Dear List Members, I'm presently carrying out morphological analysis of a data set of neuronal structures. These are essentially 3D binary trees. In due course I will be trying to use discriminant analysis or other methods to classify these neurons based on morphological variables such as total tree length, segment number etc. I would like to calculate a 3D convex hull for a set of X,Y,Z data points which define the tips of my neurons. I have found the R function chull which finds a 2D convex hull, but not have found any 3D routines. I wondered if there were any packages / publicly available code I could use. Having found the convex hull, it would be handy if there were also functions to find the centroid, volume etc. I've only been using R for 10 days and am not much of a programmer, so I would rather not have to write code to interface to external C routines etc if possible. Very many thanks for any suggestions, Greg. P.S. I'm running R 1.3.1 on MacOS 9.1 __________________________________________________________________________ Greg Jefferis, Lab Address: Liqun Luo, Herrin 144 Neurosciences PhD Programme & e-mail: jefferis at stanford.edu Dept Biological Sciences, Lab: (650) 725 5809 Gilbert Biology Building, Fax: (650) 723 0589 371 Serra Mall, Stanford, CA 94305-5020. Home: (650) 497 1135 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
On Fri, 21 Sep 2001, Greg Jefferis wrote:> Dear List Members, > > I'm presently carrying out morphological analysis of a data set of neuronal > structures. These are essentially 3D binary trees. In due course I will be > trying to use discriminant analysis or other methods to classify these > neurons based on morphological variables such as total tree length, segment > number etc. > > I would like to calculate a 3D convex hull for a set of X,Y,Z data points > which define the tips of my neurons. I have found the R function chull > which finds a 2D convex hull, but not have found any 3D routines. I > wondered if there were any packages / publicly available code I could use. > Having found the convex hull, it would be handy if there were also functions > to find the centroid, volume etc. I've only been using R for 10 days and am > not much of a programmer, so I would rather not have to write code to > interface to external C routines etc if possible.3D convex hull programs are very much more specialized than 2D ones. When I added chull I looked at the possibility of allowing kD, k > 2, but it was hard to find suitable code, let alone interface to it. Known algorithms are far too complicated to implement tolerably at R level. netlib.bell-labs.com/netlib/voronoi/hull.html is one place I considered starting, but note the portability comments.> Very many thanks for any suggestions, > > Greg. > > P.S. I'm running R 1.3.1 on MacOS 9.1 > > __________________________________________________________________________ > Greg Jefferis, Lab Address: Liqun Luo, Herrin 144 > Neurosciences PhD Programme & e-mail: jefferis at stanford.edu > Dept Biological Sciences, Lab: (650) 725 5809 > Gilbert Biology Building, Fax: (650) 723 0589 > 371 Serra Mall, > Stanford, CA 94305-5020. Home: (650) 497 1135 > > -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- > r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html > Send "info", "help", or "[un]subscribe" > (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch > _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ >-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272860 (secr) Oxford OX1 3TG, UK Fax: +44 1865 272595 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
Prof. Ripley, Have you looked at the qhull software at www.geom.umn.edu/software/qhull (as I write this note, that link is not working for me. I could, however, get to http://www.cs.sunysb.edu/~algorith/implement/qhull/distrib/)? The paper that described the algorithm is http://www.acm.org/pubs/toc/Abstracts/toms/235821.html. I've thought about interfacing R to it (but have not actually tried). If it's not worth trying, I won't. Regards, Andy> -----Original Message----- > From: Prof Brian D Ripley [mailto:ripley at stats.ox.ac.uk] > Sent: Saturday, September 22, 2001 2:53 AM > To: Greg Jefferis > Cc: r-help at stat.math.ethz.ch > Subject: Re: [R] Finding a 3D convex hull in R > > > On Fri, 21 Sep 2001, Greg Jefferis wrote: > > > Dear List Members, > > > > I'm presently carrying out morphological analysis of a data > set of neuronal > > structures. These are essentially 3D binary trees. In due > course I will be > > trying to use discriminant analysis or other methods to > classify these > > neurons based on morphological variables such as total tree > length, segment > > number etc. > > > > I would like to calculate a 3D convex hull for a set of > X,Y,Z data points > > which define the tips of my neurons. I have found the R > function chull > > which finds a 2D convex hull, but not have found any 3D routines. I > > wondered if there were any packages / publicly available > code I could use. > > Having found the convex hull, it would be handy if there > were also functions > > to find the centroid, volume etc. I've only been using R > for 10 days and am > > not much of a programmer, so I would rather not have to > write code to > > interface to external C routines etc if possible. > > 3D convex hull programs are very much more specialized than 2D ones. > When I added chull I looked at the possibility of allowing kD, k > 2, > but it was hard to find suitable code, let alone interface to it. > Known algorithms are far too complicated to implement > tolerably at R level. > > netlib.bell-labs.com/netlib/voronoi/hull.html > > is one place I considered starting, but note the portability comments. > > > > Very many thanks for any suggestions, > > > > Greg. > > > > P.S. I'm running R 1.3.1 on MacOS 9.1 > > > > > ______________________________________________________________ > ____________ > > Greg Jefferis, Lab Address: Liqun > Luo, Herrin 144 > > Neurosciences PhD Programme & e-mail: > jefferis at stanford.edu > > Dept Biological Sciences, Lab: (650) 725 5809 > > Gilbert Biology Building, Fax: (650) 723 0589 > > 371 Serra Mall, > > Stanford, CA 94305-5020. Home: (650) 497 1135 > > > > > -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-. > -.-.-.-.-.-.-.-.- > > r-help mailing list -- Readhttp://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html> Send "info", "help", or "[un]subscribe" > (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch >_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._. _._>-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272860 (secr) Oxford OX1 3TG, UK Fax: +44 1865 272595 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-. -.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._. _._ -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._