Macro open each sub-folders as a stack

[duerna]

Hi, everyone,

I have a folder with multiple sub-folders, and each of which contains 18
number of tif(.tif) files.
I'd like to open every sub-folders files as a stack in imageJ.


With some online macro documentation,
I can open files in each sub-folders, and do somethings like change 16-bit
files into 8-bit files.

But I need open each sub-floder as a stacks,
I have some problem to get stack with macro,
 
Here is the code that I have currently,

inputDir = getDirectory("choose the input directory");
outputDir = getDirectory("choose the output directory");

processDir(inputDir, outputDir);

function processDir(inputDir, outputDir) {
listdir = getFileList(inputDir);
for (j = 0; j < listdir.length; j++) {
print("Processing: " + listdir[j]);
File.makeDirectory(outputDir + listdir[j]);
outputFolder = outputDir + listdir[j];
inputFolder = inputDir + listdir[j];
setBatchMode(true);
processFolder(inputFolder);
setBatchMode(false);
}
}

function processFolder(inputFolder) {
list = getFileList(inputFolder);
for (i = 0; i < list.length; i++) {
processFile(inputFolder, outputFolder, list[i]);
}
}

function processFile(inputFolder, outputFolder, file) {
print("Processing: " + inputFolder + file);
open(inputFolder + file);
*run("Image Sequence...", "open=[inputFolder + file] number=18 starting=1
increment=1 scale=100 file=[] or=[] sort");*
run("Enhance Contrast", "saturated=0.35");
run("Apply LUT", "stack");
setAutoThreshold("Otsu dark");
setThreshold(60, 255);
run("Convert to Mask", " ");

print("Saving to: " + outputFolder);
saveAs("tiff", outputFolder+file);
close();
}



If you could tell me how to open sub-folder as a stack.

Thank you in advance.



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[Herbie]

Good day!

Maybe the following macro code does what you are after:

////////
inputDir = getDirectory("choose the input directory");
listdir = getFileList( inputDir );
for (i = 0; i < listdir.length; i++) {
        path = inputDir + listdir[i];
        if ( File.isDirectory(  path  )  ) {
                run("Image Sequence...", "open=" + path + " sort");
        }
}
////////

Regards

Herbie

::::::::::::::::::::::::::::::::::::
Am 11.11.17 um 11:47 schrieb duerna:

> Hi, everyone,
>
> I have a folder with multiple sub-folders, and each of which contains 18
> number of tif(.tif) files.
> I'd like to open every sub-folders files as a stack in imageJ.
>
>
> With some online macro documentation,
> I can open files in each sub-folders, and do somethings like change 16-bit
> files into 8-bit files.
>
> But I need open each sub-floder as a stacks,
> I have some problem to get stack with macro,
>  
> Here is the code that I have currently,
>
> inputDir = getDirectory("choose the input directory");
> outputDir = getDirectory("choose the output directory");
>
> processDir(inputDir, outputDir);
>
> function processDir(inputDir, outputDir) {
> listdir = getFileList(inputDir);
> for (j = 0; j < listdir.length; j++) {
> print("Processing: " + listdir[j]);
> File.makeDirectory(outputDir + listdir[j]);
> outputFolder = outputDir + listdir[j];
> inputFolder = inputDir + listdir[j];
> setBatchMode(true);
> processFolder(inputFolder);
> setBatchMode(false);
> }
> }
>
> function processFolder(inputFolder) {
> list = getFileList(inputFolder);
> for (i = 0; i < list.length; i++) {
> processFile(inputFolder, outputFolder, list[i]);
> }
> }
>
> function processFile(inputFolder, outputFolder, file) {
> print("Processing: " + inputFolder + file);
> open(inputFolder + file);
> *run("Image Sequence...", "open=[inputFolder + file] number=18 starting=1
> increment=1 scale=100 file=[] or=[] sort");*
> run("Enhance Contrast", "saturated=0.35");
> run("Apply LUT", "stack");
> setAutoThreshold("Otsu dark");
> setThreshold(60, 255);
> run("Convert to Mask", " ");
>
> print("Saving to: " + outputFolder);
> saveAs("tiff", outputFolder+file);
> close();
> }
>
>
>
> If you could tell me how to open sub-folder as a stack.
>
> Thank you in advance.
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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[duerna]

Hi, Herbie

Thank you very much.
It's works.

Now I could open each sub-folder as a stack,

and I add my code, but it only analysis the last stack, and did not give me a .avi saving.

here is my code:

////////
inputDir = getDirectory("choose the input directory");
outputDir = getDirectory("choose the output directory");

listdir = getFileList( inputDir );
for (i = 0; i < listdir.length; i++) {
        path = inputDir + listdir[i];
        if ( File.isDirectory(  path  )  ) {
                run("Image Sequence...", "open=" + path + " sort");
        }
}

run("Enhance Contrast", "saturated=0.35");
run("Apply LUT", "stack");
setAutoThreshold("Otsu dark");
setThreshold(60, 255);
run("Convert to Mask", " ");
print("Saving to: " + outputFolder);
saveAs("AVI", outputFolder+file);
close();
}

////////

I want set contrast and threshold of all stacks,
and save each stacks as .avi into a folder.

Would you please give me some suggestion?


Best Regards.
Duerna


 



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