WIP: Update rfc5 schemas

.github/workflows/validation.yml

@@ -0,0 +1,16 @@
+name: Validation
+on:
+  push:
+  pull_request:
+
+jobs:
+  validate:
+    name: Validation
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+      - run: python -mpip install --upgrade wheel tox
+      - run: tox

ngff_spec/examples/multiscales_strict/multiscales_example.json

@@ -57,7 +57,7 @@
                   "input": "2",
                   "output": "physical"
                 }
-            ]
+              ]
             }
           ],
           "type": "gaussian",

ngff_spec/examples/multiscales_strict/multiscales_example_relative.json

@@ -1,21 +1,21 @@
 {
   "multiscales": [
     {
-      "version": "0.5-dev",
+      "version": "0.6dev2",
       "name": "example",
       "coordinateSystems" : [
         {
-          "name" : "exampleCoordinateSystem",
-          "axes": [
-            {"name": "t", "type": "time", "unit": "millisecond"},
-            {"name": "c", "type": "channel"},
-            {"name": "z", "type": "space", "unit": "micrometer"},
-            {"name": "y", "type": "space", "unit": "micrometer"},
-            {"name": "x", "type": "space", "unit": "micrometer"}
-          ]
+          "name" : "world",
+          "axes": {
+            "t": {"type": "time", "unit": "millisecond"},
+            "c": {"type": "channel"},
+            "z": {"type": "space", "unit": "micrometer"},
+            "y": {"type": "space", "unit": "micrometer"},
+            "x": {"type": "space", "unit": "micrometer"}
+          }
         },
         {
-          "name" : "array_0",
+          "name" : "intrinsic",
           "axes": [
             {"name": "t", "type": "time", "unit": "millisecond"},
             {"name": "c", "type": "channel"},
@@ -27,12 +27,14 @@
       ],
       "datasets": [
         {
-          "path": "0",
-          // the transformation of other arrays are defined relative to this, the highest resolution, array
+          "path": "s0",
+          // the transformation of other arrays are
+          // defined relative to this, the highest resolution, array
           "coordinateTransformations": [{
-            "type": "identity",
-            "input": "/0",
-            "output": "array_0"
+            "type": "scale",
+            "scale": [1, 1, 1, 1, 1],
+            "input": "s0",
+            "output": "intrinsic"
           }]
         },
         {
@@ -56,21 +58,15 @@
           }]
         }
       ],
-      "coordinateTransformations": [{
-        // the time unit (0.1 milliseconds), the voxel size for all spatial axes of "0" (0.5 micrometers)
-        "type": "scale",
-        "scale": [0.1, 1.0, 0.5, 0.5, 0.5],
-        "input" : "array_0",
-        "output" : "exampleCoordinateSystem"
-      }],
-      "type": "gaussian",
-      "metadata": {
-        "description": "the fields in metadata depend on the downscaling implementation. Here, the parameters passed to the skimage function are given",
-        "method": "skimage.transform.pyramid_gaussian",
-        "version": "0.16.1",
-        "args": "[true]",
-        "kwargs": {"multichannel": true}
-      }
+      "coordinateTransformations": [
+        {
+          "name": "additional_translation",
+          "type": "translation",
+          "translation": [0, 0, 10, 20, 30],
+          "input": "intrinsic",
+          "output": "world"
+        }
+      ]
     }
   ]
 }

ngff_spec/examples/multiscales_strict/multiscales_transformations.json

@@ -3,19 +3,39 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.5",
+      "version": "0.6dev2",
       "multiscales": [
         {
-          "axes": [
+          "coordinateSystems": [
             {
-              "name": "y",
-              "type": "space",
-              "unit": "micrometer"
+              "name": "physical",
+              "axes": [
+                {
+                  "name": "y",
+                  "type": "space",
+                  "unit": "micrometer"
+                },
+                {
+                  "name": "x",
+                  "type": "space",
+                  "unit": "micrometer"
+                }
+              ]
             },
             {
-              "name": "x",
-              "type": "space",
-              "unit": "micrometer"
+              "name": "intrinsic",
+              "axes": [
+                {
+                  "name": "y",
+                  "type": "space",
+                  "unit": "micrometer"
+                },
+                {
+                  "name": "x",
+                  "type": "space",
+                  "unit": "micrometer"
+                }
+              ]
             }
           ],
           "datasets": [
@@ -24,15 +44,19 @@
               "coordinateTransformations": [
                 {
                   "scale": [1, 1],
-                  "type": "scale"
+                  "type": "scale",
+                  "input": "0",
+                  "output": "intrinsic"
                 }
               ]
             }
           ],
           "coordinateTransformations": [
             {
               "scale": [10, 10],
-              "type": "scale"
+              "type": "scale",
+              "input": "intrinsic",
+              "output": "physical"
             }
           ],
           "name": "image_with_coordinateTransformations",

ngff_spec/schemas/_version.schema

@@ -1,10 +1,10 @@
 {
   "$schema": "https://json-schema.org/draft/2020-12/schema",
-  "$id": "https://ngff.openmicroscopy.org/0.6.dev1/schemas/_version.schema",
+  "$id": "https://ngff.openmicroscopy.org/0.6dev2/schemas/_version.schema",
   "title": "OME-Zarr Metadata version",
   "description": "The version of the OME-Zarr Metadata",
   "type": "string",
   "enum": [
-    "0.6.dev1"
+    "0.6dev2"
   ]
 }

ngff_spec/schemas/axes.schema

@@ -1,11 +1,12 @@
 {
   "$schema": "https://json-schema.org/draft/2020-12/schema",
-  "$id": "https://ngff.openmicroscopy.org/latest/schemas/axes.schema",
+  "$id": "https://ngff.openmicroscopy.org/0.6dev2/schemas/axes.schema",
   "title": "NGFF Axes",
   "description": "JSON from OME-NGFF .zattrs",
   "type": "array",
   "uniqueItems": true,
   "minItems": 1,
+  "maxItems": 5,
   "items": {
     "$ref": "#/$defs/axis"
   },
@@ -27,23 +28,24 @@
       }
     }
   },
-  "minContains": 0,
+  "minContains": 2,
   "maxContains": 3,
   "$defs": {
     "axis": {
       "type": "object",
       "properties": {
         "name": {
           "type": "string",
-          "description": "Name of the axis"
+          "minLength": 1,
+          "description": "Name of the axis. Must be unique within the coordinate system."
         },
         "longName": {
           "type": "string",
           "description": "Longer name or description of the axis."
         },
         "type": {
           "type": "string",
-          "description": "Dimension of the axis"
+          "description": "Type of the axis. Can be a predefined type or custom type."
         },
         "discrete": {
           "type": "boolean",

ngff_spec/schemas/bf2raw.schema

@@ -1,6 +1,6 @@
 {
   "$schema": "https://json-schema.org/draft/2020-12/schema",
-  "$id": "https://ngff.openmicroscopy.org/0.6.dev1/schemas/bf2raw.schema",
+  "$id": "https://ngff.openmicroscopy.org/0.6dev2/schemas/bf2raw.schema",
   "title": "OME-Zarr container produced by bioformats2raw",
   "description": "The zarr.json attributes key",
   "type": "object",
@@ -17,7 +17,7 @@
           ]
         },
         "version": {
-          "$ref": "https://ngff.openmicroscopy.org/0.6.dev1/schemas/_version.schema"
+          "$ref": "https://ngff.openmicroscopy.org/0.6dev2/schemas/_version.schema"
         }
       },
       "required": [

ngff_spec/schemas/coordinate_systems.schema

@@ -1,6 +1,6 @@
 {
   "$schema": "https://json-schema.org/draft/2020-12/schema",
-  "$id": "https://ngff.openmicroscopy.org/latest/schemas/coordinate_systems.schema",
+  "$id": "https://ngff.openmicroscopy.org/0.6dev2/schemas/coordinate_systems.schema",
   "title": "NGFF CoordinateSystem",
   "description": "JSON from OME-NGFF .zattrs",
   "type": "array",
@@ -15,7 +15,8 @@
       "properties": {
         "name": {
           "type": "string",
-          "description": "Name of coordinate system"
+          "minLength": 1,
+          "description": "Name of coordinate system. Must be unique among all coordinate systems."
         },
         "axes": {
           "$ref": "axes.schema"

ngff_spec/schemas/coordinate_systems_and_transforms.schema

@@ -1,15 +1,17 @@
 {
   "$schema": "https://json-schema.org/draft/2020-12/schema",
-  "$id": "https://ngff.openmicroscopy.org/latest/schemas/coordinate_systems_and_transforms.schema",
+  "$id": "https://ngff.openmicroscopy.org/0.6dev2/schemas/coordinate_systems_and_transforms.schema",
   "title": "NGFF Coordinate Systems and Transforms",
   "description": "Coordinate Systems and transforms for OME-NGFF",
   "type": "object",
   "properties": {
     "coordinateSystems": {
-        "$ref": "coordinate_systems.schema"
+        "$ref": "coordinate_systems.schema",
+        "description": "Coordinate systems to combine with transforms to define spatial relationships"
     },
     "coordinateTransformations": {
-        "$ref": "coordinate_transformations.schema"
+        "$ref": "coordinate_transformations.schema",
+        "description": "Coordinate transformations defining spatial relationships between coordinate systems"
     },
     "arrayCoordinateSystem": {
       "type": "object",