Author Archives: admin

New Icons for Bio7 2.5

08.12.2016

Beside many changes for the next release I was able to find the time to update the icons of Bio7 for the next release. The icons are a subset of the FontAwesome icons and some custom icons and were created with Inkscape. They will be made available for free, too.  At the moment the icons are available in two resolutions (100%, 200%) and the larger icons will be used when working with a high DPI monitor (> x dpi). For the rules see:

https://wiki.eclipse.org/Bug_421383_-_Graphics_Scaling_issues_on_high_DPI_displays

Here are two screenshots:

 

 

 

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.

 

 

New R Editor Features in Bio7

12.07.2016

Bio7 2.4 has been released for Windows, MacOSX and Linux and this release comes with a plethora of new R editor features.
The editor now supports the dynamic code analysis of R scripts, refactoring methods, improved code completions, more key shortcuts for a faster editing and improved quick fixes which now can be opened and applied directly where the warnings or errors occur.

The video below gives an overview of some new and noteworthy functions:

Bio7 2.4 for Linux Released

04.07.2016

A new Bio7 Linux release is available at http://bio7.org. The general release note for Bio7 2.4 can be found here!

linuxscreen1

Installation:

Bio7 for Linux comes bundled with the latest Java Runtime Environment.

To use R with Bio7 you have to install R for Linux.

In addition you have to install Rserve configured to use ‘cooperative mode’ (shared workspace in Rserve and R mode) which can be downloaded here:

https://bitbucket.org/maustenfeld/bio7-new/downloads

In the R prompt type the following command to install the compiled package (replace with your file path!):

install.packages(“Users/yourName/Downloads/Rserve_1.8-4_Linux_cooperative.tar.gz”, repos=NULL)

You can also compile Rserve by yourself. For an HowTo please consult the Bio7 documentation here.

Miscellaneous:

Added a tiny script to install useful default R packages for Bio7 to use all available GUI functionalities (e.g. rmarkdown, rgdal, spatstat, formatR, knitr, etc.). To install the packages start Rserve and execute the action Scripts->RScripts->Install_R_Packages in the Bio7 main menu. Please note that this only works if all dependencies for the packages are installed for compilation.

Troubleshooting Layout:

Linux comes in different flavours and it might be that you have to correct the Bio7 GTK *.css file for a little improved layout. If you see an artefact like this (‘Maximize’ button) just increase the size of the *.css toolbar variables.

linuxscreen4

The default CSS file can be found here:

/Bio7/plugins/com.eco.bio7.themes_2.0.0.201607050754/css/e4_default_gtk.css

The following changed css attributes will correct the height of the toolbars (changed attributes are bold):

.MPartStack {
……………………………………
color: ‘#org-eclipse-ui-workbench-INACTIVE_TAB_TEXT_COLOR’;
 swt-tab-height: 36.0px;

}

.MPartStack.active {
…………………………………..
swt-shadow-visible: false;
 swt-tab-height: 36.0px;
}

/*Important to set height for the view menus!*/
CTabFolder {
swt-corner-radius: 15.0;
swt-tab-height: 36.0px;
}

Of course you can change other attributes as well, e.g.,  if you want to change a color, etc. If you have good suggestions let me know.

Screenshots:

linuxscreen2

linuxscreen3