----- Forwarded message from andrea cardini <[email protected]> -----
Date: Thu, 6 Mar 2014 03:49:47 -0500
From: andrea cardini <[email protected]>
Reply-To: andrea cardini <[email protected]>
Subject: Re: missing landmark data in PAST/ error in .TPS-file?
To: [email protected]
Ben, I am not sure if the TPS format was actually
designed for 3D data too. I've always used it for
2D but possibly saw somewhere a 3D version.
However, if the reason why you're using it is
because the x, y, z coordinates are organized in
3 columns (and not in rows for each specimen as
in the PAST or MorphoJ format, there's a fairly simple way around this.
Use the 3D nts format and remove all labels
(specimens ID and variable names). NTS is fine
even if coordinates are in columns. Then import
the file in Morphologika, do the superimposition
without standardizing size, rotation and
translation (i.e., you leave the raw coordinates
as they are) and do the PCA but don't do anything
with those PCs from raw coordinates (it's only to
go to the next step). Now save the results as
CSV. You should get the coordinates reshaped as
an N by 3 times the number of your landmarks
matrix. They might be called "shape coordinates"
but since you did not really superimpose the
data, they should be identical to your orginal raw coord. Check it to be sure.
Those can be easily imported in PAST.
Good luck.
Cheers
Andrea
At 06:23 06/03/2014, you wrote:
>----- Forwarded message from [email protected] -----
>
>Date: Fri, 31 Jan 2014 20:39:55 -0800
>From: [email protected]
>Reply-To: [email protected]
>Subject: missing landmark data in PAST/ error in .TPS-file?
>To: [email protected]
>
>
>----- Forwarded message from "GRUWIER B.J." <[email protected]> -----
>
>Date: Thu, 30 Jan 2014 14:38:48 -0500
>From: "GRUWIER B.J." <[email protected]>
>Reply-To: "GRUWIER B.J." <[email protected]>
>Subject: missing landmark data in PAST/ error in .TPS-file?
>To: "[email protected]" <[email protected]>
>
>Dear Morphmet members,
>
>I've recently started experimenting with 3D gmm
>and have a (perhaps fairly basic) question about the use of certain software.
>
>I have (what I think is) a format problem... I
>used the LANDMARK-package to register a set of 8
>landmarks on a series of 3D scans. The program
>allows you to export the coordinate data to .PTS
>files, but I used a text editor to manually
>convert the files to the .TPS format (starting
>with LM=8 and then the 3 columns for the
>coordinate data) as I am more familiar with
>this. Finally I appended all data into one file.
>
>Now when I try to open this file in PAST, I
>always end up with a datamatrix containing only
>coordinates for the first five landmarks or so,
>even though there should be eight (24 columns).
>I have tried copying the missing data from the
>original .PTS-files, and that works fine, but
>there must be an easier way to solve this problem?
>
>I think there might be something wrong with the
>format in my .TPS files. Could anyone perhaps
>provide me with some examples of .TPS files with 3D-data?
>
>Thanks,
>
>Ben
>
>
>
>
>----- End forwarded message -----
>
>
>
>
>
>----- 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: [email protected], [email protected]
WEBPAGE: http://sites.google.com/site/hymsfme/drandreacardini
Summary of research interests at:
http://www.dscg.unimore.it/site/home/ricerca/aree-di-ricerca/evolution-taxonomy-and-forensics.html
FREE Yellow BOOK on Geometric Morphometrics:
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at:
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf
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 -----
