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Extract Annotated Images from IFCB Data

Source: R/ifcb_extract_annotated_images.R
ifcb_extract_annotated_images.Rd

This function extracts labelled images from IFCB (Imaging FlowCytobot) data, annotated using the MATLAB code from the ifcb-analysis repository (Sosik and Olson 2007). It reads manually classified data, maps class indices to class names, and extracts the corresponding Region of Interest (ROI) images, saving them to the specified directory.

Usage

ifcb_extract_annotated_images(
  manual_folder,
  class2use_file,
  roi_folder,
  out_folder,
  skip_class = NA,
  verbose = TRUE,
  manual_recursive = FALSE,
  roi_recursive = TRUE,
  overwrite = FALSE
)

Arguments

manual_folder

A character string specifying the path to the directory containing the manually classified .mat files.

class2use_file

A character string specifying the path to the file containing class names.

roi_folder

A character string specifying the path to the directory containing the ROI files.

out_folder

A character string specifying the output directory where the extracted images will be saved.

skip_class

A numeric vector of class IDs or a character vector of class names to be excluded from the count. Default is NULL.

verbose

A logical value indicating whether to print progress messages. Default is TRUE.

manual_recursive

Logical. If TRUE, the function will search for MATLAB files recursively within the manual_folder. Default is FALSE.

roi_recursive

Logical. If TRUE, the function will search for data files recursively within the roi_folder (if provided). Default is TRUE.

overwrite

A logical value indicating whether to overwrite existing PNG files. Default is FALSE.

Value

None. The function saves the extracted PNG images to the specified output directory.

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.

See also

ifcb_extract_pngs ifcb_extract_classified_images https://github.com/hsosik/ifcb-analysis

Examples

if (FALSE) { # \dontrun{
ifcb_extract_annotated_images(
  manual_folder = "path/to/manual_folder",
  class2use_file = "path/to/class2use_file.mat",
  roi_folder = "path/to/roi_folder",
  out_folder = "path/to/out_folder",
  skip_class = 1
)
} # }