Package: gdi 1.10.0

gdi: Volumetric Analysis using Graphic Double Integration

Tools implementing an automated version of the graphic double integration technique (GDI) for volume implementation, and some other related utilities for paleontological image-analysis. GDI was first employed by Jerison (1973) <ISBN:9780323141086> and Hurlburt (1999) <doi:10.1080/02724634.1999.10011145> and is primarily used for volume or mass estimation of (extinct) animals. The package 'gdi' aims to make this technique as convenient and versatile as possible. The core functions of 'gdi' provide utilities for automatically measuring diameters from digital silhouettes provided as image files and calculating volume via graphic double integration with simple elliptical, superelliptical (following Motani 2001 <doi:10.1666/0094-8373(2001)027%3C0735:EBMFST%3E2.0.CO;2>) or complex cross-sectional geometries (see also Zhao 2024 <doi:10.7717/peerj.17479>). Additionally, the package provides functions for estimating the center of mass position (COM), the moment of inertia (I) for 3D shapes and the second moment of area (Ix, Iy, Iz) of 2D cross-sections, as well as for the visualization of results.

Authors:Darius Nau [aut, cre]

gdi_1.10.0.tar.gz
gdi_1.10.0.zip(r-4.7-any)gdi_1.10.0.zip(r-4.6-any)gdi_1.10.0.zip(r-4.5-any)
gdi_1.10.0.tgz(r-4.6-any)gdi_1.10.0.tgz(r-4.5-any)
gdi_1.10.0.tar.gz(r-4.7-any)gdi_1.10.0.tar.gz(r-4.6-any)
gdi_1.10.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gdi/json (API)

# Install 'gdi' in R:
install.packages('gdi', repos = c('https://theropod1.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.97 score 31 scripts 235 downloads 15 exports 2 dependencies

Last updated from:e756e3ecbe. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK144
source / vignettesOK163
linux-releaseOK165
macos-releaseOK130
macos-oldrelOK132
windows-develOK77
windows-releaseOK61
windows-oldrelOK80
wasm-releaseOK107

Exports:cscorrcsIexpandConvexHullfdetectgdihCOMimghistinter_corrmeasuresilplot_silrotIsellipsesellipse.cootransfer_ratiovCOM

Dependencies:jpegpng

Estimating Center of Mass
Rendered fromestimating_COM.Rmdusingknitr::rmarkdown

Last update: 2024-04-22
Started: 2023-08-07

Miscellaneous Applications
Rendered frommisc.Rmdusingknitr::rmarkdown

Last update: 2024-04-22
Started: 2023-09-07

gdi
Rendered fromgdi.Rmdusingknitr::rmarkdown

Last update: 2023-08-07
Started: 2023-05-04

Readme and manuals

Help Manual

Help pageTopics
Measure and analyze cross-sectional geometry supplied as an image.cscorr
Calculates the second moment of area (=area moment of inertia, Ix and Iy) and polar moment of inertia (Iz or J) for a cross-section given as an image.csI
Estimate soft tissue expansion factors following Macaulay et al. 2023expandConvexHull
Tool to help determine which threshold value and method to use with measuresil() or cscorr(). The function analyzes all pixels along the edges of the image to determine the background color, to help with deciding on appropriate settings and avoid errors introduced by inappropriate settingsfdetect
Estimate volume using Graphic Double Integration.gdi
Finds the horizontal (x axis, i.e. the axis vertical to the cross-sections) position of the center of mass (COM) of the volume. Experimental; only valid for "raw" gdi results with segment volumes approximated as elliptical prisms, or for manually supplied segment COMs. COM is calculated as a weighted mean of all segment COMs, with the segment mass as the weighting factor.hCOM
Simple histogram analysis for all color values in an input image. Can be used to help assess whether a chosen threshold value is appropriate for differentiating the silhouette from the background, or for general image analysis purposes.imghist
Helper function for interpolating cross-sectional metrics over the length of a silhouetteinter_corr
Take pixel-by-pixel measurements of a silhouette in jpeg or png format for use with the gdi function.measuresil
Plots a silhouette read by measuresil()plot_sil
Calculates the rotational inertia of a body. Only works with simple circular/elliptical and rectangular cross-sections, thus pixel-precise estimates are recommended.rotI
Estimate area of a superellipse. Assistant function for gdi.sellipse
calculate coordinates for plotting a superellipse for visualizing body cross-sectionssellipse.coo
Transfer a vector of aspect ratios onto another body profiletransfer_ratio
Finds the vertical (y axis, i.e. the axis parallel to the cross-section diameter) position of the center of mass (COM) of the volume. Experimental; only valid for "raw" gdi results with segment volumes approximated as elliptical prisms, or for manually supplied segment COMs. COM is calculated as a weighted mean of all segment COMs, with the segment mass as the weighting factor. Estimates have lower accuracy compared to hCOM, because cross-sectional geometry and variation in density throughout the cross-section is not taken into account.vCOM