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Create a Manual Classification MAT File

Source: R/ifcb_create_manual_file.R
ifcb_create_manual_file.Rd

Generates a .mat file for IFCB data with classification structure using a specified number of ROIs, class names. The output_file generated by this function is compatible with the code in the ifcb-analysis repository (Sosik and Olson 2007).

Usage

ifcb_create_manual_file(
  roi_length,
  class2use,
  output_file,
  classlist = 1,
  do_compression = TRUE
)

Arguments

roi_length

Integer. The number of rows in the class list (number of ROIs).

class2use

Character vector. The names of the classes to include in the class2use_manual field of the MAT file.

output_file

Character. The path where the output MAT file will be saved.

classlist

Integer or numeric vector. Defines the values for the second column of the class list, typically representing the manual classification labels:

  • If a single value is provided, all rows will be assigned this value. For example, all ROIs can be assigned to class index 1 (default), which typically represents the unclassified category.

  • If a numeric vector of the same length as roi_length is provided, the corresponding values will be used per row.

do_compression

A logical value indicating whether to compress the .mat file. Default is TRUE.

Value

No return value. This function is called for its side effects. The created MAT file is saved at the specified output_file location.

Details

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

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{
# Initialize a python session if not already set up
ifcb_py_install()

# Create a MAT file with 100 ROIs, using a vector of class names, and save it to "output.mat"
ifcb_create_manual_file(roi_length = 100,
                        class2use = c("unclassified", "Aphanizomenon_spp"),
                        output_file = "output.mat")

# Create a MAT file with 50 unclassified ROIs (1) and 50 Aphanizomenon_spp (2) ROIs
ifcb_create_manual_file(roi_length = 100,
                        class2use = c("unclassified", "Aphanizomenon_spp"),
                        output_file = "output.mat",
                        classlist = c(rep(1, 50), rep(2, 50)))
} # }