Add axis order zarr (#904)

* Add script for debugging the creation of properties json file. * Add axisOrder to zarr properties. * Adapt zarr related test in wkcuber. * Update Changelog.md.
scalableminds · May 23, 2023 · c9a00dc · c9a00dc
1 parent 60e78be
commit c9a00dc
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Showing 4 changed files with 34 additions and 4 deletions.
diff --git a/webknossos/Changelog.md b/webknossos/Changelog.md
@@ -23,6 +23,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 
 ### Fixed
 - Fixed poetry build backend for new versions of Poetry. [#899](https://github.com/scalableminds/webknossos-libs/pull/899)
+- Added axis_order fields for Zarr data format. [#902](https://github.com/scalableminds/webknossos-libs/issues/902)
 
 
 ## [0.12.3](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.12.3) - 2023-02-22

diff --git a/webknossos/testdata/tiff/datasource-properties.zarr-fixture.json b/webknossos/testdata/tiff/datasource-properties.zarr-fixture.json
@@ -11,17 +11,35 @@
       "elementClass": "uint8",
       "mags": [
         {
-          "mag": [1, 1, 1]
+          "mag": [
+            1,
+            1,
+            1
+          ],
+          "axisOrder": {
+            "x": 1,
+            "y": 2,
+            "z": 3,
+            "c": 0
+          }
         }
       ],
       "numChannels": 1,
       "boundingBox": {
-        "topLeft": [0, 0, 0],
+        "topLeft": [
+          0,
+          0,
+          0
+        ],
         "width": 265,
         "height": 265,
         "depth": 257
       }
     }
   ],
-  "scale": [11.24, 11.24, 25.0]
-}
+  "scale": [
+    11.24,
+    11.24,
+    25.0
+  ]
+}
diff --git a/webknossos/webknossos/dataset/layer.py b/webknossos/webknossos/dataset/layer.py
@@ -415,6 +415,11 @@ def add_mag(
                     if mag_array_info.data_format == DataFormat.WKW
                     else None
                 ),
+                axis_order=(
+                    {"x": 1, "y": 2, "z": 3, "c": 0}
+                    if mag_array_info.data_format == DataFormat.Zarr
+                    else None
+                ),
             )
         ]
 
@@ -447,6 +452,11 @@ def add_mag_for_existing_files(
                     if mag_array_info.data_format == DataFormat.WKW
                     else None
                 ),
+                axis_order=(
+                    {"x": 1, "y": 2, "z": 3, "c": 0}
+                    if mag_array_info.data_format == DataFormat.Zarr
+                    else None
+                ),
             )
         )
         self.dataset._export_as_json()

diff --git a/webknossos/webknossos/dataset/properties.py b/webknossos/webknossos/dataset/properties.py
@@ -121,6 +121,7 @@ class LayerViewConfiguration:
 class MagViewProperties:
     mag: Mag
     cube_length: Optional[int] = None
+    axis_order: Optional[Dict[str, int]] = None
 
     @property
     def resolution(self) -> Mag: