Fluorophore kinetic system revamp

Contains ALICA v0.2.1

Added

• General N-state fluorophore system which replaces the individual xFluorophore
  classes
• 3D fluorophore support (needs better PSF calculation)
• Moving 2D fluorophore

Removed

• SimpleFluorophore, dSTORMFluorophore, PALMFluorophore classes (their Properties classes however stay as they are convenient to setting up these models)

Fixed

• Graph rendering in interactive mode
• Misaligned GUI glitch in InitSettingsFrame

Added SimpleMovingFluorophore

Added

• Moving variant of SimpleFluorophore (trajectory has to be specified explicitly for every frame, and there is no motion blur). See example: scripts/example_run_generator_moving.bsh

Major bugfixes

Fixed

• Class location in package ch.epfl.leb.sass
• Normalization of emitter PSF
• Parsing emitters from file now puts them at position identical with ThunderSTORM coordinate system

Fixed FIJI BeanShell console

ALICA v0.1.x support

BeanShell and FIJI support

Compatible with ALICA v0.0.2

Added

• PALM and dSTORM fluorophore blinking models (not accessible via GUI, only BeanShell)
• Analyzer and Controller are now loaded from ALICA .jar
• BeanShell integration (executing the .jar causes a standalone BeanShell console to run, running scripts possible via command line)

Removed

• Multiple simultaneous analyzers option. Create a new custom encapsulating analyzer
  if you want the same functionality.

v0.0.1

Last version before switching to ALICA's Analyzer and Controller API