Better S3 Support for MagViews

webknossos/Changelog.md

@@ -18,6 +18,9 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 
 ### Changed
 - Using `x-auth-header` to send tokens to datastore. [#1270](https://github.com/scalableminds/webknossos-libs/pull/1270)
+- The `path` of mags are now always written either as absolute path or as relative path to the Dataset path. [#1278](https://github.com/scalableminds/webknossos-libs/pull/1278)
+- The `Layer.path` property now always returns `Dataset.path / layer.name`, even if all mags are stored remotely. [#1278](https://github.com/scalableminds/webknossos-libs/pull/1278)
+- `Layer.is_remote_to_dataset` is deprecated in favor of `Layer.is_foreign` and `MagView.is_remote_to_dataset` is deprecated in favor of `MagView.is_foreign`. [#1278](https://github.com/scalableminds/webknossos-libs/pull/1278)
 
 ### Fixed
 

webknossos/pyproject.toml

@@ -76,7 +76,7 @@ examples = [
     "s3fs >=2023.9.0",
     "tabulate >=0.9.0",
     "scikit-learn ~=1.5.1",
-    "scikit-image ~=0.24.0"
+    "scikit-image ~=0.25.0"
 ]
 all = [
     "webknossos[tifffile]",

webknossos/testdata/simple_wkw_dataset/datasource-properties.json

@@ -23,7 +23,8 @@
       "wkwResolutions": [
         {
           "resolution": [1, 1, 1],
-          "cubeLength": 32
+          "cubeLength": 32,
+          "path": "color/1"
         }
       ],
       "defaultViewConfiguration": {

webknossos/testdata/simple_zarr3_dataset/datasource-properties.json

@@ -18,7 +18,8 @@
       "dataFormat": "zarr3",
       "mags": [
         {
-          "mag": [1, 1, 1]
+          "mag": [1, 1, 1],
+          "path": "color/1"
         }
       ],
       "numChannels": 3,

webknossos/testdata/simple_zarr_dataset/datasource-properties.json

@@ -1,53 +1,34 @@
 {
-    "id": {
-        "name": "simple_zarr_dataset",
-        "team": ""
-    },
-    "scale": [
-        1.0,
-        1.0,
-        1.0
-    ],
-    "dataLayers": [
+  "id": {
+    "name": "simple_zarr_dataset",
+    "team": ""
+  },
+  "scale": [1.0, 1.0, 1.0],
+  "dataLayers": [
+    {
+      "name": "color",
+      "category": "color",
+      "boundingBox": {
+        "topLeft": [0, 0, 0],
+        "width": 24,
+        "height": 24,
+        "depth": 24
+      },
+      "elementClass": "uint24",
+      "dataFormat": "zarr",
+      "mags": [
         {
-            "name": "color",
-            "category": "color",
-            "boundingBox": {
-                "topLeft": [
-                    0,
-                    0,
-                    0
-                ],
-                "width": 24,
-                "height": 24,
-                "depth": 24
-            },
-            "elementClass": "uint24",
-            "dataFormat": "zarr",
-            "mags": [
-                {
-                    "mag": [
-                        1,
-                        1,
-                        1
-                    ]
-                }
-            ],
-            "numChannels": 3,
-            "defaultViewConfiguration": {
-                "color": [
-                    255,
-                    0,
-                    0
-                ]
-            }
+          "mag": [1, 1, 1],
+          "path": "color/1-1-1"
         }
-    ],
-    "defaultViewConfiguration": {
-        "position": [
-            12,
-            12,
-            12
-        ]
+      ],
+      "numChannels": 3,
+      "defaultViewConfiguration": {
+        "color": [255, 0, 0]
+      }
     }
-}
+  ],
+  "defaultViewConfiguration": {
+    "position": [12, 12, 12]
+  }
+}

webknossos/testdata/tiff/datasource-properties.zarr-fixture.json

@@ -5,41 +5,30 @@
   },
   "scale": {
     "unit": "nanometer",
-    "factor": [
-      11.24,
-      11.24,
-      25.0
-    ]
+    "factor": [11.24, 11.24, 25.0]
   },
   "dataLayers": [
     {
       "name": "tiff",
       "category": "segmentation",
       "boundingBox": {
-        "topLeft": [
-          0,
-          0,
-          0
-        ],
+        "topLeft": [0, 0, 0],
         "width": 265,
         "height": 265,
         "depth": 257
       },
       "elementClass": "uint8",
-      "dataFormat": "zarr",
+      "dataFormat": "zarr3",
       "mags": [
         {
-          "mag": [
-            1,
-            1,
-            1
-          ],
+          "mag": [1, 1, 1],
           "axisOrder": {
             "c": 0,
             "x": 1,
             "y": 2,
             "z": 3
-          }
+          },
+          "path": "tiff/1"
         }
       ],
       "numChannels": 1,