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schema scene.coordinateTransformations path optional for input and output (#149)
* scene.coordinateTransformations path optional for input and output * tests: add json to example to CI * tests: correct version in metadata * Apply suggestions from code review Co-authored-by: Johannes Soltwedel <38459088+jo-mueller@users.noreply.github.com> * schema: add make input/output required in this context --------- Co-authored-by: Johannes Soltwedel <38459088+jo-mueller@users.noreply.github.com>
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‎schemas/scene.schema‎

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@@ -16,37 +16,43 @@
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},
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"coordinateTransformations": {
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"$comment": "Merge general coordinate transformations with constraints for scene metadata",
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"allOf": [
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{
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"$ref": "coordinate_transformations.schema",
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"description": "General coordinate transformations defining spatial relationships between coordinate systems"
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},
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{
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"type": "array",
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"items": {
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"allOf": [
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{
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"type": "array",
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"minItems": 1,
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"items": {
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"allOf": [
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{
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"$ref": "coordinate_transformations.schema#/$defs/coordinateTransformation",
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"description": "Parameters of any possible transform"
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},
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{
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"type": "object",
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"description": "Transformations between two referenced coordinate systems",
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"properties": {
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"input": {
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"type": "object",
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"properties": {
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"name": {"type": "string"},
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"path": {"type": "string"}
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},
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"required": ["name"],
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"additionalProperties": false,
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"description": "Must reference a coordinate system defined in the same metadata document (path empty) or in a subgroup (path provided)"
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},
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"output": {
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"type": "object",
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"properties": {
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"input": {
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"allOf": [
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{"$ref": "coordinate_transformations.schema#/$defs/inputOutput"},
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{"required": ["name"]}
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]
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},
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"output": {
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"allOf": [
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{"$ref": "coordinate_transformations.schema#/$defs/inputOutput"},
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{"required": ["name"]}
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]
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}
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}
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"name": {"type": "string"},
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"path": {"type": "string"}
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},
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"required": ["name"],
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"additionalProperties": false,
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"description": "Must reference a coordinate system defined in the same metadata document (path empty) or in a subgroup (path provided)"
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}
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]
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},
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"description": "Constrained input/output for coordinate transformations in scene metadata"
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}
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]
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},
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"required": ["input", "output"]
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}
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]
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}
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}
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},
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"type": "object",

‎tests/attributes/spec/valid/scene/scene.json‎

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{
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"ome": {
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"version": "0.6.dev4",
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"scene": {
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"coordinateTransformations": [
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{
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"input": {"path": "4995115_cropped_400_100_400_400_rot10.zarr", "name": "rotated"},
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"output": {"name": "translated_x50"},
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"name": "translate_tile_to_stitched_position",
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"type": "translation",
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"translation": [
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0,
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0,
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30.608878192215265,
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11.21775638443053
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]
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},
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{
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"input": {"path": "4995115_cropped_700_700_400_400_rot45.zarr", "name": "rotated"},
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"output": {"name": "translated_x50"},
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"name": "translate_tile_to_stitched_position",
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"type": "translation",
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"translation": [
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0,
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0,
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91.8266345766458,
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41.8266345766458
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]
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},
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{
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"input": {"name": "translated_x50"},
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"output": {"path": "4995115_full.zarr", "name": "physical"},
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"name": "translate_tile_to_stitched_position",
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"type": "translation",
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"translation": [
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0,
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0,
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0,
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50
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]
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}
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],
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"coordinateSystems": [
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{
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"name": "translated_x50",
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"axes": [
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{
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"name": "c",
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"type": "channel"
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},
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{
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"name": "z",
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"type": "space",
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"unit": "micrometer"
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},
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{
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"name": "y",
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"type": "space",
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"unit": "micrometer"
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},
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{
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"name": "x",
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"type": "space",
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"unit": "micrometer"
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}
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]
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}
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]
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}
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}
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}

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