vertexFindPeaks: Vertex find peaks

In Mouse-Imaging-Centre/RMINC: Statistical Tools for Medical Imaging NetCDF (MINC) Files

Vertex find peaks

Description

Find extrema of set of values given a connectivity graph

Usage

vertexFindPeaks(
  data_map,
  graph,
  mindist = 1,
  direction = c("both", "positive", "negative"),
  threshold = 0,
  output = c("mask", "indices")
)

Arguments

data_map	A vector or text file of values to search for peaks
graph	An igraph object describing the connectivity, in most cases this will be a mesh graph produced by obj_to_graph
mindist	the search radius (in number of neighbours) to consider when finding a peak. A node is considered a peak if it is more extreme than any element in it's neighbourhood up to mindist edges away
direction	Either positive, negative, or both indicating whether to consider maxima, minima or both.
threshold	threshold above or below which to consider peaks. In the both direction case a two element vector may be passed indicating positive and negative thresholds respectively. If a single element is passed in the both direction case, it is treated as c(threshold, -threshold). Defaults to 0.
output	Either mask or indices, indicating whether a logical mask or a vector of indices is desired.

Details

Note that if coordinates of peaks are desired, they can be accessed from the parent bic_obj by obj$vertex_matrix[,peaks]

Value

Either a logical vector indicating peaks or a vector of peak indices determined by output

Mouse-Imaging-Centre/RMINC documentation built on Feb. 24, 2025, 1:22 a.m.