Merge IFCB Manual Classification Data

This function merges two sets of manual classification data by combining and aligning class labels from a base set and an additional set of classifications. The merged .mat data can be used with the code in the ifcb-analysis repository (Sosik and Olson 2007).

Usage

ifcb_merge_manual(
  class2use_file_base,
  class2use_file_additions,
  class2use_file_output = NULL,
  manual_folder_base,
  manual_folder_additions,
  manual_folder_output,
  do_compression = TRUE,
  temp_index_offset = 50000,
  skip_class = NULL,
  quiet = FALSE
)

Arguments

class2use_file_base: Character. Path to the class2use file of the base manual classifications. The base set contains the original manual classifications list that form the foundation for merging.
class2use_file_additions: Character. Path to the class2use file of the additions manual classifications. The additions set contains additional classifications that need to be merged with the base set. Class labels from the class2use_file_additions that are not already included in the class2use_file_base will be added to generate the class2use_file_output.
class2use_file_output: Character. Path where the merged class2use file will be saved. If NULL, the merged file will be stored in the same directory as class2use_file_base. Default is NULL.
manual_folder_base: Character. Path to the folder containing the base set of manual classification .mat files.
manual_folder_additions: Character. Path to the folder containing the additions set of manual classification .mat files.
manual_folder_output: Character. Path to the output folder where the merged classification files will be stored.
do_compression: A logical value indicating whether to compress the .mat file. Defaults to TRUE.
temp_index_offset: Numeric. A large integer used to generate temporary indices during the merge process. Default is 50000.
skip_class: Character. A vector of class names to skip from the class2use_file_additions during the merge process. Default is NULL.
quiet: Logical. If TRUE, suppresses output messages. Default is FALSE.

Value

No return value. Outputs the combined class2use file in the same folder as class2use_file_base is located or at a user-specified location, and merged .mat files into the output folder.

Details

Python must be installed to use this function. The required python packages can be installed in a virtual environment using ifcb_py_install().

The base set consists of the original classifications that are used as a reference for the merging process. The additions set contains the additional classifications that need to be merged with the base set. When merging, unique class names from the additions set that are not present in the base set are appended.

The function works by aligning the class labels from the additions set with those in the base set, handling conflicts by using a temporary index system. It copies .mat files from both the base and additions folders into the output folder, while adjusting indices and and class names for the additions.

Note that the maximum limit for uint16 is 65,535, so ensure that temp_index_offset remains below this value.

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) { # \dontrun{
ifcb_merge_manual("path/to/class2use_base.mat", "path/to/class2use_additions.mat",
                  "path/to/class2use_combined.mat", "path/to/manual/base_folder",
                  "path/to/manual/additions_folder", "path/to/manual/output_folder",
                  do_compression = TRUE, temp_index_offset = 50000, quiet = FALSE)
} # }