16.08.2018

A new release of Bio7 is available. The new Bio7 2.9 release comes with a plethora of new R features and bugfixes.

Screenshot MacOSX with dark theme and opened ‘R ImageJ Analysis’ perspective

Screenshot ‘R’ perspective Windows and opened R-Shell code completion

Release Notes:

General:

• Based on Eclipse 4.8
• Improved the dark theme and the layout of the dark theme in many places
  
• All editor font colors are now changed automatically to default optimized colors when using the dark theme
  
• New ‘Switch Theme’ action available to easily switch to the dark theme or back to the default theme
• Java updated to 1.8.181
• New Fullscreen/Hide Menu action available (Main menu “Window” – Key: Strg+Shift+ 4)
• New Hide and Show main menu actions available (useful to hide added plugin menus again)
• Added pdf reader option “Okular” to open a R pdf plot with the okular application (used when the SWT browser + open external preference is selected)
• Added a new Table API method to transfer a matrix array form Java more efficiently
• Improved the WorldWind search function (using the photon geocoding API)
• Improved the default font size for Swing components on Retina displays (e.g., ImageJ components)

R:

• Updated R for Windows to version 3.5.1
• Added a new plot option to plot huge plots in a temporary folder and open them in ImageJ virtually (disk resident). The folder will automatically be opened after plotting (plot images have to be deleted manually!)

ImageJ

• ImageJ Updated to 1.52f18
• ImageJ toolbar improved for the dark theme (see screenshots)
• Added a new ImageJ detach image menu in the ‘Window’ menu of the ImageJ-Canvas view

R Markdown:

• Added syntax coloring of R markdown snippets
• Added new context menu actions in menu “Text” (Find and replace, Toggle Block Selection, To Upper Case, To Lower Case)
• Added a new context menu action to toggle word wrap, etc.
  

R editor:

• Added a new warning and quickfix for possibly wrong comparisons of NULL, NA, NaN

• Added a new option in the preferences for the new warning
• Added new context menu actions in menu “Text” (Find and replace, Toggle Block Selection, To Upper Case, To Lower Case)
• Improved the display for quickfix suggestion, warning and errors when the font is resized dynamically (especially for MacOSX)
  
• The help browser for code completion popups now display help sites in dark mode if the Bio7 dark theme is enabled.

ImageJ Macro Editor

• Added a general rename method to rename selected word occurences
  
• Added new context menu actions in menu “Text” (Find and replace, Toggle Block Selection, To Upper Case, To Lower Case)
• Added latest macro code completion function definitions

Download and Installation:

Windows:

Just download the *.zip distribution file from https://bio7.org and unzip it in your preferred location. Bio7 comes bundled with a Java Runtime Environment, R and Rserve distribution and works out of the box.

Linux:

Download and extract the installation file from https://bio7.org.
For Linux you have to install R and Rserve (see Rserve installation below!).

MacOSX:

Download and extract the installation file from https://bio7.org.

If you start Bio7 a warning or error can occur because of the changes how Apple treats signatures! To allow Bio7 to start see this instructions for Yosemite and Sierra:

OS X Yosemite: Open an app from an unidentified developer

macOS Sierra: Open an app from an unidentified developer

If you have still problems with Sierra see this solution!

In addition for MacOSX you have to install R and Rserve (see below!).

Linux and MacOSX Rserve (compiled for cooperative mode) installation:

To install Rserve open the R shell and then execute the menu action “Options -> Install Rserve (coop. mode) for R …” for different R versions. This will download an install Rserve in your default R library location, see video below (please make sure that your default Linux R library install location has writing permissions!). In cooperative mode only one connection at a time is allowed (which we want for this Desktop appl.) and all subsequent connections share the same namespace (default on Windows)!

Installation of Useful R Packages

R packages which are useful in combination with Bio7 can easily be installed with the R-Shell context menu “Packages” action:

R-Shell context menu->Packages->Install_Default_R_Packages

Bio7 Documentation

For more information about Bio7 please consult the soon updated Bio7 User Guide.

A plethora of Bio7 videotutorials for an introduction can be found on YouTube.

27.06.2018

In Bio7 R and Java code can be easily combined in the Bio7 platform. For instance to create Graphical User Interfaces in Java (with SWT or JavaFX), transfer image pixel/selection data from ImageJ and finally doing the analysis parts in R code/scripts which can be called from within Java (an easy to use API on top of Rserve in Bio7 is available, see, e.g., Groovy examples here).

However sometimes it is necessary to debug the Java language as part of such combined work. In Bio7 (based on Eclipse RCP) the very powerful Java debugging tools from Eclipse are available by default.

In addition in Bio7 it is possible to debug dynamically compiled Java classes in the same Bio7 process (using Java like a scripting language is a special feature of Bio7).

The video at the bottom of this page demonstrates the use of a remote debugging connection on the same computer (localhost connection) to debug dynamically compiled/executed Java code.

Debugging a Java process which has already started (Bio7 in this case) is only possible if Bio7 is started beforehand with the following Java arguments inside a shell to start a debug server connection:

Windows (started from the current directory = Bio7 installation directory):
Bio7.exe -vmargs -Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=8000

Mac (given the full path to the Bio7 executable):
/Applications/Bio7.app/Contents/MacOS/Bio7 -vmargs -Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=8000

Linux (started from the current directory = Bio7 installation directory):
./Bio7 -vmargs -Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=8000

Furthermore the compiler debug information option has to be enabled in the Bio7 Java preferences (for the dynamic compilation process) and a seperate debug connection has to be started for this Java class (with the available Eclipse debug configuration dialog).

In the video below I (hopefully) demonstrate how you can (graphically) debug a simple cellular automata simulation like the Game of Life within a running Bio7 (Java) process.

18.05.2018

The next release of Bio7 adds a lot of new R features and improvements. One minor change is that the default perspective after the startup of Bio7 now is the R perspective to emphazise the importance of R within this software.

The R-Shell view has been simplified and the R templates have been moved in it’s own simple view for an improved usability (see screenshot from R perspective below).

In addition the context menu has been enhanced to allow the creation of submenus from scripts found in folders and subfolders (recursively added) which you can create for a menu structure.
Scripts can be added created in R, JavaScript, Groovy, Jython, BeanShell, ImageJ Macros.
Java (with dependant classes) can be dynamically compiled and executed like a script, too.

Several improvements have also been added to the R-Shell and the R editor for an easier generation of valid R code. The R-Shell and the R editor now display R workspace objects with it’s class and structure in the code completion dialog (marked with a new workspace icon – see below).

R-Shell:

R editor:

In the R editor a new quick fix function has been added to detect and install missing packages (from scanned default packages folder of an R installation – has to be enabled in the Bio7 R code analysis preferences).

Also the detection of missing package imports are fixable (when a function is called but the installed package declaration is missing in the code but the package is installed to deliver the function).

The code assistance in the R-Shell and in the R editor now offers completions for, e.g., dataframes (columns) in the %>% operator of piped function calls:

In addition code assistance is available for list, vectors, dataframes and arrays of named rows and columns, etc., when available in the current R environment.

Code completion for package functions can now easily added with the R-Shell or the R editor which loads the package function help for both interfaces. The editor will automatically be updated (see updated editor marking unknown functions in screencast below).

Numerous other features, improvements and bugfixes have been added, too.

Bio7 2.8 will hopefully be available soon at:

https://bio7.org

Overview videos on YouTube