Reconstruct a QSM and all of its variables from the minimum amount of required data. The required variables are the cylinder id, parent id, 3d information and the radius. The cylinder can be defined in 3d space with either a combination of the start and end points, or the start, axis, and length. Branch and branch order information are optional. If not provided, the branches and orders are defined recursively using the growth length.
Usage
reconstruct_qsm(
cylinder,
id,
parent,
radius,
start_x,
start_y,
start_z,
end_x = NULL,
end_y = NULL,
end_z = NULL,
axis_x = NULL,
axis_y = NULL,
axis_z = NULL,
length = NULL,
branch = NULL,
branch_order = NULL,
metrics = FALSE
)Arguments
- cylinder
QSM cylinder data frame
- id
cylinder ids
- parent
cylinder parent ids
- radius
cylinder radius
- start_x
cylinder start x position
- start_y
cylinder start y position
- start_z
cylinder start z position
- end_x
cylinder end x position
- end_y
cylinder end y position
- end_z
cylinder end z position
- axis_x
cylinder end x position
- axis_y
cylinder end y position
- axis_z
cylinder end z position
- length
cylinder length
- branch
optional cylinder branch id
- branch_order
optional cylinder branch order
- metrics
Calculate tree metrics. Defaults to FALSE.
Examples
file <- system.file("extdata/QSM.csv", package = "rTwig")
qsm <- reconstruct_qsm(
cylinder = read.csv(file),
id = "ID", parent = "parentID", radius = "radius",
start_x = "startX", start_y = "startY", start_z = "startZ",
end_x = "endX", end_y = "endY", end_z = "endZ"
)
#> Updating Cylinder Ordering
#> Building Cylinder Network
#> Calculating Growth Length
#> Calculating Reverse Branch Order
#> Calculating Total Children
#> Calculating Alternate Branch Numbers
#> Calculating Branch Segments
#> Calculating Path Metrics
plot_qsm(qsm)
#> Plotting Cylinders
#> Panning plot on rgl device: 1