Index (fijiyama 4.3.1 API)

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

A

abortCurrentAction() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Abort current action.
actionAddMiddlePoints() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Action add middle points.
actionBackExtendBranch() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Action backextend branch.
actionChangeTime() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Action change time.
actionClickedInList() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Action clicked in list.
actionCreateBranch() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Action create branch.
actionExtendBranch() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Action extend branch.
actionInfo() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Action info.
actionMovePoint() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Action move point.
actionOkClicked() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Action ok clicked.
actionPerformed(ActionEvent) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Action performed.
actionPerformed(ActionEvent) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Action performed.
actionPerformed(ActionEvent) - Method in class io.github.rocsg.fijiyama.rsml.RSMLGUI: Define the different action possible in the SRWin window.
actionRemovePoint() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Action remove point.
actionResample() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Action save.
actionSave() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Action save.
actionSwitchPoint() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Action switch point.
actionUndo() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Action undo.
actualizeData(ImagePlus, ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Actualize data.
actualizeLaunchingInterface(boolean) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Actualize launching interface.
addFirstActionOfPipeline() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Adds the first action of pipeline.
addition(ImagePlus, ImagePlus, boolean) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Addition.
addLabelOnAllSlices(ImagePlus, String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Adds the label on all slices.
addLog(String, int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Adds the log.
addLog(String, int) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Adds the log.
addMark(int, String, float) - Method in class io.github.rocsg.fijiyama.rsml.Root: Add a mark to the root.
addMark(Mark) - Method in class io.github.rocsg.fijiyama.rsml.Root: Add a mark to the root.
addMiddlePointsInModel(Point3d[], RootModel) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Adds the middle points in model.
addNode(double, double, double, double, boolean) - Method in class io.github.rocsg.fijiyama.rsml.Root: Adds the node.
addNode(double, double, double, double, double, double, double, boolean) - Method in class io.github.rocsg.fijiyama.rsml.Root: Adds the node.
addNode(float, float, boolean) - Method in class io.github.rocsg.fijiyama.rsml.Root: Add a node to the root.
addSliceToImage(ImagePlus, ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Adds the slice to image.
addStepToQueue(int, int, double, int, double, Transform3DType, double[], OptimizerType, ScalerType, double[], boolean, CenteringStrategy, SamplingStrategy) - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Adds the step to queue.
addTransform(ItkTransform) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Adds the transform.
addTransform(Transform) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Adds the transform.
addTransformAndActionBlindlyForBuilding(ItkTransform, RegistrationAction) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Adds the transform and action blindly for building.
addTransformToAction(ItkTransform, RegistrationAction, int, int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Adds the transform to action.
adjustContrast3d(ImagePlus, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Adjust contrast 3 d.
adjustFrameOnScreen(Frame, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Adjust frame on screen.
adjustFrameOnScreenRelative(Frame, Frame, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Adjust frame on screen relative.
adjustImageCalibration(ImagePlus, double[], String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Adjust image calibration.
adjustImageCalibration(ImagePlus, ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Adjust image calibration.
adjustImageOnScreen(ImagePlus, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Adjust image on screen.
adjustImageOnScreenRelative(ImagePlus, ImagePlus, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Adjust image on screen relative.
adjustSettings(Fijiyama_GUI, RegistrationManager) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Adjust settings.
adjustVoxelSize(ImagePlus, double[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Adjust voxel size.
adjustVoxelSize(ImagePlus, double[], String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Adjust voxel size.
adjustZoomFactor(double) - Method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Adjust zoom factor.
AFFINE - io.github.rocsg.fijiyama.registration.Transform3DType: The affine.
anchor - Variable in class io.github.rocsg.fijiyama.rsml.Root: The mdl.
angle - Variable in class io.github.rocsg.fijiyama.rsml.Mark: The angle.
AngleComparator() - Constructor for class io.github.rocsg.fijiyama.registration.TransformUtils.AngleComparator
ANTS - io.github.rocsg.fijiyama.registration.MetricType: The ants.
applyTransformToGeometry(ItkTransform) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Apply transform to geometry.
array16ElementsToItkTransform(double[]) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Array 16 elements to itk transform.
attachChild(Root) - Method in class io.github.rocsg.fijiyama.rsml.Root: Attach the selected root to the parent and set child informations.
attachLatToPrime() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Attach lat to prime.
attachParent(Root) - Method in class io.github.rocsg.fijiyama.rsml.Root: Attach the selected root as parent.
AUTOMATIC - Static variable in interface io.github.rocsg.fijiyama.common.VitiDialogs: The Constant AUTOMATIC.
axisAlignmentDone() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Axis alignment done.
axisGP - Variable in class io.github.rocsg.fijiyama.rsml.Root: The axis GP.

B

backExtendBranchInModel(Point3d[], RootModel) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Extend branch in model.
bhsX - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The bhs X.
bhsY - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The bhs Y.
bhsZ - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The bhs Z.
binaryOperationBetweenTwoImages(ImagePlus, ImagePlus, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Binary operation between two images.
bionanoCapillaryRadius - Static variable in class io.github.rocsg.fijiyama.common.VitimageUtils: The Constant bionanoCapillaryRadius.
birthTime - Variable in class io.github.rocsg.fijiyama.rsml.Node: The birth time.
birthTimeHours - Variable in class io.github.rocsg.fijiyama.rsml.Node: The birth time.
BLOCKMATCHING - io.github.rocsg.fijiyama.registration.OptimizerType: The blockmatching.
BlockMatchingRegistration - Class in io.github.rocsg.fijiyama.registration: The Class BlockMatchingRegistration.
BlockMatchingRegistration() - Constructor for class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Instantiates a new block matching registration.
BlockMatchingRegistration(ImagePlus, ImagePlus, Transform3DType, MetricType, double, double, int, int, int, int, ImagePlus, int, int, int, int, int, int, int, int, int, int) - Constructor for class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Starting points.
blockR2ValuesAft - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The block R 2 values aft.
blockR2ValuesBef - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The block R 2 values bef.
blockSizeHalfX - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The block size half X.
blockSizeHalfY - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The block size half Y.
blockSizeHalfZ - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The block size half Z.
blockSizeX - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The block size X.
blockSizeY - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The block size Y.
blockSizeZ - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The block size Z.
blocksStrideX - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The blocks stride X.
blocksStrideY - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The blocks stride Y.
blocksStrideZ - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The blocks stride Z.
bmIsInterrupted - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The bm is interrupted.
bmIsInterruptedSucceeded - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The bm is interrupted succeeded.
Bord - Class in io.github.rocsg.fijiyama.common: The Class Bord.
Bord(Pix, Pix) - Constructor for class io.github.rocsg.fijiyama.common.Bord: Instantiates a new bord.
bordersGP - Variable in class io.github.rocsg.fijiyama.rsml.Root: The borders GP.
BOTTOM - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.ScrollUtil: The Constant SELECTED.
boxClikedInGui() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Box cliked in gui.
boxDisplay - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The box display.
boxDisplayMan - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The box display man.
boxOptimizer - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The box optimizer.
boxTypeAction - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The box type action.
boxTypeTrans - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The box type trans.
buildDistances(double) - Static method in class io.github.rocsg.fijiyama.common.MostRepresentedFilter: Builds the distances.
buildDistances(int[], double[]) - Static method in class io.github.rocsg.fijiyama.common.MostRepresentedFilter: Builds the distances.
buildImageLookup(double[][][], double[], double) - Static method in class io.github.rocsg.fijiyama.common.MostRepresentedFilter: Builds the image lookup.
buildLookup(double) - Static method in class io.github.rocsg.fijiyama.common.MostRepresentedFilter: Builds the lookup.
buildLookup3D(double, int[], double[]) - Static method in class io.github.rocsg.fijiyama.common.MostRepresentedFilter: Builds the lookup 3 D.
buildNode() - Method in class io.github.rocsg.fijiyama.rsml.Node: Build the node.
buildTestDataForJacobianStuff() - Static method in class io.github.rocsg.fijiyama.registration.TestingRegistrationPackage: Builds the test data for jacobian stuff.

C

calcCLength() - Method in class io.github.rocsg.fijiyama.rsml.Node: Compute the length between the base of the root and the node.
calcCLength(float) - Method in class io.github.rocsg.fijiyama.rsml.Node: Compute the length between the base of the root and the node.
calcNNodes() - Method in class io.github.rocsg.fijiyama.rsml.Root: /** compute the number of nodes inside the root.
calculateAngle(double, double) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: Mathematic utilities.
capillaryCoordinatesAlongZ(ImagePlus, int[], double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Capillary coordinates along Z.
capillaryValuesAlongZStatic(ImagePlus, int[], double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Capillary values along Z static.
caracterizeBackgroundOfImage(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Caracterize background of image.
CenteringStrategy - Enum in io.github.rocsg.fijiyama.registration: The Enum CenteringStrategy.
changeCurrentAction(int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Change current action.
changeTimeBasis(double, int) - Method in class io.github.rocsg.fijiyama.rsml.Root
changeTimeBasis(double, int) - Method in class io.github.rocsg.fijiyama.rsml.RootModel
changeTimeInPointInModel(Point3d[], RootModel) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Change time in point in model.
channelSplitter(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Channel splitter.
checkComputerCapacity(boolean) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Check computer capacity.
checkComputerCapacity(boolean) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Check computer capacity.
child - Variable in class io.github.rocsg.fijiyama.rsml.Node: The child.
childList - Variable in class io.github.rocsg.fijiyama.rsml.Root: The child list.
chooseDirectoryNiceUI(String, String) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: UI generic functions to open other files : directories, roiset, transforms.
chooseDirectoryUI(String, String) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Choose directory UI.
chooseNumberUI(String, int, int, int) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Choose number UI.
chooseOneImageUI(String, String) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: UI generic functions to access images.
chooseOneImageUIPath(String, String) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Choose one image UI path.
chooseOneRoiPathUI(String, String) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Choose one roi path UI.
chooseOneTransformsUI(String, String, boolean) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Choose one transforms UI.
chooseSizeUI(ImagePlus, String, boolean) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: UI generic functions to ask simple data : image dimensions, voxel size, boolean yes/no , double or integer number, or String.
chooseTransformsUI(String, boolean) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Choose transforms UI.
chooseTwoImagesUI(String, String, String) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Choose two images UI.
chooseVoxSizeUI(ImagePlus, String, boolean) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Choose vox size UI.
cleanNegativeTh() - Method in class io.github.rocsg.fijiyama.rsml.Root
cleanNegativeTh() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get the closest root from the base of a given root .
cleanWildRsml() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Clean wild rsml.
clear() - Method in class io.github.rocsg.fijiyama.rsml.Root: Delete all the root informations.
clearDatafile() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Remove all the roots from the root list.
cLength - Variable in class io.github.rocsg.fijiyama.rsml.Node: The birth time.
clipFloatImage(ImagePlus, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Clip float image.
closeAllViews() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Close all views.
closeAllViews() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Close all views.
closeLastImages() - Method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Close last images.
combine2DArrayOfImage(ImagePlus[][]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Combine 2 D array of image.
comboBoxChanged - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The combo box changed.
compare(Object, Object) - Method in class io.github.rocsg.fijiyama.registration.TransformUtils.AngleComparator: Compare.
compare(Object, Object) - Method in class io.github.rocsg.fijiyama.registration.TransformUtils.VolumeComparator: Compare.
compareTo(Root) - Method in class io.github.rocsg.fijiyama.rsml.Root: Compare to.
composeTransformsWithGui() - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Compose transforms with gui.
compositeNoAdjustOf(ImagePlus, ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Composite no adjust of.
compositeNoAdjustOf(ImagePlus, ImagePlus, String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Composite no adjust of.
compositeOf(ImagePlus, ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Composite of.
compositeOf(ImagePlus, ImagePlus, String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Composite of.
compositeRGBByte(ImagePlus, ImagePlus, ImagePlus, double, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Composite RGB byte.
compositeRGBByteTab(ImagePlus[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Composite RGB byte tab.
compositeRGBDouble(ImagePlus, ImagePlus, ImagePlus, double, double, double, String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Composite RGB double.
compositeRGBDoubleJet(ImagePlus, ImagePlus, ImagePlus, String, boolean, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Composite RGB double jet.
compositeRGBLByte(ImagePlus, ImagePlus, ImagePlus, ImagePlus, double, double, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Composite RGBL byte.
computeDenseFieldFromSparseCorrespondancePoints(Point3d[][], ImagePlus, double) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Compute dense field from sparse correspondance points.
computeDenseFieldFromSparseCorrespondancePoints(Point3d[][], ImagePlus, double, boolean) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Compute dense field from sparse correspondance points.
computeDistances() - Method in class io.github.rocsg.fijiyama.rsml.Root: Compute distances.
computeInitialFeasibleSolution() - Method in class io.github.rocsg.fijiyama.common.HungarianAlgorithm: Compute an initial feasible solution by assigning zero labels to the workers and by assigning to each job a label equal to the minimum cost among its incident edges.
computeMismatches(Point3d[][], double[], double[], String) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Compute mismatches.
computeRegisteredImage() - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Compute registered image.
computeRiceSigmaFromBackgroundValuesStatic(double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Compute rice sigma from background values static.
computeRootLength() - Method in class io.github.rocsg.fijiyama.rsml.Root: Compute root length.
computeRootLength(double) - Method in class io.github.rocsg.fijiyama.rsml.Root: Compute root length.
computeSpeedVectors(double) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Compute speed vectors.
computeSpeedVectors(double, double, boolean) - Method in class io.github.rocsg.fijiyama.rsml.Root: Compute speed vectors.
computeSummary - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The compute summary.
computeSummaryOfLacuneData(String, String, boolean) - Static method in class io.github.rocsg.fijiyama.rsml.Tests
connexe(ImagePlus, double, double, double, double, int, int, boolean) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Connexe.
connexe2d(ImagePlus, double, double, double, double, int, int, boolean) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Connexe 2 d.
connexe2dNoFuckWithVolume(ImagePlus, double, double, double, double, int, int, boolean) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Connexe 2 d no fuck with volume.
connexeBinaryEasierParamsConnexitySelectvol(ImagePlus, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Connexe binary easier params connexity selectvol.
connexeNoFuckWithVolume(ImagePlus, double, double, double, double, int, int, boolean) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Connected components utilities.
consoleOutputActivated - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The console output activated.
convertByteToFloatWithoutDynamicChanges(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Convert byte to float without dynamic changes.
convertDisplacementFieldFloatToImagePlusArray(Image) - Static method in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface: Convert displacement field float to image plus array.
convertDisplacementFieldToImagePlusArrayAndNorm(Image) - Static method in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface: Convert displacement field to image plus array and norm.
convertDoubleArrayToPoint3dArray(double[][]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Convert double array to point 3 d array.
convertFloatToByteWithoutDynamicChanges(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Convert float to byte without dynamic changes.
convertFloatToShortWithoutDynamicChanges(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Convert float to short without dynamic changes.
convertImagePlusArrayToDisplacementField(ImagePlus[]) - Static method in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface: Convert image plus array to displacement field.
convertItkTransformToImagePlusArray(ItkTransform) - Static method in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface: Convert itk transform to image plus array.
convertLandmarksToPoints(ImagePlus, ImagePlus, boolean) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Convert landmarks to points.
convertPoint3dArrayToDoubleArray(Point3d[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Convert point 3 d array to double array.
convertPointToImageSpace(Point3d, ImagePlus) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: Convert point to image space.
convertPointToRealSpace(Point3d, ImagePlus) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: Convert point to real space.
convertShortToFloatWithoutDynamicChanges(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Wrappers or implementations of some useful thresholding and dynamic adjustment.
convertToFloat(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Convert to float.
convertToGray8(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils
convexhullGP - Variable in class io.github.rocsg.fijiyama.rsml.Root: The convexhull GP.
COORD_OF_MAX_ALONG_Z - Static variable in class io.github.rocsg.fijiyama.common.VitimageUtils: The Constant COORD_OF_MAX_ALONG_Z.
COORD_OF_MAX_IN_TWO_LAST_SLICES - Static variable in class io.github.rocsg.fijiyama.common.VitimageUtils: The Constant COORD_OF_MAX_IN_TWO_LAST_SLICES.
copy(Node) - Method in class io.github.rocsg.fijiyama.rsml.Node: Copy.
copyImageCalibrationAndRange(ImagePlus, ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Copy image calibration and range.
copyWithModifiedElements(RegistrationAction, int, int, int, int, int) - Static method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Copy with modified elements.
CORRELATION - io.github.rocsg.fijiyama.registration.MetricType: The correlation.
correlationCoefficient(double[], double[]) - Method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Correlation coefficient.
correspondanceProvidedAtStart - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The correspondance provided at start.
correspondancesSummary - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The correspondances summary.
createBlockPropsFromBlockList(double[][], int) - Method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Creates the block props from block list.
createBranchInModel(Point3d[], RootModel) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Creates the branch in model.
createDirectionCosinesFromPointList(ArrayList<double[]>) - Static method in class io.github.rocsg.fijiyama.registration.Reslicer3D
createGrayScaleImage(ImagePlus, double, boolean, boolean, int) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Creates the gray scale image.
createGrayScaleImageTimeLapse(ImagePlus, double[], double[], double) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Creates the gray scale image time lapse.
createGrayScaleImageWithHours(ImagePlus, int, boolean, double, boolean, boolean[], double[]) - Method in class io.github.rocsg.fijiyama.rsml.RootModel
createGrayScaleImageWithTime(int[], int, boolean, double, boolean, boolean[], double[], boolean) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Creates the gray scale image with time.
createGrayScaleImageWithTime(ImagePlus, int, boolean, double, boolean, boolean[], double[]) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Creates the gray scale image with time.
createImage(boolean, int, boolean, boolean) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Create an image processor based on the roots contained into the root system.
createImage(boolean, int, boolean, int, int, boolean) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Create an image processor based on the roots contained into the root system.
createImage(boolean, int, boolean, int, int, boolean, double) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Create an image processor based on the roots contained into the root system.
createOutputPathAndFjmFile() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Creates the output path and fjm file.
createRegistrationAction(ImagePlus, ImagePlus, Fijiyama_GUI, RegistrationManager, int) - Static method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Creates the registration action.
createSuperpositionTimeLapseFromPath(String, String) - Static method in class io.github.rocsg.fijiyama.rsml.RootModel: Creates the superposition time lapse from path.
createUpdater() - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Creates the updater.
cropFloatImage(ImagePlus, int, int, int, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Better signature.
cropImage(ImagePlus, int, int, int, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Crop image.
cropImageByte(ImagePlus, int, int, int, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Crop image byte.
cropImageFloat(ImagePlus, int, int, int, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Crop image float.
cropImageShort(ImagePlus, int, int, int, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Crop image short.
cropMultiChannelFloatImage(ImagePlus, int, int, int, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Crop multi channel float image.
csvSendMarks(PrintWriter, boolean, String, boolean) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Csv send marks.
currentContextIsSerie() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Current context is serie.
currentTransform - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The current transform.

D

defaultCoreNumber - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The default core number.
defineDefaultSettingsForCurrentAction() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Define default settings for current action.
defineInputData() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Define input data.
defineInputDataTesting(int, String) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Define input data testing.
defineSerieRegistrationPipeline(String) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Define serie registration pipeline.
defineSettingsForRSML(ImagePlus) - Static method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Define settings for RSML.
defineSettingsFromTwoImages(ImagePlus, ImagePlus) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Define settings from two images.
defineSettingsFromTwoImages(ImagePlus, ImagePlus, RegistrationManager, boolean) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Define settings from two images.
defineSettingsSimplyFromTwoImages(ImagePlus, ImagePlus) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Define settings simply from two images.
DEMONS - io.github.rocsg.fijiyama.registration.MetricType: The demons.
DENSE - io.github.rocsg.fijiyama.registration.Transform3DType: The dense.
denseFieldSigma - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The dense field sigma.
detectAxisIrmT1(ImagePlus, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Detect axis irm T 1.
detectRX(ImagePlus) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Detect RX.
diameter - Variable in class io.github.rocsg.fijiyama.rsml.Mark: The diameter.
diameter - Variable in class io.github.rocsg.fijiyama.rsml.Node: The birth time.
diffTeta(double, double) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: Diff teta.
dimensionsMatch(ImagePlus, ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Dimensions match.
disable(int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Disable.
disable(int) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Disable.
disable(int[]) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Disable.
disable(int[]) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Disable.
displayDistanceMapOnGrid(ItkTransform, ImagePlus) - Method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Display distance map on grid.
displayedNameCombinedImage - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The displayed name combined image.
displayedNameHyperImage - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The displayed name hyper image.
displayedNameImage1 - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The displayed name image 1.
displayedNameImage2 - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The displayed name image 2.
displayEndOfRegistrationMessage() - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Functions for displaying, tracking and keep memories of registration results along the computation.
displayR2 - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The display R 2.
displayRegistration - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The display registration.
displayRegistration - Variable in class io.github.rocsg.fijiyama.registration.ItkRegistration: The display registration.
displaySosMessage(int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Display sos message.
dispose() - Method in class io.github.rocsg.fijiyama.rsml.RSML_reader: Close the window.
dispose() - Method in class io.github.rocsg.fijiyama.rsml.RSMLGUI: Dispose.
dist - Variable in class io.github.rocsg.fijiyama.common.Pix: The dist.
distance - Variable in class io.github.rocsg.fijiyama.rsml.Node: The distance.
distance(double, double, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Distance.
distance(double, double, double, double) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Distance.
distance(double, double, double, double, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Distance.
distance(Node, Node) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Distance.
distanceBetween(Node, Node) - Static method in class io.github.rocsg.fijiyama.rsml.Node: Distance between.
distanceBetweenPointAndSegmentOrTenTimesVitimageUtilsLargeValueIfTheProjectionDoesNotFallIntoTheSegment(double[], double[], double[]) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Distance between point and segment or ten times vitimage utils large value if the projection does not fall into the segment.
distanceMap(ImagePlus, boolean) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Distance map.
distanceToSkeleton - Variable in class io.github.rocsg.fijiyama.common.Pix: The distance to skeleton.
distOut - Variable in class io.github.rocsg.fijiyama.common.Pix: The dist out.
divide(ImagePlus, ImagePlus, boolean) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Divide.
doDataInTestPablo() - Static method in class io.github.rocsg.fijiyama.rsml.Tests: The main method.
doSomething(ItkTransform) - Static method in class io.github.rocsg.fijiyama.registration.TestGargee
doStressTest - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The do stress test.
dot() - Static method in class io.github.rocsg.fijiyama.rsml.Tests
dou(double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Dou.
dou(double) - Static method in class io.github.rocsg.fijiyama.rsml.Tests
dou(double, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Dou.
dou(Point3d) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Dou.
doubleArraySort(double[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Double array sort.
doubleArrayToPoint3d(double[]) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: Double array to point 3 d.
doubleArrayToVectorDouble(double[]) - Static method in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface: Double array to vector double.
DouglasPeuckerSimplify - Class in io.github.rocsg.fijiyama.common: The Class DouglasPeuckerSimplify.
DouglasPeuckerSimplify() - Constructor for class io.github.rocsg.fijiyama.common.DouglasPeuckerSimplify
drawableString() - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Drawable string.
drawCircleInImage(ImagePlus, double, int, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Draw circle in image.
drawCircleIntoImage(ImagePlus, double, int, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Draw circle into image.
drawCircleIntoImageFloat(ImagePlus, double, int, int, int, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Draw circle into image float.
drawCircleNoFillInImage(ImagePlus, double, int, int, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Draw circle no fill in image.
drawCylinderInImage(ImagePlus, double, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Draw cylinder in image.
drawDotline(ImagePlus, int, int, int, int, int, double, double) - Static method in class io.github.rocsg.fijiyama.rsml.RootModel: Adapted from ImageProcessor in IJ v1.53i
drawDotline(ImageProcessor, int, int, int, int, int, int, double, double) - Static method in class io.github.rocsg.fijiyama.rsml.RootModel: Adapted from ImageProcessor in IJ v1.53i
drawParallepipedInImage(ImagePlus, int, int, int, int, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Draw parallepiped in image.
drawPathway(ImagePlus, List<Pix>) - Static method in class io.github.rocsg.fijiyama.common.Pix: Draw pathway.
drawPointAtPixelCoordinatesInImageModifyingIt(ImagePlus, int, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Draw point at pixel coordinates in image modifying it.
drawRectangleInImage(ImagePlus, int, int, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Draw rectangle in image.
drawSegmentInto2DByteImage(ImagePlus, double, int, double, double, double, double, boolean) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Draw segment into 2 D byte image.
drawThickLineInFloatImage(ImagePlus, double, int, int, int, double[], double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Draw thick line in float image.
drawThickLineInImage(ImagePlus, double, int, int, int, double[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Draw thick line in image.
drawThickLineInShortImage(ImagePlus, double, int, int, int, double[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Draw thick line in short image.

E

enable(int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Enable.
enable(int) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Enable.
enable(int[]) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Enable.
enable(int[]) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Enable.
enableChainIfPossible() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Enable chain if possible.
ENDING_STEP - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: The ending step.
endSetupSerieFromScratch() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: End setup serie from scratch.
EPSILON - Static variable in class io.github.rocsg.fijiyama.common.VitimageUtils: The Constant EPSILON.
eraseBorder(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Erase border.
ERROR_VALUE - Static variable in class io.github.rocsg.fijiyama.common.VitimageUtils: The Constant ERROR_VALUE.
estimateBestAffine3D(Point3d[], Point3d[]) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Estimate best affine 3 D.
estimateBestDense3D(Point3d[], Point3d[], ImagePlus, double) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Estimate best dense 3 D.
estimateBestRigid3D(Point3d[], Point3d[]) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Estimate best rigid 3 D.
estimateBestSimilarity3D(Point3d[], Point3d[]) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Estimate best similarity 3 D.
estimateBestTranslation3D(Point3d[], Point3d[]) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Estimate best translation 3 D.
estimateBlocksNumberPerLevel(int[], int, int, int, int, Transform3DType, int[], int[], int[], int, int, int, boolean) - Static method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Helper to estimate computation time, and eventually adjust parameters before launch.
estimatedTime - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The estimated time.
estimateGlobalDilationFactor(Point3d[], Point3d[]) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Estimate global dilation factor.
estimateRegistrationDuration(int[], int, int, int, int) - Static method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Estimate registration duration.
estimateRegistrationDuration(int[], int, int, int, int, Transform3DType, int[], int[], int[], int, int, int, int, boolean, int) - Static method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Estimate registration duration.
estimateTime(RegistrationAction) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Estimate time.
EULER - io.github.rocsg.fijiyama.registration.Transform3DType: The euler.
EULER2D - io.github.rocsg.fijiyama.registration.Transform3DType: The euler2d.
execute() - Method in class io.github.rocsg.fijiyama.common.HungarianAlgorithm: Execute the algorithm.
executePhase() - Method in class io.github.rocsg.fijiyama.common.HungarianAlgorithm: Execute a single phase of the algorithm.
exportImagesAndComposedTransforms(double) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Export images and composed transforms.
extendBranchInModel(Point3d[], RootModel) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Extend branch in model.

F

fade8bit(ImagePlus, ImagePlus, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Fade 8 bit.
fadeRGB(ImagePlus, ImagePlus, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Fade RGB.
fading() - Static method in class io.github.rocsg.fijiyama.rsml.PaperValidation
fastMatrixToItkTransform(FastMatrix) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Fast matrix to itk transform.
fetchUnmatchedWorker() - Method in class io.github.rocsg.fijiyama.common.HungarianAlgorithm: Fetch unmatched worker.
Fijiyama_GUI - Class in io.github.rocsg.fijiyama.fijiyamaplugin: The Class Fijiyama_GUI.
Fijiyama_GUI() - Constructor for class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Instantiates a new fijiyama GUI.
fileSuffix - Static variable in class io.github.rocsg.fijiyama.rsml.RootModel: The Constant fileSuffix.
fileSuffixRSML - Static variable in class io.github.rocsg.fijiyama.rsml.RootModel: The Constant fileSuffixRSML.
fill2dHolesInMask(ImagePlus, double, double, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Fill 2 d holes in mask.
fill3dHolesInMask(ImagePlus, double, double, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Fill 3 d holes in mask.
findCapillaryCenterInSlice(ImagePlus, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Find capillary center in slice.
findFjmFileInDir(String) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Find fjm file in dir.
finish2dEvaluation() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Finish 2 d evaluation.
finish2dManualRegistration() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Finish 2 d manual registration.
finish3dManualRegistration() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Finish 3 d manual registration.
finishActionAborted() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Finish action aborted.
finishActionThenGoOnStepSaveActionAndUpdateImage(String[]) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Finish action then go on step save rsml and update image.
finishCurrentAction(ItkTransform) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Finish current action.
firstNode - Variable in class io.github.rocsg.fijiyama.rsml.Root: /** The last node.
flag_fijiyama_IO - Static variable in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface
FLAG_OFF - Static variable in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface
FLAG_ON - Static variable in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface
FLAG_UNSET - Static variable in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface
flagRange - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The flag range.
flagRange - Variable in class io.github.rocsg.fijiyama.registration.ItkRegistration: The flag range.
flagSingleView - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The flag single view.
foreignImgName - Variable in class io.github.rocsg.fijiyama.rsml.Mark: The foreign img name.
formatInfos(String, Point3d[]) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin
frameLaunch - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The frame launch.
freeMemory() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Free memory.
freeMemory() - Method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Memory free and management.
freeMemory() - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Free memory.
from2dMatrixto1dVector() - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Converting the transformation matrix into a vector
FSR - Class in io.github.rocsg.fijiyama.rsml: The Class FSR.
FSR() - Constructor for class io.github.rocsg.fijiyama.rsml.FSR: Class constructor
fullLengthDescription() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Full length description.

G

garbageCollector() - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Garbage collector.
gather(String) - Method in class io.github.rocsg.fijiyama.common.Timer: Gather.
gaussian(float, float) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gaussian.
gaussianFiltering(ImagePlus, double, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gaussian filtering.
gaussianFilteringIJ(ImagePlus, double, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gaussian filtering IJ.
gaussianFilteringMultiChannel(ImagePlus, double, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gaussian filtering multi channel.
gaussianInterpolation(ImagePlus, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gaussian interpolation.
generateRandomDenseField(ImagePlus, int, double, double) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Generate random dense field.
getAbsoluteDay() - Method in class io.github.rocsg.fijiyama.common.Timer: Gets the absolute day.
getAndAdaptCurrentPoints(PointRoi) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Gets the and adapt current points.
getAntiCapillaryMask(ImagePlus, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the anti capillary mask.
getAutoRepMode() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Gets the auto rep mode.
getAveraging(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the averaging.
getAvgChildDens() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get the average child density of all the parent roots of the image.
getAVGDiameter() - Method in class io.github.rocsg.fijiyama.rsml.Root: The average diameter of all the nodes.
getAvgInterBranch() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get average interbranch distance.
getAVGInterBranchDistance() - Method in class io.github.rocsg.fijiyama.rsml.Root: Get the average interbanch distance of the lateral roots.
getAVGMedianDiameterInRange(double, double) - Method in class io.github.rocsg.fijiyama.rsml.Root: Gets the AVG median diameter in range.
getAvgPRDiam() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get the average diameter of primary roots.
getAvgPRLength() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get average length of primary roots.
getAvgRLength() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get the average length of all roots.
getAvgSRDiam() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get the average diameter of secondary roots.
getAvgSRInsAng() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get the average insertion angle of secondary roots.
getAvgSRLength() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get the average length of secondary roots.
getBinaryGrid(ImagePlus, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Helpers used in Registration steps (BM and ITK).
getBinaryGrid(ImagePlus, int, boolean, boolean) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the binary grid.
getBinaryMask(ImagePlus, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Main automated detectors : axis detection and inoculation point detection.
getBinaryMaskUnary(ImagePlus, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the binary mask unary.
getBinaryMaskUnaryFloat(ImagePlus, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the binary mask unary float.
getBoxName() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin
getCenter() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get the center of the tracing.
getChannelOfMaxT1MinT2Sequence(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the channel of max T 1 min T 2 sequence.
getChildDensity() - Method in class io.github.rocsg.fijiyama.rsml.Root: Get the lateral density insde the ramified region.
getChildrenAngle() - Method in class io.github.rocsg.fijiyama.rsml.Root: Return the mean children angle.
getChildrenLength() - Method in class io.github.rocsg.fijiyama.rsml.Root: Return the total length of all the children.
getChildrenSurface() - Method in class io.github.rocsg.fijiyama.rsml.Root: Get the surface of the lateral roots (if any).
getChildsRootAsRootArray() - Method in class io.github.rocsg.fijiyama.rsml.Root
getClosestNode(float) - Method in class io.github.rocsg.fijiyama.rsml.Root: get the closest node in the root from a given position on the root.
getClosestNode(Point3d) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Gets the closest node.
getClosestNodeInPrimary(Point3d) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Gets the closest node in primary.
getClosestRoot(Root) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Gets the closest root.
getColumnOfTab(double[][], int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the column of tab.
getComposedTransform(int, int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Gets the composed transform.
getComposedTransform(int, int, int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Gets the composed transform.
getConvexHull() - Method in class io.github.rocsg.fijiyama.rsml.Root: Get the root convexhull.
getConvexHull() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get the convexhull of all the roots in the image.
getConvexHullArea() - Method in class io.github.rocsg.fijiyama.rsml.Root: Get the convexhull area.
getConvexHullArea() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get the convexhull area of all the roots in the image.
getCoordsAtDistance(double) - Method in class io.github.rocsg.fijiyama.rsml.Root: Gets the coords at distance.
getCorrespondanceListAsImagePlus(ImagePlus, ArrayList<double[][]>, double[], int, int, int, int, int, int, int, boolean) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the correspondance list as image plus.
getCorrespondingSliceInHyperImage(ImagePlus, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the corresponding slice in hyper image.
getCurrentAction() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Gets the current action.
getCurrentDimensions() - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Gets the current dimensions.
getCurrentLevel() - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Gets the current level.
getCurrentMovComposedTransform() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Gets the current mov composed transform.
getCurrentMovComposedTransform(int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Gets the current mov composed transform.
getCurrentMovImage() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Gets the current mov image.
getCurrentMovRange() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Gets the current mov range.
getCurrentRefComposedTransform() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Gets the current ref composed transform.
getCurrentRefImage() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Gets the current ref image.
getCurrentRefRange() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Gets the current ref range.
getCurrentShrinkFactors() - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Gets the current shrink factors.
getCurrentSigmaFactors() - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Gets the current sigma factors.
getCurrentStep() - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Gets the current step.
getCurrentTransform() - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Gets the current transform.
getDateFromString(String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the date from string.
getDateMax() - Method in class io.github.rocsg.fijiyama.rsml.Root: Gets the date max.
getDebugMode() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Gets the debug mode.
getDefaultValue(int) - Static method in class io.github.rocsg.fijiyama.rsml.Mark: Get the default value of the mark.
getDimensions(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the dimensions.
getDimensionsRealSpace(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the dimensions real space.
getDimensionsXYZCT(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the dimensions XYZCT.
getDirectory() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Ge the directory containing the image.
getDistanceFromApex() - Method in class io.github.rocsg.fijiyama.rsml.Root: the distance of the insertion point from the parent's apex.
getDistanceFromBase() - Method in class io.github.rocsg.fijiyama.rsml.Root: Get the distance of the insertion point from the parent's base.
getDistanceTo(Node) - Method in class io.github.rocsg.fijiyama.rsml.Node: Get the distance between this node and an other one.
getDoubleSidedRangeForContrastMoreIntelligent(ImagePlus, int, int, int, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the double sided range for contrast more intelligent.
getDoubleUI(String, String, double) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Gets the double UI.
getDPI() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Ge tthe DPI value for the image.
getDPI(String, float) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Computed the scale base on an unit and a resolutiono.
getEchoTime(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the echo time.
getFijiyamaGUI() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Gets the fijiyama GUI.
getFirstChild() - Method in class io.github.rocsg.fijiyama.rsml.Root: Get the object of the lateral root the closest to the base.
getFlattenDenseField(ImagePlus) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Gets the flatten dense field.
getFlattenDenseFieldAsDisplacementFieldImage(ImagePlus) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Gets the flatten dense field as displacement field image.
getFloatBinaryMask(ImagePlus, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the float binary mask.
getGlobalRsquareWithActualTransform() - Method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Gets the global rsquare with actual transform.
getHeight(boolean) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get the height of the tracing.
getHSB(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the hsb.
getHSBOld(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the HSB old.
getIcon(int) - Static method in class io.github.rocsg.fijiyama.rsml.Mark: Get the icon for the mark.
getIdentityDenseFieldTransform(ImagePlus) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Gets the identity dense field transform.
getImageCenter(ImagePlus) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Gets the image center.
getImageCenter(ImagePlus, boolean) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the image center.
getImgViewText(int) - Static method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Gets the img view text.
getIndexFromPo(String) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get the index of the po accession.
getInitTime() - Method in class io.github.rocsg.fijiyama.common.Timer: Gets the inits the time.
getInputOutputPathForRegistrationPackage() - Static method in class io.github.rocsg.fijiyama.registration.TestingRegistrationPackage: Gets the input output path for registration package.
getInsertAngl() - Method in class io.github.rocsg.fijiyama.rsml.Root: Get the insertion angle of the root.
getInstance() - Static method in class io.github.rocsg.fijiyama.rsml.RSML_reader: Get instance.
getInstance() - Static method in class io.github.rocsg.fijiyama.rsml.RSMLGUI: Ge the GUI instance.
getInterBranch() - Method in class io.github.rocsg.fijiyama.rsml.Root: Get the interbranch distance.
getIntUI(String, int) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Temporary.
getIntUI(String, String, int) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Gets the int UI.
getInverseOfDenseField() - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Gets the inverse of dense field.
getIterationsBM() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Gets the iterations BM.
getIterationsBMLinear() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Gets the iterations BM linear.
getIterationsBMNonLinear() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Gets the iterations BM non linear.
getJacobian(ItkTransform, ImagePlus, int) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Gets the jacobian.
getJacobian(Image, int) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Gets the jacobian.
getJacobianHomeMadeBecauseOfUnavoidedCoreDumpIssueWithSimpleITKDisplacementFieldJacobianDeterminantFilter(ImagePlus, double, int) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Gets the jacobian home made because of unavoided core dump issue with simple ITK displacement field jacobian determinant filter.
getJacobianOfDisplacementField(Image, ImagePlus, int) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Gets the jacobian of displacement field.
getLastChild() - Method in class io.github.rocsg.fijiyama.rsml.Root: Get the object of the lateral root the closest to the apex.
getLateralRootsOfPlant(int) - Method in class io.github.rocsg.fijiyama.rsml.RootModel
getLateralSpeedsAndDepthOverTime(int, int) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Gets the lateral speeds and depth over time.
getLengths(double) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Gets the lengths.
getLevelMax() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Gets the level max.
getLevelMin() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Gets the level min.
getLowerStringInStringTab(String[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the lower string in string tab.
getMagnification(String) - Static method in class io.github.rocsg.fijiyama.rsml.Tests
getMaskAsCoords(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the mask as coords.
getMaxAcceptableLevelForTheCurrentAction() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Gets the max acceptable level for the current action.
getMaxValueForContrastIntelligent(ImagePlus, int, int, int, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the max value for contrast intelligent.
getMaxValueForContrastMoreIntelligent(ImagePlus, int, int, int, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the max value for contrast more intelligent.
getMinMaxByte(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the min max byte.
getMinMaxFloat(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the min max float.
getMinMaxPoints(Point3d[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the min max points.
getMinX() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get the widht of the tracing.
getMinY() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get the widht of the tracing.
getModeString() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Gets the mode string.
getName(int) - Static method in class io.github.rocsg.fijiyama.rsml.Mark: Get the name of the mark.
getNameOfUserLinux() - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the name of user linux.
getNbCores() - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the nb cores.
getNbLevels() - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Minor getters/setters.
getNbSteps() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Gets the nb steps.
getNbSteps() - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Gets the nb steps.
getNearestRootSegment(Point3d, double) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Gets the nearest root segment.
getNewRootKey() - Method in class io.github.rocsg.fijiyama.rsml.Root: Get a new root id value.
getNodeOfParentJustAfterMyAttachment() - Method in class io.github.rocsg.fijiyama.rsml.Root: Gets the node of parent just after my attachment.
getNodesList() - Method in class io.github.rocsg.fijiyama.rsml.Root: Gets the nodes list.
getNPNode() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get the number of nodes of the primary roots.
getNPRoot() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get the number of primary roots.
getNPRoot(double) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Gets the NP root.
getNRoot() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get the total number of roots.
getNSNode() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get the number of node of the secondary roots.
getNSRoot() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get the number of secondary roots.
getNSRoot(double) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Gets the NS root.
getNumber(Transform3DType) - Static method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Gets the number.
getNumberAndLenghtOverTimeSerie(int) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Gets the number and lenght over time serie.
getOtsuThreshold(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the otsu threshold.
getParent() - Method in class io.github.rocsg.fijiyama.rsml.Root: Get the object of the root parent.
getParentName() - Method in class io.github.rocsg.fijiyama.rsml.Root: Get the parent root name (id any).
getParentNode() - Method in class io.github.rocsg.fijiyama.rsml.Root: Get the parent's closest node from the base of this root.
getParentRootNameList() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get a list of strings containing all the name of roots having children.
getPathOfHomeLinux() - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the path of home linux.
getPatientName(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the patient name.
getPipelineAslistModelForGUI() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Gets the pipeline aslist model for GUI.
getPixelIndex(int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the pixel index.
getPoAccession() - Method in class io.github.rocsg.fijiyama.rsml.Root: Get the Plant Ontology accession of the root.
getPreview(String, String, int, boolean, boolean, double) - Method in class io.github.rocsg.fijiyama.rsml.RSMLNoGUI: Gets the preview.
getPreviewGreyScale(String, String, boolean) - Method in class io.github.rocsg.fijiyama.rsml.RSMLNoGUI: Gets the preview grey scale.
getPrimaryRootNameList() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get a list of strings containing all the name of primary.
getPrimaryRootOfPlant(int) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Root model wild read annotation from rsml.
getPrimaryRoots() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Gets the primary roots.
getPrimDepthOverTime(int, int) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Gets the prim depth over time.
getPrimLengthAndSpeedOverTime(int, int) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Gets the prim length over time.
getPrimLengthOverTime(int, int) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Gets the prim length over time.
getPRLength(double) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Gets the PR length.
getQuartiles(double[], double[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the quartiles.
getRadiusInVoxels(double[], double, boolean) - Static method in class io.github.rocsg.fijiyama.common.MostRepresentedFilter: Gets the radius in voxels.
getRandomSentence() - Static method in class io.github.rocsg.fijiyama.common.SentenceOfTheDay: Gets the random sentence.
getRefAndMovPaths() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Gets the ref and mov paths.
getRelativeOptimalPositionFor2DView() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Gets the relative optimal position for 2 D view.
getRelaxingPopup(String, boolean) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the relaxing popup.
getRepetitionTime(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the repetition time.
getRigidTransform(double[], double[], double[]) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Gets the rigid transform.
getRoiAsCoords(Roi) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the roi as coords.
getRoiSurface(Roi) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the roi surface.
getRoiSurface(Roi) - Static method in class io.github.rocsg.fijiyama.rsml.Tests
getRoot(int) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get a given root in the root list.
getRootCoordinates(Root) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Gets the root coordinates.
getRootID() - Method in class io.github.rocsg.fijiyama.rsml.Root: Get the root name.
getRootKey() - Method in class io.github.rocsg.fijiyama.rsml.Root: Get the root key.
getRootLength() - Method in class io.github.rocsg.fijiyama.rsml.Root: Get the root length.
getRootOrientation() - Method in class io.github.rocsg.fijiyama.rsml.Root: Return the average orientation of the root.
getRootSurface() - Method in class io.github.rocsg.fijiyama.rsml.Root: Get the surface of the root.
getRootVolume() - Method in class io.github.rocsg.fijiyama.rsml.Root: Get the volume of the root.
getRulerAtOrigin() - Method in class io.github.rocsg.fijiyama.rsml.Root: Get the value of the ruelr at origin.
getRunButtonText() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Gets the run button text.
getScalerTypes() - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Gets the scaler types.
getScales() - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Gets the scales.
getSegmentDistance(Pix, Pix, Pix) - Static method in class io.github.rocsg.fijiyama.common.DouglasPeuckerSimplify: Gets the segment distance.
getSentenceOfTheDay() - Static method in class io.github.rocsg.fijiyama.common.SentenceOfTheDay: Gets the sentence of the day.
getSentenceTab() - Static method in class io.github.rocsg.fijiyama.common.SentenceOfTheDay: Gets the sentence tab.
getShortestAndDarkestPathInImage(ImagePlus, int, Pix, Pix) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the shortest and darkest path in image.
getStartingDepth(double[][][]) - Static method in class io.github.rocsg.fijiyama.rsml.RsmlPhenotypingUtils: Gets the starting depth.
getStep() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Gets the step.
getStep() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Gets the step.
getStringUI(String, String, String, boolean) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Gets the string UI.
getSystemName() - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Informations about system and virtual machine.
getSystemNeededMemory() - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the system needed memory.
getTime() - Method in class io.github.rocsg.fijiyama.common.Timer: Gets the time.
getTipDepthAndRootLengthOverTimesteps(Root) - Method in class io.github.rocsg.fijiyama.rsml.RootModel
getTipDepthSpeedAndRootLengthOverTime(Root) - Method in class io.github.rocsg.fijiyama.rsml.RootModel
getTortuosity() - Method in class io.github.rocsg.fijiyama.rsml.Root: Returns the tortuosity of the root.
getTotalPRLength() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get the total length of the primary roots.
getTotalPRLength(double) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Gets the total PR length.
getTotalRLength() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get the total root length.
getTotalSRLength() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get the total lengthd of the lateral roots.
getTotalSRLength(double) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Gets the total SR length.
getTransformedPreview(String, String, int, boolean, boolean, double) - Method in class io.github.rocsg.fijiyama.rsml.RSMLNoGUI: Gets the transformed preview.
getTransformForResampling(double[], double[]) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Gets the transform for resampling.
getTypeCount() - Static method in class io.github.rocsg.fijiyama.rsml.Mark: Get the number of possible marks.
getTypeNum(String) - Static method in class io.github.rocsg.fijiyama.rsml.Mark: Get the type of the mark, as an integer.
getUnit() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Gets the unit.
getValue() - Method in class io.github.rocsg.fijiyama.rsml.Mark: Return the value of the mark as a string.
getVectorLength() - Method in class io.github.rocsg.fijiyama.rsml.Root: Return the vector lenght of the root (as defined in Armengaud 2009).
getViewOfImagesTransformedAndSuperposedSerieWithThisReference(ImagePlus, boolean, boolean, String) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Gets the view of images transformed and superposed serie with this reference.
getViewOfImagesTransformedAndSuperposedTwoImg() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Gets the view of images transformed and superposed two img.
getVoxelSizes(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Functions for accessing basic informations about images.
getVoxelVolume(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Gets the voxel volume.
getWeightDistExt() - Method in class io.github.rocsg.fijiyama.common.Bord: Gets the weight dist ext.
getWeightEuclidian() - Method in class io.github.rocsg.fijiyama.common.Bord: Gets the weight euclidian.
getWeights() - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Gets the weights.
getWidth(boolean) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Get the widht of the tracing.
getXMax() - Method in class io.github.rocsg.fijiyama.rsml.Root: Return the max X coordinate of the root.
getXMaxTotal() - Method in class io.github.rocsg.fijiyama.rsml.Root: Return the max X coordinate of the root and its children.
getXMin() - Method in class io.github.rocsg.fijiyama.rsml.Root: Return the min X coordinate of the root.
getXMinTotal() - Method in class io.github.rocsg.fijiyama.rsml.Root: Return the min X coordinate of the root and its children.
getYesNoUI(String, String) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Gets the yes no UI.
getYMax() - Method in class io.github.rocsg.fijiyama.rsml.Root: Return the max Y coordinate of the root.
getYMaxTotal() - Method in class io.github.rocsg.fijiyama.rsml.Root: Return the max Y coordinate of the root and its children.
getYMin() - Method in class io.github.rocsg.fijiyama.rsml.Root: Return the min Y coordinate of the root.
getYMinTotal() - Method in class io.github.rocsg.fijiyama.rsml.Root: Return the min Y coordinate of the root and its children.
globalR2Values - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The global R 2 values.
globalRanges - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: The global ranges.
GREAT_RIGID - io.github.rocsg.fijiyama.registration.TransformUtils.Misalignment: The great rigid.
greedyMatch() - Method in class io.github.rocsg.fijiyama.common.HungarianAlgorithm: Find a valid matching by greedily selecting among zero-cost matchings.
gridSummary - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The grid summary.
guessCharset(String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Guess charset.

H

handleKeyPress(KeyEvent) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Handle key press.
handleKeyPress(KeyEvent) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Handle key press.
handleKeyReleased(KeyEvent) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Handle key released.
handleOutput(String) - Method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Handle output.
handleOutputNoNewline(String) - Method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Handle output no newline.
hasExactBirthTime() - Method in class io.github.rocsg.fijiyama.rsml.Node: Checks for exact birth time.
HCENTER - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.ScrollUtil: The Constant SELECTED.
HIGH_DISTANCE - Static variable in class io.github.rocsg.fijiyama.common.MostRepresentedFilter: The high distance.
higherAcc - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The higher acc.
hoursCorrespondingToTimePoints - Variable in class io.github.rocsg.fijiyama.rsml.RootModel
HungarianAlgorithm - Class in io.github.rocsg.fijiyama.common: An implementation of the Hungarian algorithm for solving the assignment problem.
HungarianAlgorithm(double[][]) - Constructor for class io.github.rocsg.fijiyama.common.HungarianAlgorithm: Construct an instance of the algorithm.
hyperStackChannelToHyperStackFrame(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Hyper stack channel to hyper stack frame.
hyperStackFrameToHyperStackChannel(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Hyper stack frame to hyper stack channel.
hyperStackingChannels(ImagePlus[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Hyper stacking channels.
hyperStackingFrames(ImagePlus[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Hyper stacking frames.
hyperUnstack(ImagePlus[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Hyper unstack.
hypot(float, float) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Hypot.

I

ij3dTransformToItkTransform(Transform3D) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Ij 3 d transform to itk transform.
ijImgRef - Variable in class io.github.rocsg.fijiyama.registration.ItkRegistration: The ij img ref.
IMAGE_CENTER - io.github.rocsg.fijiyama.registration.CenteringStrategy: The image center.
imageChecking(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Image checking.
imageChecking(ImagePlus, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Image checking.
imageChecking(ImagePlus, double, double, int, String, double, boolean) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Image checking.
imageChecking(ImagePlus, String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Image checking.
imageChecking(ImagePlus, String, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Image checking.
imageCheckingFast(ImagePlus, String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Image checking fast.
imageCopy(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Image copy.
imageCopyWithSliceLabel(ImagePlus, String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Image copy with slice label.
imageDimsAtSuccessiveLevels(int[], int[]) - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Image dims at successive levels.
imageDimsAtSuccessiveLevels(int[], int[], boolean) - Method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Image dims at successive levels.
imageExists(int, int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Image exists.
imageJOutputActivated - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The image J output activated.
imagePlusToItkImage(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface
imagePlusToItkImageNew(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface
imagePlusToItkImageOld(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface: Image plus to itk image.
imageResume(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Debugging utilities.
images - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: The images.
imagesHaveSameCharacteristics(ImagePlus, ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Images have same characteristics.
imageTabCopy(ImagePlus[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Image tab copy.
imageVoxSizesAtSuccessiveLevels(double[], int[]) - Method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Image vox sizes at successive levels.
imgMov - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The img mov.
imgMovDefaultValue - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The img mov default value.
imgName - Variable in class io.github.rocsg.fijiyama.rsml.RootModel: The img name.
imgRef - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The img ref.
imgRefDefaultValue - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The img ref default value.
imgView - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The img view.
incrIter - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The incr iter.
indmax(double[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Indmax.
indmax(int[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Indmax.
indMaxOfImage(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Ind max of image.
indMaxOfImageArrayDouble(ImagePlus[], int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Ind max of image array double.
INERTIA_AXIS - io.github.rocsg.fijiyama.registration.OptimizerType: The inertia axis.
informAboutPointInModel(Point3d[], RootModel) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Inform about point in model.
initialize() - Method in class io.github.rocsg.fijiyama.rsml.FSR: Initialization.
initializePhase(int) - Method in class io.github.rocsg.fijiyama.common.HungarianAlgorithm: Initialize the next phase of the algorithm by clearing the committed workers and jobs sets and by initializing the slack arrays to the values corresponding to the specified root worker.
inspectAxis(ImagePlus, double[], Point3d, int) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Inspect axis.
inspectInoculationPoint(ImagePlus, Point3d) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Display a point detected on an image, and ask for confirmation.
intArrayToVectorUInt32(int[]) - Static method in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface: Int array to vector U int 32.
interfaceIsRunning - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The interface is running.
interpolateTime() - Method in class io.github.rocsg.fijiyama.rsml.Root
invertBinaryMask(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Invert binary mask.
invertVector(double[]) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: Invert vector.
io.github.rocsg.fijiyama.common - package io.github.rocsg.fijiyama.common
io.github.rocsg.fijiyama.fijiyamaplugin - package io.github.rocsg.fijiyama.fijiyamaplugin
io.github.rocsg.fijiyama.registration - package io.github.rocsg.fijiyama.registration
io.github.rocsg.fijiyama.rsml - package io.github.rocsg.fijiyama.rsml
isAbortable() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Checks if is abortable.
isBionanoImagesWithCapillary - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: The is bionano images with capillary.
isBionanoImageWithCapillary(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Checks if is bionano image with capillary.
isBouture(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Checks if is bouture.
isChild() - Method in class io.github.rocsg.fijiyama.rsml.Root: Checks if is child.
isChild(int) - Method in class io.github.rocsg.fijiyama.rsml.Root: Set if the root is a child.
isDense() - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Checks if is dense.
isDone() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Checks if is done.
isEqualToAffineTransform(ItkTransform, double, double) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Checks if is equal to affine transform.
isForeign - Variable in class io.github.rocsg.fijiyama.rsml.Mark: The is foreign.
isFromBionano(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Checks if is from bionano.
isGe3d - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: The is ge 3 d.
isGe3d(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Checks if is ge 3 d.
isHyperImage(int, int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Checks if is hyper image.
isIdentityAffineTransform(double, double) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Checks if is identity affine transform.
isInteger(String) - Static method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Checks if is integer.
isLeftRight() - Method in class io.github.rocsg.fijiyama.rsml.Root: Return an integer indicating if the root is on the right or the left side of its parent (if it is a lateral).
isMac() - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Checks if is mac.
isNullFloatImage(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Checks if is null float image.
isNullImage(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Checks if is null image.
isNullShortImage(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Checks if is null short image.
isOutlier(int, int) - Static method in class io.github.rocsg.fijiyama.rsml.RsmlPhenotypingUtils: Checks if is outlier.
isParentOrEqual(Node) - Method in class io.github.rocsg.fijiyama.rsml.Node: Checks if is parent or equal.
isProgrammingSerie() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Checks if is programming serie.
isRsml - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The is rsml.
isRunningSerie() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Checks if is running serie.
isRunningTwoImagesTraining() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Checks if is running two images training.
isSerie - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: The is serie.
isSkeleton - Variable in class io.github.rocsg.fijiyama.common.Pix: The is skeleton.
isSorghoHyperImage(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Checks if is sorgho hyper image.
isStandardChar(char) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Helpers to check conformity of the String given by the user.
isStandardName(String) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Checks if is standard name.
isSurvivorVncTunnelLittleDisplay - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The is survivor vnc tunnel little display.
isTransformationAction() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Checks if is transformation action.
isValidOrder(RegistrationAction, RegistrationAction) - Static method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Checks if is valid order.
isValidOrder(Transform3DType, Transform3DType) - Static method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Checks if is valid order.
isVitimageHyperImage(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Checks if is vitimage hyper image.
isWindowsOS() - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Checks if is windows OS.
isZuluEndangered() - Method in class io.github.rocsg.fijiyama.common.VitimageUtils
iterationsBMDen - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The iterations BM den.
iterationsBMLin - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The iterations BM lin.
iterationsITK - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The iterations ITK.
ITK_AMOEBA - io.github.rocsg.fijiyama.registration.OptimizerType: The itk amoeba.
ITK_EVOLUTIONARY - io.github.rocsg.fijiyama.registration.OptimizerType: The itk evolutionary.
ITK_EXHAUSTIVE - io.github.rocsg.fijiyama.registration.OptimizerType: The itk exhaustive.
ITK_GRADIENT - io.github.rocsg.fijiyama.registration.OptimizerType: The itk gradient.
ITK_GRADIENT_CONJUGATE - io.github.rocsg.fijiyama.registration.OptimizerType: The itk gradient conjugate.
ITK_GRADIENT_LINE_SEARCH - io.github.rocsg.fijiyama.registration.OptimizerType: The itk gradient line search.
ITK_GRADIENT_REGULAR_STEP - io.github.rocsg.fijiyama.registration.OptimizerType: The itk gradient regular step.
ITK_LBFGS2 - io.github.rocsg.fijiyama.registration.OptimizerType: The itk lbfgs2.
ITK_LBFGSB - io.github.rocsg.fijiyama.registration.OptimizerType: The itk lbfgsb.
ITK_POWELL - io.github.rocsg.fijiyama.registration.OptimizerType: The itk powell.
ItkImagePlusInterface - Class in io.github.rocsg.fijiyama.common: The ImagePlus op_1add_2mult_3div_4sub.
ItkImagePlusInterface() - Constructor for class io.github.rocsg.fijiyama.common.ItkImagePlusInterface
itkImageToImagePlus(Image) - Static method in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface
itkImageToImagePlusNew(Image) - Static method in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface
itkImageToImagePlusOld(Image) - Static method in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface: Itk image to image plus.
itkImageToImagePlusSlice(Image, int) - Static method in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface: Itk image to image plus slice.
itkImageToImagePlusStack(Image, int) - Static method in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface: Itk image to image plus stack.
itkIsInterruptedSucceeded - Variable in class io.github.rocsg.fijiyama.registration.ItkRegistration: The itk is interrupted succeeded.
itkOptimizerType - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The itk optimizer type.
ItkRegistration - Class in io.github.rocsg.fijiyama.registration: The Class ItkRegistration.
ItkRegistration() - Constructor for class io.github.rocsg.fijiyama.registration.ItkRegistration: Medium level functions : constructor, and managers algorithms.
itkRegistrationInterrupted - Variable in class io.github.rocsg.fijiyama.registration.ItkRegistration: The itk registration interrupted.
ItkTransform - Class in io.github.rocsg.fijiyama.registration: The Class ItkTransform.
ItkTransform() - Constructor for class io.github.rocsg.fijiyama.registration.ItkTransform: Instantiates a new itk transform.
ItkTransform(ItkTransform) - Constructor for class io.github.rocsg.fijiyama.registration.ItkTransform: Instantiates a new itk transform.
ItkTransform(Transform) - Constructor for class io.github.rocsg.fijiyama.registration.ItkTransform: Instantiates a new itk transform.
itkTransformFromCoefs(double[]) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Itk transform from coefs.
itkTransformFromDICOMVectors(double[], double[], double[], double[]) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Itk transform from DICOM vectors.
itkTransformFromDICOMVectorsAXIAL(double[], double[], double[], double[]) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Itk transform from DICOM vectors AXIAL.
itkTransformFromDICOMVectorsNOAXIAL(double[], double[], double[], double[]) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Itk transform from DICOM vectors NOAXIAL.
itkTransformStepToArray(String) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Itk transform step to array.
itkTransformToIj3dTransform(ItkTransform) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Itk transform to ij 3 d transform.
itkTransfoStepToString(String) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Itk transfo step to string.

J

JACOBIAN_VERSOR - io.github.rocsg.fijiyama.registration.ScalerType: The jacobian versor.
jacobianSummary - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The jacobian summary.
JOINT - io.github.rocsg.fijiyama.registration.MetricType: The joint.

K

keyPressed(KeyEvent) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Key pressed.
keyReleased(KeyEvent) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Key released.
keyTyped(KeyEvent) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Key typed.

L

laplacian(double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Laplacian.
laplacian(double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Laplacian.
LARGE_VALUE - Static variable in class io.github.rocsg.fijiyama.common.VitimageUtils: The Constant LARGE_VALUE.
lastNode - Variable in class io.github.rocsg.fijiyama.rsml.Root: /** The last node.
lastValueBlocksCorr - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The last value blocks corr.
lastValueCorr - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The last value corr.
lastViewSizes - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The last view sizes.
learningRate - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The learning rate.
LEFT - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.ScrollUtil: The Constant SELECTED.
len - Variable in class io.github.rocsg.fijiyama.common.Bord: The len.
len(Pix, Pix) - Method in class io.github.rocsg.fijiyama.common.Bord: Len.
length - Variable in class io.github.rocsg.fijiyama.rsml.Node: The birth time.
levelMax - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The level max.
levelMaxDense - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The level max dense.
levelMaxLinear - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The level max linear.
levelMin - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The level min.
levelMinDense - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The level min dense.
levelMinLinear - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The level min linear.
LIGHT_DEFORMATION - io.github.rocsg.fijiyama.registration.TransformUtils.Misalignment: The light deformation.
LIGHT_RIGID - io.github.rocsg.fijiyama.registration.TransformUtils.Misalignment: The light rigid.
LIGHT_SIMILARITY - io.github.rocsg.fijiyama.registration.TransformUtils.Misalignment: The light similarity.
linearInterpolation(double, Double[], Double[]) - Static method in class io.github.rocsg.fijiyama.rsml.Root: Linear interpolation.
listForThreads(int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: List for threads.
listPo - Static variable in class io.github.rocsg.fijiyama.rsml.FSR: The list po.
listPoNames - Static variable in class io.github.rocsg.fijiyama.rsml.FSR: The list po names.
log(String) - Method in class io.github.rocsg.fijiyama.common.Timer: Log.
logActionEvent(ActionEvent) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Log action event.
logNumberOfBlocks(int) - Static method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration
lPos - Variable in class io.github.rocsg.fijiyama.rsml.Mark: The l pos.
lPosCmToPixels(float) - Method in class io.github.rocsg.fijiyama.rsml.Root: Convert the longitudinal position from cm to pixels.
lPosPixelsToCm(float) - Method in class io.github.rocsg.fijiyama.rsml.Root: Convert the longitudinal position from pixels to cm.

M

MADeIsOutlier(double, double[], double[], double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: MA de is outlier.
MADeStatsDoubleSided(double[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: MA de stats double sided.
MADeStatsDoubleSided(double[], double[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: MA de stats double sided.
MADeStatsDoubleSided(ArrayList<Double>) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: MA de stats double sided.
main(String[]) - Static method in class io.github.rocsg.fijiyama.common.HungarianAlgorithm: The main method.
main(String[]) - Static method in class io.github.rocsg.fijiyama.common.MostRepresentedFilter: The main method.
main(String[]) - Static method in class io.github.rocsg.fijiyama.common.Timer
main(String[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: The main method.
main(String[]) - Static method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The main method.
main(String[]) - Static method in class io.github.rocsg.fijiyama.fijiyamaplugin.ReproducibilityTests
main(String[]) - Static method in class io.github.rocsg.fijiyama.fijiyamaplugin.TestingFijiyamaPackage: The main method.
main(String[]) - Static method in class io.github.rocsg.fijiyama.fijiyamaplugin.TestScriptBeanshell: The main method.
main(String[]) - Static method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The main method.
main(String[]) - Static method in class io.github.rocsg.fijiyama.registration.Reslicer3D
main(String[]) - Static method in class io.github.rocsg.fijiyama.registration.TestGargee
main(String[]) - Static method in class io.github.rocsg.fijiyama.registration.TestingRegistrationPackage: The main method.
main(String[]) - Static method in class io.github.rocsg.fijiyama.rsml.PaperValidation
main(String[]) - Static method in class io.github.rocsg.fijiyama.rsml.RootModel
main(String[]) - Static method in class io.github.rocsg.fijiyama.rsml.RSML_reader: Main class.
main(String[]) - Static method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: The main method.
main(String[]) - Static method in class io.github.rocsg.fijiyama.rsml.RSMLNoGUI: The main method.
main(String[]) - Static method in class io.github.rocsg.fijiyama.rsml.RsmlPhenotypingUtils: The main method.
main(String[]) - Static method in class io.github.rocsg.fijiyama.rsml.Test_RSMLViewer: The main method.
main(String[]) - Static method in class io.github.rocsg.fijiyama.rsml.Tests
mainThread - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The main thread.
makeLittleTests() - Static method in class io.github.rocsg.fijiyama.registration.TestingRegistrationPackage: Make little tests.
makeOperationBetweenTwoImages(ImagePlus, ImagePlus, int, boolean) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Make operation between two images.
makeOperationOnOneImage(ImagePlus, int, double, boolean) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Make operation on one image.
MANUAL - io.github.rocsg.fijiyama.registration.ScalerType: The manual.
manualRegistrationIn3D(ImagePlus, ImagePlus) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Manual registration in 3 D.
mark() - Method in class io.github.rocsg.fijiyama.common.Timer: Mark.
Mark - Class in io.github.rocsg.fijiyama.rsml: The Class Mark.
Mark(int, Root, float, float, String, boolean, String) - Constructor for class io.github.rocsg.fijiyama.rsml.Mark: Instantiates a new mark.
Mark(int, Root, float, String) - Constructor for class io.github.rocsg.fijiyama.rsml.Mark: Instantiates a new mark.
Mark(int, Root, float, String, boolean, String) - Constructor for class io.github.rocsg.fijiyama.rsml.Mark: Instantiates a new mark.
markList - Variable in class io.github.rocsg.fijiyama.rsml.Root: The mark list.
mask - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The mask.
maskWithoutCapillaryInGe3DImage(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Mask without capillary in ge 3 D image.
MASS_CENTER - io.github.rocsg.fijiyama.registration.CenteringStrategy: The mass center.
MASSCENTER - io.github.rocsg.fijiyama.registration.OptimizerType: The masscenter.
match(int, int) - Method in class io.github.rocsg.fijiyama.common.HungarianAlgorithm: Helper method to record a matching between worker w and job j.
MATTES - io.github.rocsg.fijiyama.registration.MetricType: The mattes.
max(double[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Max.
max(int[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Max.
MAX_NB_CLASSES - Static variable in class io.github.rocsg.fijiyama.common.MostRepresentedFilter: The max nb classes.
maxAcceptableLevel - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: The max acceptable level.
maxOfHyperImage(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Max of hyper image.
maxOfImage(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Max of image.
maxOfImageArray(ImagePlus[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Max of image array.
maxOfImageArray(ImagePlus[][]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Max of image array.
maxOfImageArrayDouble(ImagePlus[][]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Max of image array double.
maxOfImageArrayShort(ImagePlus[][]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Max of image array short.
MDL - Variable in class io.github.rocsg.fijiyama.rsml.Root: The mdl.
mean(double[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Mean.
meanAndVarOnlyValidValuesByte(ImagePlus, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Mean and var only valid values byte.
meanDistanceAfterTrans(ImagePlus, int, int, int, boolean) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Mean distance after trans.
meanOfImageArray(ImagePlus[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Mean of image array.
meanOfImageArray(ImagePlus[][]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Mean of image array.
meanOfImageArrayByte(ImagePlus[][]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Mean of image array byte.
meanOfImageArrayDouble(ImagePlus[][]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Mean of image array double.
meanOfImageArrayShort(ImagePlus[][]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Mean of image array short.
MEANSQUARE - io.github.rocsg.fijiyama.registration.MetricType: The meansquare.
meanValueofImageAround(ImagePlus, int, int, int, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Mean valueof image around.
metricType - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The metric type.
MetricType - Enum in io.github.rocsg.fijiyama.registration: The Enum MetricType.
min(double[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Min.
min(int[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Min.
minAndMaxOfTab(double[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Min and max of tab.
minBlockScore - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The min block score.
minBlockVariance - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The min block variance.
minOfImage(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Min of image.
MIRROR_X - io.github.rocsg.fijiyama.registration.TransformUtils.Geometry: The mirror x.
MIRROR_Y - io.github.rocsg.fijiyama.registration.TransformUtils.Geometry: The mirror y.
MIRROR_Z - io.github.rocsg.fijiyama.registration.TransformUtils.Geometry: The mirror z.
mode - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The mode.
MODE_SERIE - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The Constant MODE_SERIE.
MODE_TWO_IMAGES - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The Constant MODE_TWO_IMAGES.
moreAboutRegAction() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: More about reg action.
MostRepresentedFilter - Class in io.github.rocsg.fijiyama.common: The Class MostRepresentedFilter.
MostRepresentedFilter() - Constructor for class io.github.rocsg.fijiyama.common.MostRepresentedFilter
mostRepresentedFilteringWithRadius(ImagePlus, double, boolean, int, boolean) - Static method in class io.github.rocsg.fijiyama.common.MostRepresentedFilter: Most represented filtering with radius.
mostRepresentedFilteringWithRadius(ImagePlus, double, double[][]) - Static method in class io.github.rocsg.fijiyama.common.MostRepresentedFilter: Most represented filtering with radius.
mostRepresentedFilteringWithRadiusWithBGExclusion(ImagePlus, double, boolean, int, boolean, int) - Static method in class io.github.rocsg.fijiyama.common.MostRepresentedFilter: Most represented filtering with radius with BG exclusion.
mostRepresentedValue(int[], double[], int) - Static method in class io.github.rocsg.fijiyama.common.MostRepresentedFilter: Most represented value.
mostRepresentedValueWithBGExclusion(int[], double[], int, int) - Static method in class io.github.rocsg.fijiyama.common.MostRepresentedFilter: Most represented value with BG exclusion.
move(float) - Method in class io.github.rocsg.fijiyama.rsml.Mark: Move the makr along the root.
movePointInModel(Point3d[], RootModel) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Move point in model.
movMod - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The mov mod.
movMod - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: The mov mod.
movRange - Variable in class io.github.rocsg.fijiyama.registration.ItkRegistration: The mov range.
movTime - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The mov time.
movTime - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: The mov time.
moyTwoMax(double[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Moy two max.
MRI_0_EXPLORER - Static variable in interface io.github.rocsg.fijiyama.common.VitiDialogs: The Constant vect.
MRI_1_T1_CALCULATION - Static variable in interface io.github.rocsg.fijiyama.common.VitiDialogs: The Constant MRI_1_T1_CALCULATION.
MRI_2_T2_CALCULATION - Static variable in interface io.github.rocsg.fijiyama.common.VitiDialogs: The Constant MRI_2_T2_CALCULATION.
multiply(ImagePlus, ImagePlus, boolean) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Multiply.
multiplyDenseField(double) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Multiply dense field.
multiplySigma(ImagePlus, int, int, int, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Multiply sigma.
multiplyVector(double[], double) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: Multiply vector.
multiplyVector(double[], double[]) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: Multiply vector.

N

nameAction - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The name action.
nameForExport(int, int, boolean) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Name for export.
nameForResultingCombinedHyperImage(String) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Name for resulting combined hyper image.
nameSubject - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The name subject.
nbIterations - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The nb iterations.
nbLatsPerPlant() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Nb lats per plant.
nbLevels - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The nb levels.
nbTransformComposed() - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Nb transform composed.
needsRefresh() - Method in class io.github.rocsg.fijiyama.rsml.Mark: Does the mark need to be refreshed.
needsTwinPosition() - Method in class io.github.rocsg.fijiyama.rsml.Mark: Is the mark a interval mark.
needsTwinPosition(int) - Static method in class io.github.rocsg.fijiyama.rsml.Mark: Is the mark a interval mark.
needsValue() - Method in class io.github.rocsg.fijiyama.rsml.Mark: Needs value.
needsValue(int) - Static method in class io.github.rocsg.fijiyama.rsml.Mark: Does the makr need a value.
neighbourhoodSizeX - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The neighbourhood size X.
neighbourhoodSizeY - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The neighbourhood size Y.
neighbourhoodSizeZ - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The neighbourhood size Z.
neighX - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The neigh X.
neighY - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The neigh Y.
neighZ - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The neigh Z.
newThreadArray(int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: New thread array.
nextAutoRootID - Variable in class io.github.rocsg.fijiyama.rsml.RootModel: The next auto root ID.
nMods - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: The n mods.
NO_AUTO_CHOICE - Static variable in interface io.github.rocsg.fijiyama.common.VitiDialogs: The vect.
Node - Class in io.github.rocsg.fijiyama.rsml: Constructor
Node(float, float, float, Node, boolean) - Constructor for class io.github.rocsg.fijiyama.rsml.Node: Constructor.
Node(float, float, Node, boolean) - Constructor for class io.github.rocsg.fijiyama.rsml.Node: Instantiates a new node.
nodesGP - Variable in class io.github.rocsg.fijiyama.rsml.Root: The nodes GP.
NONE - io.github.rocsg.fijiyama.registration.CenteringStrategy: The none.
NONE - io.github.rocsg.fijiyama.registration.SamplingStrategy: The none.
NONE - io.github.rocsg.fijiyama.registration.ScalerType: The none.
NONE - io.github.rocsg.fijiyama.registration.TransformUtils.Misalignment: The none.
NONE - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.ScrollUtil: The Constant SELECTED.
norm(double[]) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: Norm.
norm(float, float) - Static method in class io.github.rocsg.fijiyama.rsml.Node: Norm.
norm(float, float, float, float) - Static method in class io.github.rocsg.fijiyama.rsml.Node: Norm.
normalize(double[]) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: Normalize.
normOfDenseField(ImagePlus) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Norm of dense field.
noSubScaleZ - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The no sub scale Z.
notYet(String) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Not yet.
nTimes - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: The n times.
nullImage(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Null image.

O

offX - Variable in class io.github.rocsg.fijiyama.common.Pix: The off X.
offY - Variable in class io.github.rocsg.fijiyama.common.Pix: The off Y.
OLD_BEHAVIOUR - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The old behaviour.
OP_ADD - Static variable in class io.github.rocsg.fijiyama.common.VitimageUtils: The Constant OP_ADD.
OP_DIV - Static variable in class io.github.rocsg.fijiyama.common.VitimageUtils: The Constant OP_DIV.
OP_MEAN - Static variable in class io.github.rocsg.fijiyama.common.VitimageUtils: The Constant OP_MEAN.
OP_MULT - Static variable in class io.github.rocsg.fijiyama.common.VitimageUtils: The Constant OP_MULT.
OP_SUB - Static variable in class io.github.rocsg.fijiyama.common.VitimageUtils: The Constant OP_SUB.
openFjmFileAndGetItsPath() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Open fjm file and get its path.
openImagesAndCheckOversizing() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Open images and check oversizing.
openJFileUI(String, String, String) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Open J file UI.
openMacFileUI(String, String, String) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Open mac file UI.
openSettingsDialog() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Open settings dialog.
OptimizerType - Enum in io.github.rocsg.fijiyama.registration: The Enum OptimizerType.
order - Variable in class io.github.rocsg.fijiyama.rsml.Root: The order.
OS_SEPARATOR - Static variable in interface io.github.rocsg.fijiyama.common.VitiDialogs: The Constant OS_SEPARATOR.
osIndependantPath(String) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Os independant path.
otsuThreshold(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Otsu threshold.

P

PaperValidation - Class in io.github.rocsg.fijiyama.rsml
PaperValidation() - Constructor for class io.github.rocsg.fijiyama.rsml.PaperValidation
parallelsGP - Variable in class io.github.rocsg.fijiyama.rsml.Root: new.
paramOpt - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The param opt.
parent - Variable in class io.github.rocsg.fijiyama.rsml.Node: The parent.
parseTimes(String) - Static method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Parses the times.
passThrough(String) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Pass through.
passThroughActivated - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The pass through activated.
paths - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: The paths.
pathToTempImg - Static variable in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface
percentageBlocksSelectedByLTS - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The percentage blocks selected by LTS.
percentageBlocksSelectedByScore - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The percentage blocks selected by score.
percentageBlocksSelectedByVariance - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The percentage blocks selected by variance.
percentageBlocksSelectedRandomly - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The percentage blocks selected randomly.
percentileDisplay - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The Constant percentileDisplay.
performActionInLaunchingInterface(ActionEvent) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Perform action in launching interface.
performActionInProgrammingSerieInterface(ActionEvent) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Perform action in programming serie interface.
Pix - Class in io.github.rocsg.fijiyama.common: The Class Pix.
Pix(int, int, double) - Constructor for class io.github.rocsg.fijiyama.common.Pix: Instantiates a new pix.
pix1 - Variable in class io.github.rocsg.fijiyama.common.Bord: The pix 1.
pix2 - Variable in class io.github.rocsg.fijiyama.common.Bord: The pix 2.
pixelSize - Variable in class io.github.rocsg.fijiyama.rsml.RootModel: The pixel size.
pixSize4096 - Static variable in class io.github.rocsg.fijiyama.rsml.PaperValidation
pixSize512 - Static variable in class io.github.rocsg.fijiyama.rsml.PaperValidation
plantNumber - Variable in class io.github.rocsg.fijiyama.rsml.Root: The plant number.
plongement(ImagePlus, RootModel, boolean) - Static method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Plongement.
point3dToDoubleArray(Point3d) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: Point 3 d to double array.
pointStart() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Point start.
pouet() - Static method in class io.github.rocsg.fijiyama.rsml.Test_RSMLViewer: Pouet.
prefs - Static variable in class io.github.rocsg.fijiyama.rsml.FSR: The preferences in ImageJ.
previous - Variable in class io.github.rocsg.fijiyama.common.Pix: The previous.
previousMagnification - Variable in class io.github.rocsg.fijiyama.rsml.RootModel: The previous magnification.
print(String) - Method in class io.github.rocsg.fijiyama.common.Timer: Prints the.
printDebugIntro(int, String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Many useful functions not organized yet.
printImageResume(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Prints the image resume.
printImageResume(ImagePlus, String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Prints the image resume.
printLookup(double, boolean[][]) - Static method in class io.github.rocsg.fijiyama.common.MostRepresentedFilter: Prints the lookup.
printRegActions(String, ArrayList<RegistrationAction>) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Prints the reg actions.
printVector(double[], String) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: IO Utilities for Vectors and Matrices.
proj_u_of_v(double[], double[]) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: Proj u of v.
projectRoiOnSubImage(Roi) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Project roi on sub image.
projectRoiTabOnSubImage(Roi[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Project roi tab on sub image.
projectRsmlOnImage(RootModel) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Project rsml on image.
projectRsmlOnImage(RootModel, ImagePlus, int, int, int, boolean, boolean, boolean) - Static method in class io.github.rocsg.fijiyama.rsml.RootModel: Project rsml on image.
putThatImageInThatOther(ImagePlus, ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Put that image in that other.

Q

QUASI_REFERENCE - io.github.rocsg.fijiyama.registration.TransformUtils.Geometry: The quasi reference.
quickFixBrokenItkMatrixTo4x4Matrix(String) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform

R

RANDOM - io.github.rocsg.fijiyama.registration.SamplingStrategy: The random.
randomKeepingSelectedBlock - Static variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration
randomLevel - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI
randomSelection(double[][]) - Static method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration
read(Node, Root) - Static method in class io.github.rocsg.fijiyama.rsml.Mark: Read the mark information from the datafile.
read(Node, Root, boolean, String, float) - Static method in class io.github.rocsg.fijiyama.rsml.Mark: Read the mark information from the datafile.
readableString() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Readable string.
readableString(boolean) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Readable string.
readAsDenseField(String) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Read as dense field.
readDoubleArray1DFromFile(String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Read double array 1 D from file.
readDoubleArrayFromFile(String, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Read double array from file.
readDoubleFromFile(String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Read double from file.
readDoubleTabFromCsv(String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Read double tab from csv.
readExpertizedData(int) - Static method in class io.github.rocsg.fijiyama.rsml.RsmlPhenotypingUtils: Read expertized data.
readFromDenseFieldWithITKImporter(String) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Read from dense field with ITK importer.
readFromTxtFile(String) - Static method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Read from txt file.
readInfoFile() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin
readIntArray1DFromFile(String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Read int array 1 D from file.
readIntArrayFromFile(String, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Read int array from file.
readIntFromFile(String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Helpers for writing or reading data in files.
readLineAndExecuteActionOnModel(String[], RootModel) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin
readPoint3dArrayInFile(String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Read point 3 d array in file.
readRSML(String) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Read RSML.
readRSML(String, boolean) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Read RSML.
readRSML(Node, boolean) - Method in class io.github.rocsg.fijiyama.rsml.Node: Read RSML.
readRSML(Node, RootModel, Root, String) - Method in class io.github.rocsg.fijiyama.rsml.Root: Read the RSML file.
readRSML(Node, RootModel, Root, String, boolean) - Method in class io.github.rocsg.fijiyama.rsml.Root: Read RSML.
readRSML(Node, Node, float) - Method in class io.github.rocsg.fijiyama.rsml.Node: Read the node information from and RSML file.
readRSMLNew(String) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Read common datafile structure.
readStringFromFile(String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Read string from file.
readStringFromFile2(String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Read string from file 2.
readStringFromFileUTF8(String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Read string from file UTF 8.
readStringTabFromCsv(String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Some Csv helpers --------------------------------------------------------------------------------------.
readStringTabFromCsv(String) - Static method in class io.github.rocsg.fijiyama.rsml.Tests: Some Csv helpers --------------------------------------------------------------------------------------
readTransformFromFile(String) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Read transform from file.
reduce() - Method in class io.github.rocsg.fijiyama.common.HungarianAlgorithm: Reduce the cost matrix by subtracting the smallest element of each row from all elements of the row as well as the smallest element of each column from all elements of the column.
REFERENCE - io.github.rocsg.fijiyama.registration.TransformUtils.Geometry: The reference.
referenceModality - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: The reference modality.
referenceTime - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: The reference time.
refineDescription(int) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Refine description.
refMod - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The ref mod.
refMod - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: The ref mod.
refRange - Variable in class io.github.rocsg.fijiyama.registration.ItkRegistration: The ref range.
refTime - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The ref time.
refTime - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: The ref time.
regInterrogationLevel - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The reg interrogation level.
register() - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Register.
RegistrationAction - Class in io.github.rocsg.fijiyama.fijiyamaplugin: The Class RegistrationAction.
RegistrationAction() - Constructor for class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Instantiates a new registration action.
RegistrationAction(Fijiyama_GUI, RegistrationManager) - Constructor for class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Instantiates a new registration action.
RegistrationAction(RegistrationAction) - Constructor for class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Instantiates a new registration action.
registrationFrame - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The registration frame.
RegistrationManager - Class in io.github.rocsg.fijiyama.fijiyamaplugin: The Class RegistrationManager.
RegistrationManager(Fijiyama_GUI) - Constructor for class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Instantiates a new registration manager.
registrationPointsUI(int, ImagePlus, ImagePlus, boolean) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Registration points UI.
registrationThread - Variable in class io.github.rocsg.fijiyama.registration.ItkRegistration: The registration thread.
REGULAR - io.github.rocsg.fijiyama.registration.SamplingStrategy: The regular.
rejectionThreshold - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The rejection threshold.
remove2dBlopsInObject(ImagePlus, double, double, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Removes the 2 d blops in object.
removeEveryTitleTextInStandardFloatImage(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Removes the every title text in standard float image.
removeInterpolatedNodes() - Method in class io.github.rocsg.fijiyama.rsml.Root
removeInterpolatedNodes() - Method in class io.github.rocsg.fijiyama.rsml.RootModel
removeLastAction() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Removes the last action.
removePointInModel(Point3d[], RootModel) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Removes the point in model.
repairUnevenSituations() - Method in class io.github.rocsg.fijiyama.rsml.Root
ReproducibilityTests - Class in io.github.rocsg.fijiyama.fijiyamaplugin
ReproducibilityTests() - Constructor for class io.github.rocsg.fijiyama.fijiyamaplugin.ReproducibilityTests
resampleCurve(double[][], double) - Static method in class io.github.rocsg.fijiyama.registration.Reslicer3D
resampleFlyingPoints(double[]) - Method in class io.github.rocsg.fijiyama.rsml.Root: Resample flying points.
resampleFlyingRoots() - Method in class io.github.rocsg.fijiyama.rsml.RootModel
resampleImage(int[], double[], ImagePlus, boolean) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Resample image.
resampleImageReech(ImagePlus, ImagePlus) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Resample image reech.
resampleModel(RootModel, double, String) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Change time in point in model.
resampler - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The resampler.
resampleRootModelToTargetTimestep(RootModel, double) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin
resize(ImagePlus, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Resize.
resizeNearest(ImagePlus, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Resize nearest.
Reslicer3D - Class in io.github.rocsg.fijiyama.registration
Reslicer3D() - Constructor for class io.github.rocsg.fijiyama.registration.Reslicer3D
resliceTiffImageAlongCurve(ImagePlus, ArrayList<double[]>, double[][][], int) - Static method in class io.github.rocsg.fijiyama.registration.Reslicer3D
resolveConnexitiesGroupsAndExclude(int[][], int, int, int[], double[], double[], double[], double, double, int, boolean) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Resolve connexities groups and exclude.
restoreType(ImagePlus, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Restore type.
restrictionMaskForFadingHandling(ImagePlus, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Restriction mask for fading handling.
returnComposedTransformationIncludingTheInitialTransformationGiven - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The return composed transformation including the initial transformation given.
returnComposedTransformationIncludingTheInitialTransformationGiven - Variable in class io.github.rocsg.fijiyama.registration.ItkRegistration: The return composed transformation including the initial transformation given.
RIGHT - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.ScrollUtil: The Constant SELECTED.
RIGID - io.github.rocsg.fijiyama.registration.Transform3DType: The rigid.
Root - Class in io.github.rocsg.fijiyama.rsml
Root(float, Node, boolean, Root, RootModel, String) - Constructor for class io.github.rocsg.fijiyama.rsml.Root: Constructor Used when opening a xml file.
Root(float, Node, boolean, Root, RootModel, String, boolean) - Constructor for class io.github.rocsg.fijiyama.rsml.Root: Instantiates a new root.
Root(Root, RootModel, String, int) - Constructor for class io.github.rocsg.fijiyama.rsml.Root: Instantiates a new root.
rootID - Variable in class io.github.rocsg.fijiyama.rsml.Root: The root ID.
rootList - Variable in class io.github.rocsg.fijiyama.rsml.RootModel: The root list.
RootModel - Class in io.github.rocsg.fijiyama.rsml: The Class RootModel.
RootModel() - Constructor for class io.github.rocsg.fijiyama.rsml.RootModel: Constructors.
RootModel(String) - Constructor for class io.github.rocsg.fijiyama.rsml.RootModel: Constructors.
RootModel(String, boolean) - Constructor for class io.github.rocsg.fijiyama.rsml.RootModel: Constructors.
RootModelWildReadFromRsml(String) - Static method in class io.github.rocsg.fijiyama.rsml.RootModel: Root model wild read from rsml.
RSML_reader - Class in io.github.rocsg.fijiyama.rsml: The Class RSML_reader.
RSML_reader() - Constructor for class io.github.rocsg.fijiyama.rsml.RSML_reader: Constructor.
RsmlExpert_Plugin - Class in io.github.rocsg.fijiyama.rsml: The Class RsmlExpert_Plugin.
RsmlExpert_Plugin() - Constructor for class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Instantiates a new rsml expert plugin.
RsmlExpert_Plugin(String) - Constructor for class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Instantiates a new ${e.g(1).rsfl()}.
rsmlFilesList(String, String) - Static method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Rsml files list.
rsmlGui - Static variable in class io.github.rocsg.fijiyama.rsml.RSML_reader: The rsml gui.
RSMLGUI - Class in io.github.rocsg.fijiyama.rsml: The Class RSMLGUI.
RSMLGUI() - Constructor for class io.github.rocsg.fijiyama.rsml.RSMLGUI: Build the RSML importer interface.
RSMLNoGUI - Class in io.github.rocsg.fijiyama.rsml: The Class RSMLNoGUI.
RSMLNoGUI() - Constructor for class io.github.rocsg.fijiyama.rsml.RSMLNoGUI: Instantiates a new RSML no GUI.
RsmlPhenotypingUtils - Class in io.github.rocsg.fijiyama.rsml: The Class RsmlPhenotypingUtils.
RsmlPhenotypingUtils() - Constructor for class io.github.rocsg.fijiyama.rsml.RsmlPhenotypingUtils
run(String) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Run.
run(String) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Run.
runApplyTransformInBeanShellMode() - Static method in class io.github.rocsg.fijiyama.fijiyamaplugin.TestScriptBeanshell: Run apply transform in bean shell mode.
runBlockMatching(ItkTransform, boolean) - Method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Run algorithm from an initial situation (trInit), and return the final transform (including trInit).
runComposeTransformInBeanShellMode() - Static method in class io.github.rocsg.fijiyama.fijiyamaplugin.TestScriptBeanshell: Run compose transform in bean shell mode.
runNextStep() - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Run next step.
runScenarioFromGui(ItkTransform, ImagePlus, ImagePlus, Transform3DType, int, int, int, double) - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Run scenario from gui.
runSos() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Run sos.
runTest(String, String) - Static method in class io.github.rocsg.fijiyama.registration.TestingRegistrationPackage: Run test.
runTestFijiyamaSupport() - Static method in class io.github.rocsg.fijiyama.registration.TestingRegistrationPackage: Run test fijiyama support.
runTestLevel00simplePassing(String, String) - Static method in class io.github.rocsg.fijiyama.registration.TestingRegistrationPackage: Run test level 00 simple passing.
runTestLevel01failWithException(String, String) - Static method in class io.github.rocsg.fijiyama.registration.TestingRegistrationPackage: Run test level 01 fail with exception.
runTestLevel02failWithCode2(String, String) - Static method in class io.github.rocsg.fijiyama.registration.TestingRegistrationPackage: Run test level 02 fail with code 2.
runTestLevel03SimpleAccessToClassesAndObjects(String, String) - Static method in class io.github.rocsg.fijiyama.registration.TestingRegistrationPackage: Run test level 03 simple access to classes and objects.
runTestLevel04Transform2D(String, String) - Static method in class io.github.rocsg.fijiyama.registration.TestingRegistrationPackage: Run test level 04 transform 2 D.
runTestLevel05Transform3D(String, String) - Static method in class io.github.rocsg.fijiyama.registration.TestingRegistrationPackage: Run test level 05 transform 3 D.
runTestLevel06Transform4D(String, String) - Static method in class io.github.rocsg.fijiyama.registration.TestingRegistrationPackage: Run test level 06 transform 4 D.
runTestLevel07Transform5D(String, String) - Static method in class io.github.rocsg.fijiyama.registration.TestingRegistrationPackage: Run test level 07 transform 5 D.
runTestSequence() - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Top level functions : Test function, and main scenarios that will be used by customers classes.

S

safeParsePositiveInt(String) - Static method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Safe parse positive int.
SamplingStrategy - Enum in io.github.rocsg.fijiyama.registration: The Enum SamplingStrategy.
saveDenseFieldTransformUI(ItkTransform, String, boolean, String, String, ImagePlus) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: UI generic functions to save transforms, images, or text in files.
saveExpertizedModel(RootModel, String) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Save expertized model
saveImageUI(ImagePlus, String, boolean, String, String) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Save image UI.
saveImageUIPath(String, String) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Save image UI path.
saveMatrixTransformUI(ItkTransform, String, boolean, String, String) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Save matrix transform UI.
saveRSML(FileWriter) - Method in class io.github.rocsg.fijiyama.rsml.Mark: Save the mark to an RSML file.
saveRsmlModel() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Save the model into a final RSML
saveSerieToFjmFile() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Save serie to fjm file.
saveTextFileUI(String, String, String, String, String) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Save text file UI.
scalarProduct(double[], double[]) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: Scalar product.
scalarProduct(Point3d, Point3d) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: Scalar product.
SCALER_INDEX - io.github.rocsg.fijiyama.registration.ScalerType: The scaler index.
SCALER_PHYSICAL - io.github.rocsg.fijiyama.registration.ScalerType: The scaler physical.
ScalerType - Enum in io.github.rocsg.fijiyama.registration: The Enum ScalerType.
scroll(JComponent, int, int[]) - Static method in class io.github.rocsg.fijiyama.fijiyamaplugin.ScrollUtil: Scroll to specified location.
scroll(JComponent, int, int, int[]) - Static method in class io.github.rocsg.fijiyama.fijiyamaplugin.ScrollUtil: Scroll to specified location.
ScrollUtil - Class in io.github.rocsg.fijiyama.fijiyamaplugin: Original class from adamski on stack overflow : https://stackoverflow.com/questions/2544758/how-to-adjust-position-of-scroll-in-the-scrollpane
segmentationToRoi(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Segmentation to roi.
SELECTED - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.ScrollUtil: The Constant SELECTED.
selectLTS - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The select LTS.
selectRandom - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The select random.
selectScore - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The select score.
sendImageData(ResultsTable, String) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Send the image data to the Result Table.
sendingOutAnSos() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Sending out an sos.
sendNodeData(ResultsTable, String) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Send the node data to the Result Table.
sendRootData(ResultsTable, String) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Send the root data to the ResulsTable rt.
SentenceOfTheDay - Class in io.github.rocsg.fijiyama.common: The Class SentenceOfTheDay.
SentenceOfTheDay() - Constructor for class io.github.rocsg.fijiyama.common.SentenceOfTheDay
sequenceStepsOfTheCreatedPipeline(ArrayList<RegistrationAction>, ArrayList<ArrayList<RegistrationAction>>) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Sequence steps of the created pipeline.
serieIsFinished() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Serie is finished.
serieOutputPath - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: The serie output path.
set16bitToValue(ImagePlus, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Sets the 16 bit to value.
set32bitToValue(ImagePlus, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Sets the 32 bit to value.
set32bitToValue(ImagePlus, double, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Sets the 32 bit to value.
set8bitToValue(ImagePlus, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Sets the 8 bit to value.
setActionTo(int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Sets the action to.
setChildDensity() - Method in class io.github.rocsg.fijiyama.rsml.Root: Set the child density of the root inside the ramified region.
setCurrentLevel(int) - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Sets the current level.
setCurrentStep(int) - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Sets the current step.
setDistanceFromApex() - Method in class io.github.rocsg.fijiyama.rsml.Root: Automatically set distance from parent apex.
setDistanceFromApex(float) - Method in class io.github.rocsg.fijiyama.rsml.Root: set the distance from the parent apex.
setDistanceFromBase() - Method in class io.github.rocsg.fijiyama.rsml.Root: Automatically set distance from parent base.
setDistanceFromBase(float) - Method in class io.github.rocsg.fijiyama.rsml.Root: set the distance from the parent base.
setDone() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Sets the done.
setDPI(float) - Method in class io.github.rocsg.fijiyama.rsml.Root: Set the DPI value for internal reference.
setDPI(float) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Set the DPI avlue for the image.
setFirstChild() - Method in class io.github.rocsg.fijiyama.rsml.Root: Set which child is the first one on the root (closest from the base).
setFlag() - Static method in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface
setHoursFromPph(double[]) - Method in class io.github.rocsg.fijiyama.rsml.RootModel
setImageToValue(ImagePlus, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Sets the image to value.
setImageWindowSizeTo(ImagePlus, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Sets the image window size to.
setInitialTransformation(ItkTransform) - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Sets the initial transformation.
setInsertAngl() - Method in class io.github.rocsg.fijiyama.rsml.Root: Automatically set the insertion angle of the root on its parent.
setInsertAngl(float) - Method in class io.github.rocsg.fijiyama.rsml.Root: set the insertion angle of the root in its parent.
setInterBranch() - Method in class io.github.rocsg.fijiyama.rsml.Root: Automatically set the interbranch distance between this root and the previous child on the parent.
setInterBranch(float) - Method in class io.github.rocsg.fijiyama.rsml.Root: Set the interbranch distance between this root and the previous child on the parent.
setIterationsBM(int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Sets the iterations BM.
setIterationsBMLinear(int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Sets the iterations BM linear.
setIterationsBMNonLinear(int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Sets the iterations BM non linear.
setLastChild() - Method in class io.github.rocsg.fijiyama.rsml.Root: Set which child is the last one on the root (closest from the apex).
setLastNodeHidden() - Method in class io.github.rocsg.fijiyama.rsml.Root: Sets the last node hidden.
setLevelMax(int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Sets the level max.
setLevelMaxLinear(int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Sets the level max linear.
setLevelMaxNonLinear(int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Sets the level max non linear.
setLevelMin(int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Sets the level min.
setLevelMinLinear(int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Sets the level min linear.
setLevelMinNonLinear(int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Sets the level min non linear.
setLut(ImagePlus, String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils
setLutToFire(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils
setLutToGrays(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils
setMaskImage() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Sets the mask image.
setMetric(MetricType) - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Sets the metric.
setMovingImage(ImagePlus) - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Sets the moving image.
setMovRange(double[]) - Method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Sets the mov range.
setNbLevels(ArrayList<Integer>) - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Sets the nb levels.
setNbSteps(int) - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Sets the nb steps.
setParent(Root, Root) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Attach c to p.
setParentKey(String) - Method in class io.github.rocsg.fijiyama.rsml.Root: Set the identifier of the parent (internal reference, does not change the value in the parent).
setParentName(String) - Method in class io.github.rocsg.fijiyama.rsml.Root: Set the name of the parent (internal reference, does not change the value in the parent).
setParentNode() - Method in class io.github.rocsg.fijiyama.rsml.Root: Set the parentNode, which is the closest node in the parent from the base node of root.
setPathToMask() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Sets the path to mask.
setPlantNumbers() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Sets the plant numbers.
setPoAccession(int) - Method in class io.github.rocsg.fijiyama.rsml.Root: Set the plant ontology accession to a new value.
setRandomSelection() - Static method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration
setReferenceImage(ImagePlus) - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Initializers.
setRefRange(double[]) - Method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Sets the ref range.
setRootID(String) - Method in class io.github.rocsg.fijiyama.rsml.Root: Set the root name to a new value.
setRootKey(String) - Method in class io.github.rocsg.fijiyama.rsml.Root: Set the root key to a new value.
setRulerAtOrigin(float) - Method in class io.github.rocsg.fijiyama.rsml.Root: Set the orign of the ruler (base of the root).
setRunToolTip(int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Sets the run tool tip.
setScalerTypes(ArrayList<ScalerType>) - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Sets the scaler types.
setScales(ArrayList<double[]>) - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Sets the scales.
setShrinkFactors(ArrayList<int[]>) - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Sets the shrink factors.
setSingleView() - Method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Sets the single view.
setSpeedupOnForFiji() - Static method in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface
setState(int[], boolean) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Sets the state.
setState(int[], boolean) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Sets the state.
setStep(int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Sets the step.
setStepTo(int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Sets the step to.
setTextInfoAtEachIterationOff() - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Sets the text info at each iteration off.
setTextInfoAtEachIterationOn() - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Sets the text info at each iteration on.
setTimingForPlayer() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI
settingsButton - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The settings button.
setTwinPosition(float) - Method in class io.github.rocsg.fijiyama.rsml.Mark: Get the positon of the twin mark.
setUndone() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Sets the undone.
setupAndRunRsmlBlockMatchingRegistration(String, boolean, boolean) - Static method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Setup and run rsml block matching registration.
setupBlockMatchingRegistration(ImagePlus, ImagePlus, RegistrationAction) - Static method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Setup block matching registration.
setupButtonsAndButtonPanel() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Setup buttons.
setupFrameAndLogArea() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin
setupFromFjmFile(String) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Setup from fjm file.
setupFromTwoImages(String[]) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Setup from two images.
setupImageAndRsml() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Setup image and rsml.
setupStructures() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Setup structures.
setViewSlice(int) - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Sets the view slice.
setWeights(ArrayList<double[]>) - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Sets the weights.
showAsCoordinates(String, int) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Show as coordinates.
showAsGrid3D(ImagePlus, int, String, int) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Show as grid 3 D.
showHyperImage(ImagePlus, int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Show hyper image.
showWithParams(ImagePlus, String, int, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Show with params.
showWithParams(ImagePlus, String, int, double, double, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Show with params.
sigmaDense - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The sigma dense.
sigmaDenseFieldAtSuccessiveLevels(int[], double) - Method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Sigma dense field at successive levels.
sigmaFactorsAtSuccessiveLevels(double[], int[], double) - Method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Sigma factors at successive levels.
sigmaFactorsAtSuccessiveLevels(double[], int[], double) - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Sigma factors at successive levels.
sigmaResampling - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The sigma resampling.
similarity(double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Similarity.
SIMILARITY - io.github.rocsg.fijiyama.registration.Transform3DType: The similarity.
simplify() - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Simplify.
simplify(List<Pix>, List<Integer>, double) - Static method in class io.github.rocsg.fijiyama.common.DouglasPeuckerSimplify: Simplify.
simplifySimpler(List<Pix>, List<Integer>, int) - Static method in class io.github.rocsg.fijiyama.common.DouglasPeuckerSimplify: Simplify simpler.
slash - Static variable in class io.github.rocsg.fijiyama.common.VitimageUtils: The Constant slash.
sliceCorr - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The slice corr.
sliceFuse - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The slice fuse.
sliceGrid - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The slice grid.
sliceInt - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The slice int.
sliceIntCorr - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The slice int corr.
sliceJacobian - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The slice jacobian.
sliceMov - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The slice mov.
sliceRef - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The slice ref.
slicesToStack(ImagePlus[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Slices to stack.
slicesWithChannelsToStackWithChannels(ImagePlus[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Slices with channels to stack with channels.
smoothDeformationTransform(ItkTransform, double, double, double) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Smooth deformation transform.
smoothImageFromCorrespondences(int[][], double[], ImagePlus, double, boolean) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Smooth image from correspondences.
smoothingSigmaInPixels - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The smoothing sigma in pixels.
sosLevel - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The sos level.
source - Variable in class io.github.rocsg.fijiyama.common.Pix: The source.
speedupLevel - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI
splitRGBStackHeadLess(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Split RGB stack head less.
SQUARED_CORRELATION - io.github.rocsg.fijiyama.registration.MetricType: The squared correlation.
sr - Static variable in class io.github.rocsg.fijiyama.rsml.RSML_reader: The sr.
stacksFromHyperstack(ImagePlus, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Stacks from hyperstack.
stacksFromHyperstackBis(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Stacks from hyperstack bis.
stacksFromHyperstackFast(ImagePlus, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Stacks from hyperstack fast.
stacksFromHyperstackFastBis(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Stacks from hyperstack fast bis.
stackToSlices(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Stack to slices.
stamp - Variable in class io.github.rocsg.fijiyama.common.Pix: The stamp.
standardOrderingOfRoots() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: This function modify the current object in order to respect the standard description of roots.
start2dManualRegistration(ImagePlus, ImagePlus) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Start 2 d manual registration.
start3dManualRegistration(ImagePlus, ImagePlus) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Start 3 d manual registration.
startAndJoin(Thread) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Start and join.
startAndJoin(Thread[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Start and join.
startBatchRsml(String, String, boolean) - Static method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Start batch rsml.
startCurrentAction() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Start current action.
startGui() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Start gui.
startLaunchingInterface() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Start launching interface.
startNewExpertize() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin
startNoJoin(Thread[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Start no join.
startPlugin(String) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Start plugin.
startRegistrationInterface() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Start registration interface.
startSerie() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Start serie.
startSetupSerieFromScratch(int, String) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Start setup serie from scratch.
startTheSerie() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Start the serie.
startTwoImagesRegistration() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Start two images registration.
statistics1D(double[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Statistics 1 D.
statistics1D(ArrayList<Double>) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Statistics 1 D.
statistics1DNoBlack(double[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Statistics 1 D no black.
statistics2D(double[][]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Statistics 2 D.
STD_BM_ITER - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The Constant STD_BM_ITER.
STD_ITK_ITER - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The Constant STD_ITK_ITER.
stdAndMeanValueofImageAround(ImagePlus, int, int, int, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: ?.
step - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The step.
step - Variable in class io.github.rocsg.fijiyama.registration.ItkTransform: The step.
stepBuild - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: The step build.
strideMoving - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The stride moving.
strideX - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The stride X.
strideY - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The stride Y.
strideZ - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The stride Z.
stringArraySort(String[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: String array sort.
stringArraySortByTrValue(String[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: String array sort by tr value.
stringMatrix(String, double[]) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: String matrix.
stringMatrixMN(String, double[][]) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: String matrix MN.
stringMatrixMN(String, int[][]) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: String matrix MN.
stringMatrixN(int[][], String) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: String matrix N.
stringNodes() - Method in class io.github.rocsg.fijiyama.rsml.Root: String nodes.
stringVector(double[], String) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: String vector.
stringVector(int[], String) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: String vector.
stringVectorDou(double[], String) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: String vector dou.
stringVectorDou(double[], String, int) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: String vector dou.
stringVectorN(double[], String) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: String vector N.
stringVectorN(int[], String) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: String vector N.
stringVectorNDou(double[], String) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: String vector N dou.
strInt6chars(int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Str int 6 chars.
STRONG_DEFORMATION - io.github.rocsg.fijiyama.registration.TransformUtils.Misalignment: The strong deformation.
STRONG_SIMILARITY - io.github.rocsg.fijiyama.registration.TransformUtils.Misalignment: The strong similarity.
stuff() - Static method in class io.github.rocsg.fijiyama.rsml.Test_RSMLViewer: Stuff.
Sub222(ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Sub 222.
subsampleZ - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The subsample Z.
subSamplingFactorsAtSuccessiveLevels(int, int, boolean, double) - Method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Helper functions to determine initial factors from given data and parameters .
subSamplingFactorsAtSuccessiveLevels(int, int, boolean, double) - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Helper functions to build the pyramidal scheme based on few parameters.
subScaleFactors - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The sub scale factors.
substract(ImagePlus, ImagePlus, boolean) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Substract.
subXYZ(ImagePlus, double[], boolean) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Sub XYZ.
successiveDenseFieldSigma - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The successive dense field sigma.
successiveDimensions - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The successive dimensions.
successiveSmoothingSigma - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The successive smoothing sigma.
successiveStepFactors - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The successive step factors.
successiveStepFactorsAtSuccessiveLevels(int, int, boolean, double) - Method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Successive step factors at successive levels.
successiveVoxSizes - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The successive vox sizes.
summary - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The summary.
sumOfImages(ImagePlus[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Sum of images.
sumVector(double[], double[]) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: Sum vector.
sumVector(double[], double[], double[]) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: Sum vector.
SUPERVISED - Static variable in interface io.github.rocsg.fijiyama.common.VitiDialogs: The Constant SUPERVISED.
SWITCH_XY - io.github.rocsg.fijiyama.registration.TransformUtils.Geometry: The switch xy.
SWITCH_XZ - io.github.rocsg.fijiyama.registration.TransformUtils.Geometry: The switch xz.
SWITCH_YZ - io.github.rocsg.fijiyama.registration.TransformUtils.Geometry: The switch yz.
switchAxis(ImagePlus, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Switch axis.
switchPointInModel(Point3d[], RootModel) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Switch point in model.
switchToFollowingAction() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Switch to following action.
switchTwoValuesInImage(ImagePlus, int, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Switch two values in image.
switchTwoValuesInImageFloat(ImagePlus, float, float, float, float) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Switch two values in image float.
switchValueInImage(ImagePlus, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Switch value in image.
switchValueInImageFloat(ImagePlus, float, float) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Helper functions to switch values in images.
sync() - Static method in class io.github.rocsg.fijiyama.rsml.Tests

T

test() - Static method in class io.github.rocsg.fijiyama.registration.TestGargee
Test_RSMLViewer - Class in io.github.rocsg.fijiyama.rsml: The Class Test_RSMLViewer.
Test_RSMLViewer() - Constructor for class io.github.rocsg.fijiyama.rsml.Test_RSMLViewer: Instantiates a new test RSML viewer.
test0() - Static method in class io.github.rocsg.fijiyama.rsml.RsmlPhenotypingUtils: Test 0.
test1() - Static method in class io.github.rocsg.fijiyama.rsml.RsmlPhenotypingUtils: Test 1.
test2() - Static method in class io.github.rocsg.fijiyama.rsml.RsmlPhenotypingUtils: Test 2.
test3() - Static method in class io.github.rocsg.fijiyama.rsml.RsmlPhenotypingUtils: Test 3.
test4() - Static method in class io.github.rocsg.fijiyama.rsml.RsmlPhenotypingUtils: Test 4.
test5() - Static method in class io.github.rocsg.fijiyama.rsml.RsmlPhenotypingUtils: Test 5.
testAllItkModif() - Static method in class io.github.rocsg.fijiyama.rsml.Tests
testCompareViewsOfExpert() - Static method in class io.github.rocsg.fijiyama.rsml.RsmlPhenotypingUtils: Test compare views of expert.
testConfig2() - Static method in class io.github.rocsg.fijiyama.rsml.Tests
testConfiguration() - Static method in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface
testConfiguration() - Static method in class io.github.rocsg.fijiyama.rsml.Tests
TestGargee - Class in io.github.rocsg.fijiyama.registration
TestGargee() - Constructor for class io.github.rocsg.fijiyama.registration.TestGargee
TestingFijiyamaPackage - Class in io.github.rocsg.fijiyama.fijiyamaplugin: The Class TestingFijiyamaPackage.
TestingFijiyamaPackage() - Constructor for class io.github.rocsg.fijiyama.fijiyamaplugin.TestingFijiyamaPackage: Instantiates a new testing fijiyama package.
TestingRegistrationPackage - Class in io.github.rocsg.fijiyama.registration: The Class blockSizeHalfY.
TestingRegistrationPackage() - Constructor for class io.github.rocsg.fijiyama.registration.TestingRegistrationPackage: Instantiates a new testing registration package.
testProduceSimplifyLatV1() - Static method in class io.github.rocsg.fijiyama.rsml.RsmlPhenotypingUtils: Test produce simplify lat V 1.
testProduceStatsPrimLatLengthNumber() - Static method in class io.github.rocsg.fijiyama.rsml.RsmlPhenotypingUtils: Test produce stats prim lat length number.
testRegistration() - Static method in class io.github.rocsg.fijiyama.registration.TestGargee
Tests - Class in io.github.rocsg.fijiyama.rsml: The Class Tests.
Tests() - Constructor for class io.github.rocsg.fijiyama.rsml.Tests
TestScriptBeanshell - Class in io.github.rocsg.fijiyama.fijiyamaplugin: The Class TestScriptBeanshell.
TestScriptBeanshell() - Constructor for class io.github.rocsg.fijiyama.fijiyamaplugin.TestScriptBeanshell
testStandardOrderingOfRoots(String) - Static method in class io.github.rocsg.fijiyama.rsml.RootModel: Here is a test function for the function above, standardOrderingOfRoots() It takes as an argument a rsml, read it by using the function RootModelWildReadFromRsml, then standardize ordering, and then write it back to a new rsml file
theta - Variable in class io.github.rocsg.fijiyama.rsml.Node: The birth time.
threads - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The threads.
thresholdByteImage(ImagePlus, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Threshold byte image.
thresholdByteImageToFloatMask(ImagePlus, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Threshold byte image to float mask.
thresholdFloatImage(ImagePlus, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Threshold float image.
thresholdFloatImageToFloatMask(ImagePlus, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Threshold float image to float mask.
thresholdImage(ImagePlus, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Threshold image.
thresholdImageToFloatMask(ImagePlus, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Threshold image to float mask.
thresholdShortImage(ImagePlus, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Threshold short image.
thresholdShortImageToFloatMask(ImagePlus, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Threshold short image to float mask.
thresholdSize - Static variable in class io.github.rocsg.fijiyama.rsml.PaperValidation
ticksGP - Variable in class io.github.rocsg.fijiyama.rsml.Root: The ticks GP.
time - Variable in class io.github.rocsg.fijiyama.common.Pix: The time.
timeHours - Variable in class io.github.rocsg.fijiyama.common.Pix: The time.
timeOut - Variable in class io.github.rocsg.fijiyama.common.Pix: The time out.
timeOutHours - Variable in class io.github.rocsg.fijiyama.common.Pix: The time out.
Timer - Class in io.github.rocsg.fijiyama.common: The Class Timer.
Timer() - Constructor for class io.github.rocsg.fijiyama.common.Timer: Instantiates a new timer.
timeVersionFlag - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The time version flag.
timingActivatedForPlayer - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI
timingLevel - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI
timingMeasurement - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The timing measurement.
tipsGP - Variable in class io.github.rocsg.fijiyama.rsml.Root: The tips GP.
toAffineArrayMonolineRepresentation() - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: To affine array monoline representation.
toAffineArrayRepresentation() - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: To affine array representation.
toCuteString() - Method in class io.github.rocsg.fijiyama.common.Timer: To cute string.
toImageSpace(Point3d, double[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: To image space.
TOOL_1_TRANSFORM_3D - Static variable in interface io.github.rocsg.fijiyama.common.VitiDialogs: The Constant TOOL_1_TRANSFORM_3D.
TOOL_2_MRI_WATER_TRACKER - Static variable in interface io.github.rocsg.fijiyama.common.VitiDialogs: The Constant TOOL_2_MRI_WATER_TRACKER.
TOOL_3_MULTIMODAL_ASSISTANT - Static variable in interface io.github.rocsg.fijiyama.common.VitiDialogs: The Constant TOOL_3_MULTIMODAL_ASSISTANT.
TOOL_NOTHING - Static variable in interface io.github.rocsg.fijiyama.common.VitiDialogs: The Constant TOOL_NOTHING.
TOP - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.ScrollUtil: The Constant SELECTED.
toRealSpace(Point3d, double[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Point 3d /xyz utilities.
toString() - Method in class io.github.rocsg.fijiyama.common.Pix: To string.
toString() - Method in class io.github.rocsg.fijiyama.common.Timer: To string.
toString() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: To string.
toString() - Method in class io.github.rocsg.fijiyama.rsml.Mark: Convert the mark to a string.
toString() - Method in class io.github.rocsg.fijiyama.rsml.Node: To string.
toString() - Method in class io.github.rocsg.fijiyama.rsml.Root: To string.
toString() - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Return the image name.
toString(String) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: To string.
TR3D_0_MANUAL_TR - Static variable in interface io.github.rocsg.fijiyama.common.VitiDialogs: The Constant TR3D_0_MANUAL_TR.
TR3D_1_AUTO_TR - Static variable in interface io.github.rocsg.fijiyama.common.VitiDialogs: The Constant TR3D_1_AUTO_TR.
TR3D_2_MAT_TR - Static variable in interface io.github.rocsg.fijiyama.common.VitiDialogs: The Constant TR3D_2_MAT_TR.
TR3D_3_MANALIGN_TR - Static variable in interface io.github.rocsg.fijiyama.common.VitiDialogs: The Constant TR3D_3_MANALIGN_TR.
TR3D_4_AUTOALIGN_TR - Static variable in interface io.github.rocsg.fijiyama.common.VitiDialogs: The Constant TR3D_4_AUTOALIGN_TR.
TR3D_5_MANCAP_TR - Static variable in interface io.github.rocsg.fijiyama.common.VitiDialogs: The Constant TR3D_5_MANCAP_TR.
TR3D_6_AUTOCAP_TR - Static variable in interface io.github.rocsg.fijiyama.common.VitiDialogs: The Constant TR3D_6_AUTOCAP_TR.
transferProperties(ImagePlus, ImagePlus) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Transfer properties.
Transform3DType - Enum in io.github.rocsg.fijiyama.registration: The Enum Transform3DType.
transformationType - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The transformation type.
transformImage(int[], double[], ImagePlus, boolean) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Transform image.
transformImage(ImagePlus, ImagePlus) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Transform image.
transformImage(ImagePlus, ImagePlus, boolean) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Transform image.
transformImage(ImagePlus, ImagePlus, boolean, boolean, long, boolean) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Transform image.
transformImageExtensive(int[], double[], ImagePlus, boolean) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Transform image extensive.
transformImageExtensive(ImagePlus, ImagePlus) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Transform image extensive.
transformImageExtensive(ImagePlus, ImagePlus, boolean) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Transform image extensive.
transformImageSegmentationByte(ImagePlus, ImagePlus, int, int) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Transform image segmentation byte.
transformImageWithGui() - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Transform image with gui.
transformPoint(double[]) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Transform point.
transformPoint(Point3d) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Transform point.
transformPointInverse(Point3d) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Transform point inverse.
transforms - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: The transforms.
TransformUtils - Interface in io.github.rocsg.fijiyama.registration: The Interface TransformUtils.
TransformUtils.AngleComparator - Class in io.github.rocsg.fijiyama.registration: The Class AngleComparator.
TransformUtils.Geometry - Enum in io.github.rocsg.fijiyama.registration: The Enum Geometry.
TransformUtils.Misalignment - Enum in io.github.rocsg.fijiyama.registration: The Enum Misalignment.
TransformUtils.VolumeComparator - Class in io.github.rocsg.fijiyama.registration: The Class VolumeComparator.
translate(float, float) - Method in class io.github.rocsg.fijiyama.rsml.Node: Translate.
TRANSLATION - io.github.rocsg.fijiyama.registration.Transform3DType: The translation.
transposeTab(double[][]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Transpose tab.
trimCorrespondances(Point3d[][], ImagePlus, double, double) - Static method in class io.github.rocsg.fijiyama.registration.ItkTransform: Trim correspondances.
trimUsingMaskNEW(double[][], ImagePlus, int, int, int) - Method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Trim using mask NEW.
trimUsingMaskOLD(double[][], ImagePlus, int, int, int) - Method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: Trim using mask OLD.
tuckeyIsOutlier(double, double[], double[], double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Helpers for outlier detection and removal---------------------------------------------------------.
twinLPos - Variable in class io.github.rocsg.fijiyama.rsml.Mark: The twin L pos.
type - Variable in class io.github.rocsg.fijiyama.rsml.Mark: The type.
typeAction - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The type action.
TYPEACTION_ALIGN - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The Constant TYPEACTION_ALIGN.
TYPEACTION_AUTO - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The Constant TYPEACTION_AUTO.
TYPEACTION_EVALUATE - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The Constant TYPEACTION_EVALUATE.
TYPEACTION_EXPORT - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The Constant TYPEACTION_EXPORT.
TYPEACTION_MAN - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The Constant TYPEACTION_MAN.
TYPEACTION_SAVE - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The Constant TYPEACTION_SAVE.
TYPEACTION_VIEW - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The Constant TYPEACTION_VIEW.
typeAutoDisplay - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The type auto display.
typeManViewer - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The type man viewer.
typeOpt - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The type opt.
typeTrans - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The type trans.

U

uncropImageByte(ImagePlus, int, int, int, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Uncrop image byte.
uncropImageFloat(ImagePlus, int, int, int, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Uncrop image float.
undoButtonPressed() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Undo button pressed.
undoLastActionInSerieContext() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Undo last action in serie context.
undoLastActionInTwoImagesContext() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Undo last action in two images context.
unit - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: The unit.
universe - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: The universe.
UNKNOWN - io.github.rocsg.fijiyama.registration.TransformUtils.Geometry: The unknown.
UNKNOWN - io.github.rocsg.fijiyama.registration.TransformUtils.Misalignment: The unknown.
unpassThrough(String) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Unpass through.
unsetAllStructures() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Unset all structures.
updateBoxFieldsFromRegistrationAction(RegistrationAction) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Update box fields from registration action.
updateBoxFieldsToCoherenceAndApplyToRegistrationAction(boolean) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Update box fields to coherence and apply to registration action.
updateChildren() - Method in class io.github.rocsg.fijiyama.rsml.Root: Update the children information.
updateEstimatedTime() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Update estimated time.
updateFieldsFromBoxes(int, int, int, int, int, int) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Update fields from boxes.
updateLabeling(double) - Method in class io.github.rocsg.fijiyama.common.HungarianAlgorithm: Update labels with the specified slack by adding the slack value for committed workers and by subtracting the slack value for committed jobs.
updateList() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Update list.
updateNbSteps() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Update nb steps.
updateNnodes() - Method in class io.github.rocsg.fijiyama.rsml.Root: Update nnodes.
updateRoot() - Method in class io.github.rocsg.fijiyama.rsml.Root: Update the root information relative to his parent.
updateTiming() - Method in class io.github.rocsg.fijiyama.rsml.Root
updateView() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Update view.
updateView(int[], double, int, String, ItkTransform) - Method in class io.github.rocsg.fijiyama.registration.ItkRegistration: Update view.
updateViews(int, int, int, String) - Method in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: display registration and informations during execution.

V

validate() - Method in class io.github.rocsg.fijiyama.rsml.Root: Is the root valid (has at least one node).
validatePipelineButton - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The validate pipeline button.
value - Variable in class io.github.rocsg.fijiyama.rsml.Mark: The value.
valueAllTypes() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationManager: Value all types.
valueOf(String) - Static method in enum io.github.rocsg.fijiyama.registration.CenteringStrategy: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum io.github.rocsg.fijiyama.registration.MetricType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum io.github.rocsg.fijiyama.registration.OptimizerType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum io.github.rocsg.fijiyama.registration.SamplingStrategy: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum io.github.rocsg.fijiyama.registration.ScalerType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum io.github.rocsg.fijiyama.registration.Transform3DType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum io.github.rocsg.fijiyama.registration.TransformUtils.Geometry: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum io.github.rocsg.fijiyama.registration.TransformUtils.Misalignment: Returns the enum constant of this type with the specified name.
values() - Static method in enum io.github.rocsg.fijiyama.registration.CenteringStrategy: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum io.github.rocsg.fijiyama.registration.MetricType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum io.github.rocsg.fijiyama.registration.OptimizerType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum io.github.rocsg.fijiyama.registration.SamplingStrategy: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum io.github.rocsg.fijiyama.registration.ScalerType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum io.github.rocsg.fijiyama.registration.Transform3DType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum io.github.rocsg.fijiyama.registration.TransformUtils.Geometry: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum io.github.rocsg.fijiyama.registration.TransformUtils.Misalignment: Returns an array containing the constants of this enum type, in the order they are declared.
valuesOfBlock(ImagePlus, int, int, int, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Values of block.
valuesOfBlock(ImagePlus, int, int, int, int, int, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Values of block.
valuesOfBlockDouble(ImagePlus, double, double, double, double, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Values of block double.
valuesOfBlockDoubleSlice(ImagePlus, double, double, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Values of block double slice.
valuesOfImageAround(ImagePlus, int, int, int, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Values of image around.
valuesOfImageProcessor(ImageProcessor, int, int, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Values of image processor.
VCENTER - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.ScrollUtil: The Constant SELECTED.
vectorDoubleToDoubleArray(VectorDouble) - Static method in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface: Vector double to double array.
vectorDoubleToPoint3d(VectorDouble) - Static method in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface: Vector double to point 3 d.
vectorialAddition(double[], double[]) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: Vectorial addition.
vectorialMean(double[], double[]) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: Vectorial mean.
vectorialProduct(double[], double[]) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: Vectorial product.
vectorialSubstraction(double[], double[]) - Static method in interface io.github.rocsg.fijiyama.registration.TransformUtils: Vectorial substraction.
vectorUInt32ToIntArray(VectorUInt32) - Static method in class io.github.rocsg.fijiyama.common.ItkImagePlusInterface: ${e.g(2).rsfu()}.
vectToTheta(float, float) - Static method in class io.github.rocsg.fijiyama.rsml.Node: Convert a vector to an angle.
versionFlag - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The version flag.
versionName - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The version name.
VERSOR - io.github.rocsg.fijiyama.registration.Transform3DType: The versor.
viewAsGrid3D(ImagePlus, int) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: View as grid 3 D.
VIEWER_2D - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The viewer 2d.
VIEWER_3D - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: The viewer 3d.
viewExpert() - Static method in class io.github.rocsg.fijiyama.rsml.Tests: View expert.
viewHeight - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The view height.
viewModel() - Static method in class io.github.rocsg.fijiyama.rsml.Tests: View model.
viewSlice - Variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The view slice.
viewSuperposition(String, String) - Static method in class io.github.rocsg.fijiyama.rsml.Test_RSMLViewer: View superposition.
viewSuperposition(String, String, String) - Static method in class io.github.rocsg.fijiyama.rsml.Test_RSMLViewer: View superposition.
viewThingsFifthReport() - Static method in class io.github.rocsg.fijiyama.rsml.Test_RSMLViewer: View things fifth report.
viewThingsFirstReport() - Static method in class io.github.rocsg.fijiyama.rsml.Test_RSMLViewer: View things first report.
viewThingsFourthReport() - Static method in class io.github.rocsg.fijiyama.rsml.Test_RSMLViewer: View things fourth report.
viewThingsSecondReport() - Static method in class io.github.rocsg.fijiyama.rsml.Test_RSMLViewer: View things second report.
viewThingsThirdReport() - Static method in class io.github.rocsg.fijiyama.rsml.Test_RSMLViewer: View things third report.
viewTimeLapse() - Static method in class io.github.rocsg.fijiyama.rsml.Tests: View time lapse.
viewWidth - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The view width.
VitiDialogs - Interface in io.github.rocsg.fijiyama.common: The Boolean int[] vectorUInt32ToIntArray(VectorUInt32 vect).
VitimageUtils - Class in io.github.rocsg.fijiyama.common: The Class VitimageUtils.
VitimageUtils() - Constructor for class io.github.rocsg.fijiyama.common.VitimageUtils
VolumeComparator() - Constructor for class io.github.rocsg.fijiyama.registration.TransformUtils.VolumeComparator
VOXEL_SCALE_FACTOR - io.github.rocsg.fijiyama.registration.TransformUtils.Misalignment: The voxel scale factor.
vx - Variable in class io.github.rocsg.fijiyama.rsml.Node: The vy.
vy - Variable in class io.github.rocsg.fijiyama.rsml.Node: The vy.

W

waitFor(int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Wait for.
waitForPointsUI(int, ImagePlus, boolean) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Wait for points UI.
waitForPointsUIUntilClickOnSlice1(ImagePlus, ImagePlus, ImagePlus, boolean) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: Wait for points UI until click on slice 1.
waitForReferencePointsUI(int, ImagePlus, boolean) - Static method in interface io.github.rocsg.fijiyama.common.VitiDialogs: UI generic functions to open landmark perspective, with an image (or two) open, and waiting for the points to be selected.
waitOkClicked() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Wait ok clicked.
waitPoints(int) - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Wait points.
wayFromPrim - Variable in class io.github.rocsg.fijiyama.common.Pix: The way from prim.
welcomeAndInformAboutComputerCapabilities() - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: Welcome and inform about computer capabilities.
welcomeAndInformAboutComputerCapabilities() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin: Welcome and inform about computer capabilities.
widthRangeDisplay - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The Constant widthRangeDisplay.
WINDOWIDLE - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The Constant WINDOWIDLE.
WINDOWSERIEPROGRAMMING - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The Constant WINDOWSERIEPROGRAMMING.
WINDOWSERIERUNNING - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The Constant WINDOWSERIERUNNING.
WINDOWTWOIMG - Static variable in class io.github.rocsg.fijiyama.fijiyamaplugin.Fijiyama_GUI: The Constant WINDOWTWOIMG.
withoutExtension(String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Without extension.
writableArray(double[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Writable array.
writableArray(int[]) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Writable array.
write(String) - Static method in class io.github.rocsg.fijiyama.rsml.FSR: Write
writeAsDenseField(String, ImagePlus) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Write as dense field.
writeAsDenseFieldWithITKExporter(String) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Write as dense field with ITK exporter.
writeBlackTextOnGivenImage(String, ImagePlus, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Write black text on given image.
writeBlackTextOnImage(String, ImagePlus, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Write black text on image.
writeDoubleArray1DInFile(double[], String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Write double array 1 D in file.
writeDoubleArray1DInFileSimple(double[], String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Write double array 1 D in file simple.
writeDoubleArrayInFile(double[][], String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Write double array in file.
writeDoubleInFile(String, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Write double in file.
writeDoubleTabInCsv(double[][], String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Write double tab in csv.
writeDoubleTabInCsvSimple(double[][], String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Write double tab in csv simple.
writeInfoFile() - Method in class io.github.rocsg.fijiyama.rsml.RsmlExpert_Plugin
writeIntArray1DInFile(int[], String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Write int array 1 D in file.
writeIntArrayInFile(int[][], String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Write int array in file.
writeIntInFile(String, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Write int in file.
writeMatrixTransformToFile(String) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Write matrix transform to file.
writePoint3dArrayInFile(Point3d[], String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Write point 3 d array in file.
writeRSML(String, String) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Write RSML.
writeRSML3D(String, String, boolean, boolean) - Method in class io.github.rocsg.fijiyama.rsml.RootModel: Write RSML 3 D.
writeStringInFile(String, String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Write string in file.
writeStringInFileUTF8(String, String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Write string in file UTF 8.
writeStringTabInCsv(String[][], String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Write string tab in csv.
writeStringTabInCsv2(String[][], String) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Write string tab in csv 2.
writeStringTabInCsv2(String[][], String) - Static method in class io.github.rocsg.fijiyama.rsml.Tests
writeTextOnGivenImage(String, ImagePlus, int, int, int, int, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Write text on given image.
writeTextOnImage(String, ImagePlus, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Write text on image.
writeTextOnImage(String, ImagePlus, int, int, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Write text on image.
writeTextOnImage(String, ImagePlus, int, int, double, double, double) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Write text on image.
writeToFileWithTypeDetection(String, ImagePlus) - Method in class io.github.rocsg.fijiyama.registration.ItkTransform: Write to file with type detection.
writeToTxtFile(String) - Method in class io.github.rocsg.fijiyama.fijiyamaplugin.RegistrationAction: Write to txt file.
writeWhiteOnImage(String, ImagePlus, int, int) - Static method in class io.github.rocsg.fijiyama.common.VitimageUtils: Write white on image.

X

x - Variable in class io.github.rocsg.fijiyama.common.Pix: The x.
x - Variable in class io.github.rocsg.fijiyama.rsml.Node: The birth time.

Y

y - Variable in class io.github.rocsg.fijiyama.common.Pix: The y.
y - Variable in class io.github.rocsg.fijiyama.rsml.Node: The birth time.

Z

zoomFactor - Variable in class io.github.rocsg.fijiyama.registration.BlockMatchingRegistration: The zoom factor.

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