Category Archives: Bio7

Improved ImageJ plugin

15.08.2016

Finally I had the time to improve the ImageJ plugin structure of the ‘Plugins’ view menu. Now the SWT menu structure of the plugin completely matches the AWT menu structure of  ImageJ (see screenshots below with some installed plugins).
Installed plugins, scripts and macros will be added to their defined menu path. Before this (current version) it was only possible to extend the SWT ‘Plugins’ menu and installed scripts and macros were only available if installed in the Bio7 main menu or by means of the ImageJ ‘Control Panel’.

Old:

beforeijmenu

New:

aftereijmenu

In addition I improved the image ‘Type’ menu to show checked menu items according to the opened image (see screenshot below).

checkmenu

Finally the ImageJ shortcuts will be mapped to the SWT menu if not used by the platform with a higher priority (see screenshot below).

shortcutsmenu

Some minor improvements will follow, too for the next update of the plugin which can be updated for Bio7 2.4 or any Eclipse environment soon.

 

 

Useful Eclipse Plugins for Bio7

21.02.2016

Here are some great Eclipse plugins useful in a scientific context which can be installed directly into Bio7 with the Eclipse Update-Manager of Bio7 (Help->Install New Software…).

Please note that you can also install the Eclipse Marketplace Client into Bio7 to install some of these plugins (a fancy interface to search for plugins):

EGit:
https://marketplace.eclipse.org/content/egit-git-team-provider
The powerful Git plugin to connect Bio7 with a Git repository.

TCF-Terminal:
http://marketplace.eclipse.org/content/tcf-terminals
A true native terminal with SSH,Telnet and Serial line support.

Eclipse CDT
https://marketplace.eclipse.org/content/eclipse-cdt-cc-development-tooling
C/C++ editor and development tooling.

Arduino C++ IDE:
https://marketplace.eclipse.org/content/arduino-c-ide
A great Arduino extension of the C++ editor of Eclipse.

PTP
https://eclipse.org/ptp/
An integrated development environment to support the development of parallel applications written in C, C++, and Fortran.

Photran
http://www.eclipse.org/photran/
An Integrated Development Environment and Refactoring Tool for Fortran

JSDT
https://eclipse.org/webtools/jsdt/
JavaScript editor and development tools

PyDev Editor:
https://marketplace.eclipse.org/content/pydev-python-ide-eclipse
A very powerful Python editor which can be used to execute Bio7 Jython and Python scripts instead of the Bio7 default editor. In addition Bio7 can use the PyDev editor to execute scripts running on the Bio7 Java classpath. If you open Jython/Python scripts with the PyDev editor the default Bio7 action will be visible to execute the scripts on the Bio7 classpath.

Groovy Editor:
https://marketplace.eclipse.org/content/groovy-eclipse-juno
A more powerful Groovy editor. Can also be used with the Bio7 classpath if scripts are opened with this editor instead of the default.

Jeeeyul’s Eclipse Themes
https://marketplace.eclipse.org/content/jeeeyuls-eclipse-themes
To install new styling themes into Bio7.

Eclipse Color Theme
https://marketplace.eclipse.org/content/eclipse-color-theme
If you need, e.g., a dark colored editor at night to rest your eyes.

Julia Editor
https://github.com/JuliaComputing/JuliaDT
A Julia editor in an early stage. But very promising.

Remote System Explorer
https://marketplace.eclipse.org/content/remote-system-explorer-ssh-telnet-ftp-and-dstore-protocols
A plugin to connect Bio7 with SSH, Telnet, FTP and DStore protocols.

This is a selection of a huge amount of available Eclipse plugins which can be installed into Bio7 to complement the default tools.

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.

First Screenshot With Eclipse 4.4

05.11.2013

Today i tried Bio7 1.7.1 with the new Eclipse 4.4M3 platform and it didn’t look bad. There are some minor UI bugs/defects and missing implementations (detached views, e.g.) but i’m quite confident that these bugs will be resolved soon by the Eclipse team. At all this is huge improvement to 4.3 which was not usable with my RCP application. Here a first screenshot:

screen4

As you can see some controls and menus are not in the right place. But at all 4.4 will be a huge UI improvement.

New Bio7 1.7.1 Release with Improved R Plot Image Display

05.09.2013

I released a new Windows version of Bio7. This release improves the general R plot functionality of Bio7. The default image plots are now displayed in a Image stack if more than one plot command is executed. In this way all plots are automatically openend and not only the last image plot. Multiple plots (e.g. an animation or simulation) can then be saved as an animated *.gif file (see example below) or an *.avi file, etc. with the available default ImageJ methods.

Furthermore i added some templates in the preferences to switch e.g. to a *.pdf (displaying multiple plots) or *.svg plot (displaying a single plot) which will be opened with the default registered software if available – for *.svg i recommend Inkscape).
For antialiased image plots i added an “Image Cairo” option.

 Click on the image below to open an overview video!

Plot

Animated *.gif exported with ImageJ

Changes:

  • Updated ImageJ to version 1.48b.
  • Improved the custom R plot display.
  • Synchronized the “Plot Data” actions  in the “R-Shell” view with the settings in the Bio7 Rserve preferences.
  • Added more R plot options (with templates) in the Bio7 Rserve preferences (see screenshot below).
  • Synchronized the “Plot Data” actions with the settings of the plot preferences.
  • Updated Rserve to version 1.7-3
  • Updated some useful links to R resources and documents (Menu Help->Bio7 Internet).

rserveplotpref

Bug Fixes:

  • Fixed a bug which occured when opening the 3d panels of Bio7 while a resized! ImageJ image was displayed.
  • Fixed a bug of the embedded ImageJ.

A Linux and Mac version is planned after the next Java Runtime release.

The new Bio7 release can be downloaded here!