A GNU Octave toolkit for analyzing diaphyseal long bone cross sectional geometry

long-bone-diaphyseal-CSG-Toolkit

A GNU Octave toolkit for analyzing diaphyseal long bone cross sectional geometry

The present set of GNU Octave functions provides a novel and robust algorithm foranalyzing the diaphyseal cross-sectional geometric properties of long bones, whichcan be applied to any 3D digital model of a humerus, femur or tibia bone representedas a triangular mesh in a Wavefront OBJ file format.

The CSG Toolkit requires the 'io >= 2.4.12', 'statistical >= 1.4.1' and 'matgeom >= 1.2.1'packages to be installed. Reading the .obj mesh files and calculating the cross sectionsrelies on the 'readObj', 'sliceMeshPlane', and 'longbone_Registration' functions,which should be compiled before their initial use.These can be compiled from within GNU Octave environment by issuing the following commands

mkoctfile readObj.ccmkoctfile slice_Mesh_Plane.ccmkoctfile longbone_Registration.cc

Alternatively, you may download and install the CSG Toolkit as a GNU Octave package fromthe archive 'csg-toolkit-1.2.1.tar.gz' which corresponds to the latest version. When installingthe packaged format, compiling and loaded paths are handled automatically. Download and run

pkg install csg-toolkit-1.2.1.tar.gz

to install from a locally downloaded archive, or issue the following command

pkg install "https://raw.githubusercontent.com/pr0m1th3as/long-bone-diaphyseal-CSG-Toolkit/master/csg-toolkit-1.2.1.tar.gz"

to automatically download and install it from online repository. Prior to using the CSG Toolkit,remember to run

pkg load csg-toolkit

Dependencies on aforementioned packages are still valid prior to installation , but they areautomatically loaded along with the csg-toolkit. Happy long bone analysis!

The CSG Toolkit can be called in batch processing mode using the 'longboneAnalysis'script which can handle all available 3D models found in OBJ format in the workingdirectory or any other folder path. Although this functionality is still available,there is no longer need to work with a specific bone being present in a folder for batchproccessing. The user may select a specific bone, i.e. Humerus, or may choose to processdifferent bones in a single batch process. Not selected bones are not processed.The need for MeshLab .pp side car files has been also relaxed. If they are present alongwith their OBJ counterparts, they are utilized, if not, the initial alignment points areautomatically registered with the 'longboneRegistration' function. Type

help longbone_Analysis

for information about its usage. The CSG Toolkit also provides functionality forgraphical representation of the cross-sectional contours and their respective CSGproperties, which can be accessed with the 'visualizeCrossSections.m' function byreading the output results of the longboneAnalysis stored in relevant CSV files. Whennumerous samples have been analyzed in batch mode, the function 'inspectCSG.m' can alsobe used to facilitate their visual inspection according to the files present in the workingdirectory. Furthermore, 'inspectCSG.m' will assemble all calculated values in tabularform and save them in a CSV file. Type

help inspect_CSG

for more information about how to use 'inspect_CSG.m' and the layout of the resulting CSV file.

The present toolkit has been extensively tested and these results are presentedin the relevant validation study available at doi:10.5281/zenodo.1466135.The testing dataset, which comprises three 3D mesh models of real humans bones (a humerus, a femur and a tibia, which are part of the Athens modern referenceskeletal collection), is also freely available at doi:10.5281/zenodo.1466962 and may be used with the CSG Toolkit for demonstrating its operation. Please, when using this toolkit,cite the following reference:

Bertsatos A, Chovalopoulou M-E. 2019. A novel method for analyzing long bone diaphyseal cross-sectional geometry. A GNU Octave CSG Toolkit. Forensic Science International 297: 65–71. DOI: 10.1016/j.forsciint.2019.01.041

To restore the repository download the bundle

wget https://archive.org/download/github.com-pr0m1th3as-long-bone-diaphyseal-CSG-Toolkit_-_2021-04-18_01-42-07/pr0m1th3as-long-bone-diaphyseal-CSG-Toolkit_-_2021-04-18_01-42-07.bundle

and run:

 git clone pr0m1th3as-long-bone-diaphyseal-CSG-Toolkit_-_2021-04-18_01-42-07.bundle 

Source: https://github.com/pr0m1th3as/long-bone-diaphyseal-CSG-Toolkit
Uploader: pr0m1th3as
Upload date: 2021-04-18

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