ChangeLog.txt

Version 2.10.1 - Patch release for "Blaise" 
	Release with small updates, clean-ups and bugfixes    
    - Bugfix in 3D view due to inconsistent angles in pln & stf
    - Bugfix for using incorrect dicom UID's and wrong writing order in the dicom export
    - Bugfix for weird colormap issue in plotting
    - New handling of environment checking with matRad_cfg (old function is still working)
    - Code documentation update
    - Remove hardcoded penumbra width in photon dose calculation -> can now be stored in machine file (machine.data.penumbraFWHMatIso)
    - Update to ompMC to use virtual Gaussian source (uses measured penumbra value) incld precompiled mex files
    - remove useless global statements before matRad_cfg
    - add blue/white/red difference map to colormaps (in the correct way)
    - Updated TravisCI testing (Sped up by using pre-compiled mex interfaces and including testing with Matlab (on Ubuntu), Azure DevOps as fallback
    - Github gimmicks added: Stalebot, Issue & PR Templates
	- code optimization for jacobian evaluation (x10-100 speedup)
	- New option pln.propDoseCalc.useGivenEqDensityCube (default false) to directly use the literal values from ct.cube and omit HU to WEQ conversion from ct.cubeHU
	- New option pln.propDoseCalc.ignoreOutsideDensities (default true) to disable/enable inclusion of WEPL outside the patient contour in ray-tracing

Version 2.10.0 - "Blaise"
	Second Release of matRad. Note that despite major incompatibilities with "Alan" we still chose major version number "2" to have a consistent versioning in the future.
	we want to thank all new contributing authors (see AUTHORS.txt)
	The new release contains:
	- integration tests using TravisCI (with Octave, so no GUI functionalities are tested)
	- matRad_rc script to configure matRad paths
    - matRad version can now be printed with matRad_version, version correctly shown in GUI and when using matRad_rc
	- Seven new Matlab exmaple scripts to demonstrate use of matRad 
	- added basic interfaces to the open-source photon/proton MC engines ompMC/MCsquare
	- Overhaul of the optimization interface using OOP and integration of the fmincon optimizer from Mathworks' MATLAB Optimization toolbox
	- Changes to the cst variable (new script to convert old to new cst structures in tools folder)
	- separation of ct/optimization/dose calculation grids to allow different resolutions
	- The graphical user interface can now be started in developer mode (more error information) and a simplified educational mode (some functionalities disabled, less buttons)
	- base data and default phantoms now organized in subfolders
	- DICOM export added (only script, dicomImport folder renamed to dicom)
	- DICOM import GUI
	- binary import and export functionalities (script & GUI)
	- overhauled the standalone project file
	- standalone toolbox file for matRad
	- Dose calculation now uses generalized initialization scripts
	- matRad_compareDose tool to compare two dose distributions with difference and gamma analysis
	- more tools for visualisation and data analysis in the tools folder
	- Possibility to define range shifter
	- Quality indicator & DVH display wrapper scripts
	- wrapper to allow 3D conformal planning using dij collapsing
	- new colormap handling to allow integration of custom colormaps
	- modularization of slice display by dedicated functions in plotting folder including generation of 3D views
    - New global configuration object (matRad_cfg <- MatRad_Config.m) to store default values and with logging interface
	- many bug fixes and many new bugs..	
Version 2.1 "Alan"
	First official relase of matRad including
	- new optimizer IPOPT for constrained optimization
	- validated ray tracing
	- validated pencil beam particle dose calcualtion
	- validated singular value decomposed pencil beam photon dose calculation
	- DICOM import including dose and particle pencil beam scanning plan objects
	- matRad standalone version
	- improved GUI workflow
	- many bug fixes and many new bugs...