mesh.from.bin: Creation of a mesh according to a binary volume
In espadon: Easy Study of Patient DICOM Data in Oncology

mesh.from.bin

R Documentation

Creation of a mesh according to a binary volume

Description

The mesh.from.bin function creates a mesh class object from a volume object of "binary" modality.

Usage

mesh.from.bin(
  bin,
  alias = "",
  tol = min(abs(bin$dxyz))/2,
  smooth.iteration = 10,
  smooth.type = c("taubin", "laplace", "HClaplace", "fujiLaplace", "angWeight",
    "surfPreserveLaplace"),
  smooth.lambda = 0.5,
  smooth.mu = -0.53,
  smooth.delta = 0.1,
  verbose = FALSE
)

Arguments

`bin`	"volume" class object of "binary" modality.
`alias`	Character string, `$alias` of the mesh defining the `$alias` of the created object.
`tol`	Tolerance in mm, applied for mesh simplification. See vcgClean. The default value, equal to half the smallest voxel edge, limits meshing errors.
`smooth.iteration`	Number of iterations applied in the smoothing algorithm. See vcgSmooth.
`smooth.type`	character: select smoothing algorithm. Available are "taubin", "laplace", "HClaplace", "fujiLaplace", "angWeight" (and any sensible abbreviations). By default, set to "taubin". See vcgSmooth.
`smooth.lambda`	numeric: parameter for Taubin smooth. See vcgSmooth.
`smooth.mu`	numeric: parameter for Taubin smooth. See vcgSmooth.
`smooth.delta`	numeric: parameter for Scale dependent laplacian smoothing (see reference below).and maximum allowed angle (in radians) for deviation between normals Laplacian (surface preserving). See vcgSmooth.
`verbose`	Boolean, by default set to `FALSE`. Allows you to inhibit comments.

Value

Returns a "mesh" class object. This is a list including the following 6 elements:

$patient: set to bin$patient.
$patient.bd: set to bin$patient.bd.
$patient.name: set to bin$patient.name.
$patient.sex: set to bin$patient.sex.
$file.basename: set to "".
$file.dirname: set to "".
$object.name: set to "".
$object.alias: set to the alias argument of the function.
$frame.of.reference: set to bin$frame.of.reference.
$ref.pseudo : set to bin$ref.pseudo.
$modality : set to "mesh".
$description: By default, set to paste (bin$object.alias, "mesh").
$creation.date: set to Sys.Date.
$nb.faces: set to the number of faces of the mesh.

$mesh: list of 3 elements defining the mesh:

	- `$vb`: array made up of the generalized coordinates (x, y, z, 1) of the vertices of the triangles.
	There are as many columns as there are vertices.
	- `$it`: array of the 3 indices of the vertices forming a triangle, arranged by column.
	There are as many columns as there are triangles in the mesh.
	- `$normals`: array made up of the generalized coordinates (x, y, z, 1) of the normal vectors of each triangle.
	There are as many columns as there are vertices.

Note

To compute the mesh, all NA voxels of the binary volume bin are set to FALSE. If all voxels are equal to FALSE, the function returns the code NULL.

Examples

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

# creation of the patient mesh
bin <- bin.from.roi (CT, struct = S, roi.name = "patient", verbose = FALSE)
mesh.patient <- mesh.from.bin (bin, alias = "patient", verbose = FALSE)
str (mesh.patient)

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