I wanted to do something I thought simple, but... well, I failed repetitively.
I want to create a gif or a video (.avi) from pictures in a folder with R.
I can list the path and the names of the pictures (e.g. "./folder/1.jpg" "./folder/2.jpg" "./folder/3.jpg" "./folder/4.jpg" )
I just wanted to put them the one after the other and create a video or gif file (I will treat them frame by frame later, so the speed is not important)
I found a solution with SaveGIF, it works with plots in R but I didn't find the way to use it with external jpg.
Otherwise, there was this solution with image_animate "Animated graphics", but again, I didn't manage.
Do somebody already have a solution to do that?
Thank you very much for your help!
You can do it with the magick package, which gives you access to ImageMagick functions. For example, if the frames of your movie are in files named
frames <- paste0("folder/", 1:100, ".jpg")
then you would create a movie using
library(magick)
m <- image_read(frames)
m <- image_animate(m)
image_write(m, "movie.gif")
You could choose to write to other formats as well, just by changing the filename, or using other arguments to image_write().
A better solution in my oppinion is using the av package.
example:
list_of_frames <- list.files("your/path/to/directory", full.names=T)
av::av_encode_video(list_of_frames, framerate = 30,
output = "output_animation.mp4")
Related
I am new to this platform and I hope someone can help me.
I have imported some pdf files into Rstudio using the pdftools library. Now I want to make structured columns of this text. I just can't seem to get the structure right.
This is an example of one file added that I imported. I want to make the yellow shaded lines in a data table.
This is the outcome I would ultimately like to have.
Now I have entered the code below, but I can't get it into a data table.
library(pdftools)
library(stringr)
library(dplyr)
# load the PDF-files into Rstudio
files <- list.files(pattern = "pdf$", full.names = TRUE)
# make a list of the PDF-files
filestext <- lapply(files, pdf_text)
# remove "\n"
filestext <- str_split(filestext, pattern = "\n")
This is the result I get:
Does anyone know the easiest way to solve this?
I would also give https://sensible.so a shot. We have some great documentation and a free plan just for projects like this. Plus, when you sign up there are some tutorials to help you understand how to extract different types of data. I bet you can have this extracted into a clean JSON object in no time.
I want to read 12 images at a time in R.
I don't know how to do it. I am complete new to working on images in R.
How can I read couple of images from a folder in my system?
I am using windows10 operating system. RAM 8 gb. CORE i5 processor.
GPU is Intel(R) HD Graphics 620.
I am able to read only single image in R and that image is displaying as numeric values. I tried to convert it into raster format and then tried to print image to view the image. But I am still finding the color codes in values but not the image in print.
Can anyone help me on this?
Thanks a lot.
install.packages("magick")
library(magick)
install.packages("rsvg")
install.packages("jpeg")
library(jpeg)
img <- readJPEG("C:/Users/folder/Abc.jpg", native = FALSE)
img1 <- as.raster(img, interpolate = F)
print(img1)
I want to read couple of images at a time into R console and want to view or print images.
The suggested duplicate gives you the basics for how to read in a number of files at once, but there are a few potential gotchas, and it won't help you with displaying the images.
This first bit is purely to set up the example
library(jpeg)
library(grid)
# Create a new directory and move to it
tdir <- "jpgtest"
dir.create(tdir)
setwd(tdir)
# Copy the package:jpeg test image twice, once as .jpg and once as .jpeg
# to the present working directory
file.copy(system.file("img", "Rlogo.jpg", package="jpeg"),
to=c(file.path(getwd(), "test.jpg"), file.path(getwd(), "test.jpeg")))
Then we can list the files, either using a regex match, or choose them interactively, then read and store the images in a list.
# Matches any file ending in .jpg or .jpeg
(flist <- list.files(pattern="*\\.jp[e]?g$"))
# Interactive selection
flist <- file.choose()
jpglist <- lapply(flist, readJPEG)
To display the images I tend to use grid, but there are a number of alternatives.
grid.raster(jpglist[[1]], interpolate=FALSE)
Remove temporary directory
setwd("..")
unlink(tdir)
I've made different plots (more than a hundred) for a project and I haven't capture them on the way (yes it's bad , i know). Now, I need to save them all at once but without running again my script (which takes hours). Is there a way to do so within Rstudio ?
Edit: All the plot are already there and I don't want to run them again.
In RStudio, every session has a temporary directory that can be obtained using tempdir(). Inside that temporary directory, there is another directory that always starts with "rs-graphics" and contains all the plots saved as ".png" files. Therefore, to get the list of ".png" files you can do the following:
plots.dir.path <- list.files(tempdir(), pattern="rs-graphics", full.names = TRUE);
plots.png.paths <- list.files(plots.dir.path, pattern=".png", full.names = TRUE)
Now, you can copy these files to your desired directory, as follows:
file.copy(from=plots.png.paths, to="path_to_your_dir")
Additional feature:
As you will notice, the .png file names are automatically generated (e.g., 0078cb77-02f2-4a16-bf02-0c5c6d8cc8d8.png). So if you want to number the .png files according to their plotting order in RStudio, you may do so as follows:
plots.png.detials <- file.info(plots.png.paths)
plots.png.detials <- plots.png.detials[order(plots.png.detials$mtime),]
sorted.png.names <- gsub(plots.dir.path, "path_to_your_dir", row.names(plots.png.detials), fixed=TRUE)
numbered.png.names <- paste0("path_to_your_dir/", 1:length(sorted.png.names), ".png")
# Rename all the .png files as: 1.png, 2.png, 3.png, and so on.
file.rename(from=sorted.png.names, to=numbered.png.names)
Hope it helps.
Although this discussion has been inactive for a while, there are some persons, like myself, who still come across the same problem, and the other solutions don't really seem to even get what the actual question is.
So, hands on. Your plot history gets saved in a variable called .SavedPlots. You can either access it directly, assign it to another variable in code or do the latter from the plots window.
# ph for plot history
ph <- .SavedPlots
In R 3.4.2, I could index ph to reproduce the corresponding plot in a device. What follows is rather straightforward:
Open a new device (png, jpeg, pdf...).
Reproduce your plot ph[index_of_plot_in_history].
Close the device (or keep plotting if it is a pdf with multiple pages).
Example:
for(i in 1:lastplot) {
png('plotname.png')
print(ph[i])
dev.off()
}
Note: Sometimes this doesn't happen because of poor programming. For instance, I was using the MICE package to impute many datasets with a large number of variables, and plotting as shown in section 4.3 of this paper. Problem was, that only three variables per plot were displayed, and if I used a png device in my code, only the last plot of each dataset would be saved. However, if the plots were printed to a window, all the plots of each dataset would be recorded.
If your plots are 3d, you can take a snapshot of all your plots and save them as a .png file format.
snapshot3d(filename = '../Plots/SnapshotPlots.png', fmt = 'png')
Or else, the best way is to create a multi-paneled plotting window using the par(mfrow) function. Try the following
plotsPath = "../Plots/allPlots.pdf"
pdf(file=plotsPath)
for (x in seq(1,100))
{
par(mfrow = c(2,1))
p1=rnorm(x)
p2=rnorm(x)
plot(p1,p2)
}
dev.off()
You can also use png, bmp, tiff, and jpeg functions instead of pdf. You can read their advantages and disadvantages and choose the one you think is good for your needs.
I am not sure how Rstudio opens the device where the plot are drawn, but I guess it uses dev.new(). In that case one quick way to save all opened graphs is to loop through all the devices and write them using dev.print.
Something like :
lapply(dev.list(),function(d){dev.set(d);dev.print(pdf,file=file.path(folder,paste0("graph_",d,".pdf"))})
where folder is the path of the folder where you want to store your graph (could be for example folder="~" if you are in linux and want to store all your graph in your home folder).
If you enter the following function all that will follow will be save in a document:
pdf("nameofthedocument.pdf")
plot(x~y)
plot(...
dev.off()
You can also use tiff(), jpg()... see ?pdf
I am doing java and R integration using JRI.
Please find below script
String path = "C:\\Users\\hrpatel\\Desktop\\CSVs\\DataNVOCT.csv";
rengine.eval("library(tseries)");
rengine.eval(String.format("mydata <- read.csv('%s')",path.replace('\\', '/')));
String exportFilePath= "C:\\Users\\hrpatel\\Desktop\\CSVs\\arima3.jpg";
rengine.eval("Y <- NewVisits");
rengine.eval("t <- Day.Index");
rengine.eval("summary(Y)");
rengine.eval("adf.test(Y, alternative='stationary')");
rengine.eval("adf.test(Y, alternative='stationary', k=0)");
rengine.eval("acf(Y)");
rengine.eval("pacf(Y)");
rengine.eval("mydata.arima101 <- arima(Y,order=c(1,0,1))");
rengine.eval("mydata.pred1 <- predict(mydata.arima101, n.ahead=1000)");
rengine.eval(String.format("jpeg('%s')",exportFilePath.replace('\\', '/')));
rengine.eval("plot(t,Y)");
rengine.eval("lines(mydata.pred1$pred, col='blue',size=10)");
rengine.eval("lines(mydata.pred1$pred+1*mydata.pred1$se, col='red')");
rengine.eval("lines(mydata.pred1$pred-1*mydata.pred1$se, col='red')");
rengine.eval("dev.off()");
In above codebase when i tried plot(t,Y) or plot(Y). it export a blank image, while in case of plot(mydata) it is working file.
One more thing when i run above code in R it creates the image(using JRI it shows blank image).
I have spend 1 day to solve this but i dont found any solution.
Please suggest if you have any alternatives.
Your help is needed.
Thanks in Advance
if i understand correctly, you have a data set named mydata, that has two columns, NewVisits, and Day.Index, in that case you need to change:
rengine.eval("Y <- NewVisits");
to
rengine.eval("Y <- mydata$NewVisits");
and
rengine.eval("t <- Day.Index");
to
rengine.eval("t <- mydata$Day.Index");
This also explains why plot(mydata) works for you - because R recognizes it.
if this isn't the solution, then i cant see where you are reading NewVisits and Day.Index from
BTW i stongly recommend to plot using the ggplot package
I have the following problem, please.
I need to read recursively raster images, stack and store them in a file with different names (e.g. name1.tiff, name2.tiff, ...)
I tried the following:
for (i in 10) {
fn <- system.file ("external / test.grd", package = "raster")
fn <-stack (fn) # not sure if this idea can work.
fnSTACK[,, i] <-fn
}
here expect a result of the form:
dim (fnSTACK)
[1] 115 80 10
or something like that
but it didn't work.
Actually, I have around 300 images that I have to be store with different names.
The purpose is to extract time series information (if you know another method or suggestions I would appreciate it)
Any suggestions are welcomed. Thank you in advance for your time.
What I would first do is put all your *.tiff in a single folder. Then read all their names into a list. Stack them and then write a multi-layered raster. I'm assuming all the images have the same extent and projection.
### Load necessary packages
library(tiff)
library(raster)
library(sp)
library(rgdal) #I cant recall what packages you might need so this is probably
library(grid) # overkill
library(car)
############ function extracts the last n characters from a string
############ without counting the last m
subs <- function(x, n=1,m=0){
substr(x, nchar(x)-n-m+1, nchar(x)-m)
}
setwd("your working directory path") # you set your wd to were all your images are
filez <- list.files() # creates a list with all the files in the wd
no <- length(filez) # amount of files found
imagestack <- stack() # you initialize your raster stack
for (i in 1:no){
if (subs(filez[i],4)=="tiff"){
image <- raster(filez[i]) # fill up raster stack with only the tiffs
imagestack <- addLayer(imagestack,image)
}
}
writeRaster(imagestack,filename="output path",options="INTERLEAVE=BAND",overwrite=TRUE)
# write stack
I did not try this, but it should work.
Your question is rather vague and it would have helped if you had provided a full example script such that it could be more easily understood. You say you need to read several (probably not recursively?) raster images (files, presumably) and create a stack. Then you need to store them in files with different names. That sounds like copying the files to new files with a different names, and there are R functions for that, but that is probably not what you intended to ask.
if you have a bunch of files (with full path names or in the working directory), e.g. from list.files()
f <- system.file ("external/test.grd", package = "raster")
ff <- rep(f, 10)
you can do
library(raster)
s <- stack(ff)
I am assuming that you simply need this stack for operations in R (it is an object, but not a file). You can extract the values in many ways (see the help files and vignette of the raster package). If you want a three dimensional array, you can do
a <- as.array(s)
dim(a)
[1] 115 80 10
thanks "JEquihua" for your suggestion, just need to add the initial variable before addLayer ie:
for (i in 1:no){
if (subs(filez[i],4)=="tiff"){
image <- raster(filez[i]) # fill up raster stack with only the tiffs
imagestack <- addLayer(imagestack,image)
}
}
And sorry "RobertH", I'm newbie about R. I will be ask, more sure or exact by next time.
Also, any suggestions for extracting data from time series of MODIS images stacked. Or examples of libraries: "rts ()", "ndvits ()" or "bfast ()"
Greetings to the entire community.
Another method for stacking
library(raster)
list<-list.files("/PATH/of/DATA/",pattern="NDVI",
recursive=T,full.names=T)
data_stack<-stack(list)