Combine_Amira_Tifs.bsh

import fiji.util.gui.GenericDialogPlus;
import ij.IJ;
import ij.ImagePlus;
import ij.Prefs;
import ij.io.FileSaver;
import ij.plugin.ImageCalculator;
import ij.process.ImageProcessor;
import java.io.File;
import java.util.regex.Pattern;
import ij.process.StackStatistics;

// Retrieve previous input and output directories from preferences
String prevInputDirectory = Prefs.get("Combine_Amira_Tifs.inputDirectory", IJ.getDirectory("current"));
String prevOutputDirectory = Prefs.get("Combine_Amira_Tifs.outputDirectory", IJ.getDirectory("current"));
String prevFilePattern = Prefs.get("Combine_Amira_Tifs.filePattern", "crop\\d+_labels_\\d+\\_.*\\.tif");

// Create a GenericDialogPlus for user input
GenericDialogPlus gd = new GenericDialogPlus("Input and Output Directories");
gd.addDirectoryField("Input Directory: ", prevInputDirectory, 70);
gd.addDirectoryField("Output Directory: ", prevOutputDirectory, 70);
gd.addStringField("File Pattern: ", prevFilePattern, 35);
gd.showDialog();

if (gd.wasCanceled()) {
    IJ.log("User canceled the operation");
} else {
    // Get user input for input and output directories
    String inputDirectory = gd.getNextString();
    String outputDirectory = gd.getNextString();
    String filePattern = gd.getNextString();

    // Use File.openDialog to allow users to select directories if needed
    if (inputDirectory.equals("")) {
        inputDirectory = IJ.getDirectory("Select Input Directory: ");
    }

    if (outputDirectory.equals("")) {
        outputDirectory = IJ.getDirectory("Select Output Directory: ");
    }

    // Save the current input and output directories to preferences
    Prefs.set("Combine_Amira_Tifs.inputDirectory", inputDirectory);
    Prefs.set("Combine_Amira_Tifs.outputDirectory", outputDirectory);
    Prefs.set("Combine_Amira_Tifs.filePattern", filePattern);

    // Append a trailing slash if necessary and ensure compatibility with different operating systems
    inputDirectory = inputDirectory.endsWith(File.separator) ? inputDirectory : inputDirectory + File.separator;
    outputDirectory = outputDirectory.endsWith(File.separator) ? outputDirectory : outputDirectory + File.separator;

    // Define the output image
    ImagePlus output = null;

    // Get the list of files in the input directory
    File[] files = new File(inputDirectory).listFiles();
    Arrays.sort(files);
    if (files != null && files.length > 0) {
        // Compile the regex pattern
        Pattern pattern = Pattern.compile(filePattern);

        // Calculate the total number of valid files
        int totalValidFiles = 0;
        for (File file : files) {
            if (pattern.matcher(file.getName()).matches()) {
                totalValidFiles++;
            }
        }
        int processedFiles = 0;

        for (File file : files) {
            // Check if the file name matches the regex pattern
            if (pattern.matcher(file.getName()).matches()) {
            	// Log the progress
                IJ.log("Processing file " + processedFiles + " of " + totalValidFiles + ": " + file.getName());
                
                // Load image        
                ImagePlus currentImage = IJ.openImage(file.getAbsolutePath());
				IJ.run(currentImage, "16-bit", "");
                
                if (output == null) {
                    // Initialize output with the first image
                    output = currentImage.duplicate();	
                } else {
                    // Duplicate the current image
                    ImagePlus binarizedImage = currentImage.duplicate();
                    IJ.setRawThreshold(binarizedImage, 0, 0); //sets background 0, foreground 255
                  	IJ.run(binarizedImage, "Convert to Mask", "background=Light black");
                    IJ.run(binarizedImage, "Invert", "stack"); //now 255 are labeled regions
                    IJ.run(binarizedImage, "Divide...", "value=" + 255 + " stack");
                    IJ.run(binarizedImage, "16-bit", "");
                    
                    statistics = new ij.process.StackStatistics(output);    
                    IJ.run(currentImage, "Add...", "value=" + statistics.max + " stack");
                    
                    // Multiply the currentImage by the binarizedImage
                    ImagePlus multipliedImage = ImageCalculator.run(binarizedImage, currentImage, "Multiply create stack");
                    
                    // Add the multiplied image to the output
                    output = ImageCalculator.run(output, multipliedImage, "Add create stack");
                }

                processedFiles++;
            }
        }

        if (output != null) {
            // Write the output image
            String outputFile = outputDirectory + "combined_labels.tif";
            new FileSaver(output).saveAsTiff(outputFile);
            IJ.log("Operation completed. Output saved to: " + outputFile);
        } else {
            IJ.log("No files matching the pattern found in the input directory.");
        }
    } else {
        IJ.log("No files found in the input directory.");
    }
}