bin.from.roi: Creation of a binary volume according to RoI

In espadon: Easy Study of Patient DICOM Data in Oncology

Creation of a binary volume according to RoI

Description

The bin.from.roi function creates a "volume" class object, of modality "binary" or "weight", by selecting the voxels defined by the RoI.

Usage

bin.from.roi(
  vol,
  struct,
  roi.name = NULL,
  roi.sname = NULL,
  roi.idx = NULL,
  T.MAT = NULL,
  within = TRUE,
  alias = "",
  description = NULL,
  modality = c("binary", "weight"),
  ...
)

Arguments

vol	"volume" class object.
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	Vector of names or parts of names of the RoI in the struct object. By default roi.sname = NULL. See Details.
roi.idx	Vector of indices of the RoI that belong to the struct object. By default roi.idx = NULL. See Details.
T.MAT	"t.mat" class object, created by load.patient.from.Rdcm or load.T.MAT. If T.MAT = NULL, struct$ref.pseudo must be equal to vol$ref.pseudo.
within	Boolean, defaults to TRUE. If within = TRUE, the contours included in a RoI are managed, depending on their $level field. If within = FALSE, only the $level = 0 fields of the RoI are used (i.e. only the external outlines).
alias	Character string, $alias of the created object.
description	Character string, describing the created object. If description = NULL (default value), it will be set to struct$roi.info$roi.pseudo[roi.idx].
modality	modality ("binary" or "weight") of the generated object.
...	additional argument.

Details

roi.name, roi.sname, and roi.idx must select only one RoI.

Value

Returns a "volume" class object of "binary" or "weight" modality (see espadon.class for class definitions), with the same grid as vol.

• In the “binary” modality, voxels with 50 percent of their volume within the ROI are set to TRUE.

• In the “weight” modality, the value of each voxel is its volume fraction included in the ROI.

See Also

bin.from.vol.

Examples

# loading of toy-patient objects (decrease dxyz for better result)
step <- 5
patient <- toy.load.patient (modality = c("ct", "rtstruct"), 
                             roi.name =  c("eye", "optical nerve", "brain"), 
                             dxyz = rep (step, 3))
CT <- patient$ct[[1]]
S <- patient$rtstruct[[1]]

# "optical nerve" binary, with  modality "binary" and "weight"
binl <- bin.from.roi (CT, struct = S, roi.sname = "left optical",
                      alias = "left_optical_nerve", verbose = FALSE,
                      modality = "binary")
binr <- bin.from.roi (CT, struct = S, roi.sname = "right optical",
                      alias = "right_optical_nerve", verbose = FALSE,
                      modality = "weight")

view.coord <- S$roi.info[S$roi.info$roi.pseudo == "leftopticalnerve",]$Gz
palette <- grey.colors(100, start = 0, end = 1, 
                       alpha = c(0, rep(1,99)))
plot(S, view.coord = view.coord, main ="optical nerves")
plot(binl, view.coord = view.coord, col = palette, 
    cut.interpolate = FALSE, add = TRUE)
plot(binr, view.coord = view.coord, col =palette, 
      cut.interpolate = FALSE, add = TRUE)
plot(S, view.coord = view.coord, lwd = 2, add= TRUE)

## Not run: 
# with a smaller step
step <- 1
patient <- toy.load.patient (modality = c("ct", "rtstruct"), 
                             roi.name =  c("eye", "optical nerve", "brain"), 
                             dxyz = rep (step, 3))
CT <- patient$ct[[1]]
S <- patient$rtstruct[[1]]
#' view.coord <- S$roi.info[S$roi.info$roi.pseudo == "leftopticalnerve",]$Gz

# "optical nerve" binary without inclusions management
bin <- bin.from.roi (CT, struct = S, roi.sname = "left optical", 
                     alias = "left_optical_nerve", within = FALSE,
                     verbose = FALSE)
display.plane (CT, top = bin, struct = S, view.coord = view.coord, 
               legend.shift = -80, interpolate = FALSE, main = "Left nerve")

# "optical nerve" binary with inclusions management
bin <- bin.from.roi (CT, struct = S, roi.sname = "left optical", 
                     alias = "left_optical_nerve", within = TRUE,
                     verbose = FALSE)
display.plane (CT, top = bin, struct = S, view.coord = view.coord, 
               legend.shift = -80, interpolate = FALSE, main = "Left nerve") 

## End(Not run)

espadon documentation built on April 11, 2025, 5:57 p.m.