Index (Stitching 3.1.10 API)

A B C D E F G H I L M N O P Q R S T U V W X Y Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

absoluteThreshold - Variable in class mpicbg.stitching.StitchingParameters
actionPerformed(ActionEvent) - Method in class tools.RoiPicker
add(double) - Method in class stitching.model.ErrorStatistic
addAllClasses(ClassifiedRegion) - Method in class mpicbg.stitching.fusion.ClassifiedRegion: Merges the classes attached to another region with the classes of this region.
addClass(int) - Method in class mpicbg.stitching.fusion.ClassifiedRegion: Add a class, in the form an int value, to this region.
addConnectedTile(Tile) - Method in class stitching.model.Tile: Add a Tile to the set of connected tiles.
addEnablerListener(Checkbox, Component[], Component[]) - Static method in class Stitching_3D
addHyperLinkListener(MultiLineLabel, String) - Static method in class stitching.CommonFunctions
addInverseEnablerListener(Checkbox, Component[], Component[]) - Static method in class Stitching_3D
addMatch(PointMatch) - Method in class stitching.model.Tile: Add one match.
addMatches(Collection<PointMatch>) - Method in class stitching.model.Tile: Add more PointMatches.
addTile(Tile) - Method in class stitching.model.TileConfiguration: Add a single tile.
addTiles(Collection<Tile>) - Method in class stitching.model.TileConfiguration: Add a collection of tiles.
addTilesAsRois - Variable in class mpicbg.stitching.StitchingParameters
addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.AveragePixelFusion
addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.AveragePixelFusionIgnoreZero
addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.BlendingPixelFusion
addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.BlendingPixelFusionIgnoreZero
addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.MaxPixelFusion
addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.MaxPixelFusionIgnoreZero
addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.MedianPixelFusion
addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.MedianPixelFusionIgnoreZero
addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.MinPixelFusion
addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.MinPixelFusionIgnoreZero
addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.OverlapFusion
addValue(double, int, double[]) - Method in interface mpicbg.stitching.fusion.PixelFusion: add a new value for the current output pixel
allChoices - Static variable in class plugin.GridType
alpha - Variable in class Stitch_Image_Collection
alpha - Variable in class Stitch_Multiple_Series_File
alpha - Variable in class Stitching_2D
alpha - Variable in class Stitching_3D
alpha - Variable in class stitching.GridLayout
alphaStatic - Static variable in class Stitch_Image_Collection
alphaStatic - Static variable in class Stitch_Image_Directory
alphaStatic - Static variable in class Stitch_Image_Grid_Sequence
alphaStatic - Static variable in class Stitch_Image_Grid
alphaStatic - Static variable in class Stitch_Many_Images
alphaStatic - Static variable in class Stitch_Multiple_Series_File
alphaStatic - Static variable in class Stitching_2D
alphaStatic - Static variable in class Stitching_3D
alwaysCopy - Static variable in class mpicbg.stitching.StitchingParameters: If you want to force that the ContainerFactory above is always used set this to true
apply(float[]) - Method in interface stitching.model.CoordinateTransform: Apply the CoordinateTransform to a location.
apply(float[]) - Method in class stitching.model.TranslationModel2D
apply(float[]) - Method in class stitching.model.TranslationModel3D
apply(Model) - Method in class stitching.model.Point: Apply a Model to the Point.
apply(Model) - Method in class stitching.model.PointMatch: Apply a Model to PointMatch.p1, update distance.
apply(Model, float) - Method in class stitching.model.Point: Apply a Model to the Point by a given amount.
applyByStrength(Model, float) - Method in class stitching.model.PointMatch: Apply a Model to PointMatch.p1 with a given amount, update distance.
applyInPlace(float[]) - Method in interface stitching.model.CoordinateTransform: Apply the CoordinateTransform to a location.
applyInPlace(float[]) - Method in class stitching.model.TranslationModel2D
applyInPlace(float[]) - Method in class stitching.model.TranslationModel3D
applyInverse(float[]) - Method in interface stitching.model.InvertibleCoordinateTransform: Apply the inverse of the model to a point location
applyInverse(float[]) - Method in class stitching.model.TranslationModel2D
applyInverse(float[]) - Method in class stitching.model.TranslationModel3D
applyInverse(InvertibleModel) - Method in class stitching.model.Point: Apply the inverse of a InvertibleModel to the Point.
applyInverseInPlace(float[]) - Method in interface stitching.model.InvertibleCoordinateTransform: apply the inverse of the model to a point location
applyInverseInPlace(float[]) - Method in class stitching.model.TranslationModel2D
applyInverseInPlace(float[]) - Method in class stitching.model.TranslationModel3D
arrangement - Variable in class stitching.GridLayout
averageAllChannels(Image<T>, int[], ImagePlus, int) - Static method in class mpicbg.stitching.PairWiseStitchingImgLib: Averages all channels into the target image.
averageAllChannels(Image<T>, ArrayList<Image<S>>, int[]) - Static method in class mpicbg.stitching.PairWiseStitchingImgLib: Averages all channels into the target image.
AveragePixelFusion - Class in mpicbg.stitching.fusion
AveragePixelFusion() - Constructor for class mpicbg.stitching.fusion.AveragePixelFusion
AveragePixelFusionIgnoreZero - Class in mpicbg.stitching.fusion
AveragePixelFusionIgnoreZero() - Constructor for class mpicbg.stitching.fusion.AveragePixelFusionIgnoreZero
AVG - Static variable in class stitching.CommonFunctions

B

betterThan(Model) - Method in class stitching.model.Model: less than operater to make the models comparable, returns false for error < 0
BlendingPixelFusion - Class in mpicbg.stitching.fusion
BlendingPixelFusion(ArrayList<? extends ImageInterpolation<?>>) - Constructor for class mpicbg.stitching.fusion.BlendingPixelFusion: Instantiates the per-pixel blending
BlendingPixelFusionIgnoreZero - Class in mpicbg.stitching.fusion
BlendingPixelFusionIgnoreZero(ArrayList<? extends ImageInterpolation<?>>) - Constructor for class mpicbg.stitching.fusion.BlendingPixelFusionIgnoreZero: Instantiates the per-pixel blending

C

calculateWeight() - Method in class stitching.model.PointMatch
canWrapIntoImgLib(ImagePlus, Roi, int) - Static method in class mpicbg.stitching.PairWiseStitchingImgLib: Determines if this imageplus with these parameters can be wrapped directly into an Image<T>.
channel1 - Variable in class mpicbg.stitching.StitchingParameters
channel2 - Variable in class mpicbg.stitching.StitchingParameters
checkPeaks - Variable in class mpicbg.stitching.StitchingParameters
checkPeaks - Variable in class Stitching_2D
checkPeaks - Variable in class Stitching_3D
checkPeaksStatic - Static variable in class Stitching_2D
checkPeaksStatic - Static variable in class Stitching_3D
choose1 - Static variable in class plugin.GridType
choose2 - Static variable in class plugin.GridType
classArray() - Method in class mpicbg.stitching.fusion.ClassifiedRegion
ClassifiedRegion - Class in mpicbg.stitching.fusion: Representation of a N-dimensional region with one or more classes/labels applied to it.
ClassifiedRegion(int) - Constructor for class mpicbg.stitching.fusion.ClassifiedRegion: Creates an empty ClassifiedRegion of the indicated size (dimensionality).
ClassifiedRegion(ClassifiedRegion) - Constructor for class mpicbg.stitching.fusion.ClassifiedRegion: Copying constructor.
ClassifiedRegion(Interval...) - Constructor for class mpicbg.stitching.fusion.ClassifiedRegion: Creates a new region using the given list of intervals.
clear() - Method in class mpicbg.stitching.fusion.AveragePixelFusion
clear() - Method in class mpicbg.stitching.fusion.BlendingPixelFusion
clear() - Method in class mpicbg.stitching.fusion.MaxPixelFusion
clear() - Method in class mpicbg.stitching.fusion.MedianPixelFusion
clear() - Method in class mpicbg.stitching.fusion.MinPixelFusion
clear() - Method in class mpicbg.stitching.fusion.OverlapFusion
clear() - Method in interface mpicbg.stitching.fusion.PixelFusion: reset for the next output pixel
clone() - Method in class stitching.CrossCorrelationResult2D
clone() - Method in class stitching.CrossCorrelationResult3D
clone() - Method in class stitching.FloatArray
clone() - Method in class stitching.FloatArray2D
clone() - Method in class stitching.FloatArray3D
clone() - Method in class stitching.model.InvertibleModel
clone() - Method in class stitching.model.Model: Clone the model.
clone() - Method in class stitching.model.Point: Clone this Point instance.
clone() - Method in class stitching.model.TranslationModel2D
clone() - Method in class stitching.model.TranslationModel3D
clone() - Method in class stitching.Point2D
clone() - Method in class stitching.Point3D
close() - Method in class mpicbg.stitching.ImageCollectionElement
closeAtEnd - Variable in class stitching.ImageInformation
CollectionStitchingImgLib - Class in mpicbg.stitching
CollectionStitchingImgLib() - Constructor for class mpicbg.stitching.CollectionStitchingImgLib
colorList - Static variable in class stitching.CommonFunctions
CommonFunctions - Class in stitching
CommonFunctions() - Constructor for class stitching.CommonFunctions
ComparePair - Class in mpicbg.stitching
ComparePair(ImagePlusTimePoint, ImagePlusTimePoint) - Constructor for class mpicbg.stitching.ComparePair
compareTo(ImagePlusTimePoint) - Method in class mpicbg.stitching.ImagePlusTimePoint
compareTo(ImageInformation) - Method in class stitching.ImageInformation
complexConjugate(float[]) - Static method in class stitching.CommonFunctions
CompositeImageFixer - Class in stitching.utils: Utility class to work around the CompositeImage nature of converting stacks to channels.
CompositeImageFixer() - Constructor for class stitching.utils.CompositeImageFixer
computeFFT(FloatArray2D) - Static method in class stitching.CommonFunctions
computeFFT(FloatArray3D) - Static method in class stitching.CommonFunctions
computeOverlap - Variable in class mpicbg.stitching.StitchingParameters
computeOverlap - Variable in class Stitching_2D
computeOverlap - Variable in class Stitching_3D
computeOverlapStatic - Static variable in class Stitch_Image_Collection
computeOverlapStatic - Static variable in class Stitch_Image_Grid_Sequence
computeOverlapStatic - Static variable in class Stitch_Image_Grid
computeOverlapStatic - Static variable in class Stitch_Many_Images
computeOverlapStatic - Static variable in class Stitch_Multiple_Series_File
computeOverlapStatic - Static variable in class Stitching_2D
computeOverlapStatic - Static variable in class Stitching_3D
computePhaseCorrelation(Image<T>, Image<S>, int, boolean) - Static method in class mpicbg.stitching.PairWiseStitchingImgLib
computePhaseCorrelationMatrix(float[], float[], boolean) - Static method in class stitching.CommonFunctions
computePhaseCorrelationMatrix(FloatArray2D, FloatArray2D, int) - Static method in class stitching.CommonFunctions
computePhaseCorrelationMatrix(FloatArray3D, FloatArray3D, int) - Static method in class stitching.CommonFunctions
computeWeight(double[], long[], double[], double) - Static method in class mpicbg.stitching.fusion.BlendingPixelFusion: From SPIM Registration
connect(Tile, Collection<PointMatch>) - Method in class stitching.model.Tile: connect two tiles by a set of point correspondences re-weighs the point correpondences We set a weigh of 1.0 / num_matches to each correspondence to equalize the connections between tiles during minimization.
contains(int) - Method in class mpicbg.stitching.fusion.Interval
CoordinateTransform - Interface in stitching.model: TODO
copy() - Method in class mpicbg.stitching.fusion.AveragePixelFusion
copy() - Method in class mpicbg.stitching.fusion.AveragePixelFusionIgnoreZero
copy() - Method in class mpicbg.stitching.fusion.BlendingPixelFusion
copy() - Method in class mpicbg.stitching.fusion.BlendingPixelFusionIgnoreZero
copy() - Method in class mpicbg.stitching.fusion.MaxPixelFusion
copy() - Method in class mpicbg.stitching.fusion.MaxPixelFusionIgnoreZero
copy() - Method in class mpicbg.stitching.fusion.MedianPixelFusion
copy() - Method in class mpicbg.stitching.fusion.MedianPixelFusionIgnoreZero
copy() - Method in class mpicbg.stitching.fusion.MinPixelFusion
copy() - Method in class mpicbg.stitching.fusion.MinPixelFusionIgnoreZero
copy() - Method in class mpicbg.stitching.fusion.OverlapFusion
copy() - Method in interface mpicbg.stitching.fusion.PixelFusion: Convinience method for multi-threading
coregister - Variable in class Stitching_3D
coregisterStatic - Static variable in class Stitching_3D
cost - Variable in class stitching.model.Model: The cost depends on what kind of algorithm is running.
coversClasses(ClassifiedRegion) - Method in class mpicbg.stitching.fusion.ClassifiedRegion
cpuMemChoice - Variable in class mpicbg.stitching.StitchingParameters
cpuMemSelect - Static variable in class stitching.CommonFunctions
createInterpolator() - Method in class mpicbg.stitching.fusion.ImageInterpolation
createOverlay(T, ImagePlus, ImagePlus, InvertibleBoundable, InvertibleBoundable, int) - Static method in class mpicbg.stitching.fusion.OverlayFusion
createOverlay(T, ArrayList<ImagePlus>, ArrayList<InvertibleBoundable>, int, int, InterpolatorFactory<FloatType, RandomAccessible<FloatType>>) - Static method in class mpicbg.stitching.fusion.OverlayFusion
createReRegisteredSeries(T, ImagePlus, ArrayList<InvertibleBoundable>, int) - Static method in class mpicbg.stitching.fusion.OverlayFusion
CrossCorrelationResult2D - Class in stitching
CrossCorrelationResult2D() - Constructor for class stitching.CrossCorrelationResult2D
CrossCorrelationResult3D - Class in stitching
CrossCorrelationResult3D() - Constructor for class stitching.CrossCorrelationResult3D

D

d - Variable in class stitching.ImageInformation
data - Variable in class stitching.FloatArray
debug(String) - Static method in class stitching.utils.Log: Issues a message to the ImageJ log window, but only in debug mode.
defaultAddTilesAsRois - Static variable in class plugin.Stitching_Grid
defaultChannel1 - Static variable in class plugin.Stitching_Pairwise
defaultChannel2 - Static variable in class plugin.Stitching_Pairwise
defaultCheckPeaks - Static variable in class plugin.Stitching_Pairwise
defaultComputeOverlap - Static variable in class plugin.Stitching_Grid
defaultComputeOverlap - Static variable in class plugin.Stitching_Pairwise
defaultConfirmFiles - Static variable in class plugin.Stitching_Grid
defaultDirectory - Static variable in class plugin.Stitching_Grid
defaultDisplacementThresholdAbsolute - Static variable in class plugin.Stitching_Grid
defaultDisplacementThresholdAbsolute - Static variable in class plugin.Stitching_Pairwise
defaultDisplacementThresholdRelative - Static variable in class plugin.Stitching_Grid
defaultDisplacementThresholdRelative - Static variable in class plugin.Stitching_Pairwise
defaultDisplayFusion - Static variable in class plugin.Stitching_Grid
defaultDownSample - Static variable in class plugin.Stitching_Grid
defaultFileNames - Static variable in class plugin.Stitching_Grid
defaultFuseImages - Static variable in class plugin.Stitching_Pairwise
defaultFusionMethod - Static variable in class plugin.Stitching_Grid
defaultFusionMethod - Static variable in class plugin.Stitching_Pairwise
defaultGridChoice1 - Static variable in class plugin.Stitching_Grid
defaultGridChoice2 - Static variable in class plugin.Stitching_Grid
defaultGridSizeX - Static variable in class plugin.Stitching_Grid
defaultGridSizeY - Static variable in class plugin.Stitching_Grid
defaultHandleChannel1 - Static variable in class plugin.Stitching_Pairwise
defaultHandleChannel2 - Static variable in class plugin.Stitching_Pairwise
defaultIgnoreCalibration - Static variable in class plugin.Stitching_Grid
defaultIgnoreZeroValues - Static variable in class plugin.Stitching_Pairwise
defaultIgnoreZStage - Static variable in class plugin.Stitching_Grid
defaultImg1 - Static variable in class plugin.Stitching_Pairwise
defaultImg2 - Static variable in class plugin.Stitching_Pairwise
defaultIncreaseOverlap - Static variable in class plugin.Stitching_Grid
defaultInvertX - Static variable in class plugin.Stitching_Grid
defaultInvertY - Static variable in class plugin.Stitching_Grid
defaultMemorySpeedChoice - Static variable in class plugin.Stitching_Grid
defaultMemorySpeedChoice - Static variable in class plugin.Stitching_Pairwise
defaultOnlyPreview - Static variable in class plugin.Stitching_Grid
defaultOutputDirectory - Static variable in class plugin.Stitching_Grid
defaultOverlapX - Static variable in class plugin.Stitching_Grid
defaultOverlapY - Static variable in class plugin.Stitching_Grid
defaultQuickFusion - Static variable in class plugin.Stitching_Grid
defaultR - Static variable in class plugin.Stitching_Grid
defaultRegressionThreshold - Static variable in class plugin.Stitching_Grid
defaultResult - Static variable in class plugin.Stitching_Grid
defaultSeqRange - Static variable in class plugin.Stitching_Grid
defaultSeriesFile - Static variable in class plugin.Stitching_Grid
defaultStartI - Static variable in class plugin.Stitching_Grid
defaultStartX - Static variable in class plugin.Stitching_Grid
defaultStartY - Static variable in class plugin.Stitching_Grid
defaultSubpixelAccuracy - Static variable in class plugin.Stitching_Grid
defaultSubpixelAccuracy - Static variable in class plugin.Stitching_Pairwise
defaultTileConfiguration - Static variable in class plugin.Stitching_Grid
defaultTimeSelect - Static variable in class plugin.Stitching_Pairwise
defaultVirtualInput - Static variable in class plugin.Stitching_Grid
defaultxOffset - Static variable in class plugin.Stitching_Pairwise
defaultyOffset - Static variable in class plugin.Stitching_Pairwise
defaultzOffset - Static variable in class plugin.Stitching_Pairwise
DeltaVision_Converter - Class in Unnamed Package
DeltaVision_Converter() - Constructor for class DeltaVision_Converter
depth - Variable in class stitching.FloatArray3D
diceBetterModel(int, float) - Method in class stitching.model.Tile: randomly dice new model until the error is smaller than the old one
dim - Variable in class Stitch_Image_Collection
dim - Variable in class stitching.GridLayout
dim - Variable in class stitching.ImageInformation
dimensionality - Variable in class mpicbg.stitching.StitchingParameters
directoryStatic - Static variable in class Stitch_Image_Grid
displayFusion - Variable in class mpicbg.stitching.StitchingParameters
distance(Point, Point) - Static method in class stitching.model.Point: Estimate the Euclidean distance of two Points in the world.
doLogging - Variable in class Stitching_2D
doLogging - Variable in class Stitching_3D
downSample - Variable in class mpicbg.stitching.StitchingParameters
Downsampler - Class in mpicbg.stitching: Helper class for running the "Image > Scale..." plugin on a collection of ImagePlus objects.
Downsampler() - Constructor for class mpicbg.stitching.Downsampler
dvLogFileStatic - Variable in class DeltaVision_Converter

E

equalsInterval(Interval) - Method in class mpicbg.stitching.fusion.Interval: Check to see if another interval is the same as this interval.
equalsRegion(ClassifiedRegion) - Method in class mpicbg.stitching.fusion.ClassifiedRegion: Test if this region is identical to another region
error(String) - Static method in class stitching.utils.Log: Issues an error message to the ImageJ log window.
error(String, Throwable) - Static method in class stitching.utils.Log: Issues an error message to the ImageJ log window, plus an exception stack trace to an ImageJ exception window.
error(Throwable) - Static method in class stitching.utils.Log: Issues an exception stack trace to an ImageJ exception window.
errorMapImp - Variable in class stitching.CrossCorrelationResult2D
errorMapImp - Variable in class stitching.CrossCorrelationResult3D
ErrorStatistic - Class in stitching.model: TODO
ErrorStatistic() - Constructor for class stitching.model.ErrorStatistic
estimateBounds(double[], int[], int[][], ArrayList<InvertibleBoundable>, int) - Static method in class mpicbg.stitching.fusion.Fusion: Estimate the bounds of the output image.
estimateBounds(double[], int[], List<ImagePlus>, ArrayList<InvertibleBoundable>, int) - Static method in class mpicbg.stitching.fusion.Fusion: Estimate the bounds of the output image.

F

fileNamesStatic - Static variable in class Stitch_Image_Grid_Sequence
fileNamesStatic - Static variable in class Stitch_Image_Grid
fileNameStatic - Static variable in class Stitch_Image_Collection
fileNameStatic - Static variable in class Stitch_Many_Images: Static variables for the individual dialogs
fileNameStatic - Static variable in class Stitch_Multiple_Series_File
fillInChannel(Image<T>, int[], ImagePlus, int, int) - Static method in class mpicbg.stitching.PairWiseStitchingImgLib: Averages all channels into the target image.
filter(Class<M>, Collection<PointMatch>, Collection<PointMatch>) - Static method in class stitching.model.Model: Estimate a Model and filter potential outliers by robust iterative regression.
filterRansac(Class<M>, List<PointMatch>, Collection<PointMatch>, int, float, float) - Static method in class stitching.model.Model: Estimate the best model for a set of feature correspondence candidates.
findOverlappingTiles(ArrayList<ImageCollectionElement>, StitchingParameters) - Static method in class mpicbg.stitching.CollectionStitchingImgLib
findPeaks(FloatArray3D, Point3D, Point3D, Point3D, Point3D, int) - Static method in class Stitching_3D
fit(Collection<PointMatch>) - Method in class stitching.model.Model: Fit the Model to a set of data points minimizing the global transfer error.
fit(Collection<PointMatch>) - Method in class stitching.model.TranslationModel2D
fit(Collection<PointMatch>) - Method in class stitching.model.TranslationModel3D
fitModel() - Method in class stitching.model.Tile: Update the transformation Model.
fixTile(Tile) - Method in class stitching.model.TileConfiguration: Fix a single tile.
flip(Collection<PointMatch>) - Static method in class stitching.model.PointMatch: Flip symmetrically, weights remains unchanged.
FloatArray - Class in stitching
FloatArray() - Constructor for class stitching.FloatArray
FloatArray2D - Class in stitching
FloatArray2D(float[], int, int) - Constructor for class stitching.FloatArray2D
FloatArray2D(int, int) - Constructor for class stitching.FloatArray2D
FloatArray3D - Class in stitching
FloatArray3D(float[], int, int, int) - Constructor for class stitching.FloatArray3D
FloatArray3D(int, int, int) - Constructor for class stitching.FloatArray3D
fractionBlended - Static variable in class mpicbg.stitching.fusion.BlendingPixelFusion
fuse(T, ImagePlus, ImagePlus, ArrayList<InvertibleBoundable>, StitchingParameters) - Static method in class plugin.Stitching_Pairwise
fuse(T, ArrayList<ImagePlus>, ArrayList<InvertibleBoundable>, int, boolean, int, String, boolean, boolean, boolean) - Static method in class mpicbg.stitching.fusion.Fusion
fuseBlock(Img<T>, ArrayList<? extends ImageInterpolation<? extends RealType<?>>>, double[], ArrayList<InvertibleBoundable>, PixelFusion, boolean) - Static method in class mpicbg.stitching.fusion.Fusion: Fuse one slice/volume (one channel)
fuseBlockNoOverlap(Img<T>, ArrayList<? extends ImageInterpolation<? extends RealType<?>>>, double[], ArrayList<InvertibleBoundable>, boolean) - Static method in class mpicbg.stitching.fusion.Fusion: Fuse one slice/volume (one channel)
fuseChannel(Img<T>, RealRandomAccessible<FloatType>, double[], InvertibleCoordinateTransform) - Static method in class mpicbg.stitching.fusion.OverlayFusion: Fuse one slice/volume (one channel)
fusedImageName - Variable in class Stitching_2D
fusedImageName - Variable in class Stitching_3D
fusedName - Variable in class mpicbg.stitching.StitchingParameters
fuseImages - Variable in class Stitching_2D
fuseImages - Variable in class Stitching_3D
fuseImages(ArrayList<ImageInformation>, float[], String, String, String, int, double, boolean) - Static method in class Stitch_Image_Collection
fuseImagesStatic - Static variable in class Stitching_2D
fuseImagesStatic - Static variable in class Stitching_3D
Fusion - Class in mpicbg.stitching.fusion: Manages the fusion for all types except the overlayfusion
Fusion() - Constructor for class mpicbg.stitching.fusion.Fusion
fusionMethod - Variable in class mpicbg.stitching.StitchingParameters
fusionMethod - Variable in class stitching.GridLayout
fusionMethodList - Static variable in class stitching.CommonFunctions
fusionMethodListGrid - Static variable in class stitching.CommonFunctions
fusionMethodListSimple - Static variable in class stitching.CommonFunctions
fusionMethodStatic - Static variable in class Stitch_Image_Collection
fusionMethodStatic - Static variable in class Stitch_Image_Directory
fusionMethodStatic - Static variable in class Stitch_Image_Grid_Sequence
fusionMethodStatic - Static variable in class Stitch_Image_Grid
fusionMethodStatic - Static variable in class Stitch_Many_Images
fusionMethodStatic - Static variable in class Stitch_Multiple_Series_File

G

generateRois(double[], ArrayList<ImagePlusTimePoint>) - Method in class plugin.Stitching_Grid: Generates a ROI for each tile in the list of optimized images.
get(int) - Method in class mpicbg.stitching.fusion.ClassifiedRegion: Gets the interval of this region for the specified axis (index)
get(int, int) - Method in class stitching.FloatArray2D
get(int, int, int) - Method in class stitching.FloatArray3D
getAllFilesInDirectory(String, boolean) - Method in class plugin.Stitching_Grid
getAndApplyMinMax(ArrayList<ImageInformation>, int) - Static method in class Stitch_Image_Collection
getAvgError() - Method in class stitching.model.TileConfiguration
getCommonRectangle(ImagePlus[], Point2D[], boolean) - Static method in class Stitching_2D
getComparePairs(ImagePlus, ImagePlus, int, int) - Static method in class plugin.Stitching_Pairwise
getConnectedTiles() - Method in class stitching.model.Tile
getCost() - Method in class stitching.model.Model
getCrossCorrelation() - Method in class mpicbg.stitching.ComparePair
getCrossCorrelation() - Method in class mpicbg.stitching.PairWiseStitchingResult
getCrossCorrelationResult() - Method in class Stitching_2D
getCrossCorrelationResult() - Method in class Stitching_3D
getCrossCorrelationResults() - Method in class Stitching_2D
getCrossCorrelationResults() - Method in class Stitching_3D
getDimension(int) - Method in class mpicbg.stitching.ImageCollectionElement
getDimensionality() - Method in class mpicbg.stitching.ImageCollectionElement
getDimensions() - Method in class mpicbg.stitching.ImageCollectionElement
getDistance() - Method in class stitching.model.PointMatch
getDistance() - Method in class stitching.model.Tile
getElement() - Method in class mpicbg.stitching.ImagePlusTimePoint
getError() - Method in class stitching.model.Model: Deprecated.
The term Error may be missleading---use Model.getCost() instead
getError() - Method in class stitching.model.Tile
getFile() - Method in class mpicbg.stitching.ImageCollectionElement
getFixedTiles() - Method in class stitching.model.TileConfiguration
getGridLayout(GridType, int, int, double, double, String, String, int, int, int, boolean, Downsampler) - Method in class plugin.Stitching_Grid
getHeight() - Method in class stitching.model.Tile
getImage(ImagePlus, Roi, ImageFactory<T>, int, int) - Static method in class mpicbg.stitching.PairWiseStitchingImgLib: return an Image<T> as input for the PhaseCorrelation.
getImagePlus() - Method in class mpicbg.stitching.ImagePlusTimePoint
getImagePlus1() - Method in class mpicbg.stitching.ComparePair
getImagePlus2() - Method in class mpicbg.stitching.ComparePair
getImg() - Method in class mpicbg.stitching.fusion.ImageInterpolation
getImpId() - Method in class mpicbg.stitching.ImagePlusTimePoint
getIndex() - Method in class mpicbg.stitching.ImageCollectionElement
getInput(int, int) - Method in class mpicbg.stitching.Downsampler: Displays a dialog to harvest user input, allowing scaling from a specified image width and height.
getIsValidOverlap() - Method in class mpicbg.stitching.ComparePair
getL() - Method in class stitching.model.Point
getLayoutFromFile(String, String, Downsampler) - Method in class plugin.Stitching_Grid
getLayoutFromMultiSeriesFile(String, double, boolean, boolean, boolean, boolean, Downsampler) - Method in class plugin.Stitching_Grid
getLeadingZeros(int, int) - Static method in class plugin.Stitching_Grid
getLeadingZeros(int, int) - Static method in class Stitch_Image_Grid
getMatches() - Method in class stitching.model.Tile
getMaxError() - Method in class stitching.model.TileConfiguration
getMinError() - Method in class stitching.model.TileConfiguration
getMinSetSize() - Method in class stitching.model.Model
getMinSetSize() - Method in class stitching.model.TranslationModel2D
getMinSetSize() - Method in class stitching.model.TranslationModel3D
getMirror(int, int) - Method in class stitching.FloatArray2D
getMirror(int, int, int) - Method in class stitching.FloatArray3D
getModel() - Method in class mpicbg.stitching.ImageCollectionElement
getModel() - Method in class stitching.model.Tile
getModel1() - Method in class mpicbg.stitching.ComparePair
getModel2() - Method in class mpicbg.stitching.ComparePair
getNumDimensions() - Method in class mpicbg.stitching.PairWiseStitchingResult
getOffset() - Method in class mpicbg.stitching.ImageCollectionElement
getOffset() - Method in class mpicbg.stitching.PairWiseStitchingResult
getOffset(int) - Method in class mpicbg.stitching.ImageCollectionElement
getOffset(int) - Method in class mpicbg.stitching.PairWiseStitchingResult
getOnlyRectangularRoi(Roi) - Static method in class mpicbg.stitching.PairWiseStitchingImgLib
getOrder() - Method in class plugin.GridType
getP1() - Method in class stitching.model.PointMatch
getP2() - Method in class stitching.model.PointMatch
getPair() - Method in class mpicbg.stitching.PointMatchStitching
getPCPeak() - Method in class mpicbg.stitching.Peak
getPhaseCorrelation() - Method in class mpicbg.stitching.PairWiseStitchingResult
getPixelMin(int, Object[], int, int, int, int, int, int, double) - Static method in class stitching.CommonFunctions
getPixelMinRGB(Object[], int, int, int, int, int, int, double) - Static method in class stitching.CommonFunctions
getPixelValueRGB(int, int) - Static method in class stitching.CommonFunctions
getPlanePosition(IFormatReader, MetadataRetrieve, int, int) - Static method in class stitching.CommonFunctions
getPlanePosition(IFormatReader, MetadataRetrieve, int, int, boolean, boolean, boolean) - Static method in class stitching.CommonFunctions
getPos(int, int) - Method in class stitching.FloatArray2D
getPos(int, int, int) - Method in class stitching.FloatArray3D
getPosition(int[], int, int, int, int, int) - Method in class plugin.Stitching_Grid
getQuicksortValue() - Method in class stitching.CrossCorrelationResult2D
getQuicksortValue() - Method in class stitching.CrossCorrelationResult3D
getQuicksortValue() - Method in interface stitching.Quicksortable
getRelativeShift() - Method in class mpicbg.stitching.ComparePair
getROI(ImageCollectionElement, ImageCollectionElement) - Static method in class mpicbg.stitching.CollectionStitchingImgLib
getTile1() - Method in class mpicbg.stitching.ComparePair
getTile2() - Method in class mpicbg.stitching.ComparePair
getTiles() - Method in class stitching.model.TileConfiguration
getTimePoint() - Method in class mpicbg.stitching.ImagePlusTimePoint
getTimePoint1() - Method in class mpicbg.stitching.ComparePair
getTimePoint2() - Method in class mpicbg.stitching.ComparePair
getToolIcon() - Method in class tools.RoiPicker
getToolName() - Method in class tools.RoiPicker
getTranslation() - Method in class Stitching_2D
getTranslation() - Method in class Stitching_3D
getTranslation() - Method in class stitching.model.TranslationModel2D
getTranslation() - Method in class stitching.model.TranslationModel3D
getType() - Method in class plugin.GridType
getValue() - Method in class mpicbg.stitching.fusion.AveragePixelFusion
getValue() - Method in class mpicbg.stitching.fusion.BlendingPixelFusion
getValue() - Method in class mpicbg.stitching.fusion.MaxPixelFusion
getValue() - Method in class mpicbg.stitching.fusion.MedianPixelFusion
getValue() - Method in class mpicbg.stitching.fusion.MinPixelFusion
getValue() - Method in class mpicbg.stitching.fusion.OverlapFusion
getValue() - Method in interface mpicbg.stitching.fusion.PixelFusion: return the result for the current pixel
getW() - Method in class stitching.model.Point
getWC() - Method in class stitching.model.Tile
getWeight() - Method in class stitching.model.PointMatch
getWeights() - Method in class stitching.model.PointMatch
getWideSlope(int) - Method in class stitching.model.ErrorStatistic
getWidth() - Method in class stitching.model.Tile
getWorstError() - Method in class stitching.model.TileConfiguration
getWorstTile() - Method in class mpicbg.stitching.TileConfigurationStitching
getWrappedImageFloat(ImagePlus, int, int) - Static method in class mpicbg.stitching.PairWiseStitchingImgLib: return an Image of FloatType as input for the PhaseCorrelation.
getWrappedImageUnsignedByte(ImagePlus, int, int) - Static method in class mpicbg.stitching.PairWiseStitchingImgLib: return an Image of UnsignedByteType as input for the PhaseCorrelation.
getWrappedImageUnsignedShort(ImagePlus, int, int) - Static method in class mpicbg.stitching.PairWiseStitchingImgLib: return an Image of UnsignedShortType as input for the PhaseCorrelation.
getZero(double, double) - Method in class stitching.FloatArray2D
getZero(int, int) - Method in class stitching.FloatArray2D
getZero(int, int, int) - Method in class stitching.FloatArray3D
GlobalOptimization - Class in mpicbg.stitching
GlobalOptimization() - Constructor for class mpicbg.stitching.GlobalOptimization
GridLayout - Class in stitching
GridLayout() - Constructor for class stitching.GridLayout
gridSizeXStatic - Static variable in class Stitch_Image_Grid_Sequence
gridSizeXStatic - Static variable in class Stitch_Image_Grid
gridSizeYStatic - Static variable in class Stitch_Image_Grid_Sequence
gridSizeYStatic - Static variable in class Stitch_Image_Grid
gridSizeZStatic - Static variable in class Stitch_Image_Grid_Sequence
GridType - Class in plugin
GridType() - Constructor for class plugin.GridType

H

h - Variable in class stitching.ImageInformation
handleRecording() - Method in class tools.RoiPicker
handleRGB - Variable in class stitching.GridLayout
handleRGB1 - Variable in class Stitching_2D
handleRGB1 - Variable in class Stitching_3D
handleRGB1Static - Static variable in class Stitching_2D
handleRGB1Static - Static variable in class Stitching_3D
handleRGB2 - Variable in class Stitching_2D
handleRGB2 - Variable in class Stitching_3D
handleRGB2Static - Static variable in class Stitching_2D
handleRGB2Static - Static variable in class Stitching_3D
handleRGBStatic - Static variable in class Stitch_Image_Collection
handleRGBStatic - Static variable in class Stitch_Image_Directory
handleRGBStatic - Static variable in class Stitch_Image_Grid_Sequence
handleRGBStatic - Static variable in class Stitch_Image_Grid
handleRGBStatic - Static variable in class Stitch_Many_Images
hasInput() - Method in class mpicbg.stitching.Downsampler
height - Variable in class stitching.FloatArray2D
height - Variable in class stitching.FloatArray3D

I

i1 - Variable in class stitching.OverlapProperties
i2 - Variable in class stitching.OverlapProperties
id - Variable in class stitching.ImageInformation
identifyConnectedGraphs(Collection<Tile>) - Static method in class stitching.model.Tile: Identify the set of connected graphs that contains all given tiles.
ignoreCalibrationStatic - Static variable in class Stitch_Multiple_Series_File
ignoreZ - Static variable in class mpicbg.stitching.GlobalOptimization
ignoreZeroValuesFusion - Variable in class mpicbg.stitching.StitchingParameters
ignoreZStage - Variable in class mpicbg.stitching.StitchingParameters
ignoreZStageStatic - Static variable in class Stitch_Multiple_Series_File
image1 - Variable in class Stitching_2D
image2 - Variable in class Stitching_2D
ImageCollectionElement - Class in mpicbg.stitching
ImageCollectionElement(File, int) - Constructor for class mpicbg.stitching.ImageCollectionElement
imageDirectoryStatic - Static variable in class Stitch_Image_Directory
ImageInformation - Class in stitching
ImageInformation(int, int, Model) - Constructor for class stitching.ImageInformation
imageInformationList - Variable in class stitching.GridLayout
ImageInterpolation<T> - Class in mpicbg.stitching.fusion: This class is necessary as it can create an InterpolatorFactory for an Img even if hold it as < ? extends RealType< ? > >.
ImageInterpolation(Img<T>, InterpolatorFactory<T, RandomAccessible<T>>, boolean) - Constructor for class mpicbg.stitching.fusion.ImageInterpolation
imageName - Variable in class stitching.ImageInformation
ImagePlusTimePoint - Class in mpicbg.stitching
ImagePlusTimePoint(ImagePlus, int, int, Model, ImageCollectionElement) - Constructor for class mpicbg.stitching.ImagePlusTimePoint
images - Variable in class plugin.GridType
imageStack - Variable in class stitching.ImageInformation
imageSwitch(Choice, Choice, ImageIcon[][], ImageIcon, JLabel) - Method in class plugin.GridType
ImageToFloatArray(ImageProcessor, String) - Method in class Stitching_2D
imageType - Variable in class stitching.ImageInformation
imgStack1 - Variable in class Stitching_3D
imgStack2 - Variable in class Stitching_3D
imp - Variable in class stitching.ImageInformation
imp - Variable in class stitching.model.PaintInvertibleCoordinateTransformThread
imp1 - Variable in class Stitching_2D
imp1 - Variable in class Stitching_3D
imp2 - Variable in class Stitching_2D
imp2 - Variable in class Stitching_3D
info(String) - Static method in class stitching.utils.Log: Issues an informational message to the ImageJ log window.
initializeReader(IFormatReader, String) - Method in class plugin.Stitching_Grid: Initializes an ImageReader if the provided reader is null, or does not match the given file id.
inputDirectoryStatic - Static variable in class Stitch_Image_Grid_Sequence
intersects(ClassifiedRegion) - Method in class mpicbg.stitching.fusion.ClassifiedRegion: Returns true if this region intersects with the provided target region.
intersects(Interval) - Method in class mpicbg.stitching.fusion.Interval: Determines if this interval has an intersection with another interval.
intersects(Tile) - Method in class stitching.model.Tile: Check if the Tile intersects another.
Interval - Class in mpicbg.stitching.fusion: A range on the number line with a Interval.min() and Interval.max() point.
Interval(int...) - Constructor for class mpicbg.stitching.fusion.Interval: Constructs a new Interval using the smallest and largest values in the provided points.
Interval(Interval) - Constructor for class mpicbg.stitching.fusion.Interval: Copying constructor
IntroItemListener(Checkbox, Vector<?>) - Constructor for class Stitch_Many_Images.IntroItemListener
invalid - Variable in class stitching.ImageInformation
InvertibleCoordinateTransform - Interface in stitching.model: TODO
InvertibleModel - Class in stitching.model: TODO
InvertibleModel() - Constructor for class stitching.model.InvertibleModel
invertX - Variable in class mpicbg.stitching.StitchingParameters
invertXStatic - Static variable in class Stitch_Multiple_Series_File
invertY - Variable in class mpicbg.stitching.StitchingParameters
invertYStatic - Static variable in class Stitch_Multiple_Series_File
isInside(float[]) - Method in class stitching.model.Tile: Check if a point that is given in world coordinates is inside the tile.
isVirtual() - Method in class mpicbg.stitching.ImageCollectionElement
itemStateChanged(ItemEvent) - Method in class Stitch_Many_Images.IntroItemListener

L

LIN_BLEND - Static variable in class stitching.CommonFunctions
loadImage(String, String, int) - Static method in class stitching.CommonFunctions
loadImage(String, String, int, String) - Static method in class stitching.CommonFunctions
Log - Class in stitching.utils: Utility class to deal with logging.
Log() - Constructor for class stitching.utils.Log

M

main(String[]) - Static method in class DeltaVision_Converter
main(String[]) - Static method in class mpicbg.stitching.fusion.Fusion
makeComposite(ImagePlus) - Static method in class stitching.utils.CompositeImageFixer: see CompositeImageFixer.makeComposite(ImagePlus, int)
makeComposite(ImagePlus, int) - Static method in class stitching.utils.CompositeImageFixer: -- HACK --
max - Variable in class stitching.model.ErrorStatistic
max() - Method in class mpicbg.stitching.fusion.Interval
MAX - Static variable in class stitching.CommonFunctions
maxIntensity - Variable in class stitching.ImageInformation
MaxPixelFusion - Class in mpicbg.stitching.fusion
MaxPixelFusion() - Constructor for class mpicbg.stitching.fusion.MaxPixelFusion
MaxPixelFusionIgnoreZero - Class in mpicbg.stitching.fusion
MaxPixelFusionIgnoreZero() - Constructor for class mpicbg.stitching.fusion.MaxPixelFusionIgnoreZero
mean - Variable in class stitching.model.ErrorStatistic
median - Variable in class stitching.model.ErrorStatistic
MedianPixelFusion - Class in mpicbg.stitching.fusion
MedianPixelFusion() - Constructor for class mpicbg.stitching.fusion.MedianPixelFusion
MedianPixelFusionIgnoreZero - Class in mpicbg.stitching.fusion
MedianPixelFusionIgnoreZero() - Constructor for class mpicbg.stitching.fusion.MedianPixelFusionIgnoreZero
method - Variable in class Stitching_2D
method - Variable in class Stitching_3D
methodList - Static variable in class stitching.CommonFunctions
methodListCollection - Static variable in class stitching.CommonFunctions
methodStatic - Static variable in class Stitching_2D
methodStatic - Static variable in class Stitching_3D
min - Variable in class stitching.model.ErrorStatistic
min() - Method in class mpicbg.stitching.fusion.Interval
MIN - Static variable in class stitching.CommonFunctions
MIN_SET_SIZE - Static variable in class stitching.model.TranslationModel2D
MIN_SET_SIZE - Static variable in class stitching.model.TranslationModel3D
minOverlap - Variable in class Stitching_3D
MinPixelFusion - Class in mpicbg.stitching.fusion
MinPixelFusion() - Constructor for class mpicbg.stitching.fusion.MinPixelFusion
MinPixelFusionIgnoreZero - Class in mpicbg.stitching.fusion
MinPixelFusionIgnoreZero() - Constructor for class mpicbg.stitching.fusion.MinPixelFusionIgnoreZero
Model - Class in stitching.model: Abstract class for arbitrary transformation models to be applied to Points in n-dimensional space.
Model() - Constructor for class stitching.model.Model
mouseClicked(MouseEvent) - Method in class tools.RoiPicker
mouseDragged(MouseEvent) - Method in class tools.RoiPicker
mouseEntered(MouseEvent) - Method in class tools.RoiPicker
mouseExited(MouseEvent) - Method in class tools.RoiPicker
mouseMoved(MouseEvent) - Method in class tools.RoiPicker
mousePressed(MouseEvent) - Method in class tools.RoiPicker
mouseReleased(MouseEvent) - Method in class tools.RoiPicker: Functional method of the RoiPicker.
mouseWheelMoved(MouseWheelEvent) - Method in class tools.RoiPicker
mpicbg.stitching - package mpicbg.stitching
mpicbg.stitching.fusion - package mpicbg.stitching.fusion
multiply(float[], float[], boolean) - Static method in class stitching.CommonFunctions
multiplyComplexImg(float, float, float, float) - Static method in class stitching.CommonFunctions
multiplyComplexReal(float, float, float, float) - Static method in class stitching.CommonFunctions

N

newThreads() - Static method in class stitching.CommonFunctions
newThreads(int) - Static method in class stitching.CommonFunctions
NONE - Static variable in class stitching.CommonFunctions
NoninvertibleModelException - Exception Class in stitching.model: Signalizes that the Model is not invertible.
NoninvertibleModelException() - Constructor for exception class stitching.model.NoninvertibleModelException
NoninvertibleModelException(String) - Constructor for exception class stitching.model.NoninvertibleModelException
NoninvertibleModelException(String, Throwable) - Constructor for exception class stitching.model.NoninvertibleModelException
NoninvertibleModelException(Throwable) - Constructor for exception class stitching.model.NoninvertibleModelException
normalizeComplexVectorsToUnitVectors(float[]) - Static method in class stitching.CommonFunctions
NotEnoughDataPointsException - Exception Class in stitching.model: Signalizes that there were not enough data points available to estimate the Model.
NotEnoughDataPointsException() - Constructor for exception class stitching.model.NotEnoughDataPointsException
NotEnoughDataPointsException(String) - Constructor for exception class stitching.model.NotEnoughDataPointsException
NotEnoughDataPointsException(String, Throwable) - Constructor for exception class stitching.model.NotEnoughDataPointsException
NotEnoughDataPointsException(Throwable) - Constructor for exception class stitching.model.NotEnoughDataPointsException
numberOfChannels - Variable in class Stitching_3D
numberOfChannelsStatic - Static variable in class Stitching_3D

O

o - Variable in class stitching.model.PointMatch
offset - Variable in class stitching.ImageInformation
open(boolean) - Method in class mpicbg.stitching.ImageCollectionElement
openBF(String, boolean, boolean, boolean, boolean, boolean, boolean) - Method in class plugin.Stitching_Grid
openBFDefault(String) - Method in class plugin.Stitching_Grid
openFileRead(File) - Static method in class mpicbg.stitching.TextFileAccess
openFileRead(String) - Static method in class mpicbg.stitching.TextFileAccess
openFileRead(String) - Static method in class Stitch_Image_Collection
openFileReadEx(File) - Static method in class mpicbg.stitching.TextFileAccess
openFileReadEx(String) - Static method in class DeltaVision_Converter
openFileReadEx(String) - Static method in class mpicbg.stitching.TextFileAccess
openFileWrite(File) - Static method in class mpicbg.stitching.TextFileAccess
openFileWrite(String) - Static method in class mpicbg.stitching.TextFileAccess
openFileWrite(String) - Static method in class Stitch_Image_Grid
openFileWriteEx(File) - Static method in class mpicbg.stitching.TextFileAccess
openFileWriteEx(String) - Static method in class DeltaVision_Converter
openFileWriteEx(String) - Static method in class mpicbg.stitching.TextFileAccess
openLOCIImagePlus(String, String, int) - Static method in class stitching.CommonFunctions
openLOCIImagePlus(String, String, int, String) - Static method in class stitching.CommonFunctions
openLOCIImagePlus(String, String, int, String, int, int) - Static method in class stitching.CommonFunctions
optimize(float, int, int) - Method in class stitching.model.TileConfiguration: Minimize the displacement of all correspondence pairs of all tiles.
optimize(Vector<ComparePair>, ImagePlusTimePoint, StitchingParameters) - Static method in class mpicbg.stitching.GlobalOptimization
outputDirectory - Variable in class mpicbg.stitching.StitchingParameters
outputDirectoryStatic - Static variable in class Stitch_Image_Grid_Sequence
outputVariant - Variable in class mpicbg.stitching.StitchingParameters
OverlapFusion - Class in mpicbg.stitching.fusion: This class implements a fusion where only the pixel value of one of the images is used.
OverlapFusion() - Constructor for class mpicbg.stitching.fusion.OverlapFusion
overlapImp - Variable in class stitching.CrossCorrelationResult2D
overlapImp - Variable in class stitching.CrossCorrelationResult3D
overlappingPixels - Variable in class stitching.CrossCorrelationResult2D
overlappingPixels - Variable in class stitching.CrossCorrelationResult3D
OverlapProperties - Class in stitching
OverlapProperties() - Constructor for class stitching.OverlapProperties
overlaps - Variable in class stitching.ImageInformation
overlapStatic - Static variable in class Stitch_Image_Grid_Sequence
overlapStatic - Static variable in class Stitch_Image_Grid
overlapStatic - Static variable in class Stitch_Multiple_Series_File
OverlayFusion - Class in mpicbg.stitching.fusion
OverlayFusion() - Constructor for class mpicbg.stitching.fusion.OverlayFusion

P

PaintInvertibleCoordinateTransformThread - Class in stitching.model: TODO
PaintInvertibleCoordinateTransformThread(ImagePlus, ImageProcessor, ImageProcessor, AtomicBoolean, InvertibleCoordinateTransform) - Constructor for class stitching.model.PaintInvertibleCoordinateTransformThread
PairWiseStitchingImgLib - Class in mpicbg.stitching: Pairwise Stitching of two ImagePlus using ImgLib1 and PhaseCorrelation.
PairWiseStitchingImgLib() - Constructor for class mpicbg.stitching.PairWiseStitchingImgLib
PairWiseStitchingResult - Class in mpicbg.stitching
PairWiseStitchingResult(float[], float, float) - Constructor for class mpicbg.stitching.PairWiseStitchingResult
parseMultiSeriesFile(String, double, boolean, boolean, boolean, boolean) - Method in class Stitch_Multiple_Series_File
PCMValue - Variable in class stitching.CrossCorrelationResult2D
PCMValue - Variable in class stitching.CrossCorrelationResult3D
Peak - Class in mpicbg.stitching
Peak(PhaseCorrelationPeak) - Constructor for class mpicbg.stitching.Peak
performPairWiseStitching(ImagePlus, ImagePlus, StitchingParameters) - Static method in class plugin.Stitching_Pairwise
performStitching(Image<T>, Image<S>, StitchingParameters) - Static method in class mpicbg.stitching.PairWiseStitchingImgLib
pffft2D(FloatArray2D, boolean) - Static method in class stitching.CommonFunctions
pffft3DMT(FloatArray3D, boolean) - Static method in class stitching.CommonFunctions
pffftInv2D(FloatArray2D, int) - Static method in class stitching.CommonFunctions
pffftInv3DMT(FloatArray3D, int) - Static method in class stitching.CommonFunctions
phaseCorrelationFactory - Static variable in class mpicbg.stitching.StitchingParameters: If we cannot wrap, which factory do we use for computing the phase correlation
PixelFusion - Interface in mpicbg.stitching.fusion
pleaseRepaint - Variable in class stitching.model.PaintInvertibleCoordinateTransformThread
plugin - package plugin
Point - Class in stitching.model: An n-dimensional point.
Point(float[]) - Constructor for class stitching.model.Point: Constructor Sets Point.l to the given float[] reference.
Point2D - Class in stitching
Point2D(int, int) - Constructor for class stitching.Point2D
Point2D(int, int, float) - Constructor for class stitching.Point2D
Point3D - Class in stitching
Point3D(int, int, int) - Constructor for class stitching.Point3D
Point3D(int, int, int, float) - Constructor for class stitching.Point3D
PointMatch - Class in stitching.model: A link between two Points that are expected to be ideally at the same location in the world coordinate space.
PointMatch(Point, Point) - Constructor for class stitching.model.PointMatch: Constructor Create a PointMatch without weight.
PointMatch(Point, Point, float) - Constructor for class stitching.model.PointMatch: Constructor Create a PointMatch with one weight.
PointMatch(Point, Point, float[]) - Constructor for class stitching.model.PointMatch: Constructor Create a PointMatch with an Array of weights.
PointMatch(Point, Point, float[], float) - Constructor for class stitching.model.PointMatch: Constructor Create a PointMatch with an Array of weights and a strength.
PointMatch(Point, Point, float, float) - Constructor for class stitching.model.PointMatch: Constructor Create a PointMatch with one weight and strength.
PointMatch(Point, Point, float, OverlapProperties) - Constructor for class stitching.model.PointMatch
PointMatchStitching - Class in mpicbg.stitching
PointMatchStitching(Point, Point, float, ComparePair) - Constructor for class mpicbg.stitching.PointMatchStitching: Constructor Create a PointMatch with one weight.
position - Variable in class stitching.ImageInformation
previewOnlyStatic - Static variable in class Stitch_Image_Collection
previewOnlyStatic - Static variable in class Stitch_Image_Grid_Sequence
previewOnlyStatic - Static variable in class Stitch_Image_Grid
previewOnlyStatic - Static variable in class Stitch_Many_Images
previewOnlyStatic - Static variable in class Stitch_Multiple_Series_File
printValue - Variable in class stitching.Point3D

Q

quicksort(Quicksortable[], int, int) - Static method in class stitching.CommonFunctions
Quicksortable - Interface in stitching

R

R - Variable in class stitching.CrossCorrelationResult2D
R - Variable in class stitching.CrossCorrelationResult3D
R - Variable in class stitching.OverlapProperties
ransac(Class<M>, List<PointMatch>, Collection<PointMatch>, int, double, double) - Static method in class stitching.model.Model: Estimate a Model from a set with many outliers by first filtering the worst outliers with ransac \citet[{FischlerB81} tand filter potential outliers by robust iterative regression.
RED_CYAN - Static variable in class stitching.CommonFunctions
redrawDelay - Static variable in class mpicbg.stitching.fusion.Fusion
regThreshold - Variable in class mpicbg.stitching.StitchingParameters
relativeThreshold - Variable in class mpicbg.stitching.StitchingParameters
removeConnectedTile(Tile) - Method in class stitching.model.Tile: Remove a Tile from the set of connected Tiles.
resetConnectedTiles() - Method in class stitching.model.Tile
resetMatches() - Method in class stitching.model.Tile
resetTile() - Method in class stitching.model.Tile
resultChoices - Static variable in class plugin.Stitching_Grid
rgbOrder - Variable in class Stitch_Image_Collection
rgbOrder - Variable in class stitching.GridLayout
rgbOrderStatic - Static variable in class Stitch_Image_Collection
rgbOrderStatic - Static variable in class Stitch_Image_Directory
rgbOrderStatic - Static variable in class Stitch_Image_Grid_Sequence
rgbOrderStatic - Static variable in class Stitch_Image_Grid
rgbOrderStatic - Static variable in class Stitch_Many_Images
rgbTypes - Static variable in class stitching.CommonFunctions
rnd - Static variable in class stitching.model.Model
RoiPicker - Class in tools: This tool is used to select the Rois containing a specific x, y position (obtained by a mouse click).
RoiPicker() - Constructor for class tools.RoiPicker
run() - Method in class stitching.model.PaintInvertibleCoordinateTransformThread
run(ImagePlus...) - Method in class mpicbg.stitching.Downsampler: Runs the "Image > Scale..." plugin on all provided ImagePlus objects, based on the previous Downsampler.getInput(int, int) call.
run(String) - Method in class DeltaVision_Converter
run(String) - Method in class plugin.Stitching_Grid
run(String) - Method in class plugin.Stitching_Pairwise
run(String) - Method in class Stitch_Image_Collection
run(String) - Method in class Stitch_Image_Directory
run(String) - Method in class Stitch_Image_Grid_Sequence
run(String) - Method in class Stitch_Image_Grid
run(String) - Method in class Stitch_Many_Images
run(String) - Method in class Stitch_Multiple_Series_File
run(String) - Method in class Stitching_2D
run(String) - Method in class Stitching_3D
run(String) - Method in class tools.RoiPicker
run(List<ImageCollectionElement>) - Method in class mpicbg.stitching.Downsampler: Scales all provided ImageCollectionElements based on the previous Downsampler.getInput(int, int) call.
run(ImageCollectionElement) - Method in class mpicbg.stitching.Downsampler: Scales the specified ImageCollectionElement based on the previous Downsampler.getInput(int, int) call.
runStitching() - Method in class Stitch_Many_Images: Calls the Stitching with the parameters provided

S

select(String, String, String, String, String, String, String) - Static method in class tools.RoiPicker
seperateOverlapY - Static variable in class plugin.Stitching_Grid
seqRange - Variable in class mpicbg.stitching.StitchingParameters
sequential - Variable in class mpicbg.stitching.StitchingParameters
seriesNumber - Variable in class stitching.ImageInformation
set(float, int, int) - Method in class stitching.FloatArray2D
set(float, int, int, int) - Method in class stitching.FloatArray3D
set(Interval, int) - Method in class mpicbg.stitching.fusion.ClassifiedRegion: Sets the interval of this region for the specified axis (index)
setCost(double) - Method in class stitching.model.Model
setCrossCorrelation(float) - Method in class mpicbg.stitching.ComparePair
setDimensionality(int) - Method in class mpicbg.stitching.ImageCollectionElement
setError(double) - Method in class stitching.model.Model: Deprecated.
The term Error may be missleading---use Model.getCost() instead
setImagePlus(ImagePlus) - Method in class mpicbg.stitching.ImageCollectionElement: Used by the multi-series stitching
setIsValidOverlap(boolean) - Method in class mpicbg.stitching.ComparePair
setMax(int) - Method in class mpicbg.stitching.fusion.Interval: Update the end position of this interval.
setMin(int) - Method in class mpicbg.stitching.fusion.Interval: Update the start position of this interval.
setModel(Model<?>) - Method in class mpicbg.stitching.ImageCollectionElement
setOffset(float[]) - Method in class mpicbg.stitching.ImageCollectionElement
setRelativeShift(float[]) - Method in class mpicbg.stitching.ComparePair
setWeight(int, float) - Method in class stitching.model.PointMatch
setWeights(float[]) - Method in class stitching.model.PointMatch
shake(Collection<PointMatch>, float, float[]) - Method in class stitching.model.Model: randomly change the model a bit estimates the necessary amount of shaking for each single dimensional distance in the set of matches
shake(Collection<PointMatch>, float, float[]) - Method in class stitching.model.TranslationModel2D: change the model a bit estimates the necessary amount of shaking for each single dimensional distance in the set of matches
shake(Collection<PointMatch>, float, float[]) - Method in class stitching.model.TranslationModel3D: change the model a bit estimates the necessary amount of shaking for each single dimensional distance in the set of matches
shift - Variable in class Stitching_2D
shift - Variable in class stitching.CrossCorrelationResult2D
shift - Variable in class stitching.CrossCorrelationResult3D
showOptionDialog() - Method in class tools.RoiPicker
size - Variable in class stitching.ImageInformation
size() - Method in class mpicbg.stitching.fusion.ClassifiedRegion
sizeX - Variable in class stitching.GridLayout
sizeY - Variable in class stitching.GridLayout
slope - Variable in class stitching.model.ErrorStatistic
sortedValues - Variable in class stitching.model.ErrorStatistic
source - Variable in class stitching.model.PaintInvertibleCoordinateTransformThread
squareDistance(Point, Point) - Static method in class stitching.model.Point: Estimate the square distance of two Points in the world.
SSQ - Variable in class stitching.CrossCorrelationResult2D
SSQ - Variable in class stitching.CrossCorrelationResult3D
startAndJoin(Thread[]) - Static method in class stitching.CommonFunctions
startIStatic - Static variable in class Stitch_Image_Grid_Sequence
startIStatic - Static variable in class Stitch_Image_Grid
startTask(Runnable, int) - Static method in class stitching.CommonFunctions
startXStatic - Static variable in class Stitch_Image_Grid_Sequence
startXStatic - Static variable in class Stitch_Image_Grid
startYStatic - Static variable in class Stitch_Image_Grid_Sequence
startYStatic - Static variable in class Stitch_Image_Grid
startZStatic - Static variable in class Stitch_Image_Grid_Sequence
std - Variable in class stitching.model.ErrorStatistic
std0 - Variable in class stitching.model.ErrorStatistic
Stitch_Image_Collection - Class in Unnamed Package
Stitch_Image_Collection() - Constructor for class Stitch_Image_Collection
Stitch_Image_Directory - Class in Unnamed Package
Stitch_Image_Directory() - Constructor for class Stitch_Image_Directory
Stitch_Image_Grid - Class in Unnamed Package
Stitch_Image_Grid() - Constructor for class Stitch_Image_Grid
Stitch_Image_Grid_Sequence - Class in Unnamed Package: Plugin class to stitch a sequence of grid of images (fixed X/Y configuration)
Stitch_Image_Grid_Sequence() - Constructor for class Stitch_Image_Grid_Sequence
Stitch_Many_Images - Class in Unnamed Package
Stitch_Many_Images() - Constructor for class Stitch_Many_Images
Stitch_Many_Images.IntroItemListener - Class in Unnamed Package: Makes sure that only one item is selected at a time
Stitch_Multiple_Series_File - Class in Unnamed Package
Stitch_Multiple_Series_File() - Constructor for class Stitch_Multiple_Series_File
stitchCollection() - Method in class Stitch_Many_Images: Manages the dialog for stitching a collection of images defined by a Tileconfiguration file
stitchCollection(ArrayList<ImageCollectionElement>, StitchingParameters) - Static method in class mpicbg.stitching.CollectionStitchingImgLib
stitchDirectory() - Method in class Stitch_Many_Images: Manages the dialog for stitching all files in a directory with unknown configuration
stitchGrid() - Method in class Stitch_Many_Images: Manages the dialog for stitching a grid of images
stitchImageGrid(String, String, GridLayout, String, String, String, double, int, int, int, boolean, boolean, boolean) - Static method in class Stitch_Image_Grid: Stitch grid of 2D images
stitchImageGridSequence(int, String, String, GridLayout, String, String, String, String, double, int, int, int, int, boolean, boolean, boolean) - Static method in class Stitch_Image_Grid_Sequence: Stitch sequence of image grids (all grids must have the same X/Y configuration)
stitching - package stitching
Stitching_2D - Class in Unnamed Package
Stitching_2D() - Constructor for class Stitching_2D
Stitching_2D(boolean, int, boolean, String, String) - Constructor for class Stitching_2D
Stitching_3D - Class in Unnamed Package
Stitching_3D() - Constructor for class Stitching_3D
Stitching_3D(boolean, int, boolean, String, String) - Constructor for class Stitching_3D
Stitching_Grid - Class in plugin
Stitching_Grid() - Constructor for class plugin.Stitching_Grid
Stitching_Pairwise - Class in plugin
Stitching_Pairwise() - Constructor for class plugin.Stitching_Pairwise
stitching.model - package stitching.model
stitching.utils - package stitching.utils
StitchingParameters - Class in mpicbg.stitching
StitchingParameters() - Constructor for class mpicbg.stitching.StitchingParameters
stitchingType - Static variable in class Stitch_Many_Images
stitchMultiSeriesFile() - Method in class Stitch_Many_Images: Manages the dialog for stitching all tiles in a multi-series file
stitchPairwise(ImagePlus, ImagePlus, Roi, Roi, int, int, StitchingParameters) - Static method in class mpicbg.stitching.PairWiseStitchingImgLib
strength - Variable in class stitching.model.PointMatch
subpixelAccuracy - Variable in class mpicbg.stitching.StitchingParameters
switchZCinXYCZT(ImagePlus) - Static method in class mpicbg.stitching.fusion.OverlayFusion: Rearranges an ImageJ XYCZT Hyperstack into XYZCT without wasting memory for processing 3d images as a chunk, if it is already XYZCT it will shuffle it back to XYCZT
switchZTinXYCZT(ImagePlus) - Static method in class mpicbg.stitching.fusion.OverlayFusion: Rearranges an ImageJ XYCTZ Hyperstack into XYCZT without wasting memory for processing 3d images as a chunk, if it is already XYCTZ it will shuffle it back to XYCZT

T

target - Variable in class stitching.model.PaintInvertibleCoordinateTransformThread
test(Model, Collection<PointMatch>, Collection<PointMatch>, double, double) - Static method in class stitching.model.Model: Test the Model for a set of point correspondence candidates.
testRegistrationCompatibility(ImagePlus, ImagePlus) - Static method in class plugin.Stitching_Pairwise
TextFileAccess - Class in mpicbg.stitching
TextFileAccess() - Constructor for class mpicbg.stitching.TextFileAccess
thresholdDisplacementAbsolute - Variable in class Stitch_Image_Collection
thresholdDisplacementAbsolute - Variable in class Stitch_Multiple_Series_File
thresholdDisplacementAbsolute - Variable in class stitching.GridLayout
thresholdDisplacementAbsoluteStatic - Static variable in class Stitch_Image_Collection
thresholdDisplacementAbsoluteStatic - Static variable in class Stitch_Image_Directory
thresholdDisplacementAbsoluteStatic - Static variable in class Stitch_Image_Grid_Sequence
thresholdDisplacementAbsoluteStatic - Static variable in class Stitch_Image_Grid
thresholdDisplacementAbsoluteStatic - Static variable in class Stitch_Many_Images
thresholdDisplacementAbsoluteStatic - Static variable in class Stitch_Multiple_Series_File
thresholdDisplacementRelative - Variable in class Stitch_Image_Collection
thresholdDisplacementRelative - Variable in class Stitch_Multiple_Series_File
thresholdDisplacementRelative - Variable in class stitching.GridLayout
thresholdDisplacementRelativeStatic - Static variable in class Stitch_Image_Collection
thresholdDisplacementRelativeStatic - Static variable in class Stitch_Image_Directory
thresholdDisplacementRelativeStatic - Static variable in class Stitch_Image_Grid_Sequence
thresholdDisplacementRelativeStatic - Static variable in class Stitch_Image_Grid
thresholdDisplacementRelativeStatic - Static variable in class Stitch_Many_Images
thresholdDisplacementRelativeStatic - Static variable in class Stitch_Multiple_Series_File
thresholdR - Variable in class Stitch_Image_Collection
thresholdR - Variable in class Stitch_Multiple_Series_File
thresholdR - Variable in class stitching.GridLayout
thresholdRStatic - Static variable in class Stitch_Image_Collection
thresholdRStatic - Static variable in class Stitch_Image_Directory
thresholdRStatic - Static variable in class Stitch_Image_Grid_Sequence
thresholdRStatic - Static variable in class Stitch_Image_Grid
thresholdRStatic - Static variable in class Stitch_Many_Images
thresholdRStatic - Static variable in class Stitch_Multiple_Series_File
Tile - Class in stitching.model: TODO
Tile(double, double, Model) - Constructor for class stitching.model.Tile: Constructor
Tile(float, float, Model) - Constructor for class stitching.model.Tile: Constructor
TileConfiguration - Class in stitching.model: A configuration of rigidly transformed tiles.
TileConfiguration() - Constructor for class stitching.model.TileConfiguration
TileConfigurationStitching - Class in mpicbg.stitching
TileConfigurationStitching() - Constructor for class mpicbg.stitching.TileConfigurationStitching
tileConfStatic - Static variable in class Stitch_Image_Directory
tileConfStatic - Static variable in class Stitch_Image_Grid_Sequence
tileConfStatic - Static variable in class Stitch_Image_Grid
timeSelect - Variable in class mpicbg.stitching.StitchingParameters
timeSelect - Static variable in class stitching.CommonFunctions
timestamp(String) - Static method in class stitching.utils.Log: Issues an informational message with timestamp to the ImageJ log window.
tmp - Variable in class stitching.ImageInformation
tools - package tools
toString() - Method in class mpicbg.stitching.fusion.ClassifiedRegion
toString() - Method in class mpicbg.stitching.fusion.Interval
toString() - Method in class stitching.ImageInformation
toString() - Method in class stitching.model.Model: Create a meaningful string representation of the model for save into text-files or display on terminals.
toString() - Method in class stitching.model.TranslationModel2D
toString() - Method in class stitching.model.TranslationModel3D
toString() - Method in class stitching.Point2D
toString() - Method in class stitching.Point3D
transform - Variable in class stitching.model.PaintInvertibleCoordinateTransformThread
translation - Variable in class stitching.model.TranslationModel2D
translation - Variable in class stitching.model.TranslationModel3D
translation2D - Variable in class stitching.OverlapProperties
translation3D - Variable in class stitching.OverlapProperties
TranslationModel2D - Class in stitching.model: TODO
TranslationModel2D() - Constructor for class stitching.model.TranslationModel2D
TranslationModel3D - Class in stitching.model: TODO
TranslationModel3D() - Constructor for class stitching.model.TranslationModel3D

U

update() - Method in class stitching.model.Tile: Apply the current Model to all local point coordinates.
updateByStrength(float) - Method in class stitching.model.Tile: Apply the current Model to all local point coordinates by weight.
updateCalibration(Calibration, Calibration) - Static method in class Stitch_Image_Collection
updateErrors() - Method in class mpicbg.stitching.TileConfigurationStitching: Estimate min/max/average displacement of all PointMatches in all Tiles.

V

validOverlap - Variable in class stitching.OverlapProperties
value - Variable in class stitching.Point2D
value - Variable in class stitching.Point3D
values - Variable in class stitching.model.ErrorStatistic
var - Variable in class stitching.model.ErrorStatistic
var0 - Variable in class stitching.model.ErrorStatistic
version - Static variable in class plugin.Stitching_Grid
virtual - Variable in class mpicbg.stitching.StitchingParameters

W

w - Variable in class stitching.ImageInformation
warn(String) - Static method in class stitching.utils.Log: Issues a warning message to the ImageJ log window.
wasIndexed - Variable in class Stitching_3D
weight - Variable in class stitching.model.PointMatch
weights - Variable in class stitching.model.PointMatch
width - Variable in class stitching.FloatArray2D
width - Variable in class stitching.FloatArray3D
windowing - Variable in class Stitching_2D
windowing - Variable in class Stitching_3D
windowingStatic - Static variable in class Stitching_2D
windowingStatic - Static variable in class Stitching_3D
work() - Method in class Stitching_2D
work() - Method in class Stitching_3D
work(String, boolean, boolean, String, String, boolean) - Method in class Stitch_Image_Collection
work(ArrayList<ImageInformation>, boolean, boolean, String, String, String, boolean) - Method in class Stitch_Image_Collection
work(FloatArray2D, FloatArray2D) - Method in class Stitching_2D
work(FloatArray3D, FloatArray3D) - Method in class Stitching_3D
work(GridLayout, boolean, boolean, String, boolean) - Method in class Stitch_Image_Collection
worstTile - Variable in class mpicbg.stitching.TileConfigurationStitching
writeBlock(Img<T>, int, int, int, int, int, ArrayList<? extends ImageInterpolation<? extends RealType<?>>>, double[], ArrayList<InvertibleBoundable>, PixelFusion, String) - Static method in class mpicbg.stitching.fusion.Fusion: Fuse one slice/volume (one channel)
writeOnlyTileConfStatic - Static variable in class plugin.Stitching_Grid
writeOnlyTileConfStatic - Static variable in class Stitch_Image_Grid_Sequence
writeOnlyTileConfStatic - Static variable in class Stitch_Image_Grid
writeOutputConfiguration(String, ArrayList<ImageInformation>) - Method in class Stitch_Image_Collection
writeRegisteredTileConfiguration(File, ArrayList<ImageCollectionElement>) - Method in class plugin.Stitching_Grid
writeTileConfiguration(File, ArrayList<ImageCollectionElement>) - Method in class plugin.Stitching_Grid

X

x - Variable in class stitching.Point2D
x - Variable in class stitching.Point3D
xOffset - Variable in class mpicbg.stitching.StitchingParameters
xOffset - Variable in class Stitching_2D
xOffset - Variable in class Stitching_3D
xOffsetStatic - Static variable in class Stitching_2D
xOffsetStatic - Static variable in class Stitching_3D

Y

y - Variable in class stitching.Point2D
y - Variable in class stitching.Point3D
yOffset - Variable in class mpicbg.stitching.StitchingParameters
yOffset - Variable in class Stitching_2D
yOffset - Variable in class Stitching_3D
yOffsetStatic - Static variable in class Stitching_2D
yOffsetStatic - Static variable in class Stitching_3D

Z

z - Variable in class stitching.Point3D
zeroPad(FloatArray2D, int, int) - Static method in class stitching.CommonFunctions
zeroPad(FloatArray3D, int, int, int) - Static method in class stitching.CommonFunctions
zeroPadImages(FloatArray2D, FloatArray2D) - Static method in class stitching.CommonFunctions
zeroPadImages(FloatArray3D, FloatArray3D) - Static method in class stitching.CommonFunctions
zOffset - Variable in class mpicbg.stitching.StitchingParameters
zOffset - Variable in class Stitching_3D
zOffsetStatic - Static variable in class Stitching_3D

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