Scripting toolbox
This page is meant to provide small code snippets as a starting point for writing scripts.
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
- 2 Opening an image using Bio-Formats
- 3 Opening, processing, and saving a sequence of files in a folder
- 4 Wait a given amount of time, or until user presses OK
- 5 Select multiple ROIs from ROI manager and combine them
- 6 Unlocking an image
- 7 Scripting SIFT
- 8 Plotting charts with JFreeChart
- 9 Writing out movie files with JavaCV
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
See also this python example script
- Ruby
- Clojure
- Beanshell
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("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);
or
waitForUser();
Javascript
Thread.sleep(100);
or
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 ImageJ.app/lib/<platform>/ (or Fiji.app/lib/<platform>/) to let JavaCV find the native libraries (e.g. unpack ffmpeg-macosx-x86_64.jar's .dylib files directly into ImageJ.app/lib/macosx/) before starting ImageJ/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); }