ifcb_replace_mat_values: Replace Values in MATLAB Classlist

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

Replace Values in MATLAB Classlist

Description

This function replaces a target class ID with a new ID in MATLAB classlist files, generated by the code in the ifcb-analysis repository (Sosik and Olson 2007).

Usage

ifcb_replace_mat_values(
  manual_folder,
  out_folder,
  target_id,
  new_id,
  column_index = 1,
  do_compression = TRUE
)

Arguments

manual_folder	A character string specifying the path to the folder containing MAT classlist files to be updated.
out_folder	A character string specifying the path to the folder where updated MAT classlist files will be saved.
target_id	The target class ID to be replaced.
new_id	The new class ID to replace the target ID.
column_index	An integer value specifying which classlist column to edit. Default is 1 (manual).
do_compression	A logical value indicating whether to compress the .mat file. Default is TRUE.

Details

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

Value

This function does not return any value; it updates the classlist files in the specified 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_py_install https://github.com/hsosik/ifcb-analysis

Examples

## Not run: 
# Initialize a python session if not already set up
ifcb_py_install()

# Replace class ID 99 with 1 in .mat classlist files
ifcb_replace_mat_values("output/manual", "output/manual", 99, 1, column_index = 1)

## End(Not run)

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