[MORPHMET] tpsUtil update

2019-04-10 Thread f.james.rohlf 


I have uploaded ver. 1.78 of tpsUtil to the http://life.bio.sunysb.edu/morph
website.

 

It just fixes an internal exception error when one completes the "unbending"
option (after the output file was saved). Thanks to Gabriel Gazzana Barros
for reporting the problem.

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

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RE: [MORPHMET] Statistics software question

2019-01-31 Thread f.james.rohlf 
An improved version of this  type of correction  (the delta-corrected K-S test 
for an intrinsic null hypothesis) is discussed in the text Biometry (Sokal and 
Rohlf, 4th ed. 2012) and a table Y is also provided for this test.  It should 
be more widely known and appreciated.

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

From: Novack-Gottshall, Philip M.  
Sent: Thursday, January 31, 2019 7:54 AM
To: Justin Bagley 
Cc: Novack-Gottshall, Philip M. ; 
morphmet@morphometrics.org
Subject: Re: [MORPHMET] Statistics software question

 

Thanks, Justin! I've checked out whichever help docs I can find, but I've 
discovered that sometimes a particular "correct" is not always mentioned, even 
when used in the software.

The reason I'm checking is that I'm a co-author on an R package (LcKS) that 
implements the Lilliefors correction for the one-sample goodness-of-fit 
Kolmogorov-Smirnoff test and we're writing a manuscript to accompany it. 
Apparently the correction is not widely used or known about (outside of the 
statistical community), and it's a major oversight. (For example, ks.test in R 
[very subtly] cautions the user about the violation but does not actually offer 
a fix, and it's not available in base R or 'stats'.) We've discovered many 
published articles that appear to do the test in the incorrect manner. Our 
package and manuscript, we hope, will help improve the situation by calling 
attention to the bias and offering a simple solution.

Best wishes,
Phil

On 1/31/2019 11:46 AM, Justin Bagley wrote:

Dear Phil, 

 

SAS has excellent support and documentation. Just go to their website at 
https://support.sas.com/en/documentation.html, type in a search query for the 
statistical test of interest, and you'll get links to the appropriate section 
of the SAS/STAT 14.3 User's Guide. Detailed information is given on statements 
to call different tests. You should be able to quickly find the information you 
need using this procedure (with a statistics text in hand), and I imagine that 
similar online documentation resources are available for the other major 
programs that you mentioned. 

 

Nevertheless, all in all, I don't recommend that you go with _any_ of the 
software programs in your list for statistical analyses of biological data, 
unless they are the only software programs that implement the test you need. 
Instead, I suggest that you conduct statistical analyses in the R environment 
for statistical computing (https://cran.r-project.org) or write bash or Python 
wrapper scripts around existing programs to conduct your analyses. Is there not 
an R package that will conduct the test you need to do?

 

Since we received this through MORPHMET, perhaps you could state the question 
you have about the "particular statistical test" in question in a way that is 
specific and that relates to morphometrics, and I'm sure that someone would be 
able to help you out in more detail.

 

Good luck.

 

Best,

 

Justin C. Bagley, Ph.D.

Postdoctoral Research Associate

Department of Biology

University of Missouri-St. Louis

One University Boulevard, 223 Research Building

St. Louis, MO 63121-4499

E-mail: bagl...@umsl.edu  

Website: https://justinbagley.org

CV: https://justinbagley.org/pages/cv.html

Blog: https://justinbagley.rbind.io

 

Affiliate Researcher

Department of Biology

Virginia Commonwealth University

1000 W Cary St, Rm 126,

Richmond, VA 23284-2012

 

 

 

On Thu, Jan 31, 2019 at 11:04 AM Novack-Gottshall, Philip M. 
mailto:pnovack-gottsh...@ben.edu> > wrote:

Hi all,

Apologies for cross-posting, but I'm not sure where this best lands.

I'm trying to find people who have access to (preferably some experience
with) any of the following statistical software programs:
-MiniTab
-SAS
-SPSS
-S-Plus
-STATA
-SYSTAT

If you do, might you contact me off-list mailto:pnovack-gottsh...@ben.edu> >?
I'm trying to find out how each program handles a particular statistical
test. My question can likely be answered with a quick check of the help
documentation for the software or by running a sample data set I can
provide, if interested.

Thanks,
Phil

~
  Phil Novack-Gottshall, PhD
  Professorpnovack-gottsh...@ben.edu 
 
  Department of Biological Sciences
  Benedictine University
  5700 College Road 
  Lisle, IL 60532

  Office: 332 Birck Hall
  Lab: 316 Birck Hall
  Phone: 630-829-6514
  Fax: 630-829-6547
  https://pnovack-gottshall.wixsite.com/home

  Spring 2019 office hours:  Tues/Thurs 9:30-11:00 AM
 Wed 10 AM - 12:15 PM

  If you have urgent academic advising questions, please contact
  Anne Baysinger (Birck 130)
 ~


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Re: [MORPHMET] MorphoJ: problem with reading the tps files

2019-01-02 Thread f.james.rohlf 
Yes, on the options menu there is an option to set the decimal charactet.


__F. James Rohlf, Distinguished Prof. Emeritus Dept. 
Anthropology and Ecology & Evolution Stonybrook University
 Original message From: morphmet  
Date: 1/2/19  7:02 AM  (GMT-10:00) To: morphmet@morphometrics.org Subject: Re: 
[MORPHMET] MorphoJ: problem with reading the tps files 
Your system is set up to us commas (',') to mark the decimal instead of 
the period ('.'). I think there is an option as to which to use within 
the tps programs. Some morphometrics programs assume the use of the 
period. -ds

On 12/31/18 2:55 PM, Ewa Krzeminska wrote:
> When trying to create a dataset from a tps file I got a response: Invalid 
> number format in the file. The file was created in TpsDig, and the text in a 
> notepad is:
> LM=18
> 943,0 1455,0
> 902,0 1097,0
> 947,0 981,0
> 954,0 866,0
> 945,0 632,0
> 954,0 397,0
> 817,0 1313,0
> 664,0 1335,0
> 797,0 1429,0
> 559,0 1477,0
> 679,0 1503,0
> 391,0 1217,0
> 485,0 1093,0
> 533,0 914,0
> 880,0 809,0
> 849,0 715,0
> 707,0 802,0
> 496,0 632,0
> IMAGE=3572.jpg
> ID=0
> 
> The option "tps" was chosen. What can be wrong?
> 

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RE: [MORPHMET] PC1 correlation with CS and length

2018-12-26 Thread f.james.rohlf 
PC1 by definition corresponds to the direction of maximum variance in your 
data. Within a species and sex this usually corresponds to size and/or age if 
you include specimens that do vary in size. However, if you include different 
species and sexes or specimens that are about the same size then the direction 
of maximum variation could be anything depending on how you choose which 
species or morphs to include.

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

From: Tarek Ismail  
Sent: Wednesday, December 26, 2018 5:17 AM
To: MORPHMET 
Subject: [MORPHMET] PC1 correlation with CS and length

 


Hi all
I wish to discuss a part of my work result. Studying ontogeny of a land isopod, 
and after PCA analysis, I have  no correlation between PC1 and body length as 
well as with centroid size of pooled data (adults and juveniles) and also for 
adults. Since PC1 usually interpreted  as a size related axis, what can be the 
reason beyond this unexpected relationship. Gardner et al., (2016) study the 
Symmetry in the Core Goodeniaceae (not the case here) and found no correlation 
between length and centroid size. They attributed that to the Symmetrical 
variation rather than as a consequence of asymmetric or allometric factors. 
I decrease the number of landmarks, but have the same result.

I attach the PCA Fig., it represent half number of specimens, F=females; 
M=males and U=juveniles. 

 

Thanks in advance

 

Tarek G. Ismail

Sohag University, Egypt

t_gad_2...@sohag.edu.eg  

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Re: [MORPHMET] Setting Scale for a large group of images on tpsDIG2

2018-12-21 Thread f.james.rohlf 
If you set the scale for the first one it will be used for all the rest.
__F. James Rohlf, Distinguished Prof. Emeritus Dept. 
Anthropology and Ecology & Evolution Stonybrook University
 Original message From: marcos patricio 
 Date: 12/21/18  1:21 AM  (GMT-10:00) To: 
morphmet@morphometrics.org Subject: [MORPHMET] Setting Scale for a large group 
of images on tpsDIG2 
Greetings,
I'm curently working with a set of images and I photographed all my subjects 
under the same conditions (zoom, lens, lights, etc). I have a scale, I used 
tpsDIG2 for placing the landmarks and I wish to place scales in all images 
(over 1000 images) but I wish to set scales for all images at once, and not go 
to each image and set over 1000 scales individually.I think I've seen this 
feature before on tpsDIG but I can't find it now, so, if any of you could help 
me with this issue, I appreciate.
Thanks a lot



-- 
Marcos Patrício Macedo, 
Laboratório de Biologia Evolutiva, Departamento de Genética e Morfologia
Universidade de Brasília, Brasília, DF, 70910-900, Brasil




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Re: [MORPHMET] Re: Multivariate PICs?

2018-03-29 Thread f.james.rohlf 
The thing to remember is that the comparative methods adjust for the lack of 
independence of the observations. Thus variables being multivariate does not 
change the computation of PICs or, preferred,  the use of generalized least 
squares.
__F. James Rohlf, Distinguished Prof. Emeritus Dept. 
Anthropology and Ecology & Evolution Stonybrook University
 Original message From: Sarah Friedman  
Date: 3/29/18  8:08 AM  (GMT-10:00) To: MORPHMET  
Subject: [MORPHMET] Re: Multivariate PICs? 
Dean,
Thank you for the thorough and informative response.  For the record, I checked 
with Chris Klingenberg and he confirmed that MorphoJ calculates PICs along each 
dimension individually as well. I think I'll opt for this method over the 
McPeek procedure. 
Much appreciated,Sarah

On Tuesday, March 27, 2018 at 11:02:10 AM UTC-7, Sarah Friedman wrote:Hi all,



Primarily, I'm wondering if there is a way to calculate phylogenetic 
independent contrasts on multivariate shape data in R. However if no R method 
exists, I know a method to do this is implemented in MorphoJ, and I could 
possibly code an analogous method in R but I'm unsure how the contrasts are 
calculated. Does anybody know if the independent contrasts are calculated using 
the method described in McPeek (1994), the Euclidean distances between 
contrasts on each branch, or another method? 



Thanks,

Sarah



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RE: [MORPHMET] digitizing very variable leaves

2018-03-15 Thread f.james.rohlf 
One could do that computationally but I would worry about the homology it might 
imply for such variable leaf shapes. You might try it and then check to see if, 
for example, a lobe on one leaf might be 20% of the linear distance around the 
outline but in another it might be 30% of the way around. In such a case the 
lobe on one leaf would effectively be treated as homologous to a location 
between lobes on another leaf. If so, does that make biological sense for your 
study? If simple leaves were also included the implied homology of a point 
along its outline to that of one of the lobed leaves might be pretty arbitrary. 
Would be better if one knew something about the development of these leaves 
(which I do not!) and used that knowledge. 

 

An alternative would be to use outline methods to group shapes for the purpose 
of say identification with little implication that groups need be biologically 
meaningful. Sorry to be rather negative but I find highly variable leaf shapes 
difficult to put in a simple standard framework. Perhaps others will have 
better suggestions.

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

From: Tina Klenovšek <tina.klenov...@um.si> 
Sent: Wednesday, March 14, 2018 12:28 AM
To: f.james.rohlf <f.james.ro...@stonybrook.edu>
Cc: morphmet@morphometrics.org
Subject: RE: [MORPHMET] digitizing very variable leaves

 

Thanks to everyone who answered.

 

Dear Dr. Rohlf,

I assumed great variability would be a problem.

I was thinking the best way of digitizing would be to draw a curve on the 
outline of each leaf (simple and lobed leaves). Resample curves by length with 
approx. 40 landmarks. Then append curves to landmarks. Two landmarks, the leaf 
tip and base, would be fixed others could be defined as semi-landmarks. Is this 
sensible?

Alternatively, we could analyse simple and lobed leaves separately.

Thank you a lot for your help.

 

Tina

  

 

From: f.james.rohlf [mailto:f.james.ro...@stonybrook.edu] 
Sent: Wednesday, March 14, 2018 3:59 AM
To: Tina Klenovšek
Subject: Re: [MORPHMET] digitizing very variable leaves

 

An assumption of the usual GMM methods is that shape variation is "small". I 
think these leaves exceed this quite a bit! Another problem is landmarks. How 
to match leaves with and without lobes?

 

__

F. James Rohlf, Distinguished Prof. Emeritus 

Dept. Anthropology and Ecology & Evolution 

Stonybrook University

 

 Original message 

From: 'Tina Klenovšek' via MORPHMET <morphmet@morphometrics.org 
<mailto:morphmet@morphometrics.org> > 

Date: 3/12/18 10:56 AM (GMT-10:00) 

To: morphmet@morphometrics.org <mailto:morphmet@morphometrics.org>  

Subject: [MORPHMET] digitizing very variable leaves 

 

Hello everyone,

 

we would like to digitize tree leaves that are very variable (from simple oval 
to strongly lobed on one tree). 

1.)I am wondering if TpsDig can do some kind of automatic digitizing like 
the LeafAnalyser software: 
http://www.plant-image-analysis.org/software/leaf-gp, which evenly distributes 
a defined number of landmarks on the leaf outline... 

LeafAnalyser does not seem flexible or precise enough. Or I can’t use it 
properly. Any experience?

 

2.)Is it possible/sensible to put objects that are so differently shaped 
(photos attached) into the same group or is it better to analyse simple and 
lobed leaves separately?

 

I apologize if similar questions have been already answered... 

 

Kind regards,

Tina

 

 

 

 

 




doc. dr. Tina Klenovšek, koordinatorica doktorskega 

študijskega programa Ekološke znanosti
Univerza v Mariboru | University of Maribor

Fakulteta za naravoslovje in matematiko
Faculty of Natural Sciences and Mathematics
Koroška cesta 160, 2000 Maribor, Slovenija

T: +386 41 808 366

E:  <mailto:ime.prii...@um.si> tina.klenov...@um.si,  
<http://www.fnm.uni-mb.si> www.fnm.um.si

 

 

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Re: ***SPAM*** [MORPHMET] Re: Digitizing landmarks on live larvae

2018-03-13 Thread f.james.rohlf 
Actually the rule is that the number of specimens should be larger than the 
number of variables 2p-4 not p landmarks in the case of 2D data.


__F. James Rohlf, Distinguished Prof. Emeritus Dept. 
Anthropology and Ecology & Evolution Stonybrook University
 Original message From: Carmelo Fruciano  
Date: 3/12/18  9:51 PM  (GMT-10:00) To: MORPHMET  
Subject: Re: ***SPAM*** [MORPHMET] Re: Digitizing landmarks on live larvae 

Dear Avi,
I guess it's hard to formulate any rule of thumb.
Some analyses might not be defined if the number of variables
  exceed the number of observations. Some other analyses might be
  defined (there is many distance-based analyses nowadays which
  circumvent that problem).
However, whether a given analysis is defined doesn't mean that
  the inference is necessarily accurate. I guess it depends on what
  you plan to test/measure and the effect size you expect.



Andrea Cardini has some papers that can give you some hint on
  this, such as:
Cardini & Elton 2007 - Zoomorphology


Cardini et al. 2015 - Zoomorphology
Cardini & Elton 2017 - Hystrix


They should be downloadable from his website
  https://sites.google.com/site/alcardini/home/pubs






Obviously, having an idea of variation on your own data would be
better.

I hope this helps.

Carmelo









On 3/12/2018 8:27 PM, Avi Koplovich
  wrote:



  Hi Carmelo,

Thank you for those answers.

One more question please:

I know that the number of specimens should exceed the number of
the total landmarks (fixed-landmarks + semi-landmarks). Is there
a rule of thumb of by how much or what ratio between specimens
to semi-landmarks one should keep?
Thank you,
Avi




On Sunday, March 11, 2018 at 5:15:24 PM UTC+2, Carmelo Fruciano
wrote:

  

  

  Il 6/03/2018 4:44 PM, Avi Koplovich ha scritto:
  

  > Hi Carmelo,
  

  > Thank you for your answer.
  

  > My project tests for the influence of kairomones of a
  predator fish on 

  > the morphology of Salamander larvae during its
  development. To do this, 

  > I take pictures every other week of larvae spawned from
  six different 

  > females and assigned to 3 treatments: No fish, 3 caged
  fish, 6 caged fish.
  

  

  Hi Avi,
  

  it sounds like an interesting experiment. I will try to answer
  to your 

  questions but keeping in mind that I'm not very knowledgeable
  on 

  salamander development.
  

  

  >  1. I intend to use landmark 1 (dorsal connection of the
  tail fin) as a
  

  >     fixed factor. But I thought I may be able to use the
  tail tip
  

  >     (landmark 20) and head tip (landmark 48) as fixed
  landmarks as well.
  

  >     Do you think it's ok in an ontogeny experiment?
  

  

  I guess it will depend on how long into ontogeny you will
  track the 

  larvae and whether or not that point will "disappear" over
  ontogeny 

  and/or slide unreasonably (depends also on your question).
  You, being 

  knowledgeable on their biology, are the best judge on that.
  

  

  > If not, do you think
  

  >     it's ok to slide all semi-landmarks of the tail on
  landmark 1, and
  

  >     all head semi-landmarks on an eye landmark? Since the
  eye isn't part
  

  >     of the head contour, is it ok if I slide one
  semi-landmark to the
  

  >     eye and all rest semi-landmarks of the head one to
  each other as a
  

  >     closed shape?
  

  

  The point(s) slid relative to the eye won't be sliding along
  the 

  direction tangent to the curve you want to approximate (i.e.,
  the 

  curvature of the head). A good starting point on the method
  could be
  

  Gunz & Mitteroecker 2013 - Hystrix
  

  

  >  2. Is it ok if landmarks 1 and 39 slid relative to each
  other as well
  

  >     as 41 and 55, since both describe a closed shape?
  

  

  It's not particularly desirable (see answer above).
  

  

  >  3. Another worry I have is that landmark 40 which I used
  to create the
  

  >     comb fan for both the tail and the head

RE: [MORPHMET] Digitizing landmarks on live larvae

2018-02-28 Thread f.james.rohlf 
Bending of long slender organisms (or other structures) can be an important 
practical problem. Changes due to bending could dominate the results. 
Separating sets of landmarks into more rigid sublets can help as long as the 
endpoints of the subsets are homologous and not arbitrary or dependent on the 
bending of a particular specimen. The tpsUtil program has an "unending" option 
if one has a subset of points that one knows should be in a straight line. That 
would be difficult for larvae.

Note: I see you are using ver. 2.30 of tpsDig. Version 2.31 is current. I do 
try to keep fixing bugs so It can be useful to stay current.


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

-Original Message-
From: Avi Koplovich [mailto:netbird.porta...@gmail.com] 
Sent: Tuesday, February 27, 2018 3:09 AM
To: MORPHMET 
Subject: [MORPHMET] Digitizing landmarks on live larvae

Hi,
I've started a new project and came to the point of marking fixed and semi 
landmarks.
Not all pictures are satisfying, mostly because of the posture of the larvae 
during photographing (sometimes raising it's tail). So in order to reduce the 
noise by the animal posture, I thought it would be helpful to separate head and 
tail as was done in Levis et. al. 2016, Biol. J. Linn. Soc.
I'm using the landmarks 1, 20 and 48 as fixed landmarks, and all the rest are 
semi landmarks. I'm not sure of using 20 and 48 as fixed landmarks, and I 
wonder if I can use landmark 40 as fixed landmark since it is restricted by 
both x (side line) and y (dorsal connection of the tail fin). Can/Should I use 
the eye as a fixed landmark for the head (i.e. can it interfere with 
interpreting the head contour)?
Here is an example to show what I mean:
https://drive.google.com/file/d/1iO7lCN3ZCtV7DF9vsczkb_EYoSli1Orr/view?usp=sharing
I'll be happy if you can advise on that.
Thank you,
Avi

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[MORPHMET] tpsUtil update

2018-02-20 Thread f.james.rohlf 


I have  just uploaded tpsUtil with a small update - version 1.76. The
area/perimeter option can now use .nts files and not just .tps file. It also
now includes a PDF file copy of the help file. Some may find that helpful.

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

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RE: [MORPHMET] Problems importing file in TPSrelw

2018-02-07 Thread f.james.rohlf 
You need to use the decimal character option in tpsRelw to select “.” Rather 
than “,”.

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

From: Waira Saravia [mailto:w.sm...@gmail.com] 
Sent: Friday, February 2, 2018 10:18 AM
To: morphmet@morphometrics.org
Subject: [MORPHMET] Problems importing file in TPSrelw

 

Dear all, 

 

I'm a bachelor student and I'm working with a 2D dataset from roedent skull. 
I'm trying to analyze my dataset in TPSrelw, but any file I uploaded appears 
the message: "'757.0' is not a valid floating point value. Bad decimal 
character in coordinates?". I thought that the problem was on my laptop, but 
running the same file in other computer appears the same message. What should I 
do?

 

Best regards,

 

Waira Machida

Universidade de Brasília (UnB)

 

 

 

 

 

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RE: [MORPHMET] problem with tps Relw

2018-02-07 Thread f.james.rohlf 
You can only process one file at a time. If your data are in many files then 
combine them using the tpsUtil program.

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

From: Ritu YADAV [mailto:y.ritik...@gmail.com] 
Sent: Friday, January 26, 2018 10:31 PM
To: MORPHMET 
Subject: [MORPHMET] problem with tps Relw

 

hllo every one,

 

i have problem in uploading files on Tps Relw, i cant select more than one 
file. I dont know how to select more than one files. If any one knows then plzz 
help me.

 

With regards 

Ritu yadav

 

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[MORPHMET] tps updates

2018-01-30 Thread f.james.rohlf 


I have just uploaded ver. 2.05 of tpsSuper, 2.31 of tpsDig2, and 1.75 of
tpsUtil.

 

Main change to all three was to add additional image file formats - most
importantly camera raw images files. See the list below. This change was
suggested by Jennifer Valvo. In addition, I fixed a problem reading .nts
files for the creation of slider files in tpsUtil -- reported by Andrea
Cardini.

 

Many thanks to both!

Input image file formats for tpsDig2, tpsSuper, and tpsUtil.


Format

Notes


JPEG (jpg)

Supports 1/2, 1/4 and 1/8 sub-sizes for fast preview


JPEG2000

 


GIF

Including editing and display of animated GIFs


PNG

 


BMP

Compressed and uncompressed


TIFF (tif)

Editing and display of single and multipage TIFF. Also supports FAX, G3F and
G3N sub-formats


BigTIFF

Single and multipage BigTIFF. Also supports FAX, G3F and G3N sub-formats


PCX

Including DCX (Multipage PCX) format


Raw Camera Formats

Including Digital Negative Format (*.dng), Canon (*.cr2, *.crw), Kodak
(*.dcr), Minolta (*.mrw), Nikon (*.nef), Olympus (*.orf), Pentax (*.pef),
Fuji (*.raf), Leica (*.raw), Sony (*.srf) and Sigma (*.x3f)


Icons (ICO)

With multiple resolution and color depth support


DICOM (Medical Imaging)

Single and multipage. Can be compressed with RLE, jpeg2000 and lossy-jpeg


Adobe Photoshop (PSD/PSB)

With multiple layer and large document support


WMP

Also known as Microsoft HD Photo


Metafiles (WMF and EMF)

 


AVI

Including retrieval and modification of frames

Note: some TIF files use a special compression that this program may not be
able to read.

 

Images can be saved in the following formats:


Format

Notes


JPEG (JPG)

 


JPEG2000

 


GIF

 


PNG

 


BMP

Compressed and uncompressed


TIFF (TIF)

 


PCX

Including DCX (Multipage PCX) format


Raw Camera Formats

Including Digital Negative Format (*.dng), Canon (*.cr2, *.crw), Kodak
(*.dcr), Minolta (*.mrw), Nikon (*.nef), Olympus (*.orf), Pentax (*.pef),
Fuji (*.raf), Leica (*.raw), Sony (*.srf) and Sigma (*.x3f)


Icons (ICO)

 


DICOM (Medical Imaging)

 


Adobe Photoshop (PSD)

With multiple layer support


WMP

Also known as Microsoft HD Photo


PostScript (PS and EPS)

 


Adobe PDF

 


AVI



 

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

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Re: [MORPHMET] Landmarks coming up funny in MorphoJ

2017-11-06 Thread f.james.rohlf 
Let it save it as a txt file then just rename the file.
-F. James RohlfDepts. of Ecology & Evolution and of 
Anthropology Stony Brook University 
 Original message From: Candice Neves 
<536...@students.wits.ac.za> Date: 11/6/17  12:59 PM  (GMT-05:00) To: Guido 
Rocatti  Cc: MORPHMET  
Subject: Re: [MORPHMET] Landmarks coming up funny in MorphoJ 
Hi Guido
Thanks so much for the suggestion, I'll definitely do that. Is there a 
particular way to save a wordpad/notepad file as a .tps format file? I've tried 
to do this before but it kept saving as a .txt file, or would this still work?
Thanks for the helpCandice Neves
On 6 November 2017 at 19:44, Guido Rocatti  wrote:
Hi Candice, 
I think that maybe you should try to organize both coordinate sets directly 
using notepad or wordpad and saving the file as a .tps format file. Doing so, 
you won't depend on the tpsUtil. Also, I understand that you have missing data. 
You can try and estimate those missing landmarks with the estimate.missing 
function of the  geomorph package for R. It uses thin-plate spline to 
interpolate landmarks, or a linear regression model to predict them (the method 
election is up to you).Once you managed to put both sets together and you 
obtained your missing landmarks, you can export your new dataset and open it on 
MorphoJ.Hope this helps somehow.
Good Luck.

Guido RocattiLic. en Antropología.División Antropología, Facultad de Ciencias 
Naturales y Museo.Universidad Nacional de La Plata.
CONICET

 

  
Libre de virus. www.avg.com 








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RE: [MORPHMET] Use of outline tool on TPSDig

2016-10-07 Thread f.james.rohlf 
If you set a number of points less than the digitized number of points then the 
software has to interpolate and that is likely to cut off the corners. This is 
especially true if the shape is irregular. No easy solution except that you can 
edit the points and push them around to where you would like them to be.


-F. James RohlfDepts. of Ecology & Evolution and of 
Anthropology Stony Brook University 
 Original message From: Serita Savolainen 
 Date: 10/6/16  8:01 AM  (GMT-05:00) To: MORPHMET 
 Subject: [MORPHMET] Use of outline tool on TPSDig 
Hello! Before I get started, I am not an experienced user of software like 
TPSDig.Anyway, I am trying to use the outline tool in TPSDig to outline the 
edges of iliac crests in order to plot a specific number of points on the 
edges. For some reason, everytime I actually set the outline and choose the 
number of co-ordinate points, the outline does not actually run all the way 
round the crest but cuts off towards the end of its loop and makes a shortcut 
to the start which is not helpful since it means I am not actually getting the 
outline of the whole bone. The yellow line that shows the initial outline does 
run around the whole bone, but the red line with the points does not. Anybody 
know why this might be happening and how I could fix it? Thank you very much!
Kind regards,Serita Savolainen



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