-------- Original Message --------
Subject: R-package for for shape analysis and mesh operations [under
development]
Date: Fri, 20 Jan 2012 04:33:23 -0500
From: Stefan Schlager <[email protected]>
To: [email protected]
Dear all,
as it seems that more and more people are using R and also are working
with triangular meshes, I also take the opportunity to share some
scripts with you:
I am developing an R package (which are basically functions coded for my
dissertation) called Morpho which allows a lot of mesh operations.
Including:
* importing all kinds of mesh formats (e.g. obj,ply,stl,...)
(file2mesh) and
* exporting objects of class "mesh3d" to ascii-ply format (mesh2ply)
* operations like TPS deformation, and affine transformations based on
landmark informations (warp.mesh, rotmesh.onto, scalemesh),
including the updating of faces’ normals.
* the imported objects are of class "mesh3d" so that they can be
rendered by the functions shade3d and wire3d from the rgl-package
* a function (called slider3d) allowing sliding of points, surfaces
and curves (using the bending energy criterion) and projecting the
slidden points back onto the 3D-mesh.
* There is also a function for semi-automatic placement of surface
patches (place.patch - yet undocumented) onto a whole sample based
on a initially defined atlas configuration.
* I’ve included functions for im- and exporting landmark-data from
landmark-IDAV (read.pts,write.pts,read.lmdta) and extracting the
information, if the coordinate belongs to a curve or surface from
imported pts files (c.extract), as I used this program to place the
curves and the atlas surface.
* There is also a GPA algorithm optimised for speed (procSym), useful
for big sample sizes and many (semi-)landmarks, that also allows
analysis of symmetry/asymmetry.
* CVA (thanks to M. Rufino from this mailing list for providing nice
examples in the documentation)
* some permutation tests
* graphical interface to find outliers (similar to MorphoJ)
And here comes the bad part: I’m a bit behind with the documentation, so
a lot code remains unexplained :(
If you're interested, you can download precompiled packages or the
source code from
https://sourceforge.net/projects/morpho-rpackage/files/
It is optimised for Linux but also works on OSX and Windows (with some
restrictions)!!!
For the full functionality you must also download some command line
tools which I coded using the header files of the meshlab/vcglib project
(http://meshlab.sourceforge.net/ ,
http://vcg.sourceforge.net/index.php/Main_Page) and install them (add
them to your system’s path). I recently managed to compile those not
only for Linux but also for OSX and Windows.
Read the README!!
It’s all licensed under GPL, so you also can rip it apart and improve or
adapt it, if necessary.
Best regards
Stefan
Stefan Schlager M.A.
Anthropologie
Medizinische Fakultät der der Albert Ludwigs- Universität Freiburg
Hebelstr. 29
79104 Freiburg
Anthropology
Faculty of Medicine, Albert-Ludwigs-University Freiburg
Hebelstr. 29
D- 79104 Freiburg
phone +49 (0)761 203-5522
fax +49 (0)761 203-6898
