RELEASE_NOTES.txt

MUSICardio 4.0.7:
- PolygonROI:
    * fix drawing a contour with shift-click to be able to change zoom/contrast with click.
    * fix removing a last contour/node which reset the label tool and allow to draw again.
- Registration step in pipelines allows to use Mouse Interaction Toolbox.
- VOICutterToolBox fix a crash with metadata in pipelines sometimes if a cut has been made.

MUSICardio 4.0.6:
- Debug import of Carto .zip archives and .mesh files.
- PolygonROI: remove shift-click to draw, fix contrast after deactivation of repulsor and hide deactivated widgets.
- Pipelines: 
    * put back the possibility of closing layers at result steps,
    * fix VOICutter if no segmentation is done,
    * fix Histogram Analysis non manual algorithms.
    * fix pipeline crash when saving data.

MUSICardio 4.0.5:
- Allow to use data with different size or spacing in LCCLogDemons and DiffeomorphicDemons.
- Manual Registration: enhance landmark numbers for better user understanding.
- Fix Histogram Analysis width problem displaying multi-results.

MUSICardio 4.0.4:
- Fix some plugins wrongly loaded on Windows.

MUSICardio 4.0.3:
- Switch to Ubuntu 22.
- PolygonROI: update icons, fix a glitch when users change ROI label, hide label panel in pipelines.
- Histogram Analysis: enhance memory management and remove useless computation.
- Pipelines: correct arithmetic filters computation. 

MUSICardio 4.0.2:
- Fix drawing problem in pipelines with custom step of PolygonROI.

MUSICardio 4.0.1:
- Fix Python module installation bug on macOS.
- Fix Real Time compilation on Ubuntu/Fedora/macOS and Windows.
- Fix a pop-up problem with wrongly imported pipeline scripts.

MUSICardio 4.0:
- Put back the Pipelines workspace.
MUSICardio 4 provides its own embedded Python 3.10 interpreter. This facilitates the development of Python scripts and components within the application. 
A Python console and plugin API will be added in an upcoming version. Contact us at music-dev@inria.fr to discuss how this Python integration can help you.
Check the Pipelines documentation to see if your scripts need to be updated: https://music-test.inria.fr/musicardio/ in Development menu, or you can ask the team to help you.
Main change: switch "from medPipelineObjectWrapper import *" and "from medPipeline import *" to "from mscPipeline import *".
- Toolboxes in the application have been updated to fit the new Pipelines system.
- We worked on the stability of the application concerning database connections and memory leaks.
- Fix Paint toolbox widgets when the user switches from Paint/Erase to Magic Wand or clear the view.
- Fix a freeze in PolygonROI toolbox if the user contours outside the image borders.
- Fix the "clear" button to effectivaly clear the view.
- Stop some toolboxes compatible with 3D data if the user is using 4D data.
- Small enhancement of the GUI of Histogram Analysis, and debug a crash leaving the toolbox without creating containers.
- Video: default frame rate a 24.
- DICOM: handle if the origin is missing.
- Switch to Fedora 37.

medInria 3.4:
- Fix an incorrect zoom for some data displayed in a view. The zoom is now calculated with x and y dims, and not z
- N4 Bias Correction process can stop now if the user wants to quit the application, it will stop at some algorithm checkpoints
- Reslice toolbox: changing the dimension of spacing parameters does not zoom one of the views
- Paint toolbox: the first click on the view quickly displays the drawing, instead of waiting for the mask to be created
- Update loading window logo at application start, and speed up the start removing text display
- Fix a bug with inrimage data type
- We have done some work to avoid memory leaks to get a more stable application
- Solve some graphical problem with settings widgets
- Add a setting in Browser to deactivate or activate the computation of thumbnail at import. Deactivation uses less RAM, if needed
- Avoid a crash importing wrong version of VTK files

MUSICardio-LITE v3.3:

Information:
- The application has a new name: MUSICardio
- MUSICardio core is now on medInria 3.3 and includes all its new features and fixes
- MUSICardio 3.3 is a LITE version which do not include the pipeline system. We will release a future version with the pipelines system and a wide use of Python
- MUSICardio 3.3 is compatible with Ubuntu 20.04, Fedora 33, macOS 10.15 and Windows 10
- Concerning the Non Local Means plugins, users are asked to use the plugin directly from the medInria binary: https://med.inria.fr/ for now

Fixes and enhancements: 
- Solve a crash in Convert Mesh To Mask with empty landmarks
- Solve a crash closing layers in CatheterManagerToolBox
- Fem inverse problem: add Finite Element Method to solve inverse problem
- Fem inverse problem: possibility to choose different conductivity depending on the zone
- Fem inverse problem: add open MP loop
- Add Boolean operation toolbox: compute the difference, the union or the intersection between 2 meshes
- Add MinThickness toolbox: impose a minimum distance between 2 meshes. The second mesh is modified to impose this distance moreover 
this minimum distance is apply only on specified (label) part of the mesh
- Solve a bug in DataInterpolation switching from a map to a mesh
- Plot tool: add interpolation button
- MeshInteractor: automatic change of selection mode when attribute changes
- EP maps: Carto Reader now reads zipped archives, and read the header to determine if it's a CARTO file or not
- Add DICOM export plugin
- Add DICOM Rt Export plugin: write DICOMS that are compatible with Varian Eclipse RT planning suite
- Add MaskToRtStruct toolbox, a toolbox that exports masks to DICOM RT structures
- EP map: fix Rhythmia study import (out-of-bound reading and writing in some cases)
- Mesh Utility: bug fix + improvements, uses robust algorithm provided by tetgen for triangle-triangle intersection, mesh consistency check, etc
- Catheter: support new ablation message, improve undo calibration Point, calibration's Tag management is simpler to use
- Add Radiotherapy planning workspace
- Add Transmural Paint: experimental toolbox that creates transmural masks from painted (or selected in any way) cells on the epi mesh
- ApplyTransform toolbox: catheter electrode and sensor positions are now transformed
- Coronary Segmentation becomes Vessel Segmentation
- Solve crashes in Channelness and Laplacian toolboxes with wrong input data 

medInria 3.3:
- Fix mirrored DICOM images problem
- Fix a bug in Paint toolbox with Retina screens
- Clear some toolboxes view when the user switches to an other one
- Add vtu reader and writer for mesh of type unstructured grid
- Check the version of the vtk file to avoid crash due to the new format introduced in vtk 9
- ManualRegistration, avoid duplication in outputs
- Reslice, solve crashs after removing a data in view
- PolygonROI, solve graphical/ergonomy pb and crashes (split, clear)
- Variational Segmentation: enhance GUI, solve a spacing error on output masks
- BUGFIX 3.3.1: [Four-views] solve crash closing the views
- BUGFIX 3.3.2: 
    * Avoid corruption of exported/imported dcm with odd axis
    * Fix errors with view tabs if the user switch 2 of them, or remove some of them

medInria 3.2:
- Add some tooltips in view navigator
- Avoid crashes if you try to open fibers data in some toolboxes
- DICOM: keep more metadata
- Remove the Generic Workspace, you can use the many existing workspaces, or create your own easily if needed
- Fix a bug where, if there is a volume and a mesh in the 2D view, changing the LUT of the mesh would also change the LUT of the image
- Fix a bug double-cliking in Polygon ROI
- Scenes: add an import and export functionality, to save the view and your parameters
- Video Export: add the export of a view as .ogv [or .mp4 possibility] or batch of .jpeg. By time, rotation of a mesh or slice

medInria v3.1.1:
- Viewer optimization: opening data is quicker, debug a window/level lag
- The annotation cube can be hidden in 3D view
- Solve some annotation text problems
- DB: remove a bug in the creation of the series
- Fix DICOM import bug with special characters
- Solve SH data image, and 4D image bugs
- PolygonROI segmentation labels enhanced
- Tools button icon, allow opening data in fix views
- Plugins from Asclepios in medInria repository
- Fix Retina screen problems with segmentations
- Registration - fix LCC Log Demons transformation crash
- Registration - put back name in undo-redo tool
- Improve 3D rendering behavior
- Add a DICOM exporter

medInria v3.1:
- Switch ITK to version 5.0.0
- Switch VTK to version 8.1.2
- Create Meshing workspace with 5 toolboxes: Create Mesh from Mask, Mesh Manipulation, Mesh Mapping, Remeshing and Iterative Closest Point
- Create Reformat workspace with 2 toolboxes: Cropping and Reslice
- Filtering workspace becomes Filtering dtk2
- Create Filtering workspace with 5 toolboxes: Binary Operation, ITK Basic Filters, Mask Application, Morphological Filters and N4 Bias Correction
- Segmentation workspace, add new toolboxes: VOI Cutter, Variational Segmentation and Polygon ROI
- Registration workspace, add a new toolbox: Manual Registration
- Paint toolbox in Segmentation is updated, can do region growing algorithm
- A log system has been added, you can find the log file on homepage -> Logs
- Histogram in views Tools button
- Possibility to open a study, dropping it in a view
- Reset camera on layer double click
- 3D orientation, change the color of the background
- Browser -> File System, path saved each time you open a directory
- Improve visibility of 2D meshes
- Pop-up to validate application exit: avoid misclicks
- Search toolbox tool in the quick access menu to find toolboxes
- Standardize Selector workspaces (with a selector combobox of toolboxes)
- Filter tool added on the top on database column in workspaces
- Right-click on a data in the database: Metadata tool lists the data metadata
- Possibility to rename data in database column with the OS shortcut (ex. F2 on Linux)
- Clarify the use of Load/Import data which become Temporary Import/Import
- Remove homepage animation, and update minimum size of the application
- Splash screen design updated, and fix transparency problem on some computers
- Improve Mouse Interaction/View settings/Layer settings ergonomy
- Fix Tensor view crash, and mesh + data display in view
- Fix save and load settings for PACS system
- Fix Dicom import with non axial acquisition
- Fix a synchronisation bug between views
- Fix a 4-split bug with the slicing
- Fix a 4-split views bug with scrolling, button in view Tools button
- Fix command-line bugs
- Fix import errors of DICOM and mha
- Fix default database path
- Fix hidden layer visibility when add a new data in a view
- Fix Composer button, and Diffusion toolboxes sizes
- Fix memory leak with meshes after view closing
- Fix thumbnail size
- Fix the slice number and location on the view when the orientation changes
- Improve packaging

MUSIC v2.4.0:
- Application compiles on Ubuntu 18
- Video export in ffmpeg (Linux-Mac) or MPEG2 (Windows)
- Median Filter: can choose neighborhood size
- Closing pop-up in case of misclick
- Add Binary Threshold process to Threshold toolbox
- Add parameters for Threshold process: lower/upper/outside values
- Add Histogram to Threshold toolbox
- Path saved in Browser workspace
- Add a Search Toolbox tool in quick menu, bottom left of application
- Access to default Python interpreter in pipelines (simpleITK, tensorFlow, numpy, keras. Cf MUSIC website)
- User can choose own Python interpreter (Python 2 required)
- Vessel Segmentation: ability to generate multiple branches without bifurcation
- Add support for 4D meshes attribute curve plotting
- Add new Carto signal reader class
- Add new E.A.M. Analysis workspace, to interact with EP maps
- Add E.A.M Analysis toolboxes: "Data projection", "Data interpolation", "Border zone", "Map Utility" and "EAM Point Distribution"
- Mesh Interactor: there are now two modes: point picking and cell picking.
- Cell Cutter: toolbox for pipelines only. Enables to remove parts of meshes using interactor tools
- Vest Similarity: sock similarity toolbox
- Mask Projection toolbox: project one or more masks onto a mesh.
- Add Thickness filter process 

MUSIC v2.3.0:
- New user manuals on GitLab Pages website
- Add Doxygen files on the website for pipelines scripts dev
- Adapt some toolboxes to 4D meshes and volumes
- Add a new light theme: Home -> Settings -> Theme. Save and reopen the application
- Screenshot can handle multiple views
- Browser: "Load" button becomes "Temporary import" for clarity
- Database: data generated by MUSIC have a "generated by MUSIC x.y.y" metadata
- Database: can edit name with F2 key
- Database: right-click on a series and "Metadata" shows a window with metadata
- Mesh: reset camera double-clicking on a view
- New "Channelness" lookup and toolbox
- Solve icon size problem on mac
- Change the way done, to do and not done steps are displayed in pipelines: add icons
- Add a Histogram Matching toolbox
- Enhancement on Paint Toolbox interpolation
- EP map improvements
- Add MFS new features: temporal correlation coefficients map, etc
- Add Transmurality toolbox computing intermediate surfaces between the inner surface and outer surface of 2 masks
- Add Laplacian filter in mscFilters

MUSIC v2.2.0:
- Add Translation volume toolbox
- Export Video from view: by rotation or time. Export in OGG VORBIS or batch of JPEG.
- MFS Simulation: add Inverse Problem Methods utility with methods that can be used in inverse problems in general and not only in MFS.
- MFS Simulation: add automatic determination of the optimal regularization parameter using Creso, Zero Crossing, GCV, RGCV, ADPC and U-Curve methods.
- MFS Simulation: can now save singular values, relative errors, correlation coefficients.
- Import (CARTO) EPMap
- Pipelines: export to RYTHMIA
- Add Jenkins Ubuntu 12.04 server (in addition to 16.04)
- Add Jenkins Windows 10 server
- Adapt MUSIC to Visual Studio 2015 compilation
- Switch to C++11 code
- Switch to ITK 4.11
- Change the view background color
- Diffeormorphic toolbox can be used with different origins
- Ergonomic changes on view buttons
- Ctrl Space to switch between workspaces, add new icons
- Manual Registration uses the undo/redo tool
- OBJ writer/reader
- STL writer/reader
- Merge data, add fuse method for meshes and volumes

MUSIC v2.1.0:
- Fix pipeline export to other computer
- Morphological kernel maximum value updated
- Debug import of RGB DICOMs files
- MUSIC-private toolboxes added on Linux and Mac binaries
- Polygon ROI several debug

MUSIC v2.0.0:
- Python pipelines
- MAIN files in XML
- Histogram Analysis: solve a bug in UTAH3D
- Workspace comboboxes show toolboxes alphabetically
- Solve some DICOM import errors
- Cropping: box in green
- DB: possibility to drop a study with several series in a view
- DB: improve the search bar
- Manual Registration: add Affine transformation
- Sliders: larger handle
- Enhancement of the Help (?) buttons in the toolboxes headers
- Add a unique progress bar for processes
- ... many other enhancements and bug fixes.

MUSIC v1.1.2:
- New Tools added since the switch medInria -> MUSIC
- Logs: save debug, info, error messages in a log file (Homepage ->Log)
- NavX export :  take into account the number of triangles limitation
- PolygonROI: new interpolation algorithm with the introduction of master ROIs (defined as new polygons or a modified ones)
- PolygonROI: extraction of a polygonROI from a binary mask
- PolygonROI: positions of segmented slices notified by a tick on the slice slider
- Invert intensity filter: correct output's dynamic range
- Ease of use improved with more explanations, tooltips
- ... many other enhancements and bug fixes.

medInria v3.0:
- Switch Qt backend to Qt 5.x
- Switch VTK to version 8.1, including a switch to OpenGL2 backend
- new, experimental composer workspace to run pipelines
- Introduce a new plugin framework for the previous purpose
- A bunch of new image processing algorithms: ITK basic operations (morphology, arithmetic...), bias correction...
- New data types for diffusion: multi-compartment models (view and estimation)
- enable image drag and drop on the application
- scale colormaps option for surface and fibers attributes
- many more things under the hood !

medInria v2.2.3:
- Fix registration of images encoded in unsigned short
- Add a colormap for label images
- Fix rare window-level crash
- Fix rare thumbnail creation crash
- Various bugs corrections

medInria v2.2.2:
- Minimum CMake version is now 2.8.10, as it corrects problem with automoc
- Window/Level sliders are now expressed as Min/Max for easier manipulation
- Fixed a bug that was wasting disk space by saving non persistent items on disk
- Restore split presets, ROI file loading, RGB(A) image support
- Undo/Redo support in paint segmentation
- Allow coloring of vector field by a single color for field comparisons
- Fixed Depth-Peeling on NVidia cards, improved general performance a bit
- Various bugs and crashes corrections

medInria v2.2.1:
- Presets for images are back
- Reversed Loni Lut added
- Diffusion workspace bug correction
- File association on Mac corrected
- Crashing bug in ITK basic filters solved
- Various bugs corrections

medInria v2.2.0:
- Rubber band zoom
- Add support for VTK vtp file format
- New application design 
- DICOM import robustness improved
- Morphological filters (dilate, erode, open, close) added
- ITK 4.6 and VTK5.10 migration
- Vector field visualization
- HighDPI support on OSX
- New navigator to explore patients/studies/series
- New view container management system
- MPR feature added to visualize an image in all orientations 
- Diffusion workspace refactored
- View and Data Management API updated
- View properties toolbox improved and a new system to link properties set up
- Corrections in time line management
- 2 new registration plugins are added : LCC log-Demons and non linear block-matching registration
- Many bug corrections

medInria v2.1.2:
- Bug fixes on view/layer synchronisation in the registration workspace
- Made image annotations more legible on any background by adding text shadows
- Fixed a crash in medPluginGenerator as well as tests
- DICOM import fixes
- Added keyboard shortcuts for orientation buttons
- Simplified paint segmentation toolbox
- File browser settings are now saved
- Mesh thumbnails are now properly rendered on Mac, no more popups on other platforms

medInria v2.1.1:
- Win64 package was using Qt 4.7 instead of 4.8
- Unix packages were using a dynamic boost, instead of static
- Temporarily disable mesh thumbnail generation on Mac due to crashes, will be fixed in 2.1.2

medInria v2.1.0:

- First open-source release, code available on github
- Database edition
- Undo-redo for registration algorithms
- New registration algorithm: pyramidal block-matching registration
- Experimental ODF visualization (for ODF in a spherical harmonics basis)
- Inter-hemispheric symmetry plane computation
- Rewritten NL-Means denoising, now includes DWI denoising
- Improved paint segmentation tool: magic wand, multi-label segmentation, controls simplification
- View orientation controls moved from right-click to the view properties toolbox
- Remove, save data, double-click to view data from any workspace using patient navigator
- Simplified ROI filtering of fiber tracts
- Direct image file opening from command line, file type association (double click on a file in Finder to view it: Mac only)
- Screenshot button and shortcut (Ctrl F)
- "Alt-Tab" like shortcut to switch between workspaces (Ctrl Shift)
- Many bug corrections and other improvements

medInria v2.0.1-1:

- Fix Dicom plugins load failures on Macos Mountain Lion

medInria v2.0.1:

- Improved UI
- Added registration algorithms: Baloo, Super Baloo, iLogDemons
- Registration always performed in float for now
- Added Segmentation Configuration preview
- Improved layer aware window level interactions
- Added INRImage support


medInria v2.0.0:

Total rewrite of the code from v 1.9.0