16.05.2012

At the moment i migrate the Bio7 source to Bitbucket a GIT provider which is offering free webspace for an unlimited amount of projects. With this migration i can easier update code from different computers (with a different OS) and i hope that i can improve my productivity e.g. for the next Bio7 1.6 release.

12.04.2012

Currently i’m working on the next release of Bio7. One of the biggest changes of Bio7 1.6 will be the possibility to dynamically compile and load Java 7 code. In addition the compiler will produce more useful error messages if the written source code is erroneous. The next version will also allow the update of selected Bio7 plugins from a repository location for a faster update of some important applications and libraries integrated in the platform.
My hope is that i can release the next version within a month (at least for Windows and Linux).

18.03.2012

Bio7 can be extended in several different ways with Eclipse plugins, R packages, ImageJ plugins and custom scripts (scripts to extend a menu or executed at startup).

1. To install (suitable) Eclipse plugins the Update-Manager can be used to install plugins from a remote website. An How-To was already posted with the GIT plugin as an example, see: http://bio7.org/?p=1066

2. R packages can be added in two different ways. One way is to use the package installer GUI of Bio7:
http://www.uni-bielefeld.de/biologie/Oekosystembiologie/bio7app/flashtut/rpackagesinstall.htm
Additionally the command line in R can be used to install packages.

3. ImageJ plugins (*.class or *.jar files) have to be installed in the plugins folder of the ImageJ Eclipse plugin which is e.g.: Bio7/plugins/com.eco.bio7.image_1.45.1/plugins.
Note: In the ImageJ Eclipse plugin the typical ImageJ folder structure can be found!

4. Groovy, BeanShell and R scripts, as well as ImageJ macros can be dropped to special folders to extend the default Bio7 menu (startup) functionality. The folders which are scanned by default are:

Path to folders: Bio7/plugins/com.eco.bio7_1.5.0/

01.02.2012

Landscape metrics were developed to analyze spatial patterns of landscapes (e.g. composition and spatial arrangement). In R it is possible to calculate these metrics with the “SDMTools” package. Bio7 offers an easy to use interface to R and ImageJ and can use these tools to simplify a workflow to analyze image data (e.g. vegetation data) with landscape metrics. A typical workflow would include to cluster available image data into different classes and then analyze the data with the available metrics.

In the video below a simple artificial example is given of the workflow in Bio7 with the help of ImageJ, R and the “SDMTools” package:

http://bio7.org/flash/landscape.htm

Beside this possibility it is also possible to calculate a subset of landscape metrics with a Java API available in Bio7 for simulation purposes.

Apropos:

Landscape metrics algorithms are quite similar to some algorithms which are default available in ImageJ and these measurements can maybe complement an analysis of landscape structures, see:

http://rsbweb.nih.gov/ij/docs/menus/analyze.html
http://bio7.org/flash/clusterParticles.htm

Be aware that it is of importance to define the neighborhood rule (e.g. 4- neighbor rule or 8-neighbor rule) beside several other aspects which have to be considered. For an overview about landscape analysis and landscape ecology follow the link to a literature database at the end of this post.

Related to this article:

Creating fractal categorical maps and images with Bio7
http://www.uni-bielefeld.de/biologie/Oekosystembiologie/bio7app/flashtut/fractalrandom.htm

Supervised classification of images with Bio7 and R
http://www.uni-bielefeld.de/biologie/Oekosystembiologie/bio7app/flashtut/supervisedimages.htm

SDMTools package
http://cran.r-project.org/web/packages/SDMTools/index.html

Literature (see Landscape Analysis – if you know good papers or books let me know!)
https://www.zotero.org/groups/ecological_modelling/items

17.01.2012

Bio7 contains a functionality to save models in a special file. The primary purpose of this file type was to save grid models and the patterns in a file. However with this method Java code can be saved in the file, too. If this file then is dragged on the GUI of Bio7 the file will be loaded, the embedded Java source will be compiled and the setup method (if available) will be executed.

This action can also be used to save other model types beside grid models e.g. 3d models or 2d continous models or models using R with the Rserve API by means of Java code. Additonally methods of the Bio7 API can be used to open views, perspectives or call the fullscreen functionality (ImageJ-Canvas view, Space view, WorldWind view) e.g. inside the setup method (which will be invoked after file loading).

On GitHub i started to create examples which can be downloaded and simply dragged on the Bio7 GUI to demonstrate this functionality (Folder “Drag and Drop Examples”.):

https://github.com/Bio7/Bio7 (download all as GitHub *.zip file or open the file and then switch to the raw visualization for a single download. Do not simple download a single file with a right-click of the mouse device. This will download a wrong formatted file!).

Video tutorial:

http://www.uni-bielefeld.de/biologie/Oekosystembiologie/bio7app/flashtut/gridmodels.htm

This feature is extremely useful if you would like to show some models in a presentation or an exhibition.

22.12.2011

Several external file types can be dragged on the Bio7 interface. Here is an overview of the supported file types and the action involved:

¹Except some Bio7 components with special drag and drop support and the editor area.
²All supported ImageJ file types and libs.
³Default Java supported image types.

05.12.2011

Since Bio7 is based on Eclipse and integrates the current Update Manager (p2) of Eclipse some useful plugins can be installed to extend the default Bio7 framework functionality. Here are some links to useful plugins.

EGIT - EGit is an Eclipse Team provider for the Git version control system (see previous article!)
SFTP - A SFTP-plugin to access remote resources.
Wicked Shell -  is an Eclipse plugin providing direct access to your system’s shell.
RSS Eclipse Plugin – RSS View is an RSS/Atom reader.
TeXlipse - TeXlipse is a plugin that adds Latex support to the Eclipse IDE
AnyEdit tools plugin – AnyEdit plugin adds several new tools to the context menu of text- based Eclipse editors, to output consoles, to Eclipse main menu and editor toolbar.
RegEx Util – Eclipse plugin for testing/editing regular expressions flavor of the Sun Java standard API (java.util.regex).

Please add the Update site (if necessary):

http://download.eclipse.org/releases/helios

to the Update Manager of Bio7 to install the afore mentioned plugins if they depend on plugins available in the default Eclipse “Helios” repository.

08.11.2011

Bio7 is based on the Eclipse platform and integrates the powerful Eclipse Update Manager. Using the Update Manager it is possible to install many useful Eclipse plugins which are compatible with the Bio7 environment. One of this useful plugins is the EGit plugin.

“EGit is an Eclipse Team provider for the Git version control system. Git is a distributed SCM, which means every developer has a full copy of all history of every revision of the code, making queries
against the history very fast and versatile.” (source: http://eclipse.org/egit/)

To install the plugin it is necessary to add two Update Sites to the configuration dialog (Select menu: Help->Install New Software…) of the Update Manager of Bio7 (in a regular Eclipse installation the first site below is default available!):

http://download.eclipse.org/releases/helios

http://download.eclipse.org/egit/updates-1.2

The Helios site has already access to the EGit plugin (see screenshot 3 below) but with the second link the latest version of the EGit plugin can be installed (see this website!)

After you’ve added the repository (plugin location) to the Update Manager select the Eclipse EGit and Eclipse JGit plugin (see second screenshot below) and accept the license agreement (see third screenshot below).

Please restart the application after the installation process has finished (confirm the restart dialog). After the restart there are new actions available in the menubar and in the toolbar. To share a Git project select the project and use e.g. the context menu in the Bio7 Navigator view.

To clone an existing repository use the import action of the Bio7 platform. For instance the Bio7 examples can be fetched from GitHub: https://github.com/Bio7/Bio7.git (Read-only. No password required!)

If you have a regular Git repository availabe Git actions will e.g. show up in the context menu.

Beside the different actions there will be also new views availabe for different Git tasks.

For the documentation of the EGit plugin visit: http://eclipse.org/egit/.
Free Git repositories (with some limitations)  can be created e.g. on GitHub, Gitorious or on Google Code.

01.11.2011

In the next release of Bio7 the full Java 7 Syntax will be availabe for the compilation of custom models. In addition the Java error messages will be more informative and errors can be easier detected in the Java source.
At the moment a combination of the Janino compiler and the standard Java compiler makes this possible. I hope to integrate the Eclipse compiler for the compilation support but there seems to be a bug in the classpath options of the compiler when used programmatically (standard compilation works dynamically).

However, this is definitevely a great compilation improvement for the next Bio7 release.