In png(), the first argument is filename = "Rplot%03d.png" which causes files to be generated with ascending numbers. However, in ggsave, this doesn't work, the number always stays at the lowest number (Rplots001.png") and this file is always overwritten.
Looking at the code of the grDevices-functions (e.g. grDevices::png() it appears that the automatic naming happens in functions which are called by .External()
Is there already an implementation of this file naming functionality in R such that it is accessible outside of the grDevices functions?
Edit:
asked differently, is there a way to continue automatic numbering after shutting off and restarting a device? For example, in this code, the two later files overwrite the former ones:
png(width = 100)
plot(1:10)
plot(1:10)
dev.off()
png(width = 1000)
plot(1:10)
plot(1:10)
dev.off()
You can write a function to do this. For example, how about simply adding a time stamp. something like:
fname = function(basename = 'myfile', fileext = 'png'){
paste(basename, format(Sys.time(), " %b-%d-%Y %H-%M-%S."), fileext, sep="")
}
ggsave(fname())
Or, if you prefer sequential numbering, then something along the lines of
next_file = function(basename = 'myfile', fileext = 'png', filepath = '.'){
old.fnames = grep(paste0(basename,' \\d+\\.', fileext,'$'),
list.files(filepath), value = T)
lastnum = gsub(paste0(basename,' (\\d+)\\.', fileext,'$'), '\\1', old.fnames)
if (!length(lastnum)) {
lastnum = 1
} else {
lastnum = sort(as.integer(lastnum),T)[1] + 1L
}
return(paste0(basename, ' ', sprintf('%03i', lastnum), '.', fileext))
}
ggsave(next_file())
Related
Trying to cut a bunch of audio (.WAV) files into smaller samples in R. For this example, I'm using a loop to cut out 1 minute samples at 140 minutes.
For some files, the recording ends before 140 minutes due to an error in the recording device. When this occurs, an error appears -- and the loop stops. I'm trying to make it so the loop continues by using the try or tryCatch function however keep getting errors.
The code is as follows:
for(i in 1:length(AR_CD288)){
CUT_AR288_5 <- try({readWave(AR_CD288[i], from = 140, to = 141, units = "minutes")})
FILE.OUT_AR288_5<- sub("\\.wav$", "_140.wav", AR_CD288)
OUT.PATH_AR288_5 <- file.path("New files", basename(FILE.OUT_AR288_5))
writeWave(CUT_AR288_5, extensible=FALSE, filename = OUT.PATH_AR288_5[i])
}
I get the following two errors from the code:
Error in readBin(con, int, n = N, size = bytes, signed = (bytes != 1), :
invalid 'n' argument
Error in writeWave(CUT_AR288_5, extensible = FALSE, filename = OUT.PATH_AR288_5[i]) :
'object' needs to be of class 'Wave' or 'WaveMC
The loop still saves some samples into the "New files" directory, however, once the loop reaches a file <140 minutes, the loop stops.
I am very stuck! Any help would be greatly appreciated.
Cheers.
When I use try, I always do one (or both) of:
check the return value to see if it inherits "try-error", indicating that the command failed; or
add try(., silent = TRUE), indicating that I don't care if it succeeded (but this implies that I will not use its return value, either).
Try this:
for (i in seq_along(AR_CD288)) {
CUT_AR288_5 <- try({
readWave(AR_CD288[i], from = 140, to = 141, units = "minutes")
}, silent = TRUE)
if (!inherits(CUT_AR288_5, "try_error")) {
FILE.OUT_AR288_5 <- sub("\\.wav$", "_140.wav", AR_CD288)
OUT.PATH_AR288_5 <- file.path("New files", basename(FILE.OUT_AR288_5))
writeWave(CUT_AR288_5, extensible = FALSE, filename = OUT.PATH_AR288_5[i])
}
}
Three notes:
I changed 1:length(.) to seq_along(.); the latter is more resilient in an automated use when it is feasible that the vector might be length 0. For example, if AR_CD288 can ever be length 2, intuitively we expect 1:length(AR_CD288) to return nothing so that the for loop will not run; unfortunately, it resolves to 1:0 which returns a vector of length 2, which will often fail (based on whatever code is operating in the loop). The use of seq_along(.) will always return a vector of length 0 with an empty input, which is what we need. (Alternatively and equivalent, seq_len(length(AR_CD288)), though that's really what seq_along is intended to do.)
If you do not add silent=TRUE (or explicitly add silent=FALSE), then you will get an error message indicating that the command failed. Unfortunately, the error message may not indicate which i failed, so you may be left in the dark as far as fixing or removing the errant file. You may prefer to add an else to the if (inherits(.,"try-error")) clause so that you can provide a clearer error, such as
if (inherits(CUT_AR288_5, "try_error")) {
warning("'readWave' failed on ", sQuote(AR_CD288[i]), call. = FALSE)
} else {
FILE.OUT_AR288_5 <- sub("\\.wav$", "_140.wav", AR_CD288)
# ...
}
(noting that I put the "things worked" code in the else clause here ... I find it odd to do if (!...) {} else {}, seems like a double-negation :-).
The choice to wrap one function or the whole block depends on your needs: I tend to prefer to know exactly where things fail, so the will-possibly-fail functions are often individually wrapped with try so that I can react (or log/message) accordingly. If you don't need that resolution of error-detection, then you can certainly wrap the whole code-block in a sense:
for (i in seq_along(AR_CD288)) {
ret <- try({
CUT_AR288_5 <- readWave(AR_CD288[i], from = 140, to = 141, units = "minutes")
FILE.OUT_AR288_5 <- sub("\\.wav$", "_140.wav", AR_CD288)
OUT.PATH_AR288_5 <- file.path("New files", basename(FILE.OUT_AR288_5))
writeWave(CUT_AR288_5, extensible = FALSE, filename = OUT.PATH_AR288_5[i])
}, silent = TRUE)
if (inherits(ret, "try-error")) {
# do or log something
}
}
I'm using slackr to send alert messages to a Slack channel. It works great except the message format is not great and I want to improve it.
install_github("hrbrmstr/slackr")
library(slackr)
slackr_setup(channel="#alerts", username="Mark Davis",
incoming_webhook_url = "https://hooks.slack.com/services/T31P8UDAB/BCH4HKQSC/*********",
api_token = "*********", echo = F)
alert="On Monday, 2018-09-03 # 2pm Pacific..."
slackr(alert)
Here is an example of how a message from slackr looks in Slack:
Here is an example of how I'd like it to look:
slackr doesn't seem to have many options in the way of formatting. I was thinking of building an image and inserting that, but I'm having trouble building an image out of a text file using R.
Perhaps there is another api I could call that could take my text and format it for slack?
I'm open to any suggestions.
Addendum:
Slackr has an option to upload files, so my latest attempt is to create an image from the text message and upload that object.
I am able to create a png file from the text message using the magick library. I created an image with a colored background, and I simply add the message text to the image:
library(magick)
alert_picture <- image_read('alert_480x150_dark_red.png')
alert_picture=image_annotate(alert_picture, DreamCloud_Alert, size = 20, gravity = "southwest",
color = "white", location = "+10+10")
image_write(alert_picture, path = "alert_picture.png", format = "png")
The image looks pretty good (although there doesn't seem to be an easy way to bold or underline specific words in the message), but the obstacle now is that I can't get the upload command to work.
slackr_upload(filename = "alert_picture.png")
I don't get any error messages but nothing is uploaded to slack.
I got around this issue by using the httr package to execute the post image function to slack.
Thanks to Adil B. for providing the solution:
Post Image to Slack Using HTTR package in R
I am not sure this is what you meant, but I solved allowing formatting like in a regular slack message by altering the slackr_bot() function and just removing the 2 sets of 3 back-ticks at the end of the code where it says text. Then just call it slackr_bot1() or something, and then you can post formatted messages. This is the function after the back-ticks removal:
slackr_bot1 <- function(...,
channel=Sys.getenv("SLACK_CHANNEL"),
username=Sys.getenv("SLACK_USERNAME"),
icon_emoji=Sys.getenv("SLACK_ICON_EMOJI"),
incoming_webhook_url=Sys.getenv("SLACK_INCOMING_URL_PREFIX")) {
if (incoming_webhook_url == "") {
stop("No incoming webhook URL specified. Did you forget to call slackr_setup()?", call. = FALSE)
}
if (icon_emoji != "") { icon_emoji <- sprintf(', "icon_emoji": "%s"', icon_emoji) }
resp_ret <- ""
if (!missing(...)) {
# mimics capture.output
# get the arglist
args <- substitute(list(...))[-1L]
# setup in-memory sink
rval <- NULL
fil <- textConnection("rval", "w", local = TRUE)
sink(fil)
on.exit({
sink()
close(fil)
})
# where we'll need to eval expressions
pf <- parent.frame()
# how we'll eval expressions
evalVis <- function(expr) withVisible(eval(expr, pf))
# for each expression
for (i in seq_along(args)) {
expr <- args[[i]]
# do something, note all the newlines...Slack ``` needs them
tmp <- switch(mode(expr),
# if it's actually an expresison, iterate over it
expression = {
cat(sprintf("> %s\n", deparse(expr)))
lapply(expr, evalVis)
},
# if it's a call or a name, eval, printing run output as if in console
call = ,
name = {
cat(sprintf("> %s\n", deparse(expr)))
list(evalVis(expr))
},
# if pretty much anything else (i.e. a bare value) just output it
integer = ,
double = ,
complex = ,
raw = ,
logical = ,
numeric = cat(sprintf("%s\n\n", as.character(expr))),
character = cat(sprintf("%s\n\n", expr)),
stop("mode of argument not handled at present by slackr"))
for (item in tmp) if (item$visible) { print(item$value, quote = FALSE); cat("\n") }
}
on.exit()
sink()
close(fil)
# combined all of them (rval is a character vector)
output <- paste0(rval, collapse="\n")
loc <- Sys.getlocale('LC_CTYPE')
Sys.setlocale('LC_CTYPE','C')
on.exit(Sys.setlocale("LC_CTYPE", loc))
resp <- POST(url = incoming_webhook_url, encode = "form",
add_headers(`Content-Type` = "application/x-www-form-urlencoded",
Accept = "*/*"), body = URLencode(sprintf("payload={\"channel\": \"%s\", \"username\": \"%s\", \"text\": \"%s\"%s}",
channel, username, output, icon_emoji)))
warn_for_status(resp)
}
return(invisible())
}
slackr_bot1("*test* on time")
So, I am running the following code:
dirtyFolder = "Myfolder/test"
filenames = list.files(dirtyFolder, pattern="*.png")
for (f in filenames)
{
print(f)
imgX = readPNG(file.path(dirtyFolder, f))
x = data.table(img2vec(imgX), kmeansThreshold(imgX))
setnames(x, c("raw", "thresholded"))
yHat = predict(gbm.mod, newdata=x, n.trees = best.iter)
img = matrix(yHat, nrow(imgX), ncol(imgX))
img.dt=data.table(melt(img))
names.dt<-names(img.dt)
setnames(img.dt,names.dt[1],"X1")
setnames(img.dt,names.dt[2],"X2")
Numfile = gsub(".png", "", f, fixed=TRUE)
img.dt[,id:=paste(Numfile,X1,X2,sep="_")]
write.table(img.dt[,c("id","value"),with=FALSE], file = "submission.csv", sep = ",", col.names = (f == filenames[1]),row.names = FALSE,quote = FALSE,append=(f != filenames[1]))
# show a sample
if (f == "4.png")
{
writePNG(imgX, "train_101.png")
writePNG(img, "train_cleaned_101.png")
}
}
What it does is basically, takes as input images which have noise in them and removes noise from them. This is only the later part of the code which applies the algorithm prepared from a training dataset (not shown here).
Now, I am not able to figure out, how can I save the cleaned image for each of the images in the test folder. That is, I wish to save the cleaned image for each of the images in the folder and not just the 4.png image. The output image should have the name as 4_cleaned.png if the input image has the name 4.png and it should be saved in a separate folder in the same directory. That is, if input image has the name x.png, the output image should have the name x_cleaned.png and saved in a separate folder. How can I do it?
Tldr; I just want to save the variable named img for each of the filename as number_cleaned.png where number corresponds to the original file name. These new files should be saved in a separate folder.
Tldr; I just want to save the variable named img for each of the filename as number_cleaned.png where number corresponds to the original file name. These new files should be saved in a separate folder.
Alright, so construct the output filename using file.path and a function such as paste or sprintf:
folder_name = 'test'
output_filename_pattern = file.path(folder_name, '%s_cleaned.png')
remove_extension = function (filename)
gsub('\\.[^.]$', '', filename)
for (f in filenames) {
# … your code her …
new_filename = sprintf(output_filename_pattern, remove_extension(f))
# … save file here …
}
Consider either function which (for rstudio) will open something in the viewer if y = TRUE and in your browser if y = FALSE. You can force the whatever to open in your browser via options(viewer = NULL) (and then you need to reset to before), but I can't get this to work inside functions using the normal on.exit approach. Tested on windows and osx.
f <- function(x, y = TRUE) {
if (y) {
oo <- getOption('viewer')
on.exit(options(viewer = oo))
options(viewer = NULL)
} else options(viewer = NULL)
print(getOption('viewer'))
DT::datatable(x)
}
g <- function(x, y = TRUE) {
if (y) {
oo <- getOption('viewer')
on.exit(options(viewer = oo))
options(viewer = NULL)
} else options(viewer = NULL)
print(getOption('viewer'))
htmlTable::htmlTable(x)
}
## in rstudio, returns the viewer function
getOption('viewer')
# function (url, height = NULL)
# ...
## opens in viewer despite `options(viewer = NULL)`
g(mtcars)
# NULL
## again returns the function, ie, reset my options to before g call successfully
getOption('viewer')
# function (url, height = NULL)
# ...
## opens in browser but leaves `options(viewer = NULL)` after exiting
g(mtcars, FALSE)
# NULL
getOption('viewer')
# NULL
It seems like the viewer isn't respecting my options within the function environment with either just some html (g) or a widget (f). I thought both would use viewer = NULL inside the function and return my options the way they were upon exiting so that I can control where I want to view the result.
Or is there a better way of doing this for both html and widgets? I have tried the options argument in DT::datatable to no avail, but this wouldn't help for the htmlTable::htmlTable case.
The only other approach I can think of is to write all the code to a temp file and use if (rstudio) rstudio::viewer(tempfile) else browseURL(tempfile) which I think is a lot of work for something seemingly so straight-forward.
Although this isn't a fix, I think it illustrates what's going on. Try adding a Sys.sleep() call in the on.exit() handler:
f <- function(x) {
viewer <- getOption("viewer")
on.exit({
print("Restoring viewer...")
Sys.sleep(3)
options(viewer = viewer)
}, add = TRUE)
options(viewer = NULL)
DT::datatable(x)
}
## opens in viewer despite `options(viewer = NULL)`
f(mtcars)
You'll notice that RStudio doesn't 'decide' what to do with the result of DT::datatable() call until after the on.exit() handler has finished execution. This means that, by the time RStudio wants to figure out to do with the result, the viewer has already been restored! Odds are, RStudio waits until R is no longer 'busy' to decide how to display the resulting content, and by then is too late for temporary changes to the viewer option.
Note that this doesn't explain the htmlTable behaviour. My best guess is that there is some kind of race condition going on; the lost viewer option seems to go away with strategically placed Sys.sleep() calls...
Unfortunately, working around this means avoiding the use of on.exit() call -- unless we can figure out to handle this in RStudio, of course.
Here's one way you could get this functionality by writing the code to a temporary file and using browseURL or whatever you like.
The gist of both f and g are the same, so you could have one function to handle any type of html code or widget I suppose. And probably widgets need to be selfcontained = TRUE.
f <- function(x, y = TRUE) {
x <- if ((inherits(x, 'iplot'))) x else DT::datatable(x)
if (!y) {
htmlFile <- tempfile(fileext = '.html')
htmlwidgets::saveWidget(x, htmlFile, selfcontained = TRUE)
utils::browseURL(htmlFile)
} else x
}
g <- function(x, y = TRUE) {
x <- htmlTable::htmlTable(x)
if (!y) {
htmlFile <- tempfile(fileext = '.html')
writeLines(x, con = htmlFile)
utils::browseURL(htmlFile)
} else x
}
## opens in viewer
g(mtcars)
## opens in browser
g(mtcars, FALSE)
## same for widgets
f(mtcars)
f(mtcars, FALSE)
f(qtlcharts::iplot(1:5, 1:5), FALSE)
## and my options haven't changed
getOption('viewer')
# function (url, height = NULL)
# ...
Side note that this is actually the proper way to have htmlTable::htmlTable use a different viewer, but g should work for any html.
library('htmlTable')
print(htmlTable(mtcars), useViewer = utils::browseURL)
There are some .fcs files in a data.000X format (where X = 1, 2, 3...) in a directory.
I want to rename every n file to the following format: exp.fcs (where exp is a text from a vector) if the file to be renamed is an .fcs file.
in other words: I want to rename files to exp.txt, where exp is a text and not a consecutive letter(s) i.e. F, cA, K, etc.
For example, from:
data.0001, data.0002, data.0003, data.0004, data.0005, data.0006...
to
textF_a.fcs, textF_b.fcs, textF_c.fcs, textVv_a.fcs, textVv_b.fcs, textVv_c.fcs ...
I tried to do it with file.rename(from, to) but failed as the arguments have different lengths (and I don't know what it means):
a <- list.files(path = ".", pattern = "data.*$")
b <- paste("data", 1:1180, ".fcs", sep = "")
file.rename(a, b)
Based on your comments, one issue is that your first file isn't named "data.001" - it's named "data.1". Use this:
b <- sprintf("data%.4d.fcs", seq(a))
It prepends up to 3 0s (since it seems you have 1000+ files, this may be better) to indices < 1000, so that all names have the same width. If you really just want to see things like "data.001", then use %.3d in the command.
Your code "works" on my machine ("works" in the sense that, when I created a set of files and followed your procedure, the renaming happened correctly). The error is likely that the number of files that you have (length(a)) is different from the number of new names that you give (length(b)). Post back if it turns out that these objects do have the same length.
As with the (very similar) question here, this function might be of use to you. I wrote it to allow regex find and replace in R. If you're on a mac it can detect and use the frontmost Finder window as a target. Also supports test runs, over-write control, and filtering large folders.
umxRenameFile <- function(baseFolder = "Finder", findStr = NA, replaceStr = NA, listPattern = NA, test = T, overwrite = F) {
# uppercase = u$1
if(baseFolder == "Finder"){
baseFolder = system(intern = T, "osascript -e 'tell application \"Finder\" to get the POSIX path of (target of front window as alias)'")
message("Using front-most Finder window:", baseFolder)
} else if(baseFolder == "") {
baseFolder = paste(dirname(file.choose(new = FALSE)), "/", sep = "") ## choose a directory
message("Using selected folder:", baseFolder)
}
if(is.na(listPattern)){
listPattern = findStr
}
a = list.files(baseFolder, pattern = listPattern)
message("found ", length(a), " possible files")
changed = 0
for (fn in a) {
findB = grepl(pattern = findStr, fn) # returns 1 if found
if(findB){
fnew = gsub(findStr, replace = replaceStr, fn) # replace all instances
if(test){
message("would change ", fn, " to ", fnew)
} else {
if((!overwrite) & file.exists(paste(baseFolder, fnew, sep = ""))){
message("renaming ", fn, "to", fnew, "failed as already exists. To overwrite set T")
} else {
file.rename(paste(baseFolder, fn, sep = ""), paste(baseFolder, fnew, sep = ""))
changed = changed + 1;
}
}
}else{
if(test){
# message(paste("bad file",fn))
}
}
}
message("changed ", changed)
}