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Import EBImage Object into BioThermR

Source: R/io.r
from_EBImage.Rd

Converts an 'EBImage' class object back into the 'BioThermR' framework. This function is designed to integrate results from external morphological operations (e.g., watershed segmentation, filtering) back into the standard BioThermR analytical workflow.

Usage

from_EBImage(
  eb_img,
  template_obj = NULL,
  name = "Imported_EBImage",
  mask_zero = FALSE
)

Arguments

eb_img

An Image object (from the 'EBImage' package).

template_obj

Optional. An existing 'BioThermR' object to update. Providing this ensures that original metadata (like filenames and original raw data) is retained. Default is NULL.

name

String. The name assigned to the new object (used only if template_obj is NULL). Default is "Imported_EBImage".

mask_zero

Logical. If TRUE, converts values of 0 in the imported matrix to NA. This is particularly useful when importing binary masks where 0 represents the background, as BioThermR uses NA to exclude background pixels from statistical calculations. Default is FALSE.

Value

A 'BioThermR' object with the imported matrix stored in the processed slot.

Details

This function supports two modes:

  • Update Mode: If template_obj is provided, the input image replaces the processed matrix of the template. Metadata (filename, path) is preserved. Statistics are reset to NULL as the data has changed.

  • Create Mode: If template_obj is NULL, a new 'BioThermR' object is created from scratch using the input matrix.

If the input eb_img has more than 2 dimensions (e.g., color/RGB), only the first channel is utilized, and a warning is issued.