3.2 ARU (acoustic) projects

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Clicking on the ARU sensor on the main project dashboard will show which projects you have access to. The list of projects you see is determined by your organization membership, project membership and status of the project. You can use the filter and sort some of the project attributes to find what you’re looking for:

 

  • Project name
  • Organization
  • Project status
  • Due date
  • Total number of tasks
  • Total number of completed tasks

 

You can also click on the  to find out more details about the project or to Request Access. The toggle filters the default view to only projects to which you are a member (either administrator or read-only).

 

3.2.1 ARU project management

3.2.1.1 Setting up an ARU project

 

As mentioned, the goals of an ARU project are to upload media, process tasks, verify tags and publish the results. Click on  . This will open the Project Settings form allowing you to add information to the project including:

  • Project Title: A short name to identify the project
  • Organization: Drop-down list of all existing organizations of which you are an admin. This field allows you to group all of your projects together in the database. Once your project is saved you will be unable to change the organization to which it belongs.
  • Year: The year the data was collected.
  • Data Source: If you are importing data from an outside source (e.g. previously tagged data), please specify the original source of the data.
  • Due Date: The anticipated processing completion date. Your taggers can use this as a guideline as to when their image sets are due.
  • Description: This field allows you to outline the purpose, goals, objectives, and methods of your project.
  • Status: See more in publishing projects

 

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3.2.1.2 User management

 

Once you've created and saved your project details, you’ll be able to manage the users who are part of the project. Select the  tab to add and view current administrator and read-only project members.

 

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  • Project administrators have both read and write access to the project details, settings. They can add users to the project and can assign taggers to tasks.
  • Project read access members can view project details, and settings, and all tasks within the project. However, they can only edit tasks assigned to them.

Once you have created your project and close the window, the new project will be visible in the ARU project list. Click on the project title to enter the project page or click to edit project details, settings or users.

 

Users are granted their respective membership levels to an organization's projects. You don't need to add an organization member to a project unless you need to grant them administrator privileges and they only have organization read-only. 

3.2.2 Location management

 

Project administrators can benefit from managing only the locations from the media in the project, This differs from location management at the organization level, where locations from all projects can be managed. The functions to manage locations work the same as organization level management:

 

  • Click the and go to  to obtain the current list of locations in the project. If you don't have any locations yet, a template will be provided.
  • Make the changes or additions you'd like in the csv and re-upload the csv with the modifications using 

 

3.2.3 Recording management

 

A recording is the raw media or audio file that is uploaded to an ARU project in WildTrax.

 

WildTrax supports four major file types: wac, wav, flac, mp3

 

  • wac are proprietary, lossless compressed file formats developed by Wildlife Acoustics
  • wav is the standard, ubiquitous uncompressed audio file format
  • mp3 a lossy compressed audio file format; works by reducing the accuracy of certain sound components, and eliminating others
  • flac is a lossless compressed audio file format

 

A recording uploaded to WildTrax must also contain two important pieces of information, a location prefix and a timestamp. This allows WildTrax to generate or append the media to the locations stored in the organization as well as tell you when the recording took place. Managing locations at the project (see previous section) or organization level allows you to further add spatial coordinates to the locations providing both a spatial and temporal component to your uploaded media. This way you can always know when and where a recording took place. 

 

When data are uploaded, WildTrax converts and stores the audio as mp3 at a bit rate of 192 kbps. The spectrograms however are generated using the raw audio file format. 

 

A typical 10-minute, CD quality wav file (44,100 Hz) is ~105 MB. Depending on the scale of your monitoring program, you may be quickly collecting terabytes of data. It can be more efficient and cost-effective to choose which recordings will be uploaded to WildTrax for processing rather than uploading the entire volume of media. What recordings you choose to upload is dependent on your project's goals. See the ARU section of FAQ for more information.

 

wildRtrax, pronounced ‘wilder tracks’, is an R package for ecologists and advanced users who work with environmental sensor data. It contains functions designed to meet most needs in order to organize, analyze and standardize data to the WildTrax infrastructure. It is self-contained and must be run under an R statistical environment, and it also depends on many other R packages. It is also set by a free software and distributed under MIT License (c) 2020.

 

Even using a high bit rate (b = 320), mp3s significantly reduce an audio file's size. Nevertheless, loss of information in the audio data is an important consideration to make when converting or analyzing audio files. mp3 files that are stored in WildTrax for transcription, for example, truncate all spectrogram data above 12 kHz.

 

Another important aspect of collecting long-duration acoustic data is ensuring that the number of recordings that were planned on being collected are in fact there. Different makes and models of ARUs have proprietary formatting mechanisms that can be used to program to a set schedule. This functionality is not transferable between different makes of ARUs, so a standard needs to be established. Given that each make and model will have a way of programming this schedule, wildRtrax indexes it by the spatial and temporal information to match distinct recordings like in WildTrax. 

 

Once you have your recordings selected that you wish to upload for processing, go to the desired project and click and then . The recording upload panel will open providing settings before you choose your files for upload. This first step will scan the files you selected files prior to setting them up for upload. 

 

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  • Including subdirectories to scan if your media is layered in a hierarchical structure
  • Removing leading zeros after delimiters helps to clean up the location naming to a generic WildTrax standard. It is not obligatory to use this function but is recommended
  • Recordings uploaded to WildTrax automatically have a task generated for them. This allows a spectrogram to be generated and the task added to the project dashboard. If you un-check this box, the recording will be uploaded to WildTrax and stored in the organization. See media management for more information.
  • The default method will be applied to all the recordings you’re uploading - you can select a different method for individual recordings in the next form

 

If you don't want to create tasks yet, uncheck the Create Tasks box in the settings. This will still upload all the media to the organization but will not generate tasks in the project. You'll need to be or contact an organization administrator in order to generate tasks (see next section).

 

  • Click and select the directory that contains your recordings. WildTrax will identify how many files it has scanned which will then allow you to go to the next step.

 

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The next form shows the details of your recording upload prior to initiating it. It’s an important step to review the errors, messages and tabs before proceeding. Here are some things to look out when you’re uploading media:

 

  • If the location prefix does not fit the WildTrax standard, the row will be returned as NA
  • If the location doesn’t exist yet in the organization, WildTrax will create it
  • If the recording is shorter than the method you indicated by more than 3 seconds (e.g. 56 seconds for a 1 minute method), you’ll be prompted with an error that a recording shorter in length than the desired method should not be uploaded to WildTrax

 

When you’ve completed reviewing the form, click on to initiate the upload. It is strongly recommended to connect via ethernet if you want to stabilize and ensure internet connectivity while you upload media.

 

 

Another way to upload recordings into a project is to download a recording list from the organization. You'll need to be an organization administrator in order to use this function. 

 

  • Go to the organization to which the project belongs to 
  • Click on the  tab and then the button; there will only be one option in the dropdown to ; this will create a csv with the recordings and required metadata in order to create tasks for project.
    • Organization
    • Location
    • Longitude
    • Latitude
    • Recording date (YYYY-MM-DD HH:MM:SS)
    • Length of the recording (in seconds)
    • Land features (indicated in the visit metadata)
    • Location visit images

 

 

When your recording upload is complete, the [DOWNLOAD LOG] button will appear allowing you to save a record of the upload and the stauts of each recording, whether it was succesfully uploaded or failed and what the error was. At any time, you can return to the organization (or notify your organization administrator if you don't have privileges) so they can manage the media accordingly in the organization.

 

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3.2.4 Task management

 

If you’ve checked the box during a recording upload, the new tasks generated from the media are added to the project dashboard under .

 

A task is a unique combination of a user, a processing method and a recording. This flexibility allows you to generate tasks using the same recording but allow for multiple users or processing methods. 

 

Go to the project dashboard and click . The form will display the list of tasks currently in view depending on the toggle - switching the toggle to red allows you to filter the list to only your assigned tasks. The metadata for each one includes the location name, the date and time of the recording, the method it was assigned, the status of the task and the assigned user. 

 

If you didn't generate tasks when you uploaded recordings to the project, or, if you're using an organization's recordings to create tasks, you can also use the  tool under the button to automatically generate the tasks you need. Use the Download Tasks or Download csv template button if you haven't created any tasks yet to download the csv with the following fields:

 

  • Location: Name of the location
  • Recording Date and Time: The date and time the recording took place (YYYY-MM-DD)
  • Method: The method of the task
  • Transcriber: The user who processed / will be processing the task - this can be left blank and will automatically default to Not Assigned
  • Status: Task status - this can be left blank and will automatically default to New.
  • Rain: The average rain on the task
  • Wind: The average wind on the task
  • Industry noise: The average chronic industrial noise on the task
  • Other noise: Other noise averages on the task
  • Audio quality: The audio quality of the task

 

If you have hundreds or thousands of tasks without an assigned user, you can use the  button and select users from the dropdown list on the left to assign tasks to. It will randomly, and equally, assign unassigned tasks to the selected user(s).

 

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Alternatively you can click the  individual tasks and assign them to specific members from the dropdown.

 

 

You can always go to the organization to look at your summarized media (remember projects are part of organizations). All location media and metadata will be summarized in the organization with links to the project where needed.

 

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If you're a project administrator, you can also delete tasks from the project dashboard by clicking the  beside the desired task and clicking . Follow the prompts and warnings accordingly as task deletion is permanent and irreversible. 

 

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3.2.5 Tag management

 

The button also contains functions that allow you to upload and download tags to and from a project. This is useful if you've ever tagged acoustic data in another database and wish to sync it to WildTrax standard or you're looking for downloadable record of the tags and their metadata. Here are the csv fields required in order to upload - if you're project doesn't contain any tags, you'll be able to download a template first by clicking .
 

Before you can upload tags into the system, you'll need to first upload the recordings and create tasks in order to have the proper metadata needed to populate the tag csvs. You cannot generate tags for tasks or recordings that don't exist.

 

  • Location: Name of the location
  • Recording Date and Time: The date and time the recording took place (YYYY-MM-DD HH:MM:SS)
  • Method: The method of the task
  • Transcriber: The user who processed / will be processing the task
  • Species: The species of the tag - if you don't know the species ID use UNKN for unknown.
  • Individual: The individual of the species, for example the first Tennessee Warbler would be TEWA and the second TEWA 
  • Vocalization type: Whether the sound was a song, call or non-vocal 
  • Start time (seconds): The start time of the tag in seconds, for example if you heard the Ovenbird at 1:25 seconds in the recording, indicate 85.
  • Length (seconds): The length of the tag - this field is optional and can be left blank. WildTrax will use the average size of the tag for that species / vocalization type combination to create a box.
  • Mininimum frequency (kHz): The minimum frequency of the tag - this field is also optional 
  • Maximum frequency (kHz): The maximum frequency of the tag - this field is also optional 

 

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Click on the  button and select . In the new pop-up window, select  to select your tag data. When the file is uploaded the  button will turn green. Click it and WildTrax will ensure that the data you're uploading fits the WildTrax standard. This may take a few minutes depending how large your file is. 

 

3.2.6 - Single-species projects

 

If you're only interested in looking for one or a few species on your media, using processes like visual scanning and automated recognition may be right for you. If you're new to automated recognizers, have a read through the tab under Methods and Protocols to learn more. You can use the WildTrax workflow to upload recordings and tags generated from an automated recognizer in order to validate the hits using acoustic species verification

 

  • Download any of the free Bioacoustic Unit single-species recognizers available on the WildTrax website
  • Run the recognizer on your media
  • Upload recordings and tasks for the media tags you want to validate
  • Use the Tag CSV template to populate tags where the hits are located in the media
  • Use species verification to verify the tags