Dear experts,
A few weeks ago I tried to get your advise on an error I run into when running FIX. I have been using FIX on the melodic.ica output created with AROMA (renamed to filtered_func_data.ica). Is that output by any chance different from what FIX is expecting and could that be what is causing FIX to quit?
I have been receiving the Rlog files described below when trying to create a train-weights file.
Thanks!
Sandra
R version 3.3.3 (2017-03-06) -- "Another Canoe”
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
library(party)
Loading required package: grid
Loading required package: mvtnorm
Loading required package: modeltools
Loading required package: stats4Loading required package: strucchange
Loading required package: zoo
Attaching package: âzooâ
The following objects are masked from âpackage:baseâ:
as.Date, as.Date.numeric
Loading required package: sandwic
library(e1071
library(kernlab)
Attaching package: âkernlabâ
The following object is masked from âpackage:modeltoolsâ:
prior
library(class
library(ROCR)
Loading required package: gplots
Attaching package: âgplotsâ
The following object is masked from âpackage:statsâ:
lowess
library(randomForest)
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes
library(MASS)
# R CMD BATCH "--no-restore --args ${FIXDIR}/ ${MELOUT}/ Standard 0.1" ${FIXDIR}/fix_2_PREDICT.R ${MELOUT}/fix/logR_Standard_0.1.tx
if (T) {
+ args <- commandArgs(TRUE)
+ path.to.fix <- args[[1]]
+ print(path.to.fix)
+ path.to.train.files <- args[[2]]
+ print(path.to.train.files)
+ weight.file.name <- args[[3]]
+ print(weight.file.name)
+ #
+ #which.fix <- args[[4]]
+ #print(which.fix)
+ } else {
+ path.to.fix <- "/Users/reza/Documents/Academic/FIX/fix1.02”
+ path.to.train.files <- "/Users/reza/Documents/Academic/FIX/raw_data/EXAMPLEL/TRAIN”
+ weight.file.name <- "/Users/reza/Documents/Academic/FIX/raw_data/EXAMPLEL/TRAIN.RData”
+
[1] "/home/lucianam/sthijsse/fix1.067”
[1] "/home/lucianam/shared/DataAnalysis/MRIdata/ABCDrfMRIscripts/ABCDscripts_minimallyProcessed/ABCD_FIXtraining/ABCDtraining_test”
[1] "/home/lucianam/shared/DataAnalysis/MRIdata/ABCDrfMRIscripts/ABCDscripts_minimallyProcessed/ABCD_FIXtraining/ABCDtraining_test.RData
if (substr(path.to.fix, nchar(path.to.fix), nchar(path.to.fix))!="/“)
+ path.to.fix <- paste(path.to.fix, "/", sep = “")
if (substr(path.to.train.files, nchar(path.to.train.files), nchar(path.to.train.files))!="/“)
+ path.to.train.files <- paste(path.to.train.files, "/", sep = “”
readMelView <- function(file.path) {
+ tmp <- readLines(file.path, -1) # read the full text file
+ tmp <- tmp[grepl("^\\[", tmp) & grepl("\\]$", tmp)] # get THE line
+ noise.list <- as.numeric(strsplit(gsub("\\]", "", gsub("\\[", "", gsub(" ", "", tmp))), ',')[[1]]) # only keep the comma-separated noise IDs > split them
+ return(noise.list) # return a vector, containing noise IDs
+ }
#readMelView <- function(file.path) {
# numb <- runif(1,0,100000000000000)*10
# system(paste("cat ", file.path, " | grep '^\\[' > ", file.path, numb, sep="”))
# con <- file(paste(file.path, numb, sep=""), "rt”)
# tmp <- readLines(con, 1) # Read one line
# close(con)
# noise.list <- as.numeric(strsplit(gsub("\\]", "", gsub("\\[", "", gsub(" ", "", tmp))), ',')[[1]])
# system(paste("rm ", file.path, numb, sep="”))
# return(noise.list)
#}
# pre-processing (e.g., concatenate all files, etc.)
is.consistent <- T
file.feats <- list.files(path.to.train.files, "*csv”)
file.label <- list.files(path.to.train.files, "*txt”)
for(i.feat in file.feats)
+ if(sum(substr(i.feat, 1, nchar(i.feat)-3)==substr(file.label, 1, nchar(file.feats)-3))==0)
+ is.consistent <- F
if (!is.consistent) {
+ print("There is a problem in that the required files are not arranged properly”)
+ print("In order for this function to work, there needs to be two files per MELODIC folder”)
+ print(" 1) a features file | CSV extracted by FIX”)
+ print(" 2) a MELVIEW-compatible label file | TXT from manual or FIX labeling”)
+ } else {
+ for(i in c(1:length(file.feats))) {
+ tmpf <- read.csv(paste(path.to.train.files, file.feats[i], sep = ""), header = F)
+ tmpl <- readMelView(paste(path.to.train.files, substr(file.feats[i], 1, nchar(file.feats[i])-3), "txt", sep = "”))
+ tmpf$labs <- 1
+ tmpf$labs[tmpl] <- 0
+ if(i==1) train.mat <- tmpf else train.mat <- rbind(train.mat, tmpf)
+ }
+ }
Error in file(file, "rt") : cannot open the connection
Calls: read.csv -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file '/home/lucianam/shared/DataAnalysis/MRIdata/ABCDrfMRIscripts/ABCDscripts_minimallyProcessed/ABCD_FIXtraining/ABCDtraining_test/NA': No such file or directory
Execution halted
> On Jun 4, 2019, at 13:45, Sandra Thijssen <[log in to unmask]> wrote:
>
> Dear experts,
>
> Does anyone have an idea what is going wrong when I try to create a train-weights file using FIX? My Rlog files shows the error below.
>
> Thanks for your help and apologies for reposting.
>
> Kind regards,
> Sandra
>
>
>
> R version 3.3.3 (2017-03-06) -- "Another Canoe"
> Copyright (C) 2017 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>>
>> library(party)
> Loading required package: grid
> Loading required package: mvtnorm
> Loading required package: modeltools
> Loading required package: stats4
> Loading required package: strucchange
> Loading required package: zoo
>
> Attaching package: âzooâ
>
> The following objects are masked from âpackage:baseâ:
>
> as.Date, as.Date.numeric
>
> Loading required package: sandwich
>> library(e1071)
>> library(kernlab)
>
> Attaching package: âkernlabâ
>
> The following object is masked from âpackage:modeltoolsâ:
>
> prior
>
>> library(class)
>> library(ROCR)
> Loading required package: gplots
>
> Attaching package: âgplotsâ
>
> The following object is masked from âpackage:statsâ:
>
> lowess
>
>> library(randomForest)
> randomForest 4.6-14
> Type rfNews() to see new features/changes/bug fixes.
>> library(MASS)
>>
>>
>> # R CMD BATCH "--no-restore --args ${FIXDIR}/ ${MELOUT}/ Standard 0.1" ${FIXDIR}/fix_2_PREDICT.R ${MELOUT}/fix/logR_Standard_0.1.txt
>>
>> if (T) {
> + args <- commandArgs(TRUE)
> + path.to.fix <- args[[1]]
> + print(path.to.fix)
> + path.to.train.files <- args[[2]]
> + print(path.to.train.files)
> + weight.file.name <- args[[3]]
> + print(weight.file.name)
> + #
> + #which.fix <- args[[4]]
> + #print(which.fix)
> + } else {
> + path.to.fix <- "/Users/reza/Documents/Academic/FIX/fix1.02"
> + path.to.train.files <- "/Users/reza/Documents/Academic/FIX/raw_data/EXAMPLEL/TRAIN"
> + weight.file.name <- "/Users/reza/Documents/Academic/FIX/raw_data/EXAMPLEL/TRAIN.RData"
> + }
> [1] "/home/lucianam/sthijsse/fix1.067"
> [1] "/home/lucianam/shared/DataAnalysis/MRIdata/ABCDrfMRIscripts/ABCDscripts_minimallyProcessed/ABCD_FIXtraining/ABCDtraining_test"
> [1] "/home/lucianam/shared/DataAnalysis/MRIdata/ABCDrfMRIscripts/ABCDscripts_minimallyProcessed/ABCD_FIXtraining/ABCDtraining_test.RData"
>>
>> if (substr(path.to.fix, nchar(path.to.fix), nchar(path.to.fix))!="/")
> + path.to.fix <- paste(path.to.fix, "/", sep = "")
>> if (substr(path.to.train.files, nchar(path.to.train.files), nchar(path.to.train.files))!="/")
> + path.to.train.files <- paste(path.to.train.files, "/", sep = "")
>>
>> readMelView <- function(file.path) {
> + tmp <- readLines(file.path, -1) # read the full text file
> + tmp <- tmp[grepl("^\\[", tmp) & grepl("\\]$", tmp)] # get THE line
> + noise.list <- as.numeric(strsplit(gsub("\\]", "", gsub("\\[", "", gsub(" ", "", tmp))), ',')[[1]]) # only keep the comma-separated noise IDs > split them
> + return(noise.list) # return a vector, containing noise IDs
> + }
>>
>> #readMelView <- function(file.path) {
>> # numb <- runif(1,0,100000000000000)*10
>> # system(paste("cat ", file.path, " | grep '^\\[' > ", file.path, numb, sep=""))
>> # con <- file(paste(file.path, numb, sep=""), "rt")
>> # tmp <- readLines(con, 1) # Read one line
>> # close(con)
>> # noise.list <- as.numeric(strsplit(gsub("\\]", "", gsub("\\[", "", gsub(" ", "", tmp))), ',')[[1]])
>> # system(paste("rm ", file.path, numb, sep=""))
>> # return(noise.list)
>> #}
>>
>> # pre-processing (e.g., concatenate all files, etc.)
>> is.consistent <- T
>> file.feats <- list.files(path.to.train.files, "*csv")
>> file.label <- list.files(path.to.train.files, "*txt")
>> for(i.feat in file.feats)
> + if(sum(substr(i.feat, 1, nchar(i.feat)-3)==substr(file.label, 1, nchar(file.feats)-3))==0)
> + is.consistent <- F
>>
>> if (!is.consistent) {
> + print("There is a problem in that the required files are not arranged properly")
> + print("In order for this function to work, there needs to be two files per MELODIC folder")
> + print(" 1) a features file | CSV extracted by FIX")
> + print(" 2) a MELVIEW-compatible label file | TXT from manual or FIX labeling")
> + } else {
> + for(i in c(1:length(file.feats))) {
> + tmpf <- read.csv(paste(path.to.train.files, file.feats[i], sep = ""), header = F)
> + tmpl <- readMelView(paste(path.to.train.files, substr(file.feats[i], 1, nchar(file.feats[i])-3), "txt", sep = ""))
> + tmpf$labs <- 1
> + tmpf$labs[tmpl] <- 0
> + if(i==1) train.mat <- tmpf else train.mat <- rbind(train.mat, tmpf)
> + }
> + }
> Error in file(file, "rt") : cannot open the connection
> Calls: read.csv -> read.table -> file
> In addition: Warning message:
> In file(file, "rt") :
> cannot open file '/home/lucianam/shared/DataAnalysis/MRIdata/ABCDrfMRIscripts/ABCDscripts_minimallyProcessed/ABCD_FIXtraining/ABCDtraining_test/NA': No such file or directory
> Execution halted
>
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