ifcb_get_mat_variable: Get Classes from a MAT File

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

Get Classes from a MAT File

Description

This function reads a specified variable from a .mat file generated by the ifcb-analysis repository (Sosik and Olson 2007). It can be used, for example, to extract lists of classes from the file.

Usage

ifcb_get_mat_variable(
  mat_file,
  variable_name = "class2use",
  use_python = FALSE
)

Arguments

mat_file	A character string specifying the path to the .mat file containing the class information.
variable_name	A character string specifying the variable name in the .mat file that contains the class information. The default is "class2use". Other examples include "class2use_manual" from a manual file, or "class2use_auto" for a class list used for automatic assignment. You can find available variable names using the function ifcb_get_mat_names.
use_python	Logical. If TRUE, attempts to read the .mat file using a Python-based method. Default is FALSE.

Details

If use_python = TRUE, the function tries to read the .mat file using ifcb_read_mat(), which relies on SciPy. This approach may be faster than the default approach using R.matlab::readMat(), especially for large .mat files. To enable this functionality, ensure Python is properly configured with the required dependencies. You can initialize the Python environment and install necessary packages using ifcb_py_install().

If use_python = FALSE or if SciPy is not available, the function falls back to using R.matlab::readMat().

Value

A character vector of class names.

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_get_mat_names https://github.com/hsosik/ifcb-analysis

Examples

# Example .mat file included in the package
mat_file <- system.file("exdata/example.mat", package = "iRfcb")

# Get class names from a class2use file
classifier_name <- ifcb_get_mat_variable(mat_file, "classifierName")
print(classifier_name)

# Get class names from a classifier file
class2useTB <- ifcb_get_mat_variable(mat_file, "class2useTB")
print(class2useTB)

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