ifcb_summarize_class_counts: Count Cells from TreeBagger Classifier Output

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

Count Cells from TreeBagger Classifier Output

Description

This function summarizes class results for a series of classifier output files and returns a summary data list.

Usage

ifcb_summarize_class_counts(
  classpath_generic,
  hdr_folder,
  year_range,
  use_python = FALSE
)

Arguments

classpath_generic	Character string specifying the location of the classifier output files. The path should include 'xxxx' in place of the 4-digit year (e.g., 'classxxxx_v1/').
hdr_folder	Character string specifying the directory where the data (hdr files) are located. This can be a URL for web services or a full path for local files.
year_range	Numeric vector specifying the range of years (e.g., 2013:2014) to process.
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 list containing the following elements:

class2useTB	Classes used in the TreeBagger classifier.
classcountTB	Counts of each class considering each target placed in the winning class.
classcountTB_above_optthresh	Counts of each class considering only classifications above the optimal threshold for maximum accuracy.
ml_analyzedTB	Volume analyzed for each file.
mdateTB	Dates associated with each file.
filelistTB	List of files processed.
classpath_generic	The generic classpath provided as input.
classcountTB_above_adhocthresh (optional)	Counts of each class considering only classifications above the adhoc threshold.
adhocthresh (optional)	The adhoc threshold used for classification.

Examples

## Not run: 
ifcb_summarize_class_counts('path/to/class/classxxxx_v1/',
                            'path/to/data/', 2014)

## End(Not run)

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