Re: [MORPHMET] Dennis Slice

2019-06-18 Thread Paolo Piras
Dear friends,
I want to join all of you in expressing my condolences for Dennis loss.
My grief goes to his family, friends and students.
I knew him in Isernia about ten years ago and I had the chance to speak
with him not only about morphometrics or science in general but also about
a great variety of arguments. I remember a very nice person, kind and
polite in any situation. As well as sharp and clever.
Our community will miss him so much...

Il giorno mar 18 giu 2019 alle ore 00:00 Una Vidarsdottir <> ha scritto:

> Like so many I have struggled with words. I posted some on my Facebook and
> copy them here below. Oh I miss him.
>  I first met Dennis at the beginning of my PhD work in 1995. 24 years. We
> spent many an evening debating how best to do a certain analysis or how to
> test a certain theory. I remember a night... probably in 2006, when we
> walked the streets of Vienna through a long summernight talking the entire
> time.  Dennis was not a big ego although his mind, work and ideas might
> have merited it. In his own quiet and sometimes self-deprecating way, he
> inspired and influenced the work of the morphometrics community as a whole.
> Dennis believed his role as an academic lay in supporting this community
> to produce better and better science, from lending helpful pointers to
> fledgling researchers taking their first cautious steps in the field, to
> being a fountain of knowledge and ideas to those of us who have been
> involved much longer.
> First and foremost Dennis was my very dear friend, soul mate and entrusted
> colleague. I will miss him very much.
> (Some photos from another very warm evening in Vienna in 2008)
> On Mon, 17 Jun 2019, 18:27 K. James Soda,  wrote:
>> Sent on behalf of Dean Adams:
>> Colleagues,
>> Like others I have spent the weekend grieving the passing of Dennis, and
>> trying to put my feelings of loss into words. Alas I cannot.
>> I’ve known Dennis for 25 years, since we overlapped in Jim’s lab in the
>> 1990s. He was a constant fixture in our field, and his passing has left a
>> great hole. I will miss his positive attitude, his whit, his endless and
>> entertaining stories, and his life lessons. But mostly I will miss having
>> him in our community.
>> I will miss you, Dennis.
>> Dean
>> Dr. Dean C. Adams
>> Director of Graduate Education, EEB Program
>> Professor
>> Department of Ecology, Evolution, and Organismal Biology
>> Iowa State University
>> phone: 515-294-3834
>> On Mon, Jun 17, 2019 at 3:53 AM K. James Soda 
>> wrote:
>>> Hello Everyone,
>>> Since Friday afternoon, I have struggled to put into words the kind of
>>> adviser Dennis Slice was to his students to supplement the elegant
>>> testimonies to his abilities as a researcher, but words fail me. I do not
>>> know how I can properly portray the care and compassion that he afforded
>>> us. Despite his many accomplishments, he remained humble and never spoke
>>> down to us. He listened to our concerns with compassion and our ideas with
>>> an open mind. He treated us like family, and I know that I am not alone in
>>> saying that we felt the same way about him. Our weekly lab meetings and
>>> monthly lab dinners form some of my happiest memories of graduate school
>>> because he infused humor into our every interaction. He taught me so many
>>> things, both professionally (like people are more likely to read emails
>>> that are broken into smaller blocks) and personally (like a gentleman
>>> should always carry a handkerchief in case a lady cries). I can only hope
>>> that I as a professor will be able to foster curiosity and confidence in my
>>> students half as well as Dennis did in me.
>>> I deeply miss Dennis, and I suspect I always will.
>>> Thank you for your time,
>>> James Soda
>>> On Mon, Jun 17, 2019 at 3:19 AM Carmelo Fruciano 
>>> wrote:
 This is extremely sad news. He has made enormous contributions to our
 field and his figure will be greatly missed. I have had limited
 interactions with him but, based on the interactions I had the
 to have, I also concur with Mauro Cavalcanti that he had a nice sense
 My most heartfelt condolences to his family, his friends, and all our


 Carmelo Fruciano
 Institute of Biology
 Ecole Normale Superieure - Paris

 On 15/06/2019 16:55, 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 

Re: [MORPHMET] Help with placePatch

2019-06-18 Thread Pablo Fisichella
Dear Murat and Ryan,

Thank you very much for your help. Both solutions work fine although the
Murat´s suggestions produced the following error but I was able to fix
it. Error
in dimnames(data)[[3]] = list(c(("A860ho, USNM083262hy, USNM084655pan,
USNM143590po, USNM143593po, USNM174699pan, USNM174701pan, USNM174702pan,
USNM239883go, USNM260582go"))) :   length of 'dimnames' [3] not equal to
array extent

I used these functions and worked correctly

patched.specimens <-
='', fileext=".ply")

the result and my checking of patched.specimens (Removed 0 duplicate 51977
unreferenced vertices and 0 duplicate faces) show that effectively the 60
semilandmarks were projected to all my specimens.

Now I´m trying to run the checkLM function as follows:

='', fileext=".ply")  but I got this error: Error in vcgImport(filename,
clean = clean, readcolor = readcol) :  file E:/Documents/hominoidA860ho.ply
does not exist

It seems that again the function can´t find my .ply models so I used this

checkLM(patched.specimens, path="E:/Documents/hominoid",prefix =
c(("A860ho, USNM083262hy, USNM084655pan, USNM143590po, USNM143593po,
USNM174699pan, USNM174701pan, USNM174702pan, USNM239883go, USNM260582go"),
suffix = ".ply", atlas=atlas))

but despite the RGL device is started and the r console is working
correctly the results are never returned.

Maybe you have some additional suggestions on how run the checkLM function

Thank you very much for your help, I really appreciate your time and
expertise to answer my questions,

with thanks,


de virus.


El lun., 17 jun. 2019 a las 17:02, Ryan Felice ()

> Hi Pablo,
> A small change should fix it. Remove the “prefix” argument. Whatever you
> set “prefix” to is pasted in front of each specimen name. Notice how the
> error says there is no such file "E:/Documents/hominoid/A860ho,
> USNM083262hy, USNM084655pan, USNM143590po, USNM143593po, USNM174699pan,
> USNM174701pan, USNM174702pan, USNM239883go,
> USNM260582goA860ho.landmarkAscii.ply”.
> This is your path ("E:/Documents/hominoid/“), then your “prefix”, then
> the name of the first specimen in “data”, which is “A860ho.landmarkAscii”,
> then the file extension, “.ply".
> Try it like this:
> dimnames(data)[[3]]=str_remove(dimnames(data)[[3]],".landmarkAscii”)
> patched.specimens <-
> placePatch(atlas=atlas,dat.array=data,path="E:/Documents/hominoid",prefix
> ='', fileext=".ply"))
> If the dimnames(data)[[3]] perfectly match the filenames of your ply
> files (without the “.ply”), it should work.
> Best
> Ryan
> Ryan N. Felice, Ph.D
> Lecturer in Human Anatomy
> University College London
> Department of Cell and Developmental Biology
> Anatomy Building Room G23
> On Jun 17, 2019, at 8:38 PM, Pablo Fisichella 
> wrote:
> Dear All,
> I’m using the function placePatch in Morpho to transfer semilandmarks from
> a template to all specimens in my sample (n=10). Unfortunately I have
> failed to run successfully such function. I have read some discussions here
> in the past but some solutions that apparently functioned for other persons
> do not seem to work in my case. Thus maybe somebody can help me with an
> idea or advice.
> I obtained my landmarks and semilandmarks using Amira
> I created an atlas (see attached pictures) which looks fine. I obtained 19
> landmarks and 60 semilandmarks for the template.
> I created a k x 3 x n array using the function read.amira.dir from the
> Arothron package (data=read.amira.dir("E:/Documents/landmarks","auto") my
> array is 19*3*10
> Finally I used the placePatch function as follows:
> placePatch(atlas=atlas,dat.array=data,path="E:/Documents/hominoid",prefix
> = c(("A860ho, USNM083262hy, USNM084655pan, USNM143590po, USNM143593po,
> USNM174699pan, USNM174701pan, USNM174702pan, USNM239883go, USNM260582go"),
> fileext=".ply"))
> I obtained a pxkxn array with only missing values -NAs- and I got 10
> errors like this for each one of my .ply models:
> In place.patch(dat.array, path, atlas.mesh = atlas$mesh,  ... :matching
> for specimen 1 failed with: Error in vcgImport( file
> E:/Documents/hominoid/A860ho, USNM083262hy, USNM084655pan, USNM143590po,
> USNM143593po, USNM174699pan, USNM174701pan, USNM174702pan, USNM239883go,
> USNM260582goA860ho.landmarkAscii.ply does not exist
> Evidently the function can’t find my .ply models. As I supposed this issue
> is related to the dimnames of my array