bin.cuboid: Create a volume containing predefined shapes
In espadon: Easy Study of Patient DICOM Data in Oncology

bin.cuboid

R Documentation

Create a volume containing predefined shapes

Description

These functions create espadon objects of class “volume”, and of modality “binary” or “weight”, by selecting the voxels defining a rectangular cuboid, an elliptical cylinder or an ellipsoid.

Usage

bin.cuboid(
  back.vol,
  side = c(10, 10, 10),
  center = c(0, 0, 0),
  orientation = c(1, 0, 0, 0, 1, 0),
  modality = "weight",
  alias = "",
  description = NULL,
  ...
)

bin.cylinder(
  back.vol,
  center,
  radius,
  height,
  orientation = c(1, 0, 0, 0, 1, 0),
  modality = "weight",
  alias = "",
  description = NULL,
  ...
)

bin.ellipsoid(
  back.vol,
  center,
  radius,
  orientation = c(1, 0, 0, 0, 1, 0),
  modality = "weight",
  alias = "",
  description = NULL,
  ...
)

Arguments

`back.vol`	"volume" class object.
`side`	Numerical vector of length 3, representing the length, width and height of the cuboid.
`center`	Numeric vector of length 3, representing the xyz-center of the shape, in the `back.vol` frame of reference.
`orientation`	Numerical vector of length 6, specifying the coordinates of the 2 vectors making up the shape base.
`modality`	modality ("binary" or "weight") of the generated object.
`alias`	Character string, `$alias` of the created object.
`description`	Character string, describing the created object.
`...`	Additional arguments.
`radius`	Positive number, or xy-vector or xyz-vector of 2 or 3 positive numbers, representing the radius of the cylinder or the ellipsoid.
`height`	Positive number representing the height of the cylinder.

Value

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

In the “binary” modality, voxels with 50 percent of their volume within the requested shape are set to TRUE.
In the “weight” modality, the value of each voxel is its volume fraction included in the requested shape.

Examples

# Creation of back.vol
CT <- vol.create (c(80, 80,40), c(1.2, 1.2, 2), 
                  pt000 = c(-50.4,-50.4,-39), modality = "ct", 
                  default.value = as.integer(-997), value.sd = 1)
                   
# Creation of a cuboid
cuboid <- bin.cuboid(CT, side = c(29.7, 20.0, 20.2), 
                     center = c(-10.9, -20.4, -10.6))
                       
# Creation of a cylinder 
cylinder <- bin.cylinder(CT, center =c(10.3, 15.6, 0.7), 
                         radius =  c(10, 20), height = 50, 
                         orientation = c(0.5150381, 0.7423287, 0.4285837,
                                         -0.8571673, 0.4460361, 0.2575190)) 
                      
# Creation of an ellipsoid 
ellipsoid <- bin.ellipsoid(CT, center = c(-20.1, 0.1, 5), 
                           radius =  c(3.3, 6.2, 5.3))  
                       
 # Display                         
 k.idx <- unique(which(cuboid$vol3D.data>0, arr.ind = TRUE)[,3]) - 1
 display.3D.stack(cuboid, k.idx, border = FALSE,
                  col = c("#FFFFFF00", "#EBDFDFFF", "#D8BFBFFF", "#C59F9FFF", 
                          "#B27F7FFF", "#9F5F5FFF", "#8C3F3FFF", "#791F1FFF", 
                          "#660000FF"))   
                           
 k.idx <- unique(which(cylinder$vol3D.data>0, arr.ind = TRUE)[,3]) - 1
 display.3D.stack(cylinder, k.idx, border = FALSE,
                  col = c("#FFFFFF00", "#DFEBDFFF", "#BFD8BFFF", "#9FC59FFF", 
                          "#7FB27FFF", "#5F9F5FFF", "#3F8C3FFF", "#1F791FFF", 
                          "#006600FF"))    

 k.idx <- unique(which(ellipsoid$vol3D.data>0, arr.ind = TRUE)[,3]) - 1
 display.3D.stack(ellipsoid, k.idx, border = FALSE,
                  col = c("#FFFFFF00", "#DFDFEBFF", "#BFBFD8FF", "#9F9FC5FF", 
                          "#7F7FB2FF", "#5F5F9FFF", "#3F3F8CFF", "#1F1F79FF", 
                          "#000066FF"))

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