RE: [MORPHMET] Problems with loading new files into tpsDig

2017-12-20 Thread F. James Rohlf 
1) Two possibilities: if the full path to the images option is not used then 
the images have to be in the same folder as the tps file (the solution is to 
copy the image files to the new location). Alternatively, if the full paths are 
used then the software will assume the images are still in the original 
location (solution is to edit the tps file using a simple editor such as 
Windows notepad and do a global search and replace to point to the new 
location. 

2) Seems a little odd. Note that just using a "reflex camera" is not enough - 
you have to also set the resolution to the desired level. By default tpsDig2 
should show the images to fill the screen. If they are in fact higher 
resolution then they should not be pixelated unless they are greatly enlarged. 
You could send me one image for me to look at to see if there is something 
special about the images.

F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution
Research Professor, Anthropology
Stony Brook University

-Original Message-
From: Lisa Krendl [mailto:lisa.maria.kre...@gmail.com] 
Sent: Tuesday, December 12, 2017 1:22 AM
To: MORPHMET 
Subject: [MORPHMET] Problems with loading new files into tpsDig

Dear all,

I have two problems in terms of dealing with the tpsDig program:

1)
I have been using tpsDig before to set landmarks, but since I rearranged my 
files and folders I always get an error report when I am trying to upload TPS 
files into the program. 

The error meassage is: 
Image file not found: C: 
Cannot open file "C:.". The system cannot find the indicated path.

I already tried to use different versions of tpsDig. I also deleted all the 
folders with my data and after transferring it back to my computer it still did 
not work. Why could that be?

2)
Besides that, I have one more issue with the program. For initial trials I used 
a compact camera. These pictures worked, but the pictures (image size: 1,06 MB) 
are a little blurred so I decided to use a single-lens reflex camera to obtain 
the pictures. The new pictures (image size: 5,77 MB) do not stretch across the 
whole user interface of the program and when I try to zoom in they get very 
pixelated. 
For further research I want to use the reflex camera. Do you know how I could 
solve the problem?

Your help is very much appreciated. Thank you very much in advance.

Kind regards,
Lisa Krendl

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RE: [MORPHMET] Issue with digit.fixed on 3D mesh geomorph

2017-12-20 Thread Murat Maga 
In my experience rgl tends to be slow with meshes with high number of vertices. 
You may want to do your data collection outside of R using programs optimized 
for handling high-resolution meshes, such as MeshLab or 3D Slicer, save your 
coordinates as a text file and import them into R.

M


From: Phillip Skipwith [mailto:pskipw...@gmail.com]
Sent: Friday, December 15, 2017 8:37 AM
To: MORPHMET 
Subject: [MORPHMET] Issue with digit.fixed on 3D mesh geomorph

Hi Everyone,

First: I apologize if this is a double posting.

I'm new to 3D geometric morphometrics, so this issue might turn out to be a 
trivial one with an easy fix. At the moment I'm trying to place landmarks on 
ply meshs (120 - 150k vertices) in geomorph using the digit.fixed function. 
However, when I set a landmark on a vertex of interest, the point does not 
attach to the correct spot. Rather, it vanishes somewhere deeper in the mesh. 
Increasing ptsize to something well above 3 helps a little, but not much. I 
realize that the help files use meshes below 30k vertices, but I lose a lot of 
information when I go that low. Has anyone else had this issue? Is it possible 
to select faces instead of vertices in geomorph (seems unlikely)?
I wondering if there was some special way of exporting ply files from Meshlab 
that I'm missing. At the moment I simplify my high resolution mesh with 
quadratic decimation, and then export the ASCII ply directly from Meshlab 
without fiddling with the settings. Is this right?

Any help would be greatly appreciated.

Best,

Skip
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[MORPHMET] Problems with loading new files into tpsDig

2017-12-20 Thread Lisa Krendl 
Dear all,

I have two problems in terms of dealing with the tpsDig program:

1)
I have been using tpsDig before to set landmarks, but since I rearranged my 
files and folders I always get an error report when I am trying to upload TPS 
files into the program. 

The error meassage is: 
Image file not found: C: 
Cannot open file "C:.". The system cannot find the indicated path.

I already tried to use different versions of tpsDig. I also deleted all the 
folders with my data and after transferring it back to my computer it still did 
not work. Why could that be?

2)
Besides that, I have one more issue with the program. For initial trials I used 
a compact camera. These pictures worked, but the pictures (image size: 1,06 MB) 
are a little blurred so I decided to use a single-lens reflex camera to obtain 
the pictures. The new pictures (image size: 5,77 MB) do not stretch across the 
whole user interface of the program and when I try to zoom in they get very 
pixelated. 
For further research I want to use the reflex camera. Do you know how I could 
solve the problem?

Your help is very much appreciated. Thank you very much in advance.

Kind regards,
Lisa Krendl

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[MORPHMET] Issues with placing 3D landmarks with digit.fixed

2017-12-20 Thread Phillip Skipwith 
Hi everyone,

I'm new to 3d geometric morphometrics, so this will be a very basic 
question to which there is probably a simple answer. I'm trying to place 
landmarks on meshes containing between 120,000 and 150,000 vertices using 
the digit.fixed function in geomorph. However, I'm finding it nearly 
impossible to select the desired vertex with the cursor. Rather, the point 
lands somewhere else deeper in the mesh, which is very frustrating. I've 
fiddled with ptsize, which helps a little when increased, but nothing seems 
to work without a lot of clicking around. Does anyone have any idea what's 
going on and if its possible to select the faces with this function (the 
function description makes this seem unlikely)? Alternatively, does anyone 
have any suggestions on how to best export .ply files from Meshlab that 
work best with geomorph and rgl? I've just been simplifying my hyper 
complex meshs with quadratic decimation and then exporting the ply. Should 
I be doing something in Meshlab that will make it easier to select vertices 
in R? Also, I realize that it the documentation for geomorph uses a mesh 
with less than 30,000 vertices, but I lose most of the useful information 
when I drop below 120k.

Any help would be greatly appreciated,

Skip

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