Index (SciJava Ops FLIM 1.0.0 API)

A B C D E F G I L M N O P R S T U X
All Classes All Packages

A

AbstractFitRAI,K extends RealType<K>> - Class in org.scijava.ops.flim: Shared base class for all FLIM fitting Ops
AbstractFitRAI() - Constructor for class org.scijava.ops.flim.AbstractFitRAI
AbstractFitWorker> - Class in org.scijava.ops.flim.impl: AbstractFitWorker
AbstractFitWorker(FitParams, FitResults) - Constructor for class org.scijava.ops.flim.impl.AbstractFitWorker
AbstractSingleFitWorker> - Class in org.scijava.ops.flim.impl
AbstractSingleFitWorker(FitParams, FitResults) - Constructor for class org.scijava.ops.flim.impl.AbstractSingleFitWorker
adjFitEnd - Variable in class org.scijava.ops.flim.impl.AbstractFitWorker: The adjusted FitParams.fitStart and FitParams.fitEnd taking into account leading instr prefix (see below)
adjFitStart - Variable in class org.scijava.ops.flim.impl.AbstractFitWorker: The adjusted FitParams.fitStart and FitParams.fitEnd taking into account leading instr prefix (see below)
afterFit() - Method in class org.scijava.ops.flim.impl.AbstractSingleFitWorker: A routine called after doFit().
afterFit() - Method in class org.scijava.ops.flim.impl.PhasorFit.PhasorFitWorker
afterFit() - Method in class org.scijava.ops.flim.impl.RLDFit.RLDFitWorker
AmplitudeFractions - Class in org.scijava.ops.flim: Ops pertaining to fractional contribution calculation
AmplitudeFractions() - Constructor for class org.scijava.ops.flim.AmplitudeFractions
apply(FitParams, RealMask, RandomAccessibleInterval<K>, FitWorker.FitEventHandler) - Method in class org.scijava.ops.flim.AbstractFitRAI
apply(FitResults, Float, Float, Float, Float, ColorTable) - Method in class org.scijava.ops.flim.Pseudocolor

B

baseClass() - Method in class org.scijava.ops.flim.types.FitParamsTypeExtractor
BayesFit - Class in org.scijava.ops.flim.impl
BayesFit() - Constructor for class org.scijava.ops.flim.impl.BayesFit
BayesFit.BayesFitWorker> - Class in org.scijava.ops.flim.impl
BayesFit.BayesSingleFitRAI,K extends RealType<K>> - Class in org.scijava.ops.flim.impl: Fits a RAI
BayesFitWorker(FitParams, FitResults, Function<FitParams, FitResults>, BiFunction<Img<FloatType>, Integer, FloatType>) - Constructor for class org.scijava.ops.flim.impl.BayesFit.BayesFitWorker
BayesSingleFitRAI() - Constructor for class org.scijava.ops.flim.impl.BayesFit.BayesSingleFitRAI
beforeFit() - Method in class org.scijava.ops.flim.impl.AbstractSingleFitWorker: A routine called before doFit().
beforeFit() - Method in class org.scijava.ops.flim.impl.BayesFit.BayesFitWorker
beforeFit() - Method in class org.scijava.ops.flim.impl.LMAFit.LMAFitWorker
beforeFit() - Method in class org.scijava.ops.flim.impl.PhasorFit.PhasorFitWorker
beforeFit() - Method in class org.scijava.ops.flim.impl.RLDFit.RLDFitWorker

C

chisq - Variable in class org.scijava.ops.flim.FitResults: The reduced chi-squared of the fit.
chisq_delta - Variable in class org.scijava.ops.flim.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 org.scijava.ops.flim.FitParams: Confidence interval when calculating the error axes (95% by default)
chisq_target - Variable in class org.scijava.ops.flim.FitParams: Stopping condition 1: stop if reduced chi-squared is less than FitParams.chisq_target (1 by default)
chisqBuffer - Variable in class org.scijava.ops.flim.impl.AbstractSingleFitWorker: Data buffers, all except for transBuffer are writable
chisqMap - Variable in class org.scijava.ops.flim.FitResults: The image representation of reduced chi-squared of the fit over the the dataset
commitRslts(FitParams, FitResults, int[]) - Method in class org.scijava.ops.flim.util.RAHelper: Put results back into the proper position in rslts.
copy() - Method in class org.scijava.ops.flim.FitParams: Create a new instance of FitParams with shallow copy (maps are not duplicated).
copy() - Method in class org.scijava.ops.flim.FitResults: Create a new instance of FitResults with shallow copy (maps are not duplicated).
createWorker(FitParams, FitResults) - Method in class org.scijava.ops.flim.AbstractFitRAI: Generates a worker for the actual fit.
createWorker(FitParams, FitResults) - Method in class org.scijava.ops.flim.impl.BayesFit.BayesSingleFitRAI
createWorker(FitParams, FitResults) - Method in class org.scijava.ops.flim.impl.GlobalFit.GlobalSingleFitRAI
createWorker(FitParams, FitResults) - Method in class org.scijava.ops.flim.impl.LMAFit.LMASingleFitRAI
createWorker(FitParams, FitResults) - Method in class org.scijava.ops.flim.impl.PhasorFit.PhasorSingleFitRAI
createWorker(FitParams, FitResults) - Method in class org.scijava.ops.flim.impl.RLDFit.RLDSingleFitRAI
Creators - Class in org.scijava.ops.flim.impl: create Ops for use in FLIM analysis

D

defaultAmplitudeFraction(FitResults, int) - Static method in class org.scijava.ops.flim.AmplitudeFractions
defaultMeanLifetime(FitResults) - Static method in class org.scijava.ops.flim.MeanLifetimes
doFit() - Method in class org.scijava.ops.flim.impl.AbstractSingleFitWorker: Does the actual implementation-specific fitting routine.
doFit() - Method in class org.scijava.ops.flim.impl.BayesFit.BayesFitWorker: Performs an Bayes fit.
doFit() - Method in class org.scijava.ops.flim.impl.LMAFit.LMAFitWorker: Performs an LMA fit.
doFit() - Method in class org.scijava.ops.flim.impl.PhasorFit.PhasorFitWorker
doFit() - Method in class org.scijava.ops.flim.impl.RLDFit.RLDFitWorker: Performs the RLD fit.
dropBad - Variable in class org.scijava.ops.flim.FitParams: Whether to declare FitResults.retCode as FitResults.RET_BAD_FIT_CHISQ_OUT_OF_RANGE or FitResults.RET_BAD_FIT_DIVERGED if FitResults.chisq is larger than 1e5 or less than 0.
duplicate(FitParams, FitResults) - Method in class org.scijava.ops.flim.impl.AbstractSingleFitWorker: Make a worker of the same kind but does not share any writable buffers (thread safe) if that buffer is null.
duplicate(FitParams, FitResults) - Method in class org.scijava.ops.flim.impl.BayesFit.BayesFitWorker
duplicate(FitParams, FitResults) - Method in class org.scijava.ops.flim.impl.LMAFit.LMAFitWorker
duplicate(FitParams, FitResults) - Method in class org.scijava.ops.flim.impl.PhasorFit.PhasorFitWorker
duplicate(FitParams, FitResults) - Method in class org.scijava.ops.flim.impl.RLDFit.RLDFitWorker

E

estimateIThreshold() - Method in class org.scijava.ops.flim.ParamEstimator
estimateStartEnd() - Method in class org.scijava.ops.flim.ParamEstimator

F

fitBatch(List<int[]>, FitWorker.FitEventHandler) - Method in interface org.scijava.ops.flim.FitWorker: Fit all coordinates listed and handles fit events.
fitBatch(List<int[]>, FitWorker.FitEventHandler) - Method in class org.scijava.ops.flim.impl.AbstractSingleFitWorker
fitBatch(List<int[]>, FitWorker.FitEventHandler) - Method in class org.scijava.ops.flim.impl.GlobalFit.GlobalFitWorker
fitEnd - Variable in class org.scijava.ops.flim.FitParams: The end of the decay interval
fitFunc - Variable in class org.scijava.ops.flim.FitParams: The fitting model to use (Z + A_1e^(-t/tau_1) + A_2e^(-t/tau_2) + ...
FitParams> - Class in org.scijava.ops.flim: The collection of all fit parameters required to perform a single fit of an image.
FitParams() - Constructor for class org.scijava.ops.flim.FitParams
FitParamsTypeExtractor - Class in org.scijava.ops.flim.types: A TypeExtractor that reifies FitParams.
FitParamsTypeExtractor() - Constructor for class org.scijava.ops.flim.types.FitParamsTypeExtractor
FitResults - Class in org.scijava.ops.flim: The collection of all results generated by a single fit of an image.
FitResults() - Constructor for class org.scijava.ops.flim.FitResults
fitSingle() - Method in class org.scijava.ops.flim.impl.AbstractSingleFitWorker: Fit the data in the buffer.
fitStart - Variable in class org.scijava.ops.flim.FitParams: The start of the decay interval
fitted - Variable in class org.scijava.ops.flim.FitResults: The fitted transients of the fit
fittedBuffer - Variable in class org.scijava.ops.flim.impl.AbstractSingleFitWorker: Data buffers, all except for transBuffer are writable
fittedMap - Variable in class org.scijava.ops.flim.FitResults: The image representation of fitted transients of the fit over the the dataset
FitWorker> - Interface in org.scijava.ops.flim
FitWorker.FitEventHandler> - Interface in org.scijava.ops.flim: The handler interface for fit events.
fromJSON(String) - Static method in class org.scijava.ops.flim.FitParams: Creates a FitParams from serialized JSON string.

G

getChisqMap - Variable in class org.scijava.ops.flim.FitParams: Whether to generate an image representation for chi-squred (false by default)
getFittedMap - Variable in class org.scijava.ops.flim.FitParams: Whether to generate an image representation for fitted transients (false by default)
getIntensityMap() - Method in class org.scijava.ops.flim.ParamEstimator
getParamMap - Variable in class org.scijava.ops.flim.FitParams: Whether to generate an image representation for fitted parameters (true by default)
getResidualsMap - Variable in class org.scijava.ops.flim.FitParams: Whether to generate an image representation for residuals (false by default)
getReturnCodeMap - Variable in class org.scijava.ops.flim.FitParams: Whether to generate an image representation for the return codes (false by default)
getTypeParameters(TypeReifier, FitParams<?>) - Method in class org.scijava.ops.flim.types.FitParamsTypeExtractor
GlobalFit - Class in org.scijava.ops.flim.impl
GlobalFit() - Constructor for class org.scijava.ops.flim.impl.GlobalFit
GlobalFit.GlobalFitWorker> - Class in org.scijava.ops.flim.impl
GlobalFit.GlobalSingleFitRAI,K extends RealType<K>> - Class in org.scijava.ops.flim.impl: Fits a RAI
GlobalFitWorker(FitParams, FitResults) - Constructor for class org.scijava.ops.flim.impl.GlobalFit.GlobalFitWorker
GlobalSingleFitRAI() - Constructor for class org.scijava.ops.flim.impl.GlobalFit.GlobalSingleFitRAI

I

instr - Variable in class org.scijava.ops.flim.FitParams: The array of instrument response (optional)
intensityMap - Variable in class org.scijava.ops.flim.FitResults: The image representation of the intensity distribution obtained by summing up photon counts.
iThresh - Variable in class org.scijava.ops.flim.FitParams: Intensity threshold value (overrides FitParams.iThreshPercent)
iThreshPercent - Variable in class org.scijava.ops.flim.FitParams: Intensity threshold percentage

L

LMAFit - Class in org.scijava.ops.flim.impl
LMAFit() - Constructor for class org.scijava.ops.flim.impl.LMAFit
LMAFit.LMAFitWorker> - Class in org.scijava.ops.flim.impl
LMAFit.LMASingleFitRAI,K extends RealType<K>> - Class in org.scijava.ops.flim.impl: Fits a RAI
LMAFitWorker(FitParams, FitResults) - Constructor for class org.scijava.ops.flim.impl.LMAFit.LMAFitWorker
LMASingleFitRAI() - Constructor for class org.scijava.ops.flim.impl.LMAFit.LMASingleFitRAI
loadData(float[], float[], FitParams, int[]) - Method in class org.scijava.ops.flim.util.RAHelper: Fill buffers with data from params.
ltAxis - Variable in class org.scijava.ops.flim.FitParams: The index of lifetime axis
ltAxis - Variable in class org.scijava.ops.flim.FitResults: The index of lifetime and parameter axis

M

makeSquareKernel(int) - Static method in class org.scijava.ops.flim.impl.Creators: Convenience method to generate a square kernel for use in flim Ops
MeanLifetimes - Class in org.scijava.ops.flim: Ops pertaining to mean lifetime calculation
MeanLifetimes() - Constructor for class org.scijava.ops.flim.MeanLifetimes
multithread - Variable in class org.scijava.ops.flim.FitParams: Enable multithread fitting (true by default)

N

nComp - Variable in class org.scijava.ops.flim.FitParams: The number of exponential components of the fit (1 by default).
nData - Variable in class org.scijava.ops.flim.impl.AbstractFitWorker: Should be self-explanatory
nDataOut() - Method in interface org.scijava.ops.flim.FitWorker: How many bins will be fitted?
nDataOut() - Method in class org.scijava.ops.flim.impl.AbstractFitWorker
nDataTotal - Variable in class org.scijava.ops.flim.impl.AbstractFitWorker: The number of data copied (including instr prefix/suffix and the part to fit, see below)
noise - Variable in class org.scijava.ops.flim.FitParams: The assumed noise model of the fit (Poisson by default) @see NoiseType
nParam - Variable in class org.scijava.ops.flim.impl.AbstractFitWorker: Should be self-explanatory
nParamOut() - Method in interface org.scijava.ops.flim.FitWorker: How many parameters should there be in results.param? E.g.
nParamOut() - Method in class org.scijava.ops.flim.impl.AbstractFitWorker
nParamOut() - Method in class org.scijava.ops.flim.impl.PhasorFit.PhasorFitWorker

O

onComplete(FitParams, FitResults) - Method in interface org.scijava.ops.flim.FitWorker.FitEventHandler: The handler called by FitWorkers upon completion of all fits.
onSingleComplete(int[], FitParams, FitResults) - Method in interface org.scijava.ops.flim.FitWorker.FitEventHandler: The handler called by FitWorkers upon completion of a single fit.
onThreadInit() - Method in class org.scijava.ops.flim.impl.AbstractSingleFitWorker: Called on the worker thread after worker duplication.
onThreadInit() - Method in class org.scijava.ops.flim.impl.BayesFit.BayesFitWorker
org.scijava.ops.flim - module org.scijava.ops.flim
org.scijava.ops.flim - package org.scijava.ops.flim
org.scijava.ops.flim.impl - package org.scijava.ops.flim.impl
org.scijava.ops.flim.types - package org.scijava.ops.flim.types
org.scijava.ops.flim.util - package org.scijava.ops.flim.util

P

param - Variable in class org.scijava.ops.flim.FitParams: The estimated parameters of the fit (global setting)
param - Variable in class org.scijava.ops.flim.FitResults: The fitted parameters of the fit
paramBuffer - Variable in class org.scijava.ops.flim.impl.AbstractSingleFitWorker: Data buffers, all except for transBuffer are writable
ParamEstimator> - Class in org.scijava.ops.flim: ParamEstimator
ParamEstimator(FitParams) - Constructor for class org.scijava.ops.flim.ParamEstimator
ParamEstimator(FitParams, List<int[]>) - Constructor for class org.scijava.ops.flim.ParamEstimator
paramFree - Variable in class org.scijava.ops.flim.FitParams: The indicators of which of the parameters can be changed
paramMap - Variable in class org.scijava.ops.flim.FitParams: The image representation of the estimated parameters the fit (per-pixel setting, overides FitParams.param)
paramMap - Variable in class org.scijava.ops.flim.FitResults: The image representation of fitted parameters of the fit over the the dataset
params - Variable in class org.scijava.ops.flim.impl.AbstractFitWorker: The fit parameters for this worker
PhasorFit - Class in org.scijava.ops.flim.impl
PhasorFit() - Constructor for class org.scijava.ops.flim.impl.PhasorFit
PhasorFit.PhasorFitWorker> - Class in org.scijava.ops.flim.impl
PhasorFit.PhasorSingleFitRAI,K extends RealType<K>> - Class in org.scijava.ops.flim.impl: Fits a RAI
PhasorFitWorker(FitParams, FitResults) - Constructor for class org.scijava.ops.flim.impl.PhasorFit.PhasorFitWorker
PhasorSingleFitRAI() - Constructor for class org.scijava.ops.flim.impl.PhasorFit.PhasorSingleFitRAI
populate() - Method in class org.scijava.ops.flim.impl.AbstractFitWorker: The settings passed into the fit worker is mutable.
Pseudocolor - Class in org.scijava.ops.flim: Generates an HSV pseudocolored image of FLIM fit results, where for each pixel: The Hue is a function of the lifetime fit parameters The Value is a function of the initial intensity fit parameters
Pseudocolor() - Constructor for class org.scijava.ops.flim.Pseudocolor

R

RAHelper> - Class in org.scijava.ops.flim.util
RAHelper(FitParams, FitResults) - Constructor for class org.scijava.ops.flim.util.RAHelper
rawChisq_target - Variable in class org.scijava.ops.flim.impl.AbstractFitWorker: The raw chisq target (params.chisq is reduced by DOF)
residualBuffer - Variable in class org.scijava.ops.flim.impl.AbstractSingleFitWorker: Data buffers, all except for transBuffer are writable
residuals - Variable in class org.scijava.ops.flim.FitResults: The residuals (y - y_fitted) of the fit
residualsMap - Variable in class org.scijava.ops.flim.FitResults: The image representation of residuals of the fit over the the dataset
restrain - Variable in class org.scijava.ops.flim.FitParams: The fit restraint (RestrainType.ECF_RESTRAIN_DEFAULT by default)
restraintMax - Variable in class org.scijava.ops.flim.FitParams: The fit restraints (min or max) for each parameter.
restraintMin - Variable in class org.scijava.ops.flim.FitParams: The fit restraints (min or max) for each parameter.
results - Variable in class org.scijava.ops.flim.impl.AbstractFitWorker: The fit results for this worker
RET_BAD_FIT_CHISQ_OUT_OF_RANGE - Static variable in class org.scijava.ops.flim.FitResults: The return code for a fit that succeeded but has chisq > 1e5
RET_BAD_FIT_DIVERGED - Static variable in class org.scijava.ops.flim.FitResults: The return code for a fit that failed by flimlib
RET_BAD_SETTING - Static variable in class org.scijava.ops.flim.FitResults: The return code for a fit that failed because of improper arguments
RET_INTENSITY_BELOW_THRESH - Static variable in class org.scijava.ops.flim.FitResults: The return code for a fit that was not performed because the intensity is below threshold
RET_INTERNAL_ERROR - Static variable in class org.scijava.ops.flim.FitResults: The return code for a fit that failed because of error in native code (e.g.
RET_OK - Static variable in class org.scijava.ops.flim.FitResults: The return code for a good fit
RET_UNKNOWN - Static variable in class org.scijava.ops.flim.FitResults: The return code for unknown fit status
retCode - Variable in class org.scijava.ops.flim.FitResults: The return code of the fit
retCodeMap - Variable in class org.scijava.ops.flim.FitResults: The image representation of return codes of the fit over the dataset
RLDFit - Class in org.scijava.ops.flim.impl
RLDFit() - Constructor for class org.scijava.ops.flim.impl.RLDFit
RLDFit.RLDFitWorker> - Class in org.scijava.ops.flim.impl
RLDFit.RLDSingleFitRAI,K extends RealType<K>> - Class in org.scijava.ops.flim.impl: Fits a RAI
RLDFitWorker(FitParams, FitResults) - Constructor for class org.scijava.ops.flim.impl.RLDFit.RLDFitWorker
RLDSingleFitRAI() - Constructor for class org.scijava.ops.flim.impl.RLDFit.RLDSingleFitRAI
roiMask - Variable in class org.scijava.ops.flim.FitParams: The ROI mask (test() returns true on interested regions)
runMultiThreaded() - Method in class org.scijava.ops.flim.impl.AbstractSingleFitWorker
runMultiThreaded() - Method in class org.scijava.ops.flim.impl.BayesFit.BayesFitWorker

S

sig - Variable in class org.scijava.ops.flim.FitParams: The standard deviation (sigma) of the data, used for calculating chi-squared if FitParams.noise is NoiseType.NOISE_CONST or NoiseType.NOISE_GIVEN.
spci() - Static method in class org.scijava.ops.flim.Pseudocolor: ColorTable used by the SPCI application

T

toJSON() - Method in class org.scijava.ops.flim.FitParams: Serialize this FitParams into a JSON string.
toString() - Method in class org.scijava.ops.flim.FitParams
trans - Variable in class org.scijava.ops.flim.FitParams: The transient data to fit
transBuffer - Variable in class org.scijava.ops.flim.impl.AbstractSingleFitWorker: Data buffers, all except for transBuffer are writable
transMap - Variable in class org.scijava.ops.flim.FitParams: The image representation of the dataset
tri2() - Static method in class org.scijava.ops.flim.Pseudocolor: ColorTable used by the TRI2 application

U

UNINIT - Static variable in class org.scijava.ops.flim.FitParams: Fields with this value are uninitialized

X

xInc - Variable in class org.scijava.ops.flim.FitParams: The time increment between two consecutive data points

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