BoneProfileR (version 3.1)

BP_EstimateCompactness: 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
)

Value

The orignial bone object with a new attribute for compactness

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 ?

Author

Marc Girondot

Details

BP_EstimateCompactness estimates the compactness of a bone section

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

if (FALSE) {
# 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)
}