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.

Supervised Image Classification With Bio7, R And ImageJ

27.11.2015

I created a new Bio7 example which demonstrates how to classify an image with Bio7, ImageJ and R.

classifyimage

For the classification I used the “randomForest” R package and an image example of ImageJ so you can reproduce the example quite easily. I made the example script as easy as possible and trained the classifier with 64 trees by default (see literature below). Not shown in the video is the procedure to control the prediction of the trained classifier with test data. You can find a simple script in the repository, too, which uses a method of the powerful ‘caret’ package.

Video:

If you have some recommendations of how to effectively use a decent classifier for image classification (e.g., which classifier is well suited for images, which tuning parameters are useful in this context, which additional signatures could be used, etc.) I would be happy to hear.

References:

Fernández-Delgado, M., Cernadas, E., Barro, S. & Amorim, D. Do we Need Hundreds of Classifiers to Solve Real World Classification Problems? Journal of Machine Learning Research 15, 3133–3181 (2014).

Oshiro, T. M., Perez, P. S. & Baranauskas, J. A. in Machine Learning and Data Mining in Pattern Recognition (ed. Perner, P.) 154–168 (Springer Berlin Heidelberg, 2012).

Latinne, P., Latinne, P., Debeir, O. & Decaestecker, C. Limiting the Number of Trees in Random Forests. IN PROCEEDINGS OF MCS 2001, LNCS 2096, 2001.

New R plot preferences and improvements for the R editor in Bio7

18.11.2015

In the current release of Bio7 2.3  two new plot preferences are available to automatically plot data with the size of the visible display (as an image) or with the size of available ImageSizeX and ImageSizeY R workspace variables.

The second option is handy if you transfer images from ImageJ to the R workspace (the variables ImageSizeX and ImageSizeY will be autmatically created, too). You can then create an R image plot (e.g. from a classification) in the same size as an overlay of the original image (in turn plotted and overlayed in ImageJ).

Video:

Improvements of the  R editor for the upcoming Bio7 2.4 release

For the upcoming release of Bio7 I also add new features to the Bio7 R editor.

Among other things until now I improved the code completion. If you now type a a left parenthesis you get a help tooltip if the function is known (if you load frequent used R packages with the Bio7 GUI interface the package function context will be added to the code completion, tooltip interface).

screenRTooltip

Screenshot 1: Improved tooltip when a left parenthesis is typed.

screenRCodeCompletion

Figure 2: Code completion (Keys: CTRL+Space) now preselects the right context (e.g. functions with ‘.’ char)

In addition I added a function to set right parentheses, braces, etc. automatically when left parentheses, etc.  are typed in the R editor.

Bio7 Toolbar Improved

07.11.2015

Finally I was able to find the CSS error in the toolbar layout which resulted in a visible gap when, e.g., the Flow editor was active. Now everything looks much better (see the red arrows!) especially when you install Eclipse plugins which make contributions to the main toolbar.

toolbarcss

You can also add this corrections easily to a current Bio7 2.3 installation. Just add the following lines to the default Bio7 CSS (Path: Bio7/plugins/com.eco.bio7.themes_2.0.0.201508261732/css/e4_default_yourOperatingSystem.css):

.MToolBar.Draggable {
  handle-image: url(./dragHandle.png);
}

.MToolControl.TrimStack {
  handle-image: url(./dragHandle.png);
}

.MToolControl.Draggable {
  handle-image: url(./dragHandle.png);
}

And delete the following ‘handle-image’ line in the Perspective Switch attribute:

/*Perspective Switch!*/
#org-eclipse-ui-main-toolbar #PerspectiveSwitcher {
……..
………
    handle-image: none;

Or just copy over the CSS from the default_win7.css github file.