01.12.2014

A new Windows version of Bio7 is available. Many new features have been added to Bio7 2.0 which is now based on Eclipse 4.4. Highlights are the improved R editor, the R debugging Graphical User Interface (using the standard R debugger), the integrated Java Development Tools (JDT) to create Java simulation models with a powerful Java editor and the embedded JavaFX SceneBuilder to create embeddable GUI’s on the fly.

Here an overview of the new features:

R

• Updated R to Version 3.1.2
• Updated Rserve to version 1.7.3
• Rserve is now started by default within a R process in a pseudo-terminal in Bio7.
• The R pseudo-terminal can also be started without Rserve.
• If started only in the native pseudo-terminal some Rserve functions are not available (e.g. the plots will be displayed in the default R graphic device and not in ImageJ!)
• The R terminal and Rserve are now sharing the same process.
• If you switch from Rserve to the R native pseudo-terminal all R Objects will be preserved and vice versa (same process).
• Implemented a debugging GUI interface for the R debugger visible if a breakpoint in the editor has been set.
• Added two special debug views to the R perspective.

Video:

• If a debugging process is started Rserve automatically switches to the native connection.
• Added an interrupt action to the R-Shell and the R console to interrupt an R evaluation (Strg+c in the console).
• Added console actions to kill a native process and to kill a native R (Rterm) process if necessary.
• Created a new single preferences page for the plot setting .

R Editor

• Integrated an ANTLR R parser for the R editor.
• Created an editor outline from parsed R scripts.
• Added a format action (using “formatR” package if installed).
• Extended the code completions for the R editor.
• Syntactical errors are now indicated in the editor.
• Implemented code folding for functions.
• Implemented hoover actions for the editor (R help for e.g. a function).
• Improved the recognition of numbers in the R editor.
• Implemented a marker for matching brackets.
• Implemented a function to mark reoccuring words in the editor.

Video:

ImageJ and R

• Added a new action to transfer the values of the ImageJ “Results Table” to R.
• Improved the Particles action. Now the Particle measurements are transferred from the “Results Table” to R which means that now all values from a stack can be transferred, too.
• Added a new action to transfer all stack images of an opened stack (also from a nearly non memory consuming virtual stack) to R.
• A new option is available to convert the stack images to a RasterStack (if the “raster” package is installed).
• With this action it is also possible to transfer R,G,B values from all slices (images) of a stack, too.
• Improved the ImageJ image to R API to create matrices from transferred image values.
• Created an new API method to transfer particle analysis values programmatically.

ImageJ

• Improved the display. The default image layout now works better after a resize event.
• ImageJ tabs can now be detached like an image window (see below).

• Added some improvements for external ImageJ plugins.
• Updated ImageJ to the latest version.
• Added more image examples from the ImageJ website.
• The size of the “Image-Methods” view and the ImageJ toolbar dialog can be adjusted in the Bio7 preferences.

Table

• Improved the table editing in the “Table” view of Bio7. If you now edit a value and press the return key automatically the next cell is selected for editing (arrow keys for left and right, Tab key for selecting the upper cell).
• Now the table scales if you paste values or if you transfer vector values from R.
• The scrollbars now follow the location of the next edited cell.
• The sheet tabs handle is now located at the bottom of a sheet.
• The speed of the table component has been improved.

Video:

Java

• Integrated the Eclipse Java Development Tools (JDT) into Bio7.
• Now the JDT editor is the default Java editor in Bio7.
• Embedded the JavaFX SceneBuilder with its own perspective in Bio7.

Video:

• Embedded the SceneBuilder panels as Bio7 views.
• Created several new Java wizards to create Bio7 projects, JavaFX projects, etc. in Bio7.  They are creating a Bio7 JDT project with all necessary Bio7 classpath libraries. In addition a wizard for a WindowsBuilder project is available, too.
• Bio7 is now compatible with the most Eclipse plugins which can be installed with the Update Manager of Bio7 (see “General” section below).
• Improved the compilation which now can detect main classes organized in Java packages.
• Added a new action to fix the JDT classpath (also invoked if a Bio7 JDT project gets imported). This is necessary to recalculate the JDT library paths for a local Bio7 installation.
• Hid unnecessary GUI elements from JDT.
• Updated all scientific and custom Bio7 libraries.
• Integrated two new SWT libraries to create scientific components and components in general (Nebula visalization – see below, Opal).

• The Eclipse jobs API can now be used from within Bio7.
• Ported all Java examples to JDT projects and reorganized the examples.

WorldWind

• Updated WorldWind to version 2.0.
• Added an option to select the ImageJ image tab for WorldWind (nice if you want to render a film with ImageJ images).
• An RGB image can now have transparent alpha values (RGBA) which appear translucent if rendered on the globe.

HTML Editor

• Added some actions to the editor toolbar to add Knitr templates, links and images.

General

• It is now possible to install most of the available Eclipse plugins with the update manager of Bio7 (see below – Bio7 with WindowsBuilder installed).

• Reorganized the Bio7 preferences for a better usability.
• Created a new CSS theme for Bio7 (Eclipse Themes plugin for a custom theme can be installed, too)
• Addded a LaTex editor (Texlipse) to Bio7 for the use with KnitR and Sweave.
• Added toolbar actions to start the native consoles easier (R, OS Terminal, Python).
• If you switch from one console to another the process won’t be killed and you can resume a native session (R, Python, OS Terminal).
• Improved the layout of the “Control” view.
• Many Eclipse improvements like a split editor action are available by default (Bio7 is based on Eclipse 4.4)
• Many bugfixes and other improvements.

This release can be downloaded from the Bio7 website:

http://bio7.org

Documentation and videos tutorials can be found here:

Documentation (1.7.1)

YouTube Videos