James Weaver on Quantum Computing and Java

JavaFX for Science

Note to reader: This "guest post" was written by Dr. James Thompson, who is using JavaFX to develop scientific applications.  I've included a brief bio for Dr. Thompson after this post.

Java has a rich history in the scientific community. Applications and frameworks such as the NIH's ImageJ, CERN's Colt framework and Apache Commons Math library immediately spring to mind when working in scientific computing. My first exposure to Java in science came as a graduate student at Oxford. We needed to analyze many large noisy datasets, typically stacked (multi-page) TIFF image files. ImageJ and its excellent plugin framework was the environment of choice for this work. Other groups such as the Mosaic group at the ETH in Switzerland did similar work and have extended it beyond what we did a few years ago.

So where does JavaFX 2 come in? Well, in my recent work we've had a need to develop image analysis software yet again. It turns out this is a common theme in biology, physics and engineering labs nowadays. I decided to have a look into what was available on the JVM which was when I learned of the new Java FX 2 pure Java library. It instantly appealed as it was well documented, had plenty of examples and was free! Scientists are a diverse group too, so the ability to write once and run on Macs, Windows and Linux boxes is a massive bonus. In academic science these days you often find diverse backgrounds and amalgamations of people with broadly different skill-sets. A nice user interface, easy installation and pleasant work environment on the computer desktop is therefore imperative.

A few features stood out immediately as I began browsing examples and reading the API. These included in my order of priority: extensive graphing tools, ObservableList, easy integration with native file systems (open / save dialogs), a simple syntax, great API documentation, FXML and good Netbeans tooling. Later on Scene Builder came onto the scene (pardon the terrible pun). Having done some work with XCode for Cocoa on the Mac I thought it would be hard to stand up to it. I was wrong. Scene Builder was mature out of the box. Laying out 'AnchorPanes' or anything else for that matter is very straightforward. CSS integration also enables easy skinning for apps. This is generally much more difficult in other frameworks.

Living on the JVM and being pure Java, integration with other JVM languages is easy too. My recent forays into Scala have proven very fruitful with JavaFX. I've been building some fairly involved numerical analysis code, and it's very easy to code in Scala. I've been able to use JavaFX in pure Scala classes, extending the 'Initializable' interface and load FXML classes easily.

I've had to develop a few things building directly on the JavaFX framework, such as for example tools to load multi-page TIFF files and write various bit-depth TIFF data to JavaFX 'Image' objects. But generally plotting tools and data handling are a breeze with JavaFX 2.

IntelliJ IDEA, Netbeans and Simple Build Tool for Scala all enable mixed projects and help with building greatly. I stumbled across an sbt-javafx plugin a few days ago, which has enabled me to package my projects for distribution among my colleagues.

JavaFX images from byte[]

In short, if you have a need to develop applets for scientific work, need to load and save data with a GUI, plot graphs and get actual science done, JavaFX 2 has to be given some serious consideration! I can't imagine trying to do what I've been able to in any other framework. I hope more scientists decide to develop things with JavaFX 2, so that we can extend the body of open source code and make development even easier.

Please have a look at a couple of movies I made showing my GUIs in action. These projects are a work in progress, but demonstrate the power of JavaFX and its application to scientific computing front ends.

Github repository

 

 

Regards,
Dr. James Thompson (and Jim Weaver)

James did his PhD at Oxford in the Physical and Theoretical Chemistry Laboratory, researching membrane protein biophysics. After finishing, James went to Harvard Medical School for a year to work on an imaging project before moving to his present role as a post-doc at USC in Los Angeles this year. His work revolves around biophysics but uses techniques from molecular biology, chemistry, microscopy and computer science. James maintains interests in single molecule biophysics, membranes, imaging, protein structure and function and computation with Java, Scala and GPUs. His twitter handle is:  drJamesThompson

And the winner [of the JavaFXpert RIA Exemplar Challenge] is...

In October 2009 I announced the JavaFXpert RIA Exemplar Challenge, which was to:

"Create an application in JavaFX that exemplifies the appearance and behavior of a next-generation enterprise RIA (rich internet application)".

I am pleased to announce that the winning entry, the Beechcraft Cargoloader, was submitted by Abhilshit Soni.  Here's a screen capture of Abhi's entry:

Abhilshit Soni is a 24 year old Software Engineer living in Mumbai, India. He holds a Bachelor of Technology in BioInformatics and is currently working with Zycus as a Software Engineer in the Product Engineering Team. He has been involved in developing web-based enterprise applications based on Java EE and Spring technologies for almost three years.

About Abhi's Application

According to Abhi, his Beechcraft Loader application "tries to solve a typical engineering problem of loading cargo containers into a Cargo aircraft. It needs a proper way in which your aircraft should be loaded with containers so that the resultant center of gravity of the aircraft is stable. For big cargo carriers like Boeing 747-400F or Airbus A380 there are set of calculations defined in their weight and balance handbook which are always calculated to ensure that center of gravity of the aircraft is and will be stable in all the conditions.  This application tries to calculate the same for a relatively smaller Aircraft called BeechCraft 1900C by the Hawker-Beechcraft Corporation. The cargo aircraft manufacturer describes the operational center of gravity limits (varying based on the total aircraft weight) for a particular aircraft which can be viewed by the  "Aircraft weight" vs "center of gravity" chart. The aim is to load aircraft in such a way that your current center of gravity falls between these operational limits, otherwise your aircraft is either nose heavy or tail heavy. This application considers only Beechcraft 1900C for cargo loading with a specific set of containers . All the equations and Aircraft master data are obtained from Chapter 7 of the FAA Aircraft Weight and Balance Handbook. The application currently does not cover all the functional use cases, like calculating lateral Center of Gravity and many other functional validations which are out of scope as of now".

Instructions for Using the Application

You can take the application for a test flight via Java Web Start by visiting Abhi's blog.  Here are some pre-flight instructions from Abhi:

1. Drag a cargo container from the cargo panel on the left side.
   
2. Place it on any of the sections on bechcraft 1900C main deck in the upper center.
   
3. See the change in center of gravity in the data table.
   
4. Also see the change in weight v/s CG chart, and the weight coverage pie chart, in the lower right and left respectively.
   
5. To remove a dropped container double click it.
   
6. Change the container's position by by dragging from old position to new position.
   
7. To reset the plan click 'Reset Container' button on the toolbar in the center just below the Main deck.
   
8. To enable/disable Drag and Drop animation toggle 'Disable Animation' button on the  toolbar in the center just below the Main deck.
   
9. To quick view/hide cargo weights toggle the "View Weights " button on the toolbar in the center just below the Main deck
   
10. Click on Weight Coverage chart or Weight vs CG chart to get a larger image.
    
11. The yellow dot in the Weight v/s CG chart represents the current center of gravity, and the polygons drawn in the chart are the operational limits provided by the aircraft manufacturer.
    
12. Check out Help and About buttons for more info about the application.

Closing Thoughts

Each of the participants were asked how their entry exemplifies the appearance and behavior of a next-generation enterprise RIA.  Here is Abhi's response: 

"To an end user the enterprise RIA is more about the way user sees the information shown in the application. All that an end user expects from an enterprise  RIA is to access the information in the fastest and coolest looking way. The definition of coolest may be interpreted as drag drop interfaces, animation and effects, different data viewing formats, but not at the cost of performance. By using JavaFX I have tried to achieve the same to an extent by adding drag-drop spot data update in multiple formats like grid and charts, and also onclick zooms, animations and effects with performance as priority."

Also, per the contest rules, Abhi has submitted the source code of this application to the JFXtras open source project in the samples repository.

Congratulations to Abhi, and thanks to everyone who submitted an entry to this RIA Exemplar Challenge!

Regards,

Jim Weaver

RIA Exemplar Challenge deadline extended to JavaFX SDK 1.3 release + 30 days

The JavaFXpert RIA Exemplar Challenge deadline will be extended to 30 days after the JavaFX 1.3 SDK is officially released.  I'm making the deadline dependent upon the JavaFX SDK 1.3 release, because based upon presentations at Devoxx and the Silicon Valley Java Users Group, the upcoming 1.3 release will have some features very relevant to the goals of this RIA Exemplar Challenge.  For example, this release will have several new UI controls, as well as the ability to transform nodes on the Z axis.

As a reminder, although I still recommend that the participants of this contest consist of a developer and a graphic designer, I have removed this restriction.  An individual developer can enter the contest, and win the 2000 USD.  Please be aware that two of the four judges in the contest are graphic designers, so the user experience and visual design are important aspects of a winning entry.

If you have already submitted an entry to this challenge, please feel free to resubmit an updated entry closer to the new deadline.

Thanks for your understanding on extending the contest deadline.  Although I can't officially enter the contest, this will also give me more time to work on my "entry" :-)

Regards,

Jim Weaver

Dean Iverson is Off Da [JavaFX] Charts!

Pro JavaFX co-author and homie Dean iverson is blogging again, beginning with a series on JavaFX 1.2 Charts. 

This series is based on charting content that he wrote for the book (in chapter 5), and will help you get up to speed quickly on this new feature of JavaFX.  Check out the first installment, perhaps with a cup of coffee and a piece of π.  (You'll get that pun when you read the article :-)

Congrats Dean, and keep those blog posts rolling!

Regards,
Jim Weaver