A B C D E F G H I J K L M N O P Q R S T U V W Z _ 

A

A - Static variable in interface loci.slim.fitted.FittedValue
 
A1 - Static variable in interface loci.slim.fitted.FittedValue
 
A1_INDEX - Static variable in interface loci.slim.fitted.FittedValue
 
A1_INDEX - Static variable in class loci.slim.fitting.images.FittedImageFitter
 
a1macroused - Variable in class loci.slim.paramSetMacro
 
A2 - Static variable in interface loci.slim.fitted.FittedValue
 
A2_INDEX - Static variable in interface loci.slim.fitted.FittedValue
 
A2_INDEX - Static variable in class loci.slim.fitting.images.FittedImageFitter
 
a2macroused - Variable in class loci.slim.paramSetMacro
 
A3 - Static variable in interface loci.slim.fitted.FittedValue
 
A3_INDEX - Static variable in interface loci.slim.fitted.FittedValue
 
A3_INDEX - Static variable in class loci.slim.fitting.images.FittedImageFitter
 
a3macroused - Variable in class loci.slim.paramSetMacro
 
ABatchHistogram - Class in loci.slim.analysis.batch
A batch histogram that represents A values.
ABatchHistogram() - Constructor for class loci.slim.analysis.batch.ABatchHistogram
 
About - Class in loci.slim
Displays a small information dialog about the SLIM Curve project.
About() - Constructor for class loci.slim.About
 
about() - Static method in class loci.slim.About
 
AbstractBaseFittedImage - Class in loci.slim.fitting.images
Base class for the fitted images.
AbstractBaseFittedImage(String, int[], IndexColorModel, boolean, IGrayScaleImage, IMaskGroup[]) - Constructor for class loci.slim.fitting.images.AbstractBaseFittedImage
 
AbstractBatchHistogram - Class in loci.slim.analysis.batch
Base class for a batch, cumulative histogram for a particular fitted parameter.
AbstractBatchHistogram() - Constructor for class loci.slim.analysis.batch.AbstractBatchHistogram
 
AbstractCurveFitter - Class in loci.curvefitter
Abstract base class for curve fitters.
AbstractCurveFitter() - Constructor for class loci.curvefitter.AbstractCurveFitter
 
AbstractFittedValue - Class in loci.slim.fitted
Abstract base class for dealing with fitted values.
AbstractFittedValue() - Constructor for class loci.slim.fitted.AbstractFittedValue
 
add(Mask) - Method in class loci.slim.mask.Mask
Adds given mask to current mask, generating a new mask.
addCursor(Cursor) - Method in class imagej.charts.cursors.CursorLayer
 
addCursorDragListener(ICursorDragListener) - Method in class imagej.charts.cursors.Cursor
 
addCursorMoveListener(ICursorMoveListener) - Method in class imagej.charts.cursors.Cursor
 
addCursorStretchListener(ICursorStretchListener) - Method in class imagej.charts.cursors.Cursor
 
addListener(IFittingCursorListener) - Method in class loci.slim.fitting.cursor.FittingCursor
Adds a listener for cursor changes.
addListener(FittingCursorListener) - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Adds a listener for cursor changes.
addMasks(Collection<Mask>) - Static method in class loci.slim.mask.Mask
Given a collection of masks, adds them all together.
addNode(IMaskNode) - Method in interface loci.slim.mask.IMaskGroup
Adds a mask node to group.
addNode(IMaskNode) - Method in class loci.slim.mask.MaskGroup
 
ADJUSTED_SIZE - Static variable in class loci.slim.histogram.PaletteFix
 
adjustEstimatedParams(double[], boolean[], ICurveFitter.FitFunction, double, double, double) - Method in class loci.curvefitter.DummyFitterEstimator
 
adjustEstimatedParams(double[], boolean[], ICurveFitter.FitFunction, double, double, double) - Method in interface loci.curvefitter.IFitterEstimator
Given an initial estimate of A, tau, and Z sets up the parameters for further fitting.
adjustEstimatedParams(double[], boolean[], ICurveFitter.FitFunction, double, double, double) - Method in class loci.slim.heuristics.FitterEstimator
Adjusts the mono exponential triple integral fit estimate for further mono, bi, tri, and stretched exponential fitting.
adjustEstimatedParams(double[], boolean[], ICurveFitter.FitFunction, double, double, double) - Method in class loci.slim2.heuristics.DefaultFitterEstimator
Adjusts the mono exponential triple integral fit estimate for further mono, bi, tri, and stretched exponential fitting.
adjustMinMax(double, double) - Static method in class loci.slim.histogram.PaletteFix
Given a min and max specification for a 254-color palette, turns it into a 256-color palette min and max.
AFittedValue - Class in loci.slim.fitted
Extracts A fitted values.
AFittedValue() - Constructor for class loci.slim.fitted.AFittedValue
 
AkutanCurveFitter - Class in loci.curvefitter
TODO
AkutanCurveFitter() - Constructor for class loci.curvefitter.AkutanCurveFitter
 
analyze(ImgPlus<DoubleType>, ICurveFitter.FitRegion, ICurveFitter.FitFunction, String) - Method in class loci.slim.analysis.plugins.ExportHistogramsToText
 
analyze(ImgPlus<DoubleType>, ICurveFitter.FitRegion, ICurveFitter.FitFunction, String) - Method in class loci.slim.analysis.plugins.ExportPixelsToText
 
analyze(ImgPlus<DoubleType>, ICurveFitter.FitRegion, ICurveFitter.FitFunction) - Method in class loci.slim.analysis.plugins.VisADAnalysisPlugin
 
analyze(ImgPlus<DoubleType>, ICurveFitter.FitRegion, ICurveFitter.FitFunction, String) - Method in interface loci.slim.analysis.SLIMAnalyzer
 
analyze(ImgPlus<DoubleType>, ICurveFitter.FitRegion, ICurveFitter.FitFunction, String) - Method in class loci.slim2.analysis.batch.ExportHistogramsToText
 
analyze(ImgPlus<DoubleType>, ICurveFitter.FitRegion, ICurveFitter.FitFunction, String) - Method in class loci.slim2.analysis.batch.ExportPixelsToText
 

B

BaseFitSettings - Class in loci.slim2.process.interactive
 
BaseFitSettings() - Constructor for class loci.slim2.process.interactive.BaseFitSettings
 
batch(String, String, String, String) - Static method in class loci.slim.SLIM_PlugIn
Processes an input file in batch processing.
batch(String, String, boolean, boolean) - Method in class loci.slim.SLIMProcessor
Batch process a single file.
batchFileList - Variable in class loci.slim.paramSetMacro
 
batchHisto(String, String) - Static method in class loci.slim.SLIM_PlugIn
Processes an input file in batch processing.
batchHisto(String, String) - Method in class loci.slim.SLIMProcessor
 
BatchHistogram - Interface in loci.slim.analysis.batch
 
BatchHistogramListener - Interface in loci.slim.analysis.batch.ui
Used to load images from the batch histogram UI.
BatchHistogramPanel - Class in loci.slim.analysis.batch.ui
 
BatchHistogramPanel(HistogramPanel, StatisticsPanel) - Constructor for class loci.slim.analysis.batch.ui.BatchHistogramPanel
 
BatchHistogramsFrame - Class in loci.slim.analysis.batch.ui
UI Panel to show information from several BatchHistogram.
BatchHistogramsFrame(BatchHistogramListener) - Constructor for class loci.slim.analysis.batch.ui.BatchHistogramsFrame
Constructor of invisible frame.
batchModeSet(String) - Static method in class loci.slim.SLIMProcessor
 
BatchProcessor - Interface in loci.slim2.process
 
beginFit() - Method in class loci.slim.fitting.images.AbstractBaseFittedImage
Begins a fit.
beginFit() - Method in class loci.slim.fitting.images.FittedImageFitter
Begins a fit.
beginFit() - Method in interface loci.slim.fitting.images.IFittedImage
Begins a fit.
Bin11x11 - Class in loci.slim.preprocess
Binning plugin which handles 11x11 square binning.
Bin11x11() - Constructor for class loci.slim.preprocess.Bin11x11
 
Bin3x3 - Class in loci.slim.preprocess
Binning plugin which handles 3x3 square binning.
Bin3x3() - Constructor for class loci.slim.preprocess.Bin3x3
 
Bin5x5 - Class in loci.slim.preprocess
Binning plugin which handles 5x5 square binning.
Bin5x5() - Constructor for class loci.slim.preprocess.Bin5x5
 
Bin7x7 - Class in loci.slim.preprocess
Binning plugin which handles 7x7 square binning.
Bin7x7() - Constructor for class loci.slim.preprocess.Bin7x7
 
Bin9x9 - Class in loci.slim.preprocess
Binning plugin which handles 9x9 square binning.
Bin9x9() - Constructor for class loci.slim.preprocess.Bin9x9
 
Binning - Class in loci.slim.analysis
Static utility methods to convert from a value to a bin, useful for dealing with histograms and LUTs.
Binning() - Constructor for class loci.slim.analysis.Binning
 
binToValue(int, double) - Method in class loci.curvefitter.DummyFitterEstimator
 
binToValue(int, double) - Method in interface loci.curvefitter.IFitterEstimator
Converts a bin index to a time value.
binToValue(int, double) - Method in class loci.slim.heuristics.FitterEstimator
Converts bin number to time-based value.
binToValue(int, double) - Method in class loci.slim2.heuristics.DefaultFitterEstimator
Converts bin number to time-based value.
binValues(int, double, double) - Method in class loci.slim.histogram.HistogramDataNode
Creates an array of histogram values based on the current nominal min/max range.

C

call() - Method in class loci.slim.fitting.callable.FittingEngineCallable
 
call() - Method in interface loci.slim.fitting.callable.IFittingEngineCallable
Do the fit.
call() - Method in class loci.slim2.fitting.DefaultFittingCallable
 
call() - Method in interface loci.slim2.fitting.FittingCallable
Do the fit.
cancelExcitation() - Method in interface loci.slim.ui.IUserInterfacePanelListener
Cancels the current excitation curve, if any.
cancelExcitation() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanelListener
Cancels the current excitation curve, if any.
cancelFit() - Method in class loci.slim.fitting.images.AbstractBaseFittedImage
Cancels a fit.
cancelFit() - Method in class loci.slim.fitting.images.FittedImageFitter
Cancels a fit.
cancelFit() - Method in interface loci.slim.fitting.images.IFittedImage
Cancels a fit
cancelFit() - Method in interface loci.slim.ui.IUserInterfacePanelListener
Cancels ongoing fit.
cancelFit() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanelListener
Cancels ongoing fitted image creation.
centerValuesPerBin(int, double, double) - Static method in class loci.slim.analysis.Binning
Returns array of center values for each bin.
chain(IProcessor) - Method in class loci.slim.DecayImageWrapper
Specifies a source IProcessor to be chained to this one.
chain(IProcessor) - Method in interface loci.slim.fitting.IDecayImage
Specifies a source IProcessor to be chained to this one.
chain(IProcessor) - Method in interface loci.slim.preprocess.IProcessor
Specifies a source IProcessor to be chained to this one.
chain(IProcessor) - Method in class loci.slim.preprocess.RoiProcessor
 
chain(IProcessor) - Method in class loci.slim.preprocess.SquareBinner
Specifies a source IProcessor to be chained to this one.
chain(IProcessor) - Method in class loci.slim.preprocess.Threshold
Specifies a source IProcessor to be chained to this one.
CHI - Static variable in interface loci.slim.fitted.FittedValue
 
CHI - Static variable in interface loci.slim2.process.interactive.ui.UserInterfacePanel
 
chi2MacroUsed - Static variable in class loci.slim.paramSetMacro
 
CHI_SQ - Static variable in interface loci.slim.fitted.FittedValue
 
CHI_SQ_INDEX - Static variable in interface loci.slim.fitted.FittedValue
 
CHISQ_INDEX - Static variable in class loci.slim.fitting.images.FittedImageFitter
 
ChiSqBatchHistogram - Class in loci.slim.analysis.batch
A batch histogram that represents chi square values.
ChiSqBatchHistogram() - Constructor for class loci.slim.analysis.batch.ChiSqBatchHistogram
 
ChiSqFittedValue - Class in loci.slim.fitted
Extracts Chi Square fitted values.
ChiSqFittedValue() - Constructor for class loci.slim.fitted.ChiSqFittedValue
 
CHISQUARE - Static variable in interface loci.slim2.process.interactive.ui.UserInterfacePanel
 
ChunkyPixel - Class in loci.slim
Class that handles drawing the image using progressively smaller "chunky" (larger than single pixel) pixels.
ChunkyPixel(int, int, int, int) - Constructor for class loci.slim.ChunkyPixel
Constructor.
ChunkyPixel - Class in loci.slim2.outputset.temp
Used to draw large but increasingly smaller "chunky pixels", to provide better feedback during a slow process.
ChunkyPixel(long[], long, long) - Constructor for class loci.slim2.outputset.temp.ChunkyPixel
Constructor.
ChunkyPixelEffectIterator - Class in loci.slim
Iterator that supplies a series of chunky pixels.
ChunkyPixelEffectIterator(IChunkyPixelTable, int, int) - Constructor for class loci.slim.ChunkyPixelEffectIterator
Constructor, sets up the chunky pixel iterator with a table of chunky pixels and the width and height of the image being processed.
ChunkyPixelIterator - Class in loci.slim2.outputset.temp
Iterator for progressively rendering images.
ChunkyPixelIterator(long[]) - Constructor for class loci.slim2.outputset.temp.ChunkyPixelIterator
Constructor.
ChunkyPixelTableImpl - Class in loci.slim
Table used for the "chunky pixel" effect.
ChunkyPixelTableImpl() - Constructor for class loci.slim.ChunkyPixelTableImpl
 
clone() - Method in class loci.slim.mask.Mask
 
close() - Method in class loci.slim.GrayScaleImage
 
close() - Method in interface loci.slim.IGrayScaleImage
Closes down the grayscale image window.
close() - Method in class loci.slim2.process.interactive.grayscale.GrayscaleDisplay
 
ColorBarPanel - Class in loci.slim.histogram
Displays a color bar with the current colorization scheme.
ColorBarPanel(int, int, int) - Constructor for class loci.slim.histogram.ColorBarPanel
Constructor.
ColorizedFittedImage - Class in loci.slim.fitting.images
This class maintains a colorized grayscale fitted image, similar to those in SPCImage software.
ColorizedFittedImage(IGrayScalePixelValue, double[][]) - Constructor for class loci.slim.fitting.images.ColorizedFittedImage
 
compute(double[]) - Method in class loci.slim2.outputset.IndexedMemberFormula
 
compute(double[]) - Method in interface loci.slim2.outputset.MemberFormula
Formula for calculating a value for this tuple dimension.
Configuration - Class in loci.slim.fitting.config
Handles configuration specific to the SLIM Curve plugin for ImageJ.
ConfigurationHelper - Class in loci.slim.fitting.config
 
ConfigurationHelper() - Constructor for class loci.slim.fitting.config.ConfigurationHelper
 
configure() - Method in class loci.slim.fitting.config.ConfigurationHelper
 
context() - Method in class loci.slim2.histogram.DataHistogramCommand
 
convert(DatasetService, Dataset, int, int) - Static method in class loci.slim2.decay.DecayDatasetUtility
Converts lifetime image to grayscale.
create(String, long...) - Static method in class loci.slim.ImageUtils
 
createBinner(String) - Method in class loci.slim.preprocess.SLIMBinning
 
createExcitation(String, double[], double) - Static method in class loci.slim.ExcitationFileUtility
 
createExcitation(String) - Method in interface loci.slim.ui.IUserInterfacePanelListener
Creates an excitation curve from current X, Y and saves to file.
createExcitation(String) - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanelListener
Creates an excitation curve from current X, Y and saves to file.
createFittedValues(String, int) - Static method in class loci.slim.fitted.FittedValueFactory
Creates array of FittedValue from String descriptor.
createImage(String, FittedImageFitter.FittedImageType, int, int, int[], IndexColorModel, int, boolean, IGrayScaleImage, IMaskGroup[]) - Method in class loci.slim.fitting.images.FittedImageFactory
 
CrossHairOverlay - Class in loci.slim2.process.interactive.grayscale
 
CrossHairOverlay(Context, Dataset) - Constructor for class loci.slim2.process.interactive.grayscale.CrossHairOverlay
Construct a CrossHairOverlay given a Context context.
Cursor - Class in imagej.charts.cursors
 
Cursor() - Constructor for class imagej.charts.cursors.Cursor
 
Cursor(int) - Constructor for class imagej.charts.cursors.Cursor
 
Cursor(int, Cursor.Orientation) - Constructor for class imagej.charts.cursors.Cursor
 
Cursor.Orientation - Enum in imagej.charts.cursors
 
cursorChanged(FittingCursor) - Method in interface loci.slim.fitting.cursor.IFittingCursorListener
Callback when the cursor changes.
cursorChanged(FittingCursor) - Method in interface loci.slim2.process.interactive.cursor.FittingCursorListener
Callback when the cursor changes.
CursorEstimator - Class in loci.slim.heuristics
Based on TRI2 TRCursors.c.
CursorEstimator() - Constructor for class loci.slim.heuristics.CursorEstimator
 
CursorEstimator - Class in loci.slim2.heuristics
Based on TRI2 TRCursors.c.
CursorEstimator() - Constructor for class loci.slim2.heuristics.CursorEstimator
 
CursorLayer - Class in imagej.charts.cursors
 
CursorLayer(JPanel) - Constructor for class imagej.charts.cursors.CursorLayer
 
cursorMoved(int, int, double) - Method in interface imagej.charts.cursors.ICursorDragListener
 
cursorMoved(int, int, double) - Method in interface imagej.charts.cursors.ICursorMoveListener
 
cursorMoved(int, int, double) - Method in interface imagej.charts.cursors.ICursorStretchListener
 
CurveFitData - Class in loci.curvefitter
TODO
CurveFitData() - Constructor for class loci.curvefitter.CurveFitData
 

D

DATA_START - Static variable in class loci.slim.heuristics.CursorEstimator
 
DATA_START - Static variable in class loci.slim2.heuristics.CursorEstimator
 
DataHistogramCommand - Class in loci.slim2.histogram
Plugin that sets the minimum and maximum for scaling of display values.
DataHistogramCommand() - Constructor for class loci.slim2.histogram.DataHistogramCommand
 
DataStartMacroUsed - Variable in class loci.slim.paramSetMacro
 
debug() - Method in class loci.slim.mask.Mask
 
DecayDatasetUtility - Class in loci.slim2.decay
Utility class to convert lifetime images to grayscale by summing the photons.
DecayDatasetUtility() - Constructor for class loci.slim2.decay.DecayDatasetUtility
 
DecayGraph - Class in loci.slim.ui
This is the chart that shows the transient decay data, the fitted model, and the residuals.
DecayGraph() - Constructor for class loci.slim.ui.DecayGraph
Public constructor, may be used to create non-singletons.
DecayGraph - Interface in loci.slim2.process.interactive.ui
Interface for a decay chart.
DecayImageWrapper<T extends RealType<T>> - Class in loci.slim
This class wraps an image that has a decay curve for each pixel.
DecayImageWrapper(ImgPlus<T>, int, int, int, int, int, int) - Constructor for class loci.slim.DecayImageWrapper
 
DEFAULT_BANDWIDTH - Static variable in class loci.slim.histogram.HistogramPanel
 
DEFAULT_EXCITATION_LOAD - Static variable in class loci.slim.SLIMProcessor
 
DEFAULT_X_INC - Static variable in interface loci.curvefitter.ICurveFitter
Default increment along x axis (evenly spaced).
DefaultBatchProcessor - Class in loci.slim2.process.batch
Handles batch fitting of lifetime images.
DefaultBatchProcessor() - Constructor for class loci.slim2.process.batch.DefaultBatchProcessor
 
DefaultDecayGraph - Class in loci.slim2.process.interactive.ui
This is the chart that shows the transient decay data, the fitted model, and the residuals.
DefaultDecayGraph() - Constructor for class loci.slim2.process.interactive.ui.DefaultDecayGraph
 
DefaultEstimator - Class in loci.slim2.heuristics
This class contains all estimates and rules of thumb.
DefaultEstimator() - Constructor for class loci.slim2.heuristics.DefaultEstimator
 
DefaultExcitationGraph - Class in loci.slim2.process.interactive.ui
Graph that displays the excitation (also known as the prompt, instrument response function, or lamp function).
DefaultFitResults - Class in loci.slim2.fitting
Container for local fitted results for current pixel.
DefaultFitResults() - Constructor for class loci.slim2.fitting.DefaultFitResults
 
DefaultFitSettings - Class in loci.slim2.process.interactive
Fit settings.
DefaultFitSettings() - Constructor for class loci.slim2.process.interactive.DefaultFitSettings
 
DefaultFitterEstimator - Class in loci.slim2.heuristics
Assorted rules of thumb for fitting.
DefaultFitterEstimator() - Constructor for class loci.slim2.heuristics.DefaultFitterEstimator
 
DefaultFittingCallable - Class in loci.slim2.fitting
This class brings together everything needed to fit one pixel.
DefaultFittingCallable() - Constructor for class loci.slim2.fitting.DefaultFittingCallable
 
DefaultGlobalFitParams - Class in loci.slim2.fitting
This contains the global fitting parameters, i.e.
DefaultGlobalFitParams() - Constructor for class loci.slim2.fitting.DefaultGlobalFitParams
 
DefaultIntegrator - Class in loci.slim.fitting
 
DefaultIntegrator() - Constructor for class loci.slim.fitting.DefaultIntegrator
 
DefaultInteractiveProcessor - Class in loci.slim2.process.interactive
Fits FLIM data in an interactive manner.
DefaultInteractiveProcessor() - Constructor for class loci.slim2.process.interactive.DefaultInteractiveProcessor
 
DefaultLocalFitParams - Class in loci.slim2.fitting
Container for the local fitting parameters, i.e.
DefaultLocalFitParams() - Constructor for class loci.slim2.fitting.DefaultLocalFitParams
 
DefaultUserInterfacePanel - Class in loci.slim2.process.interactive.ui
Default implementation of main UI panel.
DefaultUserInterfacePanel(boolean, boolean, int, double, String[], String[], FittingCursor, IFitterEstimator) - Constructor for class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
disable() - Method in interface loci.slim.ui.IUserInterfacePanel
Disables the UI.
disable() - Method in class loci.slim.ui.UserInterfacePanel
 
disable() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
disable() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Disables the UI.
disableButtons() - Method in interface loci.slim.ui.IUserInterfacePanel
Disables the UI buttons.
disableButtons() - Method in class loci.slim.ui.UserInterfacePanel
 
disableButtons() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
disableButtons() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Disables the UI buttons.
disableMacro() - Method in class loci.slim.paramSetMacro
this macro disables all the macro when SLIM Curve is exiting, so that normal operation can resume when restarted
discoverInterface(String, String) - Method in class loci.slim.fitting.config.ConfigurationHelper
 
doAnalysis(String, ImgPlus<DoubleType>, ICurveFitter.FitRegion, ICurveFitter.FitFunction, String) - Method in class loci.slim.analysis.SLIMAnalysis
Does image analysis.
doFit() - Method in interface loci.slim.ui.IUserInterfacePanelListener
Triggers a fit.
DOUBLE - Static variable in class loci.slim2.experimental.EnderleinErdmann
 
DOUBLE_FITTED_IMAGE_ITEMS - Static variable in class loci.slim.ui.UserInterfacePanel
 
DoubleFormatter - Class in loci.slim.histogram
Builds a maximum or minimum value, rounding and formatting appropriately.
DoubleFormatter(boolean, int, double) - Constructor for class loci.slim.histogram.DoubleFormatter
 
dragMinMaxLUT(double, double) - Method in class loci.slim.histogram.HistogramUIPanel
Called when the user is dragging the cursors on the histogram panel.
dragMinMaxPixels(int, int) - Method in interface loci.slim.histogram.IHistogramPanelListener
Called during a mouse drag.
draw(int, int, double) - Method in class loci.slim.fitting.images.ColorizedFittedImage
 
draw(int, int, double) - Method in class loci.slim.fitting.images.FloatFittedImage
 
draw(int, int, double) - Method in interface loci.slim.fitting.images.IFittedImageSlice
Draws a single pixel with current LUT and LUT range.
DummyFitterEstimator - Class in loci.curvefitter
This is a dummy implementation of the IFitterEstimator interface that turns off fit-time TRI2 behavior.
DummyFitterEstimator() - Constructor for class loci.curvefitter.DummyFitterEstimator
 

E

edgeValuesPerBin(int, double, double) - Static method in class loci.slim.analysis.Binning
Returns array of left edge values for each bin.
enable(boolean) - Method in class loci.slim.GrayScaleImage
Disables and enables channel selection, during and after a fit.
enable(boolean) - Method in interface loci.slim.IGrayScaleImage
Disables and enables channel selection, during and after a fit.
enableChannels(boolean) - Method in class loci.slim.histogram.HistogramUIPanel
Enables or disables the checkbox UI.
enablePrompt(boolean) - Method in class loci.slim.fitting.cursor.FittingCursorHelper
Turns on/off prompt cursors.
end(String) - Method in class loci.slim.analysis.batch.ExportBatchHistogram
 
end(String) - Method in class loci.slim.analysis.batch.ExportBatchHistogram2
 
endBatch() - Static method in class loci.slim.SLIM_PlugIn
Ends batch processing.
endBatch() - Method in class loci.slim.SLIMProcessor
End batch processing.
endBatchHisto() - Static method in class loci.slim.SLIM_PlugIn
Ends batch processing.
endBatchHisto() - Method in class loci.slim.SLIMProcessor
 
EnderleinErdmann - Class in loci.slim2.experimental
 
EnderleinErdmann() - Constructor for class loci.slim2.experimental.EnderleinErdmann
 
endFit() - Method in class loci.slim.fitting.images.AbstractBaseFittedImage
Ends a fit.
endFit() - Method in class loci.slim.fitting.images.FittedImageFitter
Ends a fit.
endFit() - Method in interface loci.slim.fitting.images.IFittedImage
Ends a fit.
endValueToBin(double, double) - Method in class loci.slim.heuristics.FitterEstimator
 
endValueToBin(double, double) - Method in class loci.slim2.heuristics.DefaultFitterEstimator
 
equals(Mask) - Method in class loci.slim.mask.Mask
Is mask equivalent to another mask?
ErrorDisplayOverlay - Class in loci.slim2.process.interactive.grayscale
 
ErrorDisplayOverlay() - Constructor for class loci.slim2.process.interactive.grayscale.ErrorDisplayOverlay
 
ErrorManager - Class in loci.slim.fitting
This class keeps track of bit masks that define which pixels have a fitting error.
ErrorManager(int, int, int) - Constructor for class loci.slim.fitting.ErrorManager
Creates a handler for a set of bit masks by channel.
estimateCursors(double, double[], double[], double) - Static method in class loci.slim.heuristics.CursorEstimator
Provides estimation of prompt and decay cursors.
estimateCursors() - Method in interface loci.slim.ui.IUserInterfacePanelListener
Estimates the prompt and decay cursors.
estimateCursors(double, double[], double[], double) - Static method in class loci.slim2.heuristics.CursorEstimator
Provides estimation of prompt and decay cursors.
estimateCursors() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanelListener
Estimates the prompt and decay cursors.
estimateDecayCursors(double, double[]) - Static method in class loci.slim.heuristics.CursorEstimator
Provides estimation of decay cursors.
estimateDecayCursors(double, double[]) - Static method in class loci.slim2.heuristics.CursorEstimator
Provides estimation of decay cursors.
estimateExcitation(String) - Method in interface loci.slim.ui.IUserInterfacePanelListener
Estimates an excitation curve from current X, Y and saves to file.
estimateExcitation(String) - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanelListener
Estimates an excitation curve from current X, Y and saves to file.
estimateThreshold() - Method in class loci.slim.GrayScaleImage
 
estimateThreshold() - Method in interface loci.slim.IThresholdUpdate
Gets an initial threshold estimate.
estimateThreshold() - Method in class loci.slim2.process.interactive.grayscale.GrayscaleDisplay
 
Estimator - Class in loci.slim.heuristics
This class contains all estimates and rules of thumb.
Estimator() - Constructor for class loci.slim.heuristics.Estimator
 
Estimator - Interface in loci.slim2.heuristics
Interface for a class with estimates and rules of thumb.
Excitation - Class in loci.slim
This class is a container for values for the excitation (also known as the prompt, instrument response function, or lamp function).
Excitation(String, double[], double) - Constructor for class loci.slim.Excitation
Creates an excitation with given filename and values.
excitationFileName - Variable in class loci.slim.paramSetMacro
 
ExcitationFileUtility - Class in loci.slim
Loads and saves excitation files.
ExcitationFileUtility() - Constructor for class loci.slim.ExcitationFileUtility
 
ExcitationGraph - Class in loci.slim.ui
Graph that displays the excitation or prompt.
ExcitationGraph - Interface in loci.slim2.process.interactive.ui
Interface for the graph showing the excitation curve.
ExcitationPanel - Class in loci.slim.ui
Panel that holds the excitation graph.
ExcitationPanel(Excitation, FittingCursor) - Constructor for class loci.slim.ui.ExcitationPanel
 
ExcitationPanel - Class in loci.slim2.process.interactive.ui
Panel that holds the excitation graph.
ExcitationPanel(Excitation, FittingCursor) - Constructor for class loci.slim2.process.interactive.ui.ExcitationPanel
 
ExcitationScaler - Class in loci.slim.heuristics
A class with static functions for working with the excitation.
ExcitationScaler() - Constructor for class loci.slim.heuristics.ExcitationScaler
 
ExcitationScaler - Class in loci.slim2.heuristics
A class with static functions for working with the excitation.
ExcitationScaler() - Constructor for class loci.slim2.heuristics.ExcitationScaler
 
excludePixels(boolean) - Method in class loci.slim.histogram.HistogramDataGroup
 
exclusiveValueToBin(int, double, double, double) - Static method in class loci.slim.analysis.Binning
Convert value to bin number.
exited() - Method in interface loci.slim.histogram.IHistogramPanelListener
Mouse has exited the HistogramPanel.
export(ImgPlus<DoubleType>, ICurveFitter.FitFunction) - Method in class loci.slim.analysis.batch.ExportBatchHistogram
 
export(ImgPlus<DoubleType>, ICurveFitter.FitFunction) - Method in class loci.slim.analysis.batch.ExportBatchHistogram2
 
export(String, char) - Method in class loci.slim.analysis.batch.ExportSummaryToText
Exports the summary to a file.
export(BufferedWriter, char) - Method in class loci.slim.analysis.HistogramStatistics
Exports the histogram statistics using a BufferedWriter.
export(HistogramStatistics[], BufferedWriter, char) - Static method in class loci.slim.analysis.HistogramStatistics
Exports a set of histograms.
export(HistogramStatistics[], BufferedWriter, char, String) - Static method in class loci.slim.analysis.HistogramStatistics
exports statistics only with mean values.
export(String, boolean, ImgPlus<DoubleType>, ICurveFitter.FitFunction, String, char) - Method in class loci.slim.analysis.plugins.ExportHistogramsToText
 
export(String, boolean, ImgPlus<DoubleType>, ICurveFitter.FitRegion, ICurveFitter.FitFunction, String, char) - Method in class loci.slim.analysis.plugins.ExportPixelsToText
 
export(String, boolean, ImgPlus<DoubleType>, ICurveFitter.FitFunction, String, char) - Method in class loci.slim2.analysis.batch.ExportHistogramsToText
 
export(String, boolean, ImgPlus<DoubleType>, ICurveFitter.FitRegion, ICurveFitter.FitFunction, String, char) - Method in class loci.slim2.analysis.batch.ExportPixelsToText
 
export(String, char) - Method in class loci.slim2.analysis.batch.ExportSummaryToText
Exports the summary to a file.
EXPORT_FILE - Static variable in class loci.slim.SLIMProcessor
 
ExportBatchHistogram - Class in loci.slim.analysis.batch
 
ExportBatchHistogram() - Constructor for class loci.slim.analysis.batch.ExportBatchHistogram
 
ExportBatchHistogram2 - Class in loci.slim.analysis.batch
 
ExportBatchHistogram2() - Constructor for class loci.slim.analysis.batch.ExportBatchHistogram2
 
exportFileSet(String, String, String) - Static method in class loci.slim.SLIMProcessor
 
exportHistoFileName(String, String) - Static method in class loci.slim.SLIMProcessor
 
exportHistoFileNameSingleFile - Variable in class loci.slim.paramSetMacro
 
exportHistoFileNameSingleFileSeperator - Variable in class loci.slim.paramSetMacro
 
exportHistoFileNameSingleFileSeperatorSLIM2 - Variable in class loci.slim.paramSetMacro
 
exportHistoFileNameSingleFileSLIM2 - Variable in class loci.slim.paramSetMacro
 
exportHistoFileNameSLIM2(String, String) - Static method in class loci.slim.SLIMProcessor
 
ExportHistogramsToText - Class in loci.slim.analysis.plugins
Exports histogram values as text for further analysis of SLIM Curve results.
ExportHistogramsToText() - Constructor for class loci.slim.analysis.plugins.ExportHistogramsToText
 
ExportHistogramsToText - Class in loci.slim2.analysis.batch
Exports histogram values as text for further analysis of SLIM Curve results.
ExportHistogramsToText() - Constructor for class loci.slim2.analysis.batch.ExportHistogramsToText
 
exportPixelFileName(String, String) - Static method in class loci.slim.SLIMProcessor
 
exportPixelFileNameSingleFile - Variable in class loci.slim.paramSetMacro
 
exportPixelFileNameSingleFileSeperator - Variable in class loci.slim.paramSetMacro
 
exportPixelFileNameSingleFileSeperatorSLIM2 - Variable in class loci.slim.paramSetMacro
 
exportPixelFileNameSingleFileSLIM2 - Variable in class loci.slim.paramSetMacro
 
exportPixelFileNameSLIM2(String, String) - Static method in class loci.slim.SLIMProcessor
 
ExportPixelsToText - Class in loci.slim.analysis.plugins
Exports pixel values as text for further analysis of SLIM Curve results.
ExportPixelsToText() - Constructor for class loci.slim.analysis.plugins.ExportPixelsToText
 
ExportPixelsToText - Class in loci.slim2.analysis.batch
Exports pixel values as text for further analysis of SLIM Curve results.
ExportPixelsToText() - Constructor for class loci.slim2.analysis.batch.ExportPixelsToText
 
ExportSummaryToText - Class in loci.slim.analysis.batch
Exports a summary histogram in batch mode.
ExportSummaryToText() - Constructor for class loci.slim.analysis.batch.ExportSummaryToText
 
ExportSummaryToText - Class in loci.slim2.analysis.batch
Exports a summary histogram in batch mode.
ExportSummaryToText() - Constructor for class loci.slim2.analysis.batch.ExportSummaryToText
 

F

F_CONT - Static variable in interface loci.slim.fitted.FittedValue
 
F_CONT1 - Static variable in interface loci.slim.fitted.FittedValue
 
F_CONT2 - Static variable in interface loci.slim.fitted.FittedValue
 
F_CONT3 - Static variable in interface loci.slim.fitted.FittedValue
 
F_INT - Static variable in interface loci.slim.fitted.FittedValue
 
F_INT1 - Static variable in interface loci.slim.fitted.FittedValue
 
F_INT2 - Static variable in interface loci.slim.fitted.FittedValue
 
F_INT3 - Static variable in interface loci.slim.fitted.FittedValue
 
F_LOWER - Static variable in interface loci.slim2.process.interactive.ui.UserInterfacePanel
 
F_UPPER - Static variable in interface loci.slim2.process.interactive.ui.UserInterfacePanel
 
findMinMax() - Method in class loci.slim.histogram.HistogramDataNode
Finds the actual minimum and maximum values.
findQuartiles(double[], int[], int, double, double) - Method in class loci.slim.histogram.HistogramDataNode
Finds the quartiles of the histogram distribution.
firstTime - Static variable in class loci.slim.SLIMProcessor
 
firstTimeRecordDataStart - Variable in class loci.slim.paramSetMacro
 
firstTimeRecordTransientStart - Variable in class loci.slim.paramSetMacro
 
firstTimeRecordTransientStop - Variable in class loci.slim.paramSetMacro
 
fit(IGlobalFitParams, ILocalFitParams) - Method in interface loci.slim.fitting.engine.IFittingEngine
Fit one pixel.
fit(IGlobalFitParams, List<ILocalFitParams>) - Method in interface loci.slim.fitting.engine.IFittingEngine
Fits a list of pixels.
fit(IGlobalFitParams, ILocalFitParams) - Method in class loci.slim.fitting.engine.ThreadedFittingEngine
Fits a single pixel with given parameters.
fit(IGlobalFitParams, List<ILocalFitParams>) - Method in class loci.slim.fitting.engine.ThreadedFittingEngine
Fit one or more pixels with given parameters.
fit(int, double[], double[]) - Static method in class loci.slim2.experimental.EnderleinErdmann
 
fit(GlobalFitParams, LocalFitParams) - Method in interface loci.slim2.fitting.FittingEngine
Fit one pixel.
fit(GlobalFitParams, List<LocalFitParams>) - Method in interface loci.slim2.fitting.FittingEngine
Fits a list of pixels.
fit(GlobalFitParams, LocalFitParams) - Method in class loci.slim2.fitting.ThreadedFittingEngine
 
fit(GlobalFitParams, List<LocalFitParams>) - Method in class loci.slim2.fitting.ThreadedFittingEngine
 
fit(Context, FitSettings, File) - Method in class loci.slim2.process.ImageFitter
Creates a fitted image.
fit(Context, FitSettings, File, int) - Method in class loci.slim2.process.ImageFitter
Creates a fitted image.
FIT_IMAGE_FN - Static variable in class loci.slim.SLIMProcessor
 
fitData(ICurveFitData[]) - Method in class loci.curvefitter.AbstractCurveFitter
 
fitData(ICurveFitData[]) - Method in class loci.curvefitter.AkutanCurveFitter
 
fitData(ICurveFitData[]) - Method in class loci.curvefitter.GrayCurveFitter
 
fitData(ICurveFitData[]) - Method in class loci.curvefitter.GrayNRCurveFitter
 
fitData(ICurveFitData[]) - Method in interface loci.curvefitter.ICurveFitter
Do the fit.
fitData(ICurveFitData[]) - Method in class loci.curvefitter.JaolhoCurveFitter
 
fitData(ICurveFitData[]) - Method in class loci.curvefitter.MarkwardtCurveFitter
 
fitData(ICurveFitData[]) - Method in class loci.curvefitter.SLIMCurveFitter
 
fitImages(String, String) - Static method in class loci.slim.SLIMProcessor
 
fitImages() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanelListener
Triggers a fit, creating fitted images.
FitInfo - Class in loci.slim.fitting
 
FitInfo() - Constructor for class loci.slim.fitting.FitInfo
 
fitInfo - Static variable in class loci.slim.SLIMProcessor
 
FitResults - Class in loci.slim.fitting.params
Interface for container for local fitted results for current pixel.
FitResults() - Constructor for class loci.slim.fitting.params.FitResults
 
FitResults - Interface in loci.slim2.fitting
Interface for container for local fitted results for current pixel.
FitSettings - Interface in loci.slim2.process
Holds basic FLIM fit settings.
fitSingleDecay(boolean) - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanelListener
Triggers a fitSingleDecay of pixel or summed.
FittedImageFactory - Class in loci.slim.fitting.images
Factory creates fitted images.
FittedImageFitter - Class in loci.slim.fitting.images
This class handles the fitted image fitting process.
FittedImageFitter() - Constructor for class loci.slim.fitting.images.FittedImageFitter
 
FittedImageFitter.FittedImageType - Enum in loci.slim.fitting.images
 
FittedImageParser - Class in loci.slim.fitting.images
This class parses a string containing a list of output images, such as "A T Z X2" and produces an array of ColorizedImageType.
FittedImageParser(String, int, boolean, boolean[]) - Constructor for class loci.slim.fitting.images.FittedImageParser
Creates an instance for a given input string, etc.
FittedValue - Interface in loci.slim.fitted
Interface for dealing with fitted values.
FittedValueFactory - Class in loci.slim.fitted
Creates FittedValues.
FittedValueFactory() - Constructor for class loci.slim.fitted.FittedValueFactory
 
FitterEstimator - Class in loci.slim.heuristics
Assorted rules of thumb for fitting.
FitterEstimator() - Constructor for class loci.slim.heuristics.FitterEstimator
 
FittingCallable - Interface in loci.slim2.fitting
 
FittingContext - Class in loci.slim2
Keeps track of various entities during the fit process.
FittingContext() - Constructor for class loci.slim2.FittingContext
 
FittingCursor - Class in loci.slim.fitting.cursor
Keeps cursor information.
FittingCursor(double, int, IFitterEstimator) - Constructor for class loci.slim.fitting.cursor.FittingCursor
Constructor
FittingCursor - Class in loci.slim2.process.interactive.cursor
Keeps cursor information.
FittingCursor(double, int, IFitterEstimator) - Constructor for class loci.slim2.process.interactive.cursor.FittingCursor
Constructor
FittingCursorHelper - Class in loci.slim.fitting.cursor
This is a helper class for the user interface for setting and displaying the fitting cursor start and stop values.
FittingCursorHelper() - Constructor for class loci.slim.fitting.cursor.FittingCursorHelper
 
FittingCursorListener - Interface in loci.slim2.process.interactive.cursor
Listener interface for fitting cursor changes.
fittingDone - Variable in class loci.slim.paramSetMacro
 
FittingEngine - Interface in loci.slim2.fitting
Interface for a fitting engine.
FittingEngineCallable - Class in loci.slim.fitting.callable
This class brings together everything needed to fit one pixel.
FittingEngineCallable() - Constructor for class loci.slim.fitting.callable.FittingEngineCallable
 
fixA1(String) - Static method in class loci.slim.SLIMProcessor
 
fixA2(String) - Static method in class loci.slim.SLIMProcessor
 
fixA3(String) - Static method in class loci.slim.SLIMProcessor
 
fixH(String) - Static method in class loci.slim.SLIMProcessor
 
fixIndexColorModel(IndexColorModel, Color, Color) - Static method in class loci.slim.histogram.PaletteFix
Given a 256-color palette, turns it into a 254-color palette, using the first and last palette entries for the below and above colors.
fixT1(String) - Static method in class loci.slim.SLIMProcessor
 
fixT2(String) - Static method in class loci.slim.SLIMProcessor
 
fixT3(String) - Static method in class loci.slim.SLIMProcessor
 
fixZ(String) - Static method in class loci.slim.SLIMProcessor
 
FloatFittedImage - Class in loci.slim.fitting.images
 
FloatFittedImage() - Constructor for class loci.slim.fitting.images.FloatFittedImage
 
FractionalContribBatchHistogram - Class in loci.slim.analysis.batch
A batch histogram that represents fractional contribution f values.
FractionalContribBatchHistogram() - Constructor for class loci.slim.analysis.batch.FractionalContribBatchHistogram
 
FractionalContributionFittedValue - Class in loci.slim.fitted
Extracts Fractional Intensity fitted value.
FractionalContributionFittedValue() - Constructor for class loci.slim.fitted.FractionalContributionFittedValue
 
FractionalContributionImage - Class in loci.slim.fitting.images
This class builds a fitted image that shows the fractional contribution.
FractionalContributionImage(String, int[], IndexColorModel, int, int, boolean, IGrayScaleImage, IMaskGroup[]) - Constructor for class loci.slim.fitting.images.FractionalContributionImage
Create the fitted image.
FractionalIntensityBatchHistogram - Class in loci.slim.analysis.batch
A batch histogram that represents fractional intensity F values.
FractionalIntensityBatchHistogram() - Constructor for class loci.slim.analysis.batch.FractionalIntensityBatchHistogram
 
FractionalIntensityFittedValue - Class in loci.slim.fitted
Extracts Fractional Intensity fitted value.
FractionalIntensityFittedValue() - Constructor for class loci.slim.fitted.FractionalIntensityFittedValue
 
FractionalIntensityImage - Class in loci.slim.fitting.images
This class builds a fitted image that shows the fractional intensity.
FractionalIntensityImage(String, int[], IndexColorModel, int, int, boolean, IGrayScaleImage, IMaskGroup[]) - Constructor for class loci.slim.fitting.images.FractionalIntensityImage
Create the fitted image.

G

gaussianExcitation(String) - Method in interface loci.slim.ui.IUserInterfacePanelListener
Creates excitation curve from gaussian.
gaussianExcitation(String) - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanelListener
Creates excitation curve from gaussian.
geta1() - Method in class loci.slim.paramSetMacro
 
geta2() - Method in class loci.slim.paramSetMacro
 
geta3() - Method in class loci.slim.paramSetMacro
 
getAdjustedDataStartIndex() - Method in class loci.curvefitter.CurveFitData
 
getAdjustedDataStartIndex() - Method in interface loci.curvefitter.ICurveFitData
Gets fitting start index adjusted for transient start.
getAdjustedTransEndIndex() - Method in class loci.curvefitter.CurveFitData
 
getAdjustedTransEndIndex() - Method in interface loci.curvefitter.ICurveFitData
Gets end index in transient adjusted for transient start.
getAdjustedTransient() - Method in class loci.curvefitter.CurveFitData
 
getAdjustedTransient() - Method in interface loci.curvefitter.ICurveFitData
Get input data for the fit, starting with data start index.
getAlgorithm() - Method in class loci.slim.fitting.FitInfo
Gets implementation & algorithm for the fit.
getAlgorithm() - Method in class loci.slim.paramSetMacro
 
getAlgorithm() - Method in interface loci.slim.ui.IUserInterfacePanel
Gets implementation & algorithm for the fit.
getAlgorithm() - Method in class loci.slim.ui.UserInterfacePanel
 
getAlgorithm() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
getAlgorithm() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Gets implementation & algorithm for the fit.
getAnalysisList() - Method in class loci.slim.fitting.FitInfo
Gets analysis plugin names.
getAnalysisList() - Method in interface loci.slim.ui.IUserInterfacePanel
Gets analysis plugin names.
getAnalysisList() - Method in class loci.slim.ui.UserInterfacePanel
 
getAnalysisList() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
getAnalysisList() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Gets analysis plugin names.
getAutoRange() - Method in class loci.slim.histogram.HistogramDataGroup
Gets whether or not histogram should automatically scale to values.
getAxes() - Method in class loci.slim2.decay.LifetimeDatasetWrapper
Returns external axis types (i.e.
getBandwidth() - Method in class loci.slim.histogram.HistogramPanel
 
getBase() - Method in class loci.slim.Excitation
Gets the base cursor.
getBin() - Method in class loci.slim2.process.HorzCursor
Get bin number.
getBinnedDecay(int, long[]) - Method in class loci.slim2.decay.LifetimeDatasetWrapper
Gets decay histogram at given location.
getBinning() - Method in class loci.slim.fitting.FitInfo
Gets binning plugin name.
getBinning() - Method in interface loci.slim.ui.IUserInterfacePanel
Gets binning plugin name.
getBinning() - Method in class loci.slim.ui.UserInterfacePanel
 
getBinning() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
getBinning() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Gets binning index.
getBinningFactor() - Method in interface loci.slim2.process.FitSettings
Gets binning factor.
getBinningFactor() - Method in class loci.slim2.process.interactive.BaseFitSettings
 
getBins() - Method in class loci.slim.DecayImageWrapper
Gets number of bins in decay curve of image.
getBins() - Method in interface loci.slim.fitting.IDecayImage
Gets number of parameters of image.
getBins() - Method in class loci.slim.histogram.HistogramStatistics
Gets the histogram bins
getBins() - Method in class loci.slim2.decay.LifetimeDatasetWrapper
Returns number of lifetime bins.
getBins() - Method in interface loci.slim2.process.FitSettings
Get number of bins in time histogram.
getBins() - Method in class loci.slim2.process.ImageFitter
Gets the bin count of the last execution.
getBins() - Method in class loci.slim2.process.interactive.BaseFitSettings
 
getBinValues() - Method in class loci.slim.histogram.HistogramStatistics
Gets values characterizing bins
getBits() - Method in class loci.slim.mask.Mask
Gets the boolean switches.
getBrightestPixel() - Method in class loci.slim2.decay.LifetimeGrayscaleDataset
Reports the full position of the brightest pixel in the first XY plane.
getBrightestPoint() - Method in class loci.slim.GrayScaleImage
 
getBrightestPoint() - Method in interface loci.slim.IGrayScaleImage
Gets the coordinates of the brightest point in the image.
getCancel() - Method in class loci.slim.fitting.FitInfo
Gets whether to cancel current fit.
getChannel() - Method in class loci.curvefitter.CurveFitData
 
getChannel() - Method in interface loci.curvefitter.ICurveFitData
Gets channel of the fitted pixel.
getChannel() - Method in class loci.slim.fitting.FitInfo
Gets current channel
getChannel() - Method in class loci.slim.GrayScaleImage
Gets the channel slider selection.
getChannel() - Method in interface loci.slim.IGrayScaleImage
Gets the channel slider selection.
getChannelIndex() - Method in class loci.slim.histogram.HistogramDataGroup
Gets current channel index.
getChannels() - Method in class loci.slim.DecayImageWrapper
Gets number of channels of image.
getChannels() - Method in interface loci.slim.fitting.IDecayImage
Gets number of channels of image.
getChannels() - Method in interface loci.slim.fitting.IFittedImage
Gets number of channels of image.
getChannels() - Method in class loci.slim.OutputImageWrapper
Gets number of channels of image.
getChartRectangleListener() - Method in class imagej.charts.cursors.CursorLayer
 
getChiSqTarget() - Method in class loci.slim2.process.interactive.DefaultFitSettings
Gets the target reduced chi square.
getChiSquare() - Method in class loci.curvefitter.CurveFitData
 
getChiSquare() - Method in interface loci.curvefitter.ICurveFitData
Gets fitted chi square.
getChiSquare() - Method in class loci.slim.fitting.params.FitResults
 
getChiSquare() - Method in interface loci.slim.fitting.params.IFitResults
Gets fitted chi square result.
getChiSquare() - Method in class loci.slim2.fitting.DefaultFitResults
 
getChiSquare() - Method in interface loci.slim2.fitting.FitResults
Gets fitted chi square result.
getChiSquareDelta() - Method in class loci.curvefitter.CurveFitData
 
getChiSquareDelta() - Method in interface loci.curvefitter.ICurveFitData
Sets chi square delta.
getChiSquareTarget() - Method in class loci.curvefitter.CurveFitData
 
getChiSquareTarget() - Method in interface loci.curvefitter.ICurveFitData
Gets chi square target.
getChiSquareTarget() - Method in class loci.slim.fitting.FitInfo
Gets chi square target for fit.
getChiSquareTarget() - Method in class loci.slim.fitting.params.GlobalFitParams
 
getChiSquareTarget() - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
getChiSquareTarget() - Method in class loci.slim.heuristics.Estimator
 
getChiSquareTarget() - Method in interface loci.slim.heuristics.IEstimator
Get a default chi square target.
getChiSquareTarget() - Method in class loci.slim.paramSetMacro
 
getChiSquareTarget() - Method in interface loci.slim.ui.IUserInterfacePanel
Gets chi square target for fit.
getChiSquareTarget() - Method in class loci.slim.ui.UserInterfacePanel
 
getChiSquareTarget() - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
getChiSquareTarget() - Method in interface loci.slim2.fitting.GlobalFitParams
 
getChiSquareTarget() - Method in class loci.slim2.heuristics.DefaultEstimator
 
getChiSquareTarget() - Method in interface loci.slim2.heuristics.Estimator
Get a default chi square target.
getChiSquareTarget() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
getChiSquareTarget() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Gets chi square target for fit.
getChoices() - Method in class loci.slim.analysis.SLIMAnalysis
Returns list of potential analysis plugin names.
getChoices() - Method in class loci.slim.preprocess.SLIMBinning
 
getChunkyPixel(int) - Method in class loci.slim.ChunkyPixelTableImpl
 
getChunkyPixel(int) - Method in interface loci.slim.IChunkyPixelTable
Get table entry at index.
getColorizeGrayScale() - Method in class loci.slim.fitting.FitInfo
Returns whether to create colorized grayscale images.
getColorizeGrayScale() - Method in interface loci.slim.ui.IUserInterfacePanel
Returns whether to create colorized grayscale fitted images.
getColorizeGrayScale() - Method in class loci.slim.ui.UserInterfacePanel
Returns whether to create colorized grayscale fitted images.
getColorizeGrayScale() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
Returns whether to create colorized grayscale fitted images.
getColorizeGrayScale() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Returns whether to create colorized grayscale fitted images.
getCombineChannels() - Method in class loci.slim.histogram.HistogramDataGroup
Gets whether or not histogram should combine all the channels.
getCombinedPlaneDecay(int, int, long[]) - Method in class loci.slim2.decay.LifetimeDatasetWrapper
Gets decay histogram summed for the whole plane.
getComponent() - Method in class loci.slim.ui.ExcitationGraph
Gets the chart JPanel
getComponent() - Method in class loci.slim2.process.interactive.ui.DefaultExcitationGraph
 
getComponent() - Method in interface loci.slim2.process.interactive.ui.ExcitationGraph
Gets the chart JPanel
getComponents() - Method in class loci.slim.fitting.FitInfo
Gets number of exponential components.
getCount() - Method in class loci.slim.analysis.HistogramStatistics
 
getCount() - Method in class loci.slim.mask.Mask
 
getCursorEstimator() - Method in class loci.slim.fitting.config.Configuration
 
getCurveFitter() - Method in class loci.slim.fitting.config.Configuration
 
getDataset() - Method in class loci.slim2.decay.LifetimeDatasetWrapper
Return wrapped Dataset.
getDataset() - Method in class loci.slim2.decay.LifetimeGrayscaleDataset
Gets the associated dataset.
getDataset() - Method in class loci.slim2.histogram.HistogramGraph
Gets the histogram graph dataset.
getDatasets() - Method in class loci.slim2.outputset.OutputSet
Gets list of datasets.
getDatasetWrapper() - Method in class loci.slim2.FittingContext
 
getDataStart() - Method in class loci.slim.fitting.cursor.FittingCursor
Gets the start of the data as a string.
getDataStart() - Method in class loci.slim.fitting.cursor.FittingCursorHelper
Gets the data start cursor.
getDataStart() - Method in interface loci.slim.fitting.cursor.IFittingCursorUI
Gets the data start cursor.
getDataStart() - Method in class loci.slim.fitting.FitInfo
Gets starting data bin of transient.
getDataStart() - Method in class loci.slim.fitting.params.GlobalFitParams
 
getDataStart() - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
getDataStart() - Method in class loci.slim.ui.UserInterfacePanel
Gets the data start cursor.
getDataStart() - Method in class loci.slim2.fitting.DefaultFitResults
 
getDataStart() - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
getDataStart() - Method in interface loci.slim2.fitting.FitResults
Gets start of data.
getDataStart() - Method in interface loci.slim2.fitting.GlobalFitParams
 
getDataStartBin() - Method in class loci.slim.fitting.cursor.FittingCursor
Gets the start of the data as a bin number.
getDataStartFromMacro() - Method in class loci.slim.paramSetMacro
 
getDataStartIndex() - Method in class loci.curvefitter.CurveFitData
 
getDataStartIndex() - Method in interface loci.curvefitter.ICurveFitData
Gets fitting start index in transient.
getDataStartIndex() - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Gets start of data as an index.
getDataStartTime() - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Gets start of data as a time.
getDataStartValue() - Method in class loci.slim.fitting.cursor.FittingCursor
Gets the start of the data as a time value.
getDecay(long, long, long[]) - Method in class loci.slim2.decay.LifetimeDatasetWrapper
Gets decay histogram at given location.
getDecay(long[]) - Method in class loci.slim2.decay.LifetimeDatasetWrapper
Gets decay histogram at given location.
getDecayHorzCursors() - Method in interface loci.slim2.process.FitSettings
Gets horizontal cursor positions on decay.
getDecayHorzCursors() - Method in class loci.slim2.process.interactive.BaseFitSettings
 
getDecayVertCursor() - Method in interface loci.slim2.process.FitSettings
Gets vertical cursor position on decay.
getDecayVertCursor() - Method in class loci.slim2.process.interactive.BaseFitSettings
 
getDefaultA() - Method in class loci.curvefitter.DummyFitterEstimator
 
getDefaultA() - Method in interface loci.curvefitter.IFitterEstimator
Gets default A for RLD fits.
getDefaultA() - Method in class loci.slim.heuristics.FitterEstimator
 
getDefaultA() - Method in class loci.slim2.heuristics.DefaultFitterEstimator
 
getDefaultT() - Method in class loci.curvefitter.DummyFitterEstimator
 
getDefaultT() - Method in interface loci.curvefitter.IFitterEstimator
Gets default T for RLD fits.
getDefaultT() - Method in class loci.slim.heuristics.FitterEstimator
 
getDefaultT() - Method in class loci.slim2.heuristics.DefaultFitterEstimator
 
getDefaultZ() - Method in class loci.curvefitter.DummyFitterEstimator
 
getDefaultZ() - Method in interface loci.curvefitter.IFitterEstimator
Gets default Z for RLD fits.
getDefaultZ() - Method in class loci.slim.heuristics.FitterEstimator
 
getDefaultZ() - Method in class loci.slim2.heuristics.DefaultFitterEstimator
 
getDimension() - Method in interface loci.slim.fitting.IFittedImage
Gets dimensions.
getDimension() - Method in class loci.slim.OutputImageWrapper
 
getDims() - Method in class loci.slim2.decay.LifetimeDatasetWrapper
Returns external dimensions (i.e.
getDimSize(ImgPlus<?>, AxisType) - Static method in class loci.slim.ImageUtils
 
getDisplayChannels() - Method in class loci.slim.histogram.HistogramDataGroup
Gets whether or not histogram should display all channels.
getErrorCode() - Method in class loci.slim2.fitting.DefaultFitResults
 
getErrorCode() - Method in interface loci.slim2.fitting.FitResults
Gets error code.
getErrorCode() - Method in class loci.slim2.process.ImageFitter
Gets the error code of the last execution.
getEstimateAValue(double, double[], int, int) - Method in class loci.curvefitter.DummyFitterEstimator
 
getEstimateAValue(double, double[], int, int) - Method in interface loci.curvefitter.IFitterEstimator
TRI2 adjusts the starting A estimate for the initial RLD estimate fit.
getEstimateAValue(double, double[], int, int) - Method in class loci.slim.heuristics.FitterEstimator
 
getEstimateAValue(double, double[], int, int) - Method in class loci.slim2.heuristics.DefaultFitterEstimator
 
getEstimateNoiseModel(ICurveFitter.NoiseModel) - Method in class loci.curvefitter.DummyFitterEstimator
 
getEstimateNoiseModel(ICurveFitter.NoiseModel) - Method in interface loci.curvefitter.IFitterEstimator
TRI2 uses hardcoded noise model.
getEstimateNoiseModel(ICurveFitter.NoiseModel) - Method in class loci.slim.heuristics.FitterEstimator
 
getEstimateNoiseModel(ICurveFitter.NoiseModel) - Method in class loci.slim2.heuristics.DefaultFitterEstimator
 
getEstimateStartIndex(double[], int, int) - Method in class loci.curvefitter.DummyFitterEstimator
 
getEstimateStartIndex(double[], int, int) - Method in interface loci.curvefitter.IFitterEstimator
TRI2 adjusts the start index for the initial RLD estimate.
getEstimateStartIndex(double[], int, int) - Method in class loci.slim.heuristics.FitterEstimator
 
getEstimateStartIndex(double[], int, int) - Method in class loci.slim2.heuristics.DefaultFitterEstimator
 
getEstimator() - Method in class loci.curvefitter.AbstractCurveFitter
 
getEstimator() - Method in interface loci.curvefitter.ICurveFitter
Get fitting estimator.
getEstimator() - Method in class loci.slim.fitting.params.GlobalFitParams
 
getEstimator() - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
getEstimator() - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
getEstimator() - Method in interface loci.slim2.fitting.GlobalFitParams
 
getExcitation() - Method in interface loci.slim2.process.FitSettings
Get excitation decay values.
getExcitation() - Method in class loci.slim2.process.interactive.BaseFitSettings
 
getExcitationHorzCursors() - Method in interface loci.slim2.process.FitSettings
Gets horizontal cursor positions on excitation decay.
getExcitationHorzCursors() - Method in class loci.slim2.process.interactive.BaseFitSettings
 
getExcitationVertCursor() - Method in interface loci.slim2.process.FitSettings
Gets vertical cursor position on excitation decay.
getExcitationVertCursor() - Method in class loci.slim2.process.interactive.BaseFitSettings
 
getExcludePixels() - Method in class loci.slim.histogram.HistogramDataGroup
Sets whether or not we should hide out-of-range pixels.
getExcludePixels() - Method in class loci.slim.histogram.HistogramUIPanel
Gets whether to hide out of range pixels.
getFences() - Method in class loci.slim.histogram.HistogramStatistics
Gets the 'fences' that demarcate outliers.
getFileName() - Method in class loci.slim.Excitation
Gets the file name.
getFirstQuartile() - Method in class loci.slim.analysis.HistogramStatistics
 
getFitAlgorithm() - Method in class loci.curvefitter.AbstractCurveFitter
 
getFitAlgorithm() - Method in interface loci.curvefitter.ICurveFitter
Get fitting algorithm.
getFitAlgorithm() - Method in class loci.slim.fitting.params.GlobalFitParams
 
getFitAlgorithm() - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
getFitAlgorithm() - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
getFitAlgorithm() - Method in interface loci.slim2.fitting.GlobalFitParams
 
getFitAllChannels() - Method in class loci.slim.fitting.FitInfo
Gets whether or not to fit all channels.
getFitAllChannels() - Method in interface loci.slim.ui.IUserInterfacePanel
Gets whether or not to fit all channels.
getFitAllChannels() - Method in class loci.slim.ui.UserInterfacePanel
 
getFitAllChannels() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
getFitAllChannels() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Gets whether or not to fit all channels.
getFitFunction() - Method in class loci.curvefitter.AbstractCurveFitter
 
getFitFunction() - Method in interface loci.curvefitter.ICurveFitter
Get function we are fitting.
getFitFunction() - Method in class loci.slim.fitting.params.GlobalFitParams
 
getFitFunction() - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
getFitFunction() - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
getFitFunction() - Method in interface loci.slim2.fitting.GlobalFitParams
 
getFitSettings() - Method in class loci.slim2.process.interactive.DefaultInteractiveProcessor
 
getFitSettings() - Method in interface loci.slim2.process.InteractiveProcessor
Gets current fit settings.
getFittedImages() - Method in class loci.slim.fitting.FitInfo
Returns list of fitted images to display.
getFittedImages() - Method in class loci.slim.fitting.images.FittedImageParser
Parses the input string and creates array of FittedImageType.
getFittedImages() - Method in interface loci.slim.ui.IUserInterfacePanel
Returns list of fitted images to display.
getFittedImages() - Method in class loci.slim.ui.UserInterfacePanel
Returns list of fitted images to display.
getFittedImages() - Method in interface loci.slim2.process.FitSettings
 
getFittedImages() - Method in class loci.slim2.process.interactive.BaseFitSettings
 
getFittedImages() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
Returns list of fitted images to display.
getFittedImages() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Returns list of fitted images to display.
getFittingEngine() - Method in class loci.slim.fitting.config.Configuration
 
getFittingEngine(ICurveFitter.FitAlgorithm, ICurveFitter.FitFunction, ICurveFitter.NoiseModel, double, boolean[]) - Method in class loci.slim2.process.ImageFitter
Helper routine to get and set up fitting engine.
getFitTitle() - Method in class loci.slim.fitting.FitInfo
 
getFocus() - Method in class loci.slim.fitting.ErrorManager
Updates the entire set of error masks when a new set of fitted images gets focus.
getFormula() - Method in class loci.slim2.outputset.OutputSetMember
 
getFrame() - Method in interface loci.slim.ui.IUserInterfacePanel
Gets the UI JFrame.
getFrame() - Method in class loci.slim.ui.UserInterfacePanel
 
getFrame() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
getFrame() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Gets the UI JFrame.
getFree() - Method in class loci.curvefitter.AbstractCurveFitter
 
getFree() - Method in interface loci.curvefitter.ICurveFitter
Gets which parameters are free (vs.
getFree() - Method in class loci.slim.fitting.FitInfo
Gets which parameters aren't fixed.
getFree() - Method in class loci.slim.fitting.params.GlobalFitParams
 
getFree() - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
getFree() - Method in interface loci.slim.ui.IUserInterfacePanel
Gets which parameters aren't fixed.
getFree() - Method in class loci.slim.ui.UserInterfacePanel
 
getFree() - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
getFree() - Method in interface loci.slim2.fitting.GlobalFitParams
 
getFree() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
getFree() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Gets which parameters aren't fixed.
getFunction() - Method in class loci.slim.fitting.FitInfo
Gets function to be fitted.
getFunction() - Method in class loci.slim.paramSetMacro
 
getFunction() - Method in interface loci.slim.ui.IUserInterfacePanel
Gets function to be fitted.
getFunction() - Method in class loci.slim.ui.UserInterfacePanel
 
getFunction() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
getFunction() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Gets function to be fitted.
getGlobalFitParams() - Method in interface loci.slim2.process.FitSettings
 
getGlobalFitParams() - Method in class loci.slim2.process.interactive.BaseFitSettings
 
getGrayscaleDataset() - Method in class loci.slim2.FittingContext
 
getGrayscaleDisplay() - Method in class loci.slim2.FittingContext
 
getGrayValue(int, int, int) - Method in class loci.slim.GrayScaleImage
Gets a grayscale pixel value, to test against a threshold.
getGrayValue(int, int, int) - Method in interface loci.slim.IGrayScalePixelValue
Gets a grayscale pixel value.
geth1() - Method in class loci.slim.paramSetMacro
 
getHasPrompt() - Method in class loci.slim.fitting.cursor.FittingCursor
Sets whether or not a prompt has been loaded.
getHeight() - Method in class loci.slim.ChunkyPixel
Gets the height to draw the pixel.
getHeight() - Method in class loci.slim.ChunkyPixelTableImpl
 
getHeight() - Method in class loci.slim.DecayImageWrapper
Gets height of image.
getHeight() - Method in interface loci.slim.fitting.IDecayImage
Gets height of image.
getHeight() - Method in interface loci.slim.fitting.IFittedImage
Gets height of image.
getHeight() - Method in interface loci.slim.IChunkyPixelTable
Get pixel height.
getHeight(ImgPlus<?>) - Static method in class loci.slim.ImageUtils
 
getHeight() - Method in class loci.slim.OutputImageWrapper
Gets height of image.
getHeight() - Method in class loci.slim2.outputset.temp.ChunkyPixel
Gets height of pixel.
getHistogram() - Method in class loci.slim.analysis.HistogramStatistics
 
getHistogram() - Method in class loci.slim2.histogram.HistogramGraph
 
getHistogramCount() - Method in class loci.slim.analysis.HistogramStatistics
 
getHistogramData() - Method in class loci.slim.fitting.images.AbstractBaseFittedImage
Gets the associated histogram data object.
getHistogramData() - Method in interface loci.slim.fitting.images.IFittedImage
Gets the associated histogram data object.
getImage() - Method in class loci.slim.DecayImageWrapper
Gets underlying image.
getImage() - Method in interface loci.slim.fitting.IDecayImage
Gets associated image.
getImage() - Method in interface loci.slim.fitting.IFittedImage
Gets associated image.
getImage() - Method in class loci.slim.OutputImageWrapper
Gets associated image.
getImageProcessor() - Method in class loci.slim.fitting.images.ColorizedFittedImage
 
getImageProcessor() - Method in class loci.slim.fitting.images.FloatFittedImage
 
getImageProcessor() - Method in interface loci.slim.fitting.images.IFittedImageSlice
Gets the underlying IJ image processor.
getIndex() - Method in class loci.slim2.outputset.OutputSetMember
 
getIndexColorModel() - Method in class loci.slim.fitting.FitInfo
Returns color model for fitted images.
getIndexColorModel() - Static method in class loci.slim.histogram.HistogramTool
Gets an IndexColorModel by loading a hardcoded LUT file.
getInputLocation() - Method in class loci.slim.ChunkyPixel
Gets the location of the pixel in the input image.
getInstance() - Static method in class loci.slim.fitting.config.Configuration
 
getInstance() - Static method in class loci.slim.fitting.images.FittedImageFactory
 
getInstance() - Static method in class loci.slim.histogram.HistogramTool
Class is a singleton for convenience.
getInstance() - Static method in class loci.slim.ui.DecayGraph
Gets the singleton instance.
getInstrumentResponse(int) - Method in class loci.curvefitter.AbstractCurveFitter
 
getInstrumentResponse(int) - Method in interface loci.curvefitter.ICurveFitter
Get instrument response data.
getInterface(String) - Method in class loci.slim.fitting.config.ConfigurationHelper
 
getLabel() - Method in class loci.slim2.outputset.OutputSetMember
 
getLogarithmicDisplay() - Method in class loci.slim.histogram.HistogramPanel
 
getLUT() - Static method in class loci.slim.histogram.HistogramTool
Gets a LUT.
getMask() - Method in interface loci.slim.mask.IMaskGroup
Gets the current total mask for this group.
getMask() - Method in class loci.slim.mask.MaskGroup
 
getMax() - Method in class loci.slim.analysis.HistogramStatistics
 
getMaximum() - Method in class loci.slim2.histogram.DataHistogramCommand
 
getMaxRange() - Method in class loci.slim.analysis.HistogramStatistics
 
getMaxTotalPhotons() - Method in class loci.slim.GrayScaleImage
 
getMaxTotalPhotons() - Method in interface loci.slim.IGrayScaleImage
Gets the photon count of the brightest point in the image.
getMean() - Method in class loci.slim.analysis.HistogramStatistics
 
getMedian() - Method in class loci.slim.analysis.HistogramStatistics
 
getMin() - Method in class loci.slim.analysis.HistogramStatistics
 
getMinimum() - Method in class loci.slim2.histogram.DataHistogramCommand
 
getMinMaxData() - Method in class loci.slim.histogram.HistogramDataGroup
Gets minimum and maximum extents of the data.
getMinMaxLUT() - Method in class loci.slim.histogram.HistogramDataGroup
Gets minimum and maximum extents of the LUT.
getMinMaxView() - Method in class loci.slim.histogram.HistogramDataGroup
Gets minimum and maximum extents of the view.
getMinNonZeroPhotonCount() - Method in class loci.slim.GrayScaleImage
 
getMinNonZeroPhotonCount() - Method in interface loci.slim.IGrayScaleImage
Gets the minimum, non-zero photon count encountered in the image.
getMinRange() - Method in class loci.slim.analysis.HistogramStatistics
 
getNChannels(ImgPlus<?>) - Static method in class loci.slim.ImageUtils
 
getNFrames(ImgPlus<?>) - Static method in class loci.slim.ImageUtils
 
getNoiseModel() - Method in class loci.curvefitter.AbstractCurveFitter
 
getNoiseModel() - Method in interface loci.curvefitter.ICurveFitter
Get noise model for fit.
getNoiseModel() - Method in class loci.slim.fitting.FitInfo
Gets noise model for fit.
getNoiseModel() - Method in class loci.slim.fitting.params.GlobalFitParams
 
getNoiseModel() - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
getNoiseModel() - Method in interface loci.slim.ui.IUserInterfacePanel
Gets noise model for fit.
getNoiseModel() - Method in class loci.slim.ui.UserInterfacePanel
Get noise model for fit.
getNoiseModel() - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
getNoiseModel() - Method in interface loci.slim2.fitting.GlobalFitParams
 
getNoiseModel() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
Get noise model for fit.
getNoiseModel() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Gets noise model for fit.
getNSlices(ImgPlus<?>) - Static method in class loci.slim.ImageUtils
 
getNumberComponents() - Method in class loci.curvefitter.AbstractCurveFitter
 
getNumberComponents() - Method in interface loci.curvefitter.ICurveFitter
Get number of function components.
getOtherMask() - Method in interface loci.slim.mask.IMaskNode
Gets the current mask created by all other nodes.
getOtherMask() - Method in class loci.slim.mask.MaskNode
Gets the current mask created by all other nodes.
getOutputLocation() - Method in class loci.slim.ChunkyPixel
Gets the location of the pixel in the output image.
getParameterCount() - Method in class loci.slim.fitting.FitInfo
Gets number of fit parameters
getParameterCount() - Method in interface loci.slim.ui.IUserInterfacePanel
Gets number of fit parameters
getParameterCount() - Method in class loci.slim.ui.UserInterfacePanel
 
getParameterCount(ICurveFitter.FitFunction) - Method in class loci.slim2.process.ImageFitter
 
getParameterCount() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
getParameterCount() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Gets number of fit parameters
getParameters() - Method in class loci.slim.fitting.FitInfo
Gets the parameters of the fit
getParameters() - Method in interface loci.slim.fitting.IFittedImage
Gets number of parameters of image.
getParameters(int, boolean) - Method in class loci.slim.heuristics.Estimator
 
getParameters(int, boolean) - Method in interface loci.slim.heuristics.IEstimator
Gets default parameters for given number of components or stretched exponential.
getParameters() - Method in class loci.slim.OutputImageWrapper
Gets number of parameters of image.
getParameters() - Method in interface loci.slim.ui.IUserInterfacePanel
Gets the parameters of the fit
getParameters() - Method in class loci.slim.ui.UserInterfacePanel
 
getParameters(int, boolean) - Method in class loci.slim2.heuristics.DefaultEstimator
 
getParameters(int, boolean) - Method in interface loci.slim2.heuristics.Estimator
Gets default parameters for given number of components or stretched exponential.
getParameters() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
getParameters() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Gets the parameters of the fit
getParams() - Method in class loci.curvefitter.CurveFitData
 
getParams() - Method in interface loci.curvefitter.ICurveFitData
Gets parameters of the fit.
getParams() - Method in class loci.slim.fitting.params.FitResults
 
getParams() - Method in interface loci.slim.fitting.params.IFitResults
Gets fitted parameters.
getParams() - Method in interface loci.slim.fitting.params.ILocalFitParams
 
getParams() - Method in class loci.slim.fitting.params.LocalFitParams
 
getParams() - Method in class loci.slim2.fitting.DefaultFitResults
 
getParams() - Method in class loci.slim2.fitting.DefaultLocalFitParams
 
getParams() - Method in interface loci.slim2.fitting.FitResults
Gets fitted parameters.
getParams() - Method in interface loci.slim2.fitting.LocalFitParams
 
getPartialDerivate(double, double[], int) - Method in class loci.curvefitter.JaolhoCurveFitter.ExpFunction
 
getPhotonCount() - Method in class loci.slim2.fitting.DefaultFitResults
 
getPhotonCount() - Method in interface loci.slim2.fitting.FitResults
Gets total photon count in decay.
getPhotonCountFactor() - Method in class loci.slim2.decay.LifetimeDatasetWrapper
Gets photon count factor.
getPhotons() - Method in class loci.slim2.process.VertCursor
Gets vertical cursor position.
getPixel(int[]) - Method in class loci.slim.DecayImageWrapper
Gets input pixel decay curve.
getPixel(int[]) - Method in interface loci.slim.fitting.IDecayImage
Gets input pixel value.
getPixel(int[]) - Method in interface loci.slim.fitting.IFittedImage
Gets pixel values at location.
getPixel(int[]) - Method in class loci.slim.OutputImageWrapper
 
getPixel(int[]) - Method in interface loci.slim.preprocess.IProcessor
Gets input pixel value.
getPixel(int[]) - Method in class loci.slim.preprocess.RoiProcessor
 
getPixel(int[]) - Method in class loci.slim.preprocess.SquareBinner
Gets input pixel value.
getPixel(int[]) - Method in class loci.slim.preprocess.Threshold
Gets input pixel value.
getPixels() - Method in class loci.curvefitter.CurveFitData
 
getPixels() - Method in interface loci.curvefitter.ICurveFitData
Gets how many pixels went into this data point.
getPosition() - Method in class loci.slim2.outputset.temp.ChunkyPixel
Gets position of upper left pixel.
getPreferredSize() - Method in class loci.slim.analysis.batch.ui.HistogramPanel
 
getPrompt() - Method in class loci.slim.fitting.cursor.FittingCursorHelper
Gets whether there is a prompt.
getPrompt() - Method in class loci.slim.fitting.FitInfo
Gets prompt or instrument response function.
getPrompt() - Method in class loci.slim.fitting.params.GlobalFitParams
 
getPrompt() - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
getPrompt() - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
getPrompt() - Method in interface loci.slim2.fitting.GlobalFitParams
 
getPromptBaseline() - Method in class loci.slim.fitting.cursor.FittingCursor
Gets the baseline of the prompt based on a string.
getPromptBaseline() - Method in class loci.slim.fitting.cursor.FittingCursorHelper
Gets the prompt baseline cursor as a string.
getPromptBaseline() - Method in interface loci.slim.fitting.cursor.IFittingCursorUI
Gets the prompt baseline cursor.
getPromptBaseLine() - Method in class loci.slim.paramSetMacro
 
getPromptBaseline() - Method in class loci.slim.ui.UserInterfacePanel
Gets the excitation baseline.
getPromptBaselineValue() - Method in class loci.slim.fitting.cursor.FittingCursor
Gets the baseline of the prompt as a value.
getPromptBaselineValue() - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Gets the baseline of the prompt.
getPromptDelay() - Method in class loci.slim.fitting.cursor.FittingCursor
Gets the start of the prompt as a string showing prompt delay.
getPromptDelay() - Method in class loci.slim.fitting.cursor.FittingCursorHelper
Gets the prompt delay cursor.
getPromptDelay() - Method in interface loci.slim.fitting.cursor.IFittingCursorUI
Gets the prompt delay cursor.
getPromptDelay() - Method in class loci.slim.paramSetMacro
 
getPromptDelay() - Method in class loci.slim.ui.UserInterfacePanel
Gets the excitation delay cursor.
getPromptDelayIndex() - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Gets the start of the prompt as a bin index.
getPromptDelayTime() - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Gets the start of the prompt as a time value.
getPromptStartBin() - Method in class loci.slim.fitting.cursor.FittingCursor
Gets the start of the prompt as a bin number.
getPromptStartIndex() - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Gets the start of the prompt as a bin index.
getPromptStartTime() - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Gets the start of the prompt as a time value.
getPromptStartValue() - Method in class loci.slim.fitting.cursor.FittingCursor
Gets the start of the prompt as a time value.
getPromptStopBin() - Method in class loci.slim.fitting.cursor.FittingCursor
Gets the end of the prompt as a bin number.
getPromptStopIndex() - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Gets the end of the prompt as an index.
getPromptStopTime() - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Gets the end of the prompt as a time value.
getPromptStopValue() - Method in class loci.slim.fitting.cursor.FittingCursor
Gets the end of the prompt as a time value.
getPromptWidth() - Method in class loci.slim.fitting.cursor.FittingCursor
Gets the end of the prompt as a string showing prompt width.
getPromptWidth() - Method in class loci.slim.fitting.cursor.FittingCursorHelper
Gets the prompt width cursor.
getPromptWidth() - Method in interface loci.slim.fitting.cursor.IFittingCursorUI
Gets the prompt width cursor.
getPromptWidth() - Method in class loci.slim.ui.UserInterfacePanel
Gets the excitation width cursor.
getPromptWidthIndex() - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Gets the width of the prompt as an index.
getPromptWidthTime() - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Gets the width of the prompt as a time.
getQuartileIndices() - Method in class loci.slim.histogram.HistogramStatistics
Gets the indices of the quartile values
getQuartiles() - Method in class loci.slim.histogram.HistogramStatistics
Gets the quartile values
getRawValues() - Method in class loci.slim.ui.ExcitationPanel
 
getRawValues() - Method in class loci.slim2.process.interactive.ui.ExcitationPanel
 
getRefineFit() - Method in class loci.slim.fitting.FitInfo
Gets whether to start next fit with results of last fit.
getRefineFit() - Method in interface loci.slim.ui.IUserInterfacePanel
Gets whether to start next fit with results of last fit.
getRefineFit() - Method in class loci.slim.ui.UserInterfacePanel
 
getRefineFit() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
getRefineFit() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Gets whether to start next fit with results of last fit.
getRegion() - Method in class loci.slim.fitting.FitInfo
Gets region the fit applies to.
getRegion() - Method in interface loci.slim.ui.IUserInterfacePanel
Gets region the fit applies to.
getRegion() - Method in class loci.slim.ui.UserInterfacePanel
 
getRegion() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
getRegion() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Gets region the fit applies to.
getScaledCenterValues() - Method in class loci.slim.analysis.batch.AbstractBatchHistogram
 
getScaledCenterValues(int) - Method in class loci.slim.analysis.batch.AbstractBatchHistogram
 
getScaledCenterValues() - Method in interface loci.slim.analysis.batch.BatchHistogram
Gets array of center values for 256-bin histogram.
getScaledCenterValues(int) - Method in interface loci.slim.analysis.batch.BatchHistogram
Gets array of center values for scaled histogram.
getScaledHistogram() - Method in class loci.slim.analysis.batch.AbstractBatchHistogram
Returns scaled-down 256-bin histogram adjusted to interquartile range.
getScaledHistogram(int) - Method in class loci.slim.analysis.batch.AbstractBatchHistogram
Returns scaled-down histogram adjusted to interquartile range.
getScaledHistogram() - Method in interface loci.slim.analysis.batch.BatchHistogram
Returns scaled-down 256-bin histogram adjusted to interquartile range.
getScaledHistogram(int) - Method in interface loci.slim.analysis.batch.BatchHistogram
Returns scaled-down histogram adjusted to interquartile range.
getScatter() - Method in interface loci.slim.ui.IUserInterfacePanel
Experimental: gets a scatter factor from UI.
getScatter() - Method in class loci.slim.ui.UserInterfacePanel
 
getScatter() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
getScatter() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Experimental: gets a scatter factor from UI.
getSelfMask() - Method in interface loci.slim.mask.IMaskNode
Gets the current mask created by this node.
getSelfMask() - Method in class loci.slim.mask.MaskNode
Gets the current mask created by this node.
getShowBins() - Method in class loci.slim.fitting.cursor.FittingCursor
Gets whether the UI will display bins or time values.
getShowBins() - Method in class loci.slim.fitting.cursor.FittingCursorHelper
Gets whether to show bins or time values for cursors.
getShowBins() - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Gets whether the UI will display bins or time values.
getSig() - Method in class loci.curvefitter.CurveFitData
 
getSig() - Method in interface loci.curvefitter.ICurveFitData
Get error for the fit data.
getSig() - Method in interface loci.slim.fitting.params.ILocalFitParams
 
getSig() - Method in class loci.slim.fitting.params.LocalFitParams
 
getSig() - Method in class loci.slim2.fitting.DefaultLocalFitParams
 
getSig() - Method in interface loci.slim2.fitting.LocalFitParams
 
getSize() - Static method in class loci.slim.histogram.PaletteFix
Gets the adjusted palette size.
getSlice() - Method in class loci.slim.MyStackWindow
 
getSmoothing() - Method in class loci.slim.histogram.HistogramPanel
 
getStandardDeviation() - Method in class loci.slim.analysis.HistogramStatistics
 
getStart() - Method in class loci.slim.Excitation
Gets start cursor.
getStart(int) - Method in class loci.slim.heuristics.Estimator
 
getStart(int) - Method in interface loci.slim.heuristics.IEstimator
Get a decay start estimate.
getStart(int) - Method in class loci.slim2.heuristics.DefaultEstimator
 
getStart(int) - Method in interface loci.slim2.heuristics.Estimator
Get a decay start estimate.
getStartPrompt() - Method in class loci.slim.fitting.FitInfo
Gets start of prompt.
getStartPrompt() - Method in class loci.slim.fitting.params.GlobalFitParams
 
getStartPrompt() - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
getStartPrompt() - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
getStartPrompt() - Method in interface loci.slim2.fitting.GlobalFitParams
 
getStatistics() - Method in class loci.slim.analysis.batch.AbstractBatchHistogram
Called periodically to get current statistics.
getStatistics() - Method in interface loci.slim.analysis.batch.BatchHistogram
Called periodically to get current statistics.
getStatistics(ImgPlus<DoubleType>, int, int, FittedValue) - Method in class loci.slim.analysis.plugins.ExportHistogramsToText
Builds statistics from image and single FittedValue.
getStatistics(int) - Method in class loci.slim.histogram.HistogramDataGroup
 
getStatistics(ImgPlus<DoubleType>, int, int, FittedValue) - Method in class loci.slim2.analysis.batch.ExportHistogramsToText
Builds statistics from image and single FittedValue.
getStdDev() - Method in class loci.slim.histogram.HistogramStatistics
Gets standard deviation values
getStdDevIndices() - Method in class loci.slim.histogram.HistogramStatistics
Gets indices of standard deviation values
getStop() - Method in class loci.slim.Excitation
Gets the stop cursor.
getStop(int) - Method in class loci.slim.heuristics.Estimator
 
getStop(int) - Method in interface loci.slim.heuristics.IEstimator
Get a decay stop estimate.
getStop(int) - Method in class loci.slim2.heuristics.DefaultEstimator
 
getStop(int) - Method in interface loci.slim2.heuristics.Estimator
Get a decay stop estimate.
getStopPrompt() - Method in class loci.slim.fitting.FitInfo
Gets end of prompt.
getStopPrompt() - Method in class loci.slim.fitting.params.GlobalFitParams
 
getStopPrompt() - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
getStopPrompt() - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
getStopPrompt() - Method in interface loci.slim2.fitting.GlobalFitParams
 
getStretched() - Method in class loci.slim.fitting.FitInfo
Gets whether or not this is a stretched exponential fit.
getSummedDecay(int, long[]) - Method in class loci.slim2.decay.LifetimeDatasetWrapper
Gets summed decay histogram at given location, with binning.
gett1() - Method in class loci.slim.paramSetMacro
 
gett2() - Method in class loci.slim.paramSetMacro
 
gett3() - Method in class loci.slim.paramSetMacro
 
getText() - Method in class loci.slim.histogram.DoubleFormatter
Gets the formatted string representation of value.
getThirdQuartile() - Method in class loci.slim.analysis.HistogramStatistics
 
getThreads() - Method in class loci.slim.fitting.config.Configuration
 
getThreshold() - Method in class loci.slim.fitting.FitInfo
Gets photon count threshold to fit a pixel.
getThreshold() - Method in class loci.slim.heuristics.Estimator
 
getThreshold() - Method in interface loci.slim.heuristics.IEstimator
Get a default threshold amount.
getThreshold() - Method in interface loci.slim.ui.IUserInterfacePanel
Gets photon count threshold to fit a pixel.
getThreshold() - Method in class loci.slim.ui.UserInterfacePanel
 
getThreshold() - Method in class loci.slim2.heuristics.DefaultEstimator
 
getThreshold() - Method in interface loci.slim2.heuristics.Estimator
Get a default threshold amount.
getThreshold() - Method in class loci.slim2.process.interactive.grayscale.GrayscaleDisplay
 
getThresholdMaximum() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
getThresholdMaximum() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Gets photon count threshold maximum to fit a pixel.
getThresholdMinimum() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
getThresholdMinimum() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Gets photon count threshold minimum to fit a pixel.
getThresholdValue() - Method in class loci.slim.paramSetMacro
 
getTime() - Method in class loci.slim2.process.HorzCursor
Get time value.
getTimeInc() - Method in class loci.slim.Excitation
Gets the horizontal time increment for the excitation curve.
getTimeInc() - Method in interface loci.slim2.process.FitSettings
Get time increment per time bin.
getTimeInc() - Method in class loci.slim2.process.interactive.BaseFitSettings
 
getTimeIncrement() - Method in class loci.slim2.decay.LifetimeDatasetWrapper
Gets bin width as time.
getTitle() - Method in class loci.slim.analysis.batch.AbstractBatchHistogram
 
getTitle() - Method in interface loci.slim.analysis.batch.BatchHistogram
Gets the histogram title.
getTitle() - Method in class loci.slim.analysis.HistogramStatistics
 
getTitle() - Method in class loci.slim.fitted.AbstractFittedValue
 
getTitle() - Method in interface loci.slim.fitted.FittedValue
Gets the title.
getTitle() - Method in class loci.slim.fitting.images.AbstractBaseFittedImage
Gets the title of the fitted image.
getTitle() - Method in interface loci.slim.fitting.images.IFittedImage
Gets the title of this image.
getTitle() - Method in class loci.slim.histogram.HistogramDataGroup
Gets a descriptive title to display on histogram UI for this data.
getToolTipText(MouseEvent) - Method in class loci.slim.histogram.HistogramPanel
 
getTotalMask() - Method in interface loci.slim.mask.IMaskNode
Gets the current mask.
getTotalMask() - Method in class loci.slim.mask.MaskNode
Gets the current total mask.
getTransEndIndex() - Method in class loci.curvefitter.CurveFitData
 
getTransEndIndex() - Method in interface loci.curvefitter.ICurveFitData
Gets end index in transient.
getTransient() - Method in class loci.curvefitter.CurveFitData
 
getTransient() - Method in interface loci.curvefitter.ICurveFitData
Get input data for the fit.
getTransient() - Method in class loci.slim2.fitting.DefaultFitResults
 
getTransient() - Method in interface loci.slim2.fitting.FitResults
Gets incoming transient data.
getTransientStart() - Method in class loci.slim.fitting.cursor.FittingCursor
Gets the start of the transient as a string.
getTransientStart() - Method in class loci.slim.fitting.cursor.FittingCursorHelper
Gets the transient start cursor.
getTransientStart() - Method in interface loci.slim.fitting.cursor.IFittingCursorUI
Gets the transient start cursor.
getTransientStart() - Method in class loci.slim.fitting.FitInfo
Gets starting bin of transient.
getTransientStart() - Method in class loci.slim.fitting.params.GlobalFitParams
 
getTransientStart() - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
getTransientStart() - Method in class loci.slim.ui.UserInterfacePanel
Gets the transient start cursor.
getTransientStart() - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
getTransientStart() - Method in interface loci.slim2.fitting.GlobalFitParams
 
getTransientStartBin() - Method in class loci.slim.fitting.cursor.FittingCursor
Gets the start of the transient as a bin number.
getTransientStartFromMacro() - Method in class loci.slim.paramSetMacro
 
getTransientStartIndex() - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Gets the start of the transient as an index.
getTransientStartTime() - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Gets the start of the transient as a time.
getTransientStartValue() - Method in class loci.slim.fitting.cursor.FittingCursor
Gets the start of the transient as a time value.
getTransientStop() - Method in class loci.slim.fitting.cursor.FittingCursor
Gets the end of the transient as a string.
getTransientStop() - Method in class loci.slim.fitting.cursor.FittingCursorHelper
Gets the transient end cursor.
getTransientStop() - Method in interface loci.slim.fitting.cursor.IFittingCursorUI
Gets the transient end cursor.
getTransientStop() - Method in class loci.slim.fitting.FitInfo
Gets stopping bin of transient (inclusive).
getTransientStop() - Method in class loci.slim.fitting.params.GlobalFitParams
 
getTransientStop() - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
getTransientStop() - Method in class loci.slim.ui.UserInterfacePanel
Gets the transient end cursor.
getTransientStop() - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
getTransientStop() - Method in interface loci.slim2.fitting.GlobalFitParams
 
getTransientStopBin() - Method in class loci.slim.fitting.cursor.FittingCursor
Gets the end of the transient as a bin number.
getTransientStopFromMacro() - Method in class loci.slim.paramSetMacro
 
getTransientStopIndex() - Method in class loci.slim2.process.interactive.cursor.FittingCursor
 
getTransientStopTime() - Method in class loci.slim2.process.interactive.cursor.FittingCursor
 
getTransientStopValue() - Method in class loci.slim.fitting.cursor.FittingCursor
Gets the end of the transient as a time value.
getTransStart() - Method in class loci.slim2.fitting.DefaultFitResults
 
getTransStart() - Method in interface loci.slim2.fitting.FitResults
Gets start of transient.
getTransStartIndex() - Method in class loci.curvefitter.CurveFitData
 
getTransStartIndex() - Method in interface loci.curvefitter.ICurveFitData
Gets start index in transient.
getTransStop() - Method in class loci.slim2.fitting.DefaultFitResults
 
getTransStop() - Method in interface loci.slim2.fitting.FitResults
Gets end of transient.
getValue(double[]) - Method in class loci.slim.fitted.AFittedValue
 
getValue(double[]) - Method in class loci.slim.fitted.ChiSqFittedValue
 
getValue(double[]) - Method in interface loci.slim.fitted.FittedValue
Gets the fitted value.
getValue(double[]) - Method in class loci.slim.fitted.FractionalContributionFittedValue
 
getValue(double[]) - Method in class loci.slim.fitted.FractionalIntensityFittedValue
 
getValue(double[]) - Method in class loci.slim.fitted.TFittedValue
 
getValue(double[]) - Method in class loci.slim.fitted.TMeanFittedValue
 
getValue(double[]) - Method in class loci.slim.fitted.ZFittedValue
 
getValue(double[]) - Method in class loci.slim.fitting.images.AbstractBaseFittedImage
Given the array of fitted parameters, get the value for this image.
getValue(double[]) - Method in class loci.slim.fitting.images.FractionalContributionImage
 
getValue(double[]) - Method in class loci.slim.fitting.images.FractionalIntensityImage
 
getValue(double[]) - Method in interface loci.slim.fitting.images.IFittedImage
Given the array of fitted parameters, get the value for this image.
getValue(double[]) - Method in class loci.slim.fitting.images.SimpleFittedImage
Given the array of fitted parameters, get the value for this image.
getValue(double[]) - Method in class loci.slim.fitting.images.TauMeanImage
 
getValue() - Method in class loci.slim.histogram.DoubleFormatter
Gets the rounded value.
getValue(long[]) - Method in class loci.slim2.outputset.temp.RampGenerator
 
getValue(long, long) - Method in class loci.slim2.outputset.temp.RampGenerator
 
getValues() - Method in class loci.slim.Excitation
Gets the values of the excitation curve.
getValues() - Method in class loci.slim.histogram.HistogramDataNode
Gets the values array.
getValues(int, int, double) - Method in class loci.slim.ui.ExcitationPanel
Gets the excitation values scaled for a particular start/stop/base cursor.
getValues(int, int, double) - Method in class loci.slim2.process.interactive.ui.ExcitationPanel
Gets the excitation values scaled for a particular start/stop/base cursor.
getView() - Method in class loci.slim2.histogram.DataHistogramCommand
 
getWidth() - Method in class loci.slim.ChunkyPixel
Gets the width to draw the pixel.
getWidth() - Method in class loci.slim.ChunkyPixelTableImpl
 
getWidth() - Method in class loci.slim.DecayImageWrapper
Gets width of image.
getWidth() - Method in interface loci.slim.fitting.IDecayImage
Gets width of image.
getWidth() - Method in interface loci.slim.fitting.IFittedImage
Gets width of image.
getWidth() - Method in interface loci.slim.IChunkyPixelTable
Get pixel width.
getWidth(ImgPlus<?>) - Static method in class loci.slim.ImageUtils
 
getWidth() - Method in class loci.slim.OutputImageWrapper
Gets width of image.
getWidth() - Method in class loci.slim2.outputset.temp.ChunkyPixel
Gets width of pixel.
getX() - Method in class loci.curvefitter.CurveFitData
 
getX() - Method in interface loci.curvefitter.ICurveFitData
Gets x location of the fitted pixel.
getX() - Method in class loci.slim.ChunkyPixel
Gets the x location.
getX() - Method in class loci.slim.fitting.FitInfo
Gets pixel x.
getX() - Method in interface loci.slim.ui.IUserInterfacePanel
Gets pixel x.
getX() - Method in class loci.slim.ui.UserInterfacePanel
 
getX() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
getX() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Gets pixel x.
getXInc() - Method in class loci.curvefitter.AbstractCurveFitter
 
getXInc() - Method in interface loci.curvefitter.ICurveFitter
Get increment along x axis (evenly spaced).
getXInc() - Method in class loci.slim.fitting.FitInfo
Gets x increment for each bin.
getXInc() - Method in class loci.slim.fitting.params.GlobalFitParams
 
getXInc() - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
getXInc() - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
getXInc() - Method in interface loci.slim2.fitting.GlobalFitParams
 
getY() - Method in class loci.curvefitter.CurveFitData
 
getY() - Method in interface loci.curvefitter.ICurveFitData
Gets y location of the fitted pixel.
getY(double, double[]) - Method in class loci.curvefitter.JaolhoCurveFitter.ExpFunction
 
getY() - Method in class loci.slim.ChunkyPixel
Gets the y location.
getY() - Method in class loci.slim.fitting.FitInfo
Gets pixel y.
getY() - Method in interface loci.slim.fitting.params.ILocalFitParams
 
getY() - Method in class loci.slim.fitting.params.LocalFitParams
 
getY() - Method in interface loci.slim.ui.IUserInterfacePanel
Gets pixel y.
getY() - Method in class loci.slim.ui.UserInterfacePanel
 
getY() - Method in class loci.slim2.fitting.DefaultLocalFitParams
 
getY() - Method in interface loci.slim2.fitting.LocalFitParams
 
getY() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
getY() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Gets pixel y.
getYFitted() - Method in class loci.curvefitter.CurveFitData
 
getYFitted() - Method in interface loci.curvefitter.ICurveFitData
Gets fitted data from the fit.
getYFitted() - Method in class loci.slim.fitting.params.FitResults
 
getYFitted() - Method in interface loci.slim.fitting.params.IFitResults
Gets fitted curve.
getYFitted() - Method in interface loci.slim.fitting.params.ILocalFitParams
 
getYFitted() - Method in class loci.slim.fitting.params.LocalFitParams
 
getYFitted() - Method in class loci.slim2.fitting.DefaultFitResults
 
getYFitted() - Method in class loci.slim2.fitting.DefaultLocalFitParams
 
getYFitted() - Method in interface loci.slim2.fitting.FitResults
Gets fitted curve.
getYFitted() - Method in interface loci.slim2.fitting.LocalFitParams
 
getz1() - Method in class loci.slim.paramSetMacro
 
getZoomFactor() - Method in class loci.slim.MyStackWindow
 
globalCursor(double[], double[]) - Method in interface loci.slim.fitting.cursor.ICursorEstimator
 
GlobalFitParams - Class in loci.slim.fitting.params
This contains the global fitting parameters, i.e.
GlobalFitParams() - Constructor for class loci.slim.fitting.params.GlobalFitParams
 
GlobalFitParams - Interface in loci.slim2.fitting
Interface for container for the global fitting parameters, i.e.
globalFitParams - Variable in class loci.slim2.process.interactive.BaseFitSettings
 
GrayCurveFitter - Class in loci.curvefitter
TODO
GrayCurveFitter() - Constructor for class loci.curvefitter.GrayCurveFitter
 
GrayCurveFitter.CLibrary - Interface in loci.curvefitter
 
GrayNRCurveFitter - Class in loci.curvefitter
TODO
GrayNRCurveFitter() - Constructor for class loci.curvefitter.GrayNRCurveFitter
 
GrayNRCurveFitter.CLibrary - Interface in loci.curvefitter
 
GrayscaleDisplay - Class in loci.slim2.process.interactive.grayscale
 
GrayscaleDisplay(Context, Dataset, Display) - Constructor for class loci.slim2.process.interactive.grayscale.GrayscaleDisplay
 
GrayScaleImage<T extends RealType<T>> - Class in loci.slim
The GrayScaleImage shows a grayscale representation of the input data.
GrayScaleImage(ImgPlus<T>) - Constructor for class loci.slim.GrayScaleImage
 
guiUpdateWithMacro - Static variable in class loci.slim.SLIMProcessor
 
guiUsedforValues - Static variable in class loci.slim.SLIMProcessor
 

H

h1macroused - Variable in class loci.slim.paramSetMacro
 
H_INDEX - Static variable in interface loci.slim.fitted.FittedValue
 
H_INDEX - Static variable in class loci.slim.fitting.images.FittedImageFitter
 
hasChannels() - Method in class loci.slim.histogram.HistogramDataGroup
Returns whether or not histogram has channels.
hasExcludedPixels() - Method in class loci.slim.mask.Mask
Any masking going on?
hasNext() - Method in class loci.slim.ChunkyPixelEffectIterator
 
hasNext() - Method in class loci.slim2.outputset.temp.ChunkyPixelIterator
 
hasPrompt() - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Sets whether or not a prompt has been loaded.
hideCursor() - Method in class loci.slim.GrayScaleImage
 
hideCursor() - Method in interface loci.slim.ICursorListener
Hide the cursor.
hideCursor() - Method in interface loci.slim2.process.interactive.ui.PixelPicker
Hide the cursor.
HistogramDataGroup - Class in loci.slim.histogram
Keeps an array of HistogramDataNodes for a given image.
HistogramDataGroup(IFittedImage, String, HistogramDataNode[]) - Constructor for class loci.slim.histogram.HistogramDataGroup
Constructor, takes an array of HistogramChannels.
HistogramDataNode - Class in loci.slim.histogram
This class shadows a channel in a stack for a displayed image.
HistogramDataNode(IFittedImage, double[][]) - Constructor for class loci.slim.histogram.HistogramDataNode
Constructor, takes the array of values.
HistogramGraph - Class in loci.slim2.histogram
Histogram graph Dataset drawing class.
HistogramGraph(DatasetService, RenderingService) - Constructor for class loci.slim2.histogram.HistogramGraph
Constructor
HistogramPanel - Class in loci.slim.analysis.batch.ui
 
HistogramPanel(HistogramStatistics) - Constructor for class loci.slim.analysis.batch.ui.HistogramPanel
 
HistogramPanel - Class in loci.slim.histogram
This is a panel that represents a histogram.
HistogramPanel(int, int, int) - Constructor for class loci.slim.histogram.HistogramPanel
Constructor
HistogramStatistics - Class in loci.slim.analysis
A histogram statistics class used for export to text.
HistogramStatistics() - Constructor for class loci.slim.analysis.HistogramStatistics
 
HistogramStatistics - Class in loci.slim.histogram
Container class for some histogram related statistics.
HistogramStatistics() - Constructor for class loci.slim.histogram.HistogramStatistics
 
HistogramStatisticsPanel - Class in loci.slim.analysis.batch.ui
 
HistogramStatisticsPanel(HistogramStatistics) - Constructor for class loci.slim.analysis.batch.ui.HistogramStatisticsPanel
 
HistogramStatisticsRowPanel - Class in loci.slim.analysis.batch.ui
 
HistogramStatisticsRowPanel(String, HistogramStatistics[], BatchHistogramListener) - Constructor for class loci.slim.analysis.batch.ui.HistogramStatisticsRowPanel
 
HistogramTool - Class in loci.slim.histogram
This is the main class for the histogram tool.
HistogramTool() - Constructor for class loci.slim.histogram.HistogramTool
 
HistogramUIPanel - Class in loci.slim.histogram
This class holds the text fields that show the current minimum and maximum LUT range.
HistogramUIPanel(boolean) - Constructor for class loci.slim.histogram.HistogramUIPanel
Constructor.
HorzCursor - Class in loci.slim2.process
Horizontal decay cursor.
HorzCursor(double) - Constructor for class loci.slim2.process.HorzCursor
Constructor, specifies time increment per bin.

I

IChartRectangleListener - Interface in imagej.charts
 
IChunkyPixelTable - Interface in loci.slim
Interface for a table of chunky pixels.
ICursorDragListener - Interface in imagej.charts.cursors
 
ICursorEstimator - Interface in loci.slim.fitting.cursor
 
ICursorListener - Interface in loci.slim
 
ICursorMoveListener - Interface in imagej.charts.cursors
 
ICursorStretchListener - Interface in imagej.charts.cursors
 
ICurveFitData - Interface in loci.curvefitter
Interface to the curve fitting data.
ICurveFitter - Interface in loci.curvefitter
Interface for a curve fitter.
ICurveFitter.FitAlgorithm - Enum in loci.curvefitter
Specifies fitting algorithm.
ICurveFitter.FitFunction - Enum in loci.curvefitter
Specifies curves that this fits.
ICurveFitter.FitRegion - Enum in loci.curvefitter
Specifies fitting region.
ICurveFitter.NoiseModel - Enum in loci.curvefitter
Specifies noise model for fit.
IDecayGraph - Interface in loci.slim.ui
Interface for a decay chart.
IDecayImage<T extends RealType<T>> - Interface in loci.slim.fitting
 
IErrorListener - Interface in loci.slim.fitting
Defines a listener for error mask changes.
IEstimator - Interface in loci.slim.heuristics
Interface for a class with estimates and rules of thumb.
IFitResults - Interface in loci.slim.fitting.params
Interface for container for local fitted results for current pixel.
IFittedImage - Interface in loci.slim.fitting
 
IFittedImage - Interface in loci.slim.fitting.images
Interface for a fitted image.
IFittedImageSlice - Interface in loci.slim.fitting.images
This interface is for a 2D slice of the fitted image.
IFitterEstimator - Interface in loci.curvefitter
This interface allows for some peculiarities of TRI2 to ensure matching results, particularly when doing a fit with an RLD estimate combined with an LMA fit.
IFittingCursorListener - Interface in loci.slim.fitting.cursor
Listener interface for fitting cursor changes.
IFittingCursorUI - Interface in loci.slim.fitting.cursor
This is an interface to get/set transient and prompt cursors as strings.
IFittingEngine - Interface in loci.slim.fitting.engine
Interface for a fitting engine.
IFittingEngineCallable - Interface in loci.slim.fitting.callable
 
IGlobalFitParams - Interface in loci.slim.fitting.params
Interface for container for the global fitting parameters, i.e.
IGrayScaleImage - Interface in loci.slim
Interface for the GrayScaleImage UI.
IGrayScalePixelValue - Interface in loci.slim
Interface for a grayscale pixel value getter.
IHistogramDataListener - Interface in loci.slim.histogram
Interface for a listener to catch changes in the data.
IHistogramPanelListener - Interface in loci.slim.histogram
Interface for a listener to catch the user moving the cursor on the histogram panel.
ILocalFitParams - Interface in loci.slim.fitting.params
Interface for container for the local fitting parameters, i.e.
ImageFitter - Class in loci.slim2.process
Fits an entire image.
ImageFitter() - Constructor for class loci.slim2.process.ImageFitter
 
ImageFitter.ErrorCode - Enum in loci.slim2.process
 
imagej.charts - package imagej.charts
 
imagej.charts.cursors - package imagej.charts.cursors
 
imagej.thread - package imagej.thread
 
ImageUtils - Class in loci.slim
Utility class for working with ImgLib2 images.
ImageUtils() - Constructor for class loci.slim.ImageUtils
 
IMaskGroup - Interface in loci.slim.mask
This is an interface for a group of associated mask nodes.
IMaskGroupListener - Interface in loci.slim.mask
Listener interface to receive changes in which mask group is active.
IMaskNode - Interface in loci.slim.mask
Interface for a mask node.
IMaskNodeListener - Interface in loci.slim.mask
Interface to a listener for a mask node.
IndexedMemberFormula - Class in loci.slim2.outputset
This is the simplest MemberFormula that just takes the input value at a given index.
IndexedMemberFormula(int) - Constructor for class loci.slim2.outputset.IndexedMemberFormula
 
INFINITY - Static variable in class loci.slim.histogram.DoubleFormatter
 
init(FittedValue) - Method in class loci.slim.analysis.batch.ABatchHistogram
 
init(FittedValue) - Method in interface loci.slim.analysis.batch.BatchHistogram
Sets the fitted value converter.
init(FittedValue) - Method in class loci.slim.analysis.batch.ChiSqBatchHistogram
 
init(ICurveFitter.FitFunction, FittedValue[], BatchHistogramListener) - Method in class loci.slim.analysis.batch.ExportSummaryToText
Initializes for given fitting function.
init(FittedValue) - Method in class loci.slim.analysis.batch.FractionalContribBatchHistogram
 
init(FittedValue) - Method in class loci.slim.analysis.batch.FractionalIntensityBatchHistogram
 
init(FittedValue) - Method in class loci.slim.analysis.batch.TauBatchHistogram
 
init(FittedValue) - Method in class loci.slim.analysis.batch.ZBatchHistogram
 
init(String, int) - Method in class loci.slim.fitted.AFittedValue
 
init(String) - Method in class loci.slim.fitted.ChiSqFittedValue
 
init(String, int, int) - Method in class loci.slim.fitted.FractionalContributionFittedValue
 
init(String, int, int) - Method in class loci.slim.fitted.FractionalIntensityFittedValue
 
init(String, int) - Method in class loci.slim.fitted.TFittedValue
 
init(String, int) - Method in class loci.slim.fitted.TMeanFittedValue
 
init(String) - Method in class loci.slim.fitted.ZFittedValue
 
init(int, int, int, IndexColorModel) - Method in class loci.slim.fitting.images.ColorizedFittedImage
 
init(int, int, int, IndexColorModel) - Method in class loci.slim.fitting.images.FloatFittedImage
 
init(int, int, int, IndexColorModel) - Method in interface loci.slim.fitting.images.IFittedImageSlice
Initializes a slice.
init(int, int) - Method in class loci.slim.preprocess.Bin11x11
 
init(int, int) - Method in class loci.slim.preprocess.Bin3x3
 
init(int, int) - Method in class loci.slim.preprocess.Bin5x5
 
init(int, int) - Method in class loci.slim.preprocess.Bin7x7
 
init(int, int) - Method in class loci.slim.preprocess.Bin9x9
 
init(int, int) - Method in interface loci.slim.preprocess.SLIMBinner
 
init(int, int, int) - Method in class loci.slim.preprocess.SquareBinner
Initializes the binner.
init(JFrame, int, double, ICursorListener) - Method in class loci.slim.ui.DecayGraph
Initialize the graph and returns the containing JFrame.
init(JFrame, int, double, ICursorListener) - Method in interface loci.slim.ui.IDecayGraph
Initialize the graph and returns the containing JFrame.
init(ICurveFitter.FitFunction, FittedValue[], BatchHistogramListener) - Method in class loci.slim2.analysis.batch.ExportSummaryToText
Initializes for given fitting function.
init(Context, CommandService, DatasetService, DisplayService, Estimator) - Method in class loci.slim2.process.interactive.DefaultInteractiveProcessor
 
init(JFrame, int, double, PixelPicker) - Method in interface loci.slim2.process.interactive.ui.DecayGraph
Initialize the graph and returns the containing JFrame.
init(JFrame, int, double, PixelPicker) - Method in class loci.slim2.process.interactive.ui.DefaultDecayGraph
 
init(Context, CommandService, DatasetService, DisplayService, Estimator) - Method in interface loci.slim2.process.InteractiveProcessor
Initializes with required services.
initValues() - Method in class loci.slim2.histogram.DataHistogramCommand
 
integrate(double[], double, double, int, int) - Method in class loci.slim.fitting.DefaultIntegrator
 
integrate(double[], double, double, int, int) - Method in interface loci.slim.fitting.Integrator
 
Integrator - Interface in loci.slim.fitting
 
InteractiveProcessor - Interface in loci.slim2.process
Interface for lifetime processing with interactive UI.
IProcessor - Interface in loci.slim.preprocess
Interface for an input processor.
isa1MacroRecording - Variable in class loci.slim.paramSetMacro
 
isa2MacroRecording - Variable in class loci.slim.paramSetMacro
 
isa3MacroRecording - Variable in class loci.slim.paramSetMacro
 
isAnalysisListUsed - Variable in class loci.slim.paramSetMacro
 
isAppendSet - Static variable in class loci.slim.paramSetMacro
 
isAppendUsed - Variable in class loci.slim.paramSetMacro
 
isAppendUsedPixel - Variable in class loci.slim.paramSetMacro
 
isBatchMacroUsed - Variable in class loci.slim.paramSetMacro
 
isDelayExcitationMacroused - Variable in class loci.slim.paramSetMacro
 
ISelectListener - Interface in loci.slim
Interface called by the gray scale image code when user clicks on it to select a pixel.
isExcitationChanging - Variable in class loci.slim.paramSetMacro
 
isExportFilemacroUsed - Variable in class loci.slim.paramSetMacro
 
isMacroUsedForDefaultExcitation - Variable in class loci.slim.paramSetMacro
 
isMacroUsedForExcitation - Variable in class loci.slim.paramSetMacro
 
isPromptBaseLineMacroused - Variable in class loci.slim.paramSetMacro
 
ist1MacroRecording - Variable in class loci.slim.paramSetMacro
 
ist2MacroRecording - Variable in class loci.slim.paramSetMacro
 
ist3MacroRecording - Variable in class loci.slim.paramSetMacro
 
IThresholdUpdate - Interface in loci.slim
An interface to allow updated threshold values to be communicated.
IUIPanelListener - Interface in loci.slim.histogram
 
IUserInterfacePanel - Interface in loci.slim.ui
Interface to the User Interface Panel
IUserInterfacePanelListener - Interface in loci.slim.ui
Listens for user input that triggers changes external to the ui panel.

J

JaolhoCurveFitter - Class in loci.curvefitter
Curve fitter that uses the Jaolho curve fitting package.
JaolhoCurveFitter() - Constructor for class loci.curvefitter.JaolhoCurveFitter
 
JaolhoCurveFitter.ExpFunction - Class in loci.curvefitter
A summed exponential function of the form: y(t) = a1*e^(-b1*t) + ...
JaolhoCurveFitter.ExpFunction(int) - Constructor for class loci.curvefitter.JaolhoCurveFitter.ExpFunction
Constructs a function with the given number of summed exponentials.

K

KEY_ANALYSIS_LIST - Static variable in class loci.slim.SLIMProcessor
 
KEY_ANALYSIS_NUMBER - Static variable in class loci.slim.SLIMProcessor
 
KEY_BASE_PROMPT - Static variable in class loci.slim.ui.UserInterfacePanel
 
KEY_BATCH_MODE_FILE_NUMBER - Static variable in class loci.slim.SLIMProcessor
 
KEY_DELAY_TIME - Static variable in class loci.slim.ui.UserInterfacePanel
 
KEY_EXCITATION - Static variable in class loci.slim.ui.UserInterfacePanel
 
KEY_FILE_NAMES - Static variable in class loci.slim.SLIMProcessor
 
KEY_WIDTH - Static variable in class loci.slim.ui.UserInterfacePanel
 

L

LAMBDA - Static variable in interface loci.slim.fitted.FittedValue
 
LAMBDA - Static variable in interface loci.slim2.process.interactive.ui.UserInterfacePanel
 
LEFT - Static variable in class imagej.charts.cursors.Cursor
 
LifetimeDatasetWrapper - Class in loci.slim2.decay
Wraps a Dataset that has lifetime information.
LifetimeDatasetWrapper(Dataset) - Constructor for class loci.slim2.decay.LifetimeDatasetWrapper
Constructor.
LifetimeDatasetWrapper(Context, File) - Constructor for class loci.slim2.decay.LifetimeDatasetWrapper
Constructor.
LifetimeGrayscaleDataset - Class in loci.slim2.decay
Builds a grayscale version of the lifetime decay image.
LifetimeGrayscaleDataset(DatasetService, LifetimeDatasetWrapper) - Constructor for class loci.slim2.decay.LifetimeGrayscaleDataset
Constructor.
listenToMaskGroup(IMaskGroup) - Method in class loci.slim.GrayScaleImage
 
listenToMaskGroup(IMaskGroup) - Method in interface loci.slim.IGrayScaleImage
Sets a mask group to listen for changes.
listenToMaskGroup(IMaskGroup) - Method in interface loci.slim.mask.IMaskGroupListener
Sets a mask group to listen for changes.
LMA_fit(double, double[], int, int, double[], int, double[], double[], int[], int, double[], DoubleByReference, double) - Method in interface loci.curvefitter.GrayNRCurveFitter.CLibrary
 
LMA_fit(double, double[], int, int, double[], int, int, double[], double[], int[], int, double[], DoubleByReference, double, double) - Method in interface loci.curvefitter.SLIMCurveFitter.CLibrary
 
loadDefaultExcitation(String) - Static method in class loci.slim.SLIMProcessor
 
loadExcitation(String, double) - Static method in class loci.slim.ExcitationFileUtility
 
loadExcitation(String) - Method in interface loci.slim.ui.IUserInterfacePanelListener
Loads an excitation curve from file.
loadExcitation(String) - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanelListener
Loads an excitation curve from file.
localCursor(FittingCursor, double[], double[]) - Method in interface loci.slim.fitting.cursor.ICursorEstimator
 
LocalFitParams - Class in loci.slim.fitting.params
Container for the local fitting parameters, i.e.
LocalFitParams() - Constructor for class loci.slim.fitting.params.LocalFitParams
 
LocalFitParams - Interface in loci.slim2.fitting
Interface for container for the local fitting parameters, i.e.
loci.curvefitter - package loci.curvefitter
 
loci.slim - package loci.slim
 
loci.slim.analysis - package loci.slim.analysis
 
loci.slim.analysis.batch - package loci.slim.analysis.batch
 
loci.slim.analysis.batch.ui - package loci.slim.analysis.batch.ui
 
loci.slim.analysis.plugins - package loci.slim.analysis.plugins
 
loci.slim.fitted - package loci.slim.fitted
 
loci.slim.fitting - package loci.slim.fitting
 
loci.slim.fitting.callable - package loci.slim.fitting.callable
 
loci.slim.fitting.config - package loci.slim.fitting.config
 
loci.slim.fitting.cursor - package loci.slim.fitting.cursor
 
loci.slim.fitting.engine - package loci.slim.fitting.engine
 
loci.slim.fitting.images - package loci.slim.fitting.images
 
loci.slim.fitting.params - package loci.slim.fitting.params
 
loci.slim.heuristics - package loci.slim.heuristics
 
loci.slim.histogram - package loci.slim.histogram
 
loci.slim.mask - package loci.slim.mask
 
loci.slim.preprocess - package loci.slim.preprocess
 
loci.slim.ui - package loci.slim.ui
 
loci.slim2 - package loci.slim2
 
loci.slim2.analysis.batch - package loci.slim2.analysis.batch
 
loci.slim2.decay - package loci.slim2.decay
 
loci.slim2.experimental - package loci.slim2.experimental
 
loci.slim2.fitting - package loci.slim2.fitting
 
loci.slim2.heuristics - package loci.slim2.heuristics
 
loci.slim2.histogram - package loci.slim2.histogram
 
loci.slim2.outputset - package loci.slim2.outputset
 
loci.slim2.outputset.temp - package loci.slim2.outputset.temp
 
loci.slim2.process - package loci.slim2.process
 
loci.slim2.process.batch - package loci.slim2.process.batch
 
loci.slim2.process.interactive - package loci.slim2.process.interactive
 
loci.slim2.process.interactive.cursor - package loci.slim2.process.interactive.cursor
 
loci.slim2.process.interactive.grayscale - package loci.slim2.process.interactive.grayscale
 
loci.slim2.process.interactive.ui - package loci.slim2.process.interactive.ui
 
logarithmicChanged() - Method in class loci.slim2.histogram.DataHistogramCommand
Called when logarithmic changes.
LOWER - Static variable in class imagej.charts.cursors.Cursor
 

M

macroParams - Static variable in class loci.slim.SLIMProcessor
 
main(String[]) - Static method in class loci.slim.About
 
Main - Class in loci.slim
Test class for launching the SLIM Curve plugin.
Main() - Constructor for class loci.slim.Main
 
main(String[]) - Static method in class loci.slim.Main
 
main(String...) - Static method in class loci.slim2.SLIMPlugin
Tests our command.
makeCompactGrid(Container, int, int, int, int, int, int) - Static method in class loci.slim.ui.SpringUtilities
Aligns the first rows * cols components of parent in a grid.
makeCompactGrid(Container, int, int, int, int, int, int) - Static method in class loci.slim2.process.interactive.ui.SpringUtilities
Aligns the first rows * cols components of parent in a grid.
makeGrid(Container, int, int, int, int, int, int) - Static method in class loci.slim.ui.SpringUtilities
Aligns the first rows * cols components of parent in a grid.
makeGrid(Container, int, int, int, int, int, int) - Static method in class loci.slim2.process.interactive.ui.SpringUtilities
Aligns the first rows * cols components of parent in a grid.
markwardt_fit(double, double[], int, int, double[], int[], int) - Method in interface loci.curvefitter.MarkwardtCurveFitter.CLibrary
 
MarkwardtCurveFitter - Class in loci.curvefitter
TODO
MarkwardtCurveFitter() - Constructor for class loci.curvefitter.MarkwardtCurveFitter
 
MarkwardtCurveFitter.CLibrary - Interface in loci.curvefitter
 
Mask - Class in loci.slim.mask
Class for keeping track of exclusion masks.
Mask(boolean[][]) - Constructor for class loci.slim.mask.Mask
 
Mask(int, int) - Constructor for class loci.slim.mask.Mask
 
MaskGroup - Class in loci.slim.mask
Mask group class associates a set of mask nodes.
MaskGroup() - Constructor for class loci.slim.mask.MaskGroup
 
MaskNode - Class in loci.slim.mask
Mask node class.
MaskNode(IMaskGroup, IMaskNodeListener) - Constructor for class loci.slim.mask.MaskNode
 
MAX_REFITS - Static variable in class loci.slim.fitting.RapidLifetimeDetermination
 
meanStatValues - Variable in class loci.slim.paramSetMacro
 
MemberFormula - Interface in loci.slim2.outputset
A formula for calculating the value of a member of an output set.
minMaxChanged(HistogramDataGroup, double, double, double, double) - Method in interface loci.slim.histogram.IHistogramDataListener
Called when the minimum or maximum changes.
minMaxChanged() - Method in class loci.slim2.histogram.DataHistogramCommand
Called when min or max changes.
mouseDragged(int, int) - Method in class imagej.charts.cursors.Cursor
 
mouseMoved(int, int) - Method in class imagej.charts.cursors.Cursor
 
MyStackWindow - Class in loci.slim
A kludge needed because StackWindow has issues.
MyStackWindow(ImagePlus) - Constructor for class loci.slim.MyStackWindow
 
MyStackWindow(ImagePlus, ImageCanvas) - Constructor for class loci.slim.MyStackWindow
 

N

NATIVE_SIZE - Static variable in class loci.slim.histogram.PaletteFix
 
newFittingEngineCallable() - Method in class loci.slim.fitting.config.Configuration
 
next() - Method in class loci.slim.ChunkyPixelEffectIterator
 
next() - Method in class loci.slim2.outputset.temp.ChunkyPixelIterator
 
NOISE_CONST - Static variable in class loci.slim.fitting.RapidLifetimeDetermination
 
NOISE_GAUSSIAN_FIT - Static variable in class loci.slim.fitting.RapidLifetimeDetermination
 
NOISE_GIVEN - Static variable in class loci.slim.fitting.RapidLifetimeDetermination
 
NOISE_MLE - Static variable in class loci.slim.fitting.RapidLifetimeDetermination
 
NOISE_POISSON_DATA - Static variable in class loci.slim.fitting.RapidLifetimeDetermination
 
NOISE_POISSON_FIT - Static variable in class loci.slim.fitting.RapidLifetimeDetermination
 
NoLifetimeAxisFoundException - Exception in loci.slim2.decay
Exception to throw when the lifetime file has no lifetime axis.
NoLifetimeAxisFoundException(String) - Constructor for exception loci.slim2.decay.NoLifetimeAxisFoundException
 
NONE - Static variable in class loci.slim.preprocess.SLIMBinning
 
noOfAnalysisList - Variable in class loci.slim.paramSetMacro
 
noOfFilesBatchProcessing - Variable in class loci.slim.paramSetMacro
 
noteError(int, int, int) - Method in class loci.slim.fitting.ErrorManager
Sets an error mask bit.
nr_GCI_marquardt_fitting_engine(float, float[], int, int, int, float[], int, int, float[], float[], int[], int, int, int, float[], float[], FloatByReference) - Method in interface loci.curvefitter.GrayCurveFitter.CLibrary
 
nr_GCI_triple_integral_fitting_engine(float, float[], int, int, float[], int, int, float[], FloatByReference, FloatByReference, FloatByReference, float[], float[], FloatByReference, float) - Method in interface loci.curvefitter.GrayCurveFitter.CLibrary
 

O

openFile() - Method in interface loci.slim.ui.IUserInterfacePanelListener
Opens new file(s).
openFile() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanelListener
Opens new file(s).
OutputImageWrapper - Class in loci.slim
This class wraps an image that is being used as output from a fit.
OutputImageWrapper(String, String, int, int, int, int) - Constructor for class loci.slim.OutputImageWrapper
Creates a wrapper for an output image and initial image.
OutputSet<T extends RealType<T> & NativeType<T>> - Class in loci.slim2.outputset
Builds a set of related images.
OutputSet(CommandService, DatasetService, boolean, boolean, T, long[], String, AxisType[], List<OutputSetMember>) - Constructor for class loci.slim2.outputset.OutputSet
Creates an images set.
OutputSet(CommandService, DatasetService, boolean, boolean, T, long[], String, AxisType[], String[]) - Constructor for class loci.slim2.outputset.OutputSet
Creates a set of images.
OutputSet(CommandService, DatasetService, boolean, boolean, T, Dataset, String[]) - Constructor for class loci.slim2.outputset.OutputSet
Creates a set of images.
OutputSet(CommandService, DatasetService, boolean, boolean, T, Dataset, List<OutputSetMember>) - Constructor for class loci.slim2.outputset.OutputSet
Creates a set of images.
OutputSetMember<T extends RealType<T> & NativeType<T>> - Class in loci.slim2.outputset
Class that describes a single member of the output set.
OutputSetMember(String, int, MemberFormula) - Constructor for class loci.slim2.outputset.OutputSetMember
Constructor.

P

paintComponent(Graphics) - Method in class loci.slim.analysis.batch.ui.HistogramPanel
 
paintComponent(Graphics) - Method in class loci.slim.histogram.ColorBarPanel
 
paintComponent(Graphics) - Method in class loci.slim.histogram.HistogramPanel
 
PAIR - Static variable in class imagej.charts.cursors.Cursor
 
PaletteFix - Class in loci.slim.histogram
This class fixes a problem in the way ImageJ assigns palette colors to FloatProcessor images.
PaletteFix() - Constructor for class loci.slim.histogram.PaletteFix
 
paramSetMacro - Class in loci.slim
 
paramSetMacro() - Constructor for class loci.slim.paramSetMacro
 
PixelPicker - Interface in loci.slim2.process.interactive.ui
Interface for the UI to pick a pixel to fit.
PLUGIN_NAME - Static variable in class loci.slim.SLIMProcessor
 
printSizes(Component) - Static method in class loci.slim.ui.SpringUtilities
A debugging utility that prints to stdout the component's minimum, preferred, and maximum sizes.
printSizes(Component) - Static method in class loci.slim2.process.interactive.ui.SpringUtilities
A debugging utility that prints to stdout the component's minimum, preferred, and maximum sizes.
process(List<? extends Callable<T>>) - Method in class imagej.thread.ThreadPool
Given a List of Callables defining tasks, execute them in parallel chunks using the thread pool.
process(double[]) - Method in class loci.slim.analysis.batch.AbstractBatchHistogram
 
process(double[]) - Method in interface loci.slim.analysis.batch.BatchHistogram
Processes fitted values for a pixel.
process(String, ImgPlus<DoubleType>) - Method in class loci.slim.analysis.batch.ExportSummaryToText
Processes each image in batch job.
process(String) - Method in class loci.slim.SLIMProcessor
Run method for the plugin.
process(String, ImgPlus<DoubleType>) - Method in class loci.slim2.analysis.batch.ExportSummaryToText
Processes each image in batch job.
process(Context, int, File[], FitSettings) - Method in class loci.slim2.process.batch.DefaultBatchProcessor
 
process(Context, int, File[], FitSettings) - Method in interface loci.slim2.process.BatchProcessor
Processes list of files with current settings.
process(LifetimeDatasetWrapper) - Method in class loci.slim2.process.interactive.DefaultInteractiveProcessor
 
process(LifetimeDatasetWrapper) - Method in interface loci.slim2.process.InteractiveProcessor
processImage(SCIFIOImgPlus<T>) - Method in class loci.slim.SLIMProcessor
 
PROMPT_BASELINE - Static variable in class loci.slim.heuristics.CursorEstimator
 
PROMPT_BASELINE - Static variable in class loci.slim2.heuristics.CursorEstimator
 
PROMPT_START - Static variable in class loci.slim.heuristics.CursorEstimator
 
PROMPT_START - Static variable in class loci.slim2.heuristics.CursorEstimator
 
PROMPT_STOP - Static variable in class loci.slim.heuristics.CursorEstimator
 
PROMPT_STOP - Static variable in class loci.slim2.heuristics.CursorEstimator
 
propagateMask(double, double) - Method in class loci.slim.histogram.HistogramDataNode
Builds a mask based on which values are within the LUT range and sends it out to peer nodes.

Q

quit() - Method in class loci.slim.ui.ExcitationPanel
 
quit() - Method in interface loci.slim.ui.IUserInterfacePanelListener
Quits running plugin.
quit() - Method in class loci.slim2.process.interactive.ui.ExcitationPanel
 
quit() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanelListener
Quits running plugin.

R

RampGenerator - Class in loci.slim2.outputset.temp
 
RampGenerator(RampGenerator.RampType, long, long) - Constructor for class loci.slim2.outputset.temp.RampGenerator
 
RampGenerator.RampType - Enum in loci.slim2.outputset.temp
 
rangeChanged() - Method in class loci.slim2.histogram.DataHistogramCommand
Called when show full range changes.
RapidLifetimeDetermination - Class in loci.slim.fitting
 
RapidLifetimeDetermination() - Constructor for class loci.slim.fitting.RapidLifetimeDetermination
 
record(String, String...) - Static method in class loci.slim.SLIMProcessor
Macro-record a specific command.
recordFirstTime(String, String...) - Method in class loci.slim.SLIMProcessor
 
recordRun(String, String...) - Static method in class loci.slim.SLIMProcessor
 
redisplay() - Method in class loci.slim.fitting.images.AbstractBaseFittedImage
Called from the histogram tool.
redisplay() - Method in interface loci.slim.fitting.images.IFittedImage
Redisplays the image after a LUT change.
redisplay() - Method in class loci.slim.histogram.HistogramDataGroup
 
reFit() - Method in interface loci.slim.ui.IUserInterfacePanelListener
Triggers a refit.
remove() - Method in class loci.slim.ChunkyPixelEffectIterator
 
remove() - Method in class loci.slim2.outputset.temp.ChunkyPixelIterator
 
removeCursor(Cursor) - Method in class imagej.charts.cursors.CursorLayer
 
removeCursorDragListener(ICursorDragListener) - Method in class imagej.charts.cursors.Cursor
 
removeCursorMoveListener(ICursorMoveListener) - Method in class imagej.charts.cursors.Cursor
 
removeCursorStretchListener(ICursorStretchListener) - Method in class imagej.charts.cursors.Cursor
 
removeListener(IFittingCursorListener) - Method in class loci.slim.fitting.cursor.FittingCursor
Removes a listener for cursor changes.
removeListener(FittingCursorListener) - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Removes a listener for cursor changes.
removeNode(IMaskNode) - Method in interface loci.slim.mask.IMaskGroup
Removes a mask node from group.
removeNode(IMaskNode) - Method in class loci.slim.mask.MaskGroup
 
rescindMask() - Method in class loci.slim.histogram.HistogramDataNode
Deletes our mask.
reset() - Method in interface loci.slim.ui.IUserInterfacePanel
Resets the UI after a fit.
reset() - Method in class loci.slim.ui.UserInterfacePanel
 
reset() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
reset() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Resets the UI after a fit.
resetButtons() - Method in interface loci.slim.ui.IUserInterfacePanel
Resets the UI buttons after a fit.
resetButtons() - Method in class loci.slim.ui.UserInterfacePanel
 
resetButtons() - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
resetButtons() - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Resets the UI buttons after a fit.
resetCursors() - Method in class loci.slim.histogram.HistogramPanel
Resets the cursors.
resetErrorMask(int) - Method in interface loci.slim.fitting.IErrorListener
Clears error mask.
resetErrorMask(int) - Method in class loci.slim.GrayScaleImage
 
RIGHT - Static variable in class imagej.charts.cursors.Cursor
 
RLD_fit(double, double[], int, int, double[], int, double[], DoubleByReference, DoubleByReference, DoubleByReference, double[], DoubleByReference, double) - Method in interface loci.curvefitter.GrayNRCurveFitter.CLibrary
 
RLD_fit(double, double[], int, int, double[], int, int, double[], DoubleByReference, DoubleByReference, DoubleByReference, double[], DoubleByReference, double) - Method in interface loci.curvefitter.SLIMCurveFitter.CLibrary
 
rldFit(ICurveFitter, ICurveFitData) - Method in class loci.slim.fitting.RapidLifetimeDetermination
Invokes java version of SLIMCurve C code.
RoiProcessor - Class in loci.slim.preprocess
 
RoiProcessor(Roi[]) - Constructor for class loci.slim.preprocess.RoiProcessor
 
roundToDecimalPlaces(double, int) - Method in class loci.curvefitter.DummyFitterEstimator
 
roundToDecimalPlaces(double, int) - Method in interface loci.curvefitter.IFitterEstimator
Rounds a double floating point to a specified number of decimal places.
roundToDecimalPlaces(double, int) - Method in class loci.slim.heuristics.FitterEstimator
 
roundToDecimalPlaces(double, int) - Method in class loci.slim2.heuristics.DefaultFitterEstimator
 
run(String) - Method in class loci.slim.About
 
run(String) - Method in class loci.slim.SLIM_PlugIn
 
run() - Method in class loci.slim2.histogram.DataHistogramCommand
 
run() - Method in class loci.slim2.SLIMPlugin
 

S

scale(double[], int, int, double, double, int) - Static method in class loci.slim.heuristics.ExcitationScaler
This is based on TRCursors.c UpdatePrompt in TRI2.
scale(double[], int, int, double, double, int) - Static method in class loci.slim2.heuristics.ExcitationScaler
This is based on TRCursors.c UpdatePrompt in TRI2.
selected(int, int, int) - Method in interface loci.slim.ISelectListener
Pixel was click-selected.
sendNotifications() - Method in class loci.slim.fitting.cursor.FittingCursor
Used to send listener notifications after a batched change.
sendNotifications() - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Used to send listener notifications after a batched change.
set(int, int) - Method in class loci.slim.mask.Mask
Sets a masked x and y.
SET_A1_FIX - Static variable in class loci.slim.SLIMProcessor
 
SET_A1_VALUE - Static variable in class loci.slim.SLIMProcessor
 
SET_A2_FIX - Static variable in class loci.slim.SLIMProcessor
 
SET_A2_VALUE - Static variable in class loci.slim.SLIMProcessor
 
SET_A3_FIX - Static variable in class loci.slim.SLIMProcessor
 
SET_A3_VALUE - Static variable in class loci.slim.SLIMProcessor
 
SET_ALGORITHM_TYPE - Static variable in class loci.slim.SLIMProcessor
 
SET_ANALYSIS_SET - Static variable in class loci.slim.SLIMProcessor
 
SET_APPEND_MODE - Static variable in class loci.slim.SLIMProcessor
 
SET_APPEND_MODE_PIXEL - Static variable in class loci.slim.SLIMProcessor
 
SET_BATCH_MODE - Static variable in class loci.slim.SLIMProcessor
 
SET_BINNING - Static variable in class loci.slim.SLIMProcessor
 
SET_CHI2_TARGET - Static variable in class loci.slim.SLIMProcessor
 
SET_DATA_START - Static variable in class loci.slim.SLIMProcessor
 
SET_DELAY_PROMPT - Static variable in class loci.slim.SLIMProcessor
 
SET_EXCITATION - Static variable in class loci.slim.SLIMProcessor
 
SET_EXPORT_HISTO_FILE_NAME - Static variable in class loci.slim.SLIMProcessor
 
SET_EXPORT_HISTO_FILE_NAME_SLIM2 - Static variable in class loci.slim.SLIMProcessor
 
SET_EXPORT_PIXEL_FILE_NAME - Static variable in class loci.slim.SLIMProcessor
 
SET_EXPORT_PIXEL_FILE_NAME_SLIM2 - Static variable in class loci.slim.SLIMProcessor
 
SET_FITTED_IMAGES - Static variable in class loci.slim.SLIMProcessor
 
SET_FUNCTION_TYPE - Static variable in class loci.slim.SLIMProcessor
 
SET_H1_VALUE - Static variable in class loci.slim.SLIMProcessor
 
SET_H_FIX - Static variable in class loci.slim.SLIMProcessor
 
SET_NOISE_MODEL - Static variable in class loci.slim.SLIMProcessor
 
SET_OF_EXPONENTS - Static variable in class loci.slim.SLIMProcessor
 
SET_PROMPT_BASELINE - Static variable in class loci.slim.SLIMProcessor
 
SET_REGION_TYPE - Static variable in class loci.slim.SLIMProcessor
 
SET_START_BATCH - Static variable in class loci.slim.SLIMProcessor
 
SET_START_FITTING - Static variable in class loci.slim.SLIMProcessor
 
SET_T1_FIX - Static variable in class loci.slim.SLIMProcessor
 
SET_T1_VALUE - Static variable in class loci.slim.SLIMProcessor
 
SET_T2_FIX - Static variable in class loci.slim.SLIMProcessor
 
SET_T2_VALUE - Static variable in class loci.slim.SLIMProcessor
 
SET_T3_FIX - Static variable in class loci.slim.SLIMProcessor
 
SET_T3_VALUE - Static variable in class loci.slim.SLIMProcessor
 
SET_THRESHOLD - Static variable in class loci.slim.SLIMProcessor
 
SET_TRANSIENT_START - Static variable in class loci.slim.SLIMProcessor
 
SET_TRANSIENT_STOP - Static variable in class loci.slim.SLIMProcessor
 
SET_WIDTH_PROMPT - Static variable in class loci.slim.SLIMProcessor
 
SET_Z1_FIX - Static variable in class loci.slim.SLIMProcessor
 
SET_Z1_VALUE - Static variable in class loci.slim.SLIMProcessor
 
seta1(double) - Method in class loci.slim.paramSetMacro
 
setA1value(String) - Static method in class loci.slim.SLIMProcessor
 
seta2(double) - Method in class loci.slim.paramSetMacro
 
setA2value(String) - Static method in class loci.slim.SLIMProcessor
 
seta3(double) - Method in class loci.slim.paramSetMacro
 
setA3value(String) - Static method in class loci.slim.SLIMProcessor
 
setAlgorithm(ICurveFitter.FitAlgorithm) - Method in class loci.slim.fitting.FitInfo
Sets implementation & algorithm for the fit.
setAlgorithm(String) - Method in class loci.slim.paramSetMacro
 
setAlgorithmType(String) - Static method in class loci.slim.SLIMProcessor
 
setAnalysisList(String[]) - Method in class loci.slim.fitting.FitInfo
Sets analysis plugin names.
setAnalysisList(String, String) - Static method in class loci.slim.SLIMProcessor
 
setAppendMode() - Static method in class loci.slim.SLIMProcessor
 
setAppendModePixel() - Static method in class loci.slim.SLIMProcessor
 
setAutoRange(boolean) - Method in class loci.slim.histogram.HistogramDataGroup
Sets whether or not histogram should automatically scale to values.
setAutoRange(boolean) - Method in class loci.slim.histogram.HistogramUIPanel
Sets whether to automatically set the LUT range.
setAutoRange(boolean) - Method in interface loci.slim.histogram.IUIPanelListener
User has clicked the auto ranging checkbox.
setBandwidth(double) - Method in class loci.slim.histogram.HistogramPanel
 
setBandwidth(double) - Method in interface loci.slim.histogram.IUIPanelListener
User has entered new bandwidth (used for smoothing).
setBase(double) - Method in class loci.slim.Excitation
Sets the base cursor.
setBin(int) - Method in class loci.slim2.process.HorzCursor
Set bin number.
setBinning(String) - Method in class loci.slim.fitting.FitInfo
Sets binning plugin name.
setBinningFactor(int) - Method in class loci.slim2.process.interactive.BaseFitSettings
Sets binning factor.
setBinnning(String) - Static method in class loci.slim.SLIMProcessor
 
setBins(int[]) - Method in class loci.slim.histogram.HistogramStatistics
Sets histogram bins
setBins(int) - Method in class loci.slim2.process.interactive.BaseFitSettings
Set number of time bins.
setBinValues(int[]) - Method in class loci.slim.histogram.HistogramPanel
Changes histogram counts and redraws.
setBinValues(double[]) - Method in class loci.slim.histogram.HistogramStatistics
Sets values characterizing bins
setBits(boolean[][]) - Method in class loci.slim.mask.Mask
Sets the boolean switches.
setCancel(boolean) - Method in class loci.slim.fitting.FitInfo
Sets whether to cancel current fit.
setChannel(int) - Method in class loci.curvefitter.CurveFitData
 
setChannel(int) - Method in interface loci.curvefitter.ICurveFitData
Sets channel of the fitted pixel.
setChannel(int) - Method in class loci.slim.fitting.FitInfo
Sets current channel
setChannelIndex(int) - Method in class loci.slim.histogram.HistogramDataGroup
Sets current channel index.
setChi2Target(String) - Static method in class loci.slim.SLIMProcessor
Works independent of the GUI, uses its own data type
setChiSqTarget(double) - Method in class loci.slim2.process.interactive.DefaultFitSettings
Sets the target reduced chi square.
setChiSquare(double) - Method in class loci.curvefitter.CurveFitData
 
setChiSquare(double) - Method in interface loci.curvefitter.ICurveFitData
Sets fitted chi square
setChiSquare(double) - Method in class loci.slim.fitting.params.FitResults
 
setChiSquare(double) - Method in interface loci.slim.fitting.params.IFitResults
Sets fitted chi square result.
setChiSquare(double) - Method in class loci.slim.ui.DecayGraph
Sets the reduced chi square.
setChiSquare(double) - Method in interface loci.slim.ui.IDecayGraph
Sets reduced chi square of fit.
setChiSquare(double) - Method in class loci.slim2.fitting.DefaultFitResults
 
setChiSquare(double) - Method in interface loci.slim2.fitting.FitResults
Sets fitted chi square result.
setChiSquare(double) - Method in interface loci.slim2.process.interactive.ui.DecayGraph
Sets reduced chi square of fit.
setChiSquare(double) - Method in class loci.slim2.process.interactive.ui.DefaultDecayGraph
 
setChiSquareDelta(double) - Method in class loci.curvefitter.CurveFitData
 
setChiSquareDelta(double) - Method in interface loci.curvefitter.ICurveFitData
Gets chi square delta.
setChiSquareTarget(double) - Method in class loci.curvefitter.CurveFitData
 
setChiSquareTarget(double) - Method in interface loci.curvefitter.ICurveFitData
Sets chi square target
setChiSquareTarget(double) - Method in class loci.slim.fitting.FitInfo
Sets chi square target for fit.
setChiSquareTarget(double) - Method in class loci.slim.fitting.params.GlobalFitParams
 
setChiSquareTarget(double) - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
setChiSquareTarget(double) - Method in class loci.slim.paramSetMacro
 
setChiSquareTarget(double) - Method in interface loci.slim.ui.IUserInterfacePanel
Sets chi square target for fit.
setChiSquareTarget(double) - Method in class loci.slim.ui.UserInterfacePanel
 
setChiSquareTarget(double) - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
setChiSquareTarget(double) - Method in interface loci.slim2.fitting.GlobalFitParams
 
setChiSquareTarget(double) - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
setChiSquareTarget(double) - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Sets chi square target for fit.
setColorizeGrayScale(boolean) - Method in class loci.slim.fitting.FitInfo
Sets whether to create colorized grayscale images.
setColorModel(IndexColorModel) - Method in class loci.slim.fitting.images.AbstractBaseFittedImage
Sets the color model used to display values.
setColorModel(IndexColorModel) - Method in class loci.slim.fitting.images.ColorizedFittedImage
 
setColorModel(IndexColorModel) - Method in class loci.slim.fitting.images.FloatFittedImage
 
setColorModel(IndexColorModel) - Method in interface loci.slim.fitting.images.IFittedImage
Sets the color model used to display float values.
setColorModel(IndexColorModel) - Method in interface loci.slim.fitting.images.IFittedImageSlice
Changes LUT.
setCombineChannels(boolean) - Method in class loci.slim.histogram.HistogramDataGroup
Sets whether or not histogram should combine all the channels.
setCombineChannels(boolean) - Method in class loci.slim.histogram.HistogramUIPanel
Sets whether to combine all channels.
setCombineChannels(boolean) - Method in interface loci.slim.histogram.IUIPanelListener
User has clicked the combine channels checkbox.
setCombined(boolean) - Method in class loci.slim2.outputset.OutputSetMember
 
setCount(long) - Method in class loci.slim.analysis.HistogramStatistics
 
setCursors(Integer, Integer) - Method in class loci.slim.histogram.HistogramPanel
Changes cursors and redraws.
setCurveFitter(ICurveFitter) - Method in interface loci.slim.fitting.engine.IFittingEngine
Sets the ICurveFitter for the fitting engine to use.
setCurveFitter(ICurveFitter) - Method in class loci.slim.fitting.engine.ThreadedFittingEngine
Sets curve fitter to use.
setCurveFitter(ICurveFitter) - Method in interface loci.slim2.fitting.FittingEngine
Sets the ICurveFitter for the fitting engine to use.
setCurveFitter(ICurveFitter) - Method in class loci.slim2.fitting.ThreadedFittingEngine
 
setData(int, double[], ICurveFitData) - Method in class loci.slim.ui.DecayGraph
Changes (or initializes) all of the charted data.
setData(int, double[], ICurveFitData) - Method in interface loci.slim.ui.IDecayGraph
Changes (or initializes) all of the charted data.
setData(int, double[], FitResults) - Method in interface loci.slim2.process.interactive.ui.DecayGraph
Changes (or initializes) all of the charted data.
setData(int, double[], FitResults) - Method in class loci.slim2.process.interactive.ui.DefaultDecayGraph
 
setDatasetWrapper(LifetimeDatasetWrapper) - Method in class loci.slim2.FittingContext
 
setDataStart(String) - Method in class loci.slim.fitting.cursor.FittingCursor
Sets the start of the data based on a string.
setDataStart(String) - Method in class loci.slim.fitting.cursor.FittingCursorHelper
Sets the data start cursor.
setDataStart(String) - Method in interface loci.slim.fitting.cursor.IFittingCursorUI
Sets the data start cursor.
setDataStart(int) - Method in class loci.slim.fitting.FitInfo
Sets starting data bin of transient.
setDataStart(int) - Method in class loci.slim.fitting.params.GlobalFitParams
 
setDataStart(int) - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
setDataStart(String) - Static method in class loci.slim.SLIMProcessor
Independent of the GUI like setTransientStop and setTransientStart
setDataStart(String) - Method in class loci.slim.ui.UserInterfacePanel
Sets the data start cursor.
setDataStart(int) - Method in class loci.slim2.fitting.DefaultFitResults
 
setDataStart(int) - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
setDataStart(int) - Method in interface loci.slim2.fitting.FitResults
Sets start of data.
setDataStart(int) - Method in interface loci.slim2.fitting.GlobalFitParams
 
setDataStartBin(int) - Method in class loci.slim.fitting.cursor.FittingCursor
Sets the start of the data as a bin number.
setDataStartFromMacro(double) - Method in class loci.slim.paramSetMacro
 
setDataStartIndex(int) - Method in class loci.curvefitter.CurveFitData
 
setDataStartIndex(int) - Method in interface loci.curvefitter.ICurveFitData
Sets fitting start index in transient.
setDataStartIndex(int) - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Set start of data as an index.
setDataStartTime(double) - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Sets start of data as a time.
setDataStartValue(double) - Method in class loci.slim.fitting.cursor.FittingCursor
Sets the start of the data as a time value.
setDecayCursors(HorzCursor[]) - Method in class loci.slim2.process.interactive.BaseFitSettings
Gets horizontal cursor positions on decay.
setDecayVertCursor(VertCursor) - Method in class loci.slim2.process.interactive.BaseFitSettings
Sets vertical cursor position on decay.
setDelayPrompt(double) - Method in class loci.slim.paramSetMacro
 
setDelayPrompt(String) - Static method in class loci.slim.SLIMProcessor
 
setDisplayChannels(boolean) - Method in class loci.slim.histogram.HistogramDataGroup
Sets whether or not histogram should display all channels.
setDisplayChannels(boolean) - Method in class loci.slim.histogram.HistogramUIPanel
Sets whether to display all channels.
setDisplayChannels(boolean) - Method in interface loci.slim.histogram.IUIPanelListener
User has clicked the display channels checkbox.
setDistinguishNonZero(boolean) - Method in class loci.slim2.histogram.HistogramGraph
Sets whether or not to emphasize single or low counts so they can be distinguished from a zero count.
setErrorCode(int) - Method in class loci.slim2.fitting.DefaultFitResults
 
setErrorCode(int) - Method in interface loci.slim2.fitting.FitResults
Sets error code (or 0 for no error).
setEstimator(IFitterEstimator) - Method in class loci.curvefitter.AbstractCurveFitter
 
setEstimator(IFitterEstimator) - Method in interface loci.curvefitter.ICurveFitter
Set fitting estimator.
setEstimator(IFitterEstimator) - Method in class loci.slim.fitting.params.GlobalFitParams
 
setEstimator(IFitterEstimator) - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
setEstimator(IFitterEstimator) - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
setEstimator(IFitterEstimator) - Method in interface loci.slim2.fitting.GlobalFitParams
 
setExcitation(String) - Static method in class loci.slim.SLIMProcessor
 
setExcitation(double[]) - Method in class loci.slim2.process.interactive.BaseFitSettings
Set excitation decay values.
setExcitationFileName(String) - Method in class loci.slim.paramSetMacro
 
setExcitationHorzCursors(HorzCursor[]) - Method in class loci.slim2.process.interactive.BaseFitSettings
Sets horizontal cursor positions on excitation decay.
setExcitationVertCursor(VertCursor) - Method in class loci.slim2.process.interactive.BaseFitSettings
Sets vertical cursor position on excitation decay.
setExcludePixels(boolean) - Method in class loci.slim.histogram.HistogramDataGroup
Sets whether or not we should hide out-of-range pixels.
setExcludePixels(boolean) - Method in class loci.slim.histogram.HistogramUIPanel
Sets whether to hide out of range pixels.
setExcludePixels(boolean) - Method in interface loci.slim.histogram.IUIPanelListener
User has clicked the exclude pixels checkbox.
setExponentNo(String) - Method in class loci.slim.SLIMProcessor
 
setFamily1(boolean) - Method in class loci.slim.histogram.HistogramPanel
 
setFamily2(boolean) - Method in class loci.slim.histogram.HistogramPanel
 
setFamilyStyle1(boolean) - Method in interface loci.slim.histogram.IUIPanelListener
User has clicked the family style 1 checkbox.
setFamilyStyle2(boolean) - Method in interface loci.slim.histogram.IUIPanelListener
User has clicked the family style 1 checkbox.
setFirstQuartile(double) - Method in class loci.slim.analysis.HistogramStatistics
 
setFitAlgorithm(ICurveFitter.FitAlgorithm) - Method in class loci.curvefitter.AbstractCurveFitter
 
setFitAlgorithm(ICurveFitter.FitAlgorithm) - Method in interface loci.curvefitter.ICurveFitter
Set fitting algorithm.
setFitAlgorithm(ICurveFitter.FitAlgorithm) - Method in class loci.slim.fitting.params.GlobalFitParams
 
setFitAlgorithm(ICurveFitter.FitAlgorithm) - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
setFitAlgorithm(ICurveFitter.FitAlgorithm) - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
setFitAlgorithm(ICurveFitter.FitAlgorithm) - Method in interface loci.slim2.fitting.GlobalFitParams
 
setFitAllChannels(boolean) - Method in class loci.slim.fitting.FitInfo
Sets whether or not to fit all channels.
setFitFunction(ICurveFitter.FitFunction) - Method in class loci.curvefitter.AbstractCurveFitter
 
setFitFunction(ICurveFitter.FitFunction) - Method in interface loci.curvefitter.ICurveFitter
Set function we are fitting.
setFitFunction(ICurveFitter.FitFunction) - Method in class loci.slim.fitting.params.GlobalFitParams
 
setFitFunction(ICurveFitter.FitFunction) - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
setFitFunction(ICurveFitter.FitFunction) - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
setFitFunction(ICurveFitter.FitFunction) - Method in interface loci.slim2.fitting.GlobalFitParams
 
setFittedImages(String) - Method in class loci.slim.fitting.FitInfo
Sets list of fitted images to display.
setFittedImages(String) - Method in interface loci.slim2.process.FitSettings
 
setFittedImages(String) - Method in class loci.slim2.process.interactive.BaseFitSettings
 
setFittedImagesType(String) - Static method in class loci.slim.SLIMProcessor
 
setFittedParameterCount(int) - Method in interface loci.slim.ui.IUserInterfacePanel
Sets number of fitted parameters after a successful fit.
setFittedParameterCount(int) - Method in class loci.slim.ui.UserInterfacePanel
 
setFittedParameterCount(int) - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
setFittedParameterCount(int) - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Sets number of fitted parameters after a successful fit.
setFittingCursor(FittingCursor) - Method in class loci.slim.fitting.cursor.FittingCursorHelper
Sets the fitting cursor that is keeping track of cursor settings.
setFittingCursor(FittingCursor) - Method in class loci.slim.ui.DecayGraph
Sets the fitting cursor, which keeps track of prompt and transient start and stop cursors.
setFittingCursor(FittingCursor) - Method in class loci.slim.ui.ExcitationGraph
Sets the fitting cursor.
setFittingCursor(FittingCursor) - Method in interface loci.slim.ui.IDecayGraph
Changes (or initializes) the cursor (start/stop bins/values) for the fit.
setFittingCursor(FittingCursor) - Method in interface loci.slim2.process.interactive.ui.DecayGraph
Changes (or initializes) the cursor (start/stop bins/values) for the fit.
setFittingCursor(FittingCursor) - Method in class loci.slim2.process.interactive.ui.DefaultDecayGraph
 
setFittingCursor(FittingCursor) - Method in class loci.slim2.process.interactive.ui.DefaultExcitationGraph
 
setFittingCursor(FittingCursor) - Method in interface loci.slim2.process.interactive.ui.ExcitationGraph
Sets the fitting cursor.
setFittingCursorUI(IFittingCursorUI) - Method in class loci.slim.fitting.cursor.FittingCursorHelper
Sets the UI source and destination of fitting cursor strings, e.g.
setFree(boolean[]) - Method in class loci.curvefitter.AbstractCurveFitter
 
setFree(boolean[]) - Method in interface loci.curvefitter.ICurveFitter
Sets which parameters are free (vs.
setFree(boolean[]) - Method in class loci.slim.fitting.FitInfo
Sets which parameters aren't fixed.
setFree(boolean[]) - Method in class loci.slim.fitting.params.GlobalFitParams
 
setFree(boolean[]) - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
setFree(boolean[]) - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
setFree(boolean[]) - Method in interface loci.slim2.fitting.GlobalFitParams
 
setFunction(ICurveFitter.FitFunction) - Method in class loci.slim.fitting.FitInfo
Sets function to be fitted.
setFunction(String) - Method in class loci.slim.paramSetMacro
 
setFunctionParameters(int, double[]) - Method in interface loci.slim.ui.IUserInterfacePanel
Sets the parameters of the fit by function.
setFunctionParameters(int, double[]) - Method in class loci.slim.ui.UserInterfacePanel
This version is used to initialize the parameters.
setFunctionParameters(int, double[]) - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
This version is used to initialize the parameters.
setFunctionParameters(int, double[]) - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Sets the parameters of the fit by function.
setFunctionType(String) - Static method in class loci.slim.SLIMProcessor
 
setGlobalFitParams(GlobalFitParams) - Method in interface loci.slim2.process.FitSettings
 
setGlobalFitParams(GlobalFitParams) - Method in class loci.slim2.process.interactive.BaseFitSettings
 
setGrayscaleDataset(LifetimeGrayscaleDataset) - Method in class loci.slim2.FittingContext
 
setGrayscaleDisplay(Display<?>) - Method in class loci.slim2.FittingContext
 
seth1(double) - Method in class loci.slim.paramSetMacro
 
setH1value(String) - Static method in class loci.slim.SLIMProcessor
 
setHasPrompt(boolean) - Method in class loci.slim.fitting.cursor.FittingCursor
Returns whether or not a prompt has been loaded.
setHasPrompt(boolean) - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Returns whether or not a prompt has been loaded.
setHistogram(long[]) - Method in class loci.slim.analysis.HistogramStatistics
 
setHistogramCount(long) - Method in class loci.slim.analysis.HistogramStatistics
 
setHistogramData(HistogramDataGroup) - Method in class loci.slim.histogram.HistogramTool
This method should be called whenever a new set of histogram values is to be displayed (i.e.
setIndexColorModel(IndexColorModel) - Method in class loci.slim.fitting.FitInfo
Sets color model for fitted images.
setInputLocation(int[]) - Method in class loci.slim.ChunkyPixel
Sets the location of the pixel in the input image.
setInstrumentResponse(double[]) - Method in class loci.curvefitter.AbstractCurveFitter
 
setInstrumentResponse(double[]) - Method in interface loci.curvefitter.ICurveFitter
Set instrument response data.
setListener(IErrorListener) - Method in class loci.slim.fitting.ErrorManager
Defines an error mask listener.
setListener(ISelectListener) - Method in class loci.slim.GrayScaleImage
Sets a listener for when the user clicks on the image.
setListener(IHistogramDataListener) - Method in class loci.slim.histogram.HistogramDataGroup
Sets a listener for histogram data changes.
setListener(IHistogramPanelListener) - Method in class loci.slim.histogram.HistogramPanel
Sets a listener for dragging minimum and maximum.
setListener(IUIPanelListener) - Method in class loci.slim.histogram.HistogramUIPanel
Sets a listener for this UI panel.
setListener(ISelectListener) - Method in interface loci.slim.IGrayScaleImage
Sets a listener for when the user clicks on the image.
setListener(IUserInterfacePanelListener) - Method in interface loci.slim.ui.IUserInterfacePanel
Sets the listener
setListener(IUserInterfacePanelListener) - Method in class loci.slim.ui.UserInterfacePanel
 
setListener(UserInterfacePanelListener) - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
setListener(UserInterfacePanelListener) - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Sets the listener
setLogarithmic(boolean) - Method in class loci.slim.ui.DecayGraph
 
setLogarithmic(boolean) - Method in class loci.slim2.histogram.HistogramGraph
Sets whether to graph logarithms.
setLogarithmic(boolean) - Method in class loci.slim2.process.interactive.ui.DefaultDecayGraph
 
setLogarithmicDisplay(boolean) - Method in class loci.slim.histogram.HistogramPanel
 
setLogarithmicDisplay(boolean) - Method in interface loci.slim.histogram.IUIPanelListener
User has clicked the logarithmic display checkbox.
setLUT(LUT) - Method in class loci.slim.histogram.ColorBarPanel
Changes the color look-up table and redraws.
setMaskGroup(IMaskGroup) - Method in class loci.slim.histogram.HistogramDataNode
Assigns a mask group.
setMax(double) - Method in class loci.slim.analysis.HistogramStatistics
 
setMaximum(double) - Method in class loci.slim2.histogram.DataHistogramCommand
 
setMaxRange(double) - Method in class loci.slim.analysis.HistogramStatistics
 
setMean(double) - Method in class loci.slim.analysis.HistogramStatistics
 
setMedian(double) - Method in class loci.slim.analysis.HistogramStatistics
 
setMin(double) - Method in class loci.slim.analysis.HistogramStatistics
 
setMinAndMax(double, double) - Method in class loci.slim.fitting.images.ColorizedFittedImage
 
setMinAndMax(double, double) - Method in class loci.slim.fitting.images.FloatFittedImage
 
setMinAndMax(double, double) - Method in interface loci.slim.fitting.images.IFittedImageSlice
Sets the minimum and maximum values for the LUT range.
setMinimum(double) - Method in class loci.slim2.histogram.DataHistogramCommand
 
setMinMax(double, double, double, double) - Method in class loci.slim.histogram.ColorBarPanel
Changes the values and redraws.
setMinMaxLUT(double, double) - Method in class loci.slim.histogram.ColorBarPanel
Changes the LUT ranges and redraws.
setMinMaxLUT(double, double) - Method in class loci.slim.histogram.HistogramDataGroup
Sets minimum and maximum extents of the LUT.
setMinMaxLUT(double, double) - Method in class loci.slim.histogram.HistogramUIPanel
Called when the user sets new cursors on the histogram panel.
setMinMaxLUT(double, double) - Method in interface loci.slim.histogram.IUIPanelListener
User has entered new min/max LUT value.
setMinMaxLUTPixels(int, int) - Method in interface loci.slim.histogram.IHistogramPanelListener
Sets a new minimum and maximum cursor on the histogram panel.
setMinMaxView(double, double) - Method in class loci.slim.histogram.HistogramDataGroup
Sets minimum and maximum extents of the view.
setMinRange(double) - Method in class loci.slim.analysis.HistogramStatistics
 
setNoiseModel(ICurveFitter.NoiseModel) - Method in class loci.curvefitter.AbstractCurveFitter
 
setNoiseModel(ICurveFitter.NoiseModel) - Method in interface loci.curvefitter.ICurveFitter
Sets noise model for fit.
setNoiseModel(ICurveFitter.NoiseModel) - Method in class loci.slim.fitting.FitInfo
Sets noise model for fit.
setNoiseModel(ICurveFitter.NoiseModel) - Method in class loci.slim.fitting.params.GlobalFitParams
 
setNoiseModel(ICurveFitter.NoiseModel) - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
setNoiseModel(String) - Static method in class loci.slim.SLIMProcessor
 
setNoiseModel(ICurveFitter.NoiseModel) - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
setNoiseModel(ICurveFitter.NoiseModel) - Method in interface loci.slim2.fitting.GlobalFitParams
 
setOutputLocation(int[]) - Method in class loci.slim.ChunkyPixel
Sets the location of the pixel in the output image.
setParameterCount(int) - Method in class loci.slim.fitting.FitInfo
Sets number of fitted parameters after a successful fit.
setParameters(double[]) - Method in class loci.slim.fitting.FitInfo
Sets the parameters of the fit
setParameters(double[], double) - Method in interface loci.slim.ui.IUserInterfacePanel
Sets the parameters of the fit
setParameters(double[], double) - Method in class loci.slim.ui.UserInterfacePanel
 
setParameters(double[], double) - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
setParameters(double[], double) - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Sets the parameters of the fit
setParams(double[]) - Method in class loci.curvefitter.CurveFitData
 
setParams(double[]) - Method in interface loci.curvefitter.ICurveFitData
Sets parameters of the fit.
setParams(double[]) - Method in class loci.slim.fitting.params.FitResults
 
setParams(double[]) - Method in interface loci.slim.fitting.params.IFitResults
Sets fitted parameters.
setParams(double[]) - Method in interface loci.slim.fitting.params.ILocalFitParams
 
setParams(double[]) - Method in class loci.slim.fitting.params.LocalFitParams
 
setParams(double[]) - Method in class loci.slim2.fitting.DefaultFitResults
 
setParams(double[]) - Method in class loci.slim2.fitting.DefaultLocalFitParams
 
setParams(double[]) - Method in interface loci.slim2.fitting.FitResults
Sets fitted parameters.
setParams(double[]) - Method in interface loci.slim2.fitting.LocalFitParams
 
setPhotonCount(int) - Method in class loci.slim2.fitting.DefaultFitResults
 
setPhotonCount(int) - Method in interface loci.slim2.fitting.FitResults
Sets total photon count in decay.
setPhotons(int) - Method in class loci.slim.ui.DecayGraph
Sets the displayed photon count.
setPhotons(int) - Method in interface loci.slim.ui.IDecayGraph
Sets number of photons in fit.
setPhotons(int) - Method in interface loci.slim2.process.interactive.ui.DecayGraph
Sets number of photons in fit.
setPhotons(int) - Method in class loci.slim2.process.interactive.ui.DefaultDecayGraph
 
setPhotons(double) - Method in class loci.slim2.process.VertCursor
Sets vertical cursor position.
setPixel(int[], double[]) - Method in interface loci.slim.fitting.IFittedImage
Sets pixel value at location.
setPixel(int[], double[]) - Method in class loci.slim.OutputImageWrapper
 
setPixel(long[]) - Method in class loci.slim2.process.interactive.grayscale.GrayscaleDisplay
 
setPixels(int) - Method in class loci.curvefitter.CurveFitData
 
setPixels(int) - Method in interface loci.curvefitter.ICurveFitData
Sets how many pixels went into this data point.
setPixelValue(double[], long[]) - Method in class loci.slim2.outputset.OutputSet
Inputs an array of values at a given position.
setPixelValue(double[], long[], int[]) - Method in class loci.slim2.outputset.OutputSet
Inputs an array of values at a given position.
setPixelValue(double[], long[]) - Method in class loci.slim2.outputset.OutputSetMember
 
setPixelValue(double[], long[], int[]) - Method in class loci.slim2.outputset.OutputSetMember
 
setPixelValue(double, long[]) - Method in class loci.slim2.outputset.OutputSetMember
 
setPoint(double[]) - Method in class loci.slim2.process.interactive.grayscale.CrossHairOverlay
Sets the point.
setPrompBaseLine(String) - Static method in class loci.slim.SLIMProcessor
 
setPrompt(double[]) - Method in class loci.slim.fitting.FitInfo
Sets prompt or instrument response function.
setPrompt(double[]) - Method in class loci.slim.fitting.params.GlobalFitParams
 
setPrompt(double[]) - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
setPrompt(double[]) - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
setPrompt(double[]) - Method in interface loci.slim2.fitting.GlobalFitParams
 
setPromptBaseline(String) - Method in class loci.slim.fitting.cursor.FittingCursor
Sets the baseline of the prompt based on a string.
setPromptBaseline(String) - Method in class loci.slim.fitting.cursor.FittingCursorHelper
Sets the prompt baseline cursor as a string.
setPromptBaseline(String) - Method in interface loci.slim.fitting.cursor.IFittingCursorUI
Sets the prompt baseline cursor.
setPromptBaseLine(double) - Method in class loci.slim.paramSetMacro
 
setPromptBaseline(String) - Method in class loci.slim.ui.UserInterfacePanel
Sets the excitation baseline.
setPromptBaselineValue(double) - Method in class loci.slim.fitting.cursor.FittingCursor
Sets the baseline of the prompt as a value.
setPromptBaselineValue(double) - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Sets the baseline of the prompt.
setPromptDelay(String) - Method in class loci.slim.fitting.cursor.FittingCursor
Sets the start of the prompt based on a prompt delay string.
setPromptDelay(String) - Method in class loci.slim.fitting.cursor.FittingCursorHelper
Sets the prompt delay cursor.
setPromptDelay(String) - Method in interface loci.slim.fitting.cursor.IFittingCursorUI
Sets the prompt delay cursor.
setPromptDelay(String) - Method in class loci.slim.ui.UserInterfacePanel
Sets the excitation delay cursor.
setPromptDelayIndex(int) - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Sets the prompt delay as a bin index.
setPromptDelayTime(double) - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Sets the prompt delay as a time value.
setPromptStartBin(int) - Method in class loci.slim.fitting.cursor.FittingCursor
Sets the start of the prompt as a bin number.
setPromptStartIndex(int) - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Sets the start of the prompt as a bin index.
setPromptStartTime(double) - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Sets the start of the prompt as a time value.
setPromptStartValue(double) - Method in class loci.slim.fitting.cursor.FittingCursor
Sets the start of the prompt as a time value.
setPromptStopBin(int) - Method in class loci.slim.fitting.cursor.FittingCursor
Sets the end of the prompt as a bin number.
setPromptStopIndex(int) - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Sets the end of the prompt as an index.
setPromptStopTime(double) - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Sets the end of the prompt as a time value.
setPromptStopValue(double) - Method in class loci.slim.fitting.cursor.FittingCursor
Sets the end of the prompt as a time value.
setPromptWidth(String) - Method in class loci.slim.fitting.cursor.FittingCursor
Sets the end of the prompt based on a prompt width string.
setPromptWidth(String) - Method in class loci.slim.fitting.cursor.FittingCursorHelper
Sets the prompt width cursor.
setPromptWidth(String) - Method in interface loci.slim.fitting.cursor.IFittingCursorUI
Sets the prompt width cursor.
setPromptWidth(String) - Method in class loci.slim.ui.UserInterfacePanel
Sets the excitation width cursor.
setPromptWidthIndex(int) - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Sets the end of the prompt based on a prompt width bin index.
setPromptWidthTime(double) - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Sets the end of the prompt based on a prompt width time.
setQuartileIndices(int[]) - Method in class loci.slim.histogram.HistogramStatistics
Sets the indices of the quartile values
setQuartiles(double[]) - Method in class loci.slim.histogram.HistogramStatistics
Sets the quartile values
setRandomAccess(RandomAccess<T>) - Method in class loci.slim2.outputset.OutputSetMember
 
setRectangle(Rectangle) - Method in class imagej.charts.cursors.Cursor
 
setRectangle(Rectangle) - Method in interface imagej.charts.IChartRectangleListener
 
setRefineFit(boolean) - Method in class loci.slim.fitting.FitInfo
Sets whether to start next fit with results of last fit.
setRegion(ICurveFitter.FitRegion) - Method in class loci.slim.fitting.FitInfo
Sets region the fit applies to.
setRegion(ICurveFitter.FitRegion) - Method in interface loci.slim.ui.IUserInterfacePanel
Sets region the fit applies to.
setRegion(ICurveFitter.FitRegion) - Method in class loci.slim.ui.UserInterfacePanel
 
setRegionType(String) - Static method in class loci.slim.SLIMProcessor
 
setShowBins(boolean) - Method in class loci.slim.fitting.cursor.FittingCursor
Sets whether the UI will display bins or time values.
setShowBins(boolean) - Method in class loci.slim.fitting.cursor.FittingCursorHelper
Sets whether to show bins or time values for cursors.
setShowBins(boolean) - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Sets whether the UI will display bins or time values.
setSig(double[]) - Method in class loci.curvefitter.CurveFitData
 
setSig(double[]) - Method in interface loci.curvefitter.ICurveFitData
Set error for the fit data.
setSig(double[]) - Method in interface loci.slim.fitting.params.ILocalFitParams
 
setSig(double[]) - Method in class loci.slim.fitting.params.LocalFitParams
 
setSig(double[]) - Method in class loci.slim2.fitting.DefaultLocalFitParams
 
setSig(double[]) - Method in interface loci.slim2.fitting.LocalFitParams
 
setSmoothing(boolean) - Method in class loci.slim.histogram.HistogramPanel
 
setSmoothing(boolean) - Method in interface loci.slim.histogram.IUIPanelListener
User has clicked the smoothing checkbox.
setStandardDeviation(double) - Method in class loci.slim.analysis.HistogramStatistics
 
setStart(int) - Method in class loci.slim.Excitation
Sets start cursor.
setStartPrompt(int) - Method in class loci.slim.fitting.FitInfo
Sets start of prompt.
setStartPrompt(int) - Method in class loci.slim.fitting.params.GlobalFitParams
 
setStartPrompt(int) - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
setStartPrompt(int) - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
setStartPrompt(int) - Method in interface loci.slim2.fitting.GlobalFitParams
 
setStartStop(double, double, double) - Method in class loci.slim.ui.DecayGraph
Changes or initializes the start and stop vertical bars.
setStartStop(double, double, double) - Method in interface loci.slim.ui.IDecayGraph
Changes (or initializes) the start and stop vertical bars.
setStartStop(double, double, double) - Method in interface loci.slim2.process.interactive.ui.DecayGraph
Changes (or initializes) the start and stop vertical bars.
setStartStop(double, double, double) - Method in class loci.slim2.process.interactive.ui.DefaultDecayGraph
 
setStartStopBaseProportion(double, double, double) - Method in class loci.slim.ui.ExcitationGraph
Sets stop and start time bins, based on proportions 0.0..1.0.
setStartStopBaseProportion(double, double, double) - Method in class loci.slim2.process.interactive.ui.DefaultExcitationGraph
Sets stop and start time bins, based on proportions 0.0..1.0.
setStartStopProportion(double, double, double) - Method in class loci.slim.ui.DecayGraph
Sets stop and start time bins, based on proportions 0.0..1.0.
setStartStopProportion(double, double, double) - Method in class loci.slim2.process.interactive.ui.DefaultDecayGraph
 
setStatistics(HistogramStatistics) - Method in class loci.slim.histogram.HistogramPanel
 
setStdDev(double[]) - Method in class loci.slim.histogram.HistogramStatistics
Sets standard deviation values
setStdDevIndices(int[]) - Method in class loci.slim.histogram.HistogramStatistics
Sets indices of standard deviation values
setStop(int) - Method in class loci.slim.Excitation
Sets the stop cursor.
setStopPrompt(int) - Method in class loci.slim.fitting.FitInfo
Sets start of prompt.
setStopPrompt(int) - Method in class loci.slim.fitting.params.GlobalFitParams
 
setStopPrompt(int) - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
setStopPrompt(int) - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
setStopPrompt(int) - Method in interface loci.slim2.fitting.GlobalFitParams
 
sett1(double) - Method in class loci.slim.paramSetMacro
 
setT1value(String) - Static method in class loci.slim.SLIMProcessor
 
sett2(double) - Method in class loci.slim.paramSetMacro
 
setT2value(String) - Static method in class loci.slim.SLIMProcessor
 
sett3(double) - Method in class loci.slim.paramSetMacro
 
setT3value(String) - Static method in class loci.slim.SLIMProcessor
 
setThersholdValue(String) - Static method in class loci.slim.SLIMProcessor
Works independent of the GUI, uses its own data type
setThirdQuartile(double) - Method in class loci.slim.analysis.HistogramStatistics
 
setThreads(int) - Method in class imagej.thread.ThreadPool
Sets number of threads to use.
setThreads(int) - Method in interface loci.slim.fitting.engine.IFittingEngine
Sets number of threads to use in a fit.
setThreads(int) - Method in class loci.slim.fitting.engine.ThreadedFittingEngine
Sets number of threads to use.
setThreads(int) - Method in interface loci.slim2.fitting.FittingEngine
Sets number of threads to use in a fit.
setThreads(int) - Method in class loci.slim2.fitting.ThreadedFittingEngine
 
setThreshold(int) - Method in class loci.slim.fitting.FitInfo
Sets photon count threshold to fit a pixel.
setThreshold(int) - Method in interface loci.slim.ui.IUserInterfacePanel
Sets photon count threshold to fit a pixel.
setThreshold(int) - Method in class loci.slim.ui.UserInterfacePanel
 
setThreshold(int, int) - Method in class loci.slim2.process.interactive.grayscale.GrayscaleDisplay
 
setThreshold(int, int) - Method in class loci.slim2.process.interactive.grayscale.ThresholdDisplayOverlay
Sets the threshold value.
setThresholdListener(IThresholdUpdate) - Method in interface loci.slim.ui.IUserInterfacePanel
Sets the threshold listener.
setThresholdListener(IThresholdUpdate) - Method in class loci.slim.ui.UserInterfacePanel
 
setThresholdListener(ThresholdUpdate) - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
setThresholdListener(ThresholdUpdate) - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Sets the threshold listener.
setThresholdMaximum(int) - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
setThresholdMaximum(int) - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Sets photon count threshold maximum to fit a pixel.
setThresholdMinimum(int) - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
setThresholdMinimum(int) - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Sets photon count threshold minimum to fit a pixel.
setThresholdValue(int) - Method in class loci.slim.paramSetMacro
 
setTime(double) - Method in class loci.slim2.process.HorzCursor
Set time value.
setTimeInc(double) - Method in class loci.slim2.process.interactive.BaseFitSettings
Set time increment per time bin.
setTitle(String) - Method in class loci.slim.analysis.HistogramStatistics
 
setTitle(String) - Method in class loci.slim.fitted.AbstractFittedValue
 
setTitle(String) - Method in interface loci.slim.fitted.FittedValue
Sets a title for a particular fitted value.
setTitle(String) - Method in class loci.slim.ui.DecayGraph
Set or change the title.
setTitle(String) - Method in interface loci.slim.ui.IDecayGraph
Changes (or initializes) the title of the graph.
setTitle(String) - Method in interface loci.slim2.process.interactive.ui.DecayGraph
Changes (or initializes) the title of the graph.
setTitle(String) - Method in class loci.slim2.process.interactive.ui.DefaultDecayGraph
 
setTransEndIndex(int) - Method in class loci.curvefitter.CurveFitData
 
setTransEndIndex(int) - Method in interface loci.curvefitter.ICurveFitData
Sets end index in transient.
setTransient(double[]) - Method in class loci.slim2.fitting.DefaultFitResults
 
setTransient(double[]) - Method in interface loci.slim2.fitting.FitResults
Sets incoming transient data.
setTransientStart(String) - Method in class loci.slim.fitting.cursor.FittingCursor
Sets the start of the transient based on a string.
setTransientStart(String) - Method in class loci.slim.fitting.cursor.FittingCursorHelper
Sets the transient start cursor.
setTransientStart(String) - Method in interface loci.slim.fitting.cursor.IFittingCursorUI
Sets the transient start cursor.
setTransientStart(int) - Method in class loci.slim.fitting.FitInfo
Sets starting bin of transient.
setTransientStart(int) - Method in class loci.slim.fitting.params.GlobalFitParams
 
setTransientStart(int) - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
setTransientStart(String) - Static method in class loci.slim.SLIMProcessor
This macro does not update the GUI, instead updates a value for transient start time and uses that value for fitting
setTransientStart(String) - Method in class loci.slim.ui.UserInterfacePanel
Sets the transient start cursor.
setTransientStart(int) - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
setTransientStart(int) - Method in interface loci.slim2.fitting.GlobalFitParams
 
setTransientStartBin(int) - Method in class loci.slim.fitting.cursor.FittingCursor
Sets the start of the transient as a bin number.
setTransientStartFromMacro(double) - Method in class loci.slim.paramSetMacro
 
setTransientStartIndex(int) - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Sets the start of the transient as an index.
setTransientStartTime(double) - Method in class loci.slim2.process.interactive.cursor.FittingCursor
 
setTransientStartValue(double) - Method in class loci.slim.fitting.cursor.FittingCursor
Sets the start of the transient as a time value.
setTransientStop(String) - Method in class loci.slim.fitting.cursor.FittingCursor
Sets the end of the transient based on a string.
setTransientStop(String) - Method in class loci.slim.fitting.cursor.FittingCursorHelper
Sets the transient end cursor.
setTransientStop(String) - Method in interface loci.slim.fitting.cursor.IFittingCursorUI
Sets the transient end cursor.
setTransientStop(int) - Method in class loci.slim.fitting.FitInfo
Sets stopping bin of transient.
setTransientStop(int) - Method in class loci.slim.fitting.params.GlobalFitParams
 
setTransientStop(int) - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
setTransientStop(String) - Static method in class loci.slim.SLIMProcessor
This macro calling function works independent for the GUI, updates its own data structure value
setTransientStop(String) - Method in class loci.slim.ui.UserInterfacePanel
Sets the transient end cursor.
setTransientStop(int) - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
setTransientStop(int) - Method in interface loci.slim2.fitting.GlobalFitParams
 
setTransientStopBin(int) - Method in class loci.slim.fitting.cursor.FittingCursor
Sets the end of the transient as a bin number.
setTransientStopFromMacro(double) - Method in class loci.slim.paramSetMacro
 
setTransientStopIndex(int) - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Sets end of data as an index.
setTransientStopTime(double) - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Sets end of data as a time.
setTransientStopValue(double) - Method in class loci.slim.fitting.cursor.FittingCursor
Sets the end of the transient as a time value.
setTransStart(int) - Method in class loci.slim2.fitting.DefaultFitResults
 
setTransStart(int) - Method in interface loci.slim2.fitting.FitResults
Sets start of transient (bin index in decay).
setTransStartIndex(int) - Method in class loci.curvefitter.CurveFitData
 
setTransStartIndex(int) - Method in interface loci.curvefitter.ICurveFitData
Sets start index in transient.
setTransStop(int) - Method in class loci.slim2.fitting.DefaultFitResults
 
setTransStop(int) - Method in interface loci.slim2.fitting.FitResults
Sets end of transient.
setup(ICurveFitter, IGlobalFitParams, ILocalFitParams) - Method in class loci.slim.fitting.callable.FittingEngineCallable
 
setup(ICurveFitter, IGlobalFitParams, ILocalFitParams) - Method in interface loci.slim.fitting.callable.IFittingEngineCallable
Set up for a fit.
setup(ICurveFitter, GlobalFitParams, LocalFitParams) - Method in class loci.slim2.fitting.DefaultFittingCallable
 
setup(ICurveFitter, GlobalFitParams, LocalFitParams) - Method in interface loci.slim2.fitting.FittingCallable
Set up for a fit.
setUpFit(String, FittedImageFitter.FittedImageType[], int, int, int[], IndexColorModel, int, boolean, IGrayScaleImage) - Method in class loci.slim.fitting.images.FittedImageFitter
 
setView(DatasetView) - Method in class loci.slim2.histogram.DataHistogramCommand
 
setWidthPrompt(String) - Static method in class loci.slim.SLIMProcessor
 
setX(int) - Method in class loci.curvefitter.CurveFitData
 
setX(int) - Method in interface loci.curvefitter.ICurveFitData
Sets x location of the fitted pixel.
setX(int) - Method in class loci.slim.fitting.FitInfo
Sets pixel x.
setX(int) - Method in interface loci.slim.ui.IUserInterfacePanel
Sets pixel x.
setX(int) - Method in class loci.slim.ui.UserInterfacePanel
 
setX(int) - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
setX(int) - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Sets pixel x.
setXInc(double) - Method in class loci.curvefitter.AbstractCurveFitter
 
setXInc(double) - Method in interface loci.curvefitter.ICurveFitter
Set increment along x axis (evenly spaced).
setXInc(double) - Method in class loci.slim.fitting.FitInfo
Sets x increment for each bin.
setXInc(double) - Method in class loci.slim.fitting.params.GlobalFitParams
 
setXInc(double) - Method in interface loci.slim.fitting.params.IGlobalFitParams
 
setXInc(double) - Method in class loci.slim2.fitting.DefaultGlobalFitParams
 
setXInc(double) - Method in interface loci.slim2.fitting.GlobalFitParams
 
setY(int) - Method in class loci.curvefitter.CurveFitData
 
setY(int) - Method in interface loci.curvefitter.ICurveFitData
Sets y location of the fitted pixel.
setY(int) - Method in class loci.slim.fitting.FitInfo
Sets pixel y.
setY(double[]) - Method in interface loci.slim.fitting.params.ILocalFitParams
 
setY(double[]) - Method in class loci.slim.fitting.params.LocalFitParams
 
setY(int) - Method in interface loci.slim.ui.IUserInterfacePanel
Sets pixel y.
setY(int) - Method in class loci.slim.ui.UserInterfacePanel
 
setY(double[]) - Method in class loci.slim2.fitting.DefaultLocalFitParams
 
setY(double[]) - Method in interface loci.slim2.fitting.LocalFitParams
 
setY(int) - Method in class loci.slim2.process.interactive.ui.DefaultUserInterfacePanel
 
setY(int) - Method in interface loci.slim2.process.interactive.ui.UserInterfacePanel
Sets pixel y.
setYCount(double[]) - Method in class loci.curvefitter.CurveFitData
 
setYCount(double[]) - Method in interface loci.curvefitter.ICurveFitData
Set input data for the fit.
setYFitted(double[]) - Method in class loci.curvefitter.CurveFitData
 
setYFitted(double[]) - Method in interface loci.curvefitter.ICurveFitData
Sets fitted data from the fit.
setYFitted(double[]) - Method in class loci.slim.fitting.params.FitResults
 
setYFitted(double[]) - Method in interface loci.slim.fitting.params.IFitResults
Sets fitted curve.
setYFitted(double[]) - Method in interface loci.slim.fitting.params.ILocalFitParams
 
setYFitted(double[]) - Method in class loci.slim.fitting.params.LocalFitParams
 
setYFitted(double[]) - Method in class loci.slim2.fitting.DefaultFitResults
 
setYFitted(double[]) - Method in class loci.slim2.fitting.DefaultLocalFitParams
 
setYFitted(double[]) - Method in interface loci.slim2.fitting.FitResults
Sets fitted curve.
setYFitted(double[]) - Method in interface loci.slim2.fitting.LocalFitParams
 
setz1(double) - Method in class loci.slim.paramSetMacro
 
setZ1value(String) - Static method in class loci.slim.SLIMProcessor
 
show(boolean) - Method in class loci.slim.histogram.HistogramTool
Initializer, handles layout and wiring.
showCursor(int, int) - Method in class loci.slim.GrayScaleImage
 
showCursor(int, int) - Method in interface loci.slim.ICursorListener
Show the cursor at fitted point.
showCursor(int, int) - Method in interface loci.slim2.process.interactive.ui.PixelPicker
Show the cursor at fitted point.
showLowCountsChanged() - Method in class loci.slim2.histogram.DataHistogramCommand
Called when show low counts changes.
shutdown() - Method in class imagej.thread.ThreadPool
Shut down the thread pool.
shutdown() - Method in interface loci.slim.fitting.engine.IFittingEngine
Shuts down the fitting engine.
shutdown() - Method in class loci.slim.fitting.engine.ThreadedFittingEngine
Cancel fit or done fitting.
shutdown() - Method in interface loci.slim2.fitting.FittingEngine
Shuts down the fitting engine.
shutdown() - Method in class loci.slim2.fitting.ThreadedFittingEngine
 
SIGMA - Static variable in interface loci.slim.fitted.FittedValue
 
SIGMA - Static variable in interface loci.slim2.process.interactive.ui.UserInterfacePanel
 
SimpleFittedImage - Class in loci.slim.fitting.images
Simple image that just displays one of the input parameters.
SimpleFittedImage(String, int[], IndexColorModel, int, boolean, IGrayScaleImage, IMaskGroup[]) - Constructor for class loci.slim.fitting.images.SimpleFittedImage
Constructor, giving index of input parameter to display
SINGLE - Static variable in class imagej.charts.cursors.Cursor
 
SINGLE - Static variable in class loci.slim2.experimental.EnderleinErdmann
 
SINGLE_FITTED_IMAGE_ITEMS - Static variable in class loci.slim.ui.UserInterfacePanel
 
size() - Method in class loci.slim.ChunkyPixelTableImpl
 
size() - Method in interface loci.slim.IChunkyPixelTable
Get table size.
SLIM_PlugIn - Class in loci.slim
TODO
SLIM_PlugIn() - Constructor for class loci.slim.SLIM_PlugIn
 
SLIMAnalysis - Class in loci.slim.analysis
This class runs post-fit analysis on the fitted image.
SLIMAnalysis() - Constructor for class loci.slim.analysis.SLIMAnalysis
Constructor, gets list of potential analysis plugins.
SLIMAnalyzer - Interface in loci.slim.analysis
A plugin for analyzing the results of a SLIM Curve fit.
SLIMBinner - Interface in loci.slim.preprocess
Interface for an input processor that does binning.
SLIMBinning - Class in loci.slim.preprocess
Helper class for managing binner plugins.
SLIMBinning() - Constructor for class loci.slim.preprocess.SLIMBinning
 
SLIMCurveFitter - Class in loci.curvefitter
This class is a Java wrapper around the SLIMCurve fitting C code.
SLIMCurveFitter() - Constructor for class loci.curvefitter.SLIMCurveFitter
 
SLIMCurveFitter.CLibrary - Interface in loci.curvefitter
This interface supports loading the library using JNA.
SLIMPlugin<T extends RealType<T> & NativeType<T>> - Class in loci.slim2
A command used to analyze time-based lifetime images.
SLIMPlugin() - Constructor for class loci.slim2.SLIMPlugin
 
SLIMProcessor<T extends RealType<T>> - Class in loci.slim
SLIMProcessor is the main class of the SLIM Curve plugin for ImageJ.
SLIMProcessor() - Constructor for class loci.slim.SLIMProcessor
 
SpringUtilities - Class in loci.slim.ui
A 1.4 file that provides utility methods for creating form- or grid-style layouts with SpringLayout.
SpringUtilities() - Constructor for class loci.slim.ui.SpringUtilities
 
SpringUtilities - Class in loci.slim2.process.interactive.ui
A 1.4 file that provides utility methods for creating form- or grid-style layouts with SpringLayout.
SpringUtilities() - Constructor for class loci.slim2.process.interactive.ui.SpringUtilities
 
SQUARE - Static variable in interface loci.slim.fitted.FittedValue
 
SQUARE - Static variable in interface loci.slim2.process.interactive.ui.UserInterfacePanel
 
SquareBinner - Class in loci.slim.preprocess
This class bins the image.
SquareBinner() - Constructor for class loci.slim.preprocess.SquareBinner
 
start() - Method in class loci.slim.analysis.batch.ExportBatchHistogram
 
start() - Method in class loci.slim.analysis.batch.ExportBatchHistogram2
 
START_SLIM_CURVE - Static variable in class loci.slim.SLIMProcessor
 
startBatch() - Static method in class loci.slim.SLIM_PlugIn
Starts up batch processing.
startBatch() - Method in class loci.slim.SLIMProcessor
Start batch processing.
startBatchHisto() - Static method in class loci.slim.SLIM_PlugIn
Starts up batch processing.
startBatchHisto() - Method in class loci.slim.SLIMProcessor
 
startBatchMacro(String) - Static method in class loci.slim.SLIMProcessor
 
startFileName - Variable in class loci.slim.paramSetMacro
 
startFitting(String) - Static method in class loci.slim.SLIMProcessor
 
startPathName - Variable in class loci.slim.paramSetMacro
 
startSLIMCurve(String, String, String) - Static method in class loci.slim.SLIMProcessor
macro for starting slim curve by automatic loading of file name
startSLIMCurveWithMacro - Variable in class loci.slim.paramSetMacro
 
StatisticsPanel - Class in loci.slim.analysis.batch.ui
 
StatisticsPanel(HistogramStatistics) - Constructor for class loci.slim.analysis.batch.ui.StatisticsPanel
 
storeFilesName(File[]) - Method in class loci.slim.paramSetMacro
 
STRETCHED_FITTED_IMAGE_ITEMS - Static variable in class loci.slim.ui.UserInterfacePanel
 
SUB_1 - Static variable in interface loci.slim.fitted.FittedValue
 
SUB_1 - Static variable in interface loci.slim2.process.interactive.ui.UserInterfacePanel
 
SUB_2 - Static variable in interface loci.slim.fitted.FittedValue
 
SUB_2 - Static variable in interface loci.slim2.process.interactive.ui.UserInterfacePanel
 
SUB_3 - Static variable in interface loci.slim.fitted.FittedValue
 
SUB_3 - Static variable in interface loci.slim2.process.interactive.ui.UserInterfacePanel
 
SUB_M - Static variable in interface loci.slim.fitted.FittedValue
 
SUB_M - Static variable in interface loci.slim2.process.interactive.ui.UserInterfacePanel
 
SUB_R - Static variable in interface loci.slim.fitted.FittedValue
 
SUB_R - Static variable in interface loci.slim2.process.interactive.ui.UserInterfacePanel
 
SUMMARY - Static variable in class loci.slim.analysis.batch.ui.BatchHistogramsFrame
 
suspendNotifications() - Method in class loci.slim.fitting.cursor.FittingCursor
Temporarily suspends listener notifications.
suspendNotifications() - Method in class loci.slim2.process.interactive.cursor.FittingCursor
Temporarily suspends listener notifications.
swapImage(String) - Method in interface loci.slim.analysis.batch.ui.BatchHistogramListener
 

T

T - Static variable in interface loci.slim.fitted.FittedValue
 
T1 - Static variable in interface loci.slim.fitted.FittedValue
 
T1_INDEX - Static variable in interface loci.slim.fitted.FittedValue
 
T1_INDEX - Static variable in class loci.slim.fitting.images.FittedImageFitter
 
t1macroused - Variable in class loci.slim.paramSetMacro
 
T2 - Static variable in interface loci.slim.fitted.FittedValue
 
T2_INDEX - Static variable in interface loci.slim.fitted.FittedValue
 
T2_INDEX - Static variable in class loci.slim.fitting.images.FittedImageFitter
 
t2macroused - Variable in class loci.slim.paramSetMacro
 
T3 - Static variable in interface loci.slim.fitted.FittedValue
 
T3_INDEX - Static variable in interface loci.slim.fitted.FittedValue
 
T3_INDEX - Static variable in class loci.slim.fitting.images.FittedImageFitter
 
t3macroused - Variable in class loci.slim.paramSetMacro
 
T_MEAN - Static variable in interface loci.slim.fitted.FittedValue
 
TAU - Static variable in interface loci.slim.fitted.FittedValue
 
TAU - Static variable in interface loci.slim2.process.interactive.ui.UserInterfacePanel
 
TAU1 - Static variable in interface loci.slim2.process.interactive.ui.UserInterfacePanel
 
TAU2 - Static variable in interface loci.slim2.process.interactive.ui.UserInterfacePanel
 
TAU3 - Static variable in interface loci.slim2.process.interactive.ui.UserInterfacePanel
 
TAU_CHAR - Static variable in interface loci.slim2.process.interactive.ui.UserInterfacePanel
 
TAU_MEAN - Static variable in interface loci.slim2.process.interactive.ui.UserInterfacePanel
 
TauBatchHistogram - Class in loci.slim.analysis.batch
A batch histogram that represents tau lifetime values.
TauBatchHistogram() - Constructor for class loci.slim.analysis.batch.TauBatchHistogram
 
TauMeanImage - Class in loci.slim.fitting.images
This class builds a fitted image that shows the tau mean.
TauMeanImage(String, int[], IndexColorModel, int, int, boolean, IGrayScaleImage, IMaskGroup[]) - Constructor for class loci.slim.fitting.images.TauMeanImage
Create the fitted image.
test(int, int) - Method in class loci.slim.mask.Mask
Test whether a given x and y is masked.
TFittedValue - Class in loci.slim.fitted
Extracts T fitted values.
TFittedValue() - Constructor for class loci.slim.fitted.TFittedValue
 
ThreadedFittingEngine - Class in loci.slim.fitting.engine
Fitting engine that uses a thread pool.
ThreadedFittingEngine() - Constructor for class loci.slim.fitting.engine.ThreadedFittingEngine
 
ThreadedFittingEngine - Class in loci.slim2.fitting
Fitting engine that uses a thread pool.
ThreadedFittingEngine() - Constructor for class loci.slim2.fitting.ThreadedFittingEngine
 
ThreadPool<T> - Class in imagej.thread
Manages a FixedThreadPool to parallelize Callable tasks.
ThreadPool() - Constructor for class imagej.thread.ThreadPool
 
Threshold - Class in loci.slim.preprocess
This class thresholds the image to a given photon count.
Threshold(int) - Constructor for class loci.slim.preprocess.Threshold
 
ThresholdDisplayOverlay - Class in loci.slim2.process.interactive.grayscale
The ThresholdDisplayOverlay
ThresholdDisplayOverlay(Context, Dataset, int, int) - Constructor for class loci.slim2.process.interactive.grayscale.ThresholdDisplayOverlay
Construct a ThresholdDisplayOverlay on a Dataset given an Context context.
thresholdMacroUsed - Static variable in class loci.slim.paramSetMacro
 
ThresholdUpdate - Interface in loci.slim2.process.interactive.ui
An interface to allow updated threshold values to be communicated.
TMeanFittedValue - Class in loci.slim.fitted
Extracts Tau Mean fitted values.
TMeanFittedValue() - Constructor for class loci.slim.fitted.TMeanFittedValue
 
TRANSIENT_START - Static variable in class loci.slim.heuristics.CursorEstimator
 
TRANSIENT_START - Static variable in class loci.slim2.heuristics.CursorEstimator
 
TRANSIENT_STOP - Static variable in class loci.slim.heuristics.CursorEstimator
 
TRANSIENT_STOP - Static variable in class loci.slim2.heuristics.CursorEstimator
 
transientStartMacroUsed - Variable in class loci.slim.paramSetMacro
 
transientStopMacroUsed - Variable in class loci.slim.paramSetMacro
 
trialRldFit(ICurveFitter, ICurveFitData) - Method in class loci.slim.fitting.RapidLifetimeDetermination
 
TRIPLE - Static variable in class loci.slim2.experimental.EnderleinErdmann
 
TRIPLE_FITTED_IMAGE_ITEMS - Static variable in class loci.slim.ui.UserInterfacePanel
 

U

update(String, HistogramStatistics[], HistogramStatistics[]) - Method in class loci.slim.analysis.batch.ui.BatchHistogramsFrame
 
updateChunkyPixel(int[], int[], double[]) - Method in class loci.slim.fitting.images.AbstractBaseFittedImage
Updates the fitted parameters for a pixel.
updateChunkyPixel(int[], int[], double[]) - Method in class loci.slim.fitting.images.FittedImageFitter
Updates the fitted parameters for a pixel.
updateChunkyPixel(int[], int[], double[]) - Method in interface loci.slim.fitting.images.IFittedImage
Updates the fitted parameters for a pixel.
updateErrorMask(Mask, int) - Method in interface loci.slim.fitting.IErrorListener
Updates the mask that defines error pixels.
updateErrorMask(Mask, int) - Method in class loci.slim.GrayScaleImage
 
updateHistogram(long[]) - Method in class loci.slim2.histogram.HistogramGraph
Updates the histogram data.
updateLUTRange() - Method in class loci.slim.fitting.images.FittedImageFitter
Recalculates the image histogram and resets the palette.
updateMask(Mask) - Method in class loci.slim.fitting.images.AbstractBaseFittedImage
Redraws the entire image after a masking change.
updateMask(Mask) - Method in interface loci.slim.fitting.images.IFittedImage
Redisplays the image after masking.
updateMask(IMaskNode) - Method in interface loci.slim.mask.IMaskGroup
Updates the mask, notifies group.
updateMask(IMaskNode) - Method in class loci.slim.mask.MaskGroup
 
updateMasks(Mask, Mask) - Method in interface loci.slim.mask.IMaskNodeListener
Tells listener other & total masks have been updated.
updateOtherMask(Mask) - Method in interface loci.slim.mask.IMaskNode
This method notifies a node that other nodes have changed the mask.
updateOtherMask(Mask) - Method in class loci.slim.mask.MaskNode
This method notifies this node that other nodes have changed masks.
updatePixel(int[], double[]) - Method in class loci.slim.fitting.images.AbstractBaseFittedImage
Updates the fitted parameters for a pixel.
updatePixel(int[], double[]) - Method in class loci.slim.fitting.images.FittedImageFitter
Updates the fitted parameters for a pixel.
updatePixel(int[], double[]) - Method in interface loci.slim.fitting.images.IFittedImage
Updates the fitted parameters for a pixel.
updateRanges() - Method in class loci.slim.fitting.images.AbstractBaseFittedImage
Recalculates the image histogram and resets the palette.
updateRanges() - Method in interface loci.slim.fitting.images.IFittedImage
Recalculates the image histogram and resets the palette.
updateRanges() - Method in class loci.slim.histogram.HistogramDataGroup
Sets the current min and max automatically if need be.
updateSelfMask(Mask) - Method in interface loci.slim.mask.IMaskNode
This method notifies other nodes that this node has changed the mask.
updateSelfMask(Mask) - Method in class loci.slim.mask.MaskNode
This method should be called when node has changed its mask.
updateThreshold(int) - Method in class loci.slim.GrayScaleImage
 
updateThreshold(int) - Method in interface loci.slim.IThresholdUpdate
Update the threshold value.
updateThreshold(int, int, boolean) - Method in interface loci.slim2.process.interactive.ui.ThresholdUpdate
Update the threshold values.
UPPER - Static variable in class imagej.charts.cursors.Cursor
 
URL_IMAGEJ - Static variable in class loci.slim.About
URL of SLIM Curve plugin for ImageJ web page.
URL_WEBSITE - Static variable in class loci.slim.About
URL of the SLIM Curve library web page.
useDetailStat - Static variable in class loci.slim.paramSetMacro
 
useDetailStat - Static variable in class loci.slim.ui.UserInterfacePanel
 
UserInterfacePanel - Class in loci.slim.ui
Main user interface panel for the fit.
UserInterfacePanel(boolean, boolean, int, double, String[], String[], FittingCursorHelper, IFitterEstimator) - Constructor for class loci.slim.ui.UserInterfacePanel
 
UserInterfacePanel - Interface in loci.slim2.process.interactive.ui
UI Panel interface.
UserInterfacePanelListener - Interface in loci.slim2.process.interactive.ui
Listens to UI panel.

V

valueOf(String) - Static method in enum imagej.charts.cursors.Cursor.Orientation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.curvefitter.ICurveFitter.FitAlgorithm
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.curvefitter.ICurveFitter.FitFunction
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.curvefitter.ICurveFitter.FitRegion
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.curvefitter.ICurveFitter.NoiseModel
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.slim.fitting.images.FittedImageFitter.FittedImageType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.slim2.outputset.temp.RampGenerator.RampType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.slim2.process.ImageFitter.ErrorCode
Returns the enum constant of this type with the specified name.
values() - Static method in enum imagej.charts.cursors.Cursor.Orientation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.curvefitter.ICurveFitter.FitAlgorithm
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.curvefitter.ICurveFitter.FitFunction
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.curvefitter.ICurveFitter.FitRegion
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.curvefitter.ICurveFitter.NoiseModel
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.slim.fitting.images.FittedImageFitter.FittedImageType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.slim2.outputset.temp.RampGenerator.RampType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.slim2.process.ImageFitter.ErrorCode
Returns an array containing the constants of this enum type, in the order they are declared.
valueToBin(double, double) - Method in class loci.curvefitter.DummyFitterEstimator
 
valueToBin(double, double) - Method in interface loci.curvefitter.IFitterEstimator
Converts a time value to a bin index.
valueToBin(int, double, double, double) - Static method in class loci.slim.analysis.Binning
Convert value to bin number.
valueToBin(double, double) - Method in class loci.slim.heuristics.FitterEstimator
Converts time-based value to a bin number.
valueToBin(double, double) - Method in class loci.slim2.heuristics.DefaultFitterEstimator
Converts time-based value to a bin number.
VertCursor - Class in loci.slim2.process
Vertical decay cursor.
VertCursor() - Constructor for class loci.slim2.process.VertCursor
 
viewChanged() - Method in class loci.slim2.histogram.DataHistogramCommand
Called when view changes.
VisADAnalysisPlugin - Class in loci.slim.analysis.plugins
Runs the VisADPlugin to analyze SLIM Curve results.
VisADAnalysisPlugin() - Constructor for class loci.slim.analysis.plugins.VisADAnalysisPlugin
 

W

waitRecord(int) - Static method in class loci.slim.SLIMProcessor
 
writeParamOnce - Static variable in class loci.slim.paramSetMacro
 

Z

Z - Static variable in interface loci.slim.fitted.FittedValue
 
z1macroused - Variable in class loci.slim.paramSetMacro
 
Z_INDEX - Static variable in interface loci.slim.fitted.FittedValue
 
Z_INDEX - Static variable in class loci.slim.fitting.images.FittedImageFitter
 
ZBatchHistogram - Class in loci.slim.analysis.batch
A batch histogram that represents Z baseline values.
ZBatchHistogram() - Constructor for class loci.slim.analysis.batch.ZBatchHistogram
 
ZFittedValue - Class in loci.slim.fitted
Extracts Z fitted values.
ZFittedValue() - Constructor for class loci.slim.fitted.ZFittedValue
 

_

_a1Fix2 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_a1Fix3 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_a1Param2 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_a1Param3 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_a2Fix2 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_a2Fix3 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_a2Param2 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_a2Param3 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_a3Fix3 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_a3Param3 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_aFix1 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_aFix4 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_algorithmComboBox - Static variable in class loci.slim.ui.UserInterfacePanel
 
_analysisCheckBoxList - Static variable in class loci.slim.ui.UserInterfacePanel
 
_aParam1 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_aParam4 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_binningComboBox - Static variable in class loci.slim.ui.UserInterfacePanel
 
_fitButton - Static variable in class loci.slim.ui.UserInterfacePanel
 
_fittedImagesComboBox - Static variable in class loci.slim.ui.UserInterfacePanel
 
_functionComboBox - Static variable in class loci.slim.ui.UserInterfacePanel
 
_hFix4 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_hParam4 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_meanValueComboBox - Static variable in class loci.slim.ui.UserInterfacePanel
 
_noiseModelComboBox - Static variable in class loci.slim.ui.UserInterfacePanel
 
_openButton - Static variable in class loci.slim.ui.UserInterfacePanel
 
_promptComboBox - Static variable in class loci.slim.ui.UserInterfacePanel
 
_promptDelaySpinner - Static variable in class loci.slim.ui.UserInterfacePanel
 
_promptWidthSpinner - Static variable in class loci.slim.ui.UserInterfacePanel
 
_regionComboBox - Static variable in class loci.slim.ui.UserInterfacePanel
 
_t1Fix2 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_t1Fix3 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_t1Param2 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_t1Param3 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_t2Fix2 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_t2Fix3 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_t2Param2 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_t2Param3 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_t3Fix3 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_t3Param3 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_tFix1 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_tFix4 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_thresholdSpinner - Static variable in class loci.slim.ui.UserInterfacePanel
 
_tParam1 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_tParam4 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_zFix1 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_zFix2 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_zFix3 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_zFix4 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_zParam1 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_zParam2 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_zParam3 - Static variable in class loci.slim.ui.UserInterfacePanel
 
_zParam4 - Static variable in class loci.slim.ui.UserInterfacePanel
 
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