Scripting toolbox

This page is meant to provide small code snippets as a starting point for writing scripts.

See also:

Scripting overview for a list of available scripting languages.
Scripting comparisons to compare and contrast the languages.
Broadly Applicable Routines, a curated collection of snippets.
Albert Cardona’s comprehensive Fiji Jython tutorial (please note that it is a better idea to contribute tutorials to the ImageJ Wiki directly).

💡

To copy the snippets, mouse over the code and click the Copy button that appears.

Opening an image using ImageJ

Macro

path = "/path/to/file";
open(path);

JavaScript

importClass(Packages.ij.IJ);

var path = "/path/to/file";
var imp = IJ.openImage(path);
imp.show();

Python

from ij import IJ

path = "/path/to/file"
imp = IJ.openImage(path)
imp.show()

Ruby

include_class 'ij.IJ'

path = "/path/to/file"
imp = ij.IJ.openImage(path)
imp.show

Clojure

(import 'ij.IJ)

(let [path "/path/to/file"
      imp (IJ/openImage path)]
  (.show imp))

BeanShell

import ij.IJ;

path = "/path/to/file";
imp = IJ.openImage(path);
imp.show();

Opening an image using Bio-Formats

Macro

path = "/path/to/file";
run("Bio-Formats Importer", "open=" + path + " autoscale color_mode=Default view=Hyperstack stack_order=XYCZT");

JavaScript

importClass(Packages.loci.plugins.BF);

var path = "/path/to/file";
var imps = BF.openImagePlus(path);

imps[0].show();

or, with more options:

importClass(Packages.loci.plugins.BF);
importClass(Packages['loci.plugins.in.ImporterOptions']); // 'in' is a reserved word, hence the different syntax
importClass(Packages.loci.common.Region);


var path = "/path/to/file";
var options = new ImporterOptions();
options.setId(path);
options.setAutoscale(true);
options.setCrop(true);
options.setCropRegion(0, new Region(x, y, w. h));
options.setColorMode(ImporterOptions.COLOR_MODE_COMPOSITE);
var imps = BF.openImagePlus(options);

imps[0].show();

Python

Opening, processing, and saving a sequence of files in a folder

Macro

input = getDirectory("Input directory");
output = getDirectory("Output directory");

Dialog.create("File type");
Dialog.addString("File suffix: ", ".tif", 5);
Dialog.show();
suffix = Dialog.getString();

processFolder(input);

function processFolder(input) {
	list = getFileList(input);
	for (i = 0; i < list.length; i++) {
		if(File.isDirectory(list[i]))
			processFolder("" + input + list[i]);
		if(endsWith(list[i], suffix))
			processFile(input, output, list[i]);
	}
}

function processFile(input, output, file) {
	// do the processing here by replacing
	// the following two lines by your own code
	print("Processing: " + input + file);
	open(input + file);
	print("Saving to: " + output);
	saveAs("/formats/tiff", output+file);
	close();
}

See also the tutorial How to apply a common operation to a complete directory.

Python

import os
from ij import IJ, ImagePlus
from ij.gui import GenericDialog
 
def run():
  srcDir = IJ.getDirectory("Input_directory")
  if not srcDir:
	return
  dstDir = IJ.getDirectory("Output_directory")
  if not dstDir:
	return
  gd = GenericDialog("Process Folder")
  gd.addStringField("File_extension", ".tif")
  gd.addStringField("File_name_contains", "")
  gd.addCheckbox("Keep directory structure when saving", True)
  gd.showDialog()
  if gd.wasCanceled():
	return
  ext = gd.getNextString()
  containString = gd.getNextString()
  keepDirectories = gd.getNextBoolean()
  for root, directories, filenames in os.walk(srcDir):
	for filename in filenames:
	  # Check for file extension
	  if not filename.endswith(ext):
		continue
	  # Check for file name pattern
	  if containString not in filename:
		continue
	  process(srcDir, dstDir, root, filename, keepDirectories)

def process(srcDir, dstDir, currentDir, fileName, keepDirectories):
  print "Processing:"
  
  # Opening the image
  print "Open image file", fileName
  imp = IJ.openImage(os.path.join(currentDir, fileName))
  
  # Put your processing commands here!
  
  # Saving the image
  saveDir = currentDir.replace(srcDir, dstDir) if keepDirectories else dstDir
  if not os.path.exists(saveDir):
	os.makedirs(saveDir)
  print "Saving to", saveDir
  IJ.saveAs(imp, "Tiff", os.path.join(saveDir, fileName));
  imp.close()

run()

JavaScript
Ruby
Clojure
BeanShell

Wait a given amount of time, or until user presses OK

Macro

wait(100);

waitForUser();

JavaScript

Thread.sleep(100);

new WaitForUserDialog("Action required", "Please press OK when done.").show();

Python
Ruby
Clojure
BeanShell

Select multiple ROIs from ROI manager and combine them

Macro

roiManager("select", newArray(0,2,4));
roiManager("AND");

JavaScript

importClass(Packages.ij.plugin.frame.RoiManager);

rm = RoiManager.getInstance();
rm.setSelectedIndexes([0,2,4]);
rm.runCommand("AND");

Python

from ij.plugin.frame import RoiManager

rm = RoiManager.getInstance()
rm.setSelectedIndexes([0, 2, 4])
rm.runCommand("AND")

BeanShell

import ij.plugin.frame.RoiManager;

rm = RoiManager.getInstance();
rm.setSelectedIndexes(new int[] { 0, 2, 4});
rm.runCommand("AND");

Ruby
Clojure

Unlocking an image

Sometimes things go wrong and all you see is “blabla.jpg is locked” when you try to process the image in some way. Then all you can do is to force-unlock the image, like so:

BeanShell

IJ.getImage().unlock();

Scripting SIFT

The Scale-Invariant Feature Transform poses a relatively powerful way to reduce the complexity when trying to find matching parts of large images. Fiji has an implementation of this algorithm which you can use like so:

BeanShell

import java.util.ArrayList;

import mpicbg.ij.SIFT;
import mpicbg.imagefeatures.Feature;
import mpicbg.imagefeatures.FloatArray2DSIFT;

param = new FloatArray2DSIFT.Param();
sift = new SIFT(new FloatArray2DSIFT(param));
features = new ArrayList();
// ''ip'' refers to an ImageProcessor
sift.extractFeatures(ip, features);

// print coordinates
for (Feature feature : features)
	print("x: " + feature.location[0] + ", y: " + feature.location[1]);

For more information, please browse the Javadoc of the Feature class.

Plotting charts with JFreeChart

JFreeChart is a Java library for creating various charts. You can create charts as interactive JFrames, display them as an ImagePlus, or write them to SVG format.

JavaScript

/* JavaScript to test JFreeChart functionality */

importPackage(Packages.org.jfree.chart);
importPackage(Packages.org.jfree.chart.plot);
importPackage(Packages.org.jfree.chart.axis);
importPackage(Packages.org.jfree.chart.encoders);
importPackage(Packages.org.jfree.chart.renderer.category);

importPackage(Packages.java.awt);
importPackage(Packages.java.awt.geom);
importPackage(Packages.java.io);

importPackage(Packages.org.jfree.ui);
importPackage(Packages.org.jfree.data.category);
importPackage(Packages.org.jfree.data.statistics);

importPackage(Packages.org.apache.batik.dom);
importPackage(Packages.org.apache.batik.svggen);

var dataset = new DefaultStatisticalCategoryDataset();

// dataset.add(Mean, StdDev, "Series", "Condition")
dataset.add(15.0, 2.4, "Row 1", "Column 1");
dataset.add(15.0, 4.4, "Row 1", "Column 2");
dataset.add(13.0, 2.1, "Row 1", "Column 3");
dataset.add(7.0, 1.3, "Row 1", "Column 4");
dataset.add(2.0, 2.4, "Row 2", "Column 1");
dataset.add(18.0, 4.4, "Row 2", "Column 2");
dataset.add(28.0, 2.1, "Row 2", "Column 3");
dataset.add(17.0, 1.3, "Row 2", "Column 4");

var chart = ChartFactory.createLineChart(
	null,                   // chart title
	"Treatment",                // domain axis label
	"Measurement",              // range axis label
	dataset,                // data
	PlotOrientation.VERTICAL,       // orientation
	false,                  // include legend
	true,                   // tooltips
	false                   // urls
);

// set the background color for the chart...
chart.setBackgroundPaint(Color.white);

var plot = chart.getPlot();
plot.setBackgroundPaint(Color.white);
plot.setRangeGridlinesVisible(false);
plot.setAxisOffset(RectangleInsets.ZERO_INSETS);

// customise the range axis...
var rangeAxis = plot.getRangeAxis();
rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits());
rangeAxis.setAutoRangeIncludesZero(true);
rangeAxis.setRange(0, 40);

// customise the renderer...
var renderer = new StatisticalBarRenderer();
renderer.setErrorIndicatorPaint(Color.black);
renderer.setSeriesOutlinePaint(0,Color.black);
renderer.setSeriesOutlinePaint(1,Color.black);
renderer.setSeriesPaint(0,Color.black);
renderer.setSeriesPaint(1,Color.white);
renderer.setItemMargin(0.0);
plot.setRenderer(0,renderer);

renderer.setDrawBarOutline(true);

bi = chart.createBufferedImage(600, 400);

imp = new ImagePlus("Chart Test", bi);
imp.show();

// Create SVG image
// Get a DOMImplementation and create an XML document
var domImpl = GenericDOMImplementation.getDOMImplementation();
var document = domImpl.createDocument(null, "svg", null);

// Create an instance of the SVG Generator
var svgGenerator = new SVGGraphics2D(document);

// draw the chart in the SVG generator
var bounds = new Rectangle(600, 400);
chart.draw(svgGenerator, bounds);

var dir = IJ.getDirectory("Where should the svg file be saved?");
// Write svg file
var svgFile = new File(dir + "test.svg");
var outputStream = new FileOutputStream(svgFile);
var out = new OutputStreamWriter(outputStream, "UTF-8");
svgGenerator.stream(out, true /* use css */);
outputStream.flush();
outputStream.close();

Writing out movie files with JavaCV

JavaCV is a Java wrapper around OpenCV and FFMPEG. You will have to unpack the libraries into the lib/<platform>/ folder of your Fiji installation (e.g. Fiji.app/lib/linux64/) to let JavaCV find the native libraries (e.g. unpack ffmpeg-macosx-x86_64.jar’s .dylib files directly into Fiji.app/lib/macosx/) before starting Fiji.

BeanShell

/*
 * A simple example how to write out a movie from a possibly virtual
 * image stack using JavaCV.
 * 
 * Licensed under CC-BY-SA 4.0 
 * by Johannes Schindelin on September 16th, 2014
 */

path = "/tmp/change-this-name.flv";
frameRate = 25.0;
videoBitrate = 400 * 1000;

// if you have not installed JavaCV into your jars/ directory:
import java.io.File;
binDir = new File(System.getProperty("user.home")
	+ "/downloads/javacv-bin/");
if (binDir.isDirectory()) {
	jars = binDir.list();
	for (String jar : jars) {
		if (jar.endsWith(".jar")) {
			addClassPath(new File(binDir, jar).getPath());
		}
	}
}

// use JavaCV to write out the currently active 3D image
import ij.IJ;
import org.bytedeco.javacv.FFmpegFrameRecorder;
import org.bytedeco.javacpp.opencv_core.IplImage;

void saveImageAsMovie(image, path, frameRate, videoBitrate) {
	if (image == null) {
		IJ.error("No active image!");
		return;
	}

	width = image.getWidth();
	height = image.getHeight();
	stack = image.getStack();

	recorder = FFmpegFrameRecorder.createDefault(path,
		(int) width, (int) height);
	recorder.setFormat("flv");
	recorder.setFrameRate(frameRate);
	recorder.setVideoBitrate(videoBitrate);
	recorder.start();

	for (slice = 1; slice <= stack.getSize(); slice++) {
		ip = stack.getProcessor(slice);
		recorder.record(IplImage.createFrom(ip.getBufferedImage()));
	}

	recorder.stop();
	recorder.release();
}

try {
	saveImageAsMovie(IJ.getImage(), path, frameRate, videoBitrate);
} catch (Throwable t) {
	IJ.handleException(t);
}

ImageJ Docs

Page contents

Scripting toolbox

Opening an image using ImageJ

Macro

JavaScript

Python

Ruby

Clojure

BeanShell

Opening an image using Bio-Formats

Macro

JavaScript

Python

Opening, processing, and saving a sequence of files in a folder

Macro

Python

Wait a given amount of time, or until user presses OK

Macro

JavaScript

Select multiple ROIs from ROI manager and combine them

Macro

JavaScript

Python

BeanShell

Unlocking an image

BeanShell

Scripting SIFT

BeanShell

Plotting charts with JFreeChart

JavaScript

Writing out movie files with JavaCV

BeanShell