Image Processing Course - EPFL BIOPbiop.epfl.ch/pdf/Courses/2015/JavaPlugins_2015.pdf · image, on...

Image Processing Course

Macros, Java & Plugins

Day 2 Overview

• Java– The Java Programming Language– Plugins vs. Macros– Eclipse IDE setup– Introduction to Java– The Plugin, PluginFilter and IJ Classes– Your first Plugin!

• Day 3: MathLab & CellProfiler

2

Fiji / ImageJ are Written in Java• ImageJ was written in Java because

of its platform independence and high-level programming capabilities. – People could contribute Plugins

(Small Java programs that can be read by ImageJ) with little effort.

• Fiji helped formalize the structure in the plugins and take it many steps further (Version Control, Maven Project Integration, ImgLib2, Wiki, etc…).

• We are not going to cover the perfect, programmer-indented way to create plugins, but the simpler “Classical” ImageJ approach.

3

ImageJ/Fiji Plugins and Java• Java: a computer programming language

that is concurrent, class-based, object-oriented and WORA (“write once, run anywhere”).

• To code in Java, 3 things are needed:– A Java Compiler.– A Java Virtual Machine (JVM).– A text editor, or better, an IDE

(Integrated development environment).

1. You edit your code in the IDE, which helps you navigate through your program structure.

2. You then compile it (.class file) and finally run it on the JVM.

4

Compiling• Compiling is the process through which human-

readable code is translated into machine-readable code.

5

What are JRE/JDK in Java?

• To run Fiji, you need to have Java installed– What people commonly call Java

is the JRE (Java Runtime Environment)

• To create Java code, you need the JDK (Java Development Kit)

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Compiling vs. Scripts or Macros• Scripting languages must interpret each

line as you run the command (Make a mini-compilation step and run it.). – This adds flexibility but at the cost of

speed.

• Java is a hybrid– It compiles a ‘universal’ Bytecode– The Bytecode is read by the Java Virtual

Machine– The JVM converts it to machine

language specific to your system (Mac, Win, Unix/Linux).

• It is almost as fast as compiled languages like C++

7

Same program, but compiled for different platforms

Platform independent

Vs.

Your First ImageJ Plugin

8


8

C:\Fiji\My_Plugin.java:12: cannot find symbol

symbol : variable imp

location: class My_Plugin

IJ.setAutoThreshold(imp, "Default");

^

C:\Fiji\My_Plugin.java:14: cannot find symbol

symbol : variable imp

location: class My_Plugin

IJ.run(imp, "Convert to Mask", "");

^

2 errors


• The Structure

9

Java Classes• The missing variable

imp is a Java variableof class ImagePlus. This is how Fiji stores the images.

• Similarily, the IJ classcontains a getImagefunction, and a setAutoThresholdfunction.

10

Java Classes• The missing variable

imp is a Java variableof class ImagePlus. This is how Fiji stores the images.

• Similarily, the IJ classcontains a getImagefunction, and a setAutoThresholdfunction.

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All are classes

Java Functions

• Java functions can have multiple inputs, and have only one output.

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public static void main(String[] args)

// Here is where you write // what the function does

}

public int count(String name) {// Return number of characters

return name.length()

}

public double multiply(double a, double b) {// Return multiplication

return a*b;

}

Java Variables• A variable contains something. It can be a number (int, double, float), text (String, char) or

a Class (ImageProcessor, ImagePlus) .• Java requires that each variable be given a type. This is called explicit typecasting.

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int a_number = 10; //Declaring an integerdouble another_number = 14.2; //Declaring a number with double precisionfloat and_another = (float) 35.2245; //Declaring a number with single precisionlong yet_another_number = (long) 2.3; //Declaring a number with twice the bytes as a double

String my_string = "A text string"; //Declare a string and initialize it.ImageProcessor ip = new FloatProcessor(100, 100); //Declare a new ImageProcessor

Java Variables• A variable contains something. It can be a number (int, double, float), text (String, char) or

a Class (ImageProcessor, ImagePlus) .• Java requires that each variable be given a type. This is called explicit typecasting.

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• In Java, exept for the base types, EVERYTHING is a class

int a_number = 10; //Declaring an integerdouble another_number = 14.2; //Declaring a number with double precisionfloat and_another = (float) 35.2245; //Declaring a number with single precisionlong yet_another_number = (long) 2.3; //Declaring a number with twice the bytes as a double

String my_string = "A text string"; //Declare a string and initialize it.ImageProcessor ip = new FloatProcessor(100, 100); //Declare a new ImageProcessor

Inheritance• Classes build on other classes. They inherit the functions of their

parent and can add functionality. Extends keyword.

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public class Shape {void draw() { //Draw the shape }void erase() {//Erase the shape }void move() { //move the shape the shape }int[] getColor() { //return color as int array }void setColor(int[] color) { //set the color }

}

public class Triangle extends Shape{void flipVertical() { //Flip shape}void flipHorizontal() {//Flip shape }

}

Triangle MyTriangle = new Triangle();Int[] color = myTriangle.getColor();myTriangle.setColor(new int[]{255,0,0});myTriangle.flipVertical();myTriangle.draw();

Inheritance, Interfaces• Interfaces are “empty” Java Classes that explicitly state what

functions you should write (implement, in Java slang).

• PlugIn and PlugInFilter are Interfaces

• That way ImageJ knows that whatever you write, it can use the run function to launch your plugin!

14

public class MyPlugIn implements PlugIn {…public class MyPlugIn implements PlugInFilter {…

Inheritance, Interfaces• Interfaces are “empty” Java Classes that explicitly state what

functions you should write (implement, in Java slang).

• PlugIn and PlugInFilter are Interfaces

• That way ImageJ knows that whatever you write, it can use the run function to launch your plugin!

14

PlugInFilter:void run(ImageProcessor ip)

Filters use this method to process the image.int setup(java.lang.String arg, ImagePlus imp)

This method is called once when the filter is loaded.

PlugIn:void run(java.lang.String arg)

This method is called when the plugin is loaded.

public class MyPlugIn implements PlugIn {…public class MyPlugIn implements PlugInFilter {…

27

Example PlugInFilter interface

setup () method is invoked first when plugin is executed.

run() method receives an object (ip) of type ImageProcessor.

Taken from:W. Burger, M.J. Burge Digital Image Processing, Springer Science 2008, p.33

Static variable of type integer (int)

28

Example PlugIn interface

Declaration of local variables(they can only be used inside this method).

Loop to calculate the values for the new image (iterate over all image coordinates).

Display Image (=ImagePlus)

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Usage of methods

Declaration of global variables(they can be used/modified inside the entire class).run() method calls (javaishfor executes or goto) two methods().

methods (): only executed when explicitly called.

Making Java Classes• Classes are containers• They can have methods

(functions), and fields (variables).• The fields are accessible by all

functions. They are global.• They can import other classes and

use them.• They can inherit other classes• You access what is inside a class

by using the “dot” (.) operator.• Private fields or methods are not

accessible except by the class itself.

• What does this class do?

15

public class MyNameClass {

// Class fields. These are accessible to all the functions inside the classprivate String number; //private means that other classes cannot access it.private String name;

// Constructorpublic MyNameClass(String name, String number) {

setNumber(number);setName(name);

}

// Public Methods

// Setterspublic void setNumber(String a_new_number) {

int length = a_new_number.length();if(length == 10) {

this.number = a_new_number;} else {

System.out.println("Could not set number '“+a_new_number+"'.\n is “+length+" characters. Expected 10");

}}

public void setName(String a_new_name) { this.name = a_new_name; }

// Getterspublic String getName() { return this.name; }

public String getNumber() {return this.number;}

private String prettyNumber() {String pretty_num = this.number.substring(0, 3)+"-“+this.number.substring(3, 6)+" "+this.number.substring(6, 10);

return pretty_num;}public void printData() {

System.out.println("Name: "+getName()+" \tnumber: "+prettyNumber());}

}

Making Java Classes: Getters and Setters• The best way to access

methods is through setters and getters.

• They start with the get or set words.

• This makes searching for functions easy. – For example. To set the title of an

image, on might search for a setTitlefunction

– If we are looking to get the name of the image, we should start by looking for a getTitle function.

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}

// Public Methods





}}







}

Making Java Classes: Getters and Setters

• The best way to access methods is through setters and getters.





16





}

// Public Methods





}}







}

ImagePlus Setters

Making Java Classes: Getters and Setters• The best way to access

methods is through setters and getters.





16





}

// Public Methods





}}







}

ImagePlus Setters ImagePlus Getters

36

An advanced example

Constructors; name must be identical to the class name

set() & get() methods

37

An advanced example

Can you find the differences?

public void iterate(int shift){for (int i=0;i<width;i++){

for (int j=0;j<height;j++){double dist=Math.sqrt(Math.pow(i+shift, 2)+Math.pow(j,2));int value=(int)(256*Math.sin(dist/frequ));ip.putPixel(i, j, value);

}}

}

Introducing The Eclipse IDE• IDEs Can:• Autocomplete• Detect syntax

errors• Suggest

corrections• Automate

integration (into FIJI) after compilation.

17

Installing Eclipse

• Get Java Development Kit athttp://tiny.cc/adip-java

• Download Eclipse at http://tiny.cc/adip-eclipse– Extract to Disk / Mount

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http://tiny.cc/adip-java

http://tiny.cc/adip-eclipse

Launching Eclipse

• Launch Eclipse

• Enter the folder where all your projects will be stored.

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Launching Eclipse

20

The Eclipse Layout

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The Eclipse Layout

21

All your plugins will appear here

The Eclipse Layout

21


Your code will appear here

The Eclipse Layout

21



The structure of your program will appear here

The Eclipse Layout

21



Errors and warnings will appear here.

The structure of your program will appear here

49

ImageJ-Eclipse ImageJ Wiki-The ImageJ Eclipse Howto

Author: Patrick Pirrottehttp://imagejdocu.tudor.lu/doku.php?id=howto:plugins:the_imagej_eclipse_howto

http://imagejdocu.tudor.lu/doku.php?id=howto:plugins:the_imagej_eclipse_howto

Import a Sample Java Application

• Go to tiny.cc/adip-java-sample, and unzip the file somewhere.

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Running A Java Application

• Open MyMainProgram.java• Run it

• Console output:

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public class MyMainProgram {

public static void main(String[] args) {MyNameClass MyData = new MyNameClass("Olivier Burri", "0216932629"); // Calling the constructor

System.out.println("My name is "+MyData.getName()+" and my number is: "+MyData.getNumber());

System.out.println("Changing my number to 021 369 88888");MyData.setNumber("021 369 88888");

// Prepare three copies of MyNameClass as an arrayMyNameClass[] PeopleData = new MyNameClass[3];

PeopleData[0] = new MyNameClass("Romain Guiet", "0216932629");PeopleData[1] = MyData;PeopleData[2] = new MyNameClass("Arne Seitz", "0216932632");

System.out.println("Printing contents of the PeopleData Array:");for(int i=0; i<3; i++) {

PeopleData[i].printData();

}

}

}

How Does It Run?• When a Class needs to be run, it contains the main

method.

• The JVM takes this as the starting point for the program.– It calls the main method with the arguments contained in

args.

• In ImageJ the Plugins Manager starts the Plugin by calling the run method (Or setup, then run, if it is a PlugInFilter)

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public static void main(String[] args) {

Plugins: A Minimalistic Plugin

• Go to tiny.cc/adip-first-plugin , and unzip the file somewhere.

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Minimalistic Plugin

26

Build Run

- Build creates the .jar file and copies it to the Fiji Folder.- Run launches ImageJ and runs your plugin

Configure Build and Run

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The Ant File: Building Made… “Simple”

• Open build.xml

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Where Fiji is located

The files your plugin needs in order to run.Must have same name

Why suffer?

• Get http://tiny.cc/adip-speedTest• And run the macro as well as the plugin.

29

http://tiny.cc/adip-speedTest

1 2 3

Import example plugins

30

4

Import example plugins

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Now Onwards to Java!

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32

Imports are packages that contain other java classes


32

Imports are packages that contain other java classesThis is your class. It is public and implements the PlugIn interface


32

Imports are packages that contain other java classesThis is your class. It is public and implements the PlugIn interface@ tags are annotations, a form of metadata


32

Imports are packages that contain other java classesThis is your class. It is public and implements the PlugIn interface@ tags are annotations, a form of metadatarun is a function inside the class My_First_PluginIt takes an argument called arg0 which is a String (another Class) It is a public function and has no return argument (void)


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showAbout is another function inside the class My_First_PluginIt takes no argument and is a private function.


32


showAbout is another function inside the class My_First_PluginIt takes no argument and is a private function.

In showAbout, we call the IJ class, which we imported from the ij package with importij.* and use the static function showMessage from that class to display a message.showMessage takes 2 arguments, both Strings.

How To Find Anything in Java? AutoComplete!• There are thousands of

classes, it’s impossible to remember everything.

• Eclipse can autocomplete things after you press the . operator.

33

You can get a lot of information this way. 1. A list of all methods and variables available in the class.2. It also displays whatever documentation was written by the programmer

The documentation is called JavaDoc

Getting the ImageJ Javadoc and making plugins!

• The most useful classes are – IJ (Accessing of most of ImageJ’s

menus)– GenericDialog

(Creating macro-recordable dialog boxes)

– ResultsTable(Display results after analyses)

– RoiManager(Get and manipulate ROIs)

– They are all inside the ij.jar file

– You can also navigate to • http://imagej.nih.gov/ij/developer/api/

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http://imagej.nih.gov/ij/developer/api/

Configuring the Javadoc for making plugins

http://imagej.nih.gov/ij/developer/api/

PlugIn Interface• The simplest plugin to use. May not even need an

image.

• Exercise: Get the name of the current image and display it in the log.

• Start from My_First_Plugin.java 35

public class PlugIn_Plugin implements PlugIn {

@Overridepublic void run(String arg0) {

//Your code here}

Simple Plugin

• Complete the function

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public class My_First_Plugin implements PlugIn {


// Get the current ImageImagePlus imp = IJ.getImage(); // Use IJ.getImage();

// Write this to the ImageJ logIJ.log("Image Name is: "+imp.getTitle() ); // Use IJ.log();

}}

Simple Plugin


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}}

Simple Plugin


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}}

Useful Class Functions

• IJ.run(options);

• IJ.getImage();

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Apply an ImageJ command or Plugin

• Use the recorder in Java mode• Apply a “Find Edges” Filter

to find the Java syntax.• Exercise: Get the image, duplicate it and find the

edges on the new image. Display the new image

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Apply a command or Plugin

• Correction

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ImagePlus edgeImp = imp.duplicate(); // Duplicate imageIJ.run(edgeImp, "Find Edges", ""); // Run Find Edges

edgeImp.setTitle(imp.getTitle()+" Edges"); // Rename the new imageedgeImp.show(); // Display it

The PluginFilter Interface

• Slightly more complex. Must operate on an image

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public class PlugInFilter_Plugin implements PlugInFilter {protected ImagePlus image;

@Overridepublic int setup(String arg, ImagePlus imp) {

// Is run when the plugin is launched// Your code here// You should look for or ask for parameters here.image = imp;

// Must return an int that says what the plugin can do.return DOES_8G | DOES_16 | DOES_32 | DOES_RGB | DOES_STACKS | CONVERT_TO_FLOAT;

}

@Overridepublic void run(ImageProcessor ip) {

// Your code here.

}

Add a Dialog

• When you need the user to provide data, there is the GenericDialog class.

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GenericDialog gd = new GenericDialog("pixels");

gd.addNumericField("value", 0.00, 2);

gd.showDialog();if (gd.wasCanceled())

return false;

value = gd.getNextNumber();

// Declare a new Dialog

// Add a number field

// Display the dialog// Check that the user clicked OK

// Get the number

Add a Dialog

• When you need the user to provide data, there is the GenericDialog class.

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GenericDialog gd = new GenericDialog("pixels");

gd.addNumericField("value", 0.00, 2);

gd.showDialog();if (gd.wasCanceled())

return false;

value = gd.getNextNumber();

// Declare a new Dialog

// Add a number field

// Display the dialog// Check that the user clicked OK

// Get the number

• Useful methods• addNumericField to get a number• addString to get a string• addChoice to get a dropdown menu• addCheckbox to get a checkbox

PluginFilter Dialog

• Exercise– Code a dialog box that asks the user for a value and

runs a median filter on the current image.– Use http://tiny.cc/adip-plugin-filter as a starting

point

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http://tiny.cc/adip-plugin-filter

PluginFilter Dialog

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@Overridepublic int setup(String arg, ImagePlus imp) {

this.imp = imp;GenericDialog gd = new GenericDialog("Median Filter");// Declare the dialog

gd.addNumericField("Median Filter Size", 2.0, 2); // Add the numeric field

gd.showDialog();// Display the dialog

// If the user did not click Cancel, continueif (!gd.wasCanceled()) {

medianValue = gd.getNextNumber(); // Recover the value the user entered}

// Explain the type of images that work with this pluginreturn DOES_8G | DOES_16 | DOES_32 | DOES_RGB;

}

PlugInFilter Dialog in a Macro

• What happens when we run the Macro Recorder on our plugin?

• GenericDialog creates everything for us!

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ResultsTable

• Exercise: Measure the mean intensity of the image and display it in a ResultsTable.

• Start from My_First_Plugin.java

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ResultsTable

• Solution tiny.cc/adip-measure-image

• Static variables belong to the Class and not the Instance…

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Flexibility

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Image Processing Course - EPFL BIOPbiop.epfl.ch/pdf/Courses/2015/JavaPlugins_2015.pdf · image, on...

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