plot: plot a 2D cut of a 3D object
In espadon: Easy Study of Patient DICOM Data in Oncology

plot	R Documentation

plot a 2D cut of a 3D object

Description

The plot function displays the requested map of espadon objects of class "volume", "struct", "mesh".

Usage

## S3 method for class 'volume'
plot(
  x,
  ...,
  view.type = "trans",
  view.coord = NULL,
  flip = FALSE,
  flop = FALSE,
  cut.interpolate = TRUE,
  display.interpolate = FALSE,
  col = grey.colors(255, start = 0, end = 1),
  breaks = NULL,
  sat.transp = FALSE
)

## S3 method for class 'struct'
plot(
  x,
  ...,
  view.type = "trans",
  view.coord = NULL,
  flip = FALSE,
  flop = FALSE,
  roi.name = NULL,
  roi.sname = NULL,
  roi.idx = NULL,
  back.dxyz = c(0.5, 0.5, x$thickness)
)

## S3 method for class 'mesh'
plot(
  x,
  ...,
  view.type = "trans",
  view.coord = NULL,
  flip = FALSE,
  flop = FALSE,
  col = "#ff0000"
)

Arguments

`x`	object of class "volume", "struct" or "mesh". See espadon.class
`...`	others parameters of plot functions. See details
`view.type`	character string among the values 'ij', 'ji', 'ik', 'ki', 'jk', 'kj', 'yx', 'xz', 'zx', 'yz', 'zy', 'trans', 'front' or 'sagi" representing the map to be displayed.
`view.coord`	value representing the coordinate where the map is displayed. This parameter can be a 3D-vector, representing the coordinate of the point on the displayed map. If `NULL`, the display is located in the center of the object.
`flip`	Boolean defaults to `FALSE` flipping the horizontal axis of the background image.
`flop`	Boolean defaults to `FALSE` flipping the vertical axis of the background image.
`cut.interpolate`	Boolean, indicating whether to calculate the volume cut using linear interpolation.
`display.interpolate`	Boolean, indicating whether to apply linear interpolation when displaying the cut.
`col`	Vector, representing the color palette of the image, if `x` is of class 'volume'. Color of the mesh outline if object `x` is of class 'mesh'.
`breaks`	One of : `NULL` : the minimum and the maximum value of the object `x` define the range. Vector giving the breakpoints of each color. Outside values are transparent, leaving the background visible, depending on `sat.transp`.
`sat.transp`	Boolean. If `TRUE`, outside values are transparent, else set to `breaks` limits colors.
`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.
`back.dxyz`	3D vector of voxel size, used to calculate contours in frontal or sagittal view.

Details

... can be xlim, ylim, add, bg etc. If view.type is egal to 'trans' or 'front' or 'sagi', the direction of xlim and ylim is ignored.

If roi.name, roi.sname, and roi.idx are all set to NULL, all closed planar or point RoI, present at view.coord are selected.

Value

Returns a display of the \mjeqnk^thascii image plane of x.

Examples

# loading of toy-patient objects (decrease dxyz and increase beam.nb for
# better result)
step <- 5
patient <- toy.load.patient (modality = c("ct","mr", "rtdose", "rtstruct"),
                             dxyz = rep (step, 3), beam.nb = 3)
MR <- patient$mr[[1]]
CT <- patient$ct[[1]]
D <- patient$rtdose[[1]]
S <- patient$rtstruct[[1]]

# display 1
layout (matrix(c(1,1,2,3), ncol=2), widths=c(1,0.2))
plot (CT, view.coord = 0, col = pal.RVV(255))
S_plot <- plot (S, view.coord = 0, add = TRUE, lwd = 2)
display.palette (col = pal.RVV(255), main="HU")
display.legend (S_plot, bg="white", text.col="black", lwd = 2, cex = 1.1)
# display 2
layout (matrix(c (1, 1, 2, 3), ncol = 2), widths = c (1, 0.2))
# Coordinates of the PTV barycenter in CT frame of reference
G <- as.numeric (S$roi.info[S$roi.info$roi.pseudo == "ptv", 
                            c ("Gx", "Gy", "Gz")])
# Coordinates of the PTV baricenter in MR frame of reference
G_MR <- as.numeric (c(G, 1) %*% 
                   t(get.rigid.M(CT$ref.pseudo, MR$ref.pseudo, 
                               T.MAT = patient$T.MAT)))[1:3]
plot (MR, view.type = "sagi", view.coord =  G_MR,
      col = grey.colors (255, start = 0, end = 1),
      breaks = seq (0, 500, length.out = 256) , bg = "darkblue")
plot (vol.in.new.ref(D, MR$ref.pseudo, T.MAT = patient$T.MAT),
      view.type = "sagi", view.coord = G_MR,
      col = pal.rainbow(255), add = TRUE)
display.palette (col = grey.colors (255, start = 0, end = 1),
                 breaks = seq (0, 500, length.out = 256), main="MR")
display.palette (col =  pal.rainbow(255),
                 breaks = seq (D$min.pixel, D$max.pixel, length.out = 256),
                 main="Gy")
layout(1)

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