read_tree_qsm: Read a TreeQSM

In lmterryn/ITSMe: Individual Tree Structural Metrics

Read a TreeQSM

Description

Reads a TreeQSM matlab file (.mat) and returns its' components in a list and optionally saves the TreeQSM components into the global environment. When multiple TreeQSMs are in the matlab file they are read into a list of qsms (which are a list of components).

Usage

read_tree_qsm(path, version = "2.4.1", global = FALSE)

Arguments

path	A character with the path to the TreeQSM mat file. This file contains one or multiple QSM(s) produced with https://github.com/InverseTampere/TreeQSM in matlab.
version	A character indicating the version of TreeQSM that was used to produce the TreeQSMs (Default = "2.4.1"). Other possible versions are "2.4.0", "2.0", "2.3.0", "2.3.1" and "2.3.2".
global	Logical (default=FALSE), indicates if TreeQSM components (or different qsms) should be read into the global environment.

Details

Initial reading of the .mat file uses readMat. TreeQSM versions older than 2.4.0 are converted to the 2.4.x structure, where the value of attributes not found in the older version is set NA.

Value

Returns a list with the TreeQSM components (cylinder, branch, treedata and triangulation) or a list of qsms (qsm_1, qsm_2, etc) wich are a list of the components. And optionally (global=TRUE) saves them into the global environment.

Examples

## Not run: 
# Read a TreeQSM.mat file with default settings
qsm <- read_tree_qsm(QSM_path = "path/to/TreeQSM.mat")
cylinder_data <- qsm$cylinder
# Read a TreeQSM.mat file of version 2.0
qsm <- read_tree_qsm(QSM_path = "path/to/TreeQSM.mat", version = "2.0")
# Read a TreeQSM.mat file with into the global environment
qsm <- read_tree_qsm(QSM_path = "path/to/TreeQSM.mat", global = TRUE)
cylinder_data <- cylinder
# Read a TreeQSM.mat file of multiple qsms
qsms <- read_tree_qsm(QSM_path = "path/to/TreeQSMs.mat")
cylinder_data_of_qsm_1 <- qsms$qsm1$cylinder

## End(Not run)

lmterryn/ITSMe documentation built on Feb. 4, 2025, 2:21 a.m.