BioThermR (version 0.1.0)

roi_filter_threshold: Filter Thermal Image by Temperature Thresholds

Description

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)

Value

A 'BioThermR' object with the processed matrix updated.

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).

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

# Load raw data
img_obj <- system.file("extdata", "C05.raw", package = "BioThermR")
img <- read_thermal_raw(img_obj)

# Simple background removal: Keep everything above 24 degrees
img <- roi_filter_threshold(img, threshold = c(24, Inf))