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Prune QSM

Source: R/prune_qsm.R
prune_qsm.Rd

Efficiently prune a QSM. The user can prune by cylinder, branch, and segment ids, or by height or diameter classes, individually, or all at the same time, and return either the pruned data, the remaining data, or a binary index of which cylinders are pruned.

Usage

prune_qsm(
  cylinder,
  cylinder_ids = NULL,
  branch_ids = NULL,
  segment_ids = NULL,
  height_m = NULL,
  diameter_cm = NULL,
  invert = FALSE,
  index = FALSE
)

Arguments

cylinder

QSM cylinder data frame

cylinder_ids

A single or vector of cylinder ids. Everything connected above the cylinder is pruned.

branch_ids

A single or vector of branch ids. Everything connected to the branch is pruned.

segment_ids

A single or vector of segment ids. Everything connected above the segment is pruned.

height_m

Height class in meters below which all cylinders are pruned. Valid inputs are numeric to one decimal.

diameter_cm

Branch diameter class in centimeters below which all cylinders are pruned. Valid inputs are numeric to one decimal.

invert

Return the remaining or pruned data. Defaults to TRUE (the remaining data), but can be set to FALSE.

index

Returns a column index called pruning indicating if the cylinder is pruned (1) or un-pruned (0). Defaults to FALSE, but can be set to TRUE.

Value

a data frame

Examples


## Load QSM
file <- system.file("extdata/QSM.mat", package = "rTwig")
qsm <- import_qsm(file)
#> Importing TreeQSM
cylinder <- qsm$cylinder
cylinder <- update_cylinders(cylinder)
#> Updating Cylinder Ordering
#> Calculating Total Children
#> Building Cylinder Network
#> Caching Network
#> Verifying Topology
#> Calculating Growth Length
#> Calculating Reverse Branch Order
#> Calculating Branch Segments
#> Calculating Alternate Branch Numbers
#> Calculating Path Metrics

## Pruning Index
prune1 <- prune_qsm(cylinder, height_m = 2, index = TRUE)
#> Pruning QSM
plot_qsm(prune1, color = pruning, palette = "blue2red")
#> Plotting Cylinders
#> Panning plot on rgl device: 1

## Remaining
prune2 <- prune_qsm(cylinder, height_m = 2, invert = FALSE)
#> Pruning QSM
plot_qsm(prune2)
#> Plotting Cylinders
#> Panning plot on rgl device: 1

## Pruned
prune3 <- prune_qsm(cylinder, height_m = 2, invert = TRUE)
#> Pruning QSM
plot_qsm(prune3)
#> Plotting Cylinders
#> Panning plot on rgl device: 1