deploy: 9e01a1e

.buildinfo

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+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 44bd2c705bad65b72d810df204cd1c47
+tags: 645f666f9bcd5a90fca523b33c5a78b7

CNAME

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+scout.docs.wildme.org

_sources/administration/delete.md

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+# Delete Data
+
+
+## Delete Users
+At present, there is no way to delete users.
+
+## Delete Images
+At present, there is no way through the UI to delete images from the system. Instead, you must make edits to the mongoDB directly.
+
+## Delete Tasks
+When you delete a task, the associated annotations are removed from the system. When you delete a task that has been through ground truth, the ground truth confirmations are removed from the system, which can impact annotation export analysis. When you delete a task that has the last instance of a tag on it, the tag is not removed from the system. To remove tags, you must delete them individually.

_sources/administration/index.md

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+# Administration
+
+Once Scout is running on your server, you can set up the system to be ready for data processing. You'll need to create the first login to do any other administration.
+
+## Create the First Login
+
+As a Lab Lead, your first contact with **Scout** is after the System Administrator installed it and provided you with a link. Open the link using the **Google Chrome browser** and create your Lab Lead account. *(Note: This step is not needed if the System Administrator provided you with login credentials.)*
+
+Here's how to create your Lab Lead account:
+
+1. Fill out the **Username** field.
+2. Create a password and confirm it in the **Password** and **Confirm password** fields.
+3. Click **Submit**. Your Lab Lead account is now available, and should be visible in the **Users** page. You can start creating accounts for Annotators.
+
+![firstlogin](../assets/images/first-signin.png)
+
+```{note}
+While you can perform all of the Lab Lead duties in Scout from any Chrome browser that can access it, you may also want to obtain access to the Scout Server laptop to be able to add aerial survey images to Scout’s image ingestion folder (see the Add survey images to Scout section of this document). Ask your System Administrator for an Ubuntu Desktop account to log into the server. Your account also needs access to the image ingestion folder created by the System Administrator.
+```
+
+```{toctree}
+:maxdepth: 1
+
+manage-users
+manage-labels
+manage-task
+delete
+```

_sources/administration/manage-labels.md

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+# Labels and Hot Keys
+
+Lab Leads should set up hot keys and labels before assigning tasks to annotators.
+
+## Assign hot keys to labels
+
+Hot keys are used to easily jump from one label to another. Here are the steps to follow when assigning hot keys:
+
+1. On the Scout homepage, click **Labels**.
+2. On the Label manager window, users will see the list of labels to which users can assign hotkeys. *Note: If a label needed is unavailable, users can add their own.*
+3. Click **Edit**.
+4. Select the preferred hot key from the dropdown list.
+5. Click **Save** to save all the changes.
+    *Note: Labels without assigned hot keys will not show up in the* **Shortcut Keys** *box during an annotation or ground truth task.*
+
+## Add a label
+
+Adding new labels (classifications) is useful for future model retraining but does not add classifications to the current Scout version. Here are the steps to follow when adding a label:
+
+1. On the Scout homepage, click the **Labels** button.
+2. On the Label manager window, click the **+ADD NEW LABELS** button.
+3. Enter the label on the space provided, and use the dropdown list to assign a hot key.
+    *Note: Labels without assigned hotkeys will not show up in the* **Shortcut Keys** *box during an annotation or ground truth task.*
+4. Click **Save** to save all the changes.
+
+It is recommended that you create an "Unknown" label for any annotations that cannot be classified on sight for future model training precision.

_sources/administration/manage-task.md

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+# Manage Tasks
+
+Tasks within Scout represent a group of images assigned to either a user or to a machine-learning model for annotation, which includes:
+
+* drawing a bounding box around all animals of interest
+* labeling the species for each bounding box
+
+The same image can appear in multiple Tasks, which can be duplicated for parallel annotation by different users. Different users can annotate the same images in different tasks. Tasks go through three stages:
+
+1. **Annotation**: Annotating animals in the images is the most important function of Scout. It is the only stage required for the downstream analysis of the tasks. Annotation can be performed by Lab Leads and Annotators.
+2. **Ground truth**: The ground truth stage of a task involves the *review, correction*, and ultimately the approval of all annotations in an image by the Lab Lead. Once an image has gone through ground truth in any task, it does not appear for annotation or ground truth in another task that may contain it.
+3. **Division line**: If an image is part of a sequence of images with annotated animals within them, then a Lab Lead may draw division lines to indicate overlap between images.
+4. **Export**: Once they have been through all the stages mentioned, tasks are ready to export for analysis in third-party applications. *Note*: tasks don’t strictly have to go through the stages above to be exported, aside from annotation.
+
+Once all images in a task have gone through annotation, ground truth, and division lines, the task is considered completely done. Lab Leads ultimately creates tasks to help break up large volumes of aerial survey images into manageable chunks for Annotators to work through, and many tasks may make up a single transect, flight, and survey. The following recommendations apply when creating tasks:
+
+* All images in a task should be *from a single side of the airplane*. This is important for the sequencing of images to draw division lines.
+* A task should ideally correspond to either a single transect or a subset of images from that transect.
+
+## Viewing Tasks
+
+Click the **Tasks** button on the header navigation menu to view the Tasks page.
+
+![tasktable](../assets/images/scout-task-table.png)
+
+### Task Table
+
+Tasks are listed in rows in the task table below the filters. The details for each task are displayed in a horizontal row to the right of the task name. Filter tasks to view only tasks with specified qualities.
+
+Click the action buttons on the right side in each task row to annotate, ground truth, draw division lines, delete the task, or view the images in a task.
+
+The table columns are:
+
+* **Task Name**: name given to the task when it was created.
+* **Side**: side of the airplane that images in the task were from, *Left or Right.*
+* **Order**: sequential or random.
+* **Assignee**: user assigned to the task.
+* **Date Created**: creation date of the task.
+* **A%**: percentage of image annotation complete in the task.
+* **G%**: percentage of image ground truth review complete in the task.
+* **D%**: percentage of image division line annotation complete in the task.
+* **Annotate** button: if images are still available for annotation in the task, this navigates to the annotation page.
+* **Ground Truth** button: if task annotation is 100% complete and images are still available for ground truth review in the task, this navigates to the ground truth page.
+* **Division Lines** button: if task ground truth is 100% complete and images are still available for division line annotation in the task, this navigates to the division line page.
+* **Delete** button: deletes the task. Deleting a task requires *manual confirmation* to avoid accidental data loss.
+
+![deleteconfirm](../assets/images/confirmdel.png)
+
+* **Images** button: navigates to the Image Gallery page to preview all images associated with that task.
+
+Under the table, the buttons to navigate through table data are:
+
+* **Next** button: provides access to subsequent rows of table data if more tasks match the filter criteria than can be displayed in the table
+* **Previous** button: provides access to previous rows of table data if more tasks match the filter criteria than can be displayed in the table
+
+```{note}
+You must click your browser’s reload button to see changes to the Tasks view that have occurred since you loaded the page.
+```
+
+## Filtering Tasks
+
+Filter tasks by any of the following in the **Filters** section above the tasks:
+
+* **Task Name**: Search for a task by its name.
+    Enter the task name in the **Task Name** field, then click the **Filter** button in the top right corner.
+* **Date created start**: filter tasks created from this date. *Note:* the dates are for task creation and not based on the dates of images in the tasks.
+    Click the calendar icon to the right of the **Date Created Start** field and select a date, then click the **Filter** button in the top right corner.
+* **Date created end**: filter tasks created up until this date.
+    Click the calendar icon to the right of the **Date Created End** field and select a date, then click the **Filter** button in the top right corner.
+* **Assignee**: filter tasks to the specified users or ML models.
+    Select the assignee/s in the scrollable **Assignee** list box, then click the **Filter** button in the top right corner.
+* **Stage**: filter tasks to their stage in the annotation, ground truth, and line division workflow.
+    Select the stage/s of progress in the scrollable **Stage** list box, then click the **Filter** button in the top right corner.
+* **Ordering type**: filter tasks by sequential or random ordering type.
+    Click the **Ordering type** dropdown menu, select an option, then click the **Filter** button in the top right corner.
+* Tags: filter tasks by Tags you have created.
+    Select the tag/s in the **Tags** list box, then click the **Filter** button in the top right corner.
+
+To select multiple **Assignee, Stage, or Tags** filters, hold down the Control key (Ctrl) on your keyboard while selecting multiple filters.
+
+To export a comma-separated values `(CSV)` file of annotation or image data filtered according to the Filters on the page, click the **Export Filtered Results** button and select an option. The export will be automatically generated.
+
+To return to the full view of unfiltered tasks, click the **Reset** button on the right of the **Filter** button.
+
+## Creating and assigning tasks
+
+Here's how to create a new task to assign to a user:
+
+1. Select **Tasks** from the Scout menu bar.
+2. Click the **+Create Task** button on the Tasks page.
+3. In the **New Task form**, do the following information:
+    * Enter a **unique name** for the task in the **Task Name field**. Human-readable task names are recommended, such as: `Lewa Flight 2022-09-15 Transect 1 Images 1-500`
+    * Select the appropriate annotator or ML model from the **Assignee dropdown** list.
+    * Select the appropriate side of the plane that the camera was on when it took the images of this task, **Left** or **Right**, **in the Camera Side field.**
+        ![newtask](../assets/images/newtask.png)
+4. Click **Select Images** to add images to the task using the Select Images dialog box.
+5. In the **Select Images** dialog box, leverage the following fields to specify the images you want added to the task. As you adjust filters, the matching images count updates. Each field adds a logical AND to the matched images and further subsets matching to those images that match all chosen criteria.
+    * Enter letters and numbers to filter images by **File Name**, updating the matching images count as you type.
+    * Enter or select the name of an existing task that already contains a desired subset of images in the **Duplicate From Existing Task** field.
+    * Select **Start and End dates** to further filter images by. These filters match against the `EXIF` creation dates of the images.
+    * Select a range of numbers in the Subset Range (inclusive) field. Where a large number of images might match your criteria, a range allows you to specify a fixed, sorted subset. For example, you might select criteria matching 1000 images and assign a range of 1 to 500 in the task for the first annotator and a range of 501 to 1000 in the task for the second annotator.
+
+![newtaskimage](../assets/images/newtask-imageselect.png)
+
+6. Click **Submit** to create the new task. On successful creation, the task becomes available in the **Tasks view**.
+
+```{note}
+There may be a short delay after creation of a task before it is ready for annotation, depending on the number of images in it.
+```
+
+```{warning}
+If during task creation you see the following message in the New Task form, please be aware that new images are being added to Scout.
+```
+
+![ingestionnotice](../assets/images/image-ingestion-notice.png)
+If the images you need to add to this task have already been ingested, you can ignore this message. However, it is recommended to wait for ingestion to complete and for the alert to drop before creating your new task. Having all images present is important if you wish to select a range of images for the task, and not all of those images have been added yet.
+
+## Adding Tags to Tasks
+
+Create and apply custom tags to tasks to view groups of tasks with aspects in common.
+
+### Creating New Tags
+
+1. Scroll down to the appropriate task.
+2. Locate and click the pencil icon on the left of the task row:
+3. To add the first new tag to a task, click the pencil icon next to the **Tags:** heading under the task name.
+4. To add additional new tags to a task, hover over the task row then click the pencil icon to the right of the existing tags.
+5. Type the new tag in the **Enter new tag** field.
+6. Click the **Save** button.
+
+The new tag is listed in the **Tags** list box on the right above the Tasks.
+
+### Adding Existing Tags
+
+To add existing tags to a task:
+
+1. Scroll down to the appropriate task.
+2. Locate and click the pencil icon on the left of the task row:
+    1. To add the first tag to a task, click the pencil icon next to the **Tags:** heading under the task name.
+    2. To add additional tags to a task, hover over the task row then click the pencil icon to the right of the existing tags.
+3. Click the **Choose tag** dropdown menu and select a tag.
+4. Click the **Save** button on the right of the dropdown menus.
+
+To add existing tags while creating a new task:
+
+1. Click the **+ Create Task** button in the top left corner.
+2. On the **New Task** page, select tags in the scrollable **Tags** box.
+3. Fill in and select the other details, then click the **Submit** button.
+
+### Deleting Tags
+
+Deleting a tag removes it from the list of tags and all tasks.
+
+1. Hover over the task row then click the pencil icon to the right of the existing tags.
+2. Click the **x** symbol on the right of the tag.
+
+To return to the default view of a task after clicking the pencil icon but not performing an action, hover over the task row and click the pencil icon to the right of the **Save** button.

_sources/administration/manage-users.md

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+# Manage Users
+## Creating User Accounts
+
+Only a Lab Lead can create Annotator and other Lab Lead user accounts. Here's how to create a new user account:
+
+1. Click the **Users** button in the top navigation menu.
+2. From the Users page, click the **+Create User** button.
+3. In the **New User** form, enter the following information:
+    * A unique username *(Note: case sensitive)*
+    * A unique password *(Note: case sensitive and needs to be confirmed on the **Confirm password** field )*
+    * The role for the new user in the **Role** field. Your options are:
+        * **Annotator** - an account that only let the user draw and label bounding boxes on images in assigned tasks.
+        * **Lab Lead** - an account that can also manage users and tasks, provide ground truth for annotated data, draw division lines, and export data.
+4. Your password to ensure that new users cannot be created without your consent.
+5. Click **Submit** to create a new user account. To make sure that it's successful, the new username will be listed on the Users page.
+
+```{note}
+Make sure to convey the new username and password to the new user so that they may begin using the account.
+```
+
+## Editing User Accounts
+
+Here's how to edit an existing user account:
+
+1. Click the **Users** button in the top navigation menu.
+2. From the Users page, click the **Edit** button next to the appropriate user.
+3. In the **Edit User** form, enter the following information:
+    * A unique password *(Note: case sensitive and needs to be confirmed on the **Confirm password** field)*
+    * Your password to ensure that new users cannot be created without your consent.
+4. Click **Submit** to save the changes. If the edit is successful, you will be routed to the **Users page**.
+
+```{note}
+Make sure to convey the new password to the user so that they may begin using the account.
+```
+

_sources/annotate-task.md

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+# Manually Annotate Tasks
+
+If an unfinished task is assigned to you directly, you can click the **Annotate button** next to the task on the **Tasks table** to begin annotating randomly presented images. The annotation screen allows you to *click-drag* to create a bounding box. Use the down arrow key or begin typing to select the correct label for the annotation. In addition to the *click-drag* motion for creating annotations, the following tools are available to you in the annotation interface:
+
+* zoom in button ![zoomin](assets/images/zoom-plus.png)
+* zoom out button ![zoomout](assets/images/zoom-minus.png)
+* **scroll bars** to pan across the image to look for parts to annotate
+* back button ![back](assets/images/back-button.png)
+* **Done** to finish the ground truth stage of this image, making it as completely and accurately done. If any annotations were created, modified, or destroyed, they are now saved as ground truth. If no annotations were present when Done was clicked, the image is considered empty.
+
+```{note}
+If you refresh your Chrome browser, the interface presents a new random image, and your work on the image you saw before is not stored.
+```
+![annotate](assets/images/annotation-interface.png)
+
+Once you finish annotating the images, a page noting the successful completion of annotation for the task appears. Click the **Tasks button** on the menu to return to the **Tasks view and start** your next assigned task.
+![success](assets/images/annotation-complete-success.png)
+
+## Annotation Toggle
+
+When annotating or ground truthing a task, annotation labels can be applied to specific regions or objects in an image as tags or markers.
+
+Toggle the visibility of the annotation labels and label delete buttons by clicking the **Show Labels** checkbox in the bottom left corner:
+
+* Toggle the checkbox on to view the annotation labels and trash can icons to delete annotation labels. This is the default state.
+* Toggle the checkbox off to hide the annotation labels and delete buttons, so the image and annotations are fully visible.