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A

AbstractCtrl - Class in flimlib.flimj.ui.controller
The basis for a tab controller that is Initializable and refreshable by both external control flow and other controllers backed by the same fit processor.
AbstractCtrl() - Constructor for class flimlib.flimj.ui.controller.AbstractCtrl
 
AbstractFitRAI<I extends RealType<I>> - Class in flimlib.flimj
 
AbstractFitRAI() - Constructor for class flimlib.flimj.AbstractFitRAI
 
AbstractFitWorker<I extends RealType<I>> - Class in flimlib.flimj.fitworker
AbstractFitWorker
AbstractFitWorker(FitParams<I>, FitResults, OpEnvironment) - Constructor for class flimlib.flimj.fitworker.AbstractFitWorker
 
AbstractSingleFitWorker<I extends RealType<I>> - Class in flimlib.flimj.fitworker
 
AbstractSingleFitWorker(FitParams<I>, FitResults, OpEnvironment) - Constructor for class flimlib.flimj.fitworker.AbstractSingleFitWorker
 
adjFitEnd - Variable in class flimlib.flimj.fitworker.AbstractFitWorker
The adjusted FitParams.fitStart and FitParams.fitEnd taking into account leading instr prefix (see below)
adjFitStart - Variable in class flimlib.flimj.fitworker.AbstractFitWorker
The adjusted FitParams.fitStart and FitParams.fitEnd taking into account leading instr prefix (see below)
afterFit() - Method in class flimlib.flimj.fitworker.AbstractSingleFitWorker
A routine called after AbstractSingleFitWorker.doFit().
afterFit() - Method in class flimlib.flimj.fitworker.PhasorFitWorker
 
afterFit() - Method in class flimlib.flimj.fitworker.RLDFitWorker
 
annotate(RandomAccess<FloatType>, RandomAccess<ARGBType>) - Method in interface flimlib.flimj.ui.PreviewImageDisplay.ImageAnnotator
Recolors the rendered pixel given a pointer to the source float value and the LUT converted color.
asArray() - Method in class flimlib.Float2DMatrix
 
asArray() - Method in class flimlib.Int2DMatrix
 
autoRange(double, double, double, double) - Method in class flimlib.flimj.ui.VariableScaleAxis
AxisRange(double, double, double, double, double, boolean) - Constructor for class flimlib.flimj.ui.VariableScaleAxis.AxisRange
 

B

Bayes_fitting_engine(float, float[], int, int, float, float[], float[], boolean[], float[], float[], float[], float[], int[], float[]) - Static method in class flimlib.FLIMLib
 
Bayes_fitting_engine(float, float[], int, int, float, float[], float[], boolean[], float[], float[], float[], float[], int[], float[]) - Static method in class flimlib.FLIMLibJNI
 
Bayes_set_search_grid(float[], float[]) - Static method in class flimlib.FLIMLib
 
Bayes_set_search_grid(float[], float[]) - Static method in class flimlib.FLIMLibJNI
 
BayesFitWorker<I extends RealType<I>> - Class in flimlib.flimj.fitworker
 
BayesFitWorker(FitParams<I>, FitResults, OpEnvironment) - Constructor for class flimlib.flimj.fitworker.BayesFitWorker
 
BayesSingleFitRAI() - Constructor for class flimlib.flimj.DefaultFitRAI.BayesSingleFitRAI
 
beforeFit() - Method in class flimlib.flimj.fitworker.AbstractSingleFitWorker
A routine called before AbstractSingleFitWorker.doFit().
beforeFit() - Method in class flimlib.flimj.fitworker.BayesFitWorker
 
beforeFit() - Method in class flimlib.flimj.fitworker.LMAFitWorker
 
beforeFit() - Method in class flimlib.flimj.fitworker.PhasorFitWorker
 
beforeFit() - Method in class flimlib.flimj.fitworker.RLDFitWorker
 

C

CalcAPercent() - Constructor for class flimlib.flimj.DefaultCalc.CalcAPercent
 
CalcTauMean() - Constructor for class flimlib.flimj.DefaultCalc.CalcTauMean
 
calculate(FitParams<I>) - Method in class flimlib.flimj.AbstractFitRAI
 
calculate(FitResults) - Method in class flimlib.flimj.DefaultCalc.CalcAPercent
 
calculate(FitResults) - Method in class flimlib.flimj.DefaultCalc.CalcTauMean
 
calculate(FitResults) - Method in class flimlib.flimj.DefaultDispRslt.Pseudocolor
 
calculateMinorTickMarks() - Method in class flimlib.flimj.ui.VariableScaleAxis
calculateTickValues(double, Object) - Method in class flimlib.flimj.ui.VariableScaleAxis
CBPopOverCtrl() - Constructor for class flimlib.flimj.ui.controller.PreviewCtrl.CBPopOverCtrl
 
chisq - Variable in class flimlib.flimj.FitResults
The reduced chi-squared of the fit.
chisq_delta - Variable in class flimlib.flimj.FitParams
Stopping condition 2: stop if change in chi-squared is less than FitParams.chisq_target (1E-4 by default)
chisq_percent - Variable in class flimlib.flimj.FitParams
Confidence interval when calculating the error axes (95% by default)
chisq_target - Variable in class flimlib.flimj.FitParams
Stopping condition 1: stop if reduced chi-squared is less than FitParams.chisq_target (1 by default)
chisqBuffer - Variable in class flimlib.flimj.fitworker.AbstractSingleFitWorker
Data buffers, all except for transBuffer are writable
chisqMap - Variable in class flimlib.flimj.FitResults
The image representation of reduced chi-squared of the fit over the the dataset
commitRslts(FitParams<I>, FitResults, int[]) - Method in class flimlib.flimj.utils.RAHelper
Put results back into the proper position in rslts.
conforms() - Method in class flimlib.flimj.AbstractFitRAI
 
copy() - Method in class flimlib.flimj.FitParams
Create a new instance of FitParams with shallow copy (maps are not duplicated).
copy() - Method in class flimlib.flimj.FitResults
Create a new instance of FitResults with shallow copy (maps are not duplicated).
createWorker(FitParams<I>, FitResults) - Method in class flimlib.flimj.AbstractFitRAI
Generates a worker for the actual fit.
createWorker(FitParams<I>, FitResults) - Method in class flimlib.flimj.DefaultFitRAI.BayesSingleFitRAI
 
createWorker(FitParams<I>, FitResults) - Method in class flimlib.flimj.DefaultFitRAI.LMAGlobalFitRAI
 
createWorker(FitParams<I>, FitResults) - Method in class flimlib.flimj.DefaultFitRAI.LMASingleFitRAI
 
createWorker(FitParams<I>, FitResults) - Method in class flimlib.flimj.DefaultFitRAI.PhasorSingleFitRAI
 
createWorker(FitParams<I>, FitResults) - Method in class flimlib.flimj.DefaultFitRAI.RLDSingleFitRAI
 

D

DecayModel - Class in flimlib
 
DecayModel(long, boolean) - Constructor for class flimlib.DecayModel
 
DecayModel() - Constructor for class flimlib.DecayModel
 
DecayModel(FitFunc, float[], boolean[], RestrainType, int, float, float, int) - Constructor for class flimlib.DecayModel
 
DecayModel_getAlpha(long, DecayModel) - Static method in class flimlib.FLIMLibJNI
 
DecayModel_getChisq(long, DecayModel) - Static method in class flimlib.FLIMLibJNI
 
DecayModel_getCovar(long, DecayModel) - Static method in class flimlib.FLIMLibJNI
 
DecayModel_getErraxes(long, DecayModel) - Static method in class flimlib.FLIMLibJNI
 
DecayModel_getFitfunc(long, DecayModel) - Static method in class flimlib.FLIMLibJNI
 
DecayModel_getFitted(long, DecayModel) - Static method in class flimlib.FLIMLibJNI
 
DecayModel_getParams(long, DecayModel) - Static method in class flimlib.FLIMLibJNI
 
DecayModel_getResiduals(long, DecayModel) - Static method in class flimlib.FLIMLibJNI
 
DefaultCalc - Class in flimlib.flimj
 
DefaultCalc.CalcAPercent - Class in flimlib.flimj
 
DefaultCalc.CalcTauMean - Class in flimlib.flimj
 
DefaultDispRslt - Class in flimlib.flimj
 
DefaultDispRslt.Pseudocolor - Class in flimlib.flimj
 
DefaultFitRAI - Class in flimlib.flimj
FLIMLib fitters on a RandomAccessibleInterval of time-resolved FLIM data.
DefaultFitRAI.BayesSingleFitRAI<I extends RealType<I>> - Class in flimlib.flimj
 
DefaultFitRAI.LMAGlobalFitRAI<I extends RealType<I>> - Class in flimlib.flimj
 
DefaultFitRAI.LMASingleFitRAI<I extends RealType<I>> - Class in flimlib.flimj
 
DefaultFitRAI.PhasorSingleFitRAI<I extends RealType<I>> - Class in flimlib.flimj
 
DefaultFitRAI.RLDSingleFitRAI<I extends RealType<I>> - Class in flimlib.flimj
 
delete() - Method in class flimlib.DecayModel
 
delete() - Method in class flimlib.Float2DMatrix
 
delete() - Method in class flimlib.Int2DMatrix
 
delete_DecayModel(long) - Static method in class flimlib.FLIMLibJNI
 
delete_FitFuncNative(long) - Static method in class flimlib.FLIMLibJNI
 
delete_Float2DMatrix(long) - Static method in class flimlib.FLIMLibJNI
 
delete_Int2DMatrix(long) - Static method in class flimlib.FLIMLibJNI
 
destroy() - Method in class flimlib.flimj.ui.controller.AbstractCtrl
Release the reources occupied by fields in the controller (e.g.
destroy() - Method in class flimlib.flimj.ui.controller.PreviewCtrl
 
destroy() - Method in class flimlib.flimj.ui.controller.SettingsCtrl
 
destroy() - Method in class flimlib.flimj.ui.FitProcessor
 
destroy() - Method in class flimlib.flimj.ui.PreviewImageDisplay
Clean up.
dispValue(double) - Method in class flimlib.flimj.ui.controller.PreviewCtrl.CBPopOverCtrl
Changes text and moves the cursor to indicate the new value.
doFit() - Method in class flimlib.flimj.fitworker.AbstractSingleFitWorker
Does the actual implementation-specific fitting routine.
doFit() - Method in class flimlib.flimj.fitworker.BayesFitWorker
Performs an Bayes fit.
doFit() - Method in class flimlib.flimj.fitworker.LMAFitWorker
Performs an LMA fit.
doFit() - Method in class flimlib.flimj.fitworker.PhasorFitWorker
 
doFit() - Method in class flimlib.flimj.fitworker.RLDFitWorker
Performs the RLD fit.
dropBad - Variable in class flimlib.flimj.FitParams
duplicate(FitParams<I>, FitResults) - Method in class flimlib.flimj.fitworker.AbstractSingleFitWorker
Make a worker of the same kind but does not share any writable buffers (thread safe) if that buffer is null.
duplicate(FitParams<I>, FitResults) - Method in class flimlib.flimj.fitworker.BayesFitWorker
 
duplicate(FitParams<I>, FitResults) - Method in class flimlib.flimj.fitworker.LMAFitWorker
 
duplicate(FitParams<I>, FitResults) - Method in class flimlib.flimj.fitworker.PhasorFitWorker
 
duplicate(FitParams<I>, FitResults) - Method in class flimlib.flimj.fitworker.RLDFitWorker
 

E

ECF_ExportParams_start(String) - Static method in class flimlib.FLIMLib
 
ECF_ExportParams_start(String) - Static method in class flimlib.FLIMLibJNI
 
ECF_ExportParams_stop() - Static method in class flimlib.FLIMLib
 
ECF_ExportParams_stop() - Static method in class flimlib.FLIMLibJNI
 
estimateIThreshold() - Method in class flimlib.flimj.ParamEstimator
 
estimateStartEnd() - Method in class flimlib.flimj.ParamEstimator
 
ExportCtrl - Class in flimlib.flimj.ui.controller
The controller of the "Export" tab.
ExportCtrl() - Constructor for class flimlib.flimj.ui.controller.ExportCtrl
 

F

finalize() - Method in class flimlib.DecayModel
 
finalize() - Method in class flimlib.Float2DMatrix
 
finalize() - Method in class flimlib.Int2DMatrix
 
fit(float, float[], float[]) - Method in interface flimlib.FitFunc
 
fitBatch(List<int[]>, FitWorker.FitEventHandler<I>) - Method in class flimlib.flimj.fitworker.AbstractSingleFitWorker
 
fitBatch(List<int[]>) - Method in interface flimlib.flimj.fitworker.FitWorker
Fit all coordinates listed.
fitBatch(List<int[]>, FitWorker.FitEventHandler<I>) - Method in interface flimlib.flimj.fitworker.FitWorker
Fit all coordinates listed and handles fit events.
fitBatch(List<int[]>, FitWorker.FitEventHandler<I>) - Method in class flimlib.flimj.fitworker.GlobalFitWorker
 
fitDataset() - Method in class flimlib.flimj.ui.FitProcessor
 
fitEnd - Variable in class flimlib.flimj.FitParams
The end of the decay interval
FitFunc - Interface in flimlib
 
fitFunc - Variable in class flimlib.flimj.FitParams
The fitting model to use (Z + A_1e^(-t/tau_1) + A_2e^(-t/tau_2) + ...
FitFuncNative_change_ownership(FitFuncNative, long, boolean) - Static method in class flimlib.FLIMLibJNI
 
FitFuncNative_director_connect(FitFuncNative, long, boolean, boolean) - Static method in class flimlib.FLIMLibJNI
 
FitFuncNative_fit(long, FitFuncNative, float, float[], float[], int) - Static method in class flimlib.FLIMLibJNI
 
FitFuncNative_fitSwigExplicitFitFuncNative(long, FitFuncNative, float, float[], float[], int) - Static method in class flimlib.FLIMLibJNI
 
FitParams<I extends RealType<I>> - Class in flimlib.flimj
The collection of all fit parameters required to perform a single fit of an image.
FitParams() - Constructor for class flimlib.flimj.FitParams
 
FitParamsPrompter - Class in flimlib.flimj.ui
Utility class to ease population of FitParams objects.
FitParamsPrompter() - Constructor for class flimlib.flimj.ui.FitParamsPrompter
 
FitProcessor - Class in flimlib.flimj.ui
ProcessingService
FitProcessor(Context, FitParams<FloatType>) - Constructor for class flimlib.flimj.ui.FitProcessor
 
FitProcessor.FitType - Enum in flimlib.flimj.ui
The collection of all fitting algorithms
FitResults - Class in flimlib.flimj
The collection of all results generated by a single fit of an image.
FitResults() - Constructor for class flimlib.flimj.FitResults
 
fitSingle() - Method in class flimlib.flimj.fitworker.AbstractSingleFitWorker
Fit the data in the buffer.
fitStart - Variable in class flimlib.flimj.FitParams
The start of the decay interval
fitted - Variable in class flimlib.flimj.FitResults
The fitted transients of the fit
fittedBuffer - Variable in class flimlib.flimj.fitworker.AbstractSingleFitWorker
Data buffers, all except for transBuffer are writable
fittedMap - Variable in class flimlib.flimj.FitResults
The image representation of fitted transients of the fit over the the dataset
FitType - Enum in flimlib
 
FitWorker<I extends RealType<I>> - Interface in flimlib.flimj.fitworker
 
FitWorker.FitEventHandler<I extends RealType<I>> - Interface in flimlib.flimj.fitworker
The handler interface for fit events.
FLIMJCommand - Class in flimlib.flimj.ui
 
FLIMJCommand() - Constructor for class flimlib.flimj.ui.FLIMJCommand
 
flimlib - package flimlib
 
FLIMLib - Class in flimlib
 
FLIMLib() - Constructor for class flimlib.FLIMLib
 
flimlib.flimj - package flimlib.flimj
 
flimlib.flimj.fitworker - package flimlib.flimj.fitworker
 
flimlib.flimj.ui - package flimlib.flimj.ui
 
flimlib.flimj.ui.controller - package flimlib.flimj.ui.controller
 
flimlib.flimj.ui.controls - package flimlib.flimj.ui.controls
 
flimlib.flimj.utils - package flimlib.flimj.utils
 
FLIMLibConstants - Interface in flimlib
 
FLIMLibJNI - Class in flimlib
 
FLIMLibJNI() - Constructor for class flimlib.FLIMLibJNI
 
FlimOps - Class in flimlib.flimj
 
FlimOps.BayesOp - Interface in flimlib.flimj
 
FlimOps.CalcAPercentOp - Interface in flimlib.flimj
 
FlimOps.CalcTauMOp - Interface in flimlib.flimj
 
FlimOps.GlobalOp - Interface in flimlib.flimj
 
FlimOps.LMAOp - Interface in flimlib.flimj
 
FlimOps.PhasorOp - Interface in flimlib.flimj
 
FlimOps.PseudocolorOp - Interface in flimlib.flimj
 
FlimOps.RLDOp - Interface in flimlib.flimj
 
Float2DMatrix - Class in flimlib
 
Float2DMatrix(long, boolean) - Constructor for class flimlib.Float2DMatrix
 
Float2DMatrix(int, int) - Constructor for class flimlib.Float2DMatrix
 
Float2DMatrix(float[][]) - Constructor for class flimlib.Float2DMatrix
 
Float2DMatrix_asArray(long, Float2DMatrix) - Static method in class flimlib.FLIMLibJNI
 
Float2DMatrix_ncol_get(long, Float2DMatrix) - Static method in class flimlib.FLIMLibJNI
 
Float2DMatrix_nrow_get(long, Float2DMatrix) - Static method in class flimlib.FLIMLibJNI
 
fp - Variable in class flimlib.flimj.ui.controller.AbstractCtrl
 
fromJSON(String) - Static method in class flimlib.flimj.FitParams
Creates a FitParams from serialized JSON string.
FXML_DIR - Static variable in class flimlib.flimj.ui.controller.AbstractCtrl
 

G

GCI_EcfModelSelectionEngine(float, float[], int, int, float[], NoiseType, float[], DecayModel[], float[], int[]) - Static method in class flimlib.FLIMLib
 
GCI_EcfModelSelectionEngine(float, float[], int, int, float[], int, float[], DecayModel[], float[], int[]) - Static method in class flimlib.FLIMLibJNI
 
GCI_marquardt(float[], float[], NoiseType, float[], float[], boolean[], RestrainType, FitFunc, float[], float[], Float2DMatrix, Float2DMatrix, float[], float, float, Float2DMatrix) - Static method in class flimlib.FLIMLib
 
GCI_marquardt(float[], float[], int, float[], float[], boolean[], int, long, float[], float[], long, Float2DMatrix, long, Float2DMatrix, float[], float, float, long, Float2DMatrix) - Static method in class flimlib.FLIMLibJNI
 
GCI_marquardt_cleanup() - Static method in class flimlib.FLIMLib
 
GCI_marquardt_cleanup() - Static method in class flimlib.FLIMLibJNI
 
GCI_marquardt_fitting_engine(float, float[], int, int, float[], NoiseType, float[], float[], boolean[], RestrainType, FitFunc, float[], float[], float[], Float2DMatrix, Float2DMatrix, Float2DMatrix, float, float, int) - Static method in class flimlib.FLIMLib
 
GCI_marquardt_fitting_engine(float, float[], int, int, float[], int, float[], float[], boolean[], int, long, float[], float[], float[], long, Float2DMatrix, long, Float2DMatrix, long, Float2DMatrix, float, float, int) - Static method in class flimlib.FLIMLibJNI
 
GCI_marquardt_global_exps_instr(float, Float2DMatrix, int, int, float[], NoiseType, float[], FitType, Float2DMatrix, boolean[], RestrainType, float, Float2DMatrix, Float2DMatrix, float[], float[], int[], int) - Static method in class flimlib.FLIMLib
 
GCI_marquardt_global_exps_instr(float, long, Float2DMatrix, int, int, float[], int, float[], int, long, Float2DMatrix, boolean[], int, float, long, Float2DMatrix, long, Float2DMatrix, float[], float[], int[], int) - Static method in class flimlib.FLIMLibJNI
 
GCI_marquardt_global_generic_instr(float, Float2DMatrix, int, int, float[], NoiseType, float[], Float2DMatrix, boolean[], int[], RestrainType, float, FitFunc, Float2DMatrix, Float2DMatrix, float[], float[], int[]) - Static method in class flimlib.FLIMLib
 
GCI_marquardt_global_generic_instr(float, long, Float2DMatrix, int, int, float[], int, float[], long, Float2DMatrix, boolean[], int[], int, float, long, long, Float2DMatrix, long, Float2DMatrix, float[], float[], int[]) - Static method in class flimlib.FLIMLibJNI
 
GCI_marquardt_instr(float, float[], int, int, float[], NoiseType, float[], float[], boolean[], RestrainType, FitFunc, float[], float[], Float2DMatrix, Float2DMatrix, float[], float, float, Float2DMatrix) - Static method in class flimlib.FLIMLib
 
GCI_marquardt_instr(float, float[], int, int, float[], int, float[], float[], boolean[], int, long, float[], float[], long, Float2DMatrix, long, Float2DMatrix, float[], float, float, long, Float2DMatrix) - Static method in class flimlib.FLIMLibJNI
 
GCI_MULTIEXP_LAMBDA - Static variable in interface flimlib.FitFunc
 
GCI_MULTIEXP_LAMBDA - Static variable in interface flimlib.FLIMLibConstants
 
GCI_MULTIEXP_LAMBDA_get() - Static method in class flimlib.FLIMLibJNI
 
GCI_MULTIEXP_TAU - Static variable in interface flimlib.FitFunc
 
GCI_MULTIEXP_TAU - Static variable in interface flimlib.FLIMLibConstants
 
GCI_MULTIEXP_TAU_get() - Static method in class flimlib.FLIMLibJNI
 
GCI_Phasor(float, float[], int, int, float[], float[], float[], float[], float[], float[], float[], float[], float[]) - Static method in class flimlib.FLIMLib
 
GCI_Phasor(float, float[], int, int, float[], float[], float[], float[], float[], float[], float[], float[], float[]) - Static method in class flimlib.FLIMLibJNI
 
GCI_Phasor_getPeriod() - Static method in class flimlib.FLIMLib
 
GCI_Phasor_getPeriod() - Static method in class flimlib.FLIMLibJNI
 
GCI_set_restrain_limits(boolean[], float[], float[]) - Static method in class flimlib.FLIMLib
 
GCI_set_restrain_limits(boolean[], float[], float[]) - Static method in class flimlib.FLIMLibJNI
 
GCI_SPA_1D_marquardt(float[], float[], NoiseType, float[], float[], boolean[], RestrainType, float, FitFunc, int, int, float, float, float[]) - Static method in class flimlib.FLIMLib
 
GCI_SPA_1D_marquardt(float[], float[], int, float[], float[], boolean[], int, float, long, int, int, float, float, float[]) - Static method in class flimlib.FLIMLibJNI
 
GCI_SPA_1D_marquardt_global_exps_instr(float, Float2DMatrix, int, int, float[], NoiseType, float[], FitType, Float2DMatrix, boolean[], RestrainType, float, int, int, int, float, float, float[], int[]) - Static method in class flimlib.FLIMLib
 
GCI_SPA_1D_marquardt_global_exps_instr(float, long, Float2DMatrix, int, int, float[], int, float[], int, long, Float2DMatrix, boolean[], int, float, int, int, int, float, float, float[], int[]) - Static method in class flimlib.FLIMLibJNI
 
GCI_SPA_1D_marquardt_global_generic_instr(float, Float2DMatrix, int, int, float[], NoiseType, float[], Float2DMatrix, boolean[], int[], RestrainType, float, FitFunc, int, int, float, float, float[], int[]) - Static method in class flimlib.FLIMLib
 
GCI_SPA_1D_marquardt_global_generic_instr(float, long, Float2DMatrix, int, int, float[], int, float[], long, Float2DMatrix, boolean[], int[], int, float, long, int, int, float, float, float[], int[]) - Static method in class flimlib.FLIMLibJNI
 
GCI_SPA_1D_marquardt_instr(float, float[], int, int, float[], NoiseType, float[], float[], boolean[], RestrainType, float, FitFunc, int, int, float, float, float[], float) - Static method in class flimlib.FLIMLib
 
GCI_SPA_1D_marquardt_instr(float, float[], int, int, float[], int, float[], float[], boolean[], int, float, long, int, int, float, float, float[], float) - Static method in class flimlib.FLIMLibJNI
 
GCI_SPA_2D_marquardt(float[], float[], NoiseType, float[], float[], boolean[], RestrainType, float, FitFunc, int, int, float, float, int, int, float, float, Float2DMatrix) - Static method in class flimlib.FLIMLib
 
GCI_SPA_2D_marquardt(float[], float[], int, float[], float[], boolean[], int, float, long, int, int, float, float, int, int, float, float, long, Float2DMatrix) - Static method in class flimlib.FLIMLibJNI
 
GCI_SPA_2D_marquardt_global_exps_instr(float, Float2DMatrix, int, int, float[], NoiseType, float[], FitType, Float2DMatrix, boolean[], RestrainType, float, int, int, int, float, float, int, int, float, float, Float2DMatrix, Int2DMatrix) - Static method in class flimlib.FLIMLib
 
GCI_SPA_2D_marquardt_global_exps_instr(float, long, Float2DMatrix, int, int, float[], int, float[], int, long, Float2DMatrix, boolean[], int, float, int, int, int, float, float, int, int, float, float, long, Float2DMatrix, long, Int2DMatrix) - Static method in class flimlib.FLIMLibJNI
 
GCI_SPA_2D_marquardt_global_generic_instr(float, Float2DMatrix, int, int, float[], NoiseType, float[], Float2DMatrix, boolean[], int[], RestrainType, float, FitFunc, int, int, float, float, int, int, float, float, Float2DMatrix, Int2DMatrix) - Static method in class flimlib.FLIMLib
 
GCI_SPA_2D_marquardt_global_generic_instr(float, long, Float2DMatrix, int, int, float[], int, float[], long, Float2DMatrix, boolean[], int[], int, float, long, int, int, float, float, int, int, float, float, long, Float2DMatrix, long, Int2DMatrix) - Static method in class flimlib.FLIMLibJNI
 
GCI_SPA_2D_marquardt_instr(float, float[], int, int, float[], NoiseType, float[], float[], boolean[], RestrainType, float, FitFunc, int, int, float, float, int, int, float, float, Float2DMatrix, float) - Static method in class flimlib.FLIMLib
 
GCI_SPA_2D_marquardt_instr(float, float[], int, int, float[], int, float[], float[], boolean[], int, float, long, int, int, float, float, int, int, float, float, long, Float2DMatrix, float) - Static method in class flimlib.FLIMLibJNI
 
GCI_STRETCHEDEXP - Static variable in interface flimlib.FitFunc
 
GCI_STRETCHEDEXP - Static variable in interface flimlib.FLIMLibConstants
 
GCI_STRETCHEDEXP_get() - Static method in class flimlib.FLIMLibJNI
 
GCI_triple_integral(float, float[], int, int, NoiseType, float[], float[], float[], float[], float[], float[], float[], int) - Static method in class flimlib.FLIMLib
 
GCI_triple_integral(float, float[], int, int, int, float[], float[], float[], float[], float[], float[], float[], int) - Static method in class flimlib.FLIMLibJNI
 
GCI_triple_integral_fitting_engine(float, float[], int, int, float[], NoiseType, float[], float[], float[], float[], float[], float[], float[], float) - Static method in class flimlib.FLIMLib
 
GCI_triple_integral_fitting_engine(float, float[], int, int, float[], int, float[], float[], float[], float[], float[], float[], float[], float) - Static method in class flimlib.FLIMLibJNI
 
GCI_triple_integral_instr(float, float[], int, int, float[], NoiseType, float[], float[], float[], float[], float[], float[], float[], int) - Static method in class flimlib.FLIMLib
 
GCI_triple_integral_instr(float, float[], int, int, float[], int, float[], float[], float[], float[], float[], float[], float[], int) - Static method in class flimlib.FLIMLibJNI
 
getAlpha() - Method in class flimlib.DecayModel
 
getChisq() - Method in class flimlib.DecayModel
 
getChisqMap - Variable in class flimlib.flimj.FitParams
Whether to generate an image representation for chi-squred (false by default)
getColorImage() - Method in class flimlib.flimj.ui.PreviewImageDisplay
 
getCovar() - Method in class flimlib.DecayModel
 
getCPtr(DecayModel) - Static method in class flimlib.DecayModel
 
getCPtr(Float2DMatrix) - Static method in class flimlib.Float2DMatrix
 
getCPtr(Int2DMatrix) - Static method in class flimlib.Int2DMatrix
 
getCursorXProperty() - Method in class flimlib.flimj.ui.PreviewImageDisplay
 
getCursorYProperty() - Method in class flimlib.flimj.ui.PreviewImageDisplay
 
getDisplayPosition(Number) - Method in class flimlib.flimj.ui.VariableScaleAxis
getDss() - Method in class flimlib.flimj.ui.controller.AbstractCtrl
Gets the dataset service in context.
getErraxes() - Method in class flimlib.DecayModel
 
getFitfunc() - Method in class flimlib.DecayModel
 
getFitFunc() - Method in class flimlib.flimj.ui.FitProcessor
 
getFitProgress() - Method in class flimlib.flimj.ui.FitProcessor
 
getFitted() - Method in class flimlib.DecayModel
 
getFittedMap - Variable in class flimlib.flimj.FitParams
Whether to generate an image representation for fitted transients (false by default)
getFXMLLoader(String) - Static method in class flimlib.flimj.ui.controller.AbstractCtrl
 
getIntensityMap() - Method in class flimlib.flimj.ParamEstimator
 
getIRFInfo() - Method in class flimlib.flimj.ui.controller.AbstractCtrl
Retrieves the current IRF information parameter.
getIRFInfo() - Method in class flimlib.flimj.ui.FitProcessor
 
getIsPercentageProperty() - Method in class flimlib.flimj.ui.controls.NumericHelper
Retrieves the boolean property denoting whether this numeric value is a percentage.
getIsPercentageProperty() - Method in class flimlib.flimj.ui.controls.NumericSpinner
 
getIsPercentageProperty() - Method in class flimlib.flimj.ui.controls.NumericTextField
 
getLogs() - Method in class flimlib.flimj.ui.controller.AbstractCtrl
Gets the log service in context.
getLogScale() - Method in class flimlib.flimj.ui.VariableScaleAxis
 
getMax() - Method in class flimlib.flimj.ui.controls.NumericHelper
 
getMax() - Method in class flimlib.flimj.ui.controls.NumericSpinner
 
getMin() - Method in class flimlib.flimj.ui.controls.NumericHelper
 
getMin() - Method in class flimlib.flimj.ui.controls.NumericSpinner
 
getNcol() - Method in class flimlib.Float2DMatrix
 
getNcol() - Method in class flimlib.Int2DMatrix
 
getNParam() - Method in class flimlib.flimj.ui.FitProcessor
 
getNrow() - Method in class flimlib.Float2DMatrix
 
getNrow() - Method in class flimlib.Int2DMatrix
 
getNumberProperty() - Method in class flimlib.flimj.ui.controls.NumericHelper
Retrieves the numeric property associated with this text field.
getNumberProperty() - Method in class flimlib.flimj.ui.controls.NumericSpinner
Retrieves the numeric property associated with this text field.
getNumberProperty() - Method in class flimlib.flimj.ui.controls.NumericTextField
Retrieves the numeric property associated with this text field.
getObs() - Method in class flimlib.flimj.ui.controller.AbstractCtrl
Gets the object service in context.
getOps() - Method in class flimlib.flimj.ui.controller.AbstractCtrl
Gets the Op service in context.
getOrigTrans() - Method in class flimlib.flimj.ui.FitProcessor
 
getParamMap - Variable in class flimlib.flimj.FitParams
Whether to generate an image representation for fitted parameters (true by default)
getParams() - Method in class flimlib.DecayModel
 
getParams() - Method in class flimlib.flimj.ui.controller.AbstractCtrl
Retrieves the current fitting parameter.
getParams() - Method in class flimlib.flimj.ui.FitProcessor
 
getPreviewImg(String) - Method in class flimlib.flimj.ui.FitProcessor
 
getPreviewOptions() - Method in class flimlib.flimj.ui.FitProcessor
 
getRange() - Method in class flimlib.flimj.ui.VariableScaleAxis
getResiduals() - Method in class flimlib.DecayModel
 
getResidualsMap - Variable in class flimlib.flimj.FitParams
Whether to generate an image representation for residuals (false by default)
getResults() - Method in class flimlib.flimj.ui.controller.AbstractCtrl
Retrieves the current fitted results.
getResults() - Method in class flimlib.flimj.ui.FitProcessor
 
getReturnCodeMap - Variable in class flimlib.flimj.FitParams
Whether to generate an image representation for the return codes (false by default)
getService(Class<S>) - Method in class flimlib.flimj.ui.FitProcessor
 
getSPAProgress() - Static method in class flimlib.FLIMLib
 
getSPAProgress() - Static method in class flimlib.FLIMLibJNI
 
getStepSize() - Method in class flimlib.flimj.ui.controls.NumericSpinner
 
getTickMarkLabel(Number) - Method in class flimlib.flimj.ui.VariableScaleAxis
getTickUnit() - Method in class flimlib.flimj.ui.VariableScaleAxis
 
getUIs() - Method in class flimlib.flimj.ui.controller.AbstractCtrl
Gets the UI service in context.
getValueUnderMouse(double, double) - Method in class flimlib.flimj.ui.PreviewImageDisplay
 
GlobalFitWorker<I extends RealType<I>> - Class in flimlib.flimj.fitworker
 
GlobalFitWorker(FitParams<I>, FitResults, OpEnvironment) - Constructor for class flimlib.flimj.fitworker.GlobalFitWorker
 

I

initialize() - Method in class flimlib.flimj.AbstractFitRAI
 
initialize() - Method in class flimlib.flimj.DefaultDispRslt.Pseudocolor
 
initialize() - Method in class flimlib.flimj.ui.controller.AbstractCtrl
 
initialize() - Method in class flimlib.flimj.ui.controller.ExportCtrl
 
initialize() - Method in class flimlib.flimj.ui.controller.PlotCtrl
 
initialize() - Method in class flimlib.flimj.ui.controller.PreviewCtrl.CBPopOverCtrl
 
initialize() - Method in class flimlib.flimj.ui.controller.PreviewCtrl
 
initialize() - Method in class flimlib.flimj.ui.controller.SettingsCtrl
 
instr - Variable in class flimlib.flimj.FitParams
The array of instrument response (optional)
Int2DMatrix - Class in flimlib
 
Int2DMatrix(long, boolean) - Constructor for class flimlib.Int2DMatrix
 
Int2DMatrix(int, int) - Constructor for class flimlib.Int2DMatrix
 
Int2DMatrix(int[][]) - Constructor for class flimlib.Int2DMatrix
 
Int2DMatrix_asArray(long, Int2DMatrix) - Static method in class flimlib.FLIMLibJNI
 
Int2DMatrix_ncol_get(long, Int2DMatrix) - Static method in class flimlib.FLIMLibJNI
 
Int2DMatrix_nrow_get(long, Int2DMatrix) - Static method in class flimlib.FLIMLibJNI
 
intensityMap - Variable in class flimlib.flimj.FitResults
The image representation of the intensity distribution obtained by summing up photon counts.
invalidateGlobalTrans() - Method in class flimlib.flimj.ui.FitProcessor
Force recalculate globalTrans when required.
invalidateRange(List<Number>) - Method in class flimlib.flimj.ui.VariableScaleAxis
isPickingIRF() - Method in class flimlib.flimj.ui.FitProcessor
 
iThresh - Variable in class flimlib.flimj.FitParams
Intensity threshold value (overrides FitParams.iThreshPercent)
iThreshPercent - Variable in class flimlib.flimj.FitParams
Intensity threshold percentage

L

LIFETIME_LUT - Static variable in class flimlib.flimj.ui.Utils
The LUT for colorizing image (same as the one in TRI2)
LMA_fit(double, double[], int, int, double[], int, double[], double[], boolean[], double[], double[], double, double) - Static method in class flimlib.FLIMLib
 
LMA_fit(double, double[], int, int, double[], int, double[], double[], boolean[], double[], double[], double, double) - Static method in class flimlib.FLIMLibJNI
 
LMAFitWorker<I extends RealType<I>> - Class in flimlib.flimj.fitworker
 
LMAFitWorker(FitParams<I>, FitResults, OpEnvironment) - Constructor for class flimlib.flimj.fitworker.LMAFitWorker
 
LMAGlobalFitRAI() - Constructor for class flimlib.flimj.DefaultFitRAI.LMAGlobalFitRAI
 
LMASingleFitRAI() - Constructor for class flimlib.flimj.DefaultFitRAI.LMASingleFitRAI
 
loadData(float[], float[], FitParams<I>, int[]) - Method in class flimlib.flimj.utils.RAHelper
Fill buffers with data from params.
logScale - Variable in class flimlib.flimj.ui.VariableScaleAxis.AxisRange
Is lowerBound, upperBound, tickUnit in log scale?
logScaleProperty() - Method in class flimlib.flimj.ui.VariableScaleAxis
 
lowerBound - Variable in class flimlib.flimj.ui.VariableScaleAxis.AxisRange
Lower and upper bound and tick difference of the axis (may be log values)
ltAxis - Variable in class flimlib.flimj.FitParams
The index of lifetime axis
ltAxis - Variable in class flimlib.flimj.FitResults
The index of lifetime and parameter axis

M

MainCtrl - Class in flimlib.flimj.ui.controller
The main controller.
MainCtrl() - Constructor for class flimlib.flimj.ui.controller.MainCtrl
 
makeSquareKernel(int) - Static method in class flimlib.flimj.FlimOps
 
matchesNumber(String) - Static method in class flimlib.flimj.ui.Utils
Determines if the string matches the number format.
MAXFIT - Static variable in interface flimlib.FLIMLibConstants
 
moveCursor(double, double) - Method in class flimlib.flimj.ui.PreviewImageDisplay
Moves the mouse cursor to the desired location.
multithread - Variable in class flimlib.flimj.FitParams
Enable multithread fitting (true by default)

N

NAME - Static variable in interface flimlib.flimj.FlimOps.BayesOp
 
NAME - Static variable in interface flimlib.flimj.FlimOps.CalcAPercentOp
 
NAME - Static variable in interface flimlib.flimj.FlimOps.CalcTauMOp
 
NAME - Static variable in interface flimlib.flimj.FlimOps.GlobalOp
 
NAME - Static variable in interface flimlib.flimj.FlimOps.LMAOp
 
NAME - Static variable in interface flimlib.flimj.FlimOps.PhasorOp
 
NAME - Static variable in interface flimlib.flimj.FlimOps.PseudocolorOp
 
NAME - Static variable in interface flimlib.flimj.FlimOps.RLDOp
 
nComp - Variable in class flimlib.flimj.FitParams
The number of exponential components of the fit (1 by default).
nData - Variable in class flimlib.flimj.fitworker.AbstractFitWorker
Should be self-explanatory
nDataOut() - Method in class flimlib.flimj.fitworker.AbstractFitWorker
 
nDataOut() - Method in interface flimlib.flimj.fitworker.FitWorker
How many bins will be fitted?
nDataTotal - Variable in class flimlib.flimj.fitworker.AbstractFitWorker
The number of data copied (including instr prefix/suffix and the part to fit, see below)
new_DecayModel__SWIG_0() - Static method in class flimlib.FLIMLibJNI
 
new_DecayModel__SWIG_1(long, FitFuncNative, float[], boolean[], int, int, float, float, int) - Static method in class flimlib.FLIMLibJNI
 
new_FitFuncNative() - Static method in class flimlib.FLIMLibJNI
 
new_Float2DMatrix__SWIG_0(int, int) - Static method in class flimlib.FLIMLibJNI
 
new_Float2DMatrix__SWIG_1(float[][]) - Static method in class flimlib.FLIMLibJNI
 
new_Int2DMatrix__SWIG_0(int, int) - Static method in class flimlib.FLIMLibJNI
 
new_Int2DMatrix__SWIG_1(int[][]) - Static method in class flimlib.FLIMLibJNI
 
noise - Variable in class flimlib.flimj.FitParams
The assumed noise model of the fit (Poisson by default) @see NoiseType
NoiseType - Enum in flimlib
 
nParam - Variable in class flimlib.flimj.fitworker.AbstractFitWorker
Should be self-explanatory
nParamOut() - Method in class flimlib.flimj.fitworker.AbstractFitWorker
 
nParamOut() - Method in interface flimlib.flimj.fitworker.FitWorker
How many parameters should there be in results.param? E.g.
nParamOut() - Method in class flimlib.flimj.fitworker.PhasorFitWorker
 
NumericHelper - Class in flimlib.flimj.ui.controls
The class defines a helper that takes over the control of a Control that has a TextField as text input.
NumericHelper(TextField, Control, boolean, HashMap<String, Double>) - Constructor for class flimlib.flimj.ui.controls.NumericHelper
Constructs an NumericHelper.
NumericSpinner - Class in flimlib.flimj.ui.controls
The class defines a TextField that consumes only numeric inputs.
NumericSpinner(double, double, double, boolean, HashMap<String, Double>) - Constructor for class flimlib.flimj.ui.controls.NumericSpinner
 
NumericSpinner(double, double, double, boolean) - Constructor for class flimlib.flimj.ui.controls.NumericSpinner
 
NumericSpinner(double, double, double) - Constructor for class flimlib.flimj.ui.controls.NumericSpinner
 
NumericSpinner() - Constructor for class flimlib.flimj.ui.controls.NumericSpinner
Constructs an NumericSpinner.
NumericTextField - Class in flimlib.flimj.ui.controls
The class defines a TextField that consumes only numeric inputs.
NumericTextField(boolean, HashMap<String, Double>) - Constructor for class flimlib.flimj.ui.controls.NumericTextField
Constructs an NumericTextField.
NumericTextField(boolean) - Constructor for class flimlib.flimj.ui.controls.NumericTextField
 
NumericTextField() - Constructor for class flimlib.flimj.ui.controls.NumericTextField
Constructs an NumericTextField.

O

offset - Variable in class flimlib.flimj.ui.VariableScaleAxis.AxisRange
Offset and scale in display units when calculating tick position
onComplete(FitParams<I>, FitResults) - Method in interface flimlib.flimj.fitworker.FitWorker.FitEventHandler
The handler called by FitWorkers upon completion of all fits.
onSingleComplete(int[], FitParams<I>, FitResults) - Method in interface flimlib.flimj.fitworker.FitWorker.FitEventHandler
The handler called by FitWorkers upon completion of a single fit.
onThreadInit() - Method in class flimlib.flimj.fitworker.AbstractSingleFitWorker
Called on the worker thread after worker duplication.
onThreadInit() - Method in class flimlib.flimj.fitworker.BayesFitWorker
 
ops - Variable in class flimlib.flimj.fitworker.AbstractFitWorker
The OpEnvironment the worker may use

P

param - Variable in class flimlib.flimj.FitParams
The estimated parameters of the fit (global setting)
param - Variable in class flimlib.flimj.FitResults
The fitted parameters of the fit
paramBuffer - Variable in class flimlib.flimj.fitworker.AbstractSingleFitWorker
Data buffers, all except for transBuffer are writable
ParamEstimator<I extends RealType<I>> - Class in flimlib.flimj
ParamEstimator
ParamEstimator(FitParams<I>, List<int[]>) - Constructor for class flimlib.flimj.ParamEstimator
 
ParamEstimator(FitParams<I>) - Constructor for class flimlib.flimj.ParamEstimator
 
paramFree - Variable in class flimlib.flimj.FitParams
The indicators of which of the parameters can be changed
paramMap - Variable in class flimlib.flimj.FitParams
The image representation of the estimated parameters the fit (per-pixel setting, overides FitParams.param)
paramMap - Variable in class flimlib.flimj.FitResults
The image representation of fitted parameters of the fit over the the dataset
params - Variable in class flimlib.flimj.fitworker.AbstractFitWorker
The fit parameters for this worker
parentCtrl - Variable in class flimlib.flimj.ui.controller.AbstractCtrl
 
parseDec(String) - Static method in class flimlib.flimj.ui.Utils
Parses the decimal string.
percentFmt(Number) - Static method in class flimlib.flimj.ui.Utils
Formats the value with the default scientific format.
PhasorFitWorker<I extends RealType<I>> - Class in flimlib.flimj.fitworker
 
PhasorFitWorker(FitParams<I>, FitResults, OpEnvironment) - Constructor for class flimlib.flimj.fitworker.PhasorFitWorker
 
PhasorSingleFitRAI() - Constructor for class flimlib.flimj.DefaultFitRAI.PhasorSingleFitRAI
 
PlotCtrl - Class in flimlib.flimj.ui.controller
The controller of the "Plot" tab.
PlotCtrl() - Constructor for class flimlib.flimj.ui.controller.PlotCtrl
 
populate() - Method in class flimlib.flimj.fitworker.AbstractFitWorker
The settings passed into the fit worker is mutable.
populate(FitParams<FloatType>, Dataset, Localizable) - Static method in class flimlib.flimj.ui.FitParamsPrompter
Computes reasonable default values for the given Dataset at the specified position, then confirms them with the user using a JavaFX dialog box.
prettyFmt(Number) - Static method in class flimlib.flimj.ui.Utils
Nicely format the input value to integer/float with at most 5 decimal places or scientific notion with at most 5 decimal places if the number exeeds 10000
PreviewCtrl - Class in flimlib.flimj.ui.controller
The controller of the "Preview" tab.
PreviewCtrl() - Constructor for class flimlib.flimj.ui.controller.PreviewCtrl
 
PreviewCtrl.CBPopOverCtrl - Class in flimlib.flimj.ui.controller
The controller for the colorbar pop over
PreviewImageDisplay - Class in flimlib.flimj.ui
Manages a clickable image display in the Preview pannel.
PreviewImageDisplay(Pane, Group, ImageView) - Constructor for class flimlib.flimj.ui.PreviewImageDisplay
 
PreviewImageDisplay.ImageAnnotator - Interface in flimlib.flimj.ui
Pseudocolor() - Constructor for class flimlib.flimj.DefaultDispRslt.Pseudocolor
 

R

RAHelper<I extends RealType<I>> - Class in flimlib.flimj.utils
 
RAHelper(FitParams<I>, FitResults) - Constructor for class flimlib.flimj.utils.RAHelper
 
rawChisq_target - Variable in class flimlib.flimj.fitworker.AbstractFitWorker
The raw chisq target (params.chisq is reduced by DOF)
refresh(FitParams<FloatType>, FitResults) - Method in class flimlib.flimj.ui.controller.AbstractCtrl
The callback called when the controller is supposed to refresh itself based on the parameters and the results provided by the arguments.
refresh(FitParams<FloatType>, FitResults) - Method in class flimlib.flimj.ui.controller.ExportCtrl
 
refresh(FitParams<FloatType>, FitResults) - Method in class flimlib.flimj.ui.controller.PlotCtrl
 
refresh(FitParams<FloatType>, FitResults) - Method in class flimlib.flimj.ui.controller.PreviewCtrl
 
refresh(FitParams<FloatType>, FitResults) - Method in class flimlib.flimj.ui.controller.SettingsCtrl
 
refreshControllers() - Method in class flimlib.flimj.ui.FitProcessor
Refreshes all controllers.
requestRefresh() - Method in class flimlib.flimj.ui.controller.AbstractCtrl
Called by external control flow to notify the controller to refresh itself.
requestUpdate() - Method in class flimlib.flimj.ui.controller.AbstractCtrl
Called by the controller to notify the fit processor to perform a fit and other controllers to update themselves based on the fit results.
residualBuffer - Variable in class flimlib.flimj.fitworker.AbstractSingleFitWorker
Data buffers, all except for transBuffer are writable
residuals - Variable in class flimlib.flimj.FitResults
The residuals (y - y_fitted) of the fit
residualsMap - Variable in class flimlib.flimj.FitResults
The image representation of residuals of the fit over the the dataset
restrain - Variable in class flimlib.flimj.FitParams
The fit restraint (RestrainType.ECF_RESTRAIN_DEFAULT by default)
restraintMax - Variable in class flimlib.flimj.FitParams
The fit restraints (min or max) for each parameter.
restraintMin - Variable in class flimlib.flimj.FitParams
The fit restraints (min or max) for each parameter.
RestrainType - Enum in flimlib
 
results - Variable in class flimlib.flimj.fitworker.AbstractFitWorker
The fit results for this worker
RET_BAD_FIT_CHISQ_OUT_OF_RANGE - Static variable in class flimlib.flimj.FitResults
The return code for a fit that succeeded but has chisq > 1e5
RET_BAD_FIT_DIVERGED - Static variable in class flimlib.flimj.FitResults
The return code for a fit that failed by flimlib
RET_BAD_SETTING - Static variable in class flimlib.flimj.FitResults
The return code for a fit that failed because of improper arguments
RET_INTENSITY_BELOW_THRESH - Static variable in class flimlib.flimj.FitResults
The return code for a fit that was not performed because the intensity is below threshold
RET_INTERNAL_ERROR - Static variable in class flimlib.flimj.FitResults
The return code for a fit that failed because of error in native code (e.g.
RET_OK - Static variable in class flimlib.flimj.FitResults
The return code for a good fit
RET_UNKNOWN - Static variable in class flimlib.flimj.FitResults
The return code for unknown fit status
retCode - Variable in class flimlib.flimj.FitResults
The return code of the fit
retCodeMap - Variable in class flimlib.flimj.FitResults
The image representation of return codes of the fit over the dataset
RLD_fit(double, double[], int, int, double[], int, double[], double[], double[], double[], double[], double[], double) - Static method in class flimlib.FLIMLib
 
RLD_fit(double, double[], int, int, double[], int, double[], double[], double[], double[], double[], double[], double) - Static method in class flimlib.FLIMLibJNI
 
RLDFitWorker<I extends RealType<I>> - Class in flimlib.flimj.fitworker
 
RLDFitWorker(FitParams<I>, FitResults, OpEnvironment) - Constructor for class flimlib.flimj.fitworker.RLDFitWorker
 
RLDSingleFitRAI() - Constructor for class flimlib.flimj.DefaultFitRAI.RLDSingleFitRAI
 
roiMask - Variable in class flimlib.flimj.FitParams
The ROI mask (test() returns true on interested regions)
run() - Method in class flimlib.flimj.ui.FLIMJCommand
 

S

scale - Variable in class flimlib.flimj.ui.VariableScaleAxis.AxisRange
Offset and scale in display units when calculating tick position
setAlgo(FitProcessor.FitType) - Method in class flimlib.flimj.ui.FitProcessor
 
setBinning(int) - Method in class flimlib.flimj.ui.FitProcessor
 
setCB(RealLUTConverter<FloatType>) - Method in class flimlib.flimj.ui.controller.PreviewCtrl.CBPopOverCtrl
Draw a new cb when it needs update.
setClamped(Double) - Method in class flimlib.flimj.ui.controls.NumericSpinner
 
setControllers(AbstractCtrl...) - Method in class flimlib.flimj.ui.FitProcessor
 
setFitProcessor(FitProcessor) - Method in class flimlib.flimj.ui.controller.AbstractCtrl
Sets the fit processor behind the controller.
setFitProcessor(FitProcessor) - Method in class flimlib.flimj.ui.controller.MainCtrl
 
setImage(RandomAccessibleInterval<FloatType>, RealLUTConverter<FloatType>, PreviewImageDisplay.ImageAnnotator) - Method in class flimlib.flimj.ui.PreviewImageDisplay
Shows an float-valued image, colored by a converter and possibly annotated by a annotator.
setIntOnly(boolean) - Method in class flimlib.flimj.ui.controls.NumericHelper
 
setIntOnly(boolean) - Method in class flimlib.flimj.ui.controls.NumericSpinner
 
setIntOnly(boolean) - Method in class flimlib.flimj.ui.controls.NumericTextField
 
setIRF(FitParams<FloatType>) - Method in class flimlib.flimj.ui.FitProcessor
 
setIsPickingIRF(boolean) - Method in class flimlib.flimj.ui.FitProcessor
 
setKwMap(HashMap<String, Double>) - Method in class flimlib.flimj.ui.controls.NumericHelper
 
setKwMap(HashMap<String, Double>) - Method in class flimlib.flimj.ui.controls.NumericSpinner
 
setKwMap(HashMap<String, Double>) - Method in class flimlib.flimj.ui.controls.NumericTextField
 
setLogScale(boolean) - Method in class flimlib.flimj.ui.VariableScaleAxis
 
setMax(double) - Method in class flimlib.flimj.ui.controls.NumericHelper
 
setMax(double) - Method in class flimlib.flimj.ui.controls.NumericSpinner
 
setMin(double) - Method in class flimlib.flimj.ui.controls.NumericHelper
 
setMin(double) - Method in class flimlib.flimj.ui.controls.NumericSpinner
 
setOwner(Node) - Method in class flimlib.flimj.ui.controller.PreviewCtrl.CBPopOverCtrl
setParentCtrl(AbstractCtrl) - Method in class flimlib.flimj.ui.controller.AbstractCtrl
Sets the parent controller of this controller.
setPixScale(double) - Method in class flimlib.flimj.ui.PreviewImageDisplay
 
setPopOver(PopOver) - Method in class flimlib.flimj.ui.controller.PreviewCtrl.CBPopOverCtrl
 
setPreviewOptions(List<String>) - Method in class flimlib.flimj.ui.FitProcessor
 
setPreviewPos(int, int, boolean) - Method in class flimlib.flimj.ui.FitProcessor
 
setProgress(Double) - Method in class flimlib.flimj.ui.controller.MainCtrl
Set the state of progress overlay.
setRange(Object, boolean) - Method in class flimlib.flimj.ui.VariableScaleAxis
setStepSize(double) - Method in class flimlib.flimj.ui.controls.NumericSpinner
 
setTickUnit(double) - Method in class flimlib.flimj.ui.VariableScaleAxis
 
SettingsCtrl - Class in flimlib.flimj.ui.controller
The controller of the "Settings" tab.
SettingsCtrl() - Constructor for class flimlib.flimj.ui.controller.SettingsCtrl
 
sig - Variable in class flimlib.flimj.FitParams
The standard deviation (sigma) of the data, used for calculating chi-squared if FitParams.noise is NoiseType.NOISE_CONST or NoiseType.NOISE_GIVEN.
SQUARE_KERNEL_3 - Static variable in class flimlib.flimj.FlimOps
 
SQUARE_KERNEL_5 - Static variable in class flimlib.flimj.FlimOps
 
submitRunnable(Runnable) - Method in class flimlib.flimj.ui.FitProcessor
 
swapInLtAxis(long[], int) - Static method in class flimlib.flimj.ui.FitProcessor
Permute the coordinates from ltDimension-last to ltDimension-at-ltAxis.
swapOutLtAxis(long[], int) - Static method in class flimlib.flimj.ui.FitProcessor
Permute the coordinates from ltDimension-at-ltAxis to ltDimension-last.
swigCMemOwn - Variable in class flimlib.DecayModel
 
swigCMemOwn - Variable in class flimlib.Float2DMatrix
 
swigCMemOwn - Variable in class flimlib.Int2DMatrix
 
SwigDirector_FitFuncNative_fit(FitFuncNative, float, float[], float[]) - Static method in class flimlib.FLIMLibJNI
 
swigToEnum(int) - Static method in enum flimlib.FitType
 
swigToEnum(int) - Static method in enum flimlib.NoiseType
 
swigToEnum(int) - Static method in enum flimlib.RestrainType
 
swigValue() - Method in enum flimlib.FitType
 
swigValue() - Method in enum flimlib.NoiseType
 
swigValue() - Method in enum flimlib.RestrainType
 

T

tickUnit - Variable in class flimlib.flimj.ui.VariableScaleAxis.AxisRange
Lower and upper bound and tick difference of the axis (may be log values)
tickUnitProperty() - Method in class flimlib.flimj.ui.VariableScaleAxis
 
toJSON() - Method in class flimlib.flimj.FitParams
Serialize this FitParams into a JSON string.
toString() - Method in class flimlib.flimj.FitParams
 
toString() - Method in class flimlib.Float2DMatrix
 
toString() - Method in class flimlib.Int2DMatrix
 
trans - Variable in class flimlib.flimj.FitParams
The transient data to fit
transBuffer - Variable in class flimlib.flimj.fitworker.AbstractSingleFitWorker
Data buffers, all except for transBuffer are writable
transMap - Variable in class flimlib.flimj.FitParams
The image representation of the dataset

U

UIException - Exception in flimlib.flimj.ui
Indicates that a FLIMJ-UI specific exception has occurred.
UIException(String) - Constructor for exception flimlib.flimj.ui.UIException
 
UIException(Exception) - Constructor for exception flimlib.flimj.ui.UIException
 
UNINIT - Static variable in class flimlib.flimj.FitParams
Fields with this value are uninitialized
updateFit() - Method in class flimlib.flimj.ui.FitProcessor
 
updateFit(boolean) - Method in class flimlib.flimj.ui.FitProcessor
 
updateIRFRange() - Method in class flimlib.flimj.ui.FitProcessor
 
upperBound - Variable in class flimlib.flimj.ui.VariableScaleAxis.AxisRange
Lower and upper bound and tick difference of the axis (may be log values)
Utils - Class in flimlib.flimj.ui
Utils
Utils() - Constructor for class flimlib.flimj.ui.Utils
 

V

valueOf(String) - Static method in enum flimlib.FitType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum flimlib.flimj.ui.FitProcessor.FitType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum flimlib.NoiseType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum flimlib.RestrainType
Returns the enum constant of this type with the specified name.
values() - Static method in enum flimlib.FitType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum flimlib.flimj.ui.FitProcessor.FitType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum flimlib.NoiseType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum flimlib.RestrainType
Returns an array containing the constants of this enum type, in the order they are declared.
VariableScaleAxis - Class in flimlib.flimj.ui
A variable (log/linear) scale axis implementation for JavaFX 2 charts.
VariableScaleAxis() - Constructor for class flimlib.flimj.ui.VariableScaleAxis
Creates a autoranging log axis.
VariableScaleAxis(double, double, double) - Constructor for class flimlib.flimj.ui.VariableScaleAxis
Creates a fixed range log axis.
VariableScaleAxis.AxisRange - Class in flimlib.flimj.ui
The bean for passing range information.

X

xInc - Variable in class flimlib.flimj.FitParams
The time increment between two consecutive data points
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