Macro open each sub-folders as a stack

Posted by duerna on
URL: http://imagej.273.s1.nabble.com/Macro-open-each-sub-folders-as-a-stack-tp5019681.html

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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