BioThermR (version 0.1.0)

as_EBImage: Convert BioThermR Object to EBImage Object

Description

Extracts the thermal matrix (raw or processed) from a 'BioThermR' object and converts it into an 'EBImage' class object. This conversion is essential for applying advanced morphological operations (e.g., thresholding, watershed, labeling) provided by the 'EBImage' package.

Usage

as_EBImage(img_obj, use_processed = TRUE, replace_na = 0, normalize = FALSE)

Value

An Image object (defined in the 'EBImage' package).

Arguments

img_obj

A 'BioThermR' object.

use_processed

Logical. If TRUE (default), uses the 'processed' matrix (which might already have masks applied). If FALSE, uses the 'raw' temperature matrix.

replace_na

Numeric. The value to replace NAs with, as 'EBImage' does not support missing values. Default is 0 (typically treated as background).

normalize

Logical. If TRUE, scales the matrix values linearly to the range [0, 1]. This is highly recommended for visualization or standard thresholding algorithms (like Otsu) in 'EBImage'. Default is FALSE (preserves actual temperature values).

Examples

# \donttest{
# Load data
mat <- matrix(runif(160*120, 20, 40), nrow = 120, ncol = 160)
obj <- create_BioThermR(mat, name = "Simulation_01")

# Convert to EBImage format with normalization (for thresholding)
eb_norm <- as_EBImage(obj, normalize = TRUE)

# Convert preserving temperature values (for calculation)
eb_temp <- as_EBImage(obj, normalize = FALSE)
# }