molaR: Dental Surface Complexity Measurement Tools

Surface topography calculations of Dirichlet's normal energy, relief index, surface slope, and orientation patch count for teeth using scans of enamel caps. Importantly, for the relief index and orientation patch count calculations to work, the scanned tooth files must be oriented with the occlusal plane parallel to the x and y axes, and perpendicular to the z axis. The files should also be simplified, and smoothed in some other software prior to uploading into R.

Author
James D. Pampush [aut, cre, cph], Julia M. Winchester [aut, cph], Paul E. Morse [aut, cph], Alexander Q. Vining [aut, cph]
Date of publication
2016-08-31 01:26:14
Maintainer
James D. Pampush <jdpampush@gmail.com>
License
ACM
Version
4.2

View on CRAN

Man pages

clustered_patches
A clustering function
compute_energy_per_face
Function will compute the DNE per face.
cSize
Centroid Size Function
Directional_Bins
This bins the faces into directional categories
DNE
Calculate Dirichlet normal energy of a surface
DNE3d
Plot results of a DNE analysis of a surface
DNE_Legend
Make legend for DNE3d plot
edge_vertices
Function for finding the edge vertices
Equal_Vertex_Normals
Important function for re-doing the vertex normals for the...
ex_tooth1
4149_DU-LP-09_LM1
ex_tooth2
4147_DU-LP-07_LM1
face_areas
Function to calculate face areas.
Face_Normals
Function to find Face Normals
index_paired_directed_faces
Index of paired faces with directions
molaR_Batch
Run a batch of molaR analyses
molaR_bgplot
Internal function for making molaR plot legends
molaR_Clean
Clean up problem ply files
OPC
Calculate orientation patch count of a surface
OPC3d
Plot results of OPC analysis of a surface
OPC_Legend
function for building a legend in OPC plots
OPCr
Calculate average orientation patch count after several...
patch_details
Function for gathering patch details for each Orientation...
patches_for_each_direction
Function for gathering the patches for each direction
patches_per
A function for patches within each face
plyZClip
Function which will clip a plyFile
read.AVIZO.ply
Read mesh data from ply files saved by AVIZO
remove_boundary_faces
Remove boundary faces
remove_outliers
Mask outliers on some faces
RFI
Calculate Boyer's (2008) relief index for a surface
RFI3d
Plot 3D and 2D areas of a mesh used to calculate relief index
RFI_Legend
function for building a legend for RFI
Slope
Function to calculate the average slope of a surface
Slope3d
Plot results of a Slope analysis of a surface
Slope_Legend
Plotting subfunction for making slope plot legend
tr
Trace function
vertex_to_face_list
function for making a list of faces on each vertex

Files in this package

molaR
molaR/inst
molaR/inst/doc
molaR/inst/doc/molaR_vignette.html
molaR/inst/doc/molaR_vignette.R
molaR/inst/doc/molaR_vignette.Rmd
molaR/NAMESPACE
molaR/data
molaR/data/ex_tooth2.RData
molaR/data/ex_tooth1.RData
molaR/R
molaR/R/read.AVIZO.ply.R
molaR/R/Directional_Bins.R
molaR/R/edge_vertices.R
molaR/R/molaR_Clean.R
molaR/R/RFI3d.R
molaR/R/remove_outliers.R
molaR/R/molaR_bgplot.R
molaR/R/OPC_Legend.R
molaR/R/compute_energy_per_face.R
molaR/R/molaR_Batch.R
molaR/R/OPCr.R
molaR/R/DNE.R
molaR/R/OPC3d.R
molaR/R/patch_details.R
molaR/R/DNE_Legend.R
molaR/R/Face_Normals.R
molaR/R/OPC.R
molaR/R/remove_boundary_faces.R
molaR/R/vertex_to_face_list.R
molaR/R/index_paired_directed_faces.R
molaR/R/Slope_Legend.R
molaR/R/cSize.R
molaR/R/patches_for_each_direction.R
molaR/R/RFI_Legend.R
molaR/R/patches_per.R
molaR/R/clustered_patches.R
molaR/R/face_areas.R
molaR/R/tr.R
molaR/R/RFI.R
molaR/R/Equal_Vertex_Normals.R
molaR/R/Slope3d.R
molaR/R/DNE3d.R
molaR/R/Slope.R
molaR/R/plyZClip.R
molaR/vignettes
molaR/vignettes/molaR_vignette.Rmd
molaR/MD5
molaR/build
molaR/build/vignette.rds
molaR/build/molaR.pdf
molaR/DESCRIPTION
molaR/man
molaR/man/OPCr.Rd
molaR/man/molaR_Clean.Rd
molaR/man/DNE_Legend.Rd
molaR/man/OPC3d.Rd
molaR/man/ex_tooth1.Rd
molaR/man/vertex_to_face_list.Rd
molaR/man/RFI_Legend.Rd
molaR/man/Face_Normals.Rd
molaR/man/RFI.Rd
molaR/man/plyZClip.Rd
molaR/man/Directional_Bins.Rd
molaR/man/DNE3d.Rd
molaR/man/molaR_Batch.Rd
molaR/man/edge_vertices.Rd
molaR/man/cSize.Rd
molaR/man/molaR_bgplot.Rd
molaR/man/Slope_Legend.Rd
molaR/man/compute_energy_per_face.Rd
molaR/man/patches_for_each_direction.Rd
molaR/man/ex_tooth2.Rd
molaR/man/read.AVIZO.ply.Rd
molaR/man/Equal_Vertex_Normals.Rd
molaR/man/Slope3d.Rd
molaR/man/clustered_patches.Rd
molaR/man/remove_boundary_faces.Rd
molaR/man/index_paired_directed_faces.Rd
molaR/man/OPC.Rd
molaR/man/OPC_Legend.Rd
molaR/man/face_areas.Rd
molaR/man/remove_outliers.Rd
molaR/man/DNE.Rd
molaR/man/tr.Rd
molaR/man/Slope.Rd
molaR/man/patches_per.Rd
molaR/man/patch_details.Rd
molaR/man/RFI3d.Rd