Open ImageJ Images in Different Views

22.05.2014

In the next release of Bio7 it will be possible to transfer opened ImageJ images from a tab to a detachable view. This action makes it possible to open several images side by side, detach images or translate them to a secondary monitor. In addition it is possible to nest several images in one detached window (see screenshot below).

detachableimage

 

Cellular Automata on a 3D Globe

15.04.2014

One of the features of the next release of Bio7 is the possibility to run an ImageJ simulation (dynamic image data) georeferenced on the 3D globe with – and this is new – a default transparent color (see image with running “Game of Life” below).

screen

To run a simulation on a 3D globe with the current Bio7 version without a transparent color follow this tutorial:

Visualize dynamic images on the WorldWind globe

Full JDT Support For The Next Release

18.02.2014

It was always a goal to integrate a powerful Java editor in Bio7. The current default Java editor of Bio7 is a custom editor with a set of tools to ease the creation of valid Java files and enables the compilation of Java classbodies and regular Java classes dynamically.

However the editor lacks many advanced Java editing capabilities which would be very hard to implement bottom up. So instead of trying to improve the current editor i evaluated the use of JDT  (Java development tools) inside of Bio7.

After some research and time i was finally able to embed JDT in Bio7 in a decent and easy to use way. As the result in next release you can create a Bio7 Java project with JDT support using several project creation wizards of Bio7 which create e.g. Bio7 Java templates ready for dynamic compilation (see below).

jdt1

The file(s) for compilation are created in the base src folder (the bin folder contains compiled *.class files which we don’t need for dynamic compilation – the built process can be disabled in the preferences).
As in previous releases the dynamic compilation action is available in the toolbar of Bio7 (you don’t need the Run configuration of JDT) to compile the files instantly
into the current Java process.

jdt2

The process of creation also configures the project Build Path automatically to include all necessary Bio7 runtime libraries, binaries and source folders which are needed more or less for the dynamic compilation process (see screenshot below) so that no further adjustments are needed to interact with the Bio7 environment.

jdt3

The JDT  Java editor drastically improves the creation of Java simulation models, etc. You definitely profit from the fantastic editing support of the editor with code completion, refactoring and error analysis, Quick fixes, etc. (below a screenshot shows the code completion for the available Bio7 API).

jdt4

However if the Java editor is not active the usual Bio7 GUI is not cluttered by JDT elements.

jdt5

At all JDT support for Bio7 is a huge improvement for the creation of e.g. simulation models avoiding many errors with Java classes. The Java file creation and the dynamic compilation process will be as easy as in previous releases of Bio7.

R editor improvements for Bio7

30.01.2014

For the next release of Bio7 based on Eclipse 4.4 an improvement of the R editor for a much better editing experience of R scripts will be available. The integrated editor itself is built bottom-up (based upon an Eclipse editor editor template) although there a great editor frameworks (DLTK) or frameworks to develop programming languages and domain specific languages (Xtext) for Eclipse available.

I decided to built the editor this way to avoid dependencies with Eclipse plugins adding unnecessary interfaces and complexities in a Rich Client Platform and because i wanted to understand the internals of the editor for manageable improvements of upcoming releases.

Until now i integrated a parser for R based on ANTLR, implemented error marking, code folding, a first simple version of “Quick Fixes” and an outline view for the R scripts.

This screenshot demonstrates:

screenreditor1

Here a screenshot with error marking and a “Quick Fix”:

screenreditor2

Beside other improvements coming from Eclipse (e.g. split editor capabilities) for the next release of Bio7 i hope that this new functionality will ease the development of R scripts inside of Bio7.