Bonus section: Adding a simple Graphical User Interface!#

The script we made in the previous section will apply to an entire folder of images. However, when we want to process a different folder, we would have to manually edit the code.

Which line(s) of code do would need to change to process a different folder?

folder = "path/to/file";  // (1)!
file_list = getFileList(folder);
number_of_files = file_list.length;

for (i=0; i<number_of_files; i++) {
    file_path = folder + File.separator + file_list[i];
    open(file_path);
    run("Gaussian Blur...", "sigma=2");
    save_path = folder + File.separator + "processed_" + file_list[i];
    saveAs("Tiff", save_path);
    run("Close");
}

This one.

What if we wanted to change the output folder? The same concern arises.

Instead, we can use a simple GUI to allow the user to select the folder to process. Fiji provides some handy helpers for this, called parameters. In this case, we can put at the top of our macro the following line:

#@ File (label = "Input directory", style = "directory") folder

What this will do is open a file dialog, which will allow the user to select a folder to process. The selected folder will be stored in the folder variable. Note that we could have called this whatever we want, but since we used the variable name folder already in our script, it makes sense to keep it the same.

What would happen if we changed style = "directory" to style = "file"?

The user would be prompted to select a single file, rather than a folder. This can also be useful, but is not what we want for this script.

Modify your script to add parameters for the input and output folders.

#@ File (label = "Input directory", style = "directory") input_folder
#@ File (label = "Output directory", style = "directory") output_folder

file_list = getFileList(input_folder);
number_of_files = file_list.length;

for (i=0; i<number_of_files; i++) {
    file_path = folder + File.separator + file_list[i];
    open(file_path);
    run("Gaussian Blur...", "sigma=2");
    save_path = output_folder + File.separator + "processed_" + file_list[i];
    saveAs("Tiff", save_path);
    run("Close");
}