ifcb_zip_matlab: Create a Zip Archive of Manual MATLAB Files
In iRfcb: Tools for Managing Imaging FlowCytobot (IFCB) Data

ifcb_zip_matlab

R Documentation

Create a Zip Archive of Manual MATLAB Files

Description

This function creates a zip archive containing specified files and directories for manually annotated IFCB images, organized into a structured format suitable for distribution or storage. The MATLAB files are generated by the ifcb-analysis repository (Sosik and Olson 2007). The zip archive can be used to submit IFCB data to repositories like in the SMHI IFCB Plankton Image Reference Library (Torstensson et al., 2024).

Usage

ifcb_zip_matlab(
  manual_folder,
  features_folder,
  class2use_file,
  zip_filename,
  data_folder = NULL,
  readme_file = NULL,
  matlab_readme_file = NULL,
  email_address = "",
  version = "",
  print_progress = TRUE,
  feature_recursive = TRUE,
  manual_recursive = FALSE,
  data_recursive = TRUE,
  quiet = FALSE
)

Arguments

`manual_folder`	The directory containing `.mat` files to be included in the zip archive.
`features_folder`	The directory containing `.csv` files, including subfolders, to be included in the zip archive.
`class2use_file`	The path to the file (class2use_file) that will be renamed and included in the 'config' directory of the zip archive.
`zip_filename`	The filename for the zip archive to be created.
`data_folder`	Optionally, the directory containing additional data files (`.roi`, `.adc`, `.hdr`) to be included in the zip archive.
`readme_file`	Optionally, the path to a README file that will be updated with metadata and included in the zip archive.
`matlab_readme_file`	Optionally, the path to a MATLAB README file whose content will be appended to the end of the README file in the zip archive.
`email_address`	The email address to be included in the README file for contact information.
`version`	Optionally, the version number to be included in the README file.
`print_progress`	A logical value indicating whether to print progress bar. Default is TRUE.
`feature_recursive`	Logical. If TRUE, the function will search for feature files recursively within the `feature_folder`. Default is TRUE.
`manual_recursive`	Logical. If TRUE, the function will search for MATLAB files recursively within the `manual_folder`. Default is FALSE.
`data_recursive`	Logical. If TRUE, the function will search for data files recursively within the `data_folder` (if provided). Default is TRUE.
`quiet`	Logical. If TRUE, suppresses messages about the progress and completion of the zip process. Default is FALSE.

Details

This function performs the following operations:

Lists .mat files from manual_folder.
Lists .csv files from features_folder (including subfolders).
Lists .roi, .adc, .hdr files from data_folder if provided.
Copies listed files to temporary directories (manual_dir, features_dir, data_dir, config_dir).
Renames and copies class2use_file to config_dir as class2use.mat.
Updates readme_file with metadata (if provided) and appends PNG image statistics and MATLAB README content.
Creates a manifest file (MANIFEST.txt) listing all files in the zip archive.
Creates a zip archive (zip_filename) containing all copied and updated files.
Cleans up temporary directories after creating the zip archive.

Value

No return value. This function creates a zip archive containing the specified files and directories.

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. Torstensson, Anders; Skjevik, Ann-Turi; Mohlin, Malin; Karlberg, Maria; Karlson, Bengt (2024). SMHI IFCB Plankton Image Reference Library. SciLifeLab. Dataset. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.17044/scilifelab.25883455")}

Examples

## Not run: 
ifcb_zip_matlab("path/to/manual_files", "path/to/feature_files",
                "path/to/class2use.mat", "output_zip_archive.zip",
                data_folder = "path/to/data_files",
                readme_file = system.file("exdata/README-template.md", package = "iRfcb"),
                matlab_readme_file = system.file("inst/exdata/MATLAB-template.md",
                                                 package = "iRfcb"),
                email_address = "example@email.com",
                version = "1.0")

## End(Not run)

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