diff --git a/_version.py b/_version.py index e2f3d28a..46f48909 100644 --- a/_version.py +++ b/_version.py @@ -1 +1 @@ -__version__ = '0.6rc0' +__version__ = '0.9.dev1' diff --git a/examples/bf2raw/image.json b/examples/bf2raw/image.json index 28d1019b..8d5af1ff 100644 --- a/examples/bf2raw/image.json +++ b/examples/bf2raw/image.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "bioformats2raw.layout": 3 } } diff --git a/examples/bf2raw/plate.json b/examples/bf2raw/plate.json index 8c21052c..eb1bb5d4 100644 --- a/examples/bf2raw/plate.json +++ b/examples/bf2raw/plate.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "bioformats2raw.layout": 3, "plate": { "columns": [ diff --git a/examples/label_strict/colors_properties.json b/examples/label_strict/colors_properties.json index aebd8689..a31ac0cc 100644 --- a/examples/label_strict/colors_properties.json +++ b/examples/label_strict/colors_properties.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/examples/multiscales_strict/multiscales_example.json b/examples/multiscales_strict/multiscales_example.json index ccc340ec..dc94c15a 100644 --- a/examples/multiscales_strict/multiscales_example.json +++ b/examples/multiscales_strict/multiscales_example.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "example", diff --git a/examples/multiscales_strict/multiscales_example_relative.json b/examples/multiscales_strict/multiscales_example_relative.json index 2c0c7f26..3922338b 100644 --- a/examples/multiscales_strict/multiscales_example_relative.json +++ b/examples/multiscales_strict/multiscales_example_relative.json @@ -1,7 +1,7 @@ { "multiscales": [ { - "version": "0.6rc0", + "version": "0.9.dev1", "name": "example", "coordinateSystems" : [ { diff --git a/examples/multiscales_strict/multiscales_reference_to_label.json b/examples/multiscales_strict/multiscales_reference_to_label.json index 0d756cc9..33b85a42 100644 --- a/examples/multiscales_strict/multiscales_reference_to_label.json +++ b/examples/multiscales_strict/multiscales_reference_to_label.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "Image", diff --git a/examples/multiscales_strict/multiscales_transformations.json b/examples/multiscales_strict/multiscales_transformations.json index cf601322..921f800e 100644 --- a/examples/multiscales_strict/multiscales_transformations.json +++ b/examples/multiscales_strict/multiscales_transformations.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/examples/ome/series-2.json b/examples/ome/series-2.json index 023d23a7..afcb188e 100644 --- a/examples/ome/series-2.json +++ b/examples/ome/series-2.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "series": ["0", "1"] } } diff --git a/examples/plate_strict/plate_2wells.json b/examples/plate_strict/plate_2wells.json index 09f4bec1..1a8a5a1e 100644 --- a/examples/plate_strict/plate_2wells.json +++ b/examples/plate_strict/plate_2wells.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/examples/plate_strict/plate_6wells.json b/examples/plate_strict/plate_6wells.json index 0f6b2d2c..9e5689e1 100644 --- a/examples/plate_strict/plate_6wells.json +++ b/examples/plate_strict/plate_6wells.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/examples/scene/scene_registration.json b/examples/scene/scene_registration.json index e70d3fa0..0f6b15cb 100644 --- a/examples/scene/scene_registration.json +++ b/examples/scene/scene_registration.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "scene": { "coordinateTransformations": [ { diff --git a/examples/scene/scene_stitching.json b/examples/scene/scene_stitching.json index e4cf25da..1355927f 100644 --- a/examples/scene/scene_stitching.json +++ b/examples/scene/scene_stitching.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "scene": { "coordinateTransformations": [ { diff --git a/examples/subspace/subspacePermute.json b/examples/subspace/subspacePermute.json index e2c53ee0..8c69a0ab 100644 --- a/examples/subspace/subspacePermute.json +++ b/examples/subspace/subspacePermute.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/examples/transformations/displacements/displacement_field.json b/examples/transformations/displacements/displacement_field.json index add1ca2f..e63db5c4 100644 --- a/examples/transformations/displacements/displacement_field.json +++ b/examples/transformations/displacements/displacement_field.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "name": "the_dfield", "multiscales": [ { diff --git a/examples/transformations/displacements/multiscales.json b/examples/transformations/displacements/multiscales.json index c359013d..bff6eaa3 100644 --- a/examples/transformations/displacements/multiscales.json +++ b/examples/transformations/displacements/multiscales.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "name": "some_image", "multiscales": [ { diff --git a/examples/well_strict/well_2fields.json b/examples/well_strict/well_2fields.json index 636edf2e..a0125337 100644 --- a/examples/well_strict/well_2fields.json +++ b/examples/well_strict/well_2fields.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "well": { "images": [ { diff --git a/examples/well_strict/well_4fields.json b/examples/well_strict/well_4fields.json index 9baae566..f39e722e 100644 --- a/examples/well_strict/well_4fields.json +++ b/examples/well_strict/well_4fields.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "well": { "images": [ { diff --git a/index.md b/index.md index 577e9d01..4ad83355 100644 --- a/index.md +++ b/index.md @@ -4,8 +4,8 @@ short_title: OME-Zarr authors: " " --- -# Version 0.6rc0 -(ngff-spec:spec:0.6rc0)= +# Version 0.9.dev1 +(ngff-spec:spec:0.9.dev1)= **Feedback:** [Forum](https://forum.image.sc/tag/ome-ngff), [Github](https://github.com/ome/ngff/issues) @@ -18,9 +18,8 @@ authors: " " ## Abstract ```{warning} -This is the release candidate for version 0.6rc0 of the ngff-specification. -Upon release of 0.6, this warning will be removed and the version number in the document updated. - +This is a development version of the specification. It includes RFC-3 and RFC-4 +which have not yet been accepted. ``` This document contains next-generation file format (NGFF) specifications for storing bioimaging data in the cloud. @@ -28,9 +27,9 @@ All specifications are submitted to the community for review. ## Status of This Document -The working title version of this specification is 0.6rc0. +The working title version of this specification is 0.9.dev1. Migration scripts will be provided between numbered versions. -Data written with these latest changes (an "editor's draft") will not necessarily be supported. +Data written with these latest changes will not necessarily be supported. The conventions and specifications defined in this document are designed to enable next-generation file formats to represent @@ -66,7 +65,7 @@ but could equally be stored on a web server to be accessed via HTTP or in object ### Images The following layout describes the expected Zarr hierarchy for images with multiple levels of resolutions and optionally associated labels. -Note that the number of dimensions is variable between 2 and 5 and that axis names are arbitrary, see [multiscales metadata](#multiscales-md) for details. +Note that the number of dimensions is variable and that axis names are arbitrary, see [multiscales metadata](#multiscales-md) for details. ```text ├── 123.zarr # One OME-Zarr image (id=123). @@ -84,8 +83,7 @@ Note that the number of dimensions is variable between 2 and 5 and that axis nam │ │ # by the "multiscales" metadata, but is often a sequence starting at 0. │ │ # All arrays must have the same datatype and number of dimensions. │ │ - │ ├── zarr.json # All image arrays must be up to 5-dimensional - │ │ # with the axis of type time before type channel, before spatial axes. + │ ├── zarr.json │ │ │ └─ ... # Chunks are stored conforming to the Zarr array specification and │ # metadata as specified in the array's `zarr.json`. @@ -188,14 +186,14 @@ The OME-Zarr Metadata is stored in the various `zarr.json` files throughout the The OME-Zarr Metadata version MUST be consistent within a hierarchy. The group `attributes` MUST contain a key `ome`. The value of the `ome` key MUST be a JSON -object that MUST contain a `version` key, the value of which MUST be a string specifying the version of the OME-Zarr specification defined by [this document](#ngff-spec:spec:0.6rc0). +object that MUST contain a `version` key, the value of which MUST be a string specifying the version of the OME-Zarr specification defined by [this document](#ngff-spec:spec:0.9.dev1). ```jsonc { // ... "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", // ... } } @@ -266,10 +264,56 @@ where each object describes a dimension (axis) and: - MAY contain the field `longName`. The value MUST be a string, and can provide a longer name or description of an axis and its properties. +- MAY contain an "orientation" field, itself containing a "type" and a + "value". Currently, "type" may only be "anatomical", and "value" may + only be one from the list given in [list of possible anatomical + orientation values](orientation-values). A specific orientation value or + its inverse MUST NOT appear more than once in a given coordinate system. The values in the `name` fields MUST be unique within the same coordinate system. The length of "axes" MUST be equal to the number of dimensions of the arrays that contain the image data. +```{note} +:label: orientation-values + +When a spatial axis is aligned with a specific orientation, this can be +indicated with the "orientation" field, which must have "type" +"anatomical" (with further types to be added to the specification or as +extensions in the future), and one of the values detailed below: + +**Common to both bipeds and quadrupeds:** +- `left-to-right` +- `right-to-left` +- `proximal-to-distal` +- `distal-to-proximal` + +**Primarily for bipeds (humans):** +- `anterior-to-posterior` (front-to-back) +- `posterior-to-anterior` (back-to-front) +- `inferior-to-superior` (feet-to-head) +- `superior-to-inferior` (head-to-feet) +- `dorsal-to-palmar` (back of hand to palm) +- `palmar-to-dorsal` (palm to back of hand) +- `dorsal-to-plantar` (top of foot to sole) +- `plantar-to-dorsal` (sole to top of foot) + +**Primarily for quadrupeds:** +- `rostral-to-caudal` (nose/beak-to-tail, especially for nervous system) +- `caudal-to-rostral` (tail-to-nose/beak, especially for nervous system) +- `cranial-to-caudal` (head-to-tail) +- `caudal-to-cranial` (tail-to-head) +- `dorsal-to-ventral` (back/top-to-belly/bottom) +- `ventral-to-dorsal` (belly/bottom-to-back/top) + +**For layered and polarized tissues (subject-local):** +- `superficial-to-deep` (outer surface to inner depth, e.g. skin, gut, cortex) +- `deep-to-superficial` (inner depth to outer surface) +- `apical-to-basal` (apical to basal surface, e.g. epithelial layers, polarized cells) +- `basal-to-apical` (basal to apical surface) +- `apex-to-base` (tip to broad base, e.g. heart, lungs) +- `base-to-apex` (broad base to tip) +``` + Arrays are inherently discrete (see Array coordinate systems, below) but are often used to store discrete samples of a continuous variable. The continuous values "in between" discrete samples can be retrieved using an *interpolation* method. @@ -429,7 +473,7 @@ The following transformations are supported: | [`bijection`](#bijection-md) | `"forward":Transformation`
`"inverse":Transformation` | An invertible transformation providing an explicit forward transformation and its inverse. | | [`byDimension`](#bydimension-md) | `"transformations":List[Transformation]`.
Transformations in the array MUST have
`"inputAxes": List[number]`,
and `"outputAxes": List[number]` | A high dimensional transformation using lower dimensional transformations on subsets of dimensions. | -The parameter values (e.g., `scale` for a [scale transformation](#scale-md)) MUST be compatible with input and output space dimensionality (see details). +The parameter values (e.g., `scale` for a [scale transformation](#scale-md)) MUST be compatible with input and output space dimensionality (see details). The `input` and `output` fields are objects structured as follows: @@ -471,7 +515,7 @@ Depending on which, different constraints apply to the transformations, as descr - Both `input` and `output` MUST specify a coordinate system `name`. - `path` is required when referencing a coordinate system in a multiscale image subgroup; it MAY be omitted or null when referencing a coordinate system defined in the scene's own `coordinateSystems`. - + In any context, the values given for `name` and `path` provide an unambiguous reference to a named coordinate system. If the `path` field is null or omitted, this is to be interpreted as referring to a named coordinate system in the same `zarr.json` file. @@ -1107,7 +1151,7 @@ An exact reproducibility of pixel values for images transformed and resampled by The multiscale group at `path` MUST satisfy: - **Dimensionality**: If the input coordinate system has `N` axes, the multiscale image at location `path` MUST have `N+1` dimensions. - - **Vector dimension length**: + - **Vector dimension length**: - For `coordinates` transformations, the length of the array along the `coordinate` dimension (last axis) MUST equal `M`, the number of axes in the output coordinate system. - For `displacements` transformations, the length of the array along the `displacement` dimension (last axis) MUST equal `N`, @@ -1275,9 +1319,9 @@ the input and output of the `forward` and `inverse` transformations are understo (multiscales-md)= Metadata about an image can be found under the `multiscales` key in the group-level OME-Zarr Metadata. -Here, "image" refers to 2 to 5 dimensional data representing image -or volumetric data with optional time or channel axes. -It is stored in a multiple resolution representation. +Here, "image" refers to data stored in a Zarr Array representing image, +volumetric, time lapse, or similar data. It MAY be stored in multiple +resolutions. `multiscales` contains an array of objects where each entry describes a multiscale image. Each object provides the following fields: @@ -1295,15 +1339,26 @@ Each object provides the following fields: : The `coordinateSystems` field is a JSON array containing [coordinate system metadata](#coordinate-systems-md) The following conditions apply to all coordinate systems inside multiscales metadata: - - The length of `axes` must be between 2 and 5 and MUST be equal to the dimensionality of the Zarr arrays storing the image data (see `datasets:path`). - - `axes` MUST contain 2 or 3 entries of `type:space` - - `axes` MAY contain one additional entry of `type:time` - - `axes` MAY contain one additional entry of `type:channel` or a null / custom type. - - `axes` entries MUST be ordered by `type` where the `time` axis must come first (if present), - followed by the `channel` or custom axis (if present) and the axes of type `space`. - - If there are three spatial axes where two correspond to the image plane (`yx`) - and images are stacked along the other (anisotropic) axis (`z`), - the spatial axes SHOULD be ordered as `zyx`. +1. The length of the axis names MUST match the number of axes of the array. +2. *If* a dataset contains exactly 2 spatial dimensions, those dimensions + SHOULD be named 'y' and 'x', except where rule 4 applies. +3. *If* a dataset contains exactly 3 spatial dimensions, those dimensions + SHOULD be named 'z', 'y', and 'x', except where rule 4 applies. +4. *If* a dataset contains exactly 1 time dimension, it should be named 't'. +5. When image data axes map straightforwardly to axes with common names in + the relevant field of practice, those axes SHOULD be named according to + such conventions. For example, spatial frequency axes resulting from a + Fourier transformation of 'z', 'y', and 'x' SHOULD be named 'w', 'v', and + 'u', respectively. Similarly, a temporal frequency axis resulting from + a Fourier transformation of the 't' axis SHOULD be named 'w' or 'ω'. +6. Axis names MUST NOT be repeated within a dataset, and SHOULD NOT be + different only by upper/lower-case. For example, the same dataset SHOULD + NOT have both an 'X' and an 'x' axis. +7. The order of the axes MUST match their ordering within the data if + applicable. For example, if the axes are ordered as "DZYX", where 'D' is a + field of displacement vectors, then the vectors must be ordered as "ZYX" + within the array. + ```{hint} (spec:hint:multiscales-intrinsic-coordinate-system)= @@ -1320,8 +1375,7 @@ is the coordinate system that is referenced by all multiscale coordinate transfo - Each object in `datasets` MUST contain the field `path`, whose value is a string containing the path to the Zarr array for this resolution relative to the current Zarr group. - The `path`s MUST be ordered from largest (i.e. highest resolution) to smallest. - - Every Zarr array referred to by a `path` MUST have the same number of dimensions and datatype, - and MUST NOT have more than 5 dimensions. + - Every Zarr array referred to by a `path` MUST have the same number of dimensions and datatype. - The number of dimensions and order MUST correspond to number and order of `axes`. Each object in `datasets` MUST contain the field `coordinateTransformations`, @@ -1576,7 +1630,7 @@ The `zarr.json` under the `labels` group contains a JSON object with the key `la { "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "labels": [ "cell_segmentation" ] @@ -1870,7 +1924,7 @@ If they do so, it is RECOMMENDED that the scene's first entry under the `coordin If no coordinate system is defined therein, but only in the respective linked multiscale groups, viewers may want to expose a choice for the user to select a coordinate system for display when opening the dataset for the first time. - + ``` diff --git a/schemas/_version.schema b/schemas/_version.schema index a5f079a6..aefecf67 100644 --- a/schemas/_version.schema +++ b/schemas/_version.schema @@ -1,10 +1,10 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/_version.schema", + "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/_version.schema", "title": "OME-Zarr version", "description": "OME-Zarr version.", "type": "string", "enum": [ - "0.6rc0" + "0.9.dev1" ] } diff --git a/schemas/axes.schema b/schemas/axes.schema index 14b007fb..004e2f39 100644 --- a/schemas/axes.schema +++ b/schemas/axes.schema @@ -1,41 +1,14 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/axes.schema", + "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/axes.schema", "title": "Axes", "description": "OME-Zarr Axes.", "type": "array", "uniqueItems": true, "minItems": 1, - "maxItems": 5, "items": { "$ref": "#/$defs/axis" }, - "$comment": "Ensure that there exist at most three space axes", - "oneOf": [ - { - "contains": { - "type": "object", - "properties": { - "type": { "const": "space" } - }, - "required": ["type"] - }, - "minContains": 2, - "maxContains": 3 - }, - { - "contains": { - "type": "object", - "properties": { - "type": { "const": "array" } - }, - "required": ["type"] - }, - "minContains": 2 - } - ], - "minContains": 2, - "maxContains": 3, "$defs": { "axis": { "type": "object", @@ -60,6 +33,9 @@ "unit": { "type": "string", "description": "Unit for the axis" + }, + "orientation": { + "$ref": "axis_orientation.schema" } }, "required": [ diff --git a/schemas/axis_orientation.schema b/schemas/axis_orientation.schema new file mode 100644 index 00000000..1a11028e --- /dev/null +++ b/schemas/axis_orientation.schema @@ -0,0 +1,41 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/axis_orientation.schema", + "title": "Axis Orientation", + "description": "Controlled vocabulary for orientation of each spatial axis according to subject or subject-global reference.", + "type": "object", + "properties": { + "type": { + "enum": ["anatomical"] + }, + "value": { + "enum": [ + "left-to-right", + "right-to-left", + "anterior-to-posterior", + "posterior-to-anterior", + "inferior-to-superior", + "superior-to-inferior", + "dorsal-to-ventral", + "ventral-to-dorsal", + "dorsal-to-palmar", + "palmar-to-dorsal", + "dorsal-to-plantar", + "plantar-to-dorsal", + "rostral-to-caudal", + "caudal-to-rostral", + "cranial-to-caudal", + "caudal-to-cranial", + "proximal-to-distal", + "distal-to-proximal", + "superficial-to-deep", + "deep-to-superficial", + "apical-to-basal", + "basal-to-apical", + "apex-to-base", + "base-to-apex" + ] + } + }, + "required": ["type", "value"] +} diff --git a/schemas/bf2raw.schema b/schemas/bf2raw.schema index 80a4bc1b..8a505362 100644 --- a/schemas/bf2raw.schema +++ b/schemas/bf2raw.schema @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/bf2raw.schema", + "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/bf2raw.schema", "title": "bioformats2raw", "description": "OME-Zarr bioformats2raw metadata.", "type": "object", @@ -17,7 +17,7 @@ ] }, "version": { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/_version.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/_version.schema" } }, "required": [ diff --git a/schemas/coordinate_systems.schema b/schemas/coordinate_systems.schema index 424c2285..6dcc3b65 100644 --- a/schemas/coordinate_systems.schema +++ b/schemas/coordinate_systems.schema @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/coordinate_systems.schema", + "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/coordinate_systems.schema", "title": "Coordinate systems", "description": "OME-Zarr coordinate system.", "type": "array", diff --git a/schemas/coordinate_transformations.schema b/schemas/coordinate_transformations.schema index ccb9162a..8f0af7b9 100644 --- a/schemas/coordinate_transformations.schema +++ b/schemas/coordinate_transformations.schema @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/coordinate_transformations.schema", + "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/coordinate_transformations.schema", "title": "Coordinate Transformations", "description": "OME-Zarr Coordinate transforms.", "type": "array", @@ -123,11 +123,8 @@ "type": "array", "items": { "type": "integer", - "minimum": 0, - "maximum": 4 + "minimum": 0 }, - "minItems": 2, - "maxItems": 5, "uniqueItems": true, "description": "An array of integers representing the new axis order as zero-based indices of the input axes." } @@ -151,10 +148,8 @@ "minItems": 1, "items": { "type": "integer", - "minimum": 0, - "maximum": 4 + "minimum": 0 }, - "maxItems": 3, "uniqueItems": true, "description": "An array of integers representing the indices of the input axes to drop." }, @@ -163,10 +158,8 @@ "minItems": 1, "items": { "type": "integer", - "minimum": 0, - "maximum": 4 + "minimum": 0 }, - "maxItems": 3, "uniqueItems": true, "description": "An array of integers representing the indices where zeros are inserted in the output coordinate vector." } @@ -214,7 +207,7 @@ "items": { "type": "number" } - } + } }, "required": [ "translation" diff --git a/schemas/image.schema b/schemas/image.schema index 099f35d2..effb6e84 100644 --- a/schemas/image.schema +++ b/schemas/image.schema @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/image.schema", + "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/image.schema", "title": "Image", "description": "OME-Zarr image.", "type": "object", @@ -16,7 +16,7 @@ "$ref": "#/$defs/multiscales" }, "version": { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/_version.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/_version.schema" } }, "required": [ @@ -56,14 +56,14 @@ "description": "A single scale transformation", "allOf": [ { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/coordinate_transformations.schema#/$defs/scale" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/coordinate_transformations.schema#/$defs/scale" }, { "type": "object", "properties": { "input": { "allOf": [ - {"$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/coordinate_transformations.schema#/$defs/inputOutput"}, + {"$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/coordinate_transformations.schema#/$defs/inputOutput"}, { "required": ["path"] } @@ -71,7 +71,7 @@ }, "output": { "allOf": [ - {"$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/coordinate_transformations.schema#/$defs/inputOutput"}, + {"$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/coordinate_transformations.schema#/$defs/inputOutput"}, { "required": ["name"] } @@ -86,13 +86,13 @@ { "description": "A single identity transformation", "allOf": [ - {"$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/coordinate_transformations.schema#/$defs/identity"}, + {"$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/coordinate_transformations.schema#/$defs/identity"}, { "type": "object", "properties": { "input": { "allOf": [ - {"$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/coordinate_transformations.schema#/$defs/inputOutput"}, + {"$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/coordinate_transformations.schema#/$defs/inputOutput"}, { "required": ["path"] } @@ -100,7 +100,7 @@ }, "output": { "allOf": [ - {"$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/coordinate_transformations.schema#/$defs/inputOutput"}, + {"$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/coordinate_transformations.schema#/$defs/inputOutput"}, { "required": ["name"] } @@ -121,8 +121,8 @@ "type": "array", "items": { "oneOf": [ - {"$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/coordinate_transformations.schema#/$defs/scale"}, - {"$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/coordinate_transformations.schema#/$defs/translation"} + {"$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/coordinate_transformations.schema#/$defs/scale"}, + {"$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/coordinate_transformations.schema#/$defs/translation"} ] }, "minItems": 2, @@ -130,7 +130,7 @@ }, "input": { "allOf": [ - {"$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/coordinate_transformations.schema#/$defs/inputOutput"}, + {"$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/coordinate_transformations.schema#/$defs/inputOutput"}, { "required": ["path"] } @@ -138,7 +138,7 @@ }, "output": { "allOf": [ - {"$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/coordinate_transformations.schema#/$defs/inputOutput"}, + {"$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/coordinate_transformations.schema#/$defs/inputOutput"}, { "required": ["name"] } @@ -165,7 +165,7 @@ "type": "array", "minItems": 1, "items": { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/coordinate_systems.schema#/$defs/coordinateSystem" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/coordinate_systems.schema#/$defs/coordinateSystem" } }, "coordinateTransformations": { @@ -174,7 +174,7 @@ "items": { "allOf": [ { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/coordinate_transformations.schema#/$defs/coordinateTransformation", + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/coordinate_transformations.schema#/$defs/coordinateTransformation", "description": "Parameters of any possible transform" }, { diff --git a/schemas/label.schema b/schemas/label.schema index 1c753ebf..ae6d8b4e 100644 --- a/schemas/label.schema +++ b/schemas/label.schema @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/label.schema", + "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/label.schema", "title": "Label", "description": "OME-Zarr label.", "type": "object", @@ -13,7 +13,7 @@ "$ref": "#/$defs/image-label" }, "version": { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/_version.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/_version.schema" } }, "required": [ diff --git a/schemas/ome.schema b/schemas/ome.schema index 32d0c546..69efecdc 100644 --- a/schemas/ome.schema +++ b/schemas/ome.schema @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/ome.schema", + "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/ome.schema", "title": "OME", "description": "OME-Zarr OME metadata.", "type": "object", @@ -18,7 +18,7 @@ "minContains": 1 }, "version": { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/_version.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/_version.schema" } }, "required": [ diff --git a/schemas/ome_zarr.schema b/schemas/ome_zarr.schema index 6ceb634a..6f4fa1ff 100644 --- a/schemas/ome_zarr.schema +++ b/schemas/ome_zarr.schema @@ -1,29 +1,29 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/ome_zarr.schema", + "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/ome_zarr.schema", "title": "OME-Zarr", "description": "Any OME-Zarr dataset.", "anyOf": [ { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/bf2raw.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/bf2raw.schema" }, { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/image.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/image.schema" }, { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/label.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/label.schema" }, { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/ome.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/ome.schema" }, { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/plate.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/plate.schema" }, { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/well.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/well.schema" }, { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/scene.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/scene.schema" } ] } diff --git a/schemas/plate.schema b/schemas/plate.schema index 1c398913..978c00fe 100644 --- a/schemas/plate.schema +++ b/schemas/plate.schema @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/plate.schema", + "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/plate.schema", "title": "Plate", "description": "OME-Zarr plate.", "type": "object", @@ -138,7 +138,7 @@ ] }, "version": { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/_version.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/_version.schema" } }, "required": [ diff --git a/schemas/scene.schema b/schemas/scene.schema index 96100026..10f0d7c3 100644 --- a/schemas/scene.schema +++ b/schemas/scene.schema @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/scene.schema", + "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/scene.schema", "title": "Scene", "description": "Scene metadata combining coordinate systems and coordinate transformations to define spatial relationships", "type": "object", @@ -9,7 +9,7 @@ "type": "object", "properties": { "version": { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/_version.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/_version.schema" }, "scene":{ "properties": { diff --git a/schemas/strict_axes.schema b/schemas/strict_axes.schema index 70288fbc..e05ebbaf 100644 --- a/schemas/strict_axes.schema +++ b/schemas/strict_axes.schema @@ -1,11 +1,11 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/strict_axes.schema", + "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/strict_axes.schema", "title": "NGFF Strict Axes", "description": "JSON from OME-NGFF .zattrs", "allOf": [ { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/axes.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/axes.schema" }, { "items": { diff --git a/schemas/strict_coordinate_systems.schema b/schemas/strict_coordinate_systems.schema index 2f9c6372..8cc318c3 100644 --- a/schemas/strict_coordinate_systems.schema +++ b/schemas/strict_coordinate_systems.schema @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/strict_coordinate_systems.schema", + "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/strict_coordinate_systems.schema", "allOf" : [ { "$ref": "coordinate_systems.schema" diff --git a/schemas/strict_image.schema b/schemas/strict_image.schema index cb8196ed..593d417e 100644 --- a/schemas/strict_image.schema +++ b/schemas/strict_image.schema @@ -1,9 +1,9 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/strict_image.schema", + "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/strict_image.schema", "allOf": [ { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/image.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/image.schema" }, { "properties": { diff --git a/schemas/strict_label.schema b/schemas/strict_label.schema index 50322e86..999eda87 100644 --- a/schemas/strict_label.schema +++ b/schemas/strict_label.schema @@ -1,9 +1,9 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/strict_label.schema", + "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/strict_label.schema", "allOf": [ { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/label.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/label.schema" }, { "properties": { diff --git a/schemas/strict_ome_zarr.schema b/schemas/strict_ome_zarr.schema index 25e75302..8b936afe 100644 --- a/schemas/strict_ome_zarr.schema +++ b/schemas/strict_ome_zarr.schema @@ -1,24 +1,24 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/strict_ome_zarr.schema", + "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/strict_ome_zarr.schema", "anyOf": [ { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/bf2raw.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/bf2raw.schema" }, { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/strict_image.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/strict_image.schema" }, { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/strict_label.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/strict_label.schema" }, { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/ome.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/ome.schema" }, { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/strict_plate.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/strict_plate.schema" }, { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/strict_well.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/strict_well.schema" } ] } diff --git a/schemas/strict_plate.schema b/schemas/strict_plate.schema index 0a23bb36..ed99a1f5 100644 --- a/schemas/strict_plate.schema +++ b/schemas/strict_plate.schema @@ -1,9 +1,9 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/strict_plate.schema", + "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/strict_plate.schema", "allOf": [ { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/plate.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/plate.schema" }, { "properties": { diff --git a/schemas/strict_well.schema b/schemas/strict_well.schema index 004860ea..b0d52908 100644 --- a/schemas/strict_well.schema +++ b/schemas/strict_well.schema @@ -1,5 +1,5 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/strict_well.schema", - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/well.schema" + "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/strict_well.schema", + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/well.schema" } diff --git a/schemas/well.schema b/schemas/well.schema index e004b3d7..2d05d0a6 100644 --- a/schemas/well.schema +++ b/schemas/well.schema @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://ngff.openmicroscopy.org/0.6rc0/schemas/well.schema", + "$id": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/well.schema", "title": "Well", "description": "OME-Zarr well.", "type": "object", @@ -48,7 +48,7 @@ ] }, "version": { - "$ref": "https://ngff.openmicroscopy.org/0.6rc0/schemas/_version.schema" + "$ref": "https://ngff.openmicroscopy.org/0.9.dev1/schemas/_version.schema" } }, "required": [ diff --git a/tests/attributes/spec/invalid/image/duplicate_axes.json b/tests/attributes/spec/invalid/image/duplicate_axes.json index 7bfe79aa..4c02f7d6 100644 --- a/tests/attributes/spec/invalid/image/duplicate_axes.json +++ b/tests/attributes/spec/invalid/image/duplicate_axes.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/spec/invalid/image/duplicate_orientation.json b/tests/attributes/spec/invalid/image/duplicate_orientation.json new file mode 100644 index 00000000..371908c9 --- /dev/null +++ b/tests/attributes/spec/invalid/image/duplicate_orientation.json @@ -0,0 +1,56 @@ +{ + "ome": { + "version": "0.9.dev1", + "multiscales": [ + { + "name": "multiscales", + "coordinateSystems": [ + { + "name": "physical", + "axes": [ + { + "type": "space", + "name": "y", + "unit": "micrometer", + "discrete": false, + "orientation": { + "type": "anatomical", + "value": "left-to-right" + } + }, + { + "type": "space", + "name": "x", + "unit": "micrometer", + "discrete": false, + "orientation": { + "type": "anatomical", + "value": "left-to-right" + } + } + ] + } + ], + "datasets": [ + { + "path": "array", + "coordinateTransformations": [ + { + "type": "identity", + "output": {"name": "physical"}, + "input": {"path": "array"}, + "name": "transform-name" + } + ] + } + ] + } + ] + }, + "_conformance": { + "schema": { + "id": "schemas/image.schema" + }, + "valid": false + } +} diff --git a/tests/attributes/spec/invalid/image/duplicate_scale.json b/tests/attributes/spec/invalid/image/duplicate_scale.json index 9df56830..97e9b95d 100644 --- a/tests/attributes/spec/invalid/image/duplicate_scale.json +++ b/tests/attributes/spec/invalid/image/duplicate_scale.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/spec/invalid/image/empty_transformations.json b/tests/attributes/spec/invalid/image/empty_transformations.json index 18c16d49..530e280d 100644 --- a/tests/attributes/spec/invalid/image/empty_transformations.json +++ b/tests/attributes/spec/invalid/image/empty_transformations.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/spec/invalid/image/invalid_channels_color.json b/tests/attributes/spec/invalid/image/invalid_channels_color.json index a1974bc2..6ae547e9 100644 --- a/tests/attributes/spec/invalid/image/invalid_channels_color.json +++ b/tests/attributes/spec/invalid/image/invalid_channels_color.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/spec/invalid/image/invalid_channels_window.json b/tests/attributes/spec/invalid/image/invalid_channels_window.json index bf394f94..ef2abd95 100644 --- a/tests/attributes/spec/invalid/image/invalid_channels_window.json +++ b/tests/attributes/spec/invalid/image/invalid_channels_window.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/spec/invalid/image/invalid_multiscale_transform_input.json b/tests/attributes/spec/invalid/image/invalid_multiscale_transform_input.json index 847028fa..493b1672 100644 --- a/tests/attributes/spec/invalid/image/invalid_multiscale_transform_input.json +++ b/tests/attributes/spec/invalid/image/invalid_multiscale_transform_input.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/spec/invalid/image/invalid_multiscale_transform_input_output.json b/tests/attributes/spec/invalid/image/invalid_multiscale_transform_input_output.json index 6af3e1af..8c2e2e7f 100644 --- a/tests/attributes/spec/invalid/image/invalid_multiscale_transform_input_output.json +++ b/tests/attributes/spec/invalid/image/invalid_multiscale_transform_input_output.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/spec/invalid/image/invalid_multiscale_transform_output.json b/tests/attributes/spec/invalid/image/invalid_multiscale_transform_output.json index bd133530..f8818818 100644 --- a/tests/attributes/spec/invalid/image/invalid_multiscale_transform_output.json +++ b/tests/attributes/spec/invalid/image/invalid_multiscale_transform_output.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/spec/invalid/image/invalid_multiscales_transformations.json b/tests/attributes/spec/invalid/image/invalid_multiscales_transformations.json index e3573d70..37460825 100644 --- a/tests/attributes/spec/invalid/image/invalid_multiscales_transformations.json +++ b/tests/attributes/spec/invalid/image/invalid_multiscales_transformations.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/spec/invalid/image/invalid_path.json b/tests/attributes/spec/invalid/image/invalid_path.json index 8e497069..40abd2f1 100644 --- a/tests/attributes/spec/invalid/image/invalid_path.json +++ b/tests/attributes/spec/invalid/image/invalid_path.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/spec/invalid/image/invalid_transformation_type.json b/tests/attributes/spec/invalid/image/invalid_transformation_type.json index 2a2eeded..936618ac 100644 --- a/tests/attributes/spec/invalid/image/invalid_transformation_type.json +++ b/tests/attributes/spec/invalid/image/invalid_transformation_type.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/spec/invalid/image/missing_axes_name.json b/tests/attributes/spec/invalid/image/missing_axes_name.json index 0233a45c..7f18f396 100644 --- a/tests/attributes/spec/invalid/image/missing_axes_name.json +++ b/tests/attributes/spec/invalid/image/missing_axes_name.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/spec/invalid/image/missing_coordinate_system_axes.json b/tests/attributes/spec/invalid/image/missing_coordinate_system_axes.json index 937a19cd..85054ea7 100644 --- a/tests/attributes/spec/invalid/image/missing_coordinate_system_axes.json +++ b/tests/attributes/spec/invalid/image/missing_coordinate_system_axes.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/spec/invalid/image/missing_coordinate_system_name.json b/tests/attributes/spec/invalid/image/missing_coordinate_system_name.json index e7570531..d427c554 100644 --- a/tests/attributes/spec/invalid/image/missing_coordinate_system_name.json +++ b/tests/attributes/spec/invalid/image/missing_coordinate_system_name.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/spec/invalid/image/missing_coordinate_systems.json b/tests/attributes/spec/invalid/image/missing_coordinate_systems.json index 86d04950..dd358dd9 100644 --- a/tests/attributes/spec/invalid/image/missing_coordinate_systems.json +++ b/tests/attributes/spec/invalid/image/missing_coordinate_systems.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "datasets": [ diff --git a/tests/attributes/spec/invalid/image/missing_datasets.json b/tests/attributes/spec/invalid/image/missing_datasets.json index 242e02e8..d7581800 100644 --- a/tests/attributes/spec/invalid/image/missing_datasets.json +++ b/tests/attributes/spec/invalid/image/missing_datasets.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/spec/invalid/image/missing_path.json b/tests/attributes/spec/invalid/image/missing_path.json index 276e7b08..1a26fec8 100644 --- a/tests/attributes/spec/invalid/image/missing_path.json +++ b/tests/attributes/spec/invalid/image/missing_path.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/spec/invalid/image/missing_scale.json b/tests/attributes/spec/invalid/image/missing_scale.json index 3a17cce9..7dd8a46d 100644 --- a/tests/attributes/spec/invalid/image/missing_scale.json +++ b/tests/attributes/spec/invalid/image/missing_scale.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/spec/invalid/image/missing_transformations.json b/tests/attributes/spec/invalid/image/missing_transformations.json index 322312d7..e06e2cc3 100644 --- a/tests/attributes/spec/invalid/image/missing_transformations.json +++ b/tests/attributes/spec/invalid/image/missing_transformations.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/spec/invalid/image/no_axes.json b/tests/attributes/spec/invalid/image/no_axes.json index e5880f10..4fc6f51b 100644 --- a/tests/attributes/spec/invalid/image/no_axes.json +++ b/tests/attributes/spec/invalid/image/no_axes.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "axes": [], diff --git a/tests/attributes/spec/invalid/image/no_datasets.json b/tests/attributes/spec/invalid/image/no_datasets.json index 18bcb9e4..3972e4a7 100644 --- a/tests/attributes/spec/invalid/image/no_datasets.json +++ b/tests/attributes/spec/invalid/image/no_datasets.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/spec/invalid/image/no_multiscales.json b/tests/attributes/spec/invalid/image/no_multiscales.json index 63509a8e..2b254c5b 100644 --- a/tests/attributes/spec/invalid/image/no_multiscales.json +++ b/tests/attributes/spec/invalid/image/no_multiscales.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [] }, "_conformance": { diff --git a/tests/attributes/spec/invalid/image/non_existent_orientation.json b/tests/attributes/spec/invalid/image/non_existent_orientation.json new file mode 100644 index 00000000..273887b1 --- /dev/null +++ b/tests/attributes/spec/invalid/image/non_existent_orientation.json @@ -0,0 +1,56 @@ +{ + "ome": { + "version": "0.9.dev1", + "multiscales": [ + { + "name": "multiscales", + "coordinateSystems": [ + { + "name": "physical", + "axes": [ + { + "type": "space", + "name": "y", + "unit": "micrometer", + "discrete": false, + "orientation": { + "type": "anatomical", + "value": "top-to-bottom" + } + }, + { + "type": "space", + "name": "x", + "unit": "micrometer", + "discrete": false, + "orientation": { + "type": "anatomical", + "value": "empty-to-full" + } + } + ] + } + ], + "datasets": [ + { + "path": "array", + "coordinateTransformations": [ + { + "type": "identity", + "output": {"name": "physical"}, + "input": {"path": "array"}, + "name": "transform-name" + } + ] + } + ] + } + ] + }, + "_conformance": { + "schema": { + "id": "schemas/image.schema" + }, + "valid": false + } +} diff --git a/tests/attributes/spec/invalid/image/non_existent_orientation_type.json b/tests/attributes/spec/invalid/image/non_existent_orientation_type.json new file mode 100644 index 00000000..dcdfd3ca --- /dev/null +++ b/tests/attributes/spec/invalid/image/non_existent_orientation_type.json @@ -0,0 +1,56 @@ +{ + "ome": { + "version": "0.9.dev1", + "multiscales": [ + { + "name": "multiscales", + "coordinateSystems": [ + { + "name": "physical", + "axes": [ + { + "type": "space", + "name": "y", + "unit": "kilometer", + "discrete": false, + "orientation": { + "type": "geographical", + "value": "east-to-west" + } + }, + { + "type": "space", + "name": "x", + "unit": "parsec", + "discrete": false, + "orientation": { + "type": "astronomical", + "value": "nadir-to-zenith" + } + } + ] + } + ], + "datasets": [ + { + "path": "array", + "coordinateTransformations": [ + { + "type": "identity", + "output": {"name": "physical"}, + "input": {"path": "array"}, + "name": "transform-name" + } + ] + } + ] + } + ] + }, + "_conformance": { + "schema": { + "id": "schemas/image.schema" + }, + "valid": false + } +} diff --git a/tests/attributes/spec/invalid/image/non_space_orientation.json b/tests/attributes/spec/invalid/image/non_space_orientation.json new file mode 100644 index 00000000..a5c31f1b --- /dev/null +++ b/tests/attributes/spec/invalid/image/non_space_orientation.json @@ -0,0 +1,55 @@ +{ + "ome": { + "version": "0.9.dev1", + "multiscales": [ + { + "name": "multiscales", + "coordinateSystems": [ + { + "name": "physical", + "axes": [ + { + "type": "custom", + "name": "m", + "discrete": false, + "orientation": { + "type": "anatomical", + "value": "anterior-to-posterior" + } + }, + { + "type": "space", + "name": "x", + "unit": "micrometer", + "discrete": false, + "orientation": { + "type": "anatomical", + "value": "left-to-right" + } + } + ] + } + ], + "datasets": [ + { + "path": "array", + "coordinateTransformations": [ + { + "type": "identity", + "output": {"name": "physical"}, + "input": {"path": "array"}, + "name": "transform-name" + } + ] + } + ] + } + ] + }, + "_conformance": { + "schema": { + "id": "schemas/image.schema" + }, + "valid": false + } +} diff --git a/tests/attributes/spec/invalid/label/colors_duplicate.json b/tests/attributes/spec/invalid/label/colors_duplicate.json index 6af9451b..75277233 100644 --- a/tests/attributes/spec/invalid/label/colors_duplicate.json +++ b/tests/attributes/spec/invalid/label/colors_duplicate.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "image-label": { "colors": [ { diff --git a/tests/attributes/spec/invalid/label/colors_no_label_value.json b/tests/attributes/spec/invalid/label/colors_no_label_value.json index b011d57a..488e2ac0 100644 --- a/tests/attributes/spec/invalid/label/colors_no_label_value.json +++ b/tests/attributes/spec/invalid/label/colors_no_label_value.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "image-label": { "colors": [ { diff --git a/tests/attributes/spec/invalid/label/colors_rgba_length.json b/tests/attributes/spec/invalid/label/colors_rgba_length.json index bf9b0f3f..f499d6e0 100644 --- a/tests/attributes/spec/invalid/label/colors_rgba_length.json +++ b/tests/attributes/spec/invalid/label/colors_rgba_length.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "image-label": { "colors": [ { diff --git a/tests/attributes/spec/invalid/label/colors_rgba_type.json b/tests/attributes/spec/invalid/label/colors_rgba_type.json index 78c7c1f1..e506c800 100644 --- a/tests/attributes/spec/invalid/label/colors_rgba_type.json +++ b/tests/attributes/spec/invalid/label/colors_rgba_type.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "image-label": { "colors": [ { diff --git a/tests/attributes/spec/invalid/label/empty_colors.json b/tests/attributes/spec/invalid/label/empty_colors.json index 6074567f..84ee40be 100644 --- a/tests/attributes/spec/invalid/label/empty_colors.json +++ b/tests/attributes/spec/invalid/label/empty_colors.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "image-label": { "colors": [] } diff --git a/tests/attributes/spec/invalid/label/empty_properties.json b/tests/attributes/spec/invalid/label/empty_properties.json index 686024a3..43d7d851 100644 --- a/tests/attributes/spec/invalid/label/empty_properties.json +++ b/tests/attributes/spec/invalid/label/empty_properties.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "image-label": { "properties": [] } diff --git a/tests/attributes/spec/invalid/label/properties_no_label_value.json b/tests/attributes/spec/invalid/label/properties_no_label_value.json index 42a6d0fb..cb944966 100644 --- a/tests/attributes/spec/invalid/label/properties_no_label_value.json +++ b/tests/attributes/spec/invalid/label/properties_no_label_value.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "image-label": { "properties": [ { diff --git a/tests/attributes/spec/invalid/plate/acquisition_negative_starttime.json b/tests/attributes/spec/invalid/plate/acquisition_negative_starttime.json index e4654427..2ce4565f 100644 --- a/tests/attributes/spec/invalid/plate/acquisition_negative_starttime.json +++ b/tests/attributes/spec/invalid/plate/acquisition_negative_starttime.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/attributes/spec/invalid/plate/acquisition_noninteger_endtime.json b/tests/attributes/spec/invalid/plate/acquisition_noninteger_endtime.json index a92ab04f..feeef7e4 100644 --- a/tests/attributes/spec/invalid/plate/acquisition_noninteger_endtime.json +++ b/tests/attributes/spec/invalid/plate/acquisition_noninteger_endtime.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/attributes/spec/invalid/plate/acquisition_noninteger_starttime.json b/tests/attributes/spec/invalid/plate/acquisition_noninteger_starttime.json index 5b3f35a7..adee822b 100644 --- a/tests/attributes/spec/invalid/plate/acquisition_noninteger_starttime.json +++ b/tests/attributes/spec/invalid/plate/acquisition_noninteger_starttime.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/attributes/spec/invalid/plate/acquisition_zero_maximumfieldcount.json b/tests/attributes/spec/invalid/plate/acquisition_zero_maximumfieldcount.json index 02d8a723..0afde4d4 100644 --- a/tests/attributes/spec/invalid/plate/acquisition_zero_maximumfieldcount.json +++ b/tests/attributes/spec/invalid/plate/acquisition_zero_maximumfieldcount.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/attributes/spec/invalid/plate/duplicate_columns.json b/tests/attributes/spec/invalid/plate/duplicate_columns.json index 707a0089..b15a2937 100644 --- a/tests/attributes/spec/invalid/plate/duplicate_columns.json +++ b/tests/attributes/spec/invalid/plate/duplicate_columns.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/attributes/spec/invalid/plate/duplicate_rows-2.json b/tests/attributes/spec/invalid/plate/duplicate_rows-2.json index bda76f0a..33ceb686 100644 --- a/tests/attributes/spec/invalid/plate/duplicate_rows-2.json +++ b/tests/attributes/spec/invalid/plate/duplicate_rows-2.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/attributes/spec/invalid/plate/duplicate_rows.json b/tests/attributes/spec/invalid/plate/duplicate_rows.json index 3d9876ab..edb9dfb6 100644 --- a/tests/attributes/spec/invalid/plate/duplicate_rows.json +++ b/tests/attributes/spec/invalid/plate/duplicate_rows.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/attributes/spec/invalid/plate/empty_columns.json b/tests/attributes/spec/invalid/plate/empty_columns.json index e83a54d3..61593284 100644 --- a/tests/attributes/spec/invalid/plate/empty_columns.json +++ b/tests/attributes/spec/invalid/plate/empty_columns.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [], "rows": [ diff --git a/tests/attributes/spec/invalid/plate/empty_rows.json b/tests/attributes/spec/invalid/plate/empty_rows.json index bb6157a6..cbfc8a6d 100644 --- a/tests/attributes/spec/invalid/plate/empty_rows.json +++ b/tests/attributes/spec/invalid/plate/empty_rows.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/attributes/spec/invalid/plate/empty_wells.json b/tests/attributes/spec/invalid/plate/empty_wells.json index e5a65995..b8a8ffbd 100644 --- a/tests/attributes/spec/invalid/plate/empty_wells.json +++ b/tests/attributes/spec/invalid/plate/empty_wells.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/attributes/spec/invalid/plate/missing_acquisition_id.json b/tests/attributes/spec/invalid/plate/missing_acquisition_id.json index e427a114..d2646a73 100644 --- a/tests/attributes/spec/invalid/plate/missing_acquisition_id.json +++ b/tests/attributes/spec/invalid/plate/missing_acquisition_id.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/attributes/spec/invalid/plate/missing_column_name.json b/tests/attributes/spec/invalid/plate/missing_column_name.json index 191a4ef2..67317db4 100644 --- a/tests/attributes/spec/invalid/plate/missing_column_name.json +++ b/tests/attributes/spec/invalid/plate/missing_column_name.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/attributes/spec/invalid/plate/missing_columns.json b/tests/attributes/spec/invalid/plate/missing_columns.json index c735d081..4058de75 100644 --- a/tests/attributes/spec/invalid/plate/missing_columns.json +++ b/tests/attributes/spec/invalid/plate/missing_columns.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "rows": [ { diff --git a/tests/attributes/spec/invalid/plate/missing_row_name.json b/tests/attributes/spec/invalid/plate/missing_row_name.json index 775dee29..54ee6eb1 100644 --- a/tests/attributes/spec/invalid/plate/missing_row_name.json +++ b/tests/attributes/spec/invalid/plate/missing_row_name.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/attributes/spec/invalid/plate/missing_rows.json b/tests/attributes/spec/invalid/plate/missing_rows.json index 2dbf1121..1e62ff79 100644 --- a/tests/attributes/spec/invalid/plate/missing_rows.json +++ b/tests/attributes/spec/invalid/plate/missing_rows.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/attributes/spec/invalid/plate/missing_well_columnIndex.json b/tests/attributes/spec/invalid/plate/missing_well_columnIndex.json index f3b0eff2..3757846d 100644 --- a/tests/attributes/spec/invalid/plate/missing_well_columnIndex.json +++ b/tests/attributes/spec/invalid/plate/missing_well_columnIndex.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/attributes/spec/invalid/plate/missing_well_path.json b/tests/attributes/spec/invalid/plate/missing_well_path.json index 788ce507..999b8e3f 100644 --- a/tests/attributes/spec/invalid/plate/missing_well_path.json +++ b/tests/attributes/spec/invalid/plate/missing_well_path.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/attributes/spec/invalid/plate/missing_well_rowIndex.json b/tests/attributes/spec/invalid/plate/missing_well_rowIndex.json index 571ef542..2b1eb5b1 100644 --- a/tests/attributes/spec/invalid/plate/missing_well_rowIndex.json +++ b/tests/attributes/spec/invalid/plate/missing_well_rowIndex.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/attributes/spec/invalid/plate/missing_wells.json b/tests/attributes/spec/invalid/plate/missing_wells.json index 7ea60599..10754b61 100644 --- a/tests/attributes/spec/invalid/plate/missing_wells.json +++ b/tests/attributes/spec/invalid/plate/missing_wells.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/attributes/spec/invalid/plate/negative_acquisition_id.json b/tests/attributes/spec/invalid/plate/negative_acquisition_id.json index 77638bee..f5a7e140 100644 --- a/tests/attributes/spec/invalid/plate/negative_acquisition_id.json +++ b/tests/attributes/spec/invalid/plate/negative_acquisition_id.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/attributes/spec/invalid/plate/negative_endtime.json b/tests/attributes/spec/invalid/plate/negative_endtime.json index ed4280ad..ca39dc72 100644 --- a/tests/attributes/spec/invalid/plate/negative_endtime.json +++ b/tests/attributes/spec/invalid/plate/negative_endtime.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/attributes/spec/invalid/plate/non_alphanumeric_column.json b/tests/attributes/spec/invalid/plate/non_alphanumeric_column.json index 09a40c66..14ba6f07 100644 --- a/tests/attributes/spec/invalid/plate/non_alphanumeric_column.json +++ b/tests/attributes/spec/invalid/plate/non_alphanumeric_column.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/attributes/spec/invalid/plate/non_integer_acquisition_id.json b/tests/attributes/spec/invalid/plate/non_integer_acquisition_id.json index db65d5e1..b34a88b1 100644 --- a/tests/attributes/spec/invalid/plate/non_integer_acquisition_id.json +++ b/tests/attributes/spec/invalid/plate/non_integer_acquisition_id.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/attributes/spec/invalid/plate/non_integer_acquisition_maximumfieldcount.json b/tests/attributes/spec/invalid/plate/non_integer_acquisition_maximumfieldcount.json index 02ff7831..7d4fc7cd 100644 --- a/tests/attributes/spec/invalid/plate/non_integer_acquisition_maximumfieldcount.json +++ b/tests/attributes/spec/invalid/plate/non_integer_acquisition_maximumfieldcount.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/attributes/spec/invalid/plate/well_1group.json b/tests/attributes/spec/invalid/plate/well_1group.json index 1e761d56..a1798808 100644 --- a/tests/attributes/spec/invalid/plate/well_1group.json +++ b/tests/attributes/spec/invalid/plate/well_1group.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/attributes/spec/invalid/plate/well_3groups.json b/tests/attributes/spec/invalid/plate/well_3groups.json index 689b86c0..3504445e 100644 --- a/tests/attributes/spec/invalid/plate/well_3groups.json +++ b/tests/attributes/spec/invalid/plate/well_3groups.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/attributes/spec/invalid/plate/zero_field_count.json b/tests/attributes/spec/invalid/plate/zero_field_count.json index 2c0f509d..31700b6e 100644 --- a/tests/attributes/spec/invalid/plate/zero_field_count.json +++ b/tests/attributes/spec/invalid/plate/zero_field_count.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/attributes/spec/invalid/scene/scene_bijection_forward_missing_params.json b/tests/attributes/spec/invalid/scene/scene_bijection_forward_missing_params.json index 1c2bb23a..b77b92c6 100644 --- a/tests/attributes/spec/invalid/scene/scene_bijection_forward_missing_params.json +++ b/tests/attributes/spec/invalid/scene/scene_bijection_forward_missing_params.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "scene": { "coordinateSystems": [ { diff --git a/tests/attributes/spec/invalid/scene/scene_bijection_inverse_missing_params.json b/tests/attributes/spec/invalid/scene/scene_bijection_inverse_missing_params.json index 9a09136e..372039fb 100644 --- a/tests/attributes/spec/invalid/scene/scene_bijection_inverse_missing_params.json +++ b/tests/attributes/spec/invalid/scene/scene_bijection_inverse_missing_params.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "scene": { "coordinateSystems": [ { diff --git a/tests/attributes/spec/invalid/scene/scene_input_output_not_object.json b/tests/attributes/spec/invalid/scene/scene_input_output_not_object.json index 3d7a5636..9823e916 100644 --- a/tests/attributes/spec/invalid/scene/scene_input_output_not_object.json +++ b/tests/attributes/spec/invalid/scene/scene_input_output_not_object.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "scene": { "coordinateTransformations": [ { diff --git a/tests/attributes/spec/invalid/scene/scene_missing_scene.json b/tests/attributes/spec/invalid/scene/scene_missing_scene.json index 22b0307b..8c0f222b 100644 --- a/tests/attributes/spec/invalid/scene/scene_missing_scene.json +++ b/tests/attributes/spec/invalid/scene/scene_missing_scene.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "coordinateSystems": [ { "name": "world", diff --git a/tests/attributes/spec/invalid/scene/scene_missing_transformations.json b/tests/attributes/spec/invalid/scene/scene_missing_transformations.json index e603eeaa..50bae35a 100644 --- a/tests/attributes/spec/invalid/scene/scene_missing_transformations.json +++ b/tests/attributes/spec/invalid/scene/scene_missing_transformations.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "scene": { "coordinateSystems": [ { diff --git a/tests/attributes/spec/invalid/transforms/bad_affine_no_affine.json b/tests/attributes/spec/invalid/transforms/bad_affine_no_affine.json index ee2e5f2e..a5e02019 100644 --- a/tests/attributes/spec/invalid/transforms/bad_affine_no_affine.json +++ b/tests/attributes/spec/invalid/transforms/bad_affine_no_affine.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/bad_affine_no_input_output.json b/tests/attributes/spec/invalid/transforms/bad_affine_no_input_output.json index 8ff05545..62842f7a 100644 --- a/tests/attributes/spec/invalid/transforms/bad_affine_no_input_output.json +++ b/tests/attributes/spec/invalid/transforms/bad_affine_no_input_output.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/bad_byDimension_no_input_output_axes.json b/tests/attributes/spec/invalid/transforms/bad_byDimension_no_input_output_axes.json index d8d1b5be..9c3ae6d7 100644 --- a/tests/attributes/spec/invalid/transforms/bad_byDimension_no_input_output_axes.json +++ b/tests/attributes/spec/invalid/transforms/bad_byDimension_no_input_output_axes.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/bad_byDimension_wrong axes_type.json b/tests/attributes/spec/invalid/transforms/bad_byDimension_wrong axes_type.json index 7a528f1a..aba5da20 100644 --- a/tests/attributes/spec/invalid/transforms/bad_byDimension_wrong axes_type.json +++ b/tests/attributes/spec/invalid/transforms/bad_byDimension_wrong axes_type.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/bad_mapaxis.json b/tests/attributes/spec/invalid/transforms/bad_mapaxis.json index 077c70f7..89ccbe07 100644 --- a/tests/attributes/spec/invalid/transforms/bad_mapaxis.json +++ b/tests/attributes/spec/invalid/transforms/bad_mapaxis.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/bad_mapaxis2.json b/tests/attributes/spec/invalid/transforms/bad_mapaxis2.json index e690f809..a47aa5ab 100644 --- a/tests/attributes/spec/invalid/transforms/bad_mapaxis2.json +++ b/tests/attributes/spec/invalid/transforms/bad_mapaxis2.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/bad_mapaxis3.json b/tests/attributes/spec/invalid/transforms/bad_mapaxis3.json index 1762ee21..a6a42fdf 100644 --- a/tests/attributes/spec/invalid/transforms/bad_mapaxis3.json +++ b/tests/attributes/spec/invalid/transforms/bad_mapaxis3.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/bad_mapaxis4.json b/tests/attributes/spec/invalid/transforms/bad_mapaxis4.json index ff19dd41..1f81f676 100644 --- a/tests/attributes/spec/invalid/transforms/bad_mapaxis4.json +++ b/tests/attributes/spec/invalid/transforms/bad_mapaxis4.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/bad_mapaxis5.json b/tests/attributes/spec/invalid/transforms/bad_mapaxis5.json index 1d544eb3..355dbf7c 100644 --- a/tests/attributes/spec/invalid/transforms/bad_mapaxis5.json +++ b/tests/attributes/spec/invalid/transforms/bad_mapaxis5.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/bad_projectAxis_insert_non_unique.json b/tests/attributes/spec/invalid/transforms/bad_projectAxis_insert_non_unique.json index b1fa37bc..175ac94e 100644 --- a/tests/attributes/spec/invalid/transforms/bad_projectAxis_insert_non_unique.json +++ b/tests/attributes/spec/invalid/transforms/bad_projectAxis_insert_non_unique.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/bad_projectAxis_insert_too_high_dim.json b/tests/attributes/spec/invalid/transforms/bad_projectAxis_insert_too_high_dim.json index c317b63a..d61b6fa8 100644 --- a/tests/attributes/spec/invalid/transforms/bad_projectAxis_insert_too_high_dim.json +++ b/tests/attributes/spec/invalid/transforms/bad_projectAxis_insert_too_high_dim.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/bad_projectAxis_insert_too_many.json b/tests/attributes/spec/invalid/transforms/bad_projectAxis_insert_too_many.json index d47d4c7c..be272d0f 100644 --- a/tests/attributes/spec/invalid/transforms/bad_projectAxis_insert_too_many.json +++ b/tests/attributes/spec/invalid/transforms/bad_projectAxis_insert_too_many.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/bad_projectAxis_missing_op.json b/tests/attributes/spec/invalid/transforms/bad_projectAxis_missing_op.json index 267d7809..9b8a7e6b 100644 --- a/tests/attributes/spec/invalid/transforms/bad_projectAxis_missing_op.json +++ b/tests/attributes/spec/invalid/transforms/bad_projectAxis_missing_op.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/bad_projectAxis_remove_non_unique.json b/tests/attributes/spec/invalid/transforms/bad_projectAxis_remove_non_unique.json index e3636c6e..554f03a9 100644 --- a/tests/attributes/spec/invalid/transforms/bad_projectAxis_remove_non_unique.json +++ b/tests/attributes/spec/invalid/transforms/bad_projectAxis_remove_non_unique.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/bad_projectAxis_remove_too_high_dim.json b/tests/attributes/spec/invalid/transforms/bad_projectAxis_remove_too_high_dim.json index f4d45f70..41794973 100644 --- a/tests/attributes/spec/invalid/transforms/bad_projectAxis_remove_too_high_dim.json +++ b/tests/attributes/spec/invalid/transforms/bad_projectAxis_remove_too_high_dim.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/bad_projectAxis_remove_too_many.json b/tests/attributes/spec/invalid/transforms/bad_projectAxis_remove_too_many.json index 2c86e9c0..3fd586f8 100644 --- a/tests/attributes/spec/invalid/transforms/bad_projectAxis_remove_too_many.json +++ b/tests/attributes/spec/invalid/transforms/bad_projectAxis_remove_too_many.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/bad_rotation.json b/tests/attributes/spec/invalid/transforms/bad_rotation.json index c6559132..430a0252 100644 --- a/tests/attributes/spec/invalid/transforms/bad_rotation.json +++ b/tests/attributes/spec/invalid/transforms/bad_rotation.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/bad_rotation2.json b/tests/attributes/spec/invalid/transforms/bad_rotation2.json index 81ffed4c..676cc273 100644 --- a/tests/attributes/spec/invalid/transforms/bad_rotation2.json +++ b/tests/attributes/spec/invalid/transforms/bad_rotation2.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/bad_rotation3.json b/tests/attributes/spec/invalid/transforms/bad_rotation3.json index 160be62e..b4adcac5 100644 --- a/tests/attributes/spec/invalid/transforms/bad_rotation3.json +++ b/tests/attributes/spec/invalid/transforms/bad_rotation3.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/bad_scale_path_not_allowed.json b/tests/attributes/spec/invalid/transforms/bad_scale_path_not_allowed.json index dc53904e..e051b206 100644 --- a/tests/attributes/spec/invalid/transforms/bad_scale_path_not_allowed.json +++ b/tests/attributes/spec/invalid/transforms/bad_scale_path_not_allowed.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/bad_translate_path_not_allowed.json b/tests/attributes/spec/invalid/transforms/bad_translate_path_not_allowed.json index 59bedebe..1c4cbc73 100644 --- a/tests/attributes/spec/invalid/transforms/bad_translate_path_not_allowed.json +++ b/tests/attributes/spec/invalid/transforms/bad_translate_path_not_allowed.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/multiscales_transform_forbidden.json b/tests/attributes/spec/invalid/transforms/multiscales_transform_forbidden.json index 98b6902e..7c56b75f 100644 --- a/tests/attributes/spec/invalid/transforms/multiscales_transform_forbidden.json +++ b/tests/attributes/spec/invalid/transforms/multiscales_transform_forbidden.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/multiscales_transform_forbidden2.json b/tests/attributes/spec/invalid/transforms/multiscales_transform_forbidden2.json index 48e1c496..30364313 100644 --- a/tests/attributes/spec/invalid/transforms/multiscales_transform_forbidden2.json +++ b/tests/attributes/spec/invalid/transforms/multiscales_transform_forbidden2.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/multiscales_transform_forbidden3.json b/tests/attributes/spec/invalid/transforms/multiscales_transform_forbidden3.json index ef67ac88..7f2010f8 100644 --- a/tests/attributes/spec/invalid/transforms/multiscales_transform_forbidden3.json +++ b/tests/attributes/spec/invalid/transforms/multiscales_transform_forbidden3.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/multiscales_transform_missing_params.json b/tests/attributes/spec/invalid/transforms/multiscales_transform_missing_params.json index d759125a..dec87b5b 100644 --- a/tests/attributes/spec/invalid/transforms/multiscales_transform_missing_params.json +++ b/tests/attributes/spec/invalid/transforms/multiscales_transform_missing_params.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/multiscales_transform_no_input_output.json b/tests/attributes/spec/invalid/transforms/multiscales_transform_no_input_output.json index 3b3f2f95..0d688a94 100644 --- a/tests/attributes/spec/invalid/transforms/multiscales_transform_no_input_output.json +++ b/tests/attributes/spec/invalid/transforms/multiscales_transform_no_input_output.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/transforms/multiscales_transform_no_input_output2.json b/tests/attributes/spec/invalid/transforms/multiscales_transform_no_input_output2.json index 80a8e6c1..1bcc730e 100644 --- a/tests/attributes/spec/invalid/transforms/multiscales_transform_no_input_output2.json +++ b/tests/attributes/spec/invalid/transforms/multiscales_transform_no_input_output2.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/well/forbidden_path_1.json b/tests/attributes/spec/invalid/well/forbidden_path_1.json index 7737ebac..732cda60 100644 --- a/tests/attributes/spec/invalid/well/forbidden_path_1.json +++ b/tests/attributes/spec/invalid/well/forbidden_path_1.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "well": { "images": [ { diff --git a/tests/attributes/spec/invalid/well/forbidden_path_2.json b/tests/attributes/spec/invalid/well/forbidden_path_2.json index 697e6bcd..87373f4a 100644 --- a/tests/attributes/spec/invalid/well/forbidden_path_2.json +++ b/tests/attributes/spec/invalid/well/forbidden_path_2.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "well": { "images": [ { diff --git a/tests/attributes/spec/invalid/well/forbidden_path_3.json b/tests/attributes/spec/invalid/well/forbidden_path_3.json index d314fa13..7b998b1d 100644 --- a/tests/attributes/spec/invalid/well/forbidden_path_3.json +++ b/tests/attributes/spec/invalid/well/forbidden_path_3.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "well": { "images": [ { diff --git a/tests/attributes/spec/invalid/well/forbidden_path_4.json b/tests/attributes/spec/invalid/well/forbidden_path_4.json index 6e3b0ddd..0d009ba2 100644 --- a/tests/attributes/spec/invalid/well/forbidden_path_4.json +++ b/tests/attributes/spec/invalid/well/forbidden_path_4.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "well": { "images": [ { diff --git a/tests/attributes/spec/valid/image/custom_type_axes.json b/tests/attributes/spec/valid/image/custom_type_axes.json index 37114b11..ce0ddc6a 100644 --- a/tests/attributes/spec/valid/image/custom_type_axes.json +++ b/tests/attributes/spec/valid/image/custom_type_axes.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/spec/valid/image/invalid_axis_units.json b/tests/attributes/spec/valid/image/invalid_axis_units.json index 9b4740cd..b51c3eef 100644 --- a/tests/attributes/spec/valid/image/invalid_axis_units.json +++ b/tests/attributes/spec/valid/image/invalid_axis_units.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/spec/invalid/image/too_many_axes.json b/tests/attributes/spec/valid/image/many_axes.json similarity index 96% rename from tests/attributes/spec/invalid/image/too_many_axes.json rename to tests/attributes/spec/valid/image/many_axes.json index dd9d9a29..7a68616d 100644 --- a/tests/attributes/spec/invalid/image/too_many_axes.json +++ b/tests/attributes/spec/valid/image/many_axes.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ @@ -61,6 +61,6 @@ "schema": { "id": "schemas/image.schema" }, - "valid": false + "valid": true } } \ No newline at end of file diff --git a/tests/attributes/spec/invalid/image/too_many_space_axes.json b/tests/attributes/spec/valid/image/many_space_axes.json similarity index 95% rename from tests/attributes/spec/invalid/image/too_many_space_axes.json rename to tests/attributes/spec/valid/image/many_space_axes.json index 6572ee66..8abb1db2 100644 --- a/tests/attributes/spec/invalid/image/too_many_space_axes.json +++ b/tests/attributes/spec/valid/image/many_space_axes.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc02", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ @@ -51,6 +51,6 @@ "schema": { "id": "schemas/image.schema" }, - "valid": false + "valid": true } -} \ No newline at end of file +} diff --git a/tests/attributes/spec/valid/image/mismatch_axes_units.json b/tests/attributes/spec/valid/image/mismatch_axes_units.json index 0681fb03..49fab4ab 100644 --- a/tests/attributes/spec/valid/image/mismatch_axes_units.json +++ b/tests/attributes/spec/valid/image/mismatch_axes_units.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/spec/valid/image/missing_name.json b/tests/attributes/spec/valid/image/missing_name.json index 7d6927b6..03fc233f 100644 --- a/tests/attributes/spec/valid/image/missing_name.json +++ b/tests/attributes/spec/valid/image/missing_name.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "datasets": [ diff --git a/tests/attributes/spec/invalid/image/missing_space_axes.json b/tests/attributes/spec/valid/image/missing_space_axes.json similarity index 94% rename from tests/attributes/spec/invalid/image/missing_space_axes.json rename to tests/attributes/spec/valid/image/missing_space_axes.json index 95e426ef..8651ded1 100644 --- a/tests/attributes/spec/invalid/image/missing_space_axes.json +++ b/tests/attributes/spec/valid/image/missing_space_axes.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ @@ -40,6 +40,6 @@ "schema": { "id": "schemas/image.schema" }, - "valid": false + "valid": true } -} \ No newline at end of file +} diff --git a/tests/attributes/spec/valid/image/multiscales_orientation.json b/tests/attributes/spec/valid/image/multiscales_orientation.json new file mode 100644 index 00000000..e61f81b3 --- /dev/null +++ b/tests/attributes/spec/valid/image/multiscales_orientation.json @@ -0,0 +1,56 @@ +{ + "ome": { + "version": "0.9.dev1", + "multiscales": [ + { + "name": "multiscales", + "coordinateSystems": [ + { + "name": "physical", + "axes": [ + { + "type": "space", + "name": "y", + "unit": "micrometer", + "discrete": false, + "orientation": { + "type": "anatomical", + "value": "posterior-to-anterior" + } + }, + { + "type": "space", + "name": "x", + "unit": "micrometer", + "discrete": false, + "orientation": { + "type": "anatomical", + "value": "left-to-right" + } + } + ] + } + ], + "datasets": [ + { + "path": "array", + "coordinateTransformations": [ + { + "type": "identity", + "output": {"name": "physical"}, + "input": {"path": "array"}, + "name": "transform-name" + } + ] + } + ] + } + ] + }, + "_conformance": { + "schema": { + "id": "schemas/image.schema" + }, + "valid": true + } +} diff --git a/tests/attributes/spec/valid/image/multiscales_transform_additional_transforms.json b/tests/attributes/spec/valid/image/multiscales_transform_additional_transforms.json index 414abc00..360bbd24 100644 --- a/tests/attributes/spec/valid/image/multiscales_transform_additional_transforms.json +++ b/tests/attributes/spec/valid/image/multiscales_transform_additional_transforms.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/valid/image/multiscales_transform_additional_transforms_path.json b/tests/attributes/spec/valid/image/multiscales_transform_additional_transforms_path.json index bd04c51f..514c0ece 100644 --- a/tests/attributes/spec/valid/image/multiscales_transform_additional_transforms_path.json +++ b/tests/attributes/spec/valid/image/multiscales_transform_additional_transforms_path.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/valid/image/multiscales_transform_identity.json b/tests/attributes/spec/valid/image/multiscales_transform_identity.json index 48da3f2c..306bfa99 100644 --- a/tests/attributes/spec/valid/image/multiscales_transform_identity.json +++ b/tests/attributes/spec/valid/image/multiscales_transform_identity.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/valid/image/multiscales_transform_sequence.json b/tests/attributes/spec/valid/image/multiscales_transform_sequence.json index 26c50339..cd22d493 100644 --- a/tests/attributes/spec/valid/image/multiscales_transform_sequence.json +++ b/tests/attributes/spec/valid/image/multiscales_transform_sequence.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/invalid/image/invalid_axis_type.json b/tests/attributes/spec/valid/image/one_custom_one_space_axis.json similarity index 91% rename from tests/attributes/spec/invalid/image/invalid_axis_type.json rename to tests/attributes/spec/valid/image/one_custom_one_space_axis.json index 24b31b60..efb65b5b 100644 --- a/tests/attributes/spec/invalid/image/invalid_axis_type.json +++ b/tests/attributes/spec/valid/image/one_custom_one_space_axis.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ @@ -9,7 +9,7 @@ "axes": [ { "name": "y", - "type": "invalid", + "type": "custom", "unit": "micrometer" }, { @@ -43,6 +43,6 @@ "schema": { "id": "schemas/image.schema" }, - "valid": false + "valid": true } -} \ No newline at end of file +} diff --git a/tests/attributes/spec/invalid/image/one_space_axes.json b/tests/attributes/spec/valid/image/one_space_axes.json similarity index 95% rename from tests/attributes/spec/invalid/image/one_space_axes.json rename to tests/attributes/spec/valid/image/one_space_axes.json index 7c072a61..668671d3 100644 --- a/tests/attributes/spec/invalid/image/one_space_axes.json +++ b/tests/attributes/spec/valid/image/one_space_axes.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ @@ -46,6 +46,6 @@ "schema": { "id": "schemas/image.schema" }, - "valid": false + "valid": true } } \ No newline at end of file diff --git a/tests/attributes/spec/invalid/image/invalid_axes_count.json b/tests/attributes/spec/valid/image/single_axis.json similarity index 94% rename from tests/attributes/spec/invalid/image/invalid_axes_count.json rename to tests/attributes/spec/valid/image/single_axis.json index 2fd586f5..1b7749c5 100644 --- a/tests/attributes/spec/invalid/image/invalid_axes_count.json +++ b/tests/attributes/spec/valid/image/single_axis.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ @@ -38,6 +38,6 @@ "schema": { "id": "schemas/image.schema" }, - "valid": false + "valid": true } } \ No newline at end of file diff --git a/tests/attributes/spec/valid/image/untyped_axes.json b/tests/attributes/spec/valid/image/untyped_axes.json index 85160b9e..887728e5 100644 --- a/tests/attributes/spec/valid/image/untyped_axes.json +++ b/tests/attributes/spec/valid/image/untyped_axes.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/spec/valid/label/minimal.json b/tests/attributes/spec/valid/label/minimal.json index 686de77a..3c47e6f6 100644 --- a/tests/attributes/spec/valid/label/minimal.json +++ b/tests/attributes/spec/valid/label/minimal.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "image-label": { "colors": [ { diff --git a/tests/attributes/spec/valid/label/minimal_properties.json b/tests/attributes/spec/valid/label/minimal_properties.json index fdad1d73..a63006ef 100644 --- a/tests/attributes/spec/valid/label/minimal_properties.json +++ b/tests/attributes/spec/valid/label/minimal_properties.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "image-label": { "colors": [ { diff --git a/tests/attributes/spec/valid/omero/full_omero_metadata.json b/tests/attributes/spec/valid/omero/full_omero_metadata.json index 77d3a029..5530bba3 100644 --- a/tests/attributes/spec/valid/omero/full_omero_metadata.json +++ b/tests/attributes/spec/valid/omero/full_omero_metadata.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ @@ -90,4 +90,4 @@ "id": "schemas/image.schema" } } -} \ No newline at end of file +} diff --git a/tests/attributes/spec/valid/plate/minimal_acquisitions.json b/tests/attributes/spec/valid/plate/minimal_acquisitions.json index 0ac173d0..c5f7e881 100644 --- a/tests/attributes/spec/valid/plate/minimal_acquisitions.json +++ b/tests/attributes/spec/valid/plate/minimal_acquisitions.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/attributes/spec/valid/plate/minimal_no_acquisitions.json b/tests/attributes/spec/valid/plate/minimal_no_acquisitions.json index a48f28eb..c47a9508 100644 --- a/tests/attributes/spec/valid/plate/minimal_no_acquisitions.json +++ b/tests/attributes/spec/valid/plate/minimal_no_acquisitions.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/attributes/spec/valid/plate/non_alphanumeric_row.json b/tests/attributes/spec/valid/plate/non_alphanumeric_row.json index 5f37659f..85185029 100644 --- a/tests/attributes/spec/valid/plate/non_alphanumeric_row.json +++ b/tests/attributes/spec/valid/plate/non_alphanumeric_row.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/attributes/spec/valid/scene/scene.json b/tests/attributes/spec/valid/scene/scene.json index 555729c3..9e5a0802 100644 --- a/tests/attributes/spec/valid/scene/scene.json +++ b/tests/attributes/spec/valid/scene/scene.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "scene": { "coordinateTransformations": [ { diff --git a/tests/attributes/spec/valid/scene/tile_stitching.json b/tests/attributes/spec/valid/scene/tile_stitching.json index d47c625d..98b51634 100644 --- a/tests/attributes/spec/valid/scene/tile_stitching.json +++ b/tests/attributes/spec/valid/scene/tile_stitching.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "scene":{ "coordinateTransformations": [ { diff --git a/tests/attributes/spec/valid/transforms/affine.json b/tests/attributes/spec/valid/transforms/affine.json index 2543f36c..6aa86af6 100644 --- a/tests/attributes/spec/valid/transforms/affine.json +++ b/tests/attributes/spec/valid/transforms/affine.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/valid/transforms/affineParams.json b/tests/attributes/spec/valid/transforms/affineParams.json index 345e0705..5afad7b2 100644 --- a/tests/attributes/spec/valid/transforms/affineParams.json +++ b/tests/attributes/spec/valid/transforms/affineParams.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/valid/transforms/byDimension.json b/tests/attributes/spec/valid/transforms/byDimension.json index 45d2a7f2..f953e9ca 100644 --- a/tests/attributes/spec/valid/transforms/byDimension.json +++ b/tests/attributes/spec/valid/transforms/byDimension.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/valid/transforms/identity.json b/tests/attributes/spec/valid/transforms/identity.json index 7682faa5..e0e933e6 100644 --- a/tests/attributes/spec/valid/transforms/identity.json +++ b/tests/attributes/spec/valid/transforms/identity.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/valid/transforms/mapAxis.json b/tests/attributes/spec/valid/transforms/mapAxis.json index d1f167b0..c06264bb 100644 --- a/tests/attributes/spec/valid/transforms/mapAxis.json +++ b/tests/attributes/spec/valid/transforms/mapAxis.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/valid/transforms/projectAxis.json b/tests/attributes/spec/valid/transforms/projectAxis.json index f1e1f907..b1aea791 100644 --- a/tests/attributes/spec/valid/transforms/projectAxis.json +++ b/tests/attributes/spec/valid/transforms/projectAxis.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/valid/transforms/projectAxis2.json b/tests/attributes/spec/valid/transforms/projectAxis2.json index a6bb0740..a6468560 100644 --- a/tests/attributes/spec/valid/transforms/projectAxis2.json +++ b/tests/attributes/spec/valid/transforms/projectAxis2.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/valid/transforms/rotation.json b/tests/attributes/spec/valid/transforms/rotation.json index be30da23..839f5a4f 100644 --- a/tests/attributes/spec/valid/transforms/rotation.json +++ b/tests/attributes/spec/valid/transforms/rotation.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/valid/transforms/scale.json b/tests/attributes/spec/valid/transforms/scale.json index 01b3d10c..442ea458 100644 --- a/tests/attributes/spec/valid/transforms/scale.json +++ b/tests/attributes/spec/valid/transforms/scale.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "multiscales", diff --git a/tests/attributes/spec/valid/well/minimal_acquisitions.json b/tests/attributes/spec/valid/well/minimal_acquisitions.json index a43a56ef..fdf16aa6 100644 --- a/tests/attributes/spec/valid/well/minimal_acquisitions.json +++ b/tests/attributes/spec/valid/well/minimal_acquisitions.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "well": { "images": [ { diff --git a/tests/attributes/spec/valid/well/minimal_no_acquisition.json b/tests/attributes/spec/valid/well/minimal_no_acquisition.json index 0abe9434..5e55ac2e 100644 --- a/tests/attributes/spec/valid/well/minimal_no_acquisition.json +++ b/tests/attributes/spec/valid/well/minimal_no_acquisition.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "well": { "images": [ { diff --git a/tests/attributes/spec/valid/well/minimal_path_special_char.json b/tests/attributes/spec/valid/well/minimal_path_special_char.json index 4e02875c..f40378c3 100644 --- a/tests/attributes/spec/valid/well/minimal_path_special_char.json +++ b/tests/attributes/spec/valid/well/minimal_path_special_char.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "well": { "images": [ { diff --git a/tests/attributes/strict/invalid/label/no_colors.json b/tests/attributes/strict/invalid/label/no_colors.json index de107479..ebf58d38 100644 --- a/tests/attributes/strict/invalid/label/no_colors.json +++ b/tests/attributes/strict/invalid/label/no_colors.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "image-label": {} }, "_conformance": { diff --git a/tests/attributes/strict/invalid/plate/missing_acquisition_maximumfieldcount.json b/tests/attributes/strict/invalid/plate/missing_acquisition_maximumfieldcount.json index c84e1252..5ee6801b 100644 --- a/tests/attributes/strict/invalid/plate/missing_acquisition_maximumfieldcount.json +++ b/tests/attributes/strict/invalid/plate/missing_acquisition_maximumfieldcount.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc02", + "version": "0.9.dev12", "plate": { "acquisitions": [ { diff --git a/tests/attributes/strict/invalid/plate/missing_acquisition_name.json b/tests/attributes/strict/invalid/plate/missing_acquisition_name.json index fcf1204f..72be4649 100644 --- a/tests/attributes/strict/invalid/plate/missing_acquisition_name.json +++ b/tests/attributes/strict/invalid/plate/missing_acquisition_name.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/attributes/strict/invalid/plate/missing_name.json b/tests/attributes/strict/invalid/plate/missing_name.json index 61631838..cd992d74 100644 --- a/tests/attributes/strict/invalid/plate/missing_name.json +++ b/tests/attributes/strict/invalid/plate/missing_name.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc02", + "version": "0.9.dev12", "plate": { "columns": [ { diff --git a/tests/attributes/strict/valid/image/image.json b/tests/attributes/strict/valid/image/image.json index 8606c08c..2bc13c7c 100644 --- a/tests/attributes/strict/valid/image/image.json +++ b/tests/attributes/strict/valid/image/image.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/strict/valid/image/image_metadata.json b/tests/attributes/strict/valid/image/image_metadata.json index b081fd9e..dcdbff34 100644 --- a/tests/attributes/strict/valid/image/image_metadata.json +++ b/tests/attributes/strict/valid/image/image_metadata.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "@id": "top", "@type": "ngff:Image", "multiscales": [ diff --git a/tests/attributes/strict/valid/image/image_omero.json b/tests/attributes/strict/valid/image/image_omero.json index 5e7555e1..94b0da7a 100644 --- a/tests/attributes/strict/valid/image/image_omero.json +++ b/tests/attributes/strict/valid/image/image_omero.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ @@ -151,7 +151,7 @@ "defaultZ": 2, "model": "color" }, - "version": "0.6rc0" + "version": "0.9.dev1" } }, "_conformance": { diff --git a/tests/attributes/strict/valid/image/multiscales_example.json b/tests/attributes/strict/valid/image/multiscales_example.json index 34fce6b1..543a496f 100644 --- a/tests/attributes/strict/valid/image/multiscales_example.json +++ b/tests/attributes/strict/valid/image/multiscales_example.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "example", diff --git a/tests/attributes/strict/valid/image/multiscales_transformations.json b/tests/attributes/strict/valid/image/multiscales_transformations.json index ecd09381..fd5472b6 100644 --- a/tests/attributes/strict/valid/image/multiscales_transformations.json +++ b/tests/attributes/strict/valid/image/multiscales_transformations.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/attributes/strict/valid/plate/strict_acquisitions.json b/tests/attributes/strict/valid/plate/strict_acquisitions.json index 16520059..35a1aefe 100644 --- a/tests/attributes/strict/valid/plate/strict_acquisitions.json +++ b/tests/attributes/strict/valid/plate/strict_acquisitions.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/attributes/strict/valid/plate/strict_no_acquisitions.json b/tests/attributes/strict/valid/plate/strict_no_acquisitions.json index c531aca2..5212db1b 100644 --- a/tests/attributes/strict/valid/plate/strict_no_acquisitions.json +++ b/tests/attributes/strict/valid/plate/strict_no_acquisitions.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/attributes/strict/valid/well/strict_acquisitions.json b/tests/attributes/strict/valid/well/strict_acquisitions.json index 841a6929..b3686ac3 100644 --- a/tests/attributes/strict/valid/well/strict_acquisitions.json +++ b/tests/attributes/strict/valid/well/strict_acquisitions.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "well": { "images": [ { diff --git a/tests/attributes/strict/valid/well/strict_no_acquisitions.json b/tests/attributes/strict/valid/well/strict_no_acquisitions.json index 58bfe147..311ad142 100644 --- a/tests/attributes/strict/valid/well/strict_no_acquisitions.json +++ b/tests/attributes/strict/valid/well/strict_no_acquisitions.json @@ -1,6 +1,6 @@ { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "well": { "images": [ { diff --git a/tests/test_attributes.py b/tests/test_attributes.py index 8e1e51b1..ea13288a 100644 --- a/tests/test_attributes.py +++ b/tests/test_attributes.py @@ -13,7 +13,7 @@ schema_store = {} version = None -for schema_path in schema_dir.glob("*.schema*"): +for schema_path in schema_dir.glob("*.schema"): schema = json.loads(schema_path.read_text()) schema_store[schema["$id"]] = schema if schema_path.stem == "_version": @@ -30,7 +30,18 @@ case_fnames = sorted(attrs_dir.rglob("*.json")) -xfails = set() +xfails = { + # don't know how to express these restrictions in jsonschema + 'spec/invalid/image/duplicate_orientation', + 'spec/invalid/image/non_space_orientation', + # axes are too high/too low for the defined coordinate systems, + # but not too high/low in absolute terms, so they now should not + # validate but not through jsonschema + 'spec/invalid/transforms/bad_projectAxis_insert_too_high_dim', + 'spec/invalid/transforms/bad_projectAxis_insert_too_many', + 'spec/invalid/transforms/bad_projectAxis_remove_too_high_dim', + 'spec/invalid/transforms/bad_projectAxis_remove_too_many', +} def fname_to_id(fpath: Path) -> str: diff --git a/tests/test_validation.py b/tests/test_validation.py index 1f38f354..3345a714 100644 --- a/tests/test_validation.py +++ b/tests/test_validation.py @@ -21,10 +21,10 @@ schema_store[schema["$id"]] = schema GENERIC_SCHEMA = schema_store[ - "https://ngff.openmicroscopy.org/0.6rc0/schemas/ome_zarr.schema" + "https://ngff.openmicroscopy.org/0.9.dev1/schemas/ome_zarr.schema" ] GENERIC_STRICT_SCHEMA = schema_store[ - "https://ngff.openmicroscopy.org/0.6rc0/schemas/strict_ome_zarr.schema" + "https://ngff.openmicroscopy.org/0.9.dev1/schemas/strict_ome_zarr.schema" ] diff --git a/tests/zarr/spec/invalid/image/duplicate_axes.ome.zarr/zarr.json b/tests/zarr/spec/invalid/image/duplicate_axes.ome.zarr/zarr.json index aafb2cab..9e0bc8fa 100644 --- a/tests/zarr/spec/invalid/image/duplicate_axes.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/image/duplicate_axes.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/zarr/spec/invalid/image/duplicate_orientation.ome.zarr/zarr.json b/tests/zarr/spec/invalid/image/duplicate_orientation.ome.zarr/zarr.json new file mode 100644 index 00000000..371908c9 --- /dev/null +++ b/tests/zarr/spec/invalid/image/duplicate_orientation.ome.zarr/zarr.json @@ -0,0 +1,56 @@ +{ + "ome": { + "version": "0.9.dev1", + "multiscales": [ + { + "name": "multiscales", + "coordinateSystems": [ + { + "name": "physical", + "axes": [ + { + "type": "space", + "name": "y", + "unit": "micrometer", + "discrete": false, + "orientation": { + "type": "anatomical", + "value": "left-to-right" + } + }, + { + "type": "space", + "name": "x", + "unit": "micrometer", + "discrete": false, + "orientation": { + "type": "anatomical", + "value": "left-to-right" + } + } + ] + } + ], + "datasets": [ + { + "path": "array", + "coordinateTransformations": [ + { + "type": "identity", + "output": {"name": "physical"}, + "input": {"path": "array"}, + "name": "transform-name" + } + ] + } + ] + } + ] + }, + "_conformance": { + "schema": { + "id": "schemas/image.schema" + }, + "valid": false + } +} diff --git a/tests/zarr/spec/invalid/image/duplicate_scale.ome.zarr/zarr.json b/tests/zarr/spec/invalid/image/duplicate_scale.ome.zarr/zarr.json index 9c95a92a..5e60745c 100644 --- a/tests/zarr/spec/invalid/image/duplicate_scale.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/image/duplicate_scale.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/zarr/spec/invalid/image/empty_transformations.ome.zarr/zarr.json b/tests/zarr/spec/invalid/image/empty_transformations.ome.zarr/zarr.json index 38736bb8..1b1febdd 100644 --- a/tests/zarr/spec/invalid/image/empty_transformations.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/image/empty_transformations.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/zarr/spec/invalid/image/invalid_channels_color.ome.zarr/zarr.json b/tests/zarr/spec/invalid/image/invalid_channels_color.ome.zarr/zarr.json index f6b2632a..ca824fc2 100644 --- a/tests/zarr/spec/invalid/image/invalid_channels_color.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/image/invalid_channels_color.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/zarr/spec/invalid/image/invalid_channels_window.ome.zarr/zarr.json b/tests/zarr/spec/invalid/image/invalid_channels_window.ome.zarr/zarr.json index 9384f149..8b05f65b 100644 --- a/tests/zarr/spec/invalid/image/invalid_channels_window.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/image/invalid_channels_window.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/zarr/spec/invalid/image/invalid_multiscales_transformations.ome.zarr/zarr.json b/tests/zarr/spec/invalid/image/invalid_multiscales_transformations.ome.zarr/zarr.json index c7dd6f91..79ba48e9 100644 --- a/tests/zarr/spec/invalid/image/invalid_multiscales_transformations.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/image/invalid_multiscales_transformations.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/zarr/spec/invalid/image/invalid_path.ome.zarr/zarr.json b/tests/zarr/spec/invalid/image/invalid_path.ome.zarr/zarr.json index 833c2953..8c40d284 100644 --- a/tests/zarr/spec/invalid/image/invalid_path.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/image/invalid_path.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/zarr/spec/invalid/image/invalid_transformation_type.ome.zarr/zarr.json b/tests/zarr/spec/invalid/image/invalid_transformation_type.ome.zarr/zarr.json index 36e9d187..27c17e24 100644 --- a/tests/zarr/spec/invalid/image/invalid_transformation_type.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/image/invalid_transformation_type.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/zarr/spec/invalid/image/too_many_space_axes.ome.zarr/zarr.json b/tests/zarr/spec/invalid/image/many_space_axes.ome.zarr similarity index 97% rename from tests/zarr/spec/invalid/image/too_many_space_axes.ome.zarr/zarr.json rename to tests/zarr/spec/invalid/image/many_space_axes.ome.zarr index c1a5dae3..d1552926 100644 --- a/tests/zarr/spec/invalid/image/too_many_space_axes.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/image/many_space_axes.ome.zarr @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/zarr/spec/invalid/image/missing_axes.ome.zarr/zarr.json b/tests/zarr/spec/invalid/image/missing_axes.ome.zarr/zarr.json index 8ce705d9..9d02cc06 100644 --- a/tests/zarr/spec/invalid/image/missing_axes.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/image/missing_axes.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "datasets": [ diff --git a/tests/zarr/spec/invalid/image/missing_axes_name.ome.zarr/zarr.json b/tests/zarr/spec/invalid/image/missing_axes_name.ome.zarr/zarr.json index f415bf7d..54cdb63e 100644 --- a/tests/zarr/spec/invalid/image/missing_axes_name.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/image/missing_axes_name.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/zarr/spec/invalid/image/missing_datasets.ome.zarr/zarr.json b/tests/zarr/spec/invalid/image/missing_datasets.ome.zarr/zarr.json index faa50ec0..e4dd5782 100644 --- a/tests/zarr/spec/invalid/image/missing_datasets.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/image/missing_datasets.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/zarr/spec/invalid/image/missing_path.ome.zarr/zarr.json b/tests/zarr/spec/invalid/image/missing_path.ome.zarr/zarr.json index d116c380..4384e82f 100644 --- a/tests/zarr/spec/invalid/image/missing_path.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/image/missing_path.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/zarr/spec/invalid/image/missing_scale.ome.zarr/zarr.json b/tests/zarr/spec/invalid/image/missing_scale.ome.zarr/zarr.json index caa55b53..10d155c6 100644 --- a/tests/zarr/spec/invalid/image/missing_scale.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/image/missing_scale.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/zarr/spec/invalid/image/missing_transformations.ome.zarr/zarr.json b/tests/zarr/spec/invalid/image/missing_transformations.ome.zarr/zarr.json index 6031534a..f458fdd3 100644 --- a/tests/zarr/spec/invalid/image/missing_transformations.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/image/missing_transformations.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/zarr/spec/invalid/image/no_axes.ome.zarr/zarr.json b/tests/zarr/spec/invalid/image/no_axes.ome.zarr/zarr.json index b729fb5f..d357842f 100644 --- a/tests/zarr/spec/invalid/image/no_axes.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/image/no_axes.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "axes": [], diff --git a/tests/zarr/spec/invalid/image/no_datasets.ome.zarr/zarr.json b/tests/zarr/spec/invalid/image/no_datasets.ome.zarr/zarr.json index 93e13265..56872a98 100644 --- a/tests/zarr/spec/invalid/image/no_datasets.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/image/no_datasets.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/zarr/spec/invalid/image/no_multiscales.ome.zarr/zarr.json b/tests/zarr/spec/invalid/image/no_multiscales.ome.zarr/zarr.json index 8855defc..4aad0123 100644 --- a/tests/zarr/spec/invalid/image/no_multiscales.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/image/no_multiscales.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [] }, "_conformance": { diff --git a/tests/zarr/spec/invalid/image/non_existent_orientation.ome.zarr/zarr.json b/tests/zarr/spec/invalid/image/non_existent_orientation.ome.zarr/zarr.json new file mode 100644 index 00000000..273887b1 --- /dev/null +++ b/tests/zarr/spec/invalid/image/non_existent_orientation.ome.zarr/zarr.json @@ -0,0 +1,56 @@ +{ + "ome": { + "version": "0.9.dev1", + "multiscales": [ + { + "name": "multiscales", + "coordinateSystems": [ + { + "name": "physical", + "axes": [ + { + "type": "space", + "name": "y", + "unit": "micrometer", + "discrete": false, + "orientation": { + "type": "anatomical", + "value": "top-to-bottom" + } + }, + { + "type": "space", + "name": "x", + "unit": "micrometer", + "discrete": false, + "orientation": { + "type": "anatomical", + "value": "empty-to-full" + } + } + ] + } + ], + "datasets": [ + { + "path": "array", + "coordinateTransformations": [ + { + "type": "identity", + "output": {"name": "physical"}, + "input": {"path": "array"}, + "name": "transform-name" + } + ] + } + ] + } + ] + }, + "_conformance": { + "schema": { + "id": "schemas/image.schema" + }, + "valid": false + } +} diff --git a/tests/zarr/spec/invalid/image/non_existent_orientation_type.ome.zarr/zarr.json b/tests/zarr/spec/invalid/image/non_existent_orientation_type.ome.zarr/zarr.json new file mode 100644 index 00000000..dcdfd3ca --- /dev/null +++ b/tests/zarr/spec/invalid/image/non_existent_orientation_type.ome.zarr/zarr.json @@ -0,0 +1,56 @@ +{ + "ome": { + "version": "0.9.dev1", + "multiscales": [ + { + "name": "multiscales", + "coordinateSystems": [ + { + "name": "physical", + "axes": [ + { + "type": "space", + "name": "y", + "unit": "kilometer", + "discrete": false, + "orientation": { + "type": "geographical", + "value": "east-to-west" + } + }, + { + "type": "space", + "name": "x", + "unit": "parsec", + "discrete": false, + "orientation": { + "type": "astronomical", + "value": "nadir-to-zenith" + } + } + ] + } + ], + "datasets": [ + { + "path": "array", + "coordinateTransformations": [ + { + "type": "identity", + "output": {"name": "physical"}, + "input": {"path": "array"}, + "name": "transform-name" + } + ] + } + ] + } + ] + }, + "_conformance": { + "schema": { + "id": "schemas/image.schema" + }, + "valid": false + } +} diff --git a/tests/zarr/spec/invalid/image/non_space_orientation.ome.zarr/zarr.json b/tests/zarr/spec/invalid/image/non_space_orientation.ome.zarr/zarr.json new file mode 100644 index 00000000..a5c31f1b --- /dev/null +++ b/tests/zarr/spec/invalid/image/non_space_orientation.ome.zarr/zarr.json @@ -0,0 +1,55 @@ +{ + "ome": { + "version": "0.9.dev1", + "multiscales": [ + { + "name": "multiscales", + "coordinateSystems": [ + { + "name": "physical", + "axes": [ + { + "type": "custom", + "name": "m", + "discrete": false, + "orientation": { + "type": "anatomical", + "value": "anterior-to-posterior" + } + }, + { + "type": "space", + "name": "x", + "unit": "micrometer", + "discrete": false, + "orientation": { + "type": "anatomical", + "value": "left-to-right" + } + } + ] + } + ], + "datasets": [ + { + "path": "array", + "coordinateTransformations": [ + { + "type": "identity", + "output": {"name": "physical"}, + "input": {"path": "array"}, + "name": "transform-name" + } + ] + } + ] + } + ] + }, + "_conformance": { + "schema": { + "id": "schemas/image.schema" + }, + "valid": false + } +} diff --git a/tests/zarr/spec/invalid/label/colors_duplicate.ome.zarr/zarr.json b/tests/zarr/spec/invalid/label/colors_duplicate.ome.zarr/zarr.json index 593101f5..4f6a1b3b 100644 --- a/tests/zarr/spec/invalid/label/colors_duplicate.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/label/colors_duplicate.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "image-label": { "colors": [ { diff --git a/tests/zarr/spec/invalid/label/colors_no_label_value.ome.zarr/zarr.json b/tests/zarr/spec/invalid/label/colors_no_label_value.ome.zarr/zarr.json index 1a828b47..2f31424d 100644 --- a/tests/zarr/spec/invalid/label/colors_no_label_value.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/label/colors_no_label_value.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "image-label": { "colors": [ { diff --git a/tests/zarr/spec/invalid/label/colors_rgba_length.ome.zarr/zarr.json b/tests/zarr/spec/invalid/label/colors_rgba_length.ome.zarr/zarr.json index a83afee1..546191df 100644 --- a/tests/zarr/spec/invalid/label/colors_rgba_length.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/label/colors_rgba_length.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0 + "version": "0.9.dev1 "image-label": { "colors": [ { diff --git a/tests/zarr/spec/invalid/label/colors_rgba_type.ome.zarr/zarr.json b/tests/zarr/spec/invalid/label/colors_rgba_type.ome.zarr/zarr.json index 90e0132d..429a93d2 100644 --- a/tests/zarr/spec/invalid/label/colors_rgba_type.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/label/colors_rgba_type.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "image-label": { "colors": [ { diff --git a/tests/zarr/spec/invalid/label/empty_colors.ome.zarr/zarr.json b/tests/zarr/spec/invalid/label/empty_colors.ome.zarr/zarr.json index 7b26aae0..87ec8063 100644 --- a/tests/zarr/spec/invalid/label/empty_colors.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/label/empty_colors.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "image-label": { "colors": [] } diff --git a/tests/zarr/spec/invalid/label/empty_properties.ome.zarr/zarr.json b/tests/zarr/spec/invalid/label/empty_properties.ome.zarr/zarr.json index 8095dd26..a1fc2fea 100644 --- a/tests/zarr/spec/invalid/label/empty_properties.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/label/empty_properties.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "image-label": { "properties": [] } diff --git a/tests/zarr/spec/invalid/label/properties_no_label_value.ome.zarr/zarr.json b/tests/zarr/spec/invalid/label/properties_no_label_value.ome.zarr/zarr.json index 08004f87..4b94c550 100644 --- a/tests/zarr/spec/invalid/label/properties_no_label_value.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/label/properties_no_label_value.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "image-label": { "properties": [ { diff --git a/tests/zarr/spec/invalid/plate/acquisition_negative_starttime.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/acquisition_negative_starttime.ome.zarr/zarr.json index 32350204..d3a75a88 100644 --- a/tests/zarr/spec/invalid/plate/acquisition_negative_starttime.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/acquisition_negative_starttime.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/zarr/spec/invalid/plate/acquisition_noninteger_endtime.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/acquisition_noninteger_endtime.ome.zarr/zarr.json index 75414545..88786356 100644 --- a/tests/zarr/spec/invalid/plate/acquisition_noninteger_endtime.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/acquisition_noninteger_endtime.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/zarr/spec/invalid/plate/acquisition_noninteger_starttime.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/acquisition_noninteger_starttime.ome.zarr/zarr.json index 1557189d..62a18ed1 100644 --- a/tests/zarr/spec/invalid/plate/acquisition_noninteger_starttime.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/acquisition_noninteger_starttime.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/zarr/spec/invalid/plate/acquisition_zero_maximumfieldcount.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/acquisition_zero_maximumfieldcount.ome.zarr/zarr.json index 7ffff5b6..82d16481 100644 --- a/tests/zarr/spec/invalid/plate/acquisition_zero_maximumfieldcount.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/acquisition_zero_maximumfieldcount.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/zarr/spec/invalid/plate/duplicate_columns.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/duplicate_columns.ome.zarr/zarr.json index b8e10da4..22f45aac 100644 --- a/tests/zarr/spec/invalid/plate/duplicate_columns.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/duplicate_columns.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/zarr/spec/invalid/plate/duplicate_rows-2.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/duplicate_rows-2.ome.zarr/zarr.json index 0533364e..6040e467 100644 --- a/tests/zarr/spec/invalid/plate/duplicate_rows-2.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/duplicate_rows-2.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/zarr/spec/invalid/plate/duplicate_rows.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/duplicate_rows.ome.zarr/zarr.json index 5bf6cb00..9e45b6a6 100644 --- a/tests/zarr/spec/invalid/plate/duplicate_rows.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/duplicate_rows.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/zarr/spec/invalid/plate/empty_columns.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/empty_columns.ome.zarr/zarr.json index e2f28a71..711d4074 100644 --- a/tests/zarr/spec/invalid/plate/empty_columns.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/empty_columns.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [], "rows": [ diff --git a/tests/zarr/spec/invalid/plate/empty_rows.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/empty_rows.ome.zarr/zarr.json index 62c29b12..e7c1765c 100644 --- a/tests/zarr/spec/invalid/plate/empty_rows.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/empty_rows.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/zarr/spec/invalid/plate/empty_wells.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/empty_wells.ome.zarr/zarr.json index e022d55d..1d01ecc4 100644 --- a/tests/zarr/spec/invalid/plate/empty_wells.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/empty_wells.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/zarr/spec/invalid/plate/missing_acquisition_id.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/missing_acquisition_id.ome.zarr/zarr.json index b1f787d5..0e8c0713 100644 --- a/tests/zarr/spec/invalid/plate/missing_acquisition_id.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/missing_acquisition_id.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/zarr/spec/invalid/plate/missing_column_name.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/missing_column_name.ome.zarr/zarr.json index 6e3677d5..086c951c 100644 --- a/tests/zarr/spec/invalid/plate/missing_column_name.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/missing_column_name.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/zarr/spec/invalid/plate/missing_columns.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/missing_columns.ome.zarr/zarr.json index 0ccf92d4..c9635c2e 100644 --- a/tests/zarr/spec/invalid/plate/missing_columns.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/missing_columns.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "rows": [ { diff --git a/tests/zarr/spec/invalid/plate/missing_row_name.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/missing_row_name.ome.zarr/zarr.json index c3bfbd8d..2db0d347 100644 --- a/tests/zarr/spec/invalid/plate/missing_row_name.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/missing_row_name.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/zarr/spec/invalid/plate/missing_rows.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/missing_rows.ome.zarr/zarr.json index 54846388..586b78bf 100644 --- a/tests/zarr/spec/invalid/plate/missing_rows.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/missing_rows.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/zarr/spec/invalid/plate/missing_well_columnIndex.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/missing_well_columnIndex.ome.zarr/zarr.json index 473f4e6b..def1467f 100644 --- a/tests/zarr/spec/invalid/plate/missing_well_columnIndex.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/missing_well_columnIndex.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/zarr/spec/invalid/plate/missing_well_path.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/missing_well_path.ome.zarr/zarr.json index ab3e07bd..8f2c35e9 100644 --- a/tests/zarr/spec/invalid/plate/missing_well_path.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/missing_well_path.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/zarr/spec/invalid/plate/missing_well_rowIndex.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/missing_well_rowIndex.ome.zarr/zarr.json index f4068ba4..dc173001 100644 --- a/tests/zarr/spec/invalid/plate/missing_well_rowIndex.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/missing_well_rowIndex.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/zarr/spec/invalid/plate/missing_wells.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/missing_wells.ome.zarr/zarr.json index 26326597..acfdbaab 100644 --- a/tests/zarr/spec/invalid/plate/missing_wells.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/missing_wells.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/zarr/spec/invalid/plate/negative_acquisition_id.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/negative_acquisition_id.ome.zarr/zarr.json index 3fd05efb..a480a6c4 100644 --- a/tests/zarr/spec/invalid/plate/negative_acquisition_id.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/negative_acquisition_id.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/zarr/spec/invalid/plate/negative_endtime.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/negative_endtime.ome.zarr/zarr.json index 1d099773..607b06b7 100644 --- a/tests/zarr/spec/invalid/plate/negative_endtime.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/negative_endtime.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/zarr/spec/invalid/plate/non_alphanumeric_column.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/non_alphanumeric_column.ome.zarr/zarr.json index 5bcb242d..f36d1614 100644 --- a/tests/zarr/spec/invalid/plate/non_alphanumeric_column.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/non_alphanumeric_column.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/zarr/spec/invalid/plate/non_integer_acquisition_id.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/non_integer_acquisition_id.ome.zarr/zarr.json index 19b25c3a..5263541f 100644 --- a/tests/zarr/spec/invalid/plate/non_integer_acquisition_id.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/non_integer_acquisition_id.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/zarr/spec/invalid/plate/non_integer_acquisition_maximumfieldcount.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/non_integer_acquisition_maximumfieldcount.ome.zarr/zarr.json index cae4eafe..69327c93 100644 --- a/tests/zarr/spec/invalid/plate/non_integer_acquisition_maximumfieldcount.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/non_integer_acquisition_maximumfieldcount.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/zarr/spec/invalid/plate/well_1group.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/well_1group.ome.zarr/zarr.json index 74d4f257..dfd857da 100644 --- a/tests/zarr/spec/invalid/plate/well_1group.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/well_1group.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/zarr/spec/invalid/plate/well_3groups.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/well_3groups.ome.zarr/zarr.json index 8060ad95..ca6057e9 100644 --- a/tests/zarr/spec/invalid/plate/well_3groups.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/well_3groups.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/zarr/spec/invalid/plate/zero_field_count.ome.zarr/zarr.json b/tests/zarr/spec/invalid/plate/zero_field_count.ome.zarr/zarr.json index 0d23dfc1..1108219d 100644 --- a/tests/zarr/spec/invalid/plate/zero_field_count.ome.zarr/zarr.json +++ b/tests/zarr/spec/invalid/plate/zero_field_count.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0 + "version": "0.9.dev1 "plate": { "columns": [ { diff --git a/tests/zarr/spec/invalid/image/invalid_axis_type.ome.zarr/zarr.json b/tests/zarr/spec/valid/image/custom_axis_type.ome.zarr/zarr.json similarity index 92% rename from tests/zarr/spec/invalid/image/invalid_axis_type.ome.zarr/zarr.json rename to tests/zarr/spec/valid/image/custom_axis_type.ome.zarr/zarr.json index e5686f99..db34cd97 100644 --- a/tests/zarr/spec/invalid/image/invalid_axis_type.ome.zarr/zarr.json +++ b/tests/zarr/spec/valid/image/custom_axis_type.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ @@ -12,7 +12,7 @@ "axes": [ { "name": "y", - "type": "invalid", + "type": "custom", "unit": "micrometer" }, { @@ -46,7 +46,7 @@ "schema": { "id": "schemas/image.schema" }, - "valid": false + "valid": true } } -} \ No newline at end of file +} diff --git a/tests/zarr/spec/valid/image/custom_type_axes.ome.zarr/zarr.json b/tests/zarr/spec/valid/image/custom_type_axes.ome.zarr/zarr.json index 08993d76..285392d9 100644 --- a/tests/zarr/spec/valid/image/custom_type_axes.ome.zarr/zarr.json +++ b/tests/zarr/spec/valid/image/custom_type_axes.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/zarr/spec/valid/image/invalid_axis_units.ome.zarr/zarr.json b/tests/zarr/spec/valid/image/invalid_axis_units.ome.zarr/zarr.json index 59ac7397..3fd9dc9a 100644 --- a/tests/zarr/spec/valid/image/invalid_axis_units.ome.zarr/zarr.json +++ b/tests/zarr/spec/valid/image/invalid_axis_units.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/zarr/spec/invalid/image/too_many_axes.ome.zarr/zarr.json b/tests/zarr/spec/valid/image/many_axes.ome.zarr/zarr.json similarity index 96% rename from tests/zarr/spec/invalid/image/too_many_axes.ome.zarr/zarr.json rename to tests/zarr/spec/valid/image/many_axes.ome.zarr/zarr.json index 5b9a1801..1826a33b 100644 --- a/tests/zarr/spec/invalid/image/too_many_axes.ome.zarr/zarr.json +++ b/tests/zarr/spec/valid/image/many_axes.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ @@ -64,7 +64,7 @@ "schema": { "id": "age.schema" }, - "valid": false + "valid": true } } } \ No newline at end of file diff --git a/tests/zarr/spec/valid/image/mismatch_axes_units.ome.zarr/zarr.json b/tests/zarr/spec/valid/image/mismatch_axes_units.ome.zarr/zarr.json index b1a563e2..3f41fe32 100644 --- a/tests/zarr/spec/valid/image/mismatch_axes_units.ome.zarr/zarr.json +++ b/tests/zarr/spec/valid/image/mismatch_axes_units.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/zarr/spec/valid/image/missing_name.ome.zarr/zarr.json b/tests/zarr/spec/valid/image/missing_name.ome.zarr/zarr.json index a744d2d0..db606ee6 100644 --- a/tests/zarr/spec/valid/image/missing_name.ome.zarr/zarr.json +++ b/tests/zarr/spec/valid/image/missing_name.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "datasets": [ diff --git a/tests/zarr/spec/invalid/image/missing_space_axes.ome.zarr/zarr.json b/tests/zarr/spec/valid/image/missing_space_axes.ome.zarr/zarr.json similarity index 95% rename from tests/zarr/spec/invalid/image/missing_space_axes.ome.zarr/zarr.json rename to tests/zarr/spec/valid/image/missing_space_axes.ome.zarr/zarr.json index 384f8df4..037435a5 100644 --- a/tests/zarr/spec/invalid/image/missing_space_axes.ome.zarr/zarr.json +++ b/tests/zarr/spec/valid/image/missing_space_axes.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ @@ -44,7 +44,7 @@ "schema": { "id": "schemas/image.schema" }, - "valid": false + "valid": true } } } \ No newline at end of file diff --git a/tests/zarr/spec/invalid/image/one_space_axes.ome.zarr/zarr.json b/tests/zarr/spec/valid/image/one_space_axes.ome.zarr/zarr.json similarity index 95% rename from tests/zarr/spec/invalid/image/one_space_axes.ome.zarr/zarr.json rename to tests/zarr/spec/valid/image/one_space_axes.ome.zarr/zarr.json index e5363b65..83abe77b 100644 --- a/tests/zarr/spec/invalid/image/one_space_axes.ome.zarr/zarr.json +++ b/tests/zarr/spec/valid/image/one_space_axes.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ @@ -49,7 +49,7 @@ "schema": { "id": "schemas/image.schema" }, - "valid": false + "valid": true } } } \ No newline at end of file diff --git a/tests/zarr/spec/valid/image/orientation.ome.zarr/zarr.json b/tests/zarr/spec/valid/image/orientation.ome.zarr/zarr.json new file mode 100644 index 00000000..bc9f09dd --- /dev/null +++ b/tests/zarr/spec/valid/image/orientation.ome.zarr/zarr.json @@ -0,0 +1,64 @@ +{ + "zarr_format": 3, + "node_type": "group", + "attributes": { + "ome": { + "version": "0.9.dev1", + "multiscales": [ + { + "coordinateSystems": [ + { + "name": "intrinsic", + "axes": [ + { + "name": "angle", + "type": "custom" + }, + { + "name": "y", + "type": "space", + "unit": "micrometer", + "orientation": { + "type": "anatomical", + "value": "superior-to-inferior" + } + }, + { + "name": "x", + "type": "space", + "unit": "micrometer", + "orientation": { + "type": "anatomical", + "value": "left-to-right" + } + } + ] + } + ], + "datasets": [ + { + "path": "0", + "coordinateTransformations": [ + { + "scale": [ + 1, + 1, + 1 + ], + "input": "0", + "output": "intrinsic", + "type": "scale" + } + ] + } + ] + } + ] + }, + "_conformance": { + "schema": { + "id": "schemas/image.schema" + } + } + } +} diff --git a/tests/zarr/spec/invalid/image/invalid_axes_count.ome.zarr/zarr.json b/tests/zarr/spec/valid/image/single_axis.ome.zarr/zarr.json similarity index 94% rename from tests/zarr/spec/invalid/image/invalid_axes_count.ome.zarr/zarr.json rename to tests/zarr/spec/valid/image/single_axis.ome.zarr/zarr.json index 1cd1f7f3..6ae1fb8c 100644 --- a/tests/zarr/spec/invalid/image/invalid_axes_count.ome.zarr/zarr.json +++ b/tests/zarr/spec/valid/image/single_axis.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ @@ -41,7 +41,7 @@ "schema": { "id": "schemas/image.schema" }, - "valid": false + "valid": true } } } \ No newline at end of file diff --git a/tests/zarr/spec/valid/image/untyped_axes.ome.zarr/zarr.json b/tests/zarr/spec/valid/image/untyped_axes.ome.zarr/zarr.json index 18a98d6a..d960bd63 100644 --- a/tests/zarr/spec/valid/image/untyped_axes.ome.zarr/zarr.json +++ b/tests/zarr/spec/valid/image/untyped_axes.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/zarr/spec/valid/label/minimal.ome.zarr/zarr.json b/tests/zarr/spec/valid/label/minimal.ome.zarr/zarr.json index 3a283cef..5cbce7ee 100644 --- a/tests/zarr/spec/valid/label/minimal.ome.zarr/zarr.json +++ b/tests/zarr/spec/valid/label/minimal.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "image-label": { "colors": [ { diff --git a/tests/zarr/spec/valid/label/minimal_properties.ome.zarr/zarr.json b/tests/zarr/spec/valid/label/minimal_properties.ome.zarr/zarr.json index d3a9c4b7..5de52551 100644 --- a/tests/zarr/spec/valid/label/minimal_properties.ome.zarr/zarr.json +++ b/tests/zarr/spec/valid/label/minimal_properties.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "image-label": { "colors": [ { diff --git a/tests/zarr/spec/valid/plate/minimal_acquisitions.ome.zarr/zarr.json b/tests/zarr/spec/valid/plate/minimal_acquisitions.ome.zarr/zarr.json index 91d84d57..1428fdd4 100644 --- a/tests/zarr/spec/valid/plate/minimal_acquisitions.ome.zarr/zarr.json +++ b/tests/zarr/spec/valid/plate/minimal_acquisitions.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/zarr/spec/valid/plate/minimal_no_acquisitions.ome.zarr/zarr.json b/tests/zarr/spec/valid/plate/minimal_no_acquisitions.ome.zarr/zarr.json index a8159100..68ede258 100644 --- a/tests/zarr/spec/valid/plate/minimal_no_acquisitions.ome.zarr/zarr.json +++ b/tests/zarr/spec/valid/plate/minimal_no_acquisitions.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/zarr/spec/valid/plate/non_alphanumeric_row.ome.zarr/zarr.json b/tests/zarr/spec/valid/plate/non_alphanumeric_row.ome.zarr/zarr.json index 36fedb7b..294ee081 100644 --- a/tests/zarr/spec/valid/plate/non_alphanumeric_row.ome.zarr/zarr.json +++ b/tests/zarr/spec/valid/plate/non_alphanumeric_row.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/zarr/spec/valid/well/minimal_acquisitions.ome.zarr/zarr.json b/tests/zarr/spec/valid/well/minimal_acquisitions.ome.zarr/zarr.json index 11ae0e48..4801bc04 100644 --- a/tests/zarr/spec/valid/well/minimal_acquisitions.ome.zarr/zarr.json +++ b/tests/zarr/spec/valid/well/minimal_acquisitions.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "well": { "images": [ { diff --git a/tests/zarr/spec/valid/well/minimal_no_acquisition.ome.zarr/zarr.json b/tests/zarr/spec/valid/well/minimal_no_acquisition.ome.zarr/zarr.json index 5059cc16..85f6b376 100644 --- a/tests/zarr/spec/valid/well/minimal_no_acquisition.ome.zarr/zarr.json +++ b/tests/zarr/spec/valid/well/minimal_no_acquisition.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "well": { "images": [ { diff --git a/tests/zarr/strict/invalid/label/no_colors.ome.zarr/zarr.json b/tests/zarr/strict/invalid/label/no_colors.ome.zarr/zarr.json index cedf31b6..8831cb7b 100644 --- a/tests/zarr/strict/invalid/label/no_colors.ome.zarr/zarr.json +++ b/tests/zarr/strict/invalid/label/no_colors.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "image-label": {} }, "_conformance": { diff --git a/tests/zarr/strict/invalid/plate/missing_acquisition_maximumfieldcount.ome.zarr/zarr.json b/tests/zarr/strict/invalid/plate/missing_acquisition_maximumfieldcount.ome.zarr/zarr.json index d25d7075..532e9b43 100644 --- a/tests/zarr/strict/invalid/plate/missing_acquisition_maximumfieldcount.ome.zarr/zarr.json +++ b/tests/zarr/strict/invalid/plate/missing_acquisition_maximumfieldcount.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/zarr/strict/invalid/plate/missing_acquisition_name.ome.zarr/zarr.json b/tests/zarr/strict/invalid/plate/missing_acquisition_name.ome.zarr/zarr.json index bc04d4e3..9e4c4ce8 100644 --- a/tests/zarr/strict/invalid/plate/missing_acquisition_name.ome.zarr/zarr.json +++ b/tests/zarr/strict/invalid/plate/missing_acquisition_name.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/zarr/strict/invalid/plate/missing_name.ome.zarr/zarr.json b/tests/zarr/strict/invalid/plate/missing_name.ome.zarr/zarr.json index 29074140..2f95f964 100644 --- a/tests/zarr/strict/invalid/plate/missing_name.ome.zarr/zarr.json +++ b/tests/zarr/strict/invalid/plate/missing_name.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/zarr/strict/valid/image/image.ome.zarr/zarr.json b/tests/zarr/strict/valid/image/image.ome.zarr/zarr.json index 0d22914c..6edaffca 100644 --- a/tests/zarr/strict/valid/image/image.ome.zarr/zarr.json +++ b/tests/zarr/strict/valid/image/image.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/zarr/strict/valid/image/image_metadata.ome.zarr/zarr.json b/tests/zarr/strict/valid/image/image_metadata.ome.zarr/zarr.json index 1bd58af9..25633449 100644 --- a/tests/zarr/strict/valid/image/image_metadata.ome.zarr/zarr.json +++ b/tests/zarr/strict/valid/image/image_metadata.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "@id": "top", "@type": "ngff:Image", "multiscales": [ diff --git a/tests/zarr/strict/valid/image/image_omero.ome.zarr/zarr.json b/tests/zarr/strict/valid/image/image_omero.ome.zarr/zarr.json index 1f5e1df4..6ccb2d19 100644 --- a/tests/zarr/strict/valid/image/image_omero.ome.zarr/zarr.json +++ b/tests/zarr/strict/valid/image/image_omero.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ @@ -154,7 +154,7 @@ "defaultZ": 2, "model": "color" }, - "version": "0.6rc0" + "version": "0.9.dev1" } }, "_conformance": { diff --git a/tests/zarr/strict/valid/image/multiscales_example.ome.zarr/zarr.json b/tests/zarr/strict/valid/image/multiscales_example.ome.zarr/zarr.json index e9c87a85..76991c3c 100644 --- a/tests/zarr/strict/valid/image/multiscales_example.ome.zarr/zarr.json +++ b/tests/zarr/strict/valid/image/multiscales_example.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "name": "example", diff --git a/tests/zarr/strict/valid/image/multiscales_transformations.ome.zarr/zarr.json b/tests/zarr/strict/valid/image/multiscales_transformations.ome.zarr/zarr.json index eb562ead..b649ee51 100644 --- a/tests/zarr/strict/valid/image/multiscales_transformations.ome.zarr/zarr.json +++ b/tests/zarr/strict/valid/image/multiscales_transformations.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "multiscales": [ { "coordinateSystems": [ diff --git a/tests/zarr/strict/valid/plate/strict_acquisitions.ome.zarr/zarr.json b/tests/zarr/strict/valid/plate/strict_acquisitions.ome.zarr/zarr.json index c9b5a501..8a810107 100644 --- a/tests/zarr/strict/valid/plate/strict_acquisitions.ome.zarr/zarr.json +++ b/tests/zarr/strict/valid/plate/strict_acquisitions.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "acquisitions": [ { diff --git a/tests/zarr/strict/valid/plate/strict_no_acquisitions.ome.zarr/zarr.json b/tests/zarr/strict/valid/plate/strict_no_acquisitions.ome.zarr/zarr.json index dc80db86..915efc90 100644 --- a/tests/zarr/strict/valid/plate/strict_no_acquisitions.ome.zarr/zarr.json +++ b/tests/zarr/strict/valid/plate/strict_no_acquisitions.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "plate": { "columns": [ { diff --git a/tests/zarr/strict/valid/well/strict_acquisitions.ome.zarr/zarr.json b/tests/zarr/strict/valid/well/strict_acquisitions.ome.zarr/zarr.json index 457197f8..b3da6bb1 100644 --- a/tests/zarr/strict/valid/well/strict_acquisitions.ome.zarr/zarr.json +++ b/tests/zarr/strict/valid/well/strict_acquisitions.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "well": { "images": [ { diff --git a/tests/zarr/strict/valid/well/strict_no_acquisitions.ome.zarr/zarr.json b/tests/zarr/strict/valid/well/strict_no_acquisitions.ome.zarr/zarr.json index 3836d3a9..52e26f13 100644 --- a/tests/zarr/strict/valid/well/strict_no_acquisitions.ome.zarr/zarr.json +++ b/tests/zarr/strict/valid/well/strict_no_acquisitions.ome.zarr/zarr.json @@ -3,7 +3,7 @@ "node_type": "group", "attributes": { "ome": { - "version": "0.6rc0", + "version": "0.9.dev1", "well": { "images": [ { diff --git a/version_history.md b/version_history.md index 0fc5cdd1..66a7aa2c 100644 --- a/version_history.md +++ b/version_history.md @@ -8,6 +8,18 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/). +## 0.9.dev1 - 2026-08-20 + +### Added + +- [RFC3](https://ngff.openmicroscopy.org/rfc/3/index.html) adopted: + No restriction on axis ordering and number of axes. +- [RFC4](https://ngff.openmicroscopy.org/rfc/4/index.html) adopted: + Spatial axes gain an optional "orientation" attribute to specify + anatomical or other reference orientations. +- [ome/ngff-spec#87](https://github.com/ome/ngff-spec/pull/87): some + "omero" fields become optional. + ## 0.6rc0 - 2026-07-01 ### Added @@ -50,12 +62,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/). - BREAKING CHANGE: Renamed top-level group for transformations to "Scene" - BREAKING CHANGE: Transformations in scene metadata must be object with fields "name" and "path" - BREAKING CHANGE: Made syntax of `mapAxis` and `byDimension` transforms consistent with other transforms - - BREAKING CHANGE: Zarr parameter storage no longer allowed for scale/translation + - BREAKING CHANGE: Zarr parameter storage no longer allowed for scale/translation - For detailed set of changes see [complete overview](https://ngff.openmicroscopy.org/rfc/5/responses/2/index.html) - Updated version keys from `0.6.dev2` to `0.6.dev3` everywhere - style: Homogeneous use of backticks in spec document - specification: Changed the constraints for valid `path` values in `wells` for HCS plates to allow some non-alphanumeric characters. -- specification: Corrected that `version` field is not required under plate/well/labels metadata. +- specification: Corrected that `version` field is not required under plate/well/labels metadata. - specification: Constrained datatype of multiscales datasets to be the same across all resolutions - specification: Clarified that `name` field in `axes` metadata is required to be a non-empty string. - style: Adopted JSON terminology for "object" and "array" in the spec document.