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Filter Thermal Image by Temperature Thresholds

Source: R/roi.r
roi_filter_threshold.Rd

Masks the thermal image by retaining only pixels that fall within a specified temperature window. Pixels outside this range are set to NA (background).

Usage

roi_filter_threshold(img_obj, threshold, use_processed = FALSE)

Arguments

img_obj

A 'BioThermR' object.

threshold

Numeric vector of length 2, e.g., c(22, 38). Defines the inclusive temperature range [min, max] to keep. Use Inf for open upper bounds (e.g., c(25, Inf) keeps everything above 25 degrees Celsius).

use_processed

Logical.

  • If FALSE (default): The filter is applied to the raw matrix, discarding any previous masks.

  • If TRUE: The filter is applied to the processed matrix, allowing for cumulative masking (e.g., refining an Otsu segmentation).

Value

A 'BioThermR' object with the processed matrix updated.

Details

This is the most fundamental segmentation method for thermal images. Since animals are typically warmer than their environment, a simple low-pass filter (e.g., keep > 22 degrees Celsius) is often sufficient to separate the subject from the cage. Open boundaries can be defined using Inf or -Inf.

Examples

if (FALSE) { # \dontrun{
# Simple background removal: Keep everything above 24 degrees
obj <- roi_filter_threshold(obj, threshold = c(24, Inf))

# Specific physiological window: Keep between 30 and 39 degrees
obj <- roi_filter_threshold(obj, threshold = c(30, 39))
} # }