ifcb_download_dashboard_data: Download IFCB data files from an IFCB Dashboard

In iRfcb: Tools for Managing Imaging FlowCytobot (IFCB) Data

Download IFCB data files from an IFCB Dashboard

Description

This function downloads specified IFCB data files from a given IFCB Dashboard URL. It supports optional filename conversion and ADC file adjustments from the old IFCB file format.

Usage

ifcb_download_dashboard_data(
  dashboard_url,
  samples,
  file_types,
  dest_dir,
  convert_filenames = FALSE,
  convert_adc = FALSE,
  parallel_downloads = 5,
  sleep_time = 2,
  multi_timeout = 120,
  max_retries = 3,
  quiet = FALSE
)

Arguments

dashboard_url	Character. The base URL of the IFCB dashboard (e.g., "https://ifcb-data.whoi.edu"). If no subpath (e.g., ⁠/data/⁠ or ⁠/mvco/⁠) is included, ⁠/data/⁠ will be added automatically. For the "features" and "autoclass" file_types, the dataset name needs to be included in the url (e.g. "https://ifcb-data.whoi.edu/mvco/").
samples	Character vector. The IFCB sample identifiers (e.g., "IFCB1_2014_188_222013" or "D20220807T025424_IFCB010").
file_types	Character vector. Specifies which file types to download. Allowed values: "blobs", "features", "autoclass", "roi", "zip", "hdr", "adc".
dest_dir	Character. The directory where downloaded files will be saved.
convert_filenames	Logical. If TRUE, converts filenames of the old format "IFCBxxx_YYYY_DDD_HHMMSS" to the new format (DYYYYMMDDTHHMMSS_IFCBXXX or IYYYYMMDDTHHMMSS_IFCBXXX). Default is FALSE.
convert_adc	Logical. If TRUE, 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. Default is FALSE.
parallel_downloads	Integer. The number of files to download in parallel per batch. This helps manage network load and system performance. Default is 10.
sleep_time	A numeric value indicating the number of seconds to wait between each batch of downloads. Default is 2.
multi_timeout	Numeric. The maximum time in seconds that the curl multi-download request will wait for a response before timing out. This helps prevent hanging downloads in case of slow or unresponsive servers. Default is 120 seconds.
max_retries	An integer specifying the maximum number of attempts to retrieve data in case the server is unable to handle the request. Default is 3.
quiet	Logical. If TRUE, suppresses messages about the progress and completion of the download process. Default is FALSE.

Details

This function can download several files in parallel if the server allows it. The download parameters can be adjusted using the parallel_downloads, sleep_time and multi_timeout arguments.

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. It performs the following actions:

• Downloads the requested files into dest_dir.

• If convert_adc = TRUE, modifies ADC files in place by inserting four empty columns after column 7.

• Displays messages indicating the download status.

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.

Examples

## Not run: 
ifcb_download_dashboard_data(
  dashboard_url = "https://ifcb-data.whoi.edu/mvco/",
  samples = "IFCB1_2014_188_222013",
  file_types = c("blobs", "autoclass"),
  dest_dir = "data",
  convert_filenames = FALSE,
  convert_adc = FALSE
)

## End(Not run)

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