ij-Scala Examples

Batch Processing

This script batch processes all images with extension ".png" in the input directory. Applies a median filter to each, and saves them in the output directory. 
import ij.IJ
import ij.ImagePlus
import java.io.File

//
// Process files from input directory that match an extension.
//

batchProcessing(
    inputDir = new File("my_input_dir"),
    inputExtension = ".png",
    outputDir = new File("my_output_dir"))

//-------------------------------------------------------------------------------------------------

/**
 * Prepare output directory and process all images in the input directory matching extension
 */
def batchProcessing(inputDir: File,
                    inputExtension: String,
                    outputDir: File) {
    val title = "Batch Process"

    // Input directory
    val inputDir = new File("my_input_dir")
    if (!inputDir.exists) {
        IJ.error(title, "Input directory does not exist: " + inputDir.getAbsolutePath)
        return
    }

    // Output directory
    val outputDir = new File("my_output_dir")
    if (!outputDir.mkdirs()) {
        IJ.error(title, "Failed to create output directory: " + outputDir.getAbsolutePath)
        return
    }

    // List all files with extension ".png"
    val inputFiles = inputDir.listFiles.filter(f => f.getName.endsWith(inputExtension))

    // batch process iterating through all input files
    inputFiles.foreach {
        inputFile =>
            println("Processing: " + inputFile.getAbsolutePath)
            val src = IJ.openImage(inputFile.getPath)
            val dest = process(src)
            val outputFile = new File(outputDir, inputFile.getName)
            IJ.saveAs(dest, "tif", outputFile.getAbsolutePath)
    }
}

/**
 * Custom image processing method
 * @param src input image
 * @return processed image
 */
def process(src: ImagePlus): ImagePlus = {
    // Do some processing
    IJ.run(src, "Median...", "radius=4")
    // Return modified input
    src
}

Process Current ImageJ Image

This scripts gets a reference to currently selected image in ImageJ then applies median filter to it. If no image is opened shows "No image" error message. 
import ij.IJ

process()

def process() {
    // Get currently selected image
    val imp = IJ.getImage
    if (imp == null) {
        // Show error message
        IJ.noImage()
        return
    }

    // Do some processing
    IJ.run(imp, "Median...", "radius=4")
    // ...
}