Count IFCB Annotations from .mat Files

This function processes .mat files, generated by the code in the `ifcb-analysis` repository (Sosik and Olson 2007), in a specified folder to count and summarize the annotations for each class based on the class2use information provided in a file.

ifcb_count_mat_annotations(manual_folder, class2use_file, skip_class = NULL)

Arguments

manual_folder

A character string specifying the path to the folder containing .mat files.

class2use_file

A character string specifying the path to the file containing the class2use variable.

skip_class

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

Value

A data frame with the total count of images per class.

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

if (FALSE) {
# Count annotations excluding specific class IDs
result <- ifcb_count_mat_annotations("path/to/manual_folder",
                                     "path/to/class2use_file",
                                     skip_class = c(99, 100))
print(result)

# Count annotations excluding a specific class name
result <- ifcb_count_mat_annotations("path/to/manual_folder",
                                     "path/to/class2use_file",
                                     skip_class = "unclassified")
print(result)
}