Scripting toolbox

From Fiji

This page is meant to provide small code snippets as a starting point for writing scripts. See also the Scripting comparisons and the dedicated pages for the ImageJ Macro language, Javascript, Jython, JRuby, Clojure, and Beanshell.

For scripting python/jython, see also Albert Cardona's comprehensive Fiji tutorial.

Note: To copy the snippets, just double-click somewhere into the code. If Javascript is enabled, this will automatically select the complete snippet.

Contents 1 Opening an image using ImageJ 1.1 Macro 1.2 Javascript 1.3 Python 1.4 Ruby 1.5 Clojure 1.6 Beanshell 2 Opening an image using Bio-Formats 2.1 Macro 2.2 Javascript 3 Opening, processing, and saving a sequence of files in a folder 3.1 Macro 4 Wait a given amount of time, or until user presses OK 4.1 Macro 4.2 Javascript 5 Select multiple ROIs from ROI manager and combine them 5.1 Macro 5.2 Javascript 5.3 Python 5.4 Beanshell 6 Unlocking an image 6.1 Beanshell

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

• Ruby

• Clojure

• Beanshell

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

Macro

dir1 = getDirectory("Choose Source Directory ");
dir2 = getDirectory("Choose Destination Directory ");
list = getFileList(dir1);

for (i=0; i<list.length; i++) {
  if (endsWith(list[i], ".tif")) {
    open(dir1 + list[i]);
    // process the image
    saveAs("TIFF", dir2+list[i]);
    close();
  }
}

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

• Javascript

• Python

• Ruby

• Clojure

• Beanshell

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

Macro

wait(100);

or

waitForUser();

Javascript

Thread.sleep(100);

or

• 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();