nesting.roi {espadon}

Restrict volume to RoI

Description

The nesting.roi function restricts a "volume" class object to the rectangular parallelepiped circumscribed to the chosen RoI.

Usage

nesting.roi(
  obj,
  struct,
  roi.name = NULL,
  roi.sname = NULL,
  roi.idx = NULL,
  xyz.margin = c(0, 0, 0),
  vol.restrict = FALSE,
  T.MAT = NULL,
  alias = "",
  description = NULL,
  ...
)

Arguments

obj

object of class volume or mesh.

struct

"struct" class object.

roi.name

Vector of exact names of the RoI in the struct object. By default roi.name = NULL. See Details.

roi.sname

Names or parts of names of the RoI in the struct object. By default roi.sname = NULL. See Details.

roi.idx

Index of the RoI that belong to the struct object. By default roi.idx = NULL. See Details.

xyz.margin

Vector of length 3, representing the distances in mm to be added to the x, y and z directions of the rectangular parallelepiped circumscribed to the chosen RoI, in the cutting planes frame of reference. By default xyz.margin = c (0, 0, 0).

vol.restrict

Boolean. If vol.restrict = TRUE, the rectangular parallelepiped circumscribed to the chosen RoI, enlarged by xyz.margin cannot exceed the initial volume.

T.MAT

"t.mat" class object, created by load.patient.from.dicom, load.patient.from.Rdcm or load.T.MAT. If T.MAT = NULL, struct$ref.pseudo must be equal to obj$ref.pseudo.

alias

Character string, $alias of the created object.

description

Character string, describing the the created object. If description = NULL, it will be that of the obj, plus "restricted to" the selected RoI.

...

Additional arguments vol (depracated), replaced by obj.

Details

If roi.name, roi.sname, and roi.idx are all set to NULL, all RoI are selected.

Value

Returns a "volume" class object, in which 3D volume is limited to the rectangular parallelepiped circumscribed to the chosen RoI, increased by the requested margins.

See Also

add.margin, nesting.cube and nesting.bin.

Examples

# loading of toy-patient objects (decrease dxyz for  better result)
step <- 4
patient <- toy.load.patient (modality = c("ct", "rtstruct"), 
                             roi.name = "brain", dxyz = rep (step, 3))
CT <- patient$ct[[1]]
S <- patient$rtstruct[[1]]

CT.brain <- nesting.roi (CT, S, roi.sname = "brain")
CT.brain.with.margin <- nesting.roi (CT, S, roi.sname = "brain",
                                         xyz.margin = c (10,10,10))

# display at the center of gravity of the cerebellum Gz
Gz <- S$roi.info [grep("^brain",S$roi.info$roi.pseudo),]$Gz
display.plane (bottom = CT.brain, view.coord = Gz,
               struct = S, bottom.col = pal.RVV (1000),
               bottom.breaks = seq (-1000, 1000, length.out = 1001),
               bg = "#00ff00",  interpolate  = FALSE, legend.shift = -20)
display.plane (bottom = CT.brain.with.margin,view.coord = Gz,
               struct = S,  bottom.col = pal.RVV (1000),
               bottom.breaks = seq(-1000, 1000, length.out = 1001),
               bg = "#00ff00", interpolate  = FALSE, legend.shift = -20)