shapelogic

ShapeLogic is an open source toolkit for declarative programming, image processing and computer vision. Started August 2007.

The first real application for ShapeLogic is a particle analyzer . It will find and categorize particles on a relatively uniform background then make a report of geometric properties for each of the particles. The main application is for recognizing cells in medical image processing.

Code hosted on http://code.google.com/p/shapelogic/ . From there you can download both source files and binary distributions.

Join the ShapeLogic mailing list for announcements, questions, bug reports, suggestions and feature requests. You can help improving the stability of ShapeLogic by filing a bug report.

Main ideas and motivation

ShapeLogic is a library for

Declarative programming and lazy computations in Java
Image processing and computer vision
Particle analyzer for microscopy and medical image processing

While ShapeLogic's declarative programming system was initially developed for image processing and computer vision, it is widely applicable. It is currently difficult to combine declarative programming and image processing. ShapeLogic is intended as basic plumbing software that turns a logic engine into a simple plugin component to ease entry into vision and image analysis. ShapeLogic also fills gaps missing from current Java image processing libraries, and uses a commercially friendly license.

ShapeLogic has an automatic color particle analyzer and a letter matching example .

Features

Declarative lazy stream driven logic engine with lazy computations
Specialized for the domain of image processing and computer vision
The user can store rules in either a flat file or database, decreasing user reliance on Java programming
User rules are written with Java or the Java 6 Scripting interface JSR 223. Groovy , JRuby , JavaScript have been tested
Implementation of 2D geometry primitives, vectorization and segmentation
It is free (as in free speech and free beer)
Commercially friendly MIT open source software license, also called the X11 License
Annotations of point as different type of junctions, end points, hard or soft points
Annotations of lines as straight, curved, concave or inflection points
Programmed in Java
Can be used as a plugin for ImageJ, the leading Java open source project used in medical image processing

Particle analyzer

ShapeLogic 1.3 contains a color particle analyzer .

Here is an example particle image embryos.jpg

Here is the result of running the non-customized particle analyzer on it.

The categories for the particles are only examples, it is easy to setup different rules for categorizing particles.

In ShapeLogic 1.4 there will be custom rules to categorize specific cells and it will be tested further.

ShapeLogic 1.3 also contains the second version of a color particle counter. It also prints a smaller report of the particle's properties.

Requirements

To run as a library for functional and declarative programming there are no requirements.

To run as an ImageJ plugin ShapeLogic uses the following libraries:

ImageJ ShapeLogic can either run as a plugin in popular ImageJ framework or stand alone in pure Java2D
Commons math : Math library for geometry
Antlr : For parsing build in filter language

You can run all current image processing algorithms outside ImageJ , using just a BufferedImage should you want to embed ShapeLogic in your application.

Optional requirements

These are used in unit tests, builds or old versions of image processing functionalities:

Maven 2 : Build system
Apache commons : JEXL , beanutils : For first version logic rules interpreter
Groovy , JRuby , JavaScript : For second version logic rules interpreter
Hibernate or JDBC: For database access
Google Guice : Lightweight IoC framework
HSQLDB or H2 : Embedded databases

Development Status: Beta

ShapeLogic is in Beta, as of version 1.0.
Particle counter and particle analyzer working directly on color images without manual user intervention.
Working example where ShapeLogic is used for matching capital letters.
Image processing algorithms now work both in ImageJ and on Java's BufferedImage .
The API is still under development.
Contains a framework for declarative and functional programming.
ShapeLogic currently consists of 32,000 lines of Java code including 480 unit tests.

News

2008/08/02 ShapeLogic v 1.3 released

Particle analyzer now has a manual color mode , where you can set either the foreground or background color, in addition to the automatic mode introduced in v 1.2
New edge tracer for particle analyzer, in v 1.2 the wrong perimeter lengths are sometimes found
Built for JDK 1.5 / Java 5 so it should work on the Mac without updates

Documentation will soon be updated to reflect ShapeLogic 1.3.

Future plans for ShapeLogic

For more up to date information on ongoing development work look at these

Blog Declarative Computer Vision
Roadmap

ShapeLogic v 1.4 with specific cell recognition particle analyzer soon to be released

Make custom rules to recognize specific cells . In v 1.3 the user has to make rules themselves.
Make it easier to select which particle properties to print out, currently a random selection of somewhat useful properties has been selected.
HSV mode for the particle analyzer
Possibly Perceptron styled 1 layered neural network for rules for particle analyzer
Improve the color replacer plugin, to take separate RGB values as input

The test images are taken from the sample images from ImageJ

blobs.gif

Cell_Colony.jpg

embryos.jpg

Examples applications

Automatic color and gray scale particle counter and analyzer , first medical image processing example.
Letter matching example . Very rudimentary OCR.
Mathematical problems from Project Euler . This is a list of 193 mathematical problems that can be solved by computers. They vary in complexity from simple to hard. The goal is to test ShapeLogic's new declarative and functional constructs on real problems and make sure they are terse and intuitive.