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.

AuthorJames D. Pampush [aut, cre, cph], Julia M. Winchester [aut, cph], Paul E. Morse [aut, cph], Alexander Q. Vining [aut, cph]
Date of publication2016-08-31 01:26:14
MaintainerJames D. Pampush <jdpampush@gmail.com>
LicenseACM
Version4.2

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

Functions

clustered_patches Man page
compute_energy_per_face Man page
cSize Man page
Directional_Bins Man page
DNE Man page
DNE3d Man page
DNE_Legend Man page
edge_vertices Man page
Equal_Vertex_Normals Man page
ex_tooth1 Man page
ex_tooth2 Man page
face_areas Man page
Face_Normals Man page
index_paired_directed_faces Man page
molaR_Batch Man page
molaR_bgplot Man page
molaR_Clean Man page
OPC Man page
OPC3d Man page
OPC_Legend Man page
OPCr Man page
patch_details Man page
patches_for_each_direction Man page
patches_per Man page
plyZClip Man page
read.AVIZO.ply Man page
remove_boundary_faces Man page
remove_outliers Man page
RFI Man page
RFI3d Man page
RFI_Legend Man page
Slope Man page
Slope3d Man page
Slope_Legend Man page
tr Man page
vertex_to_face_list Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.