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# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 22ac48b9583f82371e7750e2b505d70a
tags: 645f666f9bcd5a90fca523b33c5a78b7
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23 changes: 23 additions & 0 deletions _sources/codex/data/index.md
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# Data

```{toctree}
:hidden:
search
matching
sighting-page
individual-page
optimizing-photographs
managing-the-public-queue
```

The following terms are used to describe ecological data in the Codex platform.

## Animal vs Individual

An **animal** is defined as a reported entity. It has not been assigned a identifying name, but it does have an associated time and place that it was seen. Conversely, an **individual** is defined as a known animal. This is an animal that, through manual processing or matching, has been given an identifying name.
A major objective of the platform is to identify all reported animals, and curate the catalogue to get to an accurate census of the individuals.

## Sighting

A **sighting** is defined as a place and time at which one or more animals were seen. Sightings are useful for learning social, environmental, and behavior information about the animals that were seen together. They also provide logical units for researchers to group pictures of the same animal with greater certainty because the pictures are known to have been taken of the same animals.
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# Individual page

$$INFO
title: Info
In Codex, we use the term *Animal* when the reported animal does not yet have a name associated with it. We use the term *Individual* when it has a name and at least one Sighting, which means it exists in the database and can be identified again.
$$

To [merge](#merging-individuals) or [delete](#deleting-an-individual) an Individual, begin on the page for a given Individual.

## Page for an Individual

The top of the page for an Individual displays its **representative image**, **name**, an automatically-assigned **Codex ID,** and **adoption name**, which is another name the Individual is known by.

### Photo gallery

A selection of photos of the Individual is displayed in a gallery under its **name** and **representative picture**.

Click the **See all** link to see all uploaded images with their *location*, *sighting* *date*, and *reporter information*.

### Metadata for your Individual

The **Metadata** box under the photo gallery displays the following information about the Individual:

* **First name**
* **Adoption name**
* **Sex**
* **Species**
* Any custom fields you have created

To edit these details, click the pencil in the top right corner of the **Metadata** box and type in the above fields. The **First name** and **Species** are required fields, the other fields are optional.

### Sighting list

The Sightings of the Individual are listed on the right.

* To list the Sightings according to each category, click the **Date**, **Location**, and **Owner** headings. Click again on a heading to reverse the order of Sightings.
* To view details about a **Sighting owner**, click the name link for that Sighting under the **Owner** heading. The page you are routed to displays the owner’s profile information, metadata, Sightings, and collaborations.
* To view a Sighting page, click the **arrow** icon next to that Sighting under the **Actions** heading.
* To remove a Sighting from an Individual, click the **trash can** icon next to that Sighting under the **Actions** heading, then click the **DELETE** button.

### Relationships

You can add and view familial and social group connections between your Individual and others in the **Relationships** section.

1. To add either of these, click the **+ RELATIONSHIP** button.
2. On the **ADD RELATIONSHIP** pop-up, search for another Individual in the database by entering either their name or guid in the search field, then click the **SEARCH** button.
3. In the results box, select the row for the Individual you wish to create a relationship with.
4. Under the results box, click the **Select relationship type** drop-down menu, then select **familial** or **social grouping**.
5. Scroll down to click the **Select role from your Individual’s perspective** drop-down menu, then select the appropriate option.
6. Click the **Select role from the related Individual’s perspective** drop-down menu, then select the appropriate option. The role options are different for familial and social grouping relationships.
7. Click the **ADD RELATIONSHIP** button.

Your Individual’s reported relationship is listed in the **Relationships** section.

* To view the page for the other Individual yours has a relationship with, click the **arrow** icon next to that relationship under the **Actions** heading.
* To delete a relationship, click the **trash can** icon next to that relationship under the **Actions** heading, then click the **DELETE** button in the pop-up box.

### Social groups

Individuals that operate in social orders such as packs or pods can be assigned to Social groups to support the tracking of these types of animals. These can be added and viewed in the **Social groups** section.

See the **Social groups** page to find out about creating, editing, and removing Social groups.

1. To add an Individual to a Social group click the **+ ADD TO SOCIAL GROUP** button.
2. In the pop-up box click the **Social group** field, then select the appropriate option.
3. Click the **Role** field, then select the appropriate role for your individual within that social group.
4. Click the **ADD** button.

$$INFO
title: Info
Information about the addition to a Social group is now listed in the **Social groups** section.
$$

* To view a Social group page, click the **arrow** icon next to that Sighting under the **Actions** heading.
* To remove an Individual from a Social group, click the **trash can** icon next to that Sighting under the **Actions** heading, then click the **DELETE** button in the pop-up box.

***

## Merging Individuals

### Merging individuals from the **Individual Overview page**

1. Look for the 3-dot menu on the top right corner of the Individual’s page.
2. Select **Merge with another individual**.
3. On the Search bar, enter the name or guid of the other Individual you want to merge your first individual with, then select click the **Search** button.
4. Select an Individual from the results, then select the **Continue** button.
5. You will be routed to the **Merge individuals page**, where you can see the information of both the Individuals you are merging.
6. At the bottom of the screen, click the **First name** and **Sex** menu
7. Select the name of the Individual you want to retain the information on the **First name** menu.
8. Do the same Click with the **Sex** menu and select the same individual.
9. Select Click the **Merge Individuals** button to submit the changes.

### Merging individuals from the **Sighting Overview page**

1. Scroll down to from the bottom of the **Sighting Overview** page and select the **View Match Results** button.
2. You will be directed to the **Review match candidates** page. Check if the **Selected match candidate** on the right is the one you want to merge with your individual on the left. Details are provided for each individual.
3. If it is not the correct match candidate, you can view others in the **Candidate annotations** table below where candidates are listed in ranked order.
4. To view information about the sightings, scroll to the right of the box and select click the *View icon* next to the *Filename*.
5. Select the Individual you want to merge with the one on the left. Wait for its information to auto-populates on the **Selected match candidate** section of the page.
6. Once you confirm that all the information is correct, click the **Confirm Match** button on the bottom right corner of the page.

$$INFO
title: NOTE:
If you do not have ***edit access*** to a sighting for both Individuals, all the stakeholders with access toIn the database will receive a notification about the potential merge. Any stakeholder can deny the merge, but if no one does, it will gets denied automatically after **two weeks**.
$$

***

## Deleting an Individual

1. To delete an Individual, click the 3-dot menu at the top right of the page for the Individual.
2. In the drop-down menu select **Delete individual**, then on the pop-up box click the **DELETE** button.

$$INFO
title: Info
Even though the Individual has been deleted, the Sighting the Individual was part of stays in the database.
$$


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# Managing the Public Queue

The Public queue lists Sightings data submitted by citizen scientists and the public and is managed by researchers. All public-submitted Sightings data requires a process of curation that involves annotating images with bounding boxes to outline animals in images, and grouping annotations of the same animal together. This process allows submitted Sightings to be best set up for accurate identification. The Public queue displays the curation status of Sightings.

## Accessing the Public Queue

1. Click the **Actions** triangle icon at the right end of the menu bar.
2. Select **Pending citizen science sightings** from the drop-down menu.
A list of citizen science sightings that are ready to be curated will appear as a Public Queue.
* To sort the Sightings, click on any of the headings.
* To export the list as a CSV file, click the **download cloud** icon on the right above the list.
* To search the Sightings and use search filters, click the **menu** icon.

## Curating a Sighting

1. Locate a Sighting on the **Public Queue** page.
2. Click the **arrow** icon under the **Actions** heading to go to the **Sighting** page.
3. On the **Sighting** page, scroll down the Identification pipeline status box.
4. Under the **SIGHTING CURATION** heading, click the **ASSIGN ANNOTATIONS** button.

### Creating Annotations

You will be directed to the **PHOTOGRAPHS** tab on the **Sighting** page.

1. On the photo you wish to annotate, click the three vertical dots at the top right in the frame.
2. Click the **Add annotation** link. An annotation frame will appear on the photo.
3. Move and resize the annotation frame so that it fits entirely around the animal in the image:
* To move the annotation frame, hover over it and click and drag the frame to the position you require.
* To resize the annotation frame, hover over it to locate the resizing dots in the frame, then click and drag the dots on the frame around the animal in the image.
4. Click the **Viewpoint** field under the photo and select the side of the animal that is shown from the dropdown list.
5. Click the **Annotation class** field and select the species of the animal from the dropdown list.
6. Click the **SAVE** button on the bottom right of the page.

A fixed annotation box will appear on your photo. Toggle the **Show annotations** button to change its visibility.

### Assigning Annotations

Click the **ANIMALS** tab on the **Sighting** page.

1. Under the **Animal** heading, click the **+** sign in the **Annotations** box on the right. The photo of the animal will appear with the fixed annotation box around it.
2. Click the center of the annotation box.
3. Click the **ADD ANNOTATIONS** button.
4. Complete this process for all photos in the Sighting.

### Committing a Sighting

Once curation is complete for all photos, the Sighting is ready to be committed to searches and match results with other Animals in the database.

1. Click the **COMMIT** button to the right of the **Ready to commit** banner under the headings.
2. Select an option for the process of identification of animals in the photos. Choose to either:
* Run the identification job with the default settings.
* Not start an identification job.
* Customize settings for this identification job, which allows you to manage the identification algorithms used and the region of Sightings matched against.
3. Click the **COMMIT SIGHTING** button in the bottom right corner of the box.
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# Match Sighting - Codex

1. From your *Codex profile page*, click the **View** button for one of your Sightings on the *Sightings* table.
2. You will be directed to the **Sighting’s page** where you can see all the recorded information of this particular sighting.
3. On the **OVERVIEW** tab you will see *Identification pipeline status*.
4. If the **IDENTIFICATION stage** is incomplete, you will see a progress indicator bar, for the remaining validation time.
5. If the *IDENTIFICATION* is complete, there will be a **VIEW MATCH RESULTS** button underneath.

***

## Match Candidates

Use the **Review match candidates** page to compare animals and create individuals.

1. The image on the left is the **Selected query annotation** (the original image you started with).
2. On the right is the **Selected match candidate** (the image of the potential matching Individual).
3. Underneath each image is information about the **Individual**, **Region**, and **Time of Sighting**. This helps in making sure that the Sightings match.
4. If an image carousel displays, you can click through the images to see the full collection of images associated with the animal. The carousel only displays if there are additional images.
5. Above the images, click the **Inspect match area** toggle to see the visualizations to see what the algorithm is considering for the match.
6. Check if the annotated Individuals match.
7. The **Viewpoint column** on each of the tables indicates the camera’s perspective.
8. **Score** indicates how similar the Individuals are to each other. Note that a higher Score indicates how closely the Individuals are matching, but it is not accurate at all times.
9. If you want to view each Individual's Sighting page, scroll to the side of the **Candidate annotations table** and click the icon  under the **View Sighting** column.
10. The **Status** menu below the **Query annotations** table lets you mark the match as Unreviewed, In progress, Reviewed, or Unidentifiable.

***

## Confirm Match

1. On the **Sighting's page** for a particular sighting, click the **OVERVIEW** tab.
2. At the bottom of the *Identification pipeline status* click the **VIEW MATCH RESULTS** button.
3. You will be directed to the **Review match candidates** page.
4. Once you're sure which *Selected match candidate* matches the other on the left,  click the **CONFIRM MATCH** button. *Note: There are two possible pages that you will be directed to. Read on to continue*
5. You will be directed to the **Merge individuals** page where the matching Individuals are going to be displayed.
6. Below the images is the **Resolve fields** section.
7. Select the **First name** and **Sex** that you want to keep.
8. Click the **MERGE INDIVIDUALS** button.

If you were not directed to the **Merge individuals** page, then you ended up at the **Create individual** page:

1. Assign the necessary annotation to the Individuals.
2. Enter **First name**.
3. Enter **Adoption name**.
4. Enter **Sex**.
5. Enter **Species**.
6. Click the **CREATE INDIVIDUAL** button.

## Confirm No Match

If you've determined that none of the candidate annotations are a match, click the **CONFIRM NO MATCH** button below the table.
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# Photography Guidelines

When reporting a Sighting, photographs can be submitted to Codex to identify Individuals. Here are the guidelines for a greater chance of successful identification:

* The **Individual** in the photo is distinguishable (i.e. is free-standing or clearly in the foreground).
* The **Individual** occupies the majority of the frame.
* The **Individual** is located near the center of the photograph.
* The **Individual** is in focus and has good image resolution.

Here are what you need to **AVOID** for a successful identification:

* The **Individual** is part of an overlapping herd or group of animals.
* The **Individual** is obstructed by more than 25% by other animals or objects.
* The **Individual** is relatively small.
* The **Individual** is blurry and out of focus due to being too far from or too close to the camera.
* The **Individual** is located around the edges of the image.
* Part of the **Individual** is outside the edge of the frame.

Codex caters to multiple species. For best results, visit their [Codex platform](https://www.wildme.org/platforms.html) and navigate to **Learn > How to Photograph** on the menu bar.

## **Image Formats and Sizes**

* Codex accepts photographs in a variety of formats, including **.jpg, .jpeg, .png, and .bmp**. *(Note:* **.tiff** *format is not supported)*
* Use photographs between **480px** and **1600px**.
* When running detection and identification, photographs smaller than **480px** are sized up which may cause blurriness. Photographs bigger than **1600px** put a strain on the server and cause identification to take longer.
* A compression ratio of **90%** is sufficient. Uploading photographs with a higher compression ratio will not influence the identification process.
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