Hello All, I was thinking about using TpsRelw to slide semilandmarks before analysing the aligned specimens data in MorphoJ, but does it really make sense to double the alignment? Even if I have the file after TpsRelw, where landmarks and semilandmarks are treated differently, im MorphoJ I make the alignment - Procrustes fit again, in which the semilandmarks are treated as landmarks, they are computed as landmarks. So, do I lose the information on the placement of semilandmarks or not in MorphoJ? Best, Joanna
2017-06-22 11:18 GMT+02:00 Paolo Piras <paolopir...@gmail.com>: > Hi folks/Andrea, > > just to underline this: > > Andrea,when you say > > "an 'apparent size variable' which is a series of numbers virtually equal > to 1 (differences will be approximation errors)." > I think that MorphoJ "reads" the actual CS values from the aligned > coordinates saved by TPSrelw that, as you say, have lost their original > size. However, small deviations from 1 are not due to approximation error > as I *suspect* that the "aligned coordinates" saved by TPSrelw are those > projected on the tangent plane (by an orthogonal [more commonly used] or > stereographic projection) and for this reason they have necesarily a CS > larger than 1 that is the radius of the hyperspherical Kendall's Shape > Space. In order to reach the tangent plane from the sphere one necessarily > must go beyond its radius (that geometrically *IS* the size of a > configuration lying on that space) and the CS will be inevitably larger > than 1. > An indirect proof for this would be to verify that what you call > "approximation error" gives CS values always slightly larger than 1 and > never smaller. > So I think there is no error in having, for those data, CS > slightly different (=larger) from 1 as they MUST have CS larger than 1 by > construction. > However,I'm not sure at 100% if TPSrelw works as I hypothesized here.. > Playing a bit with TPSrelw could unveil this. > All the best > Paolo > > > 2017-06-22 11:00 GMT+02:00 andrea cardini <alcard...@gmail.com>: > >> Hi Pere, >> there's plenty of work arounds this. I agree with Carmelo that the nts >> format may be easier to edit manually, so that you can put back the >> necessary labels. >> >> HOWEVER, PLEASE BE CAREFUL because SIZE WILL BE MISSING from those data. >> As most of the time you may want to analyse both size and shape, instead of >> importing in MorphoJ the aligned specimens from the TPSRelw slid >> configurations, I'd suggest to save the SCALED ALIGNED SPECIMENS in >> TPSRelw. Jim added this option for this purpose: this way you get the >> aligned specimens rescaled to the original centroid size. Therefore, when >> you import them in MorphoJ and redo the Procrustes fit, you will get both >> the aligned specimens as well as their size. >> In contrast, if you import the aligned data (not rescaled), size won't be >> there but you may be easily tricked and think it is there, because MorphoJ >> requires that you redo the Procrustes fit and then you'll get an 'apparent >> size variable' which is a series of numbers virtually equal to 1 >> (differences will be approximation errors). >> Use the scaled aligned and you won't have this issue. >> >> Cheers >> >> Andrea >> >> On 22/06/17 10:07, Pere Ibáñez wrote: >> >>> Hello All, >>> >>> I am using TPSRelW to slide semilandmarks. Once I have the consensus, I >>> use Save aligned to export the aligned coordinates (including slid >>> semilandmarks) as a tps file, that I want to import into MorphoJ. >>> >>> The problem is that the file that is exported has the IDs of the >>> specimens empty, with no information. And MorphoJ doesn't import it without >>> that information, so I have to type it one by one on the tps file. Does >>> anyone know how to export that tps file from TPSRelW without losing the ID? >>> >>> Thanks! >>> >>> -- >>> 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 <mailto: >>> morphmet+unsubscr...@morphometrics.org>. >>> >> >> -- >> >> Dr. Andrea Cardini >> Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di >> Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy >> tel. 0039 059 2058472 >> >> Adjunct Associate Professor, School of Anatomy, Physiology and Human >> Biology, The University of Western Australia, 35 Stirling Highway, Crawley >> WA 6009, Australia >> >> E-mail address: alcard...@gmail.com, andrea.card...@unimore.it >> WEBPAGE: https://sites.google.com/site/alcardini/home/main >> >> FREE Yellow BOOK on Geometric Morphometrics: >> http://www.italian-journal-of-mammalogy.it/public/journals/3 >> /issue_241_complete_100.pdf >> >> ESTIMATE YOUR GLOBAL FOOTPRINT: http://www.footprintnetwork.or >> g/en/index.php/GFN/page/calculators/ >> >> -- >> 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. >> >> > -- > 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. > -- Joanna Lenarczyk Zakład Fykologii Instytut Botaniki im. W. Szafera Polskiej Akademii Nauk ul. Lubicz 46, 31-512 Kraków tel. 12 42 41 876 Department of Phycology W. Szafer Institute of Botany, Polish Academy of Sciences Lubicz 46, PL-31-512 Cracow phone +48 12 42 41 876 e-mail: j.lenarc...@botany.pl -- 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.
