WIP: port RFC5 updated proposal to ngff-spec

_version.py

@@ -1 +1 @@
-__version__ = '0.6.dev2'
+__version__ = '0.6.dev3'

contribute.md

@@ -68,8 +68,6 @@ Make sure the updated `CITATION.cff` file is included in your PR.
 Contributions should conform to [Semantic Line Breaks (SemBr)](https://sembr.org/),
 to improve change tracking.
 
-### Formatting hints
-
 The specification uses MyST extensively for a number of formatting options
 to make the text readable and improve structure.
 
@@ -97,6 +95,18 @@ make sure to prepend the reference anchor with `versionX` like so:
 Otherwise, the same anchors may not be possible to resolve
 if multiple versions of the spec document are built and viewed together.
 
+#### Highlighting
+
+If you refer to fields or values that would appear in JSON files,
+please use backticks to highlight them, like so:
+
+```markdown
+The `multiscales` field contains an array of dictionaries.
+```
+
+You may still use bold, italics or quotation marks for emphasis where appropriate,
+but please use backticks for JSON fields and values.
+
 #### Citations
 
 ngff-spec relies on [sphinxcontrib-bibtex](https://pypi.org/project/sphinxcontrib-bibtex/) for citations.

examples/bf2raw/image.json

@@ -3,7 +3,7 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.6.dev2",
+      "version": "0.6.dev3",
       "bioformats2raw.layout": 3
     }
   }

examples/bf2raw/plate.json

@@ -3,7 +3,7 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.6.dev2",
+      "version": "0.6.dev3",
       "bioformats2raw.layout": 3,
       "plate": {
         "columns": [

examples/label_strict/colors_properties.json

@@ -3,7 +3,7 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.6.dev2",
+      "version": "0.6.dev3",
       "image-label": {
         "colors": [
           {

examples/multiscales_strict/multiscales_example.json

@@ -3,7 +3,7 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.6.dev2",
+      "version": "0.6.dev3",
       "multiscales": [
         {
           "name": "example",
@@ -21,40 +21,40 @@
           ],
           "datasets": [
             {
-              "path": "0",
+              "path": "s0",
               "coordinateTransformations": [
                 {
                   // the voxel size for the first scale level (0.5 micrometer)
                   // and the time unit (0.1 milliseconds), which is the same for each scale level
                   "type": "scale",
                   "scale": [0.1, 1.0, 0.5, 0.5, 0.5],
-                  "input": "0",
+                  "input": "s0",
                   "output": "intrinsic"
                 }
               ]
             },
             {
-              "path": "1",
+              "path": "s1",
               "coordinateTransformations": [
                 {
                   // the voxel size for the second scale level (downscaled by a factor of 2 -> 1 micrometer)
                   // and the time unit (0.1 milliseconds), which is the same for each scale level
                   "type": "scale",
                   "scale": [0.1, 1.0, 1.0, 1.0, 1.0],
-                  "input": "1",
+                  "input": "s1",
                   "output": "intrinsic"
                 }
               ]
             },
             {
-              "path": "2",
+              "path": "s2",
               "coordinateTransformations": [
                 {
                   // the voxel size for the third scale level (downscaled by a factor of 4 -> 2 micrometer)
                   // and the time unit (0.1 milliseconds), which is the same for each scale level
                   "type": "scale",
                   "scale": [0.1, 1.0, 2.0, 2.0, 2.0],
-                  "input": "2",
+                  "input": "s2",
                   "output": "intrinsic"
                 }
               ]

examples/multiscales_strict/multiscales_example_relative.json

@@ -1,7 +1,7 @@
 {
   "multiscales": [
     {
-      "version": "0.6.dev2",
+      "version": "0.6.dev3",
       "name": "example",
       "coordinateSystems" : [
         {
@@ -38,23 +38,23 @@
           }]
         },
         {
-          "path": "1",
+          "path": "s1",
           "coordinateTransformations": [{
-            // the second scale level (downscaled by a factor of 2 relative to "0" in zyx)
+            // the second scale level (downscaled by a factor of 2 relative to "s0" in zyx)
             "type": "scale",
             "scale": [1, 1, 2, 2, 2],
-            "input" : "/1",
-            "output" : "array_0"
+            "input" : "s1",
+            "output" : "intrinsic"
           }]
         },
         {
-          "path": "2",
+          "path": "s2",
           "coordinateTransformations": [{
-            // the third scale level (downscaled by a factor of 4 relative to "0" in zyx)
+            // the third scale level (downscaled by a factor of 4 relative to "s0" in zyx)
             "type": "scale",
             "scale": [1, 1, 4, 4, 4],
-            "input" : "/2",
-            "output" : "array_0"
+            "input" : "s2",
+            "output" : "intrinsic"
           }]
         }
       ],

examples/multiscales_strict/multiscales_transformations.json

@@ -3,7 +3,7 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.6.dev2",
+      "version": "0.6.dev3",
       "multiscales": [
         {
           "coordinateSystems": [
@@ -40,12 +40,12 @@
           ],
           "datasets": [
             {
-              "path": "0",
+              "path": "s0",
               "coordinateTransformations": [
                 {
                   "scale": [1, 1],
                   "type": "scale",
-                  "input": "0",
+                  "input": "s0",
                   "output": "intrinsic"
                 }
               ]

examples/ome/series-2.json

@@ -3,7 +3,7 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.6.dev2",
+      "version": "0.6.dev3",
       "series": ["0", "1"]
     }
   }

examples/plate_strict/plate_2wells.json

@@ -3,7 +3,7 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.6.dev2",
+      "version": "0.6.dev3",
       "plate": {
         "acquisitions": [
           {

examples/plate_strict/plate_6wells.json

@@ -3,7 +3,7 @@
   "node_type": "group",
   "attributes": {
     "ome": {
-      "version": "0.6.dev2",
+      "version": "0.6.dev3",
       "plate": {
         "acquisitions": [
           {

examples/subspace/subspaceMultidim.json

@@ -1,44 +1,87 @@
 {
-  "coordinateSystems": [
-    {
-      "name": "in",
-      "axes": [
-        { "name": "0", "type": "array" },
-        { "name": "1", "type": "array" },
-        { "name": "2", "type": "array" },
-        { "name": "3", "type": "array" },
-        { "name": "4", "type": "array" }
-      ]
-    },
-    {
-      "name": "out",
-      "axes": [
-        { "name": "x", "type": "space" },
-        { "name": "y", "type": "space" },
-        { "name": "z", "type": "space" }
-      ]
-    }
-  ],
-  "coordinateTransformations": [
-    {
-      "type": "byDimension",
-      "name": "5D-to-3D-not-contiguous",
-      "input": "in",
-      "output": "out",
-      "transformations": [
-        {
-          "type": "mapAxis",
-          "mapAxis": { "0": "x", "2": "z" },
-          "input_axes": [ "0", "2" ],
-          "output_axes": [ "x", "z" ]
-        },
+  "zarr_format": 3,
+  "node_type": "group",
+  "attributes": {
+    "ome": {
+      "version": "0.6.dev3",
+      "multiscales": [
         {
-          "type": "scale",
-          "scale": [ 2 ],
-          "input_axes": [ "1" ],
-          "output_axes": [ "y" ]
+          "name": "multiscales",
+          "coordinateSystems": [
+            {
+              "name": "physical",
+              "axes": [
+                {
+                  "type": "space",
+                  "name": "y",
+                  "unit": "micrometer",
+                  "discrete": false
+                },
+                {
+                  "type": "space",
+                  "name": "x",
+                  "unit": "micrometer",
+                  "discrete": false
+                }
+              ]
+            },
+            {
+              "name": "array_coordinates",
+              "axes": [
+                {
+                  "type": "array",
+                  "name": "dim_0",
+                  "discrete": true
+                },
+                {
+                  "type": "array",
+                  "name": "dim_1",
+                  "discrete": true
+                }
+              ]
+            }
+          ],
+          "datasets": [
+            {
+              "path": "array",
+              "coordinateTransformations": [
+                {
+                  "type": "byDimension",
+                  "output": "physical",
+                  "input": "array",
+                  "transformations": [
+                    {
+                      "type": "scale",
+                      "output_axes": [
+                        "x"
+                      ],
+                      "input_axes": [
+                        "dim_1"
+                      ],
+                      "scale": [
+                        2
+                      ]
+                    },
+                    {
+                      "type": "translation",
+                      "output_axes": [
+                        "y"
+                      ],
+                      "input_axes": [
+                        "dim_0"
+                      ],
+                      "translation": [
+                        -10
+                      ]
+                    }
+                  ],
+                  "name": "transform-name"
+                }
+              ]
+            }
+          ]
         }
       ]
     }
-  ]
-}
+  }
+}