).open("w", encoding="utf-8") as outfile:
         json.dump(zgroup_content, outfile, indent=4)
@@ -105,7 +111,7 @@ def write_ome_0_4_metadata(dataset: Dataset) -> None:
                 )
 
 
-def write_ome_zarr3_metadata(dataset: Dataset) -> None:
+def write_ome_zarr3_metadata(dataset: "Dataset") -> None:
     with (dataset.path / ZARR_JSON_FILE_NAME).open("w", encoding="utf-8") as outfile:
         json.dump({"zarr_format": 3, "node_type": "group"}, outfile, indent=4)
     for layer in dataset.layers.values():

webknossos/webknossos/dataset/properties.py

@@ -9,7 +9,8 @@
 from webknossos.geometry import BoundingBox, Mag, Vec3Int
 from webknossos.utils import snake_to_camel_case, warn_deprecated
 
-from ._array import ArrayException, BaseArray, DataFormat
+from ._array import ArrayException, BaseArray
+from .data_format import DataFormat
 from .layer_categories import LayerCategoryType