BP_EstimateCompactness: Estimation of the compactness of a bone section

In BoneProfileR: Tools to Study Bone Compactness

Estimation of the compactness of a bone section

Description

Estimation of the compactness of a bone section.
The reference for radial estimation of compactness is the trigonometric circle for rotation.angle=0 in BP_EstimateCompactness():
- The top of the section is located at -pi/2.
- The left of the section is located at -pi and +pi.
- The bottom of the section is located at pi/2.
- The right of the section is 0.
If rotation.angle is different from 0, the value of rotation.angle is added to the angle modulo 2.pi.
The method Fast works well with the convex bone section while if the section is concave, Accurate is slower but works well in all circonstances.
Fast method is maintained here only for compatibility with versions <3.1 of BoneProfileR.
If the section is concave, the methods FastConvex and AccurateConvex return a minimum convex section.
If the center has been automatically detected, the method parameter is ignored because it has already been used with the function BP_DetectCenters().

Usage

BP_EstimateCompactness(
  bone,
  center = "ontogenetic",
  partial = FALSE,
  cut.angle = 60,
  cut.distance = 100,
  rotation.angle = 0,
  analysis = 1,
  method = "Accurate",
  show.plot = TRUE
)

Arguments

bone	The bone image to be used
center	Which center to be used: user, mineralized, unmineralized, section, ontogenetic
partial	Is the section partial?
cut.angle	Number of angles
cut.distance	Number of distances
rotation.angle	The angle of rotation for analysis
analysis	The name or rank of analysis
method	Can be Fast, Accurate, FastConvex, or AccurateConvex
show.plot	should plot is shown ?

Details

BP_EstimateCompactness estimates the compactness of a bone section

Value

The orignial bone object with a new attribute for compactness

Author(s)

Marc Girondot [e-mail]

See Also

Other BoneProfileR: BP_AutoFit(), BP_ChooseBackground(), BP_ChooseCenter(), BP_ChooseForeground(), BP_DetectBackground(), BP_DetectCenters(), BP_DetectForeground(), BP_DuplicateAnalysis(), BP_FitBayesianCompactness(), BP_FitMLCompactness(), BP_FitMLRadialCompactness(), BP_GetFittedParameters(), BP_ListAnalyses(), BP_LnLCompactness(), BP_OpenImage(), BP_Report(), Erinaceus_europaeus, plot.BoneProfileR(), summary.BoneProfileR()

Examples

## Not run: 
# Not run:
library(BoneProfileR)
 bone <- BP_OpenImage()
 # or 
path_Hedgehog <- system.file("extdata", "Erinaceus_europaeus_fem_2-1_small.png", 
                             package = "BoneProfileR")
 bone <- BP_OpenImage(file=path_Hedgehog)
 bone <- BP_DetectBackground(bone=bone)
 bone <- BP_DetectForeground(bone=bone)
 bone <- BP_DetectCenters(bone=bone)
 bone <- BP_EstimateCompactness(bone)
 plot(bone, type="original", show.grid=FALSE)
 plot(bone, type="mineralized", show.grid=FALSE)
 plot(bone, type="unmineralized", show.grid=FALSE)
 plot(bone, type="section", show.grid=FALSE)

## End(Not run)

BoneProfileR documentation built on Sept. 11, 2024, 6:07 p.m.