removeSmallObjects-ms.image-method: Remove binary ROI objects smaller than user-defined number of...

In paoloinglese/SPUTNIK: Spatially Automatic Denoising for Imaging Mass Spectrometry Toolkit

Remove binary ROI objects smaller than user-defined number of pixels

Description

Remove binary ROI objects smaller than user-defined number of pixels

Usage

## S4 method for signature 'ms.image'
removeSmallObjects(object, threshold = 5, border = 3)

Arguments

object	ms.image-class object. See msImage.
threshold	numeric. Smallest number of connected pixels.
border	numeric (default = 3). Size of the empty border to add before detecting the connected objects. The border is removed at the end of the process. If 'border = 0', no border is added.

Value

ms.image-class object after filtering.

Examples

library(SPUTNIK)

fakeBinImage <- matrix(0, 100, 100)
fakeBinImage[sample(prod(dim(fakeBinImage)), 2000)] <- 1

fakeBinMsImage <- msImage(values = fakeBinImage, name = "ROI", scale = FALSE)

# Remove the objects with a number of connected pixels smaller than 5
fakeBinMsImage <- removeSmallObjects(fakeBinMsImage, threshold = 5)

paoloinglese/SPUTNIK documentation built on April 18, 2024, 8:56 p.m.