Run the Real Twig correction and calculate tree metrics for supported QSM formats.
Usage
run_rtwig(
filename,
twig_radius,
metrics = TRUE,
version = NULL,
smooth = TRUE,
standardise = FALSE,
broken_branch = TRUE,
...
)Arguments
- filename
file path to QSM (.mat, .csv, .json)
- twig_radius
Twig radius in millimeters
- metrics
Calculate tree metrics. Defaults to TRUE.
- version
If using a specific version of TreeQSM, the user can specify the version (e.g. 2.4.1, 2.0, etc.).
- smooth
Defaults to TRUE if using TreeQSM. Can be set to FALSE.
- standardise
Standardise QSM cylinder data. Defaults to FALSE, but can be set to TRUE.
- broken_branch
Enable or disable the broken branch filter. Defaults to TRUE.
- ...
Additional arguments allowing standardise and standardize to be used as synonyms.
Examples
## TreeQSM
file <- system.file("extdata/QSM.mat", package = "rTwig")
qsm <- run_rtwig(file, twig_radius = 4.23)
#> Importing TreeQSM
#> 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
#> Smoothing QSM
#> Generating Paths
#> Filtering Paths
#> Modeling Paths
#> Updating Radii
#> Calculating Branch Metrics
#> Calculating Segment Metrics
#> Calculating Tree Metrics
#> Generating Point Cloud
#> Calculating Crown Metrics
#> Calculating Tree Distributions
#> Calculating Branch Distributions
#> Calculating Segment Distributions
#> Calculating Stem Taper
#> Calculating Spreads
#> Calculating Alternate Branch Metrics
str(qsm$cylinder)
#> Classes ‘tidytable’, ‘tbl’, ‘data.table’ and 'data.frame': 1136 obs. of 34 variables:
#> $ length : num 0.09392 0.07216 0.06654 0.00938 0.06795 ...
#> $ start.x : num 0.768 0.769 0.768 0.769 0.769 ...
#> $ start.y : num -16.4 -16.4 -16.4 -16.3 -16.3 ...
#> $ start.z : num 254 254 254 254 254 ...
#> $ axis.x : num 0.009949 -0.022059 0.016224 -0.000391 0.012068 ...
#> $ axis.y : num 0.091165 0.019722 0.034392 -0.000295 0.023483 ...
#> $ axis.z : num 0.996 1 0.999 1 1 ...
#> $ end.x : num 0.769 0.768 0.769 0.769 0.77 ...
#> $ end.y : num -16.4 -16.4 -16.3 -16.3 -16.3 ...
#> $ end.z : num 254 254 254 254 254 ...
#> $ added : num 0 0 0 0 0 0 0 0 0 0 ...
#> $ BranchOrder : int 0 0 0 0 0 0 0 0 0 0 ...
#> $ reverseBranchOrder : num 20 20 20 20 20 20 20 20 20 20 ...
#> $ PositionInBranch : int 1 2 3 4 5 6 7 8 9 10 ...
#> $ segment : int 1 1 1 1 1 1 1 1 1 1 ...
#> $ parentSegment : int 0 0 0 0 0 0 0 0 0 0 ...
#> $ mad : num 0.00072 0.000538 0.000523 0.000335 0.000438 ...
#> $ SurfCov : num 0.875 1 1 1 1 1 1 1 1 1 ...
#> $ UnmodRadius : num 0.0465 0.0454 0.0442 0.0437 0.0429 ...
#> $ OldRadius : num 0.0465 0.0454 0.0442 0.0437 0.0429 ...
#> $ growthLength : num 32.8 32.7 32.6 32.6 32.6 ...
#> $ branch : int 1 1 1 1 1 1 1 1 1 1 ...
#> $ branch_alt : int 0 0 0 0 0 0 0 0 0 0 ...
#> $ parent : num 0 1 2 3 4 5 6 7 8 9 ...
#> $ extension : int 1 2 3 4 5 6 7 8 9 10 ...
#> $ totalChildren : int 1 1 1 1 1 1 1 1 1 1 ...
#> $ index : int 1 2 3 4 5 6 7 8 9 10 ...
#> $ distanceFromBase : num 0 0.0722 0.1387 0.1481 0.216 ...
#> $ distanceToTwig : num 3.4 3.31 3.24 3.17 3.16 ...
#> $ reversePipeAreaBranchorder : int 82 82 82 82 82 82 82 82 82 82 ...
#> $ reversePipeRadiusBranchorder: num 9.06 9.06 9.06 9.06 9.06 ...
#> $ vesselVolume : num 279 271 266 260 259 ...
#> $ radius : num 0.0465 0.0454 0.0442 0.0437 0.0429 ...
#> $ modified : num 0 0 0 0 0 0 0 0 0 0 ...
#> - attr(*, ".internal.selfref")=<externalptr>