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schema: better context-dependency layering #150

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schema: better context-dependency layering #150

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41 changes: 10 additions & 31 deletions schemas/coordinate_transformations.schema
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Original file line number Diff line number Diff line change
Expand Up @@ -3,37 +3,7 @@
"$id": "https://ngff.openmicroscopy.org/0.6.dev4/schemas/coordinate_transformations.schema",
"title": "Coordinate Transformations",
"description": "OME-Zarr Coordinate transforms.",
"type": "array",
"uniqueItems": true,
"minItems": 1,
"items": {
"allOf": [
{
"$ref": "#/$defs/coordinateTransformation"
},
{
"type": "object",
"properties": {
"input": {
"allOf": [
{"$ref": "#/$defs/inputOutput"},
{"required": ["path"]}
]
},
"output": {
"allOf": [
{"$ref": "#/$defs/inputOutput"},
{"required": ["name"]}
]
}
},
"required": [
"input",
"output"
]
}
]
},
"$ref": "#/$defs/coordinateTransformations",
"$defs": {
"inputOutput": {
"type": "object",
Expand All @@ -42,6 +12,15 @@
"path": {"type": "string"}
}
},
"coordinateTransformations": {
"description": "JSON array of multiple OME-ZARR transformations",
"type": "array",
"uniqueItems": true,
"minItems": 1,
"items": {
"$ref": "#/$defs/coordinateTransformation"
}
},
"coordinateTransformation": {
"description": "OME-NGFF coordinate transformation.",
"allOf": [
Expand Down
60 changes: 29 additions & 31 deletions schemas/scene.schema
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Original file line number Diff line number Diff line change
Expand Up @@ -15,38 +15,36 @@
"description": "Coordinate systems to combine with transforms to define spatial relationships"
},
"coordinateTransformations": {
"$comment": "Merge general coordinate transformations with constraints for scene metadata",
"allOf": [
{
"$ref": "coordinate_transformations.schema",
"description": "General coordinate transformations defining spatial relationships between coordinate systems"
},
{
"type": "array",
"items": {
"allOf": [
{
"properties": {
"input": {
"allOf": [
{"$ref": "coordinate_transformations.schema#/$defs/inputOutput"},
{"required": ["name"]}
]
},
"output": {
"allOf": [
{"$ref": "coordinate_transformations.schema#/$defs/inputOutput"},
{"required": ["name"]}
]
}
}
}
]
"$comment": "Coordinate transformations defining spatial relationships between coordinate systems",
"type": "array",
"items": {
"allOf": [
{
"$ref": "coordinate_transformations.schema#/$defs/coordinateTransformation"
},
"description": "Constrained input/output for coordinate transformations in scene metadata"
}
]

{
"type": "object",
"properties": {
"input": {
"allOf": [
{"$ref": "coordinate_transformations.schema#/$defs/inputOutput"},
{"required": ["name"]}
]
},
"output": {
"allOf": [
{"$ref": "coordinate_transformations.schema#/$defs/inputOutput"},
{"required": ["name"]}
]
}
},
"required": ["input", "output"]
}
]
},
"minItems": 1,
"uniqueItems": true,
"description": "Coordinate transformations defining spatial relationships between coordinate systems with scene-specific constraints"
},
"arrayCoordinateSystem": {
"type": "object",
Expand Down
71 changes: 71 additions & 0 deletions tests/attributes/spec/valid/scene/scene.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,71 @@
{
"ome": {
"version": "0.6.dev4",
"scene": {
"coordinateTransformations": [
{
"input": {"path": "4995115_cropped_400_100_400_400_rot10.zarr", "name": "rotated"},
"output": {"name": "translated_x50"},
"name": "translate_tile_to_stitched_position",
"type": "translation",
"translation": [
0,
0,
30.608878192215265,
11.21775638443053
]
},
{
"input": {"path": "4995115_cropped_700_700_400_400_rot45.zarr", "name": "rotated"},
"output": {"name": "translated_x50"},
"name": "translate_tile_to_stitched_position",
"type": "translation",
"translation": [
0,
0,
91.8266345766458,
41.8266345766458
]
},
{
"input": {"name": "translated_x50"},
"output": {"path": "4995115_full.zarr", "name": "physical"},
"name": "translate_tile_to_stitched_position",
"type": "translation",
"translation": [
0,
0,
0,
50
]
}
],
"coordinateSystems": [
{
"name": "translated_x50",
"axes": [
{
"name": "c",
"type": "channel"
},
{
"name": "z",
"type": "space",
"unit": "micrometer"
},
{
"name": "y",
"type": "space",
"unit": "micrometer"
},
{
"name": "x",
"type": "space",
"unit": "micrometer"
}
]
}
]
}
}
}
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