Bio7 Changelog

What's new in Bio7 3.0.0

Mar 27, 2019

A new release of Bio7 is available which is built upon Eclipse 4.11 and the latest Java OpenJDK. This new version comes bundled with OpenJDK 12, supports the dynamic compilation of Java 11 and fixes several annoying bugs on MacOSX (e.g., shutdown crashes).
The R interface has been improved and the R-Shell now updates the workspace display automatically after a R code evaluation or R data transfer.
In additon for Bio7 3.0 the themes have been improved (especially for MacOSX and the Mojave dark mode) and some Touch Bar actions for MacOSX are available, too (if the MacOSX device has a Touch Bar).

New in Bio7 2.8.0 (May 30, 2018)

he 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.
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.
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.

New in Bio7 2.7.0 (May 30, 2018)

General:
Bundled with Java 1.8.52
Updated bundled R to version 3.4.3 (Windows)
Improved PDF rendering (PDF.js) with Java 1.8.52 (fixed rendering)
Updated the Windows SSH client
Simplified the dynamic java compilation
Updated the Java compiler infrastructure
Improved the context information when opening code completion (R-Shell and R editor)
Added an improved context information when openening code completion in the R-Shell
Context information of a function is shown when using code completion inside function calls
Added code completion for function arguments in the R-Shell
Added code completion help for ‘library’, ‘require’, ‘data’,’::’ and ‘:::’ functions in the R-Shell and in the R editor
Improved code completion for S3 and S4 nested attributes (e.g., x@y$z) also in function calls when cursor is set inside of a composite call
Implemented a code completion filter (when typing)
Added an option to select different key combinations for the R-Shell code completion (Strg+Space can already be occupied on MacOSX)
Added dark theme support for the help browser when opened from the R-Shell help (?)
Added a matching brackets selection action to the R-Shell view (Key+Mouse-click before opening or closing bracket)
Added an action to transfer the R-Shell history to an opened R editor (see R-Shell help (?))
The R-Shell and code completion fonts can now be changed and the size increased
The R-Shell is now faster if long text is printed (removed automatic text wrapping)
Added the Eclipse Spell Checking infrastructure to the R editor (can be enabled in the preferences)
Spell checking errors can now be fixed in the R editor (hoover action available)
Added a preference to enable/disable spell checking
Added a ‘Load packages tab’ in the ‘Packages’ view as an UI replacement for the Load packages dialog (improved usability)
Added an action to update the display list of installed packages (also triggered if you activate the tab)
Added an ‘Attached Packages’ tab to the ‘Packages’ view
Added an action to update all packages (‘Load Packages’ tab)
Improved the R-Shell code completion in general
Improved the hoover display layout (for warnings and errors)
Fixed several bugs (Reenabled loop parsing and fixed a bug to restore code folding after using code completion in the R editor!)
Updated ANTLR parser to version 4.7
Added „require“ for package code completion
Reduced the memory footprint of the R editor (OS handles)
Added missing roxygen tags for code completion of the R editor
Created a wizard to support a project template (default folders and files) for reproducible projects
Changed key binding of ‘<-‘ and ‘%>%’ operators to make them available in the R-Shell, too (see help in R-Shell)
Improved the “Evaluate Selected Line” Action for Rserve (Evaluated when successfully parsed!)
R Markdown editor:
Spell checking errors in the R markdown editor can now be fixed with a hoover action
Added a decent markdown parser (flexmark) to the editor which fixes some minor display problems
Added a format action for selected text to the markdown editor
ImageJ:
Updated ImageJ plugin to version 1.51.t16
Code completion (template) action now displays the macro documentation when typing
Code completion context information improved
Images from macros are now opened fast (before had a 2s delay because of a missing ImageJ attribute)
Cluttered MACOSX menus are now closed (added from opened application windows and frames). Some default added menus are disabled in the Bio7 preferences by default
Macros can now be executed within an external ImageJ instance in a separate Java process (if enabled in the preferences). Windows only!
Added Macro debugging context menus to the macro editor
Added an context actions to copy the Macro Recorder code to the current editor
Added an „Evaluate Line“ action
Reenabled CTRL+X as default „Cut“ text action.

New in Bio7 2.6.0 (Oct 19, 2017)

NEW FEATURES:
General:
Improved the dark theme for Bio7 2.6
Improved the theming of some Bio7 views (e.g., tables, text editors)
Added a new shortcut for Windows and Linux to show or hide the Bio7 main menus – CTRL(CMD)+2, CTRL(CMD)+3). By default the application frame, toolbar and the status bar can be hidden, too. (see screenshot below with hidden window and menu – set the key shortcuts in the preferences!)
Bio7 2.6 is based on Eclipse 4.7.1a
Added the ‘Project Explorer’ view to many perspectives and deleted the ‘Navigator’ view in some of the perspectives (the ‘Project Explorer’ view displays errors and warnings and supports pasting of clipboard Java code, etc.)
Added a break and interrupt action for the windows shell to end ,e.g., a ssh connection (CTRL+BREAK) or interrupt an ongoing shell process (CTRL+C)
Added an API to send commands to the Windows/Linux/MacOSX shell
Added SSH for Windows
Added the embedded SSH application path to the shell
Added a new ‘ImageJ Edit’ perspective to execute ImageJ scripts, macros side by side with the ImageJ-Canvas (see ImageJ section below)
Added a easy to use R API for Java/BeanShell/Jython/Groovy/JavaScript to execute R commands or scripts in an extra job (thread)
Improved several import/export scripts (now with Groovy) with the new Bio7 R API.
Improved the Linux shell (added the default xterm path)
The R package install script now works with a native R shell connection.
Shiny applications can now be tested from all folders (not only project folder – e.g.; from Git folders)
R EDITOR:
Added an action to surround selected code with a “try and catch” skeleton
Added an Project view/Navigator view popup action to start a shiny app in a arbitrary folder
Added an action to open and insert a hex color in the editor
Added a hoover dialog to display and replace selected hex and R colors
Added an action in the hoover dialog to select hex colors
Added an action in the hoover dialog to select default R colors by name
Added a new database view to the R perspectives to store or apply database profiles and connections
Added SSH support for the database view (also for Windows!). Bio7 comes bundled with the latest SSH version of Windows
Improved the code completion of the R-Shell
Improved the default R package install script for Bio7
Restructured the R editor context menu
ImageJ:
Added a full featured ImageJ macro editor with the following features:
Dynamic error detection (grammar derived from the ECMA grammar by Bart Kiers)
Toolbar action to execute ImageJ macros
Syntax highlightening
Editor debugging support (reusing and implementing interfaces and methods from – same keyboard shortcuts)
Code completion (with browser help)
Code templates (add you own templates)
Info popups (text hoover)
Outline view (var variables, variables, methods and macros)
Automatic closing of braces, parentheses and strings
Automatic indention of functions,loops, etc.
Code folding
Code formatting (based on the Eclipse-javascript-formatter by Sebastian Moran)
Resize fonts functions (with Ctrl++ or CMD++, CTRL+- or CMD +-)
Font preferences
Mark occurences (scope independant)
A copy function for the ImageJ forum
The ImageJ view menu is now right aligned and foldable to the left
Updated ImageJ to version 1.51r
Several bugfixes for the ImageJ compatibility

New in Bio7 2.5.0 (May 19, 2017)

General:
Bio7 is now based on Eclipse 4.6.3
Redesigned all Bio7 icons and created new icons, too
Nearly all icons are now available for high dpi displays
Added a dark Theme for Bio7
Added the default Eclipse theme as optional to Bio7
Added a new action for Linux and MacOSX to download and install Rserve (see Video in R section)
Added JavaScript editor support (default opened in text editor but if Eclipse JavaScript editor installed it can be opened and executed in the advanced editor)
Added a new action for the execution of JavaScript (and ImageJ macro)
JavaScript can be executed in the current opened browser if enabled in the preferences
Added JavaScript support to the console
Custom views are now entitled with the id of the view
Added a new „Document“ perspective for LaTeX, Sweave, knitr and rmarkdown documents
Added a new PDF viewer in the JavaFX browser to display PDF’s from LaTeX, knitr, rmarkdown and R plots („Display“)
Added options and actions to fullscreen a PDF on different monitors (press the key ‘t’ and the PDF will be centered and the toolbar will be removed)
Added several PDF options (scroll to selected page, etc.)
Added a new JavaFX browser for *.html and *.pdf files based on PDF.js
PDF files can be opened within the Navigator view with a double-click of the mouse device (also popular image types with ImageJ).
Added drag and drop support for the browser for *.html and *.pdf files
All editor fonts can now be scaled with the key combination ‘Ctlr +’
Added new global preferences for the editor fonts
Added preferences links for an improved navigation
Updated the default scientific Java libraries
Implemented a reload of the JavaFX Browser to avoid a cached display
Improved the resizing of the Quadgrid (Hexgrid) view
Added a new preference to disable the scrollbars of the Quadgrid (Hexgrid) view
Updated R to 3.3.3 on Windows
Added an action to download and install ‘Rserve cooperative mode’ for Linux and MacOSX
Improved the speed of the „Load packages“ dialog
Improved the speed of the „Install packages“ dialog.
Improved the speed of the refresh action in the R-Shell view
Added browser preferences to select the browser and the display
Added a new toolbar action for Sweave
Added an extra view for plots
Added the package install dialog as an view
Added an option to open a HTML package info for a selected package in the package install view (see video below).
Added a preference for a custom Rserve client connection port if you start the Rserve server with a different port
Added code completion in the R-Shell view for s3 and s4 methods (see video below)
Added an option to automatically open code completion when typing in the R-Shell
R-Shell R help now recognizes the selected browser
Added several actions to create, built, and test R packages to the context menu of the Navigator view (using the ‘devtools’ package)
Added a Shiny test action in the context menu of the Navigator view which opens a browser with the running shiny application (select a project folder with the server and ui files – to stop the server use the interrupt action in the R-Shell console or press ‘Strg c’ in the Console).
Improved the transfer of variables and sheet names from the Table view and LibreOffice
Improved the display of the R preferences (opening the default preferences structure)
R editor:
Improved the code completion in general
Code completion dialogs are now synchronized with the other dialogs
Added code completion for
S3 objects (after $)
S4 object slots (after @)
the library function (library())
the data function (data())
Added new individual images to the code completion
Improved the close parentheses functions
Improved the visual appearence of the hoover dialog
Corrected the code completion images to match the Outline view images
Improved the display of markers
Added a popup display for the ‚str‘ function when hoovering over a workspace variable
Fonts can now be scaled with the key shortcuts ‘Strg +’
Added automatic indention after parentheses (loops, function, etc.)
Added preferences for the formatR package
Added an formatR action to format editor selections only
Added a refactor rename method for a selected scope
Added roxygen code completion in comments
Added an action to create roxygen templates from selected function, S3, S4, Reference and R6 classes (see video below)
In the popup menu added several actions of the devtools package to create, test and install R packages (select a project or regular folder)
Added plot preferences to open plot images individually and an option to execute an ImageJ macro after plot creation (e.g. to scale a plot after creation, etc.)
Added an ‘Open File’ and ‘Save File’ dialog to create file templates with selected files in the R editor and the R-Shell view (see video)
Added a new shortcut to create an assign operator (‘ALT _’)
Added a new shortcut to create a pipe operator (‘CTRL SHIFT M’)
Added simple editor templates for S3, S4, Reference and R6 classes
Improved the preferences navigation
Reorganized some preferences
Updated the parser to ANTLR 4.6
R Markdown:
Improved the R markdown editor
Header and R chunks are now displayed in the Outline view
Added spell checking to the rmarkdown editor
Compiled documents are now displayed in a special custom view of Bio7 if enabled (by default enabled)
Added font and color preferences to the editor
Added new browser preferences (use of JavaFX webkit browser or system browser) and additional preferences for the control of the output
Added preferences to compile the document automatically after a specific time intervall (adjustable in the preferences – see video below)
Added code templates for popular markdown commands
Added an option to open word documents embedded in a custom view with Word (Windows only)
Added a key shortcut for the action to compile markdown documents
LaTeX:
Improved the compile actions in the Bio7 toolbar (new icon) and removed the popup actions in the Navigator view
Added a key shortcut for the compilation
By default Latex documents are opened in the new PDF viewer (custom view)
Added new Bio7 LaTeX preferences to compile documents easily (without the need to create a LaTeX project with Texclipse)
Added new preferences to optional use XeLaTex and cleanup auxiliary files in the project folder
Added an option to compile BibTeX along with the *.tex file (several compilation iterations are performed)
ImageJ:
Updated ImageJ to version1.51m
Improved the ImageJ menus to display all ImageJ menus correctly and nested (with key shortcuts and seperators)
ImageJ plugins now extend the respective SWT menu analogue to the ImageJ AWT menu.
Plugins, scripts and macros are now displayed in their defined menus or submenus.
Some popular image types can now be opened (double-click) directly from a Navigator folder (registered as a fake editor type)
Added two preferences to define the install location of plugins and macros (e.g external locations for teams).
Plugins now contribute to all ImageJ menus (SWT) like it is known from ImageJ
Dramatically improved the compatibility for ImageJ plugins (partially AWT)
Added a menu option to open images in a nested JavaFX panel (fullscreen on different monitors possible)
Addded JavaScript support for ImageJ (default editor is the text editor but a advanced Eclipse JavaScript editor can easily be installed)
Added a ImageJ macro wizard action to create ImageJ macros
Added an JavaScript wizard action to create a JavaScript file
JavaScript and ImageJ macros can now be executed with a toolbar (JavaScript) action.
WorldWind:
Updated WorldWind to version 2.1
Made improvements for the dark theme

New in Bio7 2.4.0 (Jul 19, 2016)

GENERAL:
Updated Bio7 to use Eclipse 4.6 (Neon) as RCP basis
Updated the embedded Java Runtime Environment to version 1.8.92
Updated embedded R for Windows to R 3.3.1
Improved the toolbar layout and action alignments (CSS can be edited!)
Added a new ImageJ R analysis perspective
rimagejpersp:
Added a new R debug perspective
Added a new and easy to use text preference field to execute Groovy script commands at startup (beside any scripts in the startup folder!) to open, e.g., a custom perspective, or startup R if enabled.
preferencestartup:
The Quadgrid, Linechart, Piechart and the Points view are now embedded in a Swt JavaFX panel and can be fullscreened (F1, F2, F3, F4, F5 – F1 key is Windows only!)
Added a terminate (Java controlled) and kill R process (OS controlled) action to the main toolbar of Bio7.
terninatetoolbar:
At R/Rserve startup a new check for a running R instance is executed with an option to kill all running R instances (to avoid a wrong connection to a running instance from an crashed Bio7 R session).
Added many new Bio7 R command key shortcuts
Added an install R packages script to install some useful default R packages for Bio7
R EDITOR:
The R editor has been transferred to it’s own Github repository and can be updated as a plugin
Improved and formatted the display of the error messages
Improved massively the speed for parsing and marker creation
Added many new R editor key shortcuts to speed up editing
Added an action to the context menu to open the plot preferences
Added an action to the context menu to open the font preferences
Added a RServe formatR action to the context menu
Added a Profile script action for the profvis package to the context menu
Added a Profile script selection action for the profvis package to the context menu
Added a color dialog to the context menu. A selected R,G,B color will be displayed and set in the editor
Added an “Reload Package Completion” action to the context menu to load completion help for loaded packages (decrease warnings by known methods, increase available code completion templates – The same action is available in the R-Shell view evaluation textfield).
contextRmenu:
The Load/Remove packages(s) dialog has a new action to transfer available selected package names to the R editor (as ‘library(package)’)
Now warnings and errors are displayed more consistently. If a quick fix is available it will be indicated with a warning/error quick fix icon instead of a default warning/error icon
Added new quick fixes to the R editor
Quick fixes and warning messages can now be displayed and fixed by hoovering over the underlined editor marker
Added the automatic close of {braces}, (parentheses), [brackets], “strings” and ‘strings’. It can be disabled in the preferences
Improved the speed of the ‘Mark selected word’ action (scope independant) which can be enabled in the preferences
R editor refactoring:
Added an ‘Extract Method’ action which parses and extract a method from a selected text if valid
refactordialog:
Added an ‘Extract Variable’ action which parses and extracts a variable from a selected text if valid
Added a ‘Create new File from Clipboard’ action which parses and creates a new file from the clipboard text if valid in the project folder and opens the R file for editing
Added an ‘Extract Editor Selection to File’ action which parses and creates a new file from a selection if valid in the project folder and opens the R file for editing
R EDITOR CODE ANALYSIS:
Added an analysis function to detect Unused Functions
Added an analysis function to detect if a function is available
Added an analysis function to detect if a variable is used
Added an analysis function to detect if a variable is available
Added an analysis function to check for wrong constants (na, true, false, null)
Added an analysis function to check for functions if a function (or variable) with that name is already defined
Added an analysis function to check for variables if a variable (or function) with that name is already defined
Added an analysis function to check if a function call argument is missing
Added an analysis function to check if a function call has to many arguments
Added an analysis function to check if the name of a variable assignment in a function call is wrong
Added an analysis function to check a function call with parameter on a parameterless function
Added an analysis function to check variables in function calls and square brackets
Added options in the preferences to enable/disable the code analysis functions
R Outline View:
Added the display of loop variables to the outline view
Added the display of function call variable assignments to the outline view
Added the display of S3,S4, References and R6 classes to the outline view (S3 classes are only detected with class(x), References classes and R6 classes functions are not displayed nested!)
R editor code completion:
The sorting of the code completion dialog has been improved
The code completion dialog now displays local defined variables and methods available in the current scope
Added a new function in the code completion popup dialog to open the template preferences faster
codecompletionvar:
If the code completion is opened in a method call the arguments of the function will be displayed in a new table dialog. However if an function or variable is started within the method call the regular code completion is shown (for nested functions or variables call)
codecompletioninfun:
Added two actions in the hoover help dialog to open the help browser (?) or search in the Rdocumentation website
hooveractions:
The code completion dialog can now be configured in the preferences to open automatically on key typing (number of typed chars and chars can be configured, too).
R-Shell view:
The R text is now validated with the Bio7 default R code parser
Added an error marker to the textfield if a parsing error occurs
Added code completions to the evaluate expression textfield (Ctrl+Space). Code completion is only available in nested calls after open parentheses
rshellparse:
A help file browser can now be opened from selected text (e.g., nested function).
Native connection commands can now be executed in the evaluate expression textfield
R Markdown:
Now JavaScript is enabled for the HTML-Browser by default
Added a new option to scale the JavaFX browser content if enabled (handy for R markdown presentations). The JavaFX browser can be fullscreened (F1,F2,F3 – secondary monitor…..)
Table view:
Improved massively the speed of the close operation of a table sheet
Improved the CSV importer with more options to import data with a dynamic preview
The CSV importer now accepts clipboard data if selected
The preview table is now updated dynamically if changes occur
ImageJ:
Updated ImageJ to version 1.51d
Added a subset of ImageJ2 libraries in a new ImageJ2 Eclipse plugin
Improved the ROI image pixel data transfer methods. Now selected ROI’s pixels are transferred. If no selection is available all ROI‘s will be transferred!
The ROI transfer methods now also accept points and lines (please note that line pixels are interpolated in the ImageJ results table by default)
The Bio7 ImageJ plugin can now be updated or installed individually
ImageJ panels can now be opened in a JavaFX panel embedded in SWT (experimental) if enabled in the preferences
Other:
Updated all Java libraries
Update the JavaFX SceneBuilder to version 2.2
The JavaFX SceneBuilder controller class created variables and methods are now ‘public’ by default.
Added support for LibreOffice 5. Now the Bio7 LibreOffice functions work again with LibreOffice 5.

New in Bio7 2.3.0 (Sep 2, 2015)

Updated R to 3.2.2 (Windows).
Added new R Markdown functionality – see video below (installation of ‘rmarkdown’, ‘knitr’ package and ‘pandoc’ binary required)
Added an option to use the JavaFX browser to open HTML markdown knitr documents to allow a fullscreen view (primary F1,F2, secondary F3, tertiary F4, quartary F5 monitor).
Added a simple default markdown editor to Bio7.
Added a new wizard for markdown documents.
In the ‘Navigator’ view you can now set the working dir of R (context menu action).
Added a new convert to list action in the context menu of the R-Shell.
Added a new default hidden „Custom“ perspective“ in which custom views can be opened in a predefined layout.
Added two new actions to open Bio7 views more easily (as a replacement for the disfunctional open view actions).
Improved the ImageJ ‘Zoom In’ and ‘Zoom Out’ action (now zooms correctly to the mouse pointer).
Improved the default paths for Linux and MacOSX.
Now the R system path, the R default library path and the pdflatex path is fetched from the PATH environment (as long as no specific location is set in the Bio7 preferences ).
Improved the installation of Rserve on Linux and Mac with precompiled Rserve libraries which can be installed easily from within R (R version 3.2.2 required!) .
Compiled Rserve in cooperative mode for MacOSX and Linux. This will make the installation process of Rserve very easy.
Deactivated some R editor options by default (can be enabled in the R preferences).
HTML GUI editor:
Mouse selection now works again (thanks to Java 1.8.60).
ImageJ and R:
Changed the variables names for the size of the image in the Particles transfer to ‘imageSizeX’, ‘imageSizeY’ (to be in accordance with the image matrix transfer).
Improved the ‘ImageMethods’ view ‘Selection’ action (see video below). Now it is opened as a view for multiple transfers.
Added new actions to transfer ImageJ selections as SpatialPolygons, SpatialLines or Spatial Points (or SpatialPolygonsDataframe, etc., if an available dataframe is selected). Selected objects can be transferred georeferenced if a georeferenced raster file (*.geotiff) is selected
Java:
Updated Java to Jre 1.8.60
ImageJ:
Updated to version 1.50.a

New in Bio7 2.2.0 (Jul 7, 2015)

New in Bio7 2.1.0 (May 20, 2015)

Updated R to version 3.2.0.
Improved the R perspective layout
Improved the syntax coloring and grammar (assignment, multiline string, infix operator for package ‘data.table’)
Improved the layout of the R-Shell view for higher dpi’s
Added code folding for ‘if’,’while’, ‘repeat’ and ‘for’ expressions.
Added options to enable or disable codefolding, code context (mark words, info popup) and code completion.
The line numbering of the R editor is now enabled by default.
Improved the “Install package(s)” GUI and other dialogs.
ImageJ:
Updated ImageJ to 1.49t
Added Bio7 ImageJ preferences for special dialogs to stay on top (ROI Manager, Results Table, Macro Recorder)
Added extra action panels for the histogram and profile plot to enable the new ImageJ actions
Resized the layout of the ‘ImageJ-Toolbar’ and ‘Image-Methods’ view.
Improved the compatibility for the 3D viewer plugin and the OMERO (The Open Microscopy Environment) client.
Added options to resize and store the dimensions of the ‘Image-Methods’ dialog and the ‘ImageJ-Toolbar’ in the preferences.
Added more tooltips for context information.
WorldWind:
Improved the layout for the different actions and layers.
Added an option to load a GEOTIFF image data parallel in ImageJ when added as a layer to WorldWind.
Added an easier to use alpha value function for transparent image regions
Greyscale and float images can now be displayed as RGBA if enabled (tranparent regions).
Added a ‘Location’ action for loaded shapefiles.
Improved the GDAL loading. Now GDAL (Java) can be called from within Bio7 dynamically.
3D:
Improved the layout and actions for the different 3D panels.
Python:
Added Py4J library for the communication between Java and Cpython.
Added a server start/stop action for Py4J available in the Scripts menu.
Added a Py4J example (ImageJ measurement) in the Bio7 documentation.
As an alternative you can now install the Eclipse Python editor PyDev and execute the python script within the Bio7 connection or in the PyDev editor process.
Added support to eval Python3.x scripts (can be enabled in the preferences).
Bio7 GUI:
Improved the startup layout for Bio7. The application now starts maximized.
Increased the Bio7 splashscreen.
Java:
Updated the embedded Java Runtime Environment to 1.8.45.
Updated the integrated JavaFX SceneBuilderKit.
Added support for Java3D built on JOGL.
Added a default ‘close’ action in the base (abstract) Model class.
The ‘close’ method is called automatically if a custom view is closed.
Examples:
Added and fixed some examples for Bio7

New in Bio7 2.0.0 (Dec 2, 2014)

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.
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.
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.
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.
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.

New in Bio7 1.7.1 (Nov 4, 2013)

New in Bio7 1.7 (Nov 4, 2013)

Updated RCP platform to Eclipse 3.8.2
Custom views can now be created with ID’s for Custom views inside of Bio7.
Updated ImageJ
Updated R
Updated Rserve
Changed the OpenOffice API and actions to LibreOffice
New file wizards available (Jython, Html, Knitr, JavaFX, etc.)
Removed the BeanShell menu
Removed the BeanShell console (now available as part of the Bio7 console)
Extended the console of Bio7
Added Console options and typical commands
Added console text options
Integrated a new webeditor (JavaFX) which can be opened as a regular editor in Bio7
Added new libraries for the support for e.g. serial communication (useful for Arduino boards)
New examples available (serial examples, Jython, Multiple classes, etc.)
Added native shell access to the Bio7 console
Added command templates to the shell menu
Improved R console messages
Updated embedded scientific Java libraries
Now an Bio7 editor can add code snippets from selections to the Snippets view
Rearranged the Image-Methods view
Improved the Linux R output
Startup scripts are now interpreted by Groovy for a custom startup of Bio7 (if enabled in the preferences)
Added some new API methods (e.g. function to write to the new console).
Rearranged and renamed some preferences for an improved overview.
Added editor menus for the language specific preferences.
Cleaned up the popup menu in the Navigator view and removed old BeanShell actions
Native Python execution from the shell, Jython editor and the Flow editor can be enabled in the Bio7 preferences
Native R execution from the shell, R editor, some R actions and Flow can be enabled in the Bio7 preferences
Updated all native execution methods to use the recommended ProcessBuilder for Java >=1.7.21
Resolved and fixed bugs
Added preferences for Python, R and Blender to execute native R, Python, Blender Python scripts if enabled in the Bio7 preferences.
Added default options for Python, Blender and R.
Added new examples for Bio7 1.7
Java:
Dynamic compilation support for multiple Java classes and subclasses
Compilation to *.class files is now supported for multiple Java classes
If a *.class is selected and a main method is available it can be executed with a new action in the context menu of the Navigator view.
Error indication support for multiple classes
Drag and drop support for full classes stored along with grid definitions
Added a new option to compile Java classes or classbody files in the Bio7 preferences
JRE ext directory can be used to extend the Java classpath with external Java libs
JavaFX support for Bio7
*.fxml files can now be created in the Bio7 workspace (along with a main Java file and a Controller file for the free available JavaFX Scene Builder from Oracle)
Support for JavaFX Java source files
JavaFX Scenes can be embedded into custom views
Fullscreen support for JavaFX views (F1 = Fullscreen, F2= Fullscreen frame, F3=Fullscreen frame secondary monitor, F4= Fullscreen frame tertiary monitor, F5= Fullscreen frame quartiary monitor)
If Fullscreen is activated an info message appears in the view which is in Fullscreen mode.
Java files and subfiles can be instantiated and packages will be recognized, too (only if the file is opened in the Java editor and compiled with the editor action. Compilation from the context menu is available, too (without package recognition!)
New Java wizards available (JavaFX, etc.)
The main class of a Java project (which possible consists of multiple dependent subclasses) can be dragged in the Flow editor for execution.
Added an action to compile multiple Java classes (context menu Navigator view)
Added several compiler options to the Bio7 Java Preferences
Added an editor context submenu to open the Java preferences faster
The Constructor of a Java file is executed after compilation if available.
If a main method of a regular Java class is available (not extending the Model class of Bio7!) it will be called after the compilation and instantiated.
Scripts:
Extended the default console to accept input for different Script interpreters
BeanShell, Groovy and Jython commands can be evaluated in the new console
Added a function to show a history of past commands (arrow keys)
Bio7 now supports the Jython interpreter
New Jython editor available
Added new icons for the different editors
Removed the old BeanShell console
Removed the old BeanShell menu in the main menubar of Bio7
Jython scripts can now be evaluated in the Flow editor
Jython scripts can use the Bio7 API
New file wizards for the different scripting languages available
Python scripts can be executed if the native execution is enabled in the Bio7 preferences and the path to Python has been specified in the preferences
Blender Python scripts can be executed if the native execution is enabled in the Bio7 preferences and the path to Blender has been specified in the preferences.
Knitr support to compile knitr files (*.html, *.latex, etc.) in the Navigator of Bio7
Knitr support in the Flow editor of Bio7 (for example to generate a report of simulation results,)
Plots can be created interactively with the shell or the editor and are opened in ImageJ (as a plot display)
New option in the Bio7 Rserve preferences to change the definition of the default plotting device.
Added a new option to start Rserve automatically after Bio7 startup
Experimental support to activate plots (Keys: Alt+a) in a blocking job as long as plots are opened (the R script for this functionality can be accessed and if necessary improved).
Support for the interaction with commands (Windows) which require console commands (e.g. scan() – if the console requires input the textfield will be marked with a different color).
Faster „Image“ plot in the plot section of the R-Shell view.
Added a custom menu for scripts (R, Groovy, Jython, BeanShell) in the R-Shell view menu . Scripts which can be dropped in a special Bio7 folder
Added a submenu in the context menu of the R editor to open the R preferences faster
Added R package skeleton action in the context menu of the Navigator view to create R packages (with Rserve).
Added R package built and install actions (with the native shell).
Added R action to create *.pdf files out of *.Rd files (with the native shell)
Added options in the Bio7 preferences for the built package commands
Added native R access without the necessity to use Rserve. The editor, the shell and the Flow editor can be used with this new feature.
Added fast workspace transfer function (F1-Key) from Rserve to the native R workspace
Added Drag and Drop *.Rdata file feature for the native R access.
Added Bio7 preferences options to enable the use of the native startup of R.
Added R and Rserve startup arguments in the Bio7 preferences.
Added a submenu in the packages tab of the R-Shell view to refresh the view of available packages.
Rearranged the R perspective and added the Editor Area, FileNavigator and Console view (ImageJ will be opened, too if a plot command occurs, see images below)
If a plot command occurs the ImageJ-View will be opened with the plot as a default plotting device.
R – ImageJ:
Added a new method to transfer multiple selections from all or selected slices of a Stack
Splitted the pixel selection transfer action into two different actions for a better usability.
Improved the Particles transfer method. Now uses the default ImageJ options.
Points view:
Points panel is now updated when Reset field action etc. is pressed.
Webeditor:
Added a new web editor with source and GUI support (the GUI part uses the JavaFX web editor)
Webeditor is now a regular Bio7 editor
New file wizards available to create *.html files along with *javascript files
Added action in the GUI to open the created file in the system web browser
Flow editor:
Gridsize for the layout can be configured
Flow editor can now execute Jython scripts
Flow editor can now execute either native python or Blender python scripts (if enabled in the preferences)
Flow editor can now execute knitr *.Rhtml reports
Flow editor can now execute knitr *.Rtex reports
Flow editor can now execute a Java main class (dependant subclasses will automatically compiled, too)
Improved the warnings for the access of the WorldWind API (if the WorldWind view is not active).
Updated WorldWind to version 2.0 (using JOGL 2.0)
Added a function to capture an animation to an ImageJ stack in a Bio7 job.
Added options to adjust the framerate and the amount of frames to be rendered.
Added WorldWind GeoTIFF import (coordinates will be set to the textfields)
Added a „Go to” function for the GeoTIFF
Added a first WorldWind Shapefile import
3d View:
Updated OpenGL library to JOGL 2.0
Updated all Bio7 OpenGL examples to be compatible with JOGL 2.0
Bug Fixes:
Improved overall stability
Fixed memory bugs with SWT