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Include provenance and annotation files locally #6

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Nov 7, 2024
Merged

Include provenance and annotation files locally #6

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122 changes: 122 additions & 0 deletions assets/annotation-v2.0.0.json
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{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://marine-imaging.com/fair/schemas/annotation-v2.0.0.json",
"title": "Annotations of images",
"description": "A schema to establish a format for annotations within images (photos and videos) of different shape and by different annotators",
"type": "object",
"properties": {
"image-annotation-labels": {
"description": "All the labels used in the image-annotations. Specified by an id (e.g. AphiaID), a human-readable name and an optional description.",
"type": "array",
"items": {
"$ref": "#/$defs/label"
}
},
"image-annotation-creators": {
"description": "All the annotators that created image-annotations. Specified by an id (e.g. ORCID), a human-readable name and an optional type specifying the annotator's expertise.",
"type": "array",
"items": {
"$ref": "#/$defs/annotator"
}
},
"image-annotations": {
"description": "This field stores all annotations as a list of dictionaries of 3-4 fields: shape, coordinates, labels and (optional) frames. See further explanations below. The list of labels specifies the IDs or names of objects and annotators and their confidence. These should be specified in an `image-annotation-labels` and `image-annotation-creators` field (see above) to provide more information on the values used in these fields.",
"type": "array",
"items": {
"type": "object",
"properties": {
"shape": {
"description": "The annotation shape is specified by a keyword (allowed values: see enum).",
"type": "string",
"enum": [
"single-pixel",
"polyline",
"polygon",
"circle",
"rectangle",
"ellipse",
"whole-image"
]
},
"coordinates": {
"description": "The pixel coordinates of one annotation. The top-left corner of an image is the (0,0) coordinate. The x-axis is the horizontal axis. Pixel coordinates may be fractional. Coordinates are to be given as a list of lists (only one element for photos, optionally multiple elements for videos). The required number of pixel coordinates is defined by the shape (0 for whole-image, 2 for single-pixel, 3 for circle, 8 for ellipse/rectangle, 4 or more for polyline, 8 or more for polygon). The third coordinate value of a circle defines the radius. The first and last coordinates of a polygon must be equal. Format: [[p1.x,p1.y,p2x,p2.y,...]..]",
"type": "array",
"items": {
"type": "array",
"items": {
"type": "number"
}
}
},
"labels": {
"description": "The list of labels assigned to annotations by annotators",
"type": "array",
"items": {
"$ref": "#/$defs/annotation-label"
}
},
"frames": {
"description": "(only required for video annotations) Frame times (in seconds from the beginning of a video) of a video annotation. Each frame time is linked to one entry in `image-annotations:coordinates` at the same position in the list, which specifies the current coordinates of the annotation at that frame.\nFormat: [f1,...]"
}
}
}
}
},
"$defs": {
"annotation-label": {
"type": "object",
"required": ["label","annotator","created-at"],
"properties": {
"label": {
"description": "A unique identifier to a semantic label",
"type": "string"
},
"annotator": {
"description": "A unique identifier to an annotation creator, e.g. orcid URL or handle to ML model",
"type": "string"
},
"created-at": {
"description": "The date-time stamp of label creation",
"type": "string",
"format": "date-time"
},
"confidence": {
"description": "A numerical confidence estimate of the validity of the label between 0 (untrustworthy) and 1 (100% certainty)",
"type": "number"
}
}
},
"label": {
"type": "object",
"required": ["id","name"],
"properties": {
"id": {
"description": "A unique identifier to a semantic label",
"type": "string"
},
"name": {
"description": "A human-readable name for the semantic label",
"type": "string"
},
"info": {
"description": "A description on what this semantic label represents",
"type": "string"
}
}
},
"annotator": {
"type": "object",
"required": ["id","name"],
"properties": {
"id": {
"description": "A unique identifier to an annotation creator, e.g. orcid URL or handle to ML model",
"type": "string"
},
"name": {
"description": "A human-readable name for the annotator (identifying the specific human or machine)",
"type": "string"
}
}
}
}
}
8 changes: 4 additions & 4 deletions assets/ifdo-v2.0.0.json
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}
},
"image-annotation-labels": {
"$ref": "https://marine-imaging.com/fair/schemas/annotation-v2.0.0.json#/properties/image-annotation-labels"
"$ref": "annotation-v2.0.0.json#/properties/image-annotation-labels"
},
"image-annotation-creators": {
"$ref": "https://marine-imaging.com/fair/schemas/annotation-v2.0.0.json#/properties/image-annotation-creators"
"$ref": "annotation-v2.0.0.json#/properties/image-annotation-creators"
},
"image-annotations": {
"$ref": "https://marine-imaging.com/fair/schemas/annotation-v2.0.0.json#/properties/image-annotations"
"$ref": "annotation-v2.0.0.json#/properties/image-annotations"
},
"image-acquisition": {
"description": "photo: still images, video: moving images, slide: microscopy images / slide scans",
Expand Down Expand Up @@ -717,7 +717,7 @@
}
},
"image-set-provenance": {
"$ref": "https://marine-imaging.com/fair/schemas/provenance-v0.1.0.json"
"$ref": "provenance-v0.1.0.json"
}
}
},
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8 changes: 4 additions & 4 deletions assets/ifdo-v2.0.1.json
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}
},
"image-annotation-labels": {
"$ref": "https://marine-imaging.com/fair/schemas/annotation-v2.0.0.json#/properties/image-annotation-labels"
"$ref": "annotation-v2.0.0.json#/properties/image-annotation-labels"
},
"image-annotation-creators": {
"$ref": "https://marine-imaging.com/fair/schemas/annotation-v2.0.0.json#/properties/image-annotation-creators"
"$ref": "annotation-v2.0.0.json#/properties/image-annotation-creators"
},
"image-annotations": {
"$ref": "https://marine-imaging.com/fair/schemas/annotation-v2.0.0.json#/properties/image-annotations"
"$ref": "annotation-v2.0.0.json#/properties/image-annotations"
},
"image-acquisition": {
"description": "photo: still images, video: moving images, slide: microscopy images / slide scans",
Expand Down Expand Up @@ -719,7 +719,7 @@
}
},
"image-set-provenance": {
"$ref": "https://marine-imaging.com/fair/schemas/provenance-v0.1.0.json"
"$ref": "provenance-v0.1.0.json"
}
}
},
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8 changes: 4 additions & 4 deletions assets/ifdo-v2.1.0.json
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}
},
"image-annotation-labels": {
"$ref": "https://marine-imaging.com/fair/schemas/annotation-v2.0.0.json#/properties/image-annotation-labels"
"$ref": "annotation-v2.0.0.json#/properties/image-annotation-labels"
},
"image-annotation-creators": {
"$ref": "https://marine-imaging.com/fair/schemas/annotation-v2.0.0.json#/properties/image-annotation-creators"
"$ref": "annotation-v2.0.0.json#/properties/image-annotation-creators"
},
"image-annotations": {
"$ref": "https://marine-imaging.com/fair/schemas/annotation-v2.0.0.json#/properties/image-annotations"
"$ref": "annotation-v2.0.0.json#/properties/image-annotations"
},
"image-acquisition": {
"description": "photo: still images, video: moving images, slide: microscopy images / slide scans",
Expand Down Expand Up @@ -719,7 +719,7 @@
}
},
"image-set-provenance": {
"$ref": "https://marine-imaging.com/fair/schemas/provenance-v0.1.0.json"
"$ref": "provenance-v0.1.0.json"
}
}
},
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106 changes: 106 additions & 0 deletions assets/provenance-v0.1.0.json
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{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://marine-imaging.com/fair/schemas/provenance-v0.1.0.json",
"title": "Documenting a processing workflow",
"description": "A schema to document the agents, activities and entities that led to an image set entity",
"type": "object",
"properties": {
"provenance-agents": {
"type": "array",
"description": "A list of all the agents in this provenance documentation",
"items": {
"$ref": "#/$defs/agent"
}
},
"provenance-entities": {
"type": "array",
"description": "A list of all the entities in this provenance documentation",
"items": {
"$ref": "#/$defs/entity"
}
},
"provenance-activities": {
"type": "array",
"description": "A list of all the activities in this provenance documentation",
"items": {
"$ref": "#/$defs/activity"
}
}
},
"$defs": {
"agent": {
"type": "object",
"description": "Someone or something that operates, takes responsibility, conducts, etc.",
"properties": {
"name": {
"type": "string",
"description": "A human-readable identifier of the agent"
},
"id": {
"type": "string",
"description": "A unique identifier for the agent. Could be a uri."
}
}
},
"entity": {
"type": "object",
"description": "A static instance of a virtual thing",
"properties": {
"name": {
"type": "string",
"description": "A human-readable identifier of the entity"
},
"id": {
"type": "string",
"description": "A unique identifier for the entity. Could be a uri."
},
"created-at": {
"type": "string",
"format": "date-time",
"description": "The time at which this entity was created in its entirety"
},
"attributed-to": {
"type": "array",
"description": "A list of agents that relate to this entity",
"items": {
"$ref": "#/$defs/agent"
}
},
"generated-by": {
"type": "array",
"description": "A list of activities that created this entity"
}
}
},
"activity": {
"type": "object",
"description": "A process that works with entities and is operated by agents",
"properties": {
"start-time": {
"type": "string",
"format": "date-time",
"description": "The time at which the activity began"
},
"end-time": {
"type": "string",
"format": "date-time",
"description": "The time at which the activity ended"
},
"associated-agents": {
"type": "array",
"description": "The agents that are associated to this activity",
"items": {
"$ref": "#/$defs/agent"
}
},
"used-entities": {
"type": "array",
"description": "The entities that are associated to this activity",
"items": {
"$ref": "#/$defs/entity"
}
}
}
}
}
}
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