get_persistence_diagrams: get_persistence_diagrams

In LOMAR: Localization Microscopy Data Analysis

get_persistence_diagrams

Description

Compute persistence diagrams for a list of point sets. By default, compute persistent homology from the Vietoris-Rips filtration. If use.dtm is TRUE, compute instead the persistent homology of the sublevel set of the distance to measure evaluated over a grid.

Usage

get_persistence_diagrams(
  point.sets = NULL,
  maxdimension = NULL,
  maxscale = NULL,
  use.dtm = FALSE,
  m0 = NULL,
  grid.by = NULL,
  ncpu = 1
)

Arguments

point.sets	list of point sets, each as a data frame with columns x,y,z
maxdimension	maximum dimension of the homological features to be computed
maxscale	limit of the Vietoris-Rips filtration
use.dtm	logical (default: FALSE), whether to use the distance to measure function
m0	parameter for the dtm function
grid.by	vector of space between points of the grid for the dtm function along each dimension
ncpu	number of parallel threads to use for computation

Value

a list of persistence diagrams as n x 3 matrices. Each row is a topological feature and the columns are dimension, birth and death of the feature.

Examples

PS <- list(data.frame(x = c(2.4,-6.9,4.6,-0.7,-3.3,-4.9,-3.5,-3.5,4.2,-7),
                      y = c(5.7,1.9,4.8,3.4,-3,-2.1,7.2,1.8,6.1,-1.6),
                      z = c(2.7,-0.1,-0.7,-0.6,0.4,-1.5,-0.6,-0.9,2.2,0.7)),
           data.frame(x = c(0,0,3.1,-5.6,-5,-7.4,-0.7,-7.7,-6.7,4,4.2,0.2,5.8,3.9,3.9),
                      y = c(6.3,-6.1,-3.5,4.6,-4.1,0.3,8.8,-2.3,2.9,3.7,-1.4,-3.9,5.5,-1.2,-6.7),
                      z = c(-1.5,1.7,-0.4,-1.4,1.8,1.7,-0.9,-1.8,-0.5,1.7,1.3,0.5,-1.4,1.6,-0.1)))
Diags <- get_persistence_diagrams(point.sets = PS, maxdimension = 1, maxscale = 5, ncpu = 1)

LOMAR documentation built on March 18, 2022, 6:05 p.m.