ifcb_prepare_whoi_plankton: Download and Prepare WHOI-Plankton Data
In iRfcb: Tools for Managing Imaging FlowCytobot (IFCB) Data

View source: R/ifcb_prepare_whoi_plankton.R

ifcb_prepare_whoi_plankton

R Documentation

Download and Prepare WHOI-Plankton Data

Description

This function downloads manually annotated images from the WHOI-Plankton dataset (Sosik et al. 2015) and generates manual classification files in .mat format that can be used to train an image classifier using the ifcb-analysis MATLAB package (Sosik and Olson 2007).

Usage

ifcb_prepare_whoi_plankton(
  years,
  png_folder,
  raw_folder,
  manual_folder,
  class2use_file,
  skip_classes = NULL,
  dashboard_url = "https://ifcb-data.whoi.edu/mvco/",
  extract_images = FALSE,
  download_blobs = FALSE,
  blobs_folder = NULL,
  download_features = FALSE,
  features_folder = NULL,
  parallel_downloads = 5,
  sleep_time = 2,
  multi_timeout = 120,
  convert_filenames = TRUE,
  convert_adc = TRUE,
  quiet = FALSE
)

Arguments

`years`	Character vector. Years to download and process. For available years, see https://hdl.handle.net/1912/7341 or `ifcb_download_whoi_plankton`.
`png_folder`	Character. Directory where `.png` images will be stored.
`raw_folder`	Character. Directory where raw files (`.adc`, `.hdr`, `.roi`) will be stored.
`manual_folder`	Character. Directory where manual classification files (`.mat`) will be stored.
`class2use_file`	Character. File path to `.mat` file to store the list of available classes.
`skip_classes`	Character vector. Classes to be excluded during processing. For example images, refer to https://whoigit.github.io/whoi-plankton/.
`dashboard_url`	Character. URL for the IFCB dashboard data source (default: "https://ifcb-data.whoi.edu/mvco/").
`extract_images`	Logical. If `TRUE`, extracts `.png` images from the downloaded archives and removes the `.zip` files. If `FALSE`, only downloads the archives without extracting images. Default is `FALSE`.
`download_blobs`	Logical. Whether to download blob files (default: FALSE).
`blobs_folder`	Character. Directory where blob files will be stored (required if `download_blobs = TRUE`).
`download_features`	Logical. Whether to download feature files (default: FALSE).
`features_folder`	Character. Directory where feature files will be stored (required if `download_features = TRUE`).
`parallel_downloads`	Integer. Number of parallel IFCB Dashboard downloads (default: 10).
`sleep_time`	Numeric. Seconds to wait between download requests (default: 2).
`multi_timeout`	Numeric. Timeout for multiple requests in seconds (default: 120).
`convert_filenames`	Logical. If `TRUE` (default), converts filenames of the old format `"IFCBxxx_YYYY_DDD_HHMMSS"` to the new format (`DYYYYMMDDTHHMMSS_IFCBXXX`).
`convert_adc`	Logical. If `TRUE` (default), adjusts `.adc` files from older IFCB instruments (IFCB1–6, with filenames in the format `"IFCBxxx_YYYY_DDD_HHMMSS"`) by inserting four empty columns after column 7 to match the newer format.
`quiet`	Logical. Suppress messages if TRUE (default: FALSE).

Details

This function requires a python interpreter to be installed. The required python packages can be installed in a virtual environment using ifcb_py_install().

This is a wrapper function for the ifcb_download_whoi_plankton, ifcb_download_dashboard_data and ifcb_create_empty_manual_file functions and used for downloading, processing, and converting IFCB data. Please note that this function downloads and extracts large amounts of data, which can take considerable time.

The training data prepared from this function can be merged with an existing training dataset using the ifcb_merge_manual function.

To exclude images from the training dataset, either exclude the class completely with the skip_classes argument, or set extract_images = TRUE and manually delete specific .png files from the png_folder and rerun ifcb_prepare_whoi_plankton.

If convert_filenames = TRUE , filenames in the "IFCBxxx_YYYY_DDD_HHMMSS" format (used by IFCB1-6) will be converted to IYYYYMMDDTHHMMSS_IFCBXXX, ensuring compatibility with blob extraction in ifcb-analysis (Sosik & Olson, 2007), which identified the old .adc format by the first letter of the filename.

If convert_adc = TRUE and convert_filenames = TRUE , the "IFCBxxx_YYYY_DDD_HHMMSS" format will instead be converted to DYYYYMMDDTHHMMSS_IFCBXXX. Additionally, .adc files will be modified to include four empty columns (PMT-A peak, PMT-B peak, PMT-C peak, and PMT-D peak), aligning them with the structure of modern .adc files for full compatibility with ifcb-analysis.

Value

This function does not return a value but downloads, processes, and stores IFCB data.

References

Sosik, H. M. and Olson, R. J. (2007), Automated taxonomic classification of phytoplankton sampled with imaging-in-flow cytometry. Limnol. Oceanogr: Methods 5, 204–216.

Sosik, H. M., Peacock, E. E. and Brownlee E. F. (2015), Annotated Plankton Images - Data Set for Developing and Evaluating Classification Methods. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1575/1912/7341")}

Examples

## Not run: 
# Download and prepare WHOI-Plankton for the years 2013 and 2014
ifcb_prepare_whoi_plankton(
  years = c("2013", "2014"),
  png_folder = "whoi_plankton/png",
  raw_folder = "whoi_plankton/raw",
  manual_folder = "whoi_plankton/manual",
  class2use_file = "whoi_plankton/config/class2use_whoiplankton.mat"
)

## End(Not run)

iRfcb documentation built on April 16, 2025, 1:09 a.m.