segment_annual_shoots: Annual shoot segmentation in tree skeleton

In aRchi: Quantitative Structural Model ('QSM') Treatment for Tree Architecture

Annual shoot segmentation in tree skeleton

Description

Segment the annual shoots in a tree skeleton based on the detection of the branching patterns created by acrotony.

Usage

segment_annual_shoots(aRchi, tree_age, segment_reiterations)

## S4 method for signature 'aRchi'
segment_annual_shoots(aRchi, tree_age, segment_reiterations)

Arguments

aRchi	an object of class aRchi containing at least a QSM.
tree_age	numeric, optional. The tree age. Helps to achieve more robust segmentation.
segment_reiterations	list of numeric values. The parameters to segment traumatic reiterations based on their age difference with the bearer annual shoot and their elevation. The list must have the following form: list(age_difference, elevation_angle) where age_difference and elevation_angle are numeric vectors. NOTE the elevation angle is defined relative to the zenith.

Value

The input aRchi file with an additional field in the QSM slot being the segmented annual shoots. NOTE that annual shoot = 1 correspond to the last growing season. If traumatic reiteration segmentation was achieved, an additional field labeling cylinders that belong to a reiteration is added.

References

Lecigne, B., Delagrange, S., & Taugourdeau, O. (2021). Annual Shoot Segmentation and Physiological Age Classification from TLS Data in Trees with Acrotonic Growth. Forests, 12(4), 391. https://doi.org/10.3390/f12040391

Examples

# import aRchi file
aRchi=system.file("extdata","Tree_2.aRchi",package = "aRchi")
aRchi = aRchi::read_aRchi(aRchi)

# smooth skeleton
aRchi = smooth_skeleton(aRchi)

# segment annual shoots
aRchi = aRchi::segment_annual_shoots(aRchi,tree_age = 13)

plot(aRchi,color="annual_shoots",bg = "white")

aRchi documentation built on Sept. 3, 2022, 9:06 a.m.