Package: coreCT 1.3.3

coreCT: Programmatic Analysis of Sediment Cores Using Computed Tomography Imaging

Computed tomography (CT) imaging is a powerful tool for understanding the composition of sediment cores. This package streamlines and accelerates the analysis of CT data generated in the context of environmental science. Included are tools for processing raw DICOM images to characterize sediment composition (sand, peat, etc.). Root analyses are also enabled, including measures of external surface area and volumes for user-defined root size classes. For a detailed description of the application of computed tomography imaging for sediment characterization, see: Davey, E., C. Wigand, R. Johnson, K. Sundberg, J. Morris, and C. Roman. (2011) <doi:10.1890/10-2037.1>.

Authors:Troy D. Hill [aut, cre], Earl Davey [ctb]

coreCT_1.3.3.tar.gz
coreCT_1.3.3.zip(r-4.7)coreCT_1.3.3.zip(r-4.6)coreCT_1.3.3.zip(r-4.5)
coreCT_1.3.3.tgz(r-4.6-any)coreCT_1.3.3.tgz(r-4.5-any)
coreCT_1.3.3.tar.gz(r-4.7-any)coreCT_1.3.3.tar.gz(r-4.6-any)
coreCT_1.3.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
coreCT/json (API)

# Install 'coreCT' in R:

install.packages('coreCT', repos = c('https://troyhill.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/troyhill/corect/issues

Datasets:

core_426 - Three computed tomography scans from a Spartina alterniflora core

On CRAN:

biomass computed-tomography sediment sediment-core

4.43 score 3 stars 18 scripts 301 downloads 11 exports 21 dependencies

Last updated from:1f5fd63ee6. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	NOTE	263
source / vignettes	OK	239
linux-release-x86_64	NOTE	242
macos-release-arm64	NOTE	202
macos-oldrel-arm64	NOTE	278
windows-devel	NOTE	215
windows-release	NOTE	206
windows-oldrel	NOTE	199
wasm-release	OK	125

Exports:conv convDir convert convertDir coreHist getRoots getRootsDir getSurface rootSize rootSizeDir voxDims

Dependencies:abind bitops cli cpp11 glue igraph lattice lifecycle magrittr Matrix oro.dicom oro.nifti pkgconfig plyr raster Rcpp rlang RNifti sp terra vctrs

Using coreCT

Rendered fromUsing_coreCT.Rmdusingknitr::rmarkdown

Last update: 2020-09-26
Started: 2017-08-13

Help page	Topics
Convert a matrix of semi-processed DICOM images to mass and volume of material classes. This is a deprecated version.	conv
Convert a directory of raw DICOM images to material classes	convDir
Convert a matrix of semi-processed DICOM images to mass and volume of material classes	convert
Convert a directory of raw DICOM images to material classes	convertDir
Three computed tomography scans from a Spartina alterniflora core	core_426
Whole-core frequency distribution of Hounsfield units	coreHist
Convert a matrix of semi-processed DICOM images to root particle counts, volumes, and surface areas	getRoots
Convert a directory of raw DICOM images to root particle counts and surface areas	getRootsDir
Remove artificial surface layers from processed CT data	getSurface
Convert a matrix of semi-processed DICOM images to root particle counts, volumes, and surface areas	rootSize
Convert a directory of raw DICOM images to root particle counts and surface areas	rootSizeDir
Extract voxel dimensions from DICOM image	voxDims

Package: coreCT 1.3.3

coreCT: Programmatic Analysis of Sediment Cores Using Computed Tomography Imaging

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)