Re: [MORPHMET] Dennis Slice

2019-06-15 Thread Ariadne Schulz
I never had the pleasure of meeting him. I knew him only through his work.
But his work was exceptional. This is a great loss. Condolences to those
closest to him.

On Sat, Jun 15, 2019 at 3:55 PM mitte...@univie.ac.at 
wrote:

>  Dear subscribers to morphmet,
>
>  With the deepest grief we must inform you of the sudden
>  death on June 13 of Prof. Dennis E. Slice,
>  holder of the fourth Rohlf Award for Excellence in Morphometrics
>  and tireless founder and moderator of this newsgroup,
>  who suffered a heart attack in his home town of
>  Tallahassee, Florida. Morphometrics will not be the same
>  without him.
>
> Jim Rohlf, Fred Bookstein, Paul O'Higgins,
>   Benedikt Hallgrimsson, June 15, 2019
>
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Re: [MORPHMET] Help with surface scans

2019-04-27 Thread Ariadne Schulz
I'm coming at this a bit late so I apologize if I've repeated anyone's
point. For your purposes photogrammetry is probably your best option
particularly for the lithics. Laser scanning works on bones and I used a
NextEngine scanner for human proximal long bones, but I think someone has
already mentioned that the laser doesn't capture the orbitals well and you
might have difficulty with tooth enamel. The photogrammetry software
requires a decently hefty laptop, but it's affordable and you'd be working
with normal light rather than lasers. I don't know that this clears up your
concerns about fusing scans though. If you are concerned you could do some
error testing on that comparing landmarks obtained on the scans to
landmarks obtained normally. I found the laser scans to be pretty decent,
but I unfortunately cannot speak to photogrammetry as I've never personally
tried it.

On Mon, Apr 22, 2019 at 3:29 PM Pablo Fisichella 
wrote:

> Dear All
>
> I´m trying to obtain surface scans from human skulls and lithic artifacts
> (projectile points). I wonder how can I get the most complete possible
> scans, I mean usually is not possibly to obtain a complete scan at once. I
> know that several post-scan processing software have functions to fuse
> and/or align the different surfaces obtained and then create one surface
> but perhaps several of you have some tips to obtain the most complete
> possible surface scans.
>
> Any suggestion and advice is more than welcome
>
> All best,
>
> Pablo
>
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Re: [MORPHMET] Re: NextEngine Laser Scanner

2017-11-12 Thread Ariadne Schulz
Hello all,
NextEngine sometimes has difficulty with small lithics or metals due to the
way they reflect light. It's a laser scanner so these things happen. All
the recommendations above should help, but in the end if it doesn't or if
you run into an institution that won't allow you to use sprays or powders I
would recommend photogrammetry and white light solutions. Particularly if
you are collecting samples from other institutions it will reduce the
amount of specialized equipment you have to carry around. If you go this
route there is a firm based in SF that provides starter kits (I think not
including the software but everything else) for free. Good luck!

Best,
Ari


Garanti
sans virus. www.avast.com

<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

On Sat, Nov 11, 2017 at 5:14 PM, Terrie Simmons-Ehrhardt <
terrielsimm...@gmail.com> wrote:

> Hi Mary-Margaret and Dave,
>
> I've had success with the provided powder on chunks of quartz, but in
> general, the NextEngine does not detect dark objects well, so I can see how
> it would have a hard time with obsidian.
>
> Terrie Simmons-Ehrhardt
>
> On Sat, Nov 11, 2017 at 11:49 AM, Dave Norris  wrote:
>
>> Mary-Margaret
>>
>> Could you recommend a foot spray?  I’ve been trying a quartz point with
>> no success and was think of using painters tape but if you’ve had success
>> with spray - I’d like to maybe give that a shot.
>> Cheers
>>
>> Dave Norris
>>
>> Sent from my iPhone
>>
>> On Nov 11, 2017, at 11:28 AM, Mary-Margaret Murphy 
>> wrote:
>>
>> Good morning, Callie and Terrie.
>>
>> I agree with your settings suggestions, Terrie.
>>
>> Also, the supplied powder with the NextEngine is (or at least with mine,
>> was) pretty basic and inadequate. I ran experiments with titanium dioxide,
>> bentonite power, foot powder spray, and chemical whiting. My sample
>> included 2 obsidian flakes. The easiest was the foot spray.
>>
>> As far as a reference object, i recommend something with plane geometry,
>> a matte surface and a coloration near to your objects. Something along the
>> line of a die (dice), a Lego brick, or a small 3D print sample.
>>
>> Meshlab software is helpful, as is CloudCompare. You should check them
>> out.
>>
>> Best,
>>
>> Mary-Margaret
>>
>>
>> On Sat, Nov 11, 2017, 9:10 AM terrielsimmons 
>> wrote:
>>
>>> Hi Callie,
>>>
>>> Are you using the old NextEngine or the Ultra? Since you are scanning at
>>> a small distance, make sure your scan setting is set to macro. Try fewer
>>> divisions, around 8--too many divisions for small objects causes the
>>> auto-alignment to not work. The NextEngine also has a hard time aligning
>>> flat objects, so if the scans don't align within ScanStudio, you might have
>>> to export them to Meshlab and align them. You can email me directly if you
>>> want some help with Meshlab.
>>>
>>> Terrie Simmons-Ehrhardt
>>>
>>>
>>> On Friday, November 10, 2017 at 6:25:14 PM UTC-5, Callie Diduck wrote:

 Hello,

 I am working with a NextEngine Laser scanner trying to create 3D models
 of Avonlea Projectile Points for my Masters Thesis. I am having difficulty
 with the scanner not being about to stitch the individual scans together to
 create a 3D model. I think I've tried just about everything I can think of
 to make it work but I still come up short.

 I am wondering if the problem is that the projectile points I am
 working with are just too small for the scanner to handle? The points range
 from 14 to 23mm, and about 2-3mm thick.

 I have been able to scan points that are larger about 26 to 35mm in
 length, 6mm at their widest point and get a successful 3D model out of it.
 Does anyone have any suggestions?

 The settings I am using right now are a 360 scan, 14-16 divisions, 3.3
 thousand points per inch, neutral for colour, and a distance from the
 scanner of about 9.5 inches. I am covering the scanner completely with a
 card board box to ensure there is no change in light.

 Any help or suggestions would be great. I have been trying to make this
 work for the past 2 months.

 Thanks,

 Callie Diduck
 Master's Candidate
 Department of Archaeology and Anthropology
 University of Saskatchwan

 --
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[MORPHMET] Form Space?

2016-03-29 Thread Ariadne Schulz
Hello All,

I have another rather silly question that I'm hoping either has a very
simple answer or will set off another wave of debate. I'm still on about my
3D semilandmarks and now I want to plot them in form space in R. I have my
original landmarks and my GPA coordinates and centroid size from gpagen
with a sliding function, and so forth so the new version of plotAllometry
should work, but I really want to plot in form space. It seems to me I'm
just missing something really easy. Is there a way to do this?

Best,
Ari

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Re: [MORPHMET] Sliding Semilandmarks

2016-02-18 Thread Ariadne Schulz
Will update and try again. That sounds - without being too hopeful - like
it might solve my problem. If not, I'll come back with better details.

I would also like the clarification on the point Andrea has asked about.
That sounds like a concerning issue for what I'm trying to do with this.

Thanks!
Ari

On Thu, Feb 18, 2016 at 4:06 PM, Collyer, Michael <michael.coll...@wku.edu>
wrote:

> Ari,
>
> If you are using geomorph, you might want to update it via GitHub.  Just a
> few days ago we updated the software with some bug fixes for surface points
> (one bug fix was for assuring non-arbitrary directions in PC planes for
> tangents of surface points).  If you are unsure how to do that, look at the
> post by Dean Adams on 15 February 2016.
>
> Beyond that, you are asking for assistance without defining (1) how you
> are sliding your landmarks (minimizing Procrustes Distance or Bending
> Energy) or (2) other specifics that might be important (package within R,
> maybe other inputs that might be important, such as the relative numbers of
> fixed landmarks and semilandmarks, etc.).
>
> Contrary to your logic, subsetting your sample could have an effect.  Your
> mean configuration would change in each of the subsamples, from the mean of
> your original sample, thus changing the reference configuration used in the
> separate GPAs performed.  The reference configuration has a prominent role
> in the sliding of landmarks.
>
> With the information you provided, t is not possible to discern among user
> error, program error, or analytical artifact.
>
> Mike
>
> Michael Collyer
>
> Associate Professor
> Biostatistics
> Department of Biology
> Western Kentucky University
> 1906 College Heights Blvd. #11080
> Bowling Green, KY 42101-1080
> Phone: 270-745-8765; Fax: 270-745-6856
> Email: michael.coll...@wku.edu
>
> On Feb 18, 2016, at 9:43 AM, Ariadne Schulz <ariadne.sch...@gmail.com>
> wrote:
>
> Hello all,
>
> I'm having a bit of a semilandmark problem. I'm working on 3D surfaces
> with semilandmarks. (Profuse thank yous to Emma for writing the scripts for
> that.) The issue I'm having I think is occurring in the sliding. When I do
> populations alone everything seems normal. The semilandmarks do not appear
> to be going off the surface defined for them, but if I try to do more than
> one population at once several of the semilandmarks slide off the surface
> so my PCs get rather distorted. Based on the few individuals from different
> populations I've looked at I think I do have interpopulation variation but
> I wouldn't expect that to influence the sliding of semilandmarks. Has
> anyone else encountered an issue like this with either 2D or 3D
> semilandmarks? As with all things R I expect the answer will be something
> like me omitting a comma somewhere so any suggestions you might have are
> welcome.
>
> Best,
> Ari
>
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[MORPHMET] Sliding Semilandmarks

2016-02-18 Thread Ariadne Schulz
Hello all,

I'm having a bit of a semilandmark problem. I'm working on 3D surfaces with
semilandmarks. (Profuse thank yous to Emma for writing the scripts for
that.) The issue I'm having I think is occurring in the sliding. When I do
populations alone everything seems normal. The semilandmarks do not appear
to be going off the surface defined for them, but if I try to do more than
one population at once several of the semilandmarks slide off the surface
so my PCs get rather distorted. Based on the few individuals from different
populations I've looked at I think I do have interpopulation variation but
I wouldn't expect that to influence the sliding of semilandmarks. Has
anyone else encountered an issue like this with either 2D or 3D
semilandmarks? As with all things R I expect the answer will be something
like me omitting a comma somewhere so any suggestions you might have are
welcome.

Best,
Ari

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[MORPHMET] Writing files from R

2016-01-22 Thread Ariadne Schulz
Hello all,

I have another hopefully simple geomorph question. How does one write a
.pts file? I've found how to write a .tps file, and I have managed to
create a .pts file, but it was empty as far as I could tell. (I used
writeland.tps and for the filename simply appended .pts, but I'm pretty
sure that's not how it's done) Is there a simple way of doing this?

Best,
Ari

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[MORPHMET] writing .nts files from geomorph

2016-01-19 Thread Ariadne Schulz
Hi all,

I'm hoping this will be a quick and easy question. I've even done it before
and then forgotten how.

I need to create quite a few .nts files. The easiest way to do this I think
is in R. I read in my .dta file, got my landmarks all switched the way I
want them but now for each of my elements I need to create a .nts file.
I've searched about online and the only things I could find were how to
read a .nts file and the "digitize" functions. I know it's possible to
simply write .nts files, because I have done it before ... but I've
forgotten what I did.

Help?

Best,
Ari

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Re: [MORPHMET] writing .nts files from geomorph

2016-01-19 Thread Ariadne Schulz
Dear Emma and Andrea,
Thanks for the rescue. I'll give this a try. I don't really know much about
code so some of the syntax is confusing to me, but this looks to be an
explanation I can follow after a few tries. Thank you so much.

Best,
Ari

On Tue, Jan 19, 2016 at 11:08 AM, Emma Sherratt <emma.sherr...@gmail.com>
wrote:

> Dear Ari,
>
> geomorph uses the following code to write an .nts from the digtizing
> functions. It's an .nts file for single specimens
>
> # Write .nts file for output of digitize2d(), buildtemplate()
> digit.fixed() and digitsurface()
> # A is an nx2 or nx3 matrix of the output coordinates. To be used
> internally only.
>
> writeland.nts <- function(A, spec.name, comment=NULL){
>   ntsfile=paste(spec.name,".nts",sep="")
>   file.create(file=ntsfile)
>   if(is.null(comment)){
> cat(paste('"',spec.name,sep=""),file= ntsfile,sep="\n",append=TRUE)
>   }
>   else if(!is.null(comment)){
> cat(paste('"',spec.name,sep=""),file= ntsfile,sep="\n")
> cat(paste('"',comment,sep=""),file= ntsfile,sep="\n",append=TRUE)
>   }
>   dims <- dim(A)
>   if (dims[2] == 2){
> cat(paste(1,dims[1],2,0,"dim=2"),file= ntsfile,sep="\n",append=TRUE)
>   }
>   else if (dims[2] == 3){
> cat(paste(1,dims[1],3,0, "dim=3"),file= ntsfile,sep="\n",append=TRUE)
>   }
>   write.table(A ,file= ntsfile,col.names = FALSE, row.names = FALSE,sep="
>  ",append=TRUE)
> }
>
> Emma
>
> ~~~
>
> Emma Sherratt, PhD.
>
> Lecturer in Zoology,
> Zoology Division, School of Environmental and Rural Science,
> Room L112 Bldg C02,
> University of New England,
> Armidale, NSW, Australia, 2351
> Tel: +61 2 6773 5041
> email: emma.sherr...@une.edu.au
> Twitter: @DrEmSherratt
>
> Caecilians are legless amphibians...
>
> *  __
> (\   .-.   .-.   /_")
>  \\_//^\\_//^\\_//
>   `"`   `"`   `"`*
>
> learn more about them here: www.emmasherratt.com/caecilians
>
>
>
>
> On 19 January 2016 at 20:19, Ariadne Schulz <ariadne.sch...@gmail.com>
> wrote:
>
>> Hi all,
>>
>> I'm hoping this will be a quick and easy question. I've even done it
>> before and then forgotten how.
>>
>> I need to create quite a few .nts files. The easiest way to do this I
>> think is in R. I read in my .dta file, got my landmarks all switched the
>> way I want them but now for each of my elements I need to create a .nts
>> file. I've searched about online and the only things I could find were how
>> to read a .nts file and the "digitize" functions. I know it's possible to
>> simply write .nts files, because I have done it before ... but I've
>> forgotten what I did.
>>
>> Help?
>>
>> Best,
>> Ari
>>
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>> email to morphmet+unsubscr...@morphometrics.org.
>>
>
>

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Re: [MORPHMET] 3D Shape Change Visualization

2015-12-15 Thread Ariadne Schulz
No problem! Actually, I'm pretty new to this stuff too, so explaining kinda
helps it gel. Anyway, I'm writing something up now so I'm going to come
back to this later, but I think what you want to do to get asymmetry is run
a MANOVA or an ANOVA with size as your variable. You can do MANOVA in SPSS
and there's quite a few tutorials online for how to do that. An ANOVA is
possible in MorphoJ and probably your simplest and quickest option. Once
you have everything in go to the "Variation" tab and it will be your last
option. If you've loaded your classifiers you'll be able to assign "side"
to the box that - most helpfully - is marked "side". If that's what you're
trying to do it's quite easy. Many of the people on this list have
published on it as well so the method is very nicely supported.

Best,
Ari

On Mon, Dec 14, 2015 at 7:55 PM, Jay Devine <jaypatrickdev...@gmail.com>
wrote:

> Hi, Ari-
>
> Thank you so much for input. I can't believe how helpful you are, ha. Your
> advice is not basic whatsoever - I'm fairly new to this, so laying
> everything out as you did is wonderful. Essentially what I'm trying to do
> is compare bilateral asymmetry of left and right humeri in males and
> females. My classifiers are population (NP), side (R, L), specimen (random
> #), and sex (M, F). This is all part of a directed study course I'm
> currently taking, which is meant to provide me with some knowledge for my
> honours thesis. It's all a bit overwhelming, but people like you make it
> easier!
>
> Ahh, I see, I see. I don't have experience with Morphologika, but I'll try
> this out. I've used R, so perhaps I'll try using geomorph as well.
>
> Once again, I can't thank you enough.
>
> Best wishes,
>
> Jay
>
> On Mon, Dec 14, 2015 at 7:55 AM, Ariadne Schulz <ariadne.sch...@gmail.com>
> wrote:
>
>> Hi Jay,
>> I'd be interested if MorphoJ had that option but I don't think it does.
>> To do it in Morphologika you'll have to first create a Morphologika file
>> which includes your wireframes. It took me a bit of doing to figure it out
>> and actually I'm wondering if one can do multiple classifiers or "labels"
>> in a Morphologika file without putting it through geomorph. But anyway,
>> I'll lay it out for you in case you don't know and also so those with more
>> experience here can critique. Basically, you just want to list things under
>> their categories as sketched out below.
>>
>> [individuals]
>> (n individuals)
>> [landmarks]
>> (n landmarks)
>> [dimensions]
>> (n Dimensions)
>> [names]
>> (Specimen_1
>> Specimen_2
>> ...)
>> [labels]
>> (name of label)
>> [labelvalues]
>> (specimen 1 label value
>> specimen 2 label value
>> ...)
>> [wireframe]
>> (1,2
>> 2,3
>> 1,3
>> ...)
>> [rawpoints]
>> '#1
>> (landmarks for Specimen 1)
>> '#2
>> (landmarks for Specimen 2)
>> ...
>>
>> I should note as it's not very clear, "labels" are your classifiers. I
>> think yours was "species" if I remember from before, so your label values
>> will be the species names. Mine is sex so my label values are "female,"
>> "possiblefemale," "unknown," "possiblemale," and "male." There's also a
>> category for "polygons" but I haven't yet gotten that to work so I won't
>> confuse matters by trying to tell you about it. Make sure all your
>> wireframe points correspond to landmarks that are included in your final
>> set in Morphologika or you will get an error. You can eliminate individuals
>> or landmarks or polygons and so forth before you get into the meat of
>> things. Once you do a Procrustes fit and PCA, you'll want the TPS tab in
>> the control panel. Sometimes the image comes up blank, but if you just
>> click on it it will solve itself. Morphologika also allows you to "Explore
>> Space" which is really helpful. Make sure that button in the Control Panel
>> is toggled and then click on any spot in the PC chart. You'll note that the
>> landmarks in the viewer change to correspond with the position in the PC
>> chart you've chosen.Given what you're trying to do though, I think you
>> might want to try geomorph in R. It's really quite versatile if a little
>> daunting. I hope this wasn't too basic ... let me know how you get on.
>>
>> Best,
>> Ari
>>
>> On Mon, Dec 14, 2015 at 5:18 AM, Jay Devine <jaypatrickdev...@gmail.com>
>> wrote:
>>
>>> Hello again, Morphmet!
>>>
>>> I received an immense amount of help with my 

Re: [MORPHMET] 3D Shape Change Visualization

2015-12-14 Thread Ariadne Schulz
Hi Jay,
I'd be interested if MorphoJ had that option but I don't think it does. To
do it in Morphologika you'll have to first create a Morphologika file which
includes your wireframes. It took me a bit of doing to figure it out and
actually I'm wondering if one can do multiple classifiers or "labels" in a
Morphologika file without putting it through geomorph. But anyway, I'll lay
it out for you in case you don't know and also so those with more
experience here can critique. Basically, you just want to list things under
their categories as sketched out below.

[individuals]
(n individuals)
[landmarks]
(n landmarks)
[dimensions]
(n Dimensions)
[names]
(Specimen_1
Specimen_2
...)
[labels]
(name of label)
[labelvalues]
(specimen 1 label value
specimen 2 label value
...)
[wireframe]
(1,2
2,3
1,3
...)
[rawpoints]
'#1
(landmarks for Specimen 1)
'#2
(landmarks for Specimen 2)
...

I should note as it's not very clear, "labels" are your classifiers. I
think yours was "species" if I remember from before, so your label values
will be the species names. Mine is sex so my label values are "female,"
"possiblefemale," "unknown," "possiblemale," and "male." There's also a
category for "polygons" but I haven't yet gotten that to work so I won't
confuse matters by trying to tell you about it. Make sure all your
wireframe points correspond to landmarks that are included in your final
set in Morphologika or you will get an error. You can eliminate individuals
or landmarks or polygons and so forth before you get into the meat of
things. Once you do a Procrustes fit and PCA, you'll want the TPS tab in
the control panel. Sometimes the image comes up blank, but if you just
click on it it will solve itself. Morphologika also allows you to "Explore
Space" which is really helpful. Make sure that button in the Control Panel
is toggled and then click on any spot in the PC chart. You'll note that the
landmarks in the viewer change to correspond with the position in the PC
chart you've chosen.Given what you're trying to do though, I think you
might want to try geomorph in R. It's really quite versatile if a little
daunting. I hope this wasn't too basic ... let me know how you get on.

Best,
Ari

On Mon, Dec 14, 2015 at 5:18 AM, Jay Devine 
wrote:

> Hello again, Morphmet!
>
> I received an immense amount of help with my last question, so I figured I
> would try again! My silly question this time concerns 3D visualization of
> shape change.
>
> I've been able to successfully create wireframe graphs for my data, but
> for some reason I can not create transformation grids. I'm aware that you
> need to right-click on the "PC shape changes" background to change the type
> of graph. Unfortunately, transformation grids doesn't appear as an option
> for me to choose. Is there perhaps a preliminary step I need to do?
>
> Does anyone know why this could be happening?
>
> Thanks in advance for your time and consideration.
>
> Respectfully,
>
> Jay
>
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[MORPHMET] surface semilandmarks

2015-01-09 Thread Ariadne Schulz
Dear All,
I've got about 160 3D scans of human femora and roughly the same of humeri
and before I go off and collect more, I want to collect surface and curve
semilandmarks. I've tried a few methods and looked at some of the papers
out there and I think EVAN toolbox is the way to go, but it takes a lot of
meticulous work and staring at a computer screen. I did try Landmark
Editor, but I'm not convinced that the patches really work on the diaphysis
(they seem to go beneath the surface) and the flexible patch doesn't seem
to export points. Does anyone here know a better method, have a suggestion
or know how to create curve objects that can be imported into EVAN? I can
pretty much use any and all suggestions.

Best Regards,
Ari

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