Merge branch 'main' into no-separate-field-for-arrayCoordinateSystem

Author: jo-mueller

contribute.md

@@ -167,6 +167,6 @@ Before creating a release, please make sure to go through the following items to
 
 - [ ] Update `_version.py`. Some internal code requires a version number to be provided there to auto-generate some parts of the documentation.
 - [ ] Update versions in examples. Go through the examples in the `examples/` and make sure that all version numbers in the `.json` files are up-to-date.
-- [ ] Update the specification number in the spec text. The [spec text](ngff-spec:spec) mentions its own version number in several places. Please make sure to update those to the new version.
+- [ ] Update the specification number in the spec text. The [spec text](./index.md) mentions its own version number in several places. Please make sure to update those to the new version.
 - [ ] Make sure all tests are passing. Run the test suite to make sure that all tests are passing before creating a release.
-- [ ] Update the version history. Add a new entry to the [version history](ngff-spec:history) file with the new version number and date, and a summary of the changes made in this release.
+- [ ] Update the version history. Add a new entry to the [version history](#ngff-spec:history) file with the new version number and date, and a summary of the changes made in this release.

index.md

@@ -153,7 +153,7 @@ those Zarr arrays SHOULD be stored in a Zarr group on the same level as images c
 store.zarr                      # One scene dataset
 │
 ├── zarr.json                   # coordinate transformations describing the relationship between two image coordinate systems
-│                               # are stored in the "scene" dictionary here.
+│                               # are stored in the "scene" object here.
 │                               # I.e., transformations between coordinate systems in the 'volume' and 'crop' multiscale images are stored here.
 │
 ├── coordinateTransformations   # transformations that use array storage for their parameters should go in a Zarr group named "coordinateTransformations".
@@ -520,7 +520,7 @@ The following transformations are supported:
 | [`displacements`](#coordinates-displacements-md) | `"path":str` | Displacement field transformation located at `path`. |
 | [`coordinates`](#coordinates-displacements-md) | `"path":str` | Coordinate field transformation located at `path`. |
 | [`bijection`](#bijection-md) | `"forward":Transformation`<br>`"inverse":Transformation` | An invertible transformation providing an explicit forward transformation and its inverse. |
-| [`byDimension`](#bydimension-md) | `"transformations":List[Transformation]`, <br> `"input_axes": List[str]`, <br> `"output_axes": List[str]` | A high dimensional transformation using lower dimensional transformations on subsets of dimensions. |
+| [`byDimension`](#bydimension-md) | `"transformations":List[Transformation]`.<br>Transformations in the array MUST have<br>`"input_axes": List[number]`, <br> and `"output_axes": List[number]` | A high dimensional transformation using lower dimensional transformations on subsets of dimensions. |
 
 Implementations SHOULD prefer to store transformations as a sequence of less expressive transformations where possible
 (e.g., sequence[translation, rotation], instead of affine transformation with translation/rotation). 
@@ -574,8 +574,8 @@ Coordinate transformations can be stored in multiple places to reflect different
   The output can be another coordinate system defined under `multiscales > coordinateSystems`.
 
 - **Inside `scene > coordinateTransformations`**: Transformations between two or more images
-  MUST be stored in the attributes of a [`scene` dictionary](#scene-md) in a [scene Zarr group](#scene-format).
-  In this case, the `input` and `output` values are dictionaries
+  MUST be stored in the attributes of a [`scene` object](#scene-md) in a [scene Zarr group](#scene-format).
+  In this case, the `input` and `output` values are objects
   that refer to coordinate systems in the same zarr.json or in the metadata of multiscale image subgroups.
 
 This separation of transformations (inside `multiscales > datasets`, under `multiscales > coordinateTransformations` and under `scene > coordinateTransformations`) provides flexibility for different use cases while still maintaining a level of rigidity for implementations.
@@ -1201,8 +1201,8 @@ I.e. the y-displacement is first, because the y-axis is the first element of the
 using lower dimensional transformations on subsets of dimensions.
 
 **transformations**
-: MUST be an array of wrapped transformations.
-  Each item MUST contain `input_axes`, `output_axes` and `transformation` fields.
+: MUST be an array of objects where each object MUST contain
+  the fields `input_axes`, `output_axes` and `transformation`.
   The values of `input_axes` and `output_axes` are arrays of integers.
   The integer values in these arrays correspond to the axis indices in the `byDimension`'s or its parent's
   `input` and `output` coordinate systems, respectively.
@@ -1567,7 +1567,7 @@ and MUST NOT be a duplicate of any other `name` in the `rows` array.
 Care SHOULD be taken to avoid collisions on case-insensitive filesystems
 (e.g. avoid using both `Aa` and `aA`).
 
-The `plate` dictionary MUST contain a `wells` key
+The `plate` object MUST contain a `wells` key
 whose value MUST be a list of JSON objects defining the wells of the plate.
 Each well object MUST contain a `path` key
 whose value MUST be a string specifying the path to the well subgroup.
@@ -1641,7 +1641,7 @@ The first field is part of the first acquisition, and the second field is part o
 For images that share a spatial relationship,
 the `scene` metadata layout can be used to describe the relationship between images.
 
-The `scene` dictionary MUST contain the field `coordinateTransformations`,
+The `scene` object MUST contain the field `coordinateTransformations`,
 whose value MUST be an array of valid [transformations](#trafo-types-md).
 It MAY contain the field `coordinateSystems`,
 whose values MUST be an array of valid [coordinate systems](#coordinate-systems-md).
@@ -1651,12 +1651,12 @@ which MUST contain the field `name` and MAY contain the field `path`.
 
 **name**
   Refers to the name of a `coordinateSystem` either in the multiscale image subgroup specified by the path,
-  or within the `scene` dictionary itself.
+  or within the `scene` object itself.
 
 **path**
   Refers to the path of a multiscale image subgroup in the Zarr hierarchy.
 
-If `name` refers to a coordinate system in the `scene` dictionary,
+If `name` refers to a coordinate system in the `scene` object,
 the `path` value MAY be omitted or null.
 If `name` refers to a coordinate system in the multiscale image subgroup specified by `path`,
 both `path` and `name` MUST be provided.

schemas/strict_well.schema

@@ -1,9 +1,5 @@
 {
   "$schema": "https://json-schema.org/draft/2020-12/schema",
   "$id": "https://ngff.openmicroscopy.org/0.6.dev3/schemas/strict_well.schema",
-  "allOf": [
-    {
-      "$ref": "https://ngff.openmicroscopy.org/0.6.dev3/schemas/well.schema"
-    }
-  ]
+  "$ref": "https://ngff.openmicroscopy.org/0.6.dev3/schemas/well.schema"
 }