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
dimnames(data)[[3]]=str_remove(dimnames(data)[[3]],".landmarkAscii")
patched.specimens <-
placePatch(atlas=atlas,dat.array=data,path="E:/Documents/hominoid",prefix
='', 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:
<-
placePatch(atlas=atlas,dat.array=data,path="E:/Documents/hominoid",prefix
='', 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
option:
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
properly
Thank you very much for your help, I really appreciate your time and
expertise to answer my questions,
with thanks,
Pablo
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El lun., 17 jun. 2019 a las 17:02, Ryan Felice (<ryanfel...@gmail.com>)
escribió:
> 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
> rnfelice.com
> ryanfel...@gmail.com
>
> On Jun 17, 2019, at 8:38 PM, Pablo Fisichella <fisichellapa...@gmail.com>
> 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(tmp.name): 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 (dimnames(data)[[3]]).
>
> I followed a suggestion that Antonio Profico did to another researcher in
> the past by using the function str_sub from the package stringr to try to
> delete the extension .landmarkAscii from my array dimnames but this time
> does not work and I continue obtaining the same errors
>
> I realized that the dimnames of my array changed. For instance the
> original .ply model name is USNM260582go but the name of the same model in
> the array with NAs is USNM260582go.landmarkAscii. This is the problem
> (i.e., the extension .landmarkAscii) but since the str_sub does not work I
> used several more functions from the package stringr including:
>
> dimnames(data)[[3]]=str_remove(dimnames(data)[[3]],".landmarkAscii")
>
>
> dimnames(data)[[3]]=str_replace(dimnames(data)[[3]],".landmarkAscii",".ply")
>
> But I got the same errors
>
> I have tried additional tricks like changing the dimnames (including only
> numbers) by using this function data2=array(data, dim=c(19,3,10)) and
> changing the names of my .ply models but I got always the same error
>
> Obviously the error is related with my array dimnames but I don’t know how
> I can solve this, thus I´m looking for advice
>
> Thanks in advance for any help, advice or suggestion
>
> best wishes
>
> Pablo
>
>
>
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> <NAs.jpg><Atlas.jpg>
>
>
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