-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #6 from biigle/patch-1
Include provenance and annotation files locally
- Loading branch information
Showing
5 changed files
with
240 additions
and
12 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,122 @@ | ||
| { | ||
| "$schema": "https://json-schema.org/draft/2020-12/schema", | ||
| "$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" | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,106 @@ | ||
| { | ||
| "$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" | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } |