----- Forwarded message from andrea cardini <alcard...@gmail.com> -----
Date: Thu, 23 May 2013 03:46:45 -0400
From: andrea cardini <alcard...@gmail.com>
Reply-To: andrea cardini <alcard...@gmail.com>
Subject: Re: Missing landmarks in 3D
To: morphmet@morphometrics.org
Hi Diego,
I seem to remember that there might be 'secret
commands' to do that in Morpheus. If there are,
Dennis will tell you, I am sure.
I do it manually: it's a bit tedious but not that
hard using a combination of Morpheus and xls.
Now I can remember how I do it when I collect
points only on one side (say the left) and want
to create a mirror reflected symmetric structure
(removing small asymmetries on the midplane and
creating a 'fake' right side which is identical
to the left side). This should be explained in
one of my papers (probably this one: Cardini A.,
Diniz Filho J. A. F., Polly P. D., Elton S., 2010
-
<http://docs.google.com/fileview?id=0B7MW9En7Pb3VYWQ5NWM3YzktOGU3Ny00YTE1LTg3YTYtZmFjOGNmZDVmZGIx&hl=en_GB>Biogeographic
analysis using geometric morphometrics: clines in
skull size and shape in a widespread African
arboreal monkey. A. M. T. Elewa (Ed.),
Morphometrics for Nonmorphometricians, Lecture
Notes in Earth Sciences 124, Springer-Verlag
Publishers, Heidelberg, Germany. DOI
10.1007/978-3-540-95853-6_8 - PDF IN MY PUBLICATION WEBPAGE).
If you symmetrize your skulls (or whatever the
bilaterally symmetric structure is), it should work about the same way.
For estimating just a few missing points without
symmetrizing, I would possibly try something like this:
1) load the data in Morpheus;
2) use the demote command (in the cited paper) to
exclude all points except those on the miplane
(which means that only those points will be used
in the GPA but all the others - matching
landmarks - will be also rescaled, translated and rotated);
3) do the GPA and, if the PCA orientation option
is on, that should (I guess) make the midplane
landmarks about co-planar with X Y or (X Z or Y
Z), which is about the same trick you used in 2D;
4) rescale the whole configuration, export it and
replace the missing point(s) after swapping the
sign of the coordinate axis which was not on the miplane.
I guess that point 2) can be done by actually
demoting all points except 3 miplane landmarks
(distant ones, I'd say) so that the midplane
superimposed points lie exactly on the same plane.
I may be wrong! Please, check carefully.
I'd love to try it myself but I am stuck with lectures for a few more weeks.
Good luck.
Cheers
Andrea
At 05:44 23/05/2013, you wrote:
>----- Forwarded message from Diego Astua de
>Moraes <d.a.mor...@gmail.com> -----
>
>Date: Wed, 22 May 2013 09:50:23 -0400
>From: Diego Astua de Moraes <d.a.mor...@gmail.com>
>Reply-To: Diego Astua de Moraes <d.a.mor...@gmail.com>
>Subject: Missing landmarks in 3D
>To: morphmet@morphometrics.org
>
>This may be obvious to several here, but as this
>is our first work with 3D lmks, I probably missed an easy step.
>Is there a straightforward way to obtain a
>landmark by reflecting its symmetric through the
>saggital plane (I want to replace a missing lmk
>that is present on the other side). I can do
>that easily in 2D by translating and rotating
>the midline so that it matches the x or y axis,
>and the obtain the reflected lmk, but I don´t
>deal that well with 3D translations and rotations...
>I would like to do that on my landmark set
>before "gluing" the dorsal and ventral datasets
>on DVLR. DVLR does provide the option of a
>missing landmark but it is still missing the the combined view...
>In time, I am only going through this because my
>sample size for this particular taxon is really
>small and every specimen matters, and because
>the missing landmark is a different one in each
>specimen (meaning I cannot simply discard that lmk...).
>Thanks
>Diego
>
>Diego Astúa de Moraes, D.Sc.
>Laboratório de Mastozoologia
>Departamento de Zoologia, Universidade Federal de Pernambuco
>Av. Professor Moraes Rego, s/n. Cidade Universitária
>50670-420 Recife, PE, Brasil.
>Te./Fax: (81) 2126-8353
>email:
><mailto:d.a.mor...@gmail.com>d.a.mor...@gmail.com
> / <mailto:diegoas...@ufpe.br>diegoas...@ufpe.br
><http://www.ufpe.br/mastozoologia/>http://www.ufpe.br/mastozoologia/
>
>
>
>----- End forwarded message -----
>
>
Dr. Andrea Cardini
Researcher in Animal Biology
Dipartimento di Scienze Chimiche e Geologiche,
Università di Modena e Reggio Emilia, l.go S. Eufemia 19, 41121 Modena, Italy
Honorary Fellow
Centre for Anatomical and Human Sciences
University of Hull, Cottingham Road, Hull, HU6 7RX, UK
University of York, Heslington, York YO10 5DD, UK
Adjunct Associate Professor
Centre for Forensic Science , The University of Western Australia
35 Stirling Highway, Crawley WA 6009, Australia
E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
Webpage: http://sites.google.com/site/hymsfme/drandreacardini
Datasets:
http://ads.ahds.ac.uk/catalogue/archive/cerco_lt_2007/overview.cfm#metadata
Editorial board for:
Zoomorphology:
http://www.springer.com/life+sciences/animal+sciences/journal/435
Journal of Zoological Systematics and
Evolutionary Research: http://www.wiley.com/bw/journal.asp?ref=0947-5745&site=1
Hystrix, the Italian Journal of
Mammalogy: http://www.italian-journal-of-mammalogy.it/
----- End forwarded message -----
