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So I have a folder with some n images which I want to open and save with the readImage function. Right now a colleague had written something similar for opening and storing the name only of the images. I'd like to do the following:

setwd("~/ABC/One_Folder_Up")

img_src <- "FolderOfInterest"

image_list <- list.files(path=img_src, pattern = "^closed")

But with the actual .tif images named for example: closed100, closed101,....closed201

The above code works great for getting the names. But how can I get this type of pattern but instead open and save images? The output is a large matrix for each image.

So for n = 1 to n, I want to perform the following:

closed175 <- readImage("closed175.tif")

ave175 <- mean(closed175)

SD175 <- SD(closed175)

I'm assuming the image list shown in the first part could be used in the desired loop?

Then, after the images are saved as their own matricies, and all averages and SDs are calculated, I want to put the averages and SDs in a matrix like this:

imavelist <- c(ave175, ave176,......ave200)

Sorry, not an expert coder. Thank you!

edit: maybe lapply?

edit2: if I use this suggestion,

require(imager)

closed_images <- lapply(closed_im_list, readImage)

closed_im_matrix = do.call('cbind', lapply(closed_images, as.numeric))

Then I need a loop to save each element of the image stack matrix as its own individual image.

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SqueakyBeak
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1 Answers1

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setwd("~/ABC/One_Folder_Up/FolderOfInterest/")
#for .tif format
image_list=list.files(path=getwd(), pattern = "*.tif")
# for other formats replace tif with appropriate format. 
f=function(x){
y=readImage(x)
mve=mean(y)
sd=sd(y)
c(mve,sd)
}

results=data.frame(t(sapply(image_list,f)))
colnames(results)=c("average","sd")

the resul for 3 images:

> results
                average        sd
Untitled.tif  0.9761128 0.1451167
Untitled2.tif 0.9604224 0.1861798
Untitled3.tif 0.9782997 0.1457034
>
ahmad
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  • Thank you! Is there a way to name each element as like 'ave100' for the 100th image etc? – SqueakyBeak Jun 17 '19 at 16:54
  • if you have 3 images: `rownames(results)=paste("ave",1:3,sep="")` and for 100 images: `rownames(results)=paste("ave",1:100,sep="")` – ahmad Jun 17 '19 at 16:58
  • Ok so the list.files didn't work but my colleague's did so I used that. And I didn't need the last rownames(results)=paste("ave",1:100,sep="") part because the image name is showing up automatically at the left. Thanks!! – SqueakyBeak Jun 17 '19 at 17:20