ThreeB 1.1
Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
AdvancedDialogControl panel which basically presents the .cfg file in a large edit box along with additional necessary things (frame range and pixel size)
ClassicGlowPlugin implementing the classic glow/hot LUT which seems to be missing from ImageJ
CloseButtonListenerClose button issues a window close event
ConjugateGradientOnly< Size, Precision >Class for performing optimization with Conjugate Gradient, where only the derivatives are available
DataForMCMCClosure hoding the data required do use GibbsSampler2 See FitSpots for naming of variables
EControlPanelControl panel for running 3B plugin and providing interactive update
ExportButtonListenerListener for the export button
FitSpotsMega class which actually does the meat of the spot fitting
FitSpotsGraphicsGraphics class for FittingSpots
FloatSliderWithBoxThis class makes a floating point slider bar with an edit box next to it for more precision
FreeEnergyHessianClass for computing the Hessian of the negative free energy
SampledMultispot::GibbsSamplerDraw samples from the spot states given the spots positions and some data
SampledMultispot::GibbsSampler2Gibbs sampling class which masks spots to reduce computation
GraphicsGLGraphics class which draws information to the screen using OpenGL
IndexLexicographicPosition< Cmp, First >Class for sorting a list of indexes to an array of spots lexicographically according to the 2D positions of the spots
JNIUserInterface3B User interface for the Java plugin
KahanClass implementing the Kahan summation algorithm to allow accurate summation of very large numbers of doubles
LessSecondComparator functor for the first element of a std::pair
LoadTestDataPlugin class to load the standard test data from the JAR file
LogFileParseErrorNull struct thrown if a parse error is encountered when trying to load a log file
MT19937Useful wrapper for MT19937 random number generator class
NegativeFreeEnergyClass for computing the negitve free energy using thermodynamic integration
NullGraphicsGraphics class which does absoloutely nothing
NullUICallbackUser interface callback class which does nothing
MT19937::ParseErrorNull struct thrown if attempting to load state from stream yields a parse error
SampledBackgroundDataClosure holding image data generated using samples drawn from the model
SomethingChangesListener class which triggers a complete redraw
SPairUtility class to hold a pair of strings
SpotBasic spot class, simply contains coordinates
SpotNegProbabilityDiffWithSampledBackgroundCompute the derivative of the negative log probability with respect to the parameters of one spot, given some samples of the other spots
SampledMultispot::SpotWithBackgroundMaskedThis class compute the log-diff-hess probability of a spot, given an image patch and background due to existing spots
StateParametersInternal state (excluding fixed settings) which represents the entire internal state of spot fitting
StopButtonListenerStop 3B thread
three_BImageJ plugin class
ThreeBDialogDialog box for starting 3B The dialog highlights bad things in red
ThreeBHelp3B plugin cclass to bring up a basic help window
ThreeBLoaderPlugin class to load up an old 3B run
ThreeBRunnerThis class deals with running the actual 3B code It should be run in a separate thread It will make calls back to a viewer, and accepts termination calls as well
UserInterfaceCallbackCallback class used by FitSpots to provide enough hooks for a user interface
UtilUtility calss to hold a number of handy static functions