// 1. Ask the user for the input folder
inputDir = getDirectory("Choose Input Directory");

// 2. Create the output folder automatically inside the input folder
outputDir = inputDir + "particle_analyze" + File.separator;
if (!File.exists(outputDir)) {
    File.makeDirectory(outputDir);
}

// 3. Prepare the environment (Clear old results/summaries)
run("Clear Results");
if (isOpen("Summary")) {
    selectWindow("Summary");
    run("Close");
}

list = getFileList(inputDir);
setBatchMode(true); // Run in the background (much faster)

for (i = 0; i < list.length; i++) {
    // Process only PNG files
    if (endsWith(toLowerCase(list[i]), ".png")) {
        processFile(inputDir, outputDir, list[i]);
    }
}

setBatchMode(false);

if (isOpen("Summary")) {
    selectWindow("Summary");
    saveAs("Results", outputDir + "Summary_Report.csv");
}


if (isOpen("Results")) {
    selectWindow("Results");
    run("Close");
}
print("Done! Files and summary saved to: " + outputDir);

function processFile(input, output, filename) {
    
    // Clear ROI Manager for each new image
    if (roiManager("count") > 0) {
        roiManager("deselect");
        roiManager("delete");
    }

    // Open the PNG
    open(input + filename);
    
    // Create a TIFF filename for the output
    basename = File.nameWithoutExtension;
    newName = basename + ".tif";

    // --- Your recorded steps ---
    run("Set Scale...", "distance=2691 known=1000 unit=micron global");
    run("Specify...", "width=2691 height=2691 x=476 y=476 constrain");
    run("Crop");
    
    // Save the cropped version as TIFF in the particle_analyze folder
    saveAs("Tiff", output + newName);
    currentImage = getTitle();

    // Image Processing for Masking
    run("Duplicate...", " ");
    setThreshold(0, 85, "raw");
    setOption("BlackBackground", true);
    run("Convert to Mask");
    run("Fill Holes");
    run("Watershed");
    
    // Analyze Particles (the 'summarize' flag builds the report window)
    run("Analyze Particles...", "size=78.5-120 circularity=0.75-1.00 display exclude clear summarize add");
    
    // Close the mask (duplicate)
    close(); 
    
    // Select the cropped TIFF and save it with the ROIs
    selectImage(currentImage); 
    if (roiManager("count") > 0) {
        roiManager("Show All without labels");
        run("Save"); 
    }
    
    // Close everything to free memory
    run("Close All");
}