From c9a00dc4c9a82c489b9df296d1c93fb52cd421c6 Mon Sep 17 00:00:00 2001
From: Mark Bader <markbader64@gmail.com>
Date: Tue, 23 May 2023 12:28:31 +0200
Subject: [PATCH] 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.
---
 webknossos/Changelog.md                       |  1 +
 .../datasource-properties.zarr-fixture.json   | 26 ++++++++++++++++---
 webknossos/webknossos/dataset/layer.py        | 10 +++++++
 webknossos/webknossos/dataset/properties.py   |  1 +
 4 files changed, 34 insertions(+), 4 deletions(-)

diff --git a/webknossos/Changelog.md b/webknossos/Changelog.md
index 50194ec17..d3e28b281 100644
--- 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
index a4900b3b4..e2fb5a896 100644
--- 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
+  ]
+}
\ No newline at end of file
diff --git a/webknossos/webknossos/dataset/layer.py b/webknossos/webknossos/dataset/layer.py
index bc4d8e06d..1be8ffdce 100644
--- 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
index b04df0305..49fcf605a 100644
--- 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: