biigler

biigler is an unofficial R package developed by Underwater Image Identification Working Group in ODB, IONTU mainly for substituting the repetitive operations on the BIIGLE 2.0 graphical user interface.

Features

• Work with BIIGLE API in R

  • Get images of volume, get label tree, and so on. Check out all relevant functions with ?getBIIGLE.
  • Massive post/delete label or annotation in volume. Check out all relevant functions with ?volPostNDelete.
  • Generate BIIGLE label/annotation csv-type report and download it. See function manual by ?reqNgetRep.

• Labeling assistant

  A set of functions for posting specific labels on targeting images. Check out details with ?labelingAssistant.

• Summary of label/annotation records in volume

  • Visualize label/annotation csv-type reports as a bar chart. Check out details with ?ana_sumVol.
  • This package contain 2 example dataset allowing user to test function ana_sumVol:
    • "annotation" csv-type report ex_annotation
    • "label" csv-type report ex_label

API token

Most of functions in this package work with BIIGLE RESTful API, which need to provide user's authentication information, including account (sign-up email) and API token. Hence, please generate an API token and use function genAuth to create the authentication string (see details with ?genAuth) before using these functions.

• Generate your API token on BIIGLE 2.0： BIIGLE 2.0 > Settings > Tokens > Generate

# Create the authentication string before your work
yourAuthString <- genAuth(account = "yourBiigleAccount@email.com", apiToken = "yourApiToken")

# Use the authentication string wherever the function requires it (parameter `auth`).
getVolID(url = "https://seaimage.oc.ntu.edu.tw", 
         auth = yourAuthString, 
         volName = "TTC17")
getVolImg(url = "https://seaimage.oc.ntu.edu.tw", 
          auth = yourAuthString,
          vol = 5)

Note that, the permission of requesting operation depends on the user's role in the BIIGLE project. For example, an Editor user can only use the function delAllLabs to delete labels created by itself, and labels created by other users will return as failed records. On the other hand, an Admin user can clean all labels with delAllLabs whatever it wants.

Dependencies

We developed this package based on:

• BIIGLE 2.0 v3.14.2
• R v4.1.2
• Other dependencies please check on DESCRIPTION file

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About Underwater Image Identification Working Group in ODB, IONTU

We built our BIIGLE 2.0 server by BIIGLE source code and analyze deep-see image in southwest of Taiwan (more information).