1. No category

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, objectoriented 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.
2.
You edit your code in the IDE, which
helps you navigate through your
program structure.
You then compile it (.class file) and
finally run it on the JVM.
4
Compiling
• Compiling is the process through which humanreadable 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)
6
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.
Vs.
• 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++
Platform
independent
Same
program,
but
compiled
for different
platforms
7
Your First ImageJ Plugin
8
Your First ImageJ Plugin
8
Your First ImageJ Plugin
8
Your First ImageJ Plugin
8
Your First ImageJ Plugin
8
Your First ImageJ Plugin
8
Your First ImageJ Plugin
8
Your First ImageJ Plugin
8
Your First ImageJ Plugin
8
Your First ImageJ Plugin
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
8
Your First ImageJ Plugin
• The Structure
9
Java Classes
• The missing variable
imp is a Java variable
of class ImagePlus.
This is how Fiji stores
the images.
• Similarily, the IJ class
contains a getImage
function, and a
setAutoThreshold
function.
10
Java Classes
• The missing variable
imp is a Java variable
of class ImagePlus.
This is how Fiji stores
the images.
• Similarily, the IJ class
contains a getImage
function, and a
setAutoThreshold
function.
All are classes
10
Java Functions
• Java functions can have multiple inputs, and have
only one output.
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;
}
11
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.
int a_number = 10;
//Declaring an integer
double another_number = 14.2;
//Declaring a number with double precision
float and_another = (float) 35.2245;
//Declaring a number with single precision
long 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
12
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.
int a_number = 10;
//Declaring an integer
double another_number = 14.2;
//Declaring a number with double precision
float and_another = (float) 35.2245;
//Declaring a number with single precision
long 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
• In Java, exept for the base types, EVERYTHING is
a class
12
Inheritance
• Classes build on other classes. They inherit the functions of their
parent and can add functionality. Extends keyword.
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();
13
Inheritance, Interfaces
• Interfaces are “empty” Java Classes that explicitly state what
functions you should write (implement, in Java slang).
• PlugIn and PlugInFilter are Interfaces
public class MyPlugIn implements PlugInFilter {…
public class MyPlugIn implements PlugIn {…
• That way ImageJ knows that whatever you write, it can use the
run function to launch your plugin!
14
Inheritance, Interfaces
• Interfaces are “empty” Java Classes that explicitly state what
functions you should write (implement, in Java slang).
• PlugIn and PlugInFilter are Interfaces
public class MyPlugIn implements PlugInFilter {…
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.
public class MyPlugIn implements PlugIn {…
PlugIn:
void run(java.lang.String arg)
This method is called when the plugin is loaded.
• That way ImageJ knows that whatever you write, it can use the
run function to launch your plugin!
14
Example PlugInFilter interface
setup () method is invoked
first when plugin is executed.
Static variable of
type integer (int)
run() method receives an
object (ip) of type
ImageProcessor.
Taken from:W. Burger, M.J. Burge Digital Image Processing, Springer Science 2008, p.33
27
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)
28
Usage of methods
Declaration of global variables
(they can be used/modified inside the
entire class).
run() method calls (javaish
for executes or goto) two
methods().
methods (): only executed
when explicitly called.
29
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.
public class MyNameClass {
// Class fields. These are accessible to all the functions inside the class
private String number; //private means that other classes cannot access it.
private String name;
// Constructor
public MyNameClass(String name, String number) {
setNumber(number);
setName(name);
}
// Public Methods
// Setters
public 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; }
// Getters
public String getName() { return this.name; }
public String getNumber() {return this.number;}
What does this class do?
}
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());
}
15
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.
–
–
public class MyNameClass {
// Class fields. These are accessible to all the functions inside the class
private String number; //private means that other classes cannot access it.
private String name;
// Constructor
public MyNameClass(String name, String number) {
setNumber(number);
setName(name);
}
// Public Methods
// Setters
public 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");
}
}
For example. To set the title of an
image, on might search for a setTitle
function
If we are looking to get the name of
the image, we should start by looking
for a getTitle function.
public void setName(String a_new_name) { this.name = a_new_name; }
// Getters
public 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());
}
16
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.
–
–
public class MyNameClass {
// Class fields. These are accessible to all the functions inside the class
private String number; //private means that other classes cannot access it.
private String name;
// Constructor
public MyNameClass(String name, String number) {
setNumber(number);
setName(name);
}
// Public Methods
// Setters
public 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");
}
}
For example. To set the title of an
image, on might search for a setTitle
function
If we are looking to get the name of
the image, we should start by looking
for a getTitle function.
public void setName(String a_new_name) { this.name = a_new_name; }
// Getters
public 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());
}
16
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.
–
–
public class MyNameClass {
// Class fields. These are accessible to all the functions inside the class
private String number; //private means that other classes cannot access it.
private String name;
// Constructor
public MyNameClass(String name, String number) {
setNumber(number);
setName(name);
}
// Public Methods
// Setters
public 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");
}
}
For example. To set the title of an
image, on might search for a setTitle
function
If we are looking to get the name of
the image, we should start by looking
for a getTitle function.
public void setName(String a_new_name) { this.name = a_new_name; }
// Getters
public 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());
}
16
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.
public class MyNameClass {
// Class fields. These are accessible to all the functions inside the class
private String number; //private means that other classes cannot access it.
private String name;
// Constructor
public MyNameClass(String name, String number) {
setNumber(number);
setName(name);
}
// Public Methods
// Setters
public 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");
}
}
For example. To set the title of an
image, on might search for a setTitle
ImagePlus Setters function
– If we are looking to get the name of
the image, we should start by looking
for a getTitle function.
–
public void setName(String a_new_name) { this.name = a_new_name; }
// Getters
public 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());
}
16
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.
public class MyNameClass {
// Class fields. These are accessible to all the functions inside the class
private String number; //private means that other classes cannot access it.
private String name;
// Constructor
public MyNameClass(String name, String number) {
setNumber(number);
setName(name);
}
// Public Methods
// Setters
public 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");
}
}
For example. To set the title of an
image, on might search for a setTitle
ImagePlus Setters function
ImagePlus Getters
– If we are looking to get the name of
the image, we should start by looking
for a getTitle function.
–
public void setName(String a_new_name) { this.name = a_new_name; }
// Getters
public 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());
}
16
An advanced example
Constructors; name must be
identical to the class name
set() & get() methods
36
An advanced example
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);
}
}
}
Can you find the
differences?
37
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 at
http://tiny.cc/adip-java
• Download Eclipse at http://tiny.cc/adip-eclipse
– Extract to Disk / Mount
18
Installing Eclipse
• Get Java Development Kit at
http://tiny.cc/adip-java
• Download Eclipse at http://tiny.cc/adip-eclipse
– Extract to Disk / Mount
18
Launching Eclipse
• Launch Eclipse
• Enter the folder
where all your
projects will be
stored.
19
Launching Eclipse
• Launch Eclipse
• Enter the folder
where all your
projects will be
stored.
19
Launching Eclipse
20
The Eclipse Layout
21
The Eclipse Layout
All your plugins
will appear here
21
The Eclipse Layout
Your code will appear here
All your plugins
will appear here
21
The Eclipse Layout
Your code will appear here
All your plugins
will appear here
The structure
of your
program will
appear here
21
The Eclipse Layout
Your code will appear here
All your plugins
will appear here
The structure
of your
program will
appear here
Errors and warnings will appear here.
21
ImageJ-Eclipse
ImageJ Wiki-The ImageJ Eclipse Howto
Author: Patrick Pirrotte
http://imagejdocu.tudor.lu/doku.php?id=howto:plugins:the_imagej_eclipse_howto
49
Import a Sample Java Application
• Go to tiny.cc/adip-java-sample, and unzip the file
somewhere.
22
Import a Sample Java Application
• Go to tiny.cc/adip-java-sample, and unzip the file
somewhere.
22
Import a Sample Java Application
• Go to tiny.cc/adip-java-sample, and unzip the file
somewhere.
22
Import a Sample Java Application
• Go to tiny.cc/adip-java-sample, and unzip the file
somewhere.
22
Import a Sample Java Application
• Go to tiny.cc/adip-java-sample, and unzip the file
somewhere.
22
Import a Sample Java Application
• Go to tiny.cc/adip-java-sample, and unzip the file
somewhere.
22
Import a Sample Java Application
• Go to tiny.cc/adip-java-sample, and unzip the file
somewhere.
22
Import a Sample Java Application
• Go to tiny.cc/adip-java-sample, and unzip the file
somewhere.
22
Import a Sample Java Application
• Go to tiny.cc/adip-java-sample, and unzip the file
somewhere.
22
Import a Sample Java Application
• Go to tiny.cc/adip-java-sample, and unzip the file
somewhere.
22
Running A Java Application
• Open MyMainProgram.java
• Run it
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 array
MyNameClass[] PeopleData = new MyNameClass[3];
PeopleData[0] = new MyNameClass("Romain Guiet", "0216932629");
PeopleData[1] = MyData;
PeopleData[2] = new MyNameClass("Arne Seitz", "0216932632");
• Console output:
System.out.println("Printing contents of the PeopleData Array:");
for(int i=0; i<3; i++) {
PeopleData[i].printData();
}
}
}
23
How Does It Run?
• When a Class needs to be run, it contains the main
method.
public static void main(String[] args) {
• 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)
24
Plugins: A Minimalistic Plugin
• Go to tiny.cc/adip-first-plugin , and unzip the file
somewhere.
25
Plugins: A Minimalistic Plugin
• Go to tiny.cc/adip-first-plugin , and unzip the file
somewhere.
25
Plugins: A Minimalistic Plugin
• Go to tiny.cc/adip-first-plugin , and unzip the file
somewhere.
25
Plugins: A Minimalistic Plugin
• Go to tiny.cc/adip-first-plugin , and unzip the file
somewhere.
25
Plugins: A Minimalistic Plugin
• Go to tiny.cc/adip-first-plugin , and unzip the file
somewhere.
25
Plugins: A Minimalistic Plugin
• Go to tiny.cc/adip-first-plugin , and unzip the file
somewhere.
25
Plugins: A Minimalistic Plugin
• Go to tiny.cc/adip-first-plugin , and unzip the file
somewhere.
25
Plugins: A Minimalistic Plugin
• Go to tiny.cc/adip-first-plugin , and unzip the file
somewhere.
25
Plugins: A Minimalistic Plugin
• Go to tiny.cc/adip-first-plugin , and unzip the file
somewhere.
25
Plugins: A Minimalistic Plugin
• Go to tiny.cc/adip-first-plugin , and unzip the file
somewhere.
25
Build
Run
Minimalistic Plugin
- Build creates
the .jar file and
copies it to the
Fiji Folder.
- Run launches
ImageJ and runs
your plugin
26
Configure Build and Run
27
Configure Build and Run
27
Configure Build and Run
27
Configure Build and Run
27
Configure Build and Run
27
Configure Build and Run
27
Configure Build and Run
27
Configure Build and Run
27
Configure Build and Run
27
Configure Build and Run
27
Configure Build and Run
27
Configure Build and Run
27
Configure Build and Run
27
Configure Build and Run
27
The Ant File: Building Made… “Simple”
• Open build.xml
Where Fiji is
located
Must have same name
The files your plugin
needs in order to run.
28
The Ant File: Building Made… “Simple”
• Open build.xml
Where Fiji is
located
Must have same name
The files your plugin
needs in order to run.
28
Why suffer?
• Get http://tiny.cc/adip-speedTest
• And run the macro as well as the plugin.
29
Import example plugins
1
2
3
30
Import example plugins
4
31
Now Onwards to Java!
32
Now Onwards to Java!
Imports are packages that contain other
java classes
32
Now Onwards to Java!
Imports are packages that contain other
java classes
This is your class. It is public and
implements the PlugIn interface
32
Now Onwards to Java!
Imports are packages that contain other
java classes
This is your class. It is public and
implements the PlugIn interface
@ tags are annotations, a form of
metadata
32
Now Onwards to Java!
Imports are packages that contain other
java classes
This is your class. It is public and
implements the PlugIn interface
@ tags are annotations, a form of
metadata
run is a function inside the class
My_First_Plugin
It takes an argument called arg0 which is a
String (another Class)
It is a public function and has no return
argument (void)
32
Now Onwards to Java!
Imports are packages that contain other
java classes
This is your class. It is public and
implements the PlugIn interface
@ tags are annotations, a form of
metadata
run is a function inside the class
My_First_Plugin
It takes an argument called arg0 which is a
String (another Class)
It is a public function and has no return
argument (void)
showAbout is another function inside the
class My_First_Plugin
It takes no argument and is a private
function.
32
Now Onwards to Java!
Imports are packages that contain other
java classes
This is your class. It is public and
implements the PlugIn interface
@ tags are annotations, a form of
metadata
run is a function inside the class
My_First_Plugin
It takes an argument called arg0 which is a
String (another Class)
It is a public function and has no return
argument (void)
showAbout is another function inside the
class My_First_Plugin
It takes no argument and is a private
function.
In showAbout, we call the IJ class, which we imported from the ij package with import
ij.* and use the static function showMessage from that class to display a message.
showMessage takes 2 arguments, both Strings.
32
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.
You can get a lot of information this way.
1.
2.
A list of all methods and variables available in the class.
It also displays whatever documentation was written by the programmer
The documentation is called JavaDoc
33
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/
Configuring the Javadoc for making plugins
• http://imagej.nih.gov/ij/developer/api/
34
PlugIn Interface
• The simplest plugin to use. May not even need an
image.
public class PlugIn_Plugin implements PlugIn {
@Override
public void run(String arg0) {
//Your code here
}
• Exercise: Get the name of the current image and
display it in the log.
• Start from My_First_Plugin.java
35
Simple Plugin
• Complete the function
public class My_First_Plugin implements PlugIn {
@Override
public void run(String arg0) {
// Get the current Image
ImagePlus imp = IJ.getImage();
// Use IJ.getImage();
// Write this to the ImageJ log
IJ.log("Image Name is: "+imp.getTitle() );
// Use IJ.log();
}
}
36
Simple Plugin
• Complete the function
public class My_First_Plugin implements PlugIn {
@Override
public void run(String arg0) {
// Get the current Image
ImagePlus imp = IJ.getImage();
// Use IJ.getImage();
// Write this to the ImageJ log
IJ.log("Image Name is: "+imp.getTitle() );
// Use IJ.log();
}
}
37
Simple Plugin
• Complete the function
public class My_First_Plugin implements PlugIn {
@Override
public void run(String arg0) {
// Get the current Image
ImagePlus imp = IJ.getImage();
// Use IJ.getImage();
// Write this to the ImageJ log
IJ.log("Image Name is: "+imp.getTitle() );
// Use IJ.log();
}
}
38
Useful Class Functions
• IJ.run(options);
• IJ.getImage();
39
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
40
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
40
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
40
Apply a command or Plugin
• Correction
// Get the current Image
ImagePlus imp = IJ.getImage();
// Use IJ.getImage();
// Write this to the ImageJ log
IJ.log("Image Name is: "+imp.getTitle() ); // Use IJ.log();
ImagePlus edgeImp = imp.duplicate();
IJ.run(edgeImp, "Find Edges", "");
// Duplicate image
// Run Find Edges
edgeImp.setTitle(imp.getTitle()+" Edges"); // Rename the new image
edgeImp.show();
// Display it
40
Apply a command or Plugin
• Correction
// Get the current Image
ImagePlus imp = IJ.getImage();
// Use IJ.getImage();
// Write this to the ImageJ log
IJ.log("Image Name is: "+imp.getTitle() ); // Use IJ.log();
ImagePlus edgeImp = imp.duplicate();
IJ.run(edgeImp, "Find Edges", "");
// Duplicate image
// Run Find Edges
edgeImp.setTitle(imp.getTitle()+" Edges"); // Rename the new image
edgeImp.show();
// Display it
40
Apply a command or Plugin
• Correction
// Get the current Image
ImagePlus imp = IJ.getImage();
// Use IJ.getImage();
// Write this to the ImageJ log
IJ.log("Image Name is: "+imp.getTitle() ); // Use IJ.log();
ImagePlus edgeImp = imp.duplicate();
IJ.run(edgeImp, "Find Edges", "");
// Duplicate image
// Run Find Edges
edgeImp.setTitle(imp.getTitle()+" Edges"); // Rename the new image
edgeImp.show();
// Display it
40
Apply a command or Plugin
• Correction
// Get the current Image
ImagePlus imp = IJ.getImage();
// Use IJ.getImage();
// Write this to the ImageJ log
IJ.log("Image Name is: "+imp.getTitle() ); // Use IJ.log();
ImagePlus edgeImp = imp.duplicate();
IJ.run(edgeImp, "Find Edges", "");
// Duplicate image
// Run Find Edges
edgeImp.setTitle(imp.getTitle()+" Edges"); // Rename the new image
edgeImp.show();
// Display it
40
Apply a command or Plugin
• Correction
// Get the current Image
ImagePlus imp = IJ.getImage();
// Use IJ.getImage();
// Write this to the ImageJ log
IJ.log("Image Name is: "+imp.getTitle() ); // Use IJ.log();
ImagePlus edgeImp = imp.duplicate();
IJ.run(edgeImp, "Find Edges", "");
// Duplicate image
// Run Find Edges
edgeImp.setTitle(imp.getTitle()+" Edges"); // Rename the new image
edgeImp.show();
// Display it
40
The PluginFilter Interface
• Slightly more complex. Must operate on an image
public class PlugInFilter_Plugin implements PlugInFilter {
protected ImagePlus image;
@Override
public 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;
}
@Override
public void run(ImageProcessor ip) {
// Your code here.
}
41
Add a Dialog
• When you need the user to provide data, there is
the GenericDialog class.
GenericDialog gd = new GenericDialog("pixels");
// Declare a new Dialog
gd.addNumericField("value", 0.00, 2);
// Add a number field
gd.showDialog();
if (gd.wasCanceled())
return false;
// Display the dialog
// Check that the user clicked OK
value = gd.getNextNumber();
// Get the number
42
Add a Dialog
• When you need the user to provide data, there is
the GenericDialog class.
GenericDialog gd = new GenericDialog("pixels");
// Declare a new Dialog
gd.addNumericField("value", 0.00, 2);
// Add a number field
gd.showDialog();
if (gd.wasCanceled())
return false;
// Display the dialog
// Check that the user clicked OK
value = gd.getNextNumber();
// Get the number
• Useful methods
• addNumericField
• addString
• addChoice
• addCheckbox
to get a number
to get a string
to get a dropdown menu
to get a checkbox
42
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
43
PluginFilter Dialog
@Override
public 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, continue
if (!gd.wasCanceled()) {
medianValue = gd.getNextNumber(); // Recover the value the user entered
}
// Explain the type of images that work with this plugin
return DOES_8G | DOES_16 | DOES_32 | DOES_RGB;
}
44
PlugInFilter Dialog in a Macro
• What happens when we run the Macro Recorder
on our plugin?
• GenericDialog creates everything for us!
45
ResultsTable
• Exercise: Measure the mean intensity of the
image and display it in a ResultsTable.
• Start from My_First_Plugin.java
46
ResultsTable
• Solution tiny.cc/adip-measure-image
• Static variables belong to the Class and not the
Instance…
47
ResultsTable
• Solution tiny.cc/adip-measure-image
• Static variables belong to the Class and not the
Instance…
47
Flexibility
123