Re: [MORPHMET] Re: MeshLab - setting default FOV as Ortho?
Hi all, to set the Ortho view in MeshLab: "shift" + "scroll down" (using middle click). You can see the value on the left bottom. Antonio 2017-01-20 16:17 GMT+01:00 terrielsimmons <terrielsimm...@gmail.com>: > Hi Christy, > > I don't think there's a way to set Ortho as the default view. I just > change it with Windows --> View from... Meshlab 2016 has more options under > this menu, for example, to select front with the z up, like CT scans. You > can also hold shift and scroll the mouse wheel. > > Terrie > > > On Thursday, January 19, 2017 at 9:23:09 PM UTC-5, Christy Hipsley wrote: >> >> Hi all, >> >> Does anyone know if it's possible to set the Field of View (FOV) in >> MeshLab to Ortho as a default setting? It drives me nuts each time I open a >> file to have to change it, and I don't know why anyone would work in >> MeshLab without automatically changing this anyway. I've asked a couple of >> other colleagues but no happy solution so far - I'm hoping someone here >> might have the magic answer! >> >> Thanks, >> Christy >> > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > --- > You received this message because you are subscribed to the Google Groups > "MORPHMET" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet+unsubscr...@morphometrics.org. > -- __ Antonio Profico PhD Department of Environmental Biology – Dipartimento di Biologia Ambientale SAPIENZA Università di Roma Lab. 06 4991 2690 Mob. 3293440766 -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
Re: [MORPHMET] How to export .obj with textures as .ply with colours for morphometric analyses?
Dear Viviana, you can export the 3D model from MeshLab as wrl format (export mesh as). After, you can open and display the new mesh in Avizo (Display Open Inventor Scene). In this way you can acquire the landmark in Avizo. Best, Antonio 2016-09-01 13:31 GMT+02:00 M. Viviana Toro Ibacache < mtoroibaca...@odontologia.uchile.cl>: > Deal Morphometricians, > > I have .obj files with textures from three .jpg photos. I can load and see > the textures very nicely in Meshlab, but I need the textures to be > transformed into a coloured .ply file to do geometric morphometric analyses > (the landmarks are represented in the textures). So far it has not worked > doing it from Meshlab, so my questions are: > > - I know I can place landmarks in Meshlab using the .obj file, but when I > do it, the software crashes. any thoughts? the .obj file is 16 Mb big. Is > there a limit to files size in Meshlab? I would rather not to downsample > the mesh to not lose anatomical details. > > - When using the Transfer Texture to Vertex Color function, the texture > gets messed. It seems from web forums that Mshlab takes only one of the (in > this case) three .jpg files to do the colouring of the .ply mesh. Does > anybody know how to fix this? Another freeware software? > > - Is there any landmark acquisition software that loads .obj files with > textures? So far, I have not been able to do it in Landmark Editor, Evan > toolbox, Avizo, Morpho nor Geomorph. > > Any help is greatly appreciated. > > Best (y saludos), > Viviana > > > > -- > > *Viviana Toro-Ibacache DDS MSc PhD* > Profesora Asistente *(Assistant Professor)* > Centro de Análisis Cuantitativo en Antropología Dental (CA2) > Unidad de Anatomía, Instituto de Investigación en Ciencias Odontológicas > Facultad de Odontología Universidad de Chile > > Dirección: Sergio Livingstone Pohlhammer 943 > *(address)* Independencia, Región Metropolitana > Chile > Email:mtoroibaca...@odontologia.uchile.cl > Web: www.researchgate.net/profile/Viviana_Toro_Ibacache/ > www.cienciaymemoria.cl/staff.html > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > --- > You received this message because you are subscribed to the Google Groups > "MORPHMET" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet+unsubscr...@morphometrics.org. > -- __ Antonio Profico PhD Department of Environmental Biology – Dipartimento di Biologia Ambientale SAPIENZA Università di Roma Lab. 06 4991 2690 Mob. 3293440766 -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
Re: [MORPHMET] Question on Morpho
00 1.16e+08 > 16 5.60e+08 6360 1.17e+08 > 17 5.63e+08 6120 1.19e+08 > 18 5.66e+08 5820 1.21e+08 > 19 5.69e+08 5410 1.22e+08 > 20 5.71e+08 4800 1.22e+08 > 21 5.72e+08 3960 1.20e+08 > 22 5.73e+08 2960 1.19e+08 > 23 5.71e+08 2000 1.13e+08 > 24 5.93e+08 1110 9.49e+07 > 25 5.99e+08 1380 9.20e+07 > 26 6.04e+08 1650 8.87e+07 > 27 6.08e+08 1930 8.54e+07 > 28 6.11e+08 2230 8.19e+07 > 29 6.13e+08 2530 7.83e+07 > 30 6.14e+08 2830 7.44e+07 > 31 6.13e+08 3140 7.05e+07 > 32 6.12e+08 3460 6.64e+07 > 33 6.10e+08 3810 6.21e+07 > 34 6.05e+08 5970 5.27e+07 > 35 6.05e+08 6390 5.30e+07 > 36 6.04e+08 6780 5.28e+07 > 37 6.02e+08 7150 5.25e+07 > 38 6.01e+08 7530 5.22e+07 > 39 5.99e+08 7930 5.19e+07 > 40 5.96e+08 8350 5.13e+07 > 41 5.91e+08 8720 4.98e+07 > 42 5.84e+08 8880 4.73e+07 > 43 5.77e+08 9030 4.48e+07 > > , , 1865 > > X YZ > 1 4.06e+08 -3.58e+08 5.56e+08 > 2 3.76e+08 -2.90e+08 5.60e+08 > 3 3.62e+08 -3.32e+08 5.99e+08 > 4 3.84e+08 -3.85e+08 5.76e+08 > 5 3.89e+08 -3.84e+08 5.74e+08 > 6 3.93e+08 -3.83e+08 5.73e+08 > 7 3.98e+08 -3.81e+08 5.72e+08 > 8 4.01e+08 -3.79e+08 5.70e+08 > 9 4.03e+08 -3.77e+08 5.68e+08 > 10 4.05e+08 -3.74e+08 5.67e+08 > 11 4.07e+08 -3.71e+08 5.65e+08 > 12 4.08e+08 -3.68e+08 5.63e+08 > 13 4.08e+08 -3.64e+08 5.61e+08 > 14 4.07e+08 -3.45e+08 5.55e+08 > 15 4.09e+08 -3.40e+08 5.54e+08 > 16 4.11e+08 -3.36e+08 5.54e+08 > 17 4.11e+08 -3.31e+08 5.53e+08 > 18 4.10e+08 -3.26e+08 5.53e+08 > 19 4.08e+08 -3.21e+08 5.52e+08 > 20 4.02e+08 -3.16e+08 5.51e+08 > 21 3.97e+08 -3.10e+08 5.51e+08 > 22 3.92e+08 -3.02e+08 5.51e+08 > 23 3.85e+08 -2.94e+08 5.51e+08 > 24 3.68e+08 -2.87e+08 5.71e+08 > 25 3.67e+08 -2.88e+08 5.76e+08 > 26 3.67e+08 -2.88e+08 5.81e+08 > 27 3.66e+08 -2.90e+08 5.85e+08 > 28 3.64e+08 -2.94e+08 5.88e+08 > 29 3.63e+08 -2.98e+08 5.90e+08 > 30 3.61e+08 -3.02e+08 5.93e+08 > 31 3.59e+08 -3.07e+08 5.95e+08 > 32 3.57e+08 -3.13e+08 5.95e+08 > 33 3.56e+08 -3.20e+08 5.95e+08 > 34 3.66e+08 -3.40e+08 6.04e+08 > 35 3.68e+08 -3.42e+08 6.05e+08 > 36 3.69e+08 -3.45e+08 6.06e+08 > 37 3.69e+08 -3.48e+08 6.06e+08 > 38 3.70e+08 -3.52e+08 6.06e+08 > 39 3.70e+08 -3.56e+08 6.05e+08 > 40 3.71e+08 -3.61e+08 6.04e+08 > 41 3.70e+08 -3.66e+08 6.02e+08 > 42 3.69e+08 -3.71e+08 5.99e+08 > 43 3.67e+08 -3.77e+08 5.94e+08 > > , , 1880 > > X YZ > 1 3.49e+08 -1.07e+08 6.05e+08 > 2 3.17e+08 -2.81e+07 6.07e+08 > 3 3.00e+08 -6.88e+07 6.51e+08 > 4 3.22e+08 -1.39e+08 6.27e+08 > 5 3.30e+08 -1.36e+08 6.23e+08 > 6 3.37e+08 -1.34e+08 6.20e+08 > 7 3.42e+08 -1.32e+08 6.17e+08 > 8 3.47e+08 -1.30e+08 6.15e+08 > 9 3.50e+08 -1.27e+08 6.14e+08 > 10 3.52e+08 -1.24e+08 6.12e+08 > 11 3.53e+08 -1.21e+08 6.11e+08 > 12 3.53e+08 -1.19e+08 6.11e+08 > 13 3.52e+08 -1.15e+08 6.11e+08 > 14 3.50e+08 -9.35e+07 6.04e+08 > 15 3.53e+08 -8.75e+07 6.03e+08 > 16 3.54e+08 -8.14e+07 6.01e+08 > 17 3.55e+08 -7.53e+07 6.01e+08 > 18 3.54e+08 -6.91e+07 6.00e+08 > 19 3.53e+08 -6.26e+07 6.00e+08 > 20 3.50e+08 -5.61e+07 5.99e+08 > 21 3.44e+08 -4.97e+07 5.98e+08 > 22 3.38e+08 -4.26e+07 5.98e+08 > 23 3.30e+08 -3.65e+07 5.97e+08 > 24 3.11e+08 -2.72e+07 6.21e+08 > 25 3.09e+08 -3.05e+07 6.27e+08 > 26 3.09e+08 -3.28e+07 6.33e+08 > 27 3.09e+08 -3.43e+07 6.39e+08 > 28 3.09e+08 -3.73e+07 6.44e+08 > 29 3.07e+08 -4.08e+07 6.47e+08 > 30 3.06e+08 -4.44e+07 6.49e+08 > 31 3.05e+08 -4.82e+07 6.50e+08 > 32 3.04e+08 -5.23e+07 6.51e+08 > 33 3.03e+08 -5.67e+07 6.51e+08 > 34 3.04e+08 -7.65e+07 6.56e+08 > 35 3.05e+08 -8.11e+07 6.58e+08 > 36 3.06e+08 -8.54e+07 6.60e+08 > 37 3.07e+08 -8.99e+07 6.61e+08 > 38 3.08e+08 -9.48e+07 6.62e+08 > 39 3.09e+08 -1.00e+08 6.62e+08 > 40 3.10e+08 -1.07e+08 6.60e+08 > 41 3.08e+08 -1.13e+08 6.56e+08 > 42 3.06e+08 -1.20e+08 6.48e+08 > 43 3.05e+08 -1.28e+08 6.43e+08 > > > $NAs > NULL > > $NA.list > NULL > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > --- > You received this message because you are subscribed to the Google Groups > "MORPHMET" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet+unsubscr...@morphometrics.org. > -- __ Antonio Profico PhD Department of Environmental Biology – Dipartimento di Biologia Ambientale SAPIENZA Università di Roma Lab. 06 4991 2690 Mob. 3293440766 -- ___ *Il tuo 5 diventa 1000* Fai crescere la tua università Dona il 5 per mille alla Sapienza Codice fiscale: *80209930587* -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
Re: [MORPHMET] WarpRefMesh p x k matrix read problems.
Hi Asleigh, if you send me the objects "OriginScan", "Cer19Coords", "meanshape" I could help you! Are you sure that the objects mesh.coord and ref are two matrices? Try: class(Cer19Coords) class(meanshape) dim(Cer19Coords)==dim(meanshape) Best, Antonio 2017-12-04 15:10 GMT+01:00 ashleigh.haruda <ashleigh.har...@gmail.com>: > Hello all, > > I am stuck on what is probably a very easy issue but my normal sources for > troubleshooting just haven't been very helpful lately. > > I'm trying to visualize any kind of warps on a 3D .ply file. In the past, > I used a combination of MorphoJ and Landmark (IDAV) but the quality of the > images wasn't very good, so I'm attempting to use Geomorph in R to make > better quality visualizations. > > I have managed to import a .ply file for the most 'average' shaped > specimens and .dta files created in Landmark into Geomorph with no issues, > however whenever I attempt to execute WarpRefMesh (say, to make an average > reference mesh or for shape variation along PCs), I get this error: > > Error in warpRefMesh(OriginScan, Cer19Coords, meanshape) : > Input must be a p-x-k matrix of landmark coordinates > > I've attempted to sort this error out in a number of ways- I have checked > the dimensionality of each landmark matrix (Cer19Coords, meanshape), > ensured they are matrices, and even discarded my original .dta files to > attempt to re-landmark my OriginScan in Geomorph- all to no luck. I > continue to get this error even when I attempt to warp along PCs. > > Any suggestions on how I can get this work? I feel that I am missing > something basic here, but have been backwards and forwards through the > Geomorph manual for a couple of weeks now to no avail. > > Thanks, > > Ashleigh > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > --- > You received this message because you are subscribed to the Google Groups > "MORPHMET" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet+unsubscr...@morphometrics.org. > -- __ Antonio Profico PhD Department of Environmental Biology – Dipartimento di Biologia Ambientale SAPIENZA Università di Roma Lab. 06 4991 2690 Mob. 3293440766 -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
Re: [MORPHMET] creating mirror reflection of one-side landmarks
Hi Christy, you could use the function fixLMmirror() embedded in the Morpho R package. Here an example: library(Morpho) ?fixLMmirror #create dataset mat<-matrix(NA,ncol=2,nrow=10) #first 4 landmarks along the midplane mat[1:4,]<-rbind(c(3.01,2),c(3.0,2.1),c(2.99,2.3),c(2.99,2.5)) #three landmarks on the left side mat[5:7,]<-rbind(c(2,2),c(2.5,3),c(2.5,1.5)) #three missing landmarks on the right side plot(NA,xlim=c(1,6),ylim=c(1,4)) points(mat) #define left landmarks left<-c(5:7) #define right landmarks right<-c(8:10) pairedLM<-cbind(left,right) #in this case, the missing landmarks are 8, 9, 10 onesidefixed <- fixLMmirror(mat,pairedLM) points(onesidefixed[right,],col="red") Best, Antonio 2018-08-24 6:31 GMT+02:00 Christy Hipsley : > Dear all, > > I'm working with a 2D landmark data set of vertebrae in anterior view in > which one side (right) has been landmarked, with 5 landmarks along the > midplane axis for a total of 12 points. > > I would like to generate a mirror reflection of the paired landmarks, and > wonder if there is an easy way to do this. I naively tried multiplying the > x coordinate dimensions *-1 and keeping y the same, but since the midplane > x coordinates are not at 0 this obviously doesn't work. > > Any advice or code would be greatly appreciated! > > Thanks, > Christy > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > --- > You received this message because you are subscribed to the Google Groups > "MORPHMET" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet+unsubscr...@morphometrics.org. > -- __ Antonio Profico PhD Department of Environmental Biology – Dipartimento di Biologia Ambientale SAPIENZA Università di Roma Lab. 06 4991 2690 Mob. 3293440766 -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
Re: [MORPHMET] Script to read Avizo landmarks and B-splines
Hi Miguel, please send me the two files from Avizo (.ladmarkAscii) and B-splines (.am). Are you sure that read.amira.set() doesn't work with the .landmarkAscii files from Avizo? I'll add these two functions in Arothron and before to submit the new release to the CRAN I'll send them to you. Best, Antonio Il giorno lun 15 apr 2019 alle ore 01:26 Miguel Eduardo Delgado Burbano < mdelgadoburb...@gmail.com> ha scritto: > Dear All, > > I'm using landmarks (.ladmarkAscii) and B-splines (.am) derived from Avizo > (Standard Edition 7.1.0). I have used previously the Arothron and Nat > packages to load landmarks derived from Amira into the R console. Now > using the Avizo files such packages do not seem to work. Somebody has a > script to read Avizo files in R or know a way to succesfully load such > files into the R console? Thanks for any suggestion > > All best, > > Miguel > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > --- > You received this message because you are subscribed to the Google Groups > "MORPHMET" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet+unsubscr...@morphometrics.org. > -- __ Antonio Profico PhD Department of Environmental Biology – Dipartimento di Biologia Ambientale SAPIENZA Università di Roma MicroWeaR mailing list: https://groups.google.com/forum/#!forum/microwear Subscription: https://groups.google.com/forum/#!forum/microwear/join Arothron mailing list: https://groups.google.com/forum/#!forum/arothron <https://groups.google.com/forum/#!forum/microwear> Subscription: https://groups.google.com/forum/#!forum/arothron/join Lab. 06 4991 2690 Mob. 3293440766 -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
