display.slice.all: Display a 2D slice superimposed to the CT

In planit-group/Rplanit: Radiotherapy with ion beams - planning, simulations and analysis

Display a 2D slice superimposed to the CT

Description

Display an arbitrary 2D slice (axial, coronal, sagittal) of the values stored in a values object. The slice is superimposed to the associated CT slice. Optionally ROI contours can be also displayed.

Usage

display.slice.all(ct = NULL, contours = NULL, values = NULL,
  variable = NULL, plan = NULL, x = NA, y = NA, z = NA,
  cont = FALSE, isoc = FALSE, xlim = NULL, ylim = NULL,
  zlim = NULL, vlim = NULL, file.name = NULL, width = 7,
  height = 7, HU.window = c(-1000, 3000), alpha.lower = 0,
  alpha.upper = 1, invert.y.axis = FALSE, contour.color = "green",
  dpi = 300, levels = NULL, use.contour.colors = TRUE,
  contours.legend = FALSE, cex.contours.legend = 0.8,
  contour.legend.position = "topleft", title = NULL,
  col.invert = FALSE)

Arguments

ct	the ct object (optional, if plan is specified)
contours	the contours object (optional)
values	the values object (optional, if plan is specified)
variable	the specific variable to be displayed (not needed if values contains only one variable, or if the variable is the first of the list)
plan	the plan object (optional, if values and ct are defined)
x, y, z	slice coordinate to be displayed. Only one of them should be defined, corresponding to an axial, coronal or sagittal slice (optional)
cont	display isolevel contours of the values (optional, boolean)
isoc	display the isocenter on the slice (optional, boolean)
xlim, ylim, zlim	two element vectors containing the coordinate ranges to be displayed (optional)
vlim	two element vector containing the value range to be displayed. Values outside the range are displayed as 'blank', i.e. no color tile (optional)
file.name	name of the file on which to save the figure. By default no file is written (optional)
width, height	sizes of the figure to be saved (inches) (optional)
HU.window	HU window to visualize for the CT.
alpha.lower, alpha.upperThe	opacity (alpha) is evaluated as a linear ramp (alpha.lower to alpha.upper) from alpha.lower to alpha.upper of the values range.
invert.y.axis	Invert the y axis.
contour.color	The color used for the contour of the VOI.
dpi	dpi of the saved image.
use.contour.colors	Use the colors defined in the contours object for the contours.
cex.contours.legend	Font dimension for the contour legend.
contour.legend.position	Position of the contour legend.
title	Explicitly define the text to be displayed in the plot title.
col.invert	Invert the color map (red for lower values and blue for high values)
Nx, Ny, Nz	slice index to be displayed. Only one of them should be defined, corresponding to an axial, coronal or sagittal slice (optional)
bw	display using gray color levels. It colud be used to display CT values (optional, boolean)
display.contours.legend	Display a legend for the contours.

Details

If slice index and slice coordinate are not specified, but the plan is specified, the displayed slice is axial and at the isocenter of the plan. If slice index, slice coordinate and plan are not specified, the displayed slice is axial and at the middle of the z range.

If the plan is specified, it is possible to not specify some or all of the following objects: values, CT and contours. In this case the missing ones are replaced with those associated to the plan.

See Also

Other display slices: display.slice.ct, display.slice, dumpslices.3d.2.png

planit-group/Rplanit documentation built on Dec. 5, 2022, 11:10 p.m.