Index (fijirelax 4.0.10 API)

A B C D E F G H I J K L M N O P R S T U V W X Y Z
All Classes All Packages

A

actionPerformed(ActionEvent) - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Action performed.
actionPerformed(ActionEvent) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Action performed.
actualDay - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The actual day.
actualizeCursor() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Actualize the ROI Cursor
actualizeDisplayedNumbers() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Actualize displayed numbers in the central tab
actualizeFirstPlots() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Update graphs using new computed results--------------------------------------------------------------------------------.
actualizeFirstPlotsT1() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Actualize plots of T1 spectrum.
actualizeFirstPlotsT1T2() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Actualize first plots T 1 T 2.
actualizeFirstPlotsT2() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Actualize plots of T2 spectrum.
actualizeMeanEstimations() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Actualize mean when data changed (ROI or cursor clicked)
actualizeMriObservationsBasedOnData() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Actualize mri observations based on data of the ROI or the clicked area
actualizeRangingBoundaries() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Actualize ranging boundaries for display selection in the spectrum
actualizeSecondPlots() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Actualize Secondary plots.
actualizeSelectedEcho(int) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Actualize selected echo, when scrolling the mouse
actualizeSpectrumCurves() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Actualize spectrum curves.
actualizeSpectrumCurvesT1() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Actualize spectrum curves
actualizeSpectrumCurvesT1T2() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Actualize spectrum curves when computing cross-fitting T1T2
actualizeSpectrumCurvesT2() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Actualize spectrum curves T 2.
addLog(String, int) - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Adds the log.
adjustContrast() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Adjust the contrast of all the slices in the HyperMap to provide a smooth visualization of data
alpha - Variable in class io.github.rocsg.fijirelax.curvefit.MRLMA: The alpha.
alpha - Variable in class io.github.rocsg.fijirelax.lma.LMA: The alpha.
ArrayConverter - Class in io.github.rocsg.fijirelax.lma: The Class ArrayConverter.
ArrayConverter() - Constructor for class io.github.rocsg.fijirelax.lma.ArrayConverter
ArrayConverter.SeparatedData - Class in io.github.rocsg.fijirelax.lma: The Class SeparatedData.
asDoubleArray(float[]) - Static method in class io.github.rocsg.fijirelax.lma.ArrayConverter: Get float array as a double array.
asDoubleArray(float[][]) - Static method in class io.github.rocsg.fijirelax.lma.ArrayConverter: Get float array as a double array.
asFloatArray(double[]) - Static method in class io.github.rocsg.fijirelax.lma.ArrayConverter: Get double array as float array.

B

besFunkCost(double, double) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Bes funk cost.
besFunkDeriv(double, double) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Bes funk deriv. derivative of the bessel function on the corresponding value
bessi0NoExp(double) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Bessi 0 no exp.
bessi1NoExp(double) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Bessi 1 no exp.
beta - Variable in class io.github.rocsg.fijirelax.curvefit.MRLMA: The beta.
beta - Variable in class io.github.rocsg.fijirelax.lma.LMA: The beta.
buildLookupTable() - Method in class io.github.rocsg.fijirelax.mrialgo.RiceEstimator: Builds the lookup table among possible values of sigma and observations
buildObservationRange() - Method in class io.github.rocsg.fijirelax.mrialgo.RiceEstimator: Builds the observation range.
buildSigmaRange() - Method in class io.github.rocsg.fijirelax.mrialgo.RiceEstimator: Builds the sigma range tab

C

C - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Number of channels in the HyperMaps, including original echoes, and maps if so.
calculateAlphaElement(int, int) - Method in class io.github.rocsg.fijirelax.curvefit.MRLMA
calculateAlphaElement(int, int) - Method in class io.github.rocsg.fijirelax.lma.LMA
calculateBetaElement(int) - Method in class io.github.rocsg.fijirelax.curvefit.MRLMA
calculateBetaElement(int) - Method in class io.github.rocsg.fijirelax.lma.LMA
calculateChi2() - Method in class io.github.rocsg.fijirelax.curvefit.MRLMA: Calculate chi 2.
calculateChi2() - Method in class io.github.rocsg.fijirelax.lma.LMA: Calculate chi 2.
calculateChi2(double[]) - Method in class io.github.rocsg.fijirelax.curvefit.MRLMA: Calculate chi 2.
calculateChi2(double[]) - Method in class io.github.rocsg.fijirelax.lma.LMA: Calculate chi 2.
calculateIncrementedChi2() - Method in class io.github.rocsg.fijirelax.curvefit.MRLMA: Calculate incremented chi 2.
calculateIncrementedChi2() - Method in class io.github.rocsg.fijirelax.lma.LMA: Calculate incremented chi 2.
capillaryValuesAlongZ(int, int[], double) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Measure mean capillary value along Z, if a capillary is present to set a reference in magnitude data
changeTr(boolean) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Change tr.
checkComputerCapacity(boolean) - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Check computer capacity.
checkWeights(int, double[]) - Method in class io.github.rocsg.fijirelax.curvefit.MRLMA: Checks that the given array in not null, filled with zeros or contain negative weights.
checkWeights(int, double[]) - Method in class io.github.rocsg.fijirelax.lma.LMA: Checks that the given array in not null, filled with zeros or contain negative weights.
chi2 - Variable in class io.github.rocsg.fijirelax.curvefit.MRLMA: The chi 2.
chi2 - Variable in class io.github.rocsg.fijirelax.lma.LMA: The chi 2.
chi2Goodness() - Method in class io.github.rocsg.fijirelax.curvefit.MRLMA: Chi 2 goodness.
chi2Goodness() - Method in class io.github.rocsg.fijirelax.lma.LMA: Chi 2 goodness.
closeAllViews() - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Close all the images opened
closePlotsAndRoi() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Close plots and roi.
combineMultiDimDataPoints(double[], double[][]) - Static method in class io.github.rocsg.fijirelax.lma.ArrayConverter: Combines K-dimensional input data into one 2d-array: yDataPoints = y0 y1 y2 ... yN xDataPoints[i] = xi0 xi1 xi2 ... xi[K-1] Gives result[j] = yj xj0 xj1 xj2 ... xj[K-1]
combineMultiDimDataPoints(float[], float[][]) - Static method in class io.github.rocsg.fijirelax.lma.ArrayConverter: Combines K-dimensional input data into one 2d-array: yDataPoints = y0 y1 y2 ... yN xDataPoints[i] = xi0 xi1 xi2 ... xi[K-1] Gives result[j] = yj xj0 xj1 xj2 ... xj[K-1]
computeBioNano() - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Compute approximative parameters using the three first echoes.
computeEstimationsForAllPointsMultiThreaded() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Compute estimations for all points multi threaded.
computeEstimationsForAllPointsMultiThreadedT1() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Multi-threaded estimations of curve parameters using all data points, estimating a T1 recovery fit
computeEstimationsForAllPointsMultiThreadedT1T2() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Multi-threaded estimations of curve parameters using all data points, estimating a T1T2 joint fit
computeEstimationsForAllPointsMultiThreadedT2() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Multi-threaded estimations of curve parameters using all data points, estimating a T2 recovery fit
computeMaps() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Maps computation routine, with default parameters
computeMaps(double) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Maps computation routine, with default parameters
computeMaps(double[], ImagePlus) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Compute maps according to the provided parameters.
computeMaps(NoiseManagement) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Maps computation routine, with provided parameters
computeMapsAgainAndMask(int, boolean, NoiseManagement, boolean, ImagePlus, double, boolean) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Compute maps again and mask of the current HyperMap.
computeMapsNoJoint() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Maps computation routine, with default parameters, but without joint T1-T2 fit
computeMapsNoJoint(NoiseManagement) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Maps computation routine, with default parameters, but without joint T1-T2 fit
computeMapsWithMask(ImagePlus) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Maps computation routine, with default parameters
computeMulti - Variable in class io.github.rocsg.fijirelax.gui.Custom_Format_Importer: The compute multi.
computeResultsAgain() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Read new data and update estimation and fits--------------------------------------------------------------------------------.
computeRiceSigmaFromBackgroundValuesStatic(double, double) - Static method in class io.github.rocsg.fijirelax.mrialgo.RiceEstimator: Estimation of the rice noise stddev from values measured in the background assuming that there is no object in such background.
computeSigmaAndMeanBgFromRiceSigmaStatic(double) - Static method in class io.github.rocsg.fijirelax.mrialgo.RiceEstimator: Estimation of the rice noise stddev from values measured in the background assuming that there is no object in such background.
computeSpectrumCurveT1(int) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Compute spectrum curve T1 .
computeSpectrumCurveT1T2(int) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Compute spectrum curve T1 T2, used when cross-fitting
computeSpectrumCurveT2(int) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Compute spectrum curve T1 .
computeT1Bionano() - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Computing approximative value of T1 using the three first recovery times.
computeT1T2MapMultiThreadSlices(ImagePlus[], ImagePlus, double, int, int, boolean, boolean, boolean) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Compute T1 T2 maps slice per slice, in a multi-threaded way.
computeT2Bionano() - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Computing approximative value of T2 using the three first echoes.
computeTeTrAndRiceSigmaOfEachSliceAndWriteItInTheLabels(ImagePlus, boolean, String, boolean) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Estimate rice noise in each slice from the background values.
configLMA(double, double, int) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias: Setters for LM parameters
constitems2 - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias: The Constant constitems2.
constitems2 - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant constitems2.
constructWeights(double[][]) - Method in class io.github.rocsg.fijirelax.lma.LMAFunction: The default weights-array constructor.
constructWeights(double[][]) - Method in class io.github.rocsg.fijirelax.lma.LMAMultiDimFunction: The default weights-array constructor.
convertBionanoM0InPercentage(double, boolean) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Convert data from custom MRImaging device in percentage of maximal magnitude
copyTab(boolean[]) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Copy a boolean tab
copyTab(double[]) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Copy double tab
copyTab(int[]) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Copy int tab
Ctot - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Total channel number to expect, including both original echoes and maps.
Custom_Format_Importer - Class in io.github.rocsg.fijirelax.gui: The Custom_Format_Importer class is in charge of handling importation MRI data from NIFTI, multiple NIFTI or BRUKER formats.
Custom_Format_Importer(String, String) - Constructor for class io.github.rocsg.fijirelax.gui.Custom_Format_Importer: Instantiates a new custom format importer.

D

da - Variable in class io.github.rocsg.fijirelax.curvefit.MRLMA: The da.
da - Variable in class io.github.rocsg.fijirelax.lma.LMA: The da.
data - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias: The data.
debugBionano - Static variable in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: The Constant debugBionano.
debugLM - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias: The debug LM.
DEFAULT_N_ITER_T1T2 - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant DEFAULT_N_ITER_T1T2.
defaultAlgoChoice - Static variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The default algo choice.
defaultFirstChoice - Static variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The default first choice.
defaultJointSchemeChoice - Static variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The default joint scheme choice.
defaultMaskChoice - Static variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The default mask choice.
defaultNoiseChoice - Static variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The default noise choice.
defaultOutlierAlgorithm - Static variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The default outlier algorithm.
defaultOutlierNeighbourXY - Static variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The default outlier neighbour XY.
defaultOutlierStdDev - Static variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The default outlier std dev.
defaultStdDevMask - Static variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The default std dev mask.
DELTA_TE_BOUTURE_TRICK - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant DELTA_TE_BOUTURE_TRICK.
detectBouture(ImagePlus) - Method in class io.github.rocsg.fijirelax.gui.Custom_Format_Importer: Used for detecting specific kind of experiments
detectSorgho(ImagePlus) - Method in class io.github.rocsg.fijirelax.gui.Custom_Format_Importer: Used for detecting specific kind of experiments
dims - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The dims.
disable(int) - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Disable.
disable(int[]) - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Disable.
displayedNameCombinedImage - Variable in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: The displayed name combined image.
displayedNameHyperImage - Variable in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: The displayed name hyper image.
displayedNameImage1 - Variable in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: The displayed name image 1.
displayedNameImage2 - Variable in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: The displayed name image 2.
displayResultsAgain() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Update display of both results
doFit() - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias: Run the fit using the declared setup of the current object
doFit() - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Start the fit with the defined setup in the current object
doFit(double, double, int) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias: Run the fit using the declared setup of the current object and the given LM parameters
doFit(int) - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Starts the fit with the defined setup in the current object, and the given fit type
doFit(int, boolean) - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Starts the fit with the defined setup in the current object, and the given fit type
dontShowNothing - Variable in class io.github.rocsg.fijirelax.gui.Custom_Format_Importer: The dont show nothing.
doubleArraySort(double[]) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Sort an array of double by increasing order

E

enable(int) - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Enable.
enable(int[]) - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Enable.
epsilon - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant epsilon.
ERROR_KHI2 - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant ERROR_KHI2.
ERROR_VALUE - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant ERROR_VALUE.
estimateDeltaTe - Variable in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: The estimate delta te.
estimateInitialSignal(double, double) - Method in class io.github.rocsg.fijirelax.mrialgo.RiceEstimator: Estimate the initial uncorrupted signal, given the value of sigmaRice, and the value of observation of the magnitude signal
estimateSigma(double, double) - Method in class io.github.rocsg.fijirelax.mrialgo.RiceEstimator: Estimate the besselFunction sigma for these values
estimateSigmas(double, double[]) - Method in class io.github.rocsg.fijirelax.mrialgo.RiceEstimator: Estimate the besselFunction sigma for these values
exportDataToCsv(String, String) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Export fitting data and spectrum to csv.
exportFileName - Variable in class io.github.rocsg.fijirelax.gui.Custom_Format_Importer: The export file name.

F

f(double[], double, double) - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Returns formula value for parameters 'p' at 'x'.
f(int, double[], double, double) - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Returns 'fit' formula value for parameters "p" at "x".
factorT1M0MaxRatio - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant factorT1M0MaxRatio.
factorT1MaxRatio - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant factorT1MaxRatio.
factorT1MinRatio - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant factorT1MinRatio.
factorT2M0MaxRatio - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant factorT2M0MaxRatio.
factorT2MaxRatio - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant factorT2MaxRatio.
factorT2MinRatio - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant factorT2MinRatio.
factorViewNormalisation - Static variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The factor view normalisation.
FijiRelax_Gui - Class in io.github.rocsg.fijirelax.gui: The PlugInFrame holding the main window the FijiRelax GUI, when called from the Fiji interface.
FijiRelax_Gui() - Constructor for class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Constructor of the class.
fit - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias: The fit.
fit - Variable in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: The fit.
fit() - Method in class io.github.rocsg.fijirelax.curvefit.MRLMA: The default fit.
fit() - Method in class io.github.rocsg.fijirelax.lma.LMA: The default fit.
fit(double, double, int) - Method in class io.github.rocsg.fijirelax.curvefit.MRLMA: Initializes and starts the fit.
fit(double, double, int) - Method in class io.github.rocsg.fijirelax.lma.LMA: Initializes and starts the fit.
fitAndEvaluateT1(double[], double[], double[][][], double[], double, int, int, int, boolean) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Fit selected equations and evaluate their accuracy by updating displayed Khi2 values.
fitAndEvaluateT1T2(double[], double[], double[][][], double[], double, int, int, int, boolean) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Fit selected equations and evaluate their accuracy by updating displayed Khi2 values.
fitAndEvaluateT2(double[], double[], double[][][], double[], double, int, int, int, boolean) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Fit selected equations and evaluate their accuracy by updating displayed Khi2 values.
fititems2 - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias: The Constant fititems2.
fititems2 - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant fititems2.
fittenRelaxationCurve(double[], double[], double[], double, int) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Estimate the curve corresponding to the parameters estimated, and compute the accuracy of fit, khi2, and corresponding pvalue.
fittingAccuracies(double[], double[], double[], double, double[], int, boolean, RiceEstimator, int) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Compute normalised khi2 and p values according to the sigma parameter of the Rice noise the number of points averaged for the estimation is used to estimate sigma of the sum Another interesting point is that sigma is reestimated locally for each magnitude value as the rice sigma is not equal to the observed sigma for different values of the magnitude.
forceNoBoutureTrick - Variable in class io.github.rocsg.fijirelax.gui.Custom_Format_Importer: The force no bouture trick.
forgetEarlyReps - Variable in class io.github.rocsg.fijirelax.gui.Custom_Format_Importer: The forget early reps.
forgetLastT2(double[][]) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Eliminate the first echo of the sequence
forgetLastT2(double[][][]) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Eliminate the first echo of the sequence
function - Variable in class io.github.rocsg.fijirelax.curvefit.MRLMA: The model function to be fitted, y = y(x[], a[]), where x[] the array of x-values and a is the array of fit parameters.
function - Variable in class io.github.rocsg.fijirelax.lma.LMA: The model function to be fitted, y = y(x[], a[]), where x[] the array of x-values and a is the array of fit parameters.

G

gaussianSpectrum - Variable in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: The gaussian spectrum.
GE3D - io.github.rocsg.fijirelax.mrialgo.MRDataType: The ge3d.
generateData() - Method in class io.github.rocsg.fijirelax.curvefit.MRLMA
generateData() - Method in class io.github.rocsg.fijirelax.lma.LMA
generateData(double[][], double[]) - Method in class io.github.rocsg.fijirelax.lma.LMAMultiDimFunction: Generate data.
generateData(double[], double[]) - Method in class io.github.rocsg.fijirelax.lma.LMAFunction: Generate data.
generateData(double[], double[]) - Method in class io.github.rocsg.fijirelax.lma.LMAMultiDimFunction: The one dimesional convenience method.
generateData(float[][], double[]) - Method in class io.github.rocsg.fijirelax.lma.LMAMultiDimFunction: Generate data.
generateData(float[][], float[]) - Method in class io.github.rocsg.fijirelax.lma.LMAMultiDimFunction: Generate data.
generateData(float[], double[]) - Method in class io.github.rocsg.fijirelax.lma.LMAFunction: Generate data.
generateData(float[], double[]) - Method in class io.github.rocsg.fijirelax.lma.LMAMultiDimFunction: The one dimesional convenience method.
generateData(float[], float[]) - Method in class io.github.rocsg.fijirelax.lma.LMAFunction: Generate data.
generateData(float[], float[]) - Method in class io.github.rocsg.fijirelax.lma.LMAMultiDimFunction: One dimensional convenience method.
generateData(LMA) - Method in class io.github.rocsg.fijirelax.lma.LMAMultiDimFunction: Generate data.
getAsImagePlus() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the current HyperImage as an image plus, with maps (if any) in the first channels, and echoes in the next channels.
getBackgroundStatsFromProcessor(ImageProcessor) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: This routine compute the background stats in eight little square near the border Before estimation, the 3 ones with the highest values are discarded because there is often the object somewhere on the border, or the capillary.
getBackgroundStatsFromProcessorTight(ImageProcessor) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: This routine compute the background stats in eight very little square near the border Before estimation, the 3 ones with the highest values are discarded because there is often the object somewhere on the border, or the capillary.
getCoordinatesAroundThisVoxel(int, int, int, int, int) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the absolute coordinates of neighbours around a voxel.
getCoordsOfCorrespondingVoxelsUsedInEstimationAroundThisPoint(ImagePlus, int, int, int, int, int, int, int, int, int, boolean) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Give the coords of the voxels in the neighbouring of v(xCor,yCor,curZ,curTime The neighbouring is a parallepiped of size (2*crossWidth+1) along X-Y and (2*crossThick+1) along Z.
getCopy() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets a copy of the Imageplus containing the current HyperMap data
getCovarianceMatrixOfStandardErrorsInParameters() - Method in class io.github.rocsg.fijirelax.curvefit.MRLMA: Gets the covariance matrix of standard errors in parameters.
getCovarianceMatrixOfStandardErrorsInParameters() - Method in class io.github.rocsg.fijirelax.lma.LMA: Gets the covariance matrix of standard errors in parameters.
getCuteTimesT1() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Gets the cute times T1 which are an interpolation of the actual MRI data, in order to generate smooth curves corresponding to estimate exponential parameters
getCuteTimesT1T2() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Gets the cute times T1 T2 which are an interpolation of the actual MRI data, in order to generate smooth curves corresponding to estimate exponential parameters
getCuteTimesT2() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Gets the cute times T2 which are an interpolation of the actual MRI data, in order to generate smooth curves corresponding to estimate exponential parameters
getDataForVoxel(ImagePlus, int, int, int, int, int, int, int, int, int, boolean) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Give the average decay signal of the voxels in the neighbouring of v(xCor,yCor,curZ,curTime The neighbouring is a parallepiped of size (2*crossWidth+1) along X-Y and (2*crossThick+1) along Z.
getDataForVoxelGaussian(ImagePlus, int, int, int, int, int, int, int, int, int, boolean) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Give the average decay signal of the voxels in the neighbouring of v(xCor,yCor,curZ,curTime The neighbouring is a parallepiped of size (2*crossWidth+1) along X-Y and (2*crossThick+1) along Z This method is surnumerary : with assumption of non using of sigma, it can be done with the other one.
getDataTypeOfThisMagneticResonanceSlice(ImagePlus, int, int, int) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Check data type in slice labels, by testing if it contains patterns (ex : "T1SEQ").
getDefaultParametersBoundaries(int) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias: Gets the default parameters boundaries i.e. the acceptable boundaries for the exponential curve to estimate.
getDefaultParametersBoundaries(int) - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Gets the default parameters boundaries i.e. the acceptable boundaries for the exponential curve to estimate.
getDefaultRegistrationSettings() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the default registration settings.
getDefaultRiceEstimatorForNormalizedHyperEchoesT1AndT2Images() - Static method in class io.github.rocsg.fijirelax.mrialgo.RiceEstimator: Gets the default rice estimator for normalized hyper echoes T 1 and T 2 images, includin a common scale of possible signals and possible rice values
getEchoesImage() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the echoes image.
getEchoesImageText() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the echoes image text, with metainfo stored in the slice labels
getElement(int, int) - Method in class io.github.rocsg.fijirelax.lma.implementations.JAMAMatrix: Gets the element.
getElement(int, int) - Method in interface io.github.rocsg.fijirelax.lma.LMAMatrix: Get the value of a matrix element.
getFirstImageOfT1T2Serie(String) - Method in class io.github.rocsg.fijirelax.gui.Custom_Format_Importer: Gets the first image of T1-T2 serie, when providing the input dir containing all the data.
getFit() - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Gets the fit.
getFitFunctionValue(double, double, double[], double, int) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Get the value of the fitting equation of the model described by a fit Type,(ex: MRUTils.T1_MONO), given the recovery time and the echo time
getFitGoodness() - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Get a measure of "goodness of fit" where 1.0 is best.
getFitType(int) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Gets the fit type as an int:(fitType %10)+10*this.noiseHandling)
getFullDataForVoxel(ImagePlus, int, int, int, int, int, int, int, int, int) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Give the magnitude decay signal of the voxels in the neighbouring of v(xCor,yCor,curZ,curTime The neighbouring is a parallepiped of size (2*crossWidth+1) along X-Y and (2*crossThick+1) along Z.
getFullMRISignalAroundThisVoxelT1T2(int, int, int, int, int, double) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the full MRI signal around this voxel T1 T2 in a neighbourhood defined by crossWidth x crossWidth x crossThick, after gaussian smoothing of this data with sigma parameter.
getFullMRISignalInTheseCoordinatesT1T2(int, int, int, int[][], double) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the full MRI signal around this voxel T1 T2 in neighbourhood voxels defined by their relative coordinates around x0,y0,z0, after gaussian smoothing of this data with sigma parameter.
getHelpString() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Gets the help string.
getHyperEcho(int, int) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets an echo corresponding to a channel index and a timeframe
getImgViewText(int) - Static method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Gets the title of what should be the current image
getIterations() - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Get number of iterations performed.
getLMA() - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias: Gets the lma object.
getMagPoints() - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Gets the mag points.
getMapsImage() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the maps image.
getMask() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the mask associated with this image, covering the area to be computed (where there is an object)
getMax(double[]) - Static method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Gets index of highest value in an array.
getMaxIterations() - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Get maximum number of iterations allowed.
getMaxValueForContrastMoreIntelligent(ImagePlus, int, int, int, double, double) - Static method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Compute a max value for display range by taking the percentageKeep'th value, and multiply it by provided factor
getMeanRelativeError() - Method in class io.github.rocsg.fijirelax.curvefit.MRLMA: Gets the mean relative error.
getMeanRelativeError() - Method in class io.github.rocsg.fijirelax.lma.LMA: Gets the mean relative error.
getMeanRiceOfCentralSlicesOverEchoes(ImagePlus[]) - Static method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Get the mean Rice noise computed over the imaged echoes.
getNiftiInfos(int) - Static method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the nifti infos.
getNonRicedY(double, double, double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1Mono: Gets estimates of what would be the observed value in absence of Rice noise corruption
getNonRicedY(double, double, double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1MonoBias: Gets estimates of what would be the observed value in absence of Rice noise corruption
getNonRicedY(double, double, double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1MonoRice: Gets estimates of what would be the observed value in absence of Rice noise corruption
getNonRicedY(double, double, double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2DefaultMonoRice: Gets the non riced Y.
getNonRicedY(double, double, double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2DefaultMultiRice: Gets estimates of what would be the observed value in absence of Rice noise corruption
getNonRicedY(double, double, double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2Mono: Gets estimates of what would be the observed value in absence of Rice noise corruption
getNonRicedY(double, double, double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MonoBias: Gets estimates of what would be the observed value in absence of Rice noise corruption
getNonRicedY(double, double, double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MonoRice: Gets estimates of what would be the observed value in absence of Rice noise corruption
getNonRicedY(double, double, double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2Multi: Gets estimates of what would be the observed value in absence of Rice noise corruption
getNonRicedY(double, double, double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MultiBias: Gets estimates of what would be the observed value in absence of Rice noise corruption
getNonRicedY(double, double, double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MultiRice: Gets estimates of what would be the observed value in absence of Rice noise corruption
getNonRicedY(double, double, double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2Mono: Gets estimates of what would be the observed value in absence of Rice noise corruption
getNonRicedY(double, double, double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MonoBias: Gets estimates of what would be the observed value in absence of Rice noise corruption
getNonRicedY(double, double, double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MonoRice: Gets estimates of what would be the observed value in absence of Rice noise corruption
getNonRicedY(double, double, double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2Multi: Gets estimates of what would be the observed value in absence of Rice noise corruption
getNonRicedY(double, double, double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MultiBias: Gets estimates of what would be the observed value in absence of Rice noise corruption
getNonRicedY(double, double, double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MultiRice: Gets estimates of what would be the observed value in absence of Rice noise corruption
getNparams(int) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Get the number of parameters used by a model described by a fit Type,(ex: MRUTils.T1_MONO)
getObservationCoord(double) - Method in class io.github.rocsg.fijirelax.mrialgo.RiceEstimator: Gets the coordinate corresponding to this observation
getParams() - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias: Gets the estimated params of the fitted function.
getParams() - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Get the set of parameter values from the best corner of the simplex.
getPartialDerivate(double[], double[], int) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1Mono: Gets the partial derivate of the signal according to one of the parameters
getPartialDerivate(double[], double[], int) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1MonoBias: Gets the partial derivate of the signal according to one of the parameters
getPartialDerivate(double[], double[], int) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1MonoRice: Gets the partial derivate of the signal according to one of the parameters
getPartialDerivate(double[], double[], int) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2DefaultMonoRice: Gets the partial derivate.
getPartialDerivate(double[], double[], int) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2DefaultMultiRice: Gets the partial derivate of the signal according to one of the parameters
getPartialDerivate(double[], double[], int) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2Mono: Gets the partial derivate of the signal according to one of the parameters
getPartialDerivate(double[], double[], int) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MonoBias: Gets the partial derivate of the signal according to one of the parameters
getPartialDerivate(double[], double[], int) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MonoRice: Gets the partial derivate of the signal according to one of the parameters
getPartialDerivate(double[], double[], int) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2Multi: Gets the partial derivate of the signal according to one of the parameters
getPartialDerivate(double[], double[], int) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MultiBias: Gets the partial derivate of the signal according to one of the parameters
getPartialDerivate(double[], double[], int) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MultiRice: Gets the partial derivate of the signal according to one of the parameters
getPartialDerivate(double[], double[], int) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2Mono: Gets the partial derivate of the signal according to one of the parameters
getPartialDerivate(double[], double[], int) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MonoBias: Gets the partial derivate of the signal according to one of the parameters
getPartialDerivate(double[], double[], int) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MonoRice: Gets the partial derivate of the signal according to one of the parameters
getPartialDerivate(double[], double[], int) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2Multi: Gets the partial derivate of the signal according to one of the parameters
getPartialDerivate(double[], double[], int) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MultiBias: Gets the partial derivate of the signal according to one of the parameters
getPartialDerivate(double[], double[], int) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MultiRice: Gets the partial derivate of the signal according to one of the parameters
getPartialDerivate(double[], double[], int) - Method in class io.github.rocsg.fijirelax.lma.LMAMultiDimFunction: The method which gives the partial derivates used in the LMA fit.
getPartialDerivate(double, double[], int) - Method in class io.github.rocsg.fijirelax.lma.LMAFunction: The method which gives the partial derivates used in the LMA fit.
getProportionalTimes(double, double, double) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Helper to make a linspace along relaxation times in order to prepare display of the relaxation curves.
getPvalue(double, int) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Gets the pvalue associated with the khi2 and the number of freedom degrees
getQuartiles(double[], double[]) - Static method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the quartiles of the distribution
getRandomRiceRealization(double, double) - Static method in class io.github.rocsg.fijirelax.mrialgo.RiceEstimator: Simulation of Rice Noise over an unaltered signal.
getRandomRiceRealization(double, double, int) - Static method in class io.github.rocsg.fijirelax.mrialgo.RiceEstimator: Simulation of Rice Noise over an unaltered signal.
getRangeInfos() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the current display range infos, as a String
getRelativeChi2() - Method in class io.github.rocsg.fijirelax.curvefit.MRLMA: Gets the relative chi 2.
getRelativeChi2() - Method in class io.github.rocsg.fijirelax.lma.LMA: Gets the relative chi 2.
getRelativeOptimalPositionFor2DView() - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Gets the relative optimal position on screen for 2 D view.
getResiduals() - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Returns residuals array ie. differences between data and curve.
getRestarts() - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Get number of simplex restarts to do.
getRSquared() - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Returns R^2, where 1.0 is best.
getSD() - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Returns the standard deviation of the residuals.
getSigmaCoord(double) - Method in class io.github.rocsg.fijirelax.mrialgo.RiceEstimator: Gets the coordinate to access the sigma value
getSigmaFrom3DRelaxationImageTab(ImagePlus[]) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Helper to compute sigma Rice mean over the successive echoes image If one of the sigma is +-30% from the mean, a warning is sent to the log console.
getStandardErrorsOfParameters() - Method in class io.github.rocsg.fijirelax.curvefit.MRLMA: Gets the standard errors of parameters.
getStandardErrorsOfParameters() - Method in class io.github.rocsg.fijirelax.lma.LMA: Gets the standard errors of parameters.
getSumResidualsSqr() - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Gets the sum residuals sqr.
getT1EchoesImage(int) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the stack corresponding to the t1 relaxation sequence.
getT1Indices() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the indices of the T1 relaxation images in the current HyperMap for all the timeframes
getT1Indices(int) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the indices of the T1 relaxation images in the current HyperMap
getT1SeqNumberReps(int) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the number of echoes defining the T1 relaxation sequences.
getT1T2Indices() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the indices of the T1 T2 relaxation images in the current HyperMap for all the timeframes
getT1T2Indices(int) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the indices of the T1 and T2 relaxation images in the current HyperMap
getT1T2SeqNumberReps(int) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the number of echoes defining the T1 and T2 relaxation sequences.
getT1T2TeTimes() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the echoe time of all the T1T2 relaxation images in the current HyperMap for all the timeframes
getT1T2TrTeTimes() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the recovery time and echoe time of all the T1T2 relaxation images in the current HyperMap for all the timeframes
getT1T2TrTeTimes(int) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the recovery time and echoe time of all the T1T2 relaxation images in the current HyperMap
getT1T2TrTimes() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the recovery time of all the T1T2 relaxation images in the current HyperMap for all the timeframes
getT1TeTimes() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the echoe time of all the T1 relaxation images in the current HyperMap for all the timeframes
getT1TrTeTimes() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the recovery time and echoe time of all the T1 relaxation images in the current HyperMap for all the timeframes
getT1TrTeTimes(int) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the recovery time and echoe time of all the T1 relaxation images in the current HyperMap
getT1TrTimes() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the recovery time of all the T1 relaxation images in the current HyperMap for all the timeframes
getT2EchoesImage(int) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the stack corresponding to the t2 relaxation sequence.
getT2Indices() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the indices of the T2 relaxation images in the current HyperMap for all the timeframes
getT2Indices(int) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the indices of the T2 relaxation images in the current HyperMap
getT2SeqNumberReps(int) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the number of echoes defining the T2 relaxation sequences.
getT2TeTimes() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the echoe time of all the T2 relaxation images in the current HyperMap for all the timeframes
getT2TrTeTimes() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the recovery time and echoe time of all the T2 relaxation images in the current HyperMap for all the timeframes
getT2TrTeTimes(int) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the recovery time and echoe time of all the T2 relaxation images in the current HyperMap
getT2TrTimes() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Gets the recovery time of all the T2 relaxation images in the current HyperMap for all the timeframes
getTeFrom3DRelaxationImageTab(ImagePlus[]) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Extract Te values from the relaxation images
getTePoints() - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Gets the te points.
getTrFrom3DRelaxationImageTab(ImagePlus[]) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Extract Tr values from the relaxation images by reading this in slice labels
getTrPoints() - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Gets the tr points.
getY(double[], double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1Mono: Gets estimates of what would be the observed value in absence of Rice noise corruption
getY(double[], double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1MonoBias: Gets estimates of what would be the observed value in absence of Rice noise corruption
getY(double[], double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1MonoRice: Gets estimates of what would be the observed value in absence of Rice noise corruption
getY(double[], double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2DefaultMonoRice: Gets the y.
getY(double[], double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2DefaultMultiRice: Gets estimates of what would be the observed value in presence of Rice noise corruption
getY(double[], double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2Mono: Gets estimates of what would be the observed value in absence of Rice noise corruption
getY(double[], double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MonoBias: Gets estimates of what would be the observed value in absence of Rice noise corruption
getY(double[], double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MonoRice: Gets estimates of what would be the observed value in absence of Rice noise corruption
getY(double[], double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2Multi: Gets estimates of what would be the observed value in absence of Rice noise corruption
getY(double[], double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MultiBias: Gets estimates of what would be the observed value in absence of Rice noise corruption
getY(double[], double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MultiRice: Gets estimates of what would be the observed value in absence of Rice noise corruption
getY(double[], double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2Mono: Gets estimates of what would be the observed value in absence of Rice noise corruption
getY(double[], double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MonoBias: Gets estimates of what would be the observed value in absence of Rice noise corruption
getY(double[], double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MonoRice: Gets estimates of what would be the observed value in absence of Rice noise corruption
getY(double[], double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2Multi: Gets estimates of what would be the observed value in absence of Rice noise corruption
getY(double[], double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MultiBias: Gets estimates of what would be the observed value in absence of Rice noise corruption
getY(double[], double[]) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MultiRice: Gets estimates of what would be the observed value in absence of Rice noise corruption
getY(double[], double[]) - Method in class io.github.rocsg.fijirelax.lma.LMAMultiDimFunction: Gets the y.
getY(double, double[]) - Method in class io.github.rocsg.fijirelax.lma.LMAFunction: Gets the y.
getY(double, double[]) - Method in class io.github.rocsg.fijirelax.lma.LMAMultiDimFunction: A convenience method for the one dimensional case.

H

hasMaps - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Has maps.
hasT1sequence - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Has T 1 sequence.
hasT1T2sequence - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Has joint T1-T2 sequence.
hasT2sequence - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Has T 2 sequence.
hideMessage - Variable in class io.github.rocsg.fijirelax.gui.Custom_Format_Importer: The hide message.
hyperEchoes - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The hyper echoes.
hyperImg - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The hyper img.
HyperMap - Class in io.github.rocsg.fijirelax.mrialgo: HyperMap class is the data packager for the variety of possible data processed by FijiRelax.
HyperMap() - Constructor for class io.github.rocsg.fijirelax.mrialgo.HyperMap: Default constructor with no params.
HyperMap(ImagePlus) - Constructor for class io.github.rocsg.fijirelax.mrialgo.HyperMap: Constructor of HyperMap object from an hypermap serialized as a TIFF file Runs no safety check.
hyperMapFactory(HyperMap) - Static method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: HyperMap Factory.
hyperMaps - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The hyper maps.

I

identifyRangedData() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Identify the ranged data in the spectrum, depending on the actual defined interval (in blue in the plot)
identifyRangedDataT1T2() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Identify the ranged data in the spectrum, depending on the actual defined interval (in blue in the plot), when using cross-fitting T1T2
imgView - Variable in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: The img view.
importButton - Variable in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: The import button.
importCustomDataAsHyperMap() - Method in class io.github.rocsg.fijirelax.gui.Custom_Format_Importer: Run the importation, according to defined member fields (name,inputdir) and return the imported MRI observation as an HyperMap.
importHyperMapFromCustomData(String, String) - Static method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Import hyper map from custom data.
importHyperMapFromNifti4DSequence(String, String, Object[]) - Static method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Import hyper map from nifti 4 D sequence.
importHyperMapFromNifti4DT1Sequence(String, String, double[], double) - Static method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Import a T1 relaxation experiment stored as a Nifti 3D or 4D stack
importHyperMapFromNifti4DT2Sequence(String, String, double, double) - Static method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Import a T2 relaxation experiment stored as a Nifti 3D or 4D stack
importHyperMapFromNifti4DT2Sequence(String, String, double, double[]) - Static method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Import a T2 relaxation experiment stored as a Nifti 3D or 4D stack
importHyperMapFromNifti4DUnknownSequence(String, String) - Static method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Import hyper map from nifti 4 D unknown sequence.
importHyperMapFromRawDicomData(String, String) - Static method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Import hyper map from raw dicom data organized in a directory, by calling (see fijirelax.gui.Custom_Format_Importer.importCustomDataAsHyperMap)
incrementedChi2 - Variable in class io.github.rocsg.fijirelax.curvefit.MRLMA: The incremented chi 2.
incrementedChi2 - Variable in class io.github.rocsg.fijirelax.lma.LMA: The incremented chi 2.
incrementedParameters - Variable in class io.github.rocsg.fijirelax.curvefit.MRLMA: The incremented parameters.
incrementedParameters - Variable in class io.github.rocsg.fijirelax.lma.LMA: The incremented parameters.
infinity - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant infinity.
init(LMAMultiDimFunction, double[], double[], double[][], double[], LMAMatrix) - Method in class io.github.rocsg.fijirelax.lma.LMA: Inits the.
initialize(int) - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Initialise the simplex.
initialize2DTab() - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Initialize 2 D tab for storing successive values of Repetition times and Echo times
initializeGUI() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Initialize GUI.
initializeScreenConstants() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Initialize screen constants.
inspect2DTab() - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Inspect 2 D tab storing successive values of Repetition times and Echo times
inspectT2EstimatedValues() - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Inspect values when computing approximative parameters using the three first echoes.
interfaceIsRunning - Variable in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: The interface is running.
invert() - Method in class io.github.rocsg.fijirelax.lma.implementations.JAMAMatrix: Invert.
invert() - Method in interface io.github.rocsg.fijirelax.lma.LMAMatrix: Inverts the matrix for solving linear equations for parameter increments.
InvertException(String) - Constructor for exception io.github.rocsg.fijirelax.lma.LMAMatrix.InvertException: Instantiates a new invert exception.
io.github.rocsg.fijirelax - package io.github.rocsg.fijirelax: This package is the root of the fijirelax project.
io.github.rocsg.fijirelax.curvefit - package io.github.rocsg.fijirelax.curvefit: This package contains the optimizers and the associated routines for curve fitting T1/T2/PD params using samples of MRI data Copyright (C) 2022 io.github.rocsg (except MRLMA class, which is
io.github.rocsg.fijirelax.gui - package io.github.rocsg.fijirelax.gui: This package contains classes describing the graphical user interface of the Fiji plugin Copyright (C) 2022 io.github.rocsg This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
io.github.rocsg.fijirelax.lma - package io.github.rocsg.fijirelax.lma: This package contains linear matrix algebra functions used for the curve fitting algorithms Copyright (C) 2022 io.github.rocsg ((except MRLMA class, which is
io.github.rocsg.fijirelax.lma.implementations - package io.github.rocsg.fijirelax.lma.implementations
io.github.rocsg.fijirelax.mrialgo - package io.github.rocsg.fijirelax.mrialgo: This package contains the data structure description (HyperMap), RiceEstimator functions, and utils for MR data handling Copyright (C) 2022 io.github.rocsg This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
iterationCount - Variable in class io.github.rocsg.fijirelax.curvefit.MRLMA: The iteration count.
iterationCount - Variable in class io.github.rocsg.fijirelax.lma.LMA: The iteration count.
iterationsBreak - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias: The iterations break.
iterationsBreak - Variable in class io.github.rocsg.fijirelax.curvefit.MRLMA: The iterations break.
iterationsBreak - Variable in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: The iterations break.
iterFactor - Static variable in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: The iter factor.

J

JAMAMatrix - Class in io.github.rocsg.fijirelax.lma.implementations: The Class JAMAMatrix.
JAMAMatrix(double[][]) - Constructor for class io.github.rocsg.fijirelax.lma.implementations.JAMAMatrix: Instantiates a new JAMA matrix.
JAMAMatrix(int, int) - Constructor for class io.github.rocsg.fijirelax.lma.implementations.JAMAMatrix: Instantiates a new JAMA matrix.

K

keyPressed(KeyEvent) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Key pressed.
keyReleased(KeyEvent) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Key released.
keyTyped(KeyEvent) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Gui updating functions and callbacks--------------------------------------------------------------------------------.

L

lambda - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias: The lambda.
lambda - Variable in class io.github.rocsg.fijirelax.curvefit.MRLMA: The lambda.
lambda - Variable in class io.github.rocsg.fijirelax.lma.LMA: The lambda.
lambdaFactor - Variable in class io.github.rocsg.fijirelax.curvefit.MRLMA: The lambda factor.
lambdaFactor - Variable in class io.github.rocsg.fijirelax.lma.LMA: The lambda factor.
lastViewSizes - Variable in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: The last view sizes.
lm - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1Mono: The lm.
lm - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1MonoBias: The lm.
lm - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1MonoRice: The lm.
lm - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2DefaultMonoRice: The lm.
lm - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2DefaultMultiRice: The lm.
lm - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2Mono: The lm.
lm - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MonoBias: The lm.
lm - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MonoRice: The lm.
lm - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2Multi: The lm.
lm - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MultiBias: The lm.
lm - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MultiRice: The optimiser
lm - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2Mono: The lm.
lm - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MonoBias: The lm.
lm - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MonoRice: The lm.
lm - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2Multi: The lm.
lm - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MultiBias: The lm.
lm - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MultiRice: The lm.
LM - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant LM.
LMA - Class in io.github.rocsg.fijirelax.lma: A class which implements the Levenberg-Marquardt Algorithm (LMA) fit for non-linear, multidimensional parameter space for any multidimensional fit function.
LMA(LMAFunction, double[], double[][]) - Constructor for class io.github.rocsg.fijirelax.lma.LMA: One dimensional convenience constructor for LMAFunction.
LMA(LMAFunction, double[], double[][], double[]) - Constructor for class io.github.rocsg.fijirelax.lma.LMA: One dimensional convenience constructor for LMAFunction.
LMA(LMAFunction, float[], float[][]) - Constructor for class io.github.rocsg.fijirelax.lma.LMA: One dimensional convenience constructor for LMAFunction.
LMA(LMAFunction, float[], float[][], float[]) - Constructor for class io.github.rocsg.fijirelax.lma.LMA: One dimensional convenience constructor for LMAFunction.
LMA(LMAMultiDimFunction, double[], double[][]) - Constructor for class io.github.rocsg.fijirelax.lma.LMA: Initiates the fit with function constructed weights and a JAMA matrix.
LMA(LMAMultiDimFunction, double[], double[][], double[], LMAMatrix) - Constructor for class io.github.rocsg.fijirelax.lma.LMA: Initiates the fit.
LMA(LMAMultiDimFunction, double[], double[], double[][]) - Constructor for class io.github.rocsg.fijirelax.lma.LMA: Initiates the fit with function constructed weights and a JAMA matrix.
LMA(LMAMultiDimFunction, double[], double[], double[][], double[], LMAMatrix) - Constructor for class io.github.rocsg.fijirelax.lma.LMA: Initiates the fit.
LMA(LMAMultiDimFunction, double[], float[], float[][]) - Constructor for class io.github.rocsg.fijirelax.lma.LMA: Initiates the fit with function constructed weights and a JAMA matrix.
LMA(LMAMultiDimFunction, float[], float[][]) - Constructor for class io.github.rocsg.fijirelax.lma.LMA: Initiates the fit with function constructed weights and a JAMA matrix.
LMA(LMAMultiDimFunction, float[], float[][], float[], LMAMatrix) - Constructor for class io.github.rocsg.fijirelax.lma.LMA: Initiates the fit.
LMAFunction - Class in io.github.rocsg.fijirelax.lma: Implement this for your fit function.
LMAFunction() - Constructor for class io.github.rocsg.fijirelax.lma.LMAFunction
LMAMatrix - Interface in io.github.rocsg.fijirelax.lma: The matrix to be used in LMA.
LMAMatrix.InvertException - Exception in io.github.rocsg.fijirelax.lma: The Class InvertException.
LMAMultiDimFunction - Class in io.github.rocsg.fijirelax.lma: Implement this multidimensional function y = (x[], a[]) for your fit purposes.
LMAMultiDimFunction() - Constructor for class io.github.rocsg.fijirelax.lma.LMAMultiDimFunction
LMDualCurveFitterNoBias - Class in io.github.rocsg.fijirelax.curvefit: Implements the MRLMA capabilities for fitting exponential curves to match observation points Copyright (C) 2022 io.github.rocsg This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
LMDualCurveFitterNoBias(double[], double[], double[], int, double, boolean) - Constructor for class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias: Construct a new CurveFitter object to proceed to exponential fit
LMDualCurveFitterNoBias.T1Mono - Class in io.github.rocsg.fijirelax.curvefit: The Class T1Mono.
LMDualCurveFitterNoBias.T1MonoBias - Class in io.github.rocsg.fijirelax.curvefit: The Class T1MonoBias.
LMDualCurveFitterNoBias.T1MonoRice - Class in io.github.rocsg.fijirelax.curvefit: The Class T1MonoRice.
LMDualCurveFitterNoBias.T1T2DefaultMonoRice - Class in io.github.rocsg.fijirelax.curvefit: The Class T1T2DefaultMonoRice.
LMDualCurveFitterNoBias.T1T2DefaultMultiRice - Class in io.github.rocsg.fijirelax.curvefit: The Class T1T2DefaultMultiRice.
LMDualCurveFitterNoBias.T1T2Mono - Class in io.github.rocsg.fijirelax.curvefit: The Class T1T2Mono.
LMDualCurveFitterNoBias.T1T2MonoBias - Class in io.github.rocsg.fijirelax.curvefit: The Class T1T2MonoBias.
LMDualCurveFitterNoBias.T1T2MonoRice - Class in io.github.rocsg.fijirelax.curvefit: The Class T1T2MonoRice.
LMDualCurveFitterNoBias.T1T2Multi - Class in io.github.rocsg.fijirelax.curvefit: The Class T1T2Multi.
LMDualCurveFitterNoBias.T1T2MultiBias - Class in io.github.rocsg.fijirelax.curvefit: The Class T1T2MultiBias.
LMDualCurveFitterNoBias.T1T2MultiRice - Class in io.github.rocsg.fijirelax.curvefit: The Class T1T2MultiRice.
LMDualCurveFitterNoBias.T2Mono - Class in io.github.rocsg.fijirelax.curvefit: The Class T2Mono.
LMDualCurveFitterNoBias.T2MonoBias - Class in io.github.rocsg.fijirelax.curvefit: The Class T2MonoBias.
LMDualCurveFitterNoBias.T2MonoRice - Class in io.github.rocsg.fijirelax.curvefit: The Class T2MonoRice.
LMDualCurveFitterNoBias.T2Multi - Class in io.github.rocsg.fijirelax.curvefit: The Class T2Multi.
LMDualCurveFitterNoBias.T2MultiBias - Class in io.github.rocsg.fijirelax.curvefit: The Class T2MultiBias.
LMDualCurveFitterNoBias.T2MultiRice - Class in io.github.rocsg.fijirelax.curvefit: The Class T2MultiRice.
lock() - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Lock.

M

MADeIsOutlier(double, double[], double[], double) - Static method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: MDetect outlier values using the MAD-e technique in Detecting outliers Leys (2013)
MADeStatsDoubleSided(double[], double[]) - Static method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Compute the double sided MADeStats: Median, Median-median abs. dev left wing, Median+median abs dev right wing
magData - Variable in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: The mag data.
main(String[]) - Static method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: The main method.
main(String[]) - Static method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Main function
main(String[]) - Static method in class io.github.rocsg.fijirelax.lma.implementations.JAMAMatrix: The main method.
main(String[]) - Static method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The main method.
makeBoutureTrick - Variable in class io.github.rocsg.fijirelax.gui.Custom_Format_Importer: The make bouture trick.
makeCrop - Variable in class io.github.rocsg.fijirelax.gui.Custom_Format_Importer: The make crop.
makeFit(double[], double[], double[], int, int, int, double, boolean) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Compute a simple T1 or T2 fit, or a T1T2 crossfit, using Simplex or Levenberg-Marquardt, and estimate a MONO or BI exponential, corrupted by rice Noise.
makeFitMonteCarlo(double[], double[], double[], int, int, int, double, int, int, RiceEstimator, boolean) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Compute a simple T1 or T2 fit, or a T1T2 crossfit, but compute also the distribution of estimated parameters when applying randomized modifications of the relaxation data, to check the sensibility of the operation.
makeNullMaps() - Method in class io.github.rocsg.fijirelax.gui.Custom_Format_Importer: Set member fields maps (Images) to null
makeSorghoTrick - Variable in class io.github.rocsg.fijirelax.gui.Custom_Format_Importer: The make sorgho trick.
MASKMAP - io.github.rocsg.fijirelax.mrialgo.MRDataType: The maskmap.
maxAcceptableBionanoM0 - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant maxAcceptableBionanoM0.
maxAcceptableBionanoT1 - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant maxAcceptableBionanoT1.
maxAcceptableBionanoT2 - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant maxAcceptableBionanoT2.
maxDisplayedBionanoGE3D - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant maxDisplayedBionanoGE3D.
maxDisplayedBionanoM0 - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant maxDisplayedBionanoM0.
maxDisplayedBionanoT1 - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant maxDisplayedBionanoT1.
maxDisplayedBionanoT2 - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant maxDisplayedBionanoT2.
maxDisplayedPDratio - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant maxDisplayedPDratio.
maxDisplayedT1ratio - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant maxDisplayedT1ratio.
maxDisplayedT2ratio - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant maxDisplayedT2ratio.
maxIterations - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias: The max iterations.
maxIterations - Variable in class io.github.rocsg.fijirelax.curvefit.MRLMA: The max iterations.
maxIterations - Variable in class io.github.rocsg.fijirelax.lma.LMA: The max iterations.
maxKhi2 - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The max khi 2.
maxKhi2AfterFit - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The max khi 2 after fit.
maxKhi2MONO - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The max khi 2 MONO.
maxM0BionanoForNormalization - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant maxM0BionanoForNormalization.
mean(double[]) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Compute the mean of the double tab
meanHampel(double[]) - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Used in benchmark for estimative approximation of parrameters.
measureCapillaryValuesInM0Map(int) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Measure mean capillary value along Z, if a capillary is present to set a reference in magnitude data
measureMeanCapillaryValueAlongZ(ImagePlus) - Static method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Measure mean capillary value along Z, if a capillary is present to set a reference in magnitude data
minAcceptableBionanoT1 - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant minAcceptableBionanoT1.
minAcceptableBionanoT1Bouture - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant minAcceptableBionanoT1Bouture.
minAcceptableBionanoT2 - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant minAcceptableBionanoT2.
minDeltaChi2 - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias: The min delta chi 2.
minDeltaChi2 - Variable in class io.github.rocsg.fijirelax.curvefit.MRLMA: The min delta chi 2.
minDeltaChi2 - Variable in class io.github.rocsg.fijirelax.lma.LMA: The min delta chi 2.
minDeltaChi2 - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The min delta chi 2.
minPossibleMaxT1 - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant minPossibleMaxT1.
modifySigma(ImagePlus, int, int, int, double) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Modify Rice noise sigma, and write it in the slice label
mouseClicked(MouseEvent) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Mouse clicked.
mouseDragged(MouseEvent) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Mouse dragged.
mouseEntered(MouseEvent) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Mouse entered.
mouseExited(MouseEvent) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Mouse exited.
mouseMoved(MouseEvent) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Mouse moved.
mousePressed(MouseEvent) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Mouse pressed.
mouseReleased(MouseEvent) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Mouse released.
mouseWheelMoved(MouseWheelEvent) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Mouse wheel moved.
mrDataType - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The mr data type.
MRDataType - Enum in io.github.rocsg.fijirelax.mrialgo: This enum define different common MRI imaging sequence.
MRI_HyperCurvesExplorer - Class in io.github.rocsg.fijirelax.gui: MRI_HyperCurvesExplorer is the PlugInFrame describing the curve explorer of FijiRelax, an user-friendly tool for exploration of T1 T2 relaxation curves coming from T1 and T2 sequence Copyright (C) 2022 io.github.rocsg This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
MRI_HyperCurvesExplorer() - Constructor for class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Instantiates a new MRI hyper curves explorer.
MRLMA - Class in io.github.rocsg.fijirelax.curvefit: A class which implements the Levenberg-Marquardt Algorithm (LMA) fit for non-linear, multidimensional parameter space for any multidimensional fit function.
MRLMA(LMAFunction, double[], double[][], double[], float[][]) - Constructor for class io.github.rocsg.fijirelax.curvefit.MRLMA: One dimensional convenience constructor for LMAFunction.
MRLMA(LMAFunction, double[], double[][], float[][]) - Constructor for class io.github.rocsg.fijirelax.curvefit.MRLMA: One dimensional convenience constructor for LMAFunction.
MRLMA(LMAFunction, float[], float[][], float[][]) - Constructor for class io.github.rocsg.fijirelax.curvefit.MRLMA: One dimensional convenience constructor for LMAFunction.
MRLMA(LMAFunction, float[], float[][], float[], float[][]) - Constructor for class io.github.rocsg.fijirelax.curvefit.MRLMA: One dimensional convenience constructor for LMAFunction.
MRLMA(LMAMultiDimFunction, double[], double[][], double[], LMAMatrix, float[][]) - Constructor for class io.github.rocsg.fijirelax.curvefit.MRLMA: Initiates the fit.
MRLMA(LMAMultiDimFunction, double[], double[][], float[][], boolean, double) - Constructor for class io.github.rocsg.fijirelax.curvefit.MRLMA: Initiates the fit with function constructed weights and a JAMA matrix.
MRLMA(LMAMultiDimFunction, double[], double[], double[][], double[], LMAMatrix, float[][]) - Constructor for class io.github.rocsg.fijirelax.curvefit.MRLMA: Initiates the fit.
MRLMA(LMAMultiDimFunction, double[], double[], double[][], float[][]) - Constructor for class io.github.rocsg.fijirelax.curvefit.MRLMA: Initiates the fit with function constructed weights and a JAMA matrix.
MRLMA(LMAMultiDimFunction, double[], float[], float[][], float[][]) - Constructor for class io.github.rocsg.fijirelax.curvefit.MRLMA: Initiates the fit with function constructed weights and a JAMA matrix.
MRLMA(LMAMultiDimFunction, float[], float[][], float[][]) - Constructor for class io.github.rocsg.fijirelax.curvefit.MRLMA: Initiates the fit with function constructed weights and a JAMA matrix.
MRLMA(LMAMultiDimFunction, float[], float[][], float[], LMAMatrix, float[][]) - Constructor for class io.github.rocsg.fijirelax.curvefit.MRLMA: Initiates the fit.
MRUtils - Class in io.github.rocsg.fijirelax.mrialgo: This class is a utility class to hold many helpers used for simulating MRI echoes, computing rice noise estimation, reading information into TIFF metadata.
MRUtils() - Constructor for class io.github.rocsg.fijirelax.mrialgo.MRUtils: Instantiates a new MR utils.
MSEC - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant MSEC.
multiply(double[], double[]) - Method in class io.github.rocsg.fijirelax.lma.implementations.JAMAMatrix: Multiply.
multiply(double[], double[]) - Method in interface io.github.rocsg.fijirelax.lma.LMAMatrix: Multiplies this matrix with an array (result = this * vector).

N

N_ITER_T1T2 - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant N_ITER_T1T2.
name - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The name.
nameObservation - Variable in class io.github.rocsg.fijirelax.gui.Custom_Format_Importer: The name observation.
next - Variable in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: The next.
nMaps - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The expected number of maps, given the relaxation sequences provided .
NoiseManagement - Enum in io.github.rocsg.fijirelax.mrialgo: This enum define cases of noise management.
normalizeAfterComputation - Variable in class io.github.rocsg.fijirelax.gui.Custom_Format_Importer: The normalize after computation.
normalizeBeforeComputation - Variable in class io.github.rocsg.fijirelax.gui.Custom_Format_Importer: The normalize before computation.
normalizeBeforeComputation(ImagePlus[], ImagePlus) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: A routine to normalize a z-stack along the z-axis, to compensate for the non-uniformity of the magnetic field This method detects the capillary and do the normalization of the capillary area and the rest of the image separately
NOTHING - io.github.rocsg.fijirelax.mrialgo.NoiseManagement: The nothing.
nparams - Variable in class io.github.rocsg.fijirelax.curvefit.MRLMA: The nparams.
Nparams - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1Mono: The Constant Nparams.
Nparams - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1MonoBias: The Constant Nparams.
Nparams - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1MonoRice: The Constant Nparams.
Nparams - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2DefaultMonoRice: The Constant Nparams.
Nparams - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2DefaultMultiRice: The Constant Nparams.
Nparams - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2Mono: The Constant Nparams.
Nparams - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MonoBias: The Constant Nparams.
Nparams - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MonoRice: The Constant Nparams.
Nparams - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2Multi: The Constant Nparams.
Nparams - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MultiBias: The Constant Nparams.
Nparams - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MultiRice: The Constant Nparams.
Nparams - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2Mono: The Constant Nparams.
Nparams - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MonoBias: The Constant Nparams.
Nparams - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MonoRice: The Constant Nparams.
Nparams - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2Multi: The Constant Nparams.
Nparams - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MultiBias: The Constant Nparams.
Nparams - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MultiRice: The Constant Nparams.
npts - Variable in class io.github.rocsg.fijirelax.curvefit.MRLMA: The npts.
numParams - Variable in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: The num params.
numPoints - Variable in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: The num points.
numVertices - Variable in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: The num vertices.

O

OFFSET - io.github.rocsg.fijirelax.mrialgo.NoiseManagement: The offset.
openComputeDialog() - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Open compute dialog.
openOutliersDialog() - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Open outliers dialog.
openRegistrationSettingsDialog() - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Open registration settings dialog.
OTHER - io.github.rocsg.fijirelax.mrialgo.MRDataType: The other.

P

PARAM_SIGMA - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant PARAM_SIGMA.
PARAM_TE - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant PARAM_TE.
PARAM_TR - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant PARAM_TR.
parameters - Variable in class io.github.rocsg.fijirelax.curvefit.MRLMA: The array of fit parameters (a.k.a, the a-vector).
parameters - Variable in class io.github.rocsg.fijirelax.lma.LMA: The array of fit parameters (a.k.a, the a-vector).
PDMAP - io.github.rocsg.fijirelax.mrialgo.MRDataType: The pdmap.
percentageKeepNormalisation - Static variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The percentage keep normalisation.
pruneBionanoStuff() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Specific setup for data handling

R

rangingBoundaries - Variable in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: The ranging boundaries.
rangingFactor - Variable in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: The ranging factor.
readCapValuesInSliceLabel(ImagePlus, int, int, int) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Read values of the capillary in slices label
readNifti(String) - Static method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Read nifti.
readSigmaInSliceLabel(ImagePlus, int, int, int) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Read Rice noise sigma in slice label
readT1T2() - Method in class io.github.rocsg.fijirelax.gui.Custom_Format_Importer: Read T1-T2 data from the given input dir (object member),organize it and return it as an HyperMap.
readTeInSliceLabel(ImagePlus, int, int, int) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Read the echoe time in slice label
readTrInSliceLabel(ImagePlus, int, int, int) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Read recovery time in slice label
readValueOfSigmaTrTeInSliceLabel(ImagePlus, int, int, int, int) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Read value of sigma tr te in slice label.
registerEchoes() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Register the echoes image.
registerEchoes(RegistrationAction) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Register the echoes image.
registrationFrame - Variable in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: The registration frame.
repaintAll() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Calling the sequence of GUI building helpers--------------------------------------------------------------------------------.
replaceMapsOutliersSlicePerSlice(int, double, int, boolean) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Apply the outlier detection scheme to a multi-slice MRI image, voxel after voxel by investigating the local distribution in a neighbourhood, and replace the outlier by the median computed in a local neighbourhood
RICE - io.github.rocsg.fijirelax.mrialgo.NoiseManagement: The rice.
RiceEstimator - Class in io.github.rocsg.fijirelax.mrialgo: This class provides utilities to estimate MRI relaxation parameters in presence of a Rice noise Rice noise affects the signal in a way that make it complicated to invert : its moments depend on the value of the unaltered signal For more information, refer to Fernandez et al. 2023 FijiRelax: Fast and noise-corrected estimation of MRI relaxation maps in 3D + t (in prep.)
RiceEstimator(double, double, double, double, int, int) - Constructor for class io.github.rocsg.fijirelax.mrialgo.RiceEstimator: Instantiates a new rice estimator.
run(String) - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Method called from the ImageJ interface, starting the plugin.
run(String) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Run the explorer
runActionAbort() - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Run abort current action
runActionCompute() - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Run compute maps
runActionExplorer() - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Run the curve explorer
runActionExport() - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Run exporting image to disk
runActionImport() - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Run importing image from disk
runActionOpen() - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Run the action for opening an Hypermap
runActionOutliers() - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Run outliers correction
runActionRegistration() - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Run register image sequences
runActionSos() - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Run the sos popup
runActionStress() - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Run the unstressing popup
runActionUndo() - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Run action undo.
runDebugTest() - Static method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Some debug test.
runExplorer(String) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Run explorer by specifying an HyperMap to explore
runExplorerFromHyperMap(HyperMap) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Run explorer by specifying an Hypermap to explore
runExplorerFromImage(ImagePlus) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Run explorer from a ImagePlus containing an HyperMap

S

SEC - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant SEC.
SeparatedData() - Constructor for class io.github.rocsg.fijirelax.lma.ArrayConverter.SeparatedData
separateMultiDimDataToXY(double[][]) - Static method in class io.github.rocsg.fijirelax.lma.ArrayConverter: Separates data from dataPoints[N][K+1] to yDataPoints[N] and xDatapoints[N][K].
separateNormalizationSpectrumMode - Variable in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: The separate normalization spectrum mode.
setDisplayRange() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Sets the display range according to default setup
setElement(int, int, double) - Method in class io.github.rocsg.fijirelax.lma.implementations.JAMAMatrix: Sets the element.
setElement(int, int, double) - Method in interface io.github.rocsg.fijirelax.lma.LMAMatrix: Set the value of a matrix element.
setInitialParameters(double[]) - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Sets the initial parameters, which override the default initial parameters.
setIterFactor(int) - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Sets the max number of iterations before early break
setLM(LMDualCurveFitterNoBias) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1Mono: Sets the optimiser.
setLM(LMDualCurveFitterNoBias) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1MonoBias: Sets the optimiser.
setLM(LMDualCurveFitterNoBias) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1MonoRice: Sets the optimiser.
setLM(LMDualCurveFitterNoBias) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2DefaultMonoRice: Sets the optimiser
setLM(LMDualCurveFitterNoBias) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2DefaultMultiRice: Sets the optimiser
setLM(LMDualCurveFitterNoBias) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2Mono: Sets the optimiser
setLM(LMDualCurveFitterNoBias) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MonoBias: Sets the optimiser
setLM(LMDualCurveFitterNoBias) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MonoRice: Sets the optimiser
setLM(LMDualCurveFitterNoBias) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2Multi: Sets the optimiser.
setLM(LMDualCurveFitterNoBias) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MultiBias: Sets the optimiser
setLM(LMDualCurveFitterNoBias) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MultiRice: Sets the lm.
setLM(LMDualCurveFitterNoBias) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2Mono: Sets the optimiser
setLM(LMDualCurveFitterNoBias) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MonoBias: Sets the optimiser
setLM(LMDualCurveFitterNoBias) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MonoRice: Sets the optimiser
setLM(LMDualCurveFitterNoBias) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2Multi: Sets the optimiser
setLM(LMDualCurveFitterNoBias) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MultiBias: Sets the optimiser
setLM(LMDualCurveFitterNoBias) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MultiRice: Sets the optimiser
setMaxIterations(int) - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Set maximum number of iterations allowed.
setMinDeltaChi2(double) - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Sets the min delta chi 2.
setRestarts(int) - Method in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Set number of simplex restarts to do.
setSigma(double) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1Mono: Sets the Rice sigma
setSigma(double) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1MonoBias: Sets the Rice sigma.
setSigma(double) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1MonoRice: Sets the Rice sigma.
setSigma(double) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2DefaultMonoRice: Sets the sigma.
setSigma(double) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2DefaultMultiRice: Sets the Rice sigma.
setSigma(double) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2Mono: Sets the Rice sigma.
setSigma(double) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MonoBias: Sets the Rice sigma.
setSigma(double) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MonoRice: Sets the Rice sigma.
setSigma(double) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2Multi: Sets the Rice sigma.
setSigma(double) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MultiBias: Sets the Rice sigma.
setSigma(double) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MultiRice: Sets the Rice sigma.
setSigma(double) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2Mono: Sets the Rice sigma.
setSigma(double) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MonoBias: Sets the Rice sigma.
setSigma(double) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MonoRice: Sets the Rice sigma.
setSigma(double) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2Multi: Sets the Rice sigma.
setSigma(double) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MultiBias: Sets the Rice sigma.
setSigma(double) - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MultiRice: Sets the Rice sigma.
setState(int[], boolean) - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Sets the state.
setup() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Setup the hypermap from the current configuration provided at construction
setupDataType() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Setup data type from the metainfo stored in slice labels
setupDimensions() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Setup dimensions fields from the given image
setupImages() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Setup respective images HyperMaps and HyperEchoes, storing computed maps (if any), and the echoes images
setupName() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Setup the name of image (img title) from the corresponding name field
setupScroll(int, int) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Setup scroll.
setupSigmaTabs() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Setup a tab of sigma values from the estimated sigma of the Rice noise.
setupStructures() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Setup the structures of the GUI.
setupTrTe() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Setup tab storing the values of echo time and recovery time, for each timepoint, each 2D slice, and each channel
showCopy(String) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Show a copy of the current HyperImage, with a selected text
sigma - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1Mono: The sigma.
sigma - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1MonoBias: The sigma.
sigma - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1MonoRice: The sigma.
sigma - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2DefaultMonoRice: The sigma.
sigma - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2DefaultMultiRice: The sigma.
sigma - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2Mono: The sigma.
sigma - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MonoBias: The sigma.
sigma - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MonoRice: The sigma.
sigma - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2Multi: The sigma.
sigma - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MultiBias: The sigma.
sigma - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MultiRice: The sigma.
sigma - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2Mono: The sigma.
sigma - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MonoBias: The sigma.
sigma - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MonoRice: The sigma.
sigma - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2Multi: The sigma.
sigma - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MultiBias: The sigma.
sigma - Variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MultiRice: The sigma.
sigma - Variable in class io.github.rocsg.fijirelax.curvefit.MRLMA: The sigma.
sigma - Variable in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: The sigma.
sigmaInUse - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The sigma in use.
sigmaRice - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The sigma rice.
simp - Variable in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: The simp.
SIMPLEX - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant SIMPLEX.
SimplexDualCurveFitterNoBias - Class in io.github.rocsg.fijirelax.curvefit: A simplex-based solution to curve fitting of exponential functions over MRI observations points This one is preferred as default solution, as it produce way less outliers than Levenberg implementation, is faster, and converges toward the same values in most cases Copyright (C) 2022 io.github.rocsg This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
SimplexDualCurveFitterNoBias(double[], double[], double[], int, double, boolean) - Constructor for class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: Construct a new SimplexCurveFitter.
simulateEchoesT1Relax(ImagePlus, double[], double, int, MRDataType, double, String) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Simulate echoes of a T2 relaxation sequence.
simulateEchoesT1T2Relax(ImagePlus, double[], double[], int, MRDataType[], double, String) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Simulate echoes of a T2 relaxation sequence.
simulateEchoesT2Relax(ImagePlus, double, double[], int, MRDataType, double, String) - Static method in class io.github.rocsg.fijirelax.mrialgo.MRUtils: Simulate echoes of a T2 relaxation sequence.
simulateOutlierRemoval(int, int, int, int, int, int) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Simulate outlier removal on a crop of the current HyperMap, by simulating a range of possible parameterization of outlier removal, in order to help the user to select the suitable parameters
sizeOfCursor() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Get cursor size.
smoothHisto(double[], int) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Smooth histo.
solveIncrements() - Method in class io.github.rocsg.fijirelax.curvefit.MRLMA: Solves the increments array (this.da) using alpha and beta.
solveIncrements() - Method in class io.github.rocsg.fijirelax.lma.LMA: Solves the increments array (this.da) using alpha and beta.
spectrumRangingModeT1 - Variable in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: The spectrum ranging mode T 1.
spectrumRangingModeT2 - Variable in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: The spectrum ranging mode T 2.
speedupRegistrationForTesting - Variable in class io.github.rocsg.fijirelax.gui.Custom_Format_Importer: The speedup registration for testing.
stackToSlicesTframes(ImagePlus) - Static method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Helper to convert a 3D image to a tab of 2D images (containing the succession of echoes)
start() - Method in class io.github.rocsg.fijirelax.mrialgo.RiceEstimator: Starting point after instantiating RiceEstimator
startFijiRelaxInterface() - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Start fiji relax interface.
startFromTestImage(String) - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Developer function, useful to quickstart from a test image.
startGui() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Start the GUI.
startPlotsAndRoi() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Start plotting the spectral density and the ROI over HyperMap.
stop() - Method in class io.github.rocsg.fijirelax.curvefit.MRLMA: The stop condition for the fit.
stop() - Method in class io.github.rocsg.fijirelax.lma.LMA: The stop condition for the fit.

T

T - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: number of time-frames in the HyperMap.
T1_MONO - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant T1_MONO.
T1_MONO_BIAS - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant T1_MONO_BIAS.
T1_MONO_RICE - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant T1_MONO_RICE.
T1MAP - io.github.rocsg.fijirelax.mrialgo.MRDataType: The t1map.
T1Mono() - Constructor for class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1Mono
T1MonoBias() - Constructor for class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1MonoBias
T1MonoRice() - Constructor for class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1MonoRice
t1selectCute(double[], int) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Getting if T1/T2 data should be displayed
t1SelectedCurve(int, int) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Getting if T1/T2 data should be displayed
T1SEQ - io.github.rocsg.fijirelax.mrialgo.MRDataType: The t1seq.
T1T2_BIONANO - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant T1T2_BIONANO.
T1T2_DEFAULT_T2_MONO_RICE - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant T1T2_DEFAULT_T2_MONO_RICE.
T1T2_DEFAULT_T2_MULTI_RICE - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant T1T2_DEFAULT_T2_MULTI_RICE.
T1T2_MONO - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant T1T2_MONO.
T1T2_MONO_BIAS - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant T1T2_MONO_BIAS.
T1T2_MONO_RICE - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant T1T2_MONO_RICE.
T1T2_MULTI - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant T1T2_MULTI.
T1T2_MULTI_BIAS - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant T1T2_MULTI_BIAS.
T1T2_MULTI_RICE - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant T1T2_MULTI_RICE.
T1T2DefaultMonoRice() - Constructor for class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2DefaultMonoRice
T1T2DefaultMultiRice() - Constructor for class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2DefaultMultiRice
T1T2Mono() - Constructor for class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2Mono
T1T2MonoBias() - Constructor for class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MonoBias
T1T2MonoRice() - Constructor for class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MonoRice
T1T2Multi() - Constructor for class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2Multi
T1T2MultiBias() - Constructor for class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MultiBias
T1T2MultiRice() - Constructor for class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MultiRice
t1t2selectCute(double[], int) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Selecting which T1/T2 data should be displayed
t1t2SelectedCurve(int, int) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Getting if T1/T2 data should be displayed
T1T2SEQ - io.github.rocsg.fijirelax.mrialgo.MRDataType: The t1t2seq.
T2_MONO - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant T2_MONO.
T2_MONO_BIAS - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant T2_MONO_BIAS.
T2_MONO_RICE - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant T2_MONO_RICE.
T2_MULTI - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant T2_MULTI.
T2_MULTI_BIAS - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant T2_MULTI_BIAS.
T2_MULTI_RICE - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant T2_MULTI_RICE.
T2MAP - io.github.rocsg.fijirelax.mrialgo.MRDataType: The t2map.
T2Mono() - Constructor for class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2Mono
T2MonoBias() - Constructor for class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MonoBias
T2MonoRice() - Constructor for class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MonoRice
T2Multi() - Constructor for class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2Multi
T2MultiBias() - Constructor for class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MultiBias
T2MultiRice() - Constructor for class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MultiRice
t2selectCute(double[], int) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Getting if T1/T2 data should be displayed
t2SelectedCurve(int, int) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Getting if T1/T2 data should be displayed
T2SEQ - io.github.rocsg.fijirelax.mrialgo.MRDataType: The t2seq.
T2SEQHR - io.github.rocsg.fijirelax.mrialgo.MRDataType: The t2seqhr.
tabSigmasT1Seq - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The tab sigmas T 1 seq.
tabSigmasT1T2Seq - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The tab sigmas T 1 T 2 seq.
tabSigmasT2Seq - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The tab sigmas T 2 seq.
Te - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The Te.
teData - Variable in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: The mag data.
testCorruptAndRecoverSignal() - Static method in class io.github.rocsg.fijirelax.mrialgo.RiceEstimator: Test of the random Rice simulator and correction scheme
testRandomRiceMeanDrift() - Static method in class io.github.rocsg.fijirelax.mrialgo.RiceEstimator: Test of the random Rice simulator
testSimulateAndEstimateRiceSigma() - Static method in class io.github.rocsg.fijirelax.mrialgo.RiceEstimator: Test of the random Rice simulator
textAlg(int) - Static method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: get the current estimation algo as a short String
THRESHOLD_BOUTURE_FACTOR - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant THRESHOLD_BOUTURE_FACTOR.
THRESHOLD_RATIO_BETWEEN_MAX_ECHO_AND_SIGMA_RICE - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant THRESHOLD_RATIO_BETWEEN_MAX_ECHO_AND_SIGMA_RICE.
THRESHOLD_RATIO_BETWEEN_MEAN_ECHO_AND_SIGMA_RICE - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant THRESHOLD_RATIO_BETWEEN_MEAN_ECHO_AND_SIGMA_RICE.
timeitems - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias: The Constant timeitems.
timeitems - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant timeitems.
timeunits - Static variable in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias: The Constant timeunits.
timeunits - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant timeunits.
timeVersionFlag - Variable in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: The time version flag.
toString() - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1Mono: Get the equation currently estimated
toString() - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1MonoBias: Get the equation currently estimated
toString() - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1MonoRice: Get the equation currently estimated
toString() - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2DefaultMonoRice: To string.
toString() - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2DefaultMultiRice: The equation being optimized.
toString() - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2Mono: The equation being optimized.
toString() - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MonoBias: Get the equation currently estimated
toString() - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MonoRice: Get the equation currently estimated
toString() - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2Multi: The equation being optimized.
toString() - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MultiBias: Get the equation currently estimated
toString() - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T1T2MultiRice: Get the equation currently estimated
toString() - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2Mono: Get the equation currently estimated
toString() - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MonoBias: Get the equation currently estimated
toString() - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MonoRice: Get the equation currently estimated
toString() - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2Multi: The equation being optimized.
toString() - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MultiBias: Get the equation currently estimated
toString() - Method in class io.github.rocsg.fijirelax.curvefit.LMDualCurveFitterNoBias.T2MultiRice: Get the equation currently estimated
toString() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Get current HyperMap as a String
Tr - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The Tr.
TR10000 - io.github.rocsg.fijirelax.mrialgo.MRDataType: The tr10000.
TR1200 - io.github.rocsg.fijirelax.mrialgo.MRDataType: The tr1200.
TR2400 - io.github.rocsg.fijirelax.mrialgo.MRDataType: The tr2400.
TR4800 - io.github.rocsg.fijirelax.mrialgo.MRDataType: The tr4800.
TR600 - io.github.rocsg.fijirelax.mrialgo.MRDataType: The tr600.
transpose(double[]) - Static method in class io.github.rocsg.fijirelax.lma.ArrayConverter: Transpose.
trData - Variable in class io.github.rocsg.fijirelax.curvefit.SimplexDualCurveFitterNoBias: The mag data.
tuckeyIsOutlier(double, double[], double[], double) - Static method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Detect outlier values using the tuckey fence technique
TWOPOINTS - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The Constant TWOPOINTS.

U

unlock() - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Unlock.
updateAlpha() - Method in class io.github.rocsg.fijirelax.curvefit.MRLMA: Calculates all elements for this.alpha.
updateAlpha() - Method in class io.github.rocsg.fijirelax.lma.LMA: Calculates all elements for this.alpha.
updateBeta() - Method in class io.github.rocsg.fijirelax.curvefit.MRLMA: Calculates all elements for this.beta.
updateBeta() - Method in class io.github.rocsg.fijirelax.lma.LMA: Calculates all elements for this.beta.
updateBothFromNewHyperImg(ImagePlus) - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Update both fields from a TIFF representing a new HyperMap
updateEchoesAndMaps() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Update echoes and maps images from the hyperMap when it changed
updateHyperImgFromEchoesAndMaps() - Method in class io.github.rocsg.fijirelax.mrialgo.HyperMap: Update hyper img from the members hyperMaps and hyperEchoes.
updateParameters() - Method in class io.github.rocsg.fijirelax.curvefit.MRLMA: Updates parameters from incrementedParameters.
updateParameters() - Method in class io.github.rocsg.fijirelax.lma.LMA: Updates parameters from incrementedParameters.
updatePlaying(int, int) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Update the parameters displayed in the tab, depending on the current action
updateSwitchButtons() - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Update switch buttons.
updateView() - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Update the view.
useBoundaries - Static variable in class io.github.rocsg.fijirelax.mrialgo.MRUtils: The use boundaries.

V

valueOf(String) - Static method in enum io.github.rocsg.fijirelax.mrialgo.MRDataType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum io.github.rocsg.fijirelax.mrialgo.NoiseManagement: Returns the enum constant of this type with the specified name.
values() - Static method in enum io.github.rocsg.fijirelax.mrialgo.MRDataType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum io.github.rocsg.fijirelax.mrialgo.NoiseManagement: Returns an array containing the constants of this enum type, in the order they are declared.
verbose - Variable in class io.github.rocsg.fijirelax.curvefit.MRLMA: Set true to print details while fitting.
verbose - Variable in class io.github.rocsg.fijirelax.lma.LMA: Set true to print details while fitting.
versionFlag - Variable in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: The version flag.
versionName - Variable in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: The version name.
viewSlice - Variable in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: The view slice.
voxs - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: The voxel sizes.

W

weights - Variable in class io.github.rocsg.fijirelax.curvefit.MRLMA: Weights for each data point.
weights - Variable in class io.github.rocsg.fijirelax.lma.LMA: Weights for each data point.
welcomeAndInformAboutComputerCapabilities() - Method in class io.github.rocsg.fijirelax.gui.FijiRelax_Gui: Welcome and inform about computer capabilities.
windowClosing(WindowEvent) - Method in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: Window closing.

X

X - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: HyperMap width
xDataPoints - Variable in class io.github.rocsg.fijirelax.curvefit.MRLMA: Measured x-data point arrays for which the model function is to be fitted, yDataPoints[j] = y(xDataPoints[j], a[]).
xDataPoints - Variable in class io.github.rocsg.fijirelax.lma.ArrayConverter.SeparatedData: The x data points.
xDataPoints - Variable in class io.github.rocsg.fijirelax.lma.LMA: Measured x-data point arrays for which the model function is to be fitted, yDataPoints[j] = y(xDataPoints[j], a[]).
xMouseRange - Variable in class io.github.rocsg.fijirelax.gui.MRI_HyperCurvesExplorer: The x mouse range.

Y

Y - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: HyperMap Height.
yDataPoints - Variable in class io.github.rocsg.fijirelax.curvefit.MRLMA: Measured y-data points for which the model function is to be fitted, yDataPoints[j] = y(xDataPoints[j], a[]).
yDataPoints - Variable in class io.github.rocsg.fijirelax.lma.ArrayConverter.SeparatedData: The y data points.
yDataPoints - Variable in class io.github.rocsg.fijirelax.lma.LMA: Measured y-data points for which the model function is to be fitted, yDataPoints[j] = y(xDataPoints[j], a[]).

Z

Z - Variable in class io.github.rocsg.fijirelax.mrialgo.HyperMap: HyperMap number of z-slices

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