Bio7 2.0 for Windows Released!

December 1, 2014
By

(This article was first published on » R, and kindly contributed to R-bloggers)

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).

detachedviews

  • 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

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).

visualizationlib

  • 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).

windowbuilder

  • 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

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