-------- Original Message --------
Subject: Re: EVAN toolkit help
Date: Sun, 30 Oct 2011 18:46:51 -0400
From: Helgi Pétur Gunnarsson <[email protected]>
To: [email protected]
Hello Heather,
I am happy to hear that you are using the Evan Toolbox.
Hope you find it useful when doing your PhD project.
I have been working as a programmer on the Evan Toolbox and I think I
can help you with some of your questions.
1) The semi-landmarks actually slide on tangents perpendicular to the
surface so it is perfectly normal that they slide off it.
You have to project the landmarks back onto the surface after
you slide.
You may have to repeat a couple of times
(slide-project-slide-project), 2 or 3 timeshould be enough to converge.
Just make sure that you end with projecting the landmarks to
make sure they are on the surface.
Each set of semi-landmarks slides independently of other
semi-landmark sets, so you may have many sets of semi-landmarks for one
specimen.
2) Templand saves the landmark data in form files (*.frm), one file for
each specimen.
The "append" feature does not create a larger datafile, it only
adds the path of the form file to the tableau file (*.ltb).
The tableau file is basically a list of a list of form files
(and some other settings), but the actual landmark data is in the form
files themselves.
If you want to save the data in another format, (such as
Morphologika, NTS or raw text format) then you can use the Export Node.
Import the tableau file (*.ltb) with an Import node,
Connect the Import node to an Export node,
press the Play button
double click on the Export node and export the data in a format.
But I agree it would be good if the entire dataset could be
exported more easily directly fromthe Templand node.
3) The "View" option shows the Template and the current specimen.
The Template is generally the same for all specimens.
But if you want to change the current specimen, you can use the
forward and backward buttons on the bottom.
You can also import the specimens into the network directly
from Templand.
Connect the "All specimens" output of the Templand node to a
node in the network (like GPA node or a Viewer node).
In Templand, select File->Refresh Output ports
In the network part, Press the Play button.
There have been reports that the Templand node crashes on Windows 7,
when trying to export landmark from it.
Especially if Microsoft Office Groove (or Microsoft Office
Sharepoint Workspace) is installed.
If you have problems with Evan crashing I would suggest you uninstall
this component and try again.
Hope this helps,
regards,
Helgi Petur Gunnarsson
On 28 October 2011 17:44, morphmet <[email protected]
<mailto:[email protected]>> wrote:
-------- Original Message --------
Subject: EVAN toolkit help
Date: Fri, 28 Oct 2011 09:56:04 -0400
From: Heather Garvin <[email protected] <mailto:[email protected]>>
To: [email protected] <mailto:[email protected]>
Hi All,
I just downloaded the EVAN toolkit, which looks like it's going to
be an
awesome resource. I've gone through all the tutorials/reference
manuals,
but it seems like some areas are not completed within them, and I was
wondering if anyone has had experience with using 3D surface sliding
semilandmarks within the program, and would be willing to help me out.
1) First off with Templand - I've managed to make a template, and have
figured out how to project those semilandmarks onto the next specimen.
(I do the whole "Calculate & Warp" button.) I then project the points
onto the new specimen. Then I let the semilandmarks slide. In a number
of cases the semilandmarks actually slide off of the surface. After
letting the semilandmarks slide, should I then project the points back
onto the specimen again? Should I be treated the outline of the
specimen
(for simplicity sake think of a triangle), act as a different set of
semilandmarks, so that they slide independent of the other surface
semilandmarks? I'm sorry if these are general questions.
2) Let's say I have completed the process correctly, and have my
semilandmarks & landmarks. I know I can export the points individually
for each specimen. But the manual also seemed to imply that you could
"append" them, creating one large data set with all the individuals
(instead of having to combine all the files at the end by hand). I've
used the "append" button, but can't seem to figure out where I can
export the entire data set.
3) The manual also suggests that by appending the specimens, you can
then go back to the main window and use that data in subsequent
analyses. I'm running into 2 problems here.. I've used the "view"
tab to
see what's actually being uploaded into the program, and despite the
fact that I've appended 4 specimens, it only shows 2 (the template and
one other specimen, whichever is currently being viewed in the Templand
window). And if I try to do anything other than just view the
landmarks,
the program just crashes on me. I'm thinking if I export the data,
combine it into a single data set, and then just upload the dataset
instead of trying to run stuff straight from Templand, I may be able to
avoid these issues.
Bottom line - if anyone has experience with any of these scenarios
- any
guidance would be greatly appreciated! The current tutorials and
reference manuals were great for getting introduced to the program and
simple analyses. I'm sure there is similar documentations in
preparation
for more complex scenarios, I'm just not sure that my dissertation has
the privilege of waiting that that patiently.
Thanks in advance!
--Heather
*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~__~~~~~~~~
Heather Garvin*
PhD Candidate
Center for Functional Anatomy & Evolution
Johns Hopkins School of Medicine
http://www.hopkinsmedicine.__org/fae/HMG.htm
<http://www.hopkinsmedicine.org/fae/HMG.htm>
[email protected] <mailto:[email protected]>
