Icy An open community platform for bioimage informatics

**Application**
* fixed a regression with ROI merge.
* small fix on ROI boolean operation button in ribbon.

**Application**
* fixed a regression with ROI boolean operations.
* small fix on application updater

**Application**
* Saver
- fixed FPS setting on AVI file saving
* Loader
- fixed small bug on multiple files loading
- fixed resolution level parameter which wasn't taken in account
* Canvas
- added `+` / `-` shortcuts to zoom IN / OUT in 2D canvas view
* ROI
- fixed ROI2DPoint / ROI3DPoint focused state
* fixed some issues with old internal HTTP address
* fixed invalid warning report on load
* fixed several issues with MacOS app integration
* updated Bio-Formats to version 6.11.0
* updated ImageJ to version 1.53r
* updated MacOS app launcher
* switched to Markdown for CHANGELOG file

**Developper**
* added new PluginScriptFactory interface for plugin providing ScriptEngineFactory
* cleaned up / removed some old useless classes.

Application
* Loader
- fixed unresponsive UI when loading large group of file
- improved performance on file group loading
- faster preview refresh
- fixed others smalls issues with file loading in general

Developer
* fixed a small bug where embedded sub class plugin couldn't be found in PluginLoader plugin list
* AbstractImageProvider: added InterruptedException + small fix on process interruption (we were removing interruption state)
* SequencePrefetcher: fixed incorrect InterruptedException handling
* SequenceFileGroupImporter: added 'ordering' parameter (when directly opening a list of file)

Application
* fixed a regression on signed byte image creation
* fixed possible memory leak on colormodel listener release
* updated Bio-Formats to 6.9.0 + added custom patch to fix ND2 file loading
* general better performance when dealing with many ROIs
* Loader
- fixed a bug making a new loaded image irresponsive in some situation
- better colormap restoration on group loading
- improved image paths parsing for image grouping operation
* ROI
- added shift modifier to link new created ROI to current T and Z position
- added Shift+T and Shift+Z shortcuts to attach ROI to current T and Z pos
- others smalls bug fixes and tweaks.

Developer
* added SequenceUtil.setDefaultColormaps(..) method

Application
* Viewer
- added current image name in viewer title
* ImageCache
- image cache can now be initialized and shutdown at runtime (better performance and better memory usage)
* Updater
- OSX: removed automatic native library signature
* System
- fixed and improved automatic bug report plugin detection
- re-introduced library path patching for Java version supporting it (still marked as deprecated but better to keep it when supported)
- added general 'interruptible' background process actions
- improved interrupted process handling
- small fixes for headless mode
- fixed exe launcher to accept Java 12 or above
- several bug fixes and tweaks.

Developer
* Image
- implemented proper ColorSpace sharing on IcyColorModel (not anymore using illegal reflection)
* ImageCache
- reworked image cache so it does not anymore require usage of illegal reflection
- better handling of volatile image on loading process
- removed Cache.isEnabled() method (higher level now)
- added Cache.clean() and Cache.isEmpty() methods
- improved Cache.end() implementation
* ROI
- fixed a small bug with ROIUtil.computeWatershedSeparation(..)
* System / advanced
- added ReflectionUtil.setFieldValue(..) methods
- added ClassPatcher.getField(..) and ClassPatcher.setFieldPublic(..) methods
- removed IcySecurityManager (deprecated with Java 14 or >)
- improved 'InterruptedException' throw / propagation and handling

Application
* 3D / VTK
- added new volume slicer tool
- tweaked default opacity
* Loader
- fixed loading non image files from Open command with 'All files' filter selected
* GUI
- fixed a minor viewer toolbar refresh bug when switching rendering mode
- fixed histogram log/linear display state restoration
- improved histogram info display to remain visible even when moving bounds
* ROI
- small optimization on 'Erosion' / 'Watershed' process time
* switch dataset to 'virtual' state asynchronously (as it can takes age to do so)
* fixed ImageJ / Icy image conversion switch
* improved Java 17 compatibility (replacing illegal reflective access where possible)
Still need some work to allow the image cache engine to work with Java 17
* small change to 'Updater' tool

Developer
* 3D / VTK
- added new VtkArrow/Cylinder/PlaneObject classes for easy drawing of these primitives.
* deprecated all illegal reflective access methods
* bit of refactoring / cleanup in project structure (moved all package.html file to 'javadoc' folder)

Fixed possible crash when interacting with ROIs during 3D visualization (VTK)

Application
* Loader
- fixed images grouping (could group image of different type or dimension)
* ROI
- added new 3D ROIs Rectangle3D, Cylinder3D and FlatPolygon3D which are Z extended version of ROI2DRectangle, ROI2DEllipse and ROI2DPolygon
* VTK
- upgraded VTK / 3D visualization library to version 8.0.1
- upgraded JOAMP / JOGL library to vrsion 2.4.0-rc (fix osx crash with VTK)
* general bug fixes
* fixed high resolution support on OSX
* fixed possible death locks on starting (happen only with certain OpenJDK and on Linux)
* allow illegal-access with Java 16 or above
* major rewrite of README file
* added CODE-OF-CONDUCT and CONTRIBUTING
* fixed links to LICENSE, CHANGELOG and README + tweaked About to redirect to the README.

Developer
* ROI
- added new 3D ROIs ROI3DRectangle, ROI3DCylinder and ROI3DFlatPolygon ROIs classes
- ROI3DStackEllipse, ROI3DStackRectangle and ROI3DStackPolygon are now deprecated
- added ROI2DShape getMinZ()/getMaxZ() methods for easier display evolution
- added base ROI3DZShape / ROI3DBoxShape abstract classes for easier 3D ROI implementation
- small fix to Polygon2D / Polyline2D and added getPoints() / setPoints(..) methods
- avoid throwing change event when not changed (bug touching ROIPolygon2D and ROIPolyline2D)
- replaced ROIUtil.convertToStack(roi) by ROIUtil.convertTo3D(roi) and updated ROIUtil.convertTo2D(..)
- fixed persistence (disabled Overlay persistence as ROI handle it by itself)
* VTK
- lot of changes / fixes to make it work with new VTK 8.0 and also fix all issues on recent OSX
* Overlay
- added base ZShape3D and BoxShape3D abstract classes.
- added new ZBoxAnchor3D, LineAnchor3D and RectAnchor3D classes to handle interaction with 3D objects / ROIs
* cleanup

Application
* Loader:
- fixed 'Drag and Drop' loading of multi series or folder dataset.
- ignore advanced metadata parsing for image format not supporting it (faster loading)
* Saver:
- fixed overwriting an opened image (image was locked by the Image cache so it couldn't be properly saved)
* ROI:
- added 3D ROI support to 'Separate component' ROI separation tool.
- added new Magic Wand tool and associated preferences.
- fixed global key action (unselect, delete and read-only mode).
* VTK / 3D visualization:
- added support for view synchronization.
* Preferences:
- added a section to set advanced settings for the new Magic Wand tool.
- reset cache / result path if they are not anymore valid.
* general bug fixes

Developer
* Cursor:
- fixed VolumetricCursor getter
* BooleanMask3D:
- added getComponent() method to retrieve connected component from 3D boolean mask
* LUT:
- added LUTViewer.getActiveChannelIndex() method to know which channel tab has focus
* Loader:
- added hasMetadata(path) method to know if dataset designed by given path supports metadata
* cleanup

Application
* ROI:
- added global selection and alphabetical sorting function on descriptors selector
- changed 'positive infinity' to 'ALL' value representation for size Z/T/C ROI descriptors (ROI table)
* Loader:
- small fix in 'base path' determination during stiched loading from a set of image files
* MetaData:
- better metadata preservation in general
- added 'User Name' information
- added 'Date' (dataset creation / acquisition date)
* updated Forum help URL (Image.sc)
* minors bug fixes

Developer
* Loader:
- added new openWith(path, flags, readerClass) method to select which reader to use (Bio-Formats importer)
- fixed a small issue preventing stitched loading using loadSequences(..)
* MetaData:
- added T,Z,C plane position fix in MetaDataUtil.keepPlanes(..) method
- added plane metadata preservation in buildMetaData() from group importer
- added MetaDataUtil.get/setUserName(s) methods to get/set experimenter(s) user name
- added new OMEUtil.createOMEXMLMetadata(meta, setUserName) method to define if we set the user name in the meta data
* Sequence:
- added 'user name' property (represent who created / generated the dataset)
* added new PETA / TERA prefixes to UnitPrefix class

Application
* fixed Windows launcher to not require JAVA_HOME variable to be defined.
* Sequence:
- fixed sequence filename when loading a dataset from a folder (regression)
* GUI:
- fixed support of custom ROI
- fixed a bug in ROI descriptor computation to avoid error on process interruption
* ROI:
- small optimization for .contains(..) and .intersects(..) methods
* Sequence:
- fixed timestamp metadata calculation (could generate problem when copy/pasting ROI)
* Updated Javassist library to version 3.27 to fix issues with recent Java.

Developer
* ROI:
- fixed id preservation on copyFrom(ROI) method
* Sequence:
- added getProperty(..) / setProperty(..) methods (as in ROI class)

Application
* Java 8 is now the minimum required version of Java.
* GUI:
- better headless support in general
* Metadata:
- better 'time interval' metadata retrieval
* Sequence:
- fixed fast crop operation (wasn't correctly considering ROI channel information)
* Cache:
- added option do disable cache (through command line)
* ROI:
- ROI2DArea now show its bounding box only when hovered or selected (better for visualization).
- added ROI dilatation / erosion operations
- added ROI distance map operation
- added ROI watershed separation operation
- added ROI unstack operation (convert 3D ROI to multiple 2D ROIS, one for each slice)
- added new 'Intersected' and 'Contained' ROI descriptors (number of intersected and contained ROI)
- added 'Internal id' ROI descriptor to retrieve internal ROI id (can be useful)
- fixed ROI table focusing on double click
- better handling of ROI descriptors process interruption (when switching or closing an image for ex)
- fixed BooleanMask for tiny ROI2DShape (single pixel)
- fixed area multi selection for ROI with channel position different from ALL
* Viewer:
- we can now loop in a timelaps using left/right keys.
- fixed pixel size of sequence rendering views (snapshots)
* Network:
- added option to disable network (through command line)
- ignore possible error on audit process
* Updater:
- fixed weird lockup on process execution error
* better recovery of parent / main plugin for 'Bundled Plugin'
* many others changes, tweaks or fixes

Developer
* project migrated to maven
* repository migrated to GitLab (Pasteur)
* cleanup up unused dependencies / libraries (they are now distributed as plugin)
* IcyBufferedImage:
- added IcyBufferedImageCursor class for easier / faster image data manipulation
- minor tweak on cache data management
* Sequence:
- added VolumetricImageCursor class for easier / faster 3D image data manipulation
- added SequenceCursor class for easier / faster sequence data manipulation
* Plugin:
- added static methods to extract native library files
- added getMainPlugin() method to retrieve Main Plugin descriptor (Bundled Plugin)

Application
* Canvas:
- faster and smaller memory footprint for screenshot for simple 2D image
* VTK:
- fixed colormap alpha restoration for 3D VTK canvas.
* Loader / Bio-Formats:
- fixed tile image loading.
- fixed duplicated data when opening several sequences at once.
- minor tweak to avoid using cache when not needed (better performance).
- minor change on data pre-fetch strategy.
* replaced micro character by 'u' to avoid incorrect display on non UTF-16 softwares
* updated online bug report to make it compliant with new web report.
* small fix in ROI table sorter.

Developer
- fixed MANIFEST.MF file containing an invalid character which was making Eclipse to crash.
- small tweak in XMLUtil.loadDocument(..) methods.

Application
* Loader:
- empty pre-fetch tasks on Sequence close.
* VTK:
- correct colormap alpha channel loading for IcyCanvas3D
* Search:
- general improvements on search engine (support +/- operator on keyword).
- switched online search to the new web interface

Developer
* fixed ROIUtil.convertToSequence(..) method to correctly generate labeled image.

Application
* Loader:
- fixed empty (black) image when opening multi-series Sequence (shared importer was closed)
- limited number of importer (reduce memory usage when the group contains many files)
* ImageCache:
- removed temporal images from the cache to not waste memory
- tweaked EHCache data expiration settings
- minor fix in GUI refresh
* Sequence:
- added simple data prefetch for faster initial data loading
- added getFilename(t, z, c) to get file path for image at given position when Sequence was loaded from multiple files
* added global layer enable/disable action (shift + L)
* fixed native library patching for Java 12 or above
* VTK:
- better error reporting
- minor tweak on VTK native library loading

Application
* new image cache engine.
* new packaging for easier installation on OSX system.
* GUI:
- added new Icy 'virtual mode' button to force the image cache engine to be used for all opened / created images.
- memory monitor now display image cache load level.
- Icy shows 'virtual mode' in title when image cache engine is forced ON.
- improved 'General' and 'Canvas' preferences presentation.
- added image cache settings in 'General preferences' section.
- added informations on image cache at startup.
- fixed position of Series selection dialog
* Loader:
- added lazy data loading for faster Sequence loading operation.
- improved preview display refresh.
* ROI:
- added 'ROI to Square' conversion.
- added 'ROI to Circle' conversion.
- small changes / improvements on ROI tasks GUI
* Viewer:
- timelaps are now in 'repeat' playback mode by default
- added 'SPACE' key shortcut to play/pause timelaps playback
* better background processing of some basic sequence operations ('Duplicate', 'Convert RGB', 'Convert Gray', 'Crop'...)
* minor speed improvement on application start
* added new splash screens
* many other small changes, tweaks, fixes and refactoring

Developer
* IcyBufferedImage:
- many changes to add image cache support.
- added lazy data loading support (for faster Sequence loading operation)
- added isVolatile() / setVolatile(..) method to enable/disable image caching.
- added isDataInitialized() / isDataLoaded().. methods.
- many others changes.
* Sequence:
- added isVolatile() / setVolatile(..) method to enable/disable image caching.
- added setDataXY(..) method (need to use it for image caching)
- changed the way channel bounds are updated (as data can be loaded on demand).
* SequenceUtil:
- fixed getSubSequence(...) method to work with volatile images.
- extractSlice(..) and extractFrame(..) now correctly duplicate original images data (should have been the case).
- minor fix on colormap update in utilities methods.
* Loader:
- added 'forceVolatile' parameter on some methods to force image caching.
- fixed possible Importer leak on error.
* Bio-Formats importer:
- fixed possible bugs during downscaled image/data loading
* ROIUtil:
- added convertToPoint(..), convertToEllipse(..) and convertToRectangle(..) methods
* DataIterator:
- updated to be compatible with volatile images.
* VtkUtil:
- minor change in getBinaryImageData(vtkPolyData, ...) method
* added FileUtil.getDrive(path) method
* added IcyFrame.getBorder() method
* fixed last ROIs objects retention when removing ROIS from an image while keeping the image open.
* added EHCache library.

Application
* ROI:
- fixed 3D VTK display for ROI2DPoint and ROI3DPoint
- tweaks for faster retrieve of default property value
* Saver:
- FPS is automatically determined from metadata (AVI format)
- added time interval field for easier FPS calculation (AVI format)
* Plugin: minor fix about plugin installation notification
* Network: audit methods cannot lock anymore Icy launch process.
* Minor fix on possible exception with the Clipboard.
* Other minors changes or fixes.

Application
* Loader:
- added series grouping when 'grouping' in enabled in Loader dialog
- added groupSeries(..) method to group similar series in an image
* Sequence: fixed series index reset after saving an image
* ROI:
- fixed 3D VTK display (correctly handling specific Z and T position of the ROI)
- fixed ROI Mass Center computation for single point ROI
* VtkCanvas:
- fixed layers refresh on position change
- fixed/better implementation of layers visibility
* Network:
- added warning message for HTTPS compatibility with the future web site
- fixed HTTPS support for future web site (when java version ok)
- replaced automatic redirection by manual (and safer) redirection
- better error handling in general

Developer
* Sequence: added getDataInterpolated(t, z, c, y, x) method
* IcyBufferedImage: added getDataInterpolate(x,y,c) method
* Loader: added groupSeries(..) method to group similar series in an image
* Line2DIterator / Line3DIterator: added forceLastPoint parameter.
* VtkUtil:
- added getJavaArray(vtkDataArray) method
- added getPolyDataFromDataSet(vtkDataSet) method
- added getBooleanMaskFromBinaryImage(vtkImageData..) method

Application
* Loader:
- fixed time position (timestamp) in metadata when loading sub part of sequence
- fixed a small bug in setting panel (couldn't change 'loading type' in some situation)
- fixed minor bug with possible invalid metadata when stitching was used.
- stitching disabled when 'loading type' is set to 'separate' (better implementation)
* Minor fix to update plugin processing (incorrect message report)

Developer
* Sequence:
- better metadata initialization
- added getPosition() method for fast XYZ position retrieving
- added getPositionT() / getTimeStamp() methods
- added getPositionTOffset(..) method
- added setPositionT() / setTimeStamp(..) methods
- added setPositionTOffset(..) method
* MetaDataUtil:
- added getPositionT(..) / getTimeStamp(..) methods
- changed getTimePosition(..) by getPositionTOffset(..) methods
- added setPositionT(..) / setTimeStamp(..) methods
- added setPositionTOffset(..) methods
* SequenceUtil:
- added convertPoint(..) methods for easy coordinate conversion between 2 Sequence objects
- added convertRectangle(..) methods for easy region conversion between 2 Sequence objects
* ROIUtil:
- rewrote adjustToSequence(..) method (better implementation).
* VtkUtil:
- added getROIFromBinaryImage(..) method to convert VTK binary image to ROI
- renamed method polyDataToImageDate(..) to getBinaryImageData(..)
- added getTransform(..) method
- renamed method objToMesh(..) to getSurfaceFromOBJ(..)

Application
* Several fixes and improvements on multi file loading
* Fixed updater to keep it compatible with Java 6

Application:
* fixed ImageJ issue on last OSX preventing Icy from starting.
* Search: 'Actionable' bundled plugins are not visible in search results.

Developer:
* added added Sequence.getROIs(Class roiClass, boolean sorted) method
* minor tweak/fix in MetaDataUtil.keepSingleSerie(..)tmp

Application:
- minors fixes and tweaks.

Developer:
* ROI2DArea / BooleanMask2D:
- added upscale() method for 2x up scaling.
- added downscale() method for 2x down scaling.
* ROI3DArea / BooleanMask3D:
- added upscale() method for 2x up scaling.
- added upscale2D() method for 2x up scaling (2D only).
- added downscale() method for 2x down scaling.
- added downscale2D() method for 2x down scaling (2D only).
* ROI:
- getProperty(..) / setProperty(..) property name is not anymore case sensitive.
* ROIUtil:
- added scale(ROI, ...) method (only work for ROI2DShape and ROI3DShape)
- added getUpscaled(..) method for 2x up scaled ROI.
- added getDownscaled(..) method for 2x down scaled ROI.
* Loader: fixed a minor bug on region image loading.
* Saver: fixed "origin" informations on saving operation
* Sequence: added resetOriginInformation() method

Application:
* GUI: reworked Sequence and ROI menu tasks.
* Loader:
- we can now select image series directly from Loader dialog
- some bug fixes in preview refresh
- fixed Bio-Formats sub resolution loading
- fixed some bugs in Bio-Formats importer
- preserve series information when using 'open sequence region'
* fixed colormap opacity (regression)
* better colormap preservation of some Sequence operations.
* now support HTTPS connection for plugin repository.
* OutputPanel: we can now set a maximum line limit
* several bug fixes

Developer:
* fixed IcyBufferedImage.toBufferedImage(..) method (regression)
* switched to OMEXMLMetadata class from 'ome' package when possible (refactoring)
* MetadataUtil: lot of refactoring (due to OMEXMLMetadata class change mainly)
* OMEUtil: some refactoring (due to OMEXMLMetadata class change mainly)
* added ImageProvider.getOMEXMLMetadata() method to use the good OMEXMLMetadata class ('ome' package)
* VTKUtil: added getImageData(..) method
* MainInterface: added getROIRibbonTask() method
* IcyCanvas: protected listener operations (add/remove/fireEvent)
* minor fix on ROI2DLine.setLine(..) method
* ROIActions: added fillInterior and fillExterior actions
* Sequence: some refactoring
* minor change in function ClassUtil.getFile(String className)
* minor fix in FileUtil.getFileExtension(..) method

Application:
* added new 3D ROI:
- 3D point type ROI.
- 3D line type ROI.
- 3D polyline type ROI.
- Ellipse 3D stack type ROI (available from stacking operation).
- Polygon 3D stack type ROI (available from stacking operation).
* ROI:
- more interaction with 3D VTK display (can move and modify the ROI)
- better and safer VTK rendering in general
- added 'to 3D stack' operation to convert 2D ROI to 3D Stack ROI.
- added 'to Mask' operation to convert shape ROI to Area ROI.
- added 'to Shape' operation to convert area ROI to Polygon ROI.
- added 'Separate' operation to separate unconnected object from an Area ROI.
- added 'ROI Cutter' operation to manually cut/separate ROI.
* ROI Panel:
- can now modify position / size of multiple ROI at same time.
- we can now quickly move view to a specific ROI location by double clicking on it (work in both way: from ROI panel or from the image).
- cleaned GUI:
- removed some ROI operations we usually do from keyboard (copy/paste, delete)
- moved some ROI operations to ROI band (load/save, boolean operator).
- XLS export button moved at the top of the ROI table.
* Image Loader (loader dialog):
- added Z and T range selection
- added channel selection
- added resolution level selection
- added 2D region (XY) selection
- improved preview
- better filename auto ordering
* Image Saver (saver dialog):
- removed Z and T range selection (better to do adjust range before)
- use big tiff when dataset is above 2GB
- setting are now preserved in XML preferences.
- image conversion is now automatically done when you use a save format which isn't compatible with the current image format.
A warning is displayed to inform the user about possible data loss.
* GUI:
- added a new tooltip to explain where is the main menu.
- added java 6 warning for OSX users.
- improved memory usage report in memory monitor.
- reorganized 'File & ROI tools' menu:
- added 'open region...' command to load a specific XY region of an image.
- re-organized the ROI creation actions.
- added many ROI operation actions (see the above 'ROI' and 'ROI Panel' sections).
* Canvas2D:
- reversed panning direction from keypad keys.
- image cache now use volatile accelerated image (image redraw should be much faster on some systems)
* VtkCanvas: improved overlay handling (should be a bit faster and safer)
* better metadata preservation on Sequence operation.
* sequence merging operations is now possible with Sequence of different type.
* ToolTipFrame: we can now clink on URL to open external browser.
* Updater: fixed local directory saving (it was saving in working folder instead of application folder)
* fixed wait for plugin update in headless mode.
* many bug fixes.
* several tweaks and optimizations.
* some code cleanup.

Developer:
* ROI:
- added 'group' field (will be use in future for 'group' ROI operation)
- added getLength(Sequence) method to compute length/perimeter with Sequence pixel size information.
- added getEffectiveDimension(..) dimension method.
- added unselectAllPoints() method.
- moved some methods to ROIUtil.
* ROI3D:
- added ROI3DPainter class for easier display and interaction for 3D ROI.
- added isOverEdge(..) method.
- added add(..), exclusiveAdd(..), intersects(..) and subtract(..) methods.
- added ROI3DShape: abstract class for 3D Shape ROI.
- added ROI3DPoint: 3D point type ROI.
- added ROI3DLine: 3D line type ROI.
- added ROI3DPolyline: 3D polyline type ROI.
- added ROI3DStackShape: abstract class for 3D Stack Shape ROI.
- added ROI3DStackEllipse: Ellipse 3D stack type ROI (available from stacking operation).
- added ROI3DStackPolygon: Polygon 3D stack type ROI (available from stacking operation).
* ROI3DStack:
- fixed setName(..) methods so children get modified as well.
- deprecated getUseChildColor()/setUseChildColor(..) methods.
* ROI3DArea:
- added ROI3DArea(BooleanMask2D, zMin, zMax) constructor.
- added isOverEdge(..) method.
* ROI5DArea: fixed a bug in optimizeBounds()
* ROI Overlay: drawROI(..) and drawName(..) are now public.
* ROIUtil:
- moved methods from ROI: getUnion(..), getIntersection(..), ...
- added convertToStack(..) method to convert 2D ROI to 3D Stack ROI.
- added convertToMask(..) method to convert Shape ROI to Area ROI.
- added convertToShape(..) method to convert Area ROI to Polygon ROI.
- added getConnectedComponents(..) to separate and retrieve connected components from an input ROI.
- added copyROIProperties(..) to copy properties from an input ROI.
- added split(ROI, Line2D) to cut/split a ROI from a given Line2D.
- added convertToSequence(..) method to convert a list of ROI to a labeled sequence.
* ROIDescriptor: added getDescriptor(descriptors, descriptorId) method
* ROIPerimeterDescriptor: modified to use the new ROI.getLength(..) method.
* BooleanMask2D:
- added getConnectedContourPoints(..) method to retrieve contour in 'connected' order.
- minor change to make it safer.
* added new 'geom' classes: Polygon2D, Polyline2D, Shape3D (base class for 3D shape), Line3D, Polyline3D
* Rectangle3D: added intersectsLine(..) method.
* Point3D:
- added many methods to compute distance, total distance, angle, normalize, length, dot product, cross product...
- added translate(..) method
- better hashCode() implementation.
* Anchor2D:
- added integer Z position information (for 3D position of 2D ROI)
- added VTK display and interaction support (allow ROI2D manipulation with VTK).
* PathAnchor2D: fixed visibility for closing point.
* added Rectangle2DUtil, Line2DUtil and Point2DUtil classes (utilities for the java classes)
* Sequence:
- added position X, Y, Z information (metadata)
- added 'origin' resolution, XY region, Z range, T range, channel information (when loading sub part of an image)
- added getOutputBaseName() / getOutputExtension() and getOutputFilename() to obtain wanted output filename given 'origin' informations
- trying to load too large array of data throw a TooLargeArrayException exception
* SequencePersistent: added isValidXMLPersitence(..) methods
* SequenceUtil:
- added getOriginPoint(..) / convertPoint(..) for point position conversion operation
- added getOriginRectangle(..) / convertRectangle(..) for rectangle position conversion operation
* IcyBufferedImage:
- trying to load too large array of data throw a TooLargeArrayException exception
- added copyData(array, ..) method to copy data from an array
* IcyBufferedImageUtil:
- added fast downscaleBy2(..) methods to quickly downscale image by a factor of 2
- changed toBufferedImage(..) method so it returns accelerated volatile image when possible.
* new 'undoable' operations:
- ROIReplaceSequenceEdit (replaced single ROI in a sequence)
- ROIReplacesSequenceEdit (replaced multiple ROI in a sequence)
- PositionROIEdit (modified single ROI position)
- PositionROIsEdit (modified multiple ROI position)
- BoundsROIEdit (modified single ROI bounds)
- BoundsROIsEdit (modified multiple ROI bounds)
- PropertyROIEdit (modified single ROI property)
- PropertyROIsEdit (modified multiple ROI property)
- Point3DAddedROIEdit (added a new point in a 3D ROI)
- Point3DMovedROIEdit (modified a point in a 3D ROI)
- Point3DRemovedROIEdit (removed a point in a 3D ROI)
* DefaultSequenceEdit: default undo operation on Sequence also preserve ROI and Overlays now (reference only)
* IcyCanvas:
- added canvasToImageLogDeltaZ(..) method, this is the Z equivalent to canvasToImageLogDeltaY(..) / canvasToImageLogDeltaX(..) methods.
- added centerOn(region) method for centering view on a specified image location.
* IcyCanvas2D: improved setMousePos(..) method to be safer.
* IcyCanvas3D:
- added methods to handle mouse (image) position.
- added imageToCanvas(..) and canvasToImage(..) methods (with default implementation to avoid breaking compatibility)
* Canvas2D:
- added getFitToCanvas() / setFirToCanvas() methods
- getARGBImage(..) now returns volatile accelerated image for faster image drawing operation (may consume more memory to prepare the image)
* VtkCanvas:
- added getWorldZ(Point) method to retrieve Z depth for a given 2D canvas position.
- added worldToDisplay(Point3D) method to convert a 3D world point to canvas 3D position.
- added displayToWorld(Point) method to convert a 2D canvas position to a world 3D point.
- implemented imageToCanvas(..) and canvasToImage(..) from previous added methods.
- implemented getScaleX/Y() methods.
- implemented setMouseImagePosX/Y/Z(..) methods.
- mouse event now provide a correct mouse position.
- removed the enable picking on Mouse Move switch.
* VtkUtil: simplified getSurfaceFromImage(..) method.
* IcyVtkPanel: added proper event consuming.
* Loader:
- added checkOpening(..) method to check we have enough resource to open an image
- added methods to load only sub part (Z, T and C) and sub resolution of the image.
- fixed issues while using Importer on non image files.
- many changes in general, new methods, refactoring...
* Bio-Format importer:
- added multi thread support.
- added tile loading for large image and sub resolution loading.
- better thumbnail loading.
* AbstractImageProvider / PluginSequenceFileImporter / PluginSequenceIdImporter:
- improved default getThumbnail(..) implementation
- added getImageByTile(..) method to load an image by tile (useful for large image)
* Saver:
- added many new methods to check compatibility image writing compatibility.
- reverted channel combination for 3 channels image saving in TIFF format (better for RGB image preview)
- methods doing Z/T range saving operation are now deprecated (better to do it before)
- added method getCompatibleSequenceForWriter(..) to automatically convert a Sequence so it can be save by a given writer (possible data loss)
- added SaverOptionPanel for easier setting definition
* SequenceDataIterator: fixed typo making some ROI calculations wrong in some situation.
* MetaDataUtil: replaced OMEXMLMetadataImpl class by OMEXMLMetadata in some methods (more generic, check if that bring issue)
* FileUtil: added getFiles(..) method to easily retrieve file with a specific extension without using a FileFilter.
* XMLUtil: added filtering to avoid incorrect character in name/attribute fields.
* SystemUtil:
- added getJavaVersionAsNumber() method
- getJavaFreeMemory() return the total amount of free memory available to the JVM
- getJavaMaxMemory() return the maximum amount of memory the JVM will attempt to use
- getJavaAllocatedMemory() return the memory currently *allocated* by the JVM
- getJavaUsedMemory() return an estimation of the memory currently *used* by the JVM
- getJavaTotalMemory() is deprecated (replaced by getJavaAllocatedMemory())
* ImageComponent: now use a cache for faster image drawing
* NumberTextField: added setInteger(..) method to force integer value instead of double value.
* ImageJUtil: added convertToIcyBufferedImage(..) method to convert a single image from an ImagePlus to an IcyBufferedImage
* IcyExceptionHandler: added anti spam protection for report(..) method.
* IcyCommandButton: added setPopup(..) method to enable popup action.
* RecentList: thread safe accesses, fixed possible NPE.

Application:
* fixed an issue when we tried to reload an image which has been saved after a Z slice remove operation.
* removed POI library from Icy-Kernel package (fix the infamous workbook error in protocol).
* other internals tweaks or changes.

Just some bug fixes here and there.