Re: [MORPHMET] Read .landmarkAscii file into R

[David Katz]

Thanks, Antonio! It's good to know it's a bug. Then it's just about finding
a workaround (like those you provided).

Best,
David

On Tue, Feb 16, 2016 at 10:39 AM,  wrote:

> Dear David,
>
> when you do many operations in Amira or Avizo for a bug the landmarkAscii
> file is converted in a 2setlandmarkAscii file, in fact a second empty
> matrix will be added…
>
> I report two functions to convert a landmarkAscii file or a folder
> containing the amira/avizo Landmark files in an array k*3*n, where k=number
> of landmarks and n=number of specimens.
> My functions read only the matrix between the @1 and @2.
>
> Let me know if it works or not…
>
> Best,
> Antonio
>
> #' read.amira.set
> #'
> #' This function convert a file landmark set of Amira in a array
> #' @param name.file character: path of landamrkascii file
> #' @param nland numeric: number of landmark sampled in Amira, if is set on
> "auto" will be automatically recognized the landmark number
> #' @return array.set numeric: an array with landmark coordinates (kxdxn)
> #' @author Antonio Profico
> #' @export
> #'
>
> read.amira.set=function(name.file,nland){
> A <- readLines(name.file, n = 100)
> end <- which(A == "@1")
> end_2 <- which(A == "@2")
> if(length(end_2!=0)){
> print(paste("file named",name.file, "contains a second matrix of 000"))
> B_junk=read.table(name.file,skip=end,nrows=(end_2-end-2))
> if(nland!="auto"){
> if (dim(B_junk)[1] != nland){
> print(paste("nland is different from dim(matrix)[1]:
> ",paste("nland=",nland,",",sep=""),
>   paste("dim(matrix)[1]=", dim(B_junk)[1],sep="")))
> B=matrix(NA,ncol=3,nrow=nland)}
> if(dim(B_junk)[1]==nland){
> B=B_junk
> }}
> if(nland=="auto"){
> B=read.table(name.file,skip=end,nrows=(end_2-end-2))
> }}
> if(length(end_2)==0){
> B_junk=read.table(name.file,skip=end)
> if(nland!="auto"){
> if (dim(B_junk)[1] != nland){
> print(paste("nland is different from dim(matrix)[1]:
> ",paste("nland=",nland,",",sep=""),
> paste("dim(matrix)[1]=", dim(B_junk)[1],sep="")))
> B=matrix(NA,ncol=3,nrow=nland)}
> if(dim(B_junk)[1]==nland){
> B=B_junk
> }}
> if(nland=="auto"){
> B=B_junk}}
> array.set=array(as.matrix(B),dim=c(dim(B)[1],3,1))
> dimnames(array.set)[[3]]=list(name.file)
> return(array.set)}
>
>
>
>
> #' read.amira.dir
> #'
> #' This function read and store in array the coordinated allocated in a
> folder in separate files (format
> #' @param path.dir character: path of the folder
> #' @param nland numeric: number of landmark sampled in Amira
> #' @return array.set numeric: a kxdxn array with landmark coordinates
> #' @author Antonio Profico
> #' @export
>
> read.amira.dir=function(path.dir,nland){
> names=list.files(path.dir)
> if(nland=="auto"){
> dims=c()
> for(i in 1:length(names)){
> dims[i]=dim(read.amira.set(paste(path.dir,"/",names[i],sep=""),"auto"))[1]}
>
> array.amira=array(NA,dim=c(as.numeric(names(sort(-table(dims)))[1]),3,length(names)))}
> else{array.amira=array(NA,dim=c(nland,3,length(names)))}
> for(i in 1:length(names)){
> array.amira[,,i]=read.amira.set(paste(path.dir,"/",names[i],sep=""),nland)
> }
> if(length(names)==1){
> dimnames(array.amira)[[3]]=list(names)}
> if(length(names)!=1){
> dimnames(array.amira)[[3]]=names}
> return(array.amira)
> }
>
>
> __
>
> Antonio Profico
> PhD student
> Department of Environmental Biology – Dipartimento di Biologia Ambientale
> SAPIENZA Università di Roma
>
> Lab.  06 4991 2690
> Mob. 3293440766
>
> *Da:* David Katz 
> *Data invio:* ‎mercoledì‎ ‎20‎ ‎gennaio‎ ‎2016 ‎06‎:‎49
> *A:* Emma Sherratt 
> *Cc:* MORPHMET 
>
> I won't get back to my office, and the hard drive where the files are
> stored, for about a week. I'll send something along then.
>
> Thanks, Emma.
>
> David
>
> On Wed, Jan 20, 2016 at 12:08 AM, Emma Sherratt 
> wrote:
>
>> Hi David,
>>
>> Not sure what the file actually looks like since you’ve not included a
>> sample here. However I suggest taking a look at the readland functions in
>> geomorph R package to see how we tackle the different types. If you want,
>> send it through to us and we can take a look. If there’s a lot of people
>> using AVIZO for digitising, we can include a function in geomorph.
>>
>> Regarding a read function writing? Nope, never heard of that.
>>
>> Em
>>
>> ~~~
>>
>> 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 20 January 2016 at 

Re: [MORPHMET] Read .landmarkAscii file into R

[antonio.profico]

Dear David,


when you do many operations in Amira or Avizo for a bug the landmarkAscii file 
is converted in a 2setlandmarkAscii file, in fact a second empty matrix will be 
added…


I report two functions to convert a landmarkAscii file or a folder containing 
the amira/avizo Landmark files in an array k*3*n, where k=number of landmarks 
and n=number of specimens. 

My functions read only the matrix between the @1 and @2. 



Let me know if it works or not…


Best,

Antonio


#' read.amira.set
#'
#' This function convert a file landmark set of Amira in a array
#' @param name.file character: path of landamrkascii file
#' @param nland numeric: number of landmark sampled in Amira, if is set on 
"auto" will be automatically recognized the landmark number
#' @return array.set numeric: an array with landmark coordinates (kxdxn)
#' @author Antonio Profico
#' @export
#' 


read.amira.set=function(name.file,nland){
A <- readLines(name.file, n = 100)
end <- which(A == "@1")
end_2 <- which(A == "@2")
if(length(end_2!=0)){
print(paste("file named",name.file, "contains a second matrix of 000"))
B_junk=read.table(name.file,skip=end,nrows=(end_2-end-2))
if(nland!="auto"){
if (dim(B_junk)[1] != nland){
print(paste("nland is different from dim(matrix)[1]: 
",paste("nland=",nland,",",sep=""),
  paste("dim(matrix)[1]=", dim(B_junk)[1],sep="")))  
B=matrix(NA,ncol=3,nrow=nland)}
if(dim(B_junk)[1]==nland){
B=B_junk  
}}
if(nland=="auto"){
B=read.table(name.file,skip=end,nrows=(end_2-end-2))
}}
if(length(end_2)==0){
B_junk=read.table(name.file,skip=end)
if(nland!="auto"){
if (dim(B_junk)[1] != nland){
print(paste("nland is different from dim(matrix)[1]: 
",paste("nland=",nland,",",sep=""),
paste("dim(matrix)[1]=", dim(B_junk)[1],sep="")))
B=matrix(NA,ncol=3,nrow=nland)}
if(dim(B_junk)[1]==nland){
B=B_junk  
}}
if(nland=="auto"){
B=B_junk}}
array.set=array(as.matrix(B),dim=c(dim(B)[1],3,1))
dimnames(array.set)[[3]]=list(name.file)
return(array.set)}






#' read.amira.dir
#'
#' This function read and store in array the coordinated allocated in a folder 
in separate files (format
#' @param path.dir character: path of the folder
#' @param nland numeric: number of landmark sampled in Amira
#' @return array.set numeric: a kxdxn array with landmark coordinates
#' @author Antonio Profico
#' @export


read.amira.dir=function(path.dir,nland){
names=list.files(path.dir)
if(nland=="auto"){
dims=c()
for(i in 1:length(names)){
dims[i]=dim(read.amira.set(paste(path.dir,"/",names[i],sep=""),"auto"))[1]}
array.amira=array(NA,dim=c(as.numeric(names(sort(-table(dims)))[1]),3,length(names)))}
else{array.amira=array(NA,dim=c(nland,3,length(names)))}
for(i in 1:length(names)){
array.amira[,,i]=read.amira.set(paste(path.dir,"/",names[i],sep=""),nland) 
}
if(length(names)==1){
dimnames(array.amira)[[3]]=list(names)}
if(length(names)!=1){
dimnames(array.amira)[[3]]=names}
return(array.amira)
}








__

Antonio Profico
PhD student
Department of Environmental Biology – Dipartimento di Biologia Ambientale
SAPIENZA Università di Roma

Lab.  06 4991 2690
Mob. 3293440766






Da: David Katz
Data invio: ‎mercoledì‎ ‎20‎ ‎gennaio‎ ‎2016 ‎06‎:‎49
A: Emma Sherratt
Cc: MORPHMET





I won't get back to my office, and the hard drive where the files are stored, 
for about a week. I'll send something along then. 



Thanks, Emma.

David



On Wed, Jan 20, 2016 at 12:08 AM, Emma Sherratt  wrote:



Hi David,




Not sure what the file actually looks like since you’ve not included a sample 
here. However I suggest taking a look at the readland functions in geomorph R 
package to see how we tackle the different types. If you want, send it through 
to us and we can take a look. If there’s a lot of people using AVIZO for 
digitising, we can include a function in geomorph.




Regarding a read function writing? Nope, never heard of that.




Em



~~~
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 20 January 2016 at 14:50:38, David Katz (dck...@ucdavis.edu) wrote:







Hi everyone,  



I've collected 3D landmarks on a series of cranial surface models in Avizo. 
Avizo's landmark editor outputs .landmarkAscii files, which I would like to 
read into R. The way I've done the reading has the following very unexpected 
effect: sometimes, it writes additional data to my .landmarkAscii files. I'd 
like to understand why, but am mostly interested in finding a solution.




To read in the landmark files for a specimen...





# Below, avz.file is