histo.2D: 2D histograms of 2 volumes

Description

The histo.2D function creates a "histo2D" class object, containing the two-dimensional array of histograms of two "volume" class objects that have the same grid.

Usage

histo.2D(
  x.vol,
  y.vol,
  x.breaks = NULL,
  y.breaks = NULL,
  include.outer = TRUE,
  alias = "",
  description = ""
)

Value

Returns a "histo2D" class object. This is a list including:

$patient: set to x.vol$patient.
$patient.name: set to x.vol$patient.name.
$patient.bd: set to x.vol$patient.bd.
$patient.sex: set to x.vol$patient.sex.
$file.basename: set to "".
$file.dirname: set to "".
$object.name: set to "".
$object.alias: alias of the histo2D object.
$frame.of.reference: set to x.vol$frame.of.reference.
$ref.pseudo : set to x.vol$ref.pseudo.
$modality : set to "histo2D".
$description: description of the histo2D object.
$creation.date: set to Sys.Date.
$nb.pixels: number of elements in the density.map.
$x.file.src: set to x.vol$object.alias
$y.file.src: set to y.vol$object.alias
x.breaks: vector of x-axis breakpoints.
y.breaks: vector of y-axis breakpoints.
x.mids: vector of x-axis cell centers.
y.mids: vector of y-axis cell centers.
density.map: array of densities.
total.counts: number of counted voxels.

Arguments

x.vol, y.vol: "volume" class objects. The 2 volumes must have the grid (i.e. share the same voxels location).
x.breaks, y.breaks: Vectors giving the breakpoints of x and y axes. See Details.
include.outer: Boolean. If include.outer = TRUE, the values out the x.breaks and y.breaks of each volume are counted in the first and the last cell of the histograms. They are not taken into account otherwise.
alias: Character string, $alias of the created object
description: Character string, describing the created object.

Details

The arguments x.breaks and y.breaks represent the scales of the x and y axes of 2D-histogram graph. If they are NULL, the histo.2D function defaults to 256 cells between the values vol$min.pixel and vol$max.pixel.

Examples

Run this code

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

# restriction of the volume around the RoI
CT.on.roi <- nesting.roi (CT, S, roi.name = "brain", vol.restrict = TRUE,
                          xyz.margin = c (1, 1, 1), alias = CT$description)
MR.on.CT <- vol.regrid (vol = MR, back.vol = CT.on.roi, interpolate = TRUE,
                        T.MAT = T.MAT, alias = CT$description,
                        description = NULL)
# selection of voxels included in the RoI.
roi.bin <- bin.from.roi (vol = CT.on.roi, struct = S, roi.sname = "brain", 
                         verbose = FALSE)
MR.select <- vol.from.bin (MR.on.CT, roi.bin, alias = MR$description)
CT.select <- vol.from.bin (CT.on.roi, roi.bin, alias = CT$description)
# 2D histogram
H2D <- histo.2D (MR.select, CT.select, x.breaks = seq (50, 400, 10),
			  y.breaks = seq (50, 400, 10), alias = "H2D MR CT")
str (H2D)