Index (QuimP 19.08.01 API)

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

A

about() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterController
about() - Method in class com.github.celldynamics.quimp.plugin.ana.ANA_
about() - Method in class com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentation_
about() - Method in class com.github.celldynamics.quimp.plugin.dic.DicLidReconstruction_
about() - Method in class com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping
about() - Method in class com.github.celldynamics.quimp.plugin.generatemask.GenerateMask_
about() - Method in interface com.github.celldynamics.quimp.plugin.IQuimpCorePlugin: Get short info about plugin.
about() - Method in interface com.github.celldynamics.quimp.plugin.IQuimpFilter: Return plugin description.
about() - Method in interface com.github.celldynamics.quimp.plugin.IQuimpPlugin: Return plugin description.
about() - Method in class com.github.celldynamics.quimp.plugin.protanalysis.Prot_Analysis
about() - Method in class com.github.celldynamics.quimp.plugin.qanalysis.Q_Analysis
about() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_: About string.
AboutDialog - Class in com.github.celldynamics.quimp: Build About dialog with support of mouse operations.
AboutDialog(Window, int, int) - Constructor for class com.github.celldynamics.quimp.AboutDialog: Build window and menus with given size.
AboutDialog(Window) - Constructor for class com.github.celldynamics.quimp.AboutDialog: Main constructor.
aboutWnd - Variable in class com.github.celldynamics.quimp.AboutDialog: About window.
AbstractOptionsParser - Class in com.github.celldynamics.quimp.plugin: This is template allows for serialize/deserialize plugin options to/from macro string.
AbstractOptionsParser() - Constructor for class com.github.celldynamics.quimp.plugin.AbstractOptionsParser: This default constructor must be overridden in concrete class.
AbstractOptionsParser(AbstractPluginOptions) - Constructor for class com.github.celldynamics.quimp.plugin.AbstractOptionsParser: Default constructor.
AbstractOptionsParser(String, AbstractPluginOptions) - Constructor for class com.github.celldynamics.quimp.plugin.AbstractOptionsParser: Constructor that allows to provide own parameter string.
AbstractPluginBase - Class in com.github.celldynamics.quimp.plugin: Base template of QuimP (legacy Fiji compatible) plugins.
AbstractPluginBase() - Constructor for class com.github.celldynamics.quimp.plugin.AbstractPluginBase: This default constructor must be overridden in concrete class.
AbstractPluginBase(AbstractPluginOptions, String) - Constructor for class com.github.celldynamics.quimp.plugin.AbstractPluginBase: Default constructor.
AbstractPluginBase(String, AbstractPluginOptions, String) - Constructor for class com.github.celldynamics.quimp.plugin.AbstractPluginBase: Constructor that allows to provide own parameter string.
AbstractPluginOptions - Class in com.github.celldynamics.quimp.plugin: This abstract class serves basic methods for processing parameters strings specified in macros.
AbstractPluginOptions() - Constructor for class com.github.celldynamics.quimp.plugin.AbstractPluginOptions
AbstractPluginQconf - Class in com.github.celldynamics.quimp.plugin: Template of plugin focused at processing QCONF/paQP files.
AbstractPluginQconf() - Constructor for class com.github.celldynamics.quimp.plugin.AbstractPluginQconf: This default constructor must be overridden in concrete class.
AbstractPluginQconf(AbstractPluginOptions, String) - Constructor for class com.github.celldynamics.quimp.plugin.AbstractPluginQconf: Default constructor.
AbstractPluginQconf(String, AbstractPluginOptions, String) - Constructor for class com.github.celldynamics.quimp.plugin.AbstractPluginQconf: Constructor that allows to provide own parameters.
AbstractPluginTemplate - Class in com.github.celldynamics.quimp.plugin: General purpose plugin template for UI plugins.
AbstractPluginTemplate() - Constructor for class com.github.celldynamics.quimp.plugin.AbstractPluginTemplate: This default constructor must be overridden in concrete class.
AbstractPluginTemplate(AbstractPluginOptions, String) - Constructor for class com.github.celldynamics.quimp.plugin.AbstractPluginTemplate: Default constructor.
AbstractPluginTemplate(String, AbstractPluginOptions, String) - Constructor for class com.github.celldynamics.quimp.plugin.AbstractPluginTemplate: Constructor that allows to provide own parameters.
ActionClearOverlay - Class in com.github.celldynamics.quimp.plugin.protanalysis: Action for clear overlay button.
ActionClearOverlay(String, String, ProtAnalysisUi) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ActionClearOverlay: Action creator.
ActionClearPoints - Class in com.github.celldynamics.quimp.plugin.protanalysis: Action for clear button.
ActionClearPoints(ProtAnalysisUi) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ActionClearPoints: Create action not related to UI element.
ActionClearPoints(String, String, ProtAnalysisUi) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ActionClearPoints: Action creator.
ActionClickPredefinedPoint - Class in com.github.celldynamics.quimp.plugin.protanalysis: Set mode for CustomCanvas to get reference point only.
ActionClickPredefinedPoint(String, String, ProtAnalysisUi) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ActionClickPredefinedPoint: Action creator.
ActionFromRoi - Class in com.github.celldynamics.quimp.plugin.protanalysis: Action for ROI to/from transfer.
ActionFromRoi(String, String, ProtAnalysisUi) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ActionFromRoi: Create action.
ActionGetPredefinedPoint - Class in com.github.celldynamics.quimp.plugin.protanalysis: Update reference point from predefined settings.
ActionGetPredefinedPoint(String, String, ProtAnalysisUi) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ActionGetPredefinedPoint: Action creator.
ActionNotSupported - Class in com.github.celldynamics.quimp.plugin.protanalysis: Deprecated.
ActionNotSupported(ProtAnalysisUi) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ActionNotSupported: Deprecated.

Create action not related to UI element.
ActionNotSupported(String, String, ProtAnalysisUi) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ActionNotSupported: Deprecated.

Action creator.
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.AboutDialog: Menu actions support.
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.bar.QuimP_Bar
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ActionClearOverlay
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ActionClearPoints
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ActionClickPredefinedPoint
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ActionFromRoi
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ActionGetPredefinedPoint
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ActionNotSupported: Deprecated.
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ActionPlot2d
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ActionPlotMap
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ActionPolarPlot
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ActionRoiPredefinedPoint
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ActionSaveTracks
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ActionTableFluo
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ActionTableGeom
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ActionToRoi
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ActionTrackPoints
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ActionUpdateOptionsBoolean
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ActionUpdateOptionsEnum
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ActionUpdateOptionsNumber
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ActionUpdateOptionsRadio
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisAbstractAction
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_.BgController
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_.CancelBtnController
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_.CloneController
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_.FgController
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_.LoadQconfController
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_.QconfShowSeedImageController
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_.SeedRoiController
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Create dynamic panel on window depending on state of radio buttons group.
actionPerformed(ActionEvent) - Method in class com.github.celldynamics.quimp.registration.Registration
ActionPlot2d - Class in com.github.celldynamics.quimp.plugin.protanalysis: Plot selected 2d data.
ActionPlot2d(String, String, ProtAnalysisUi) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ActionPlot2d: Action creator.
ActionPlotMap - Class in com.github.celldynamics.quimp.plugin.protanalysis: Plot selected map.
ActionPlotMap(String, String, ProtAnalysisUi, String) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ActionPlotMap: Action for plotting maps.
ActionPolarPlot - Class in com.github.celldynamics.quimp.plugin.protanalysis: Action for generating polar plots for selected point.
ActionPolarPlot(String, String, ProtAnalysisUi) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ActionPolarPlot: Action creator.
ActionRoiPredefinedPoint - Class in com.github.celldynamics.quimp.plugin.protanalysis: Get reference point from current roi.
ActionRoiPredefinedPoint(String, String, ProtAnalysisUi) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ActionRoiPredefinedPoint: Action creator.
ActionSaveTracks - Class in com.github.celldynamics.quimp.plugin.protanalysis: Action (referenced as ActionListener) for saving tracks to csv if "Track" button is hit.
ActionSaveTracks(ProtAnalysisUi) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ActionSaveTracks: Action creator.
ActionTableFluo - Class in com.github.celldynamics.quimp.plugin.protanalysis: Create table with fluorescence features for selected cell and channel.
ActionTableFluo(String, String, ProtAnalysisUi) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ActionTableFluo: Action creator.
ActionTableGeom - Class in com.github.celldynamics.quimp.plugin.protanalysis: Create table with geometric features for selected cell.
ActionTableGeom(String, String, ProtAnalysisUi) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ActionTableGeom: Action creator.
ActionToRoi - Class in com.github.celldynamics.quimp.plugin.protanalysis: Action for ROI to/from transfer.
ActionToRoi(String, String, ProtAnalysisUi) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ActionToRoi: Create action.
ActionTrackPoints - Class in com.github.celldynamics.quimp.plugin.protanalysis: Generalisation of action for tracking points.
ActionTrackPoints(String, String, ProtAnalysisUi) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ActionTrackPoints: Action creator.
ActionTrackPoints(ProtAnalysisUi) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ActionTrackPoints: Initialise this action as ActionListener without properties.
ActionUpdateOptionsBoolean - Class in com.github.celldynamics.quimp.plugin.protanalysis: Create action for updating booleans in options from JCheckboxes.
ActionUpdateOptionsBoolean(String, String, ProtAnalysisUi, MutableBoolean) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ActionUpdateOptionsBoolean: Create action.
ActionUpdateOptionsEnum - Class in com.github.celldynamics.quimp.plugin.protanalysis: Action to set Enum based types.
ActionUpdateOptionsEnum(String, String, ProtAnalysisUi, ProtAnalysisOptions.IEnumDataType) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ActionUpdateOptionsEnum: Main constructor.
ActionUpdateOptionsNumber - Class in com.github.celldynamics.quimp.plugin.protanalysis: Create action for updating numbers in options from JComboBox<>.
ActionUpdateOptionsNumber(String, String, ProtAnalysisUi, MutableInt) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ActionUpdateOptionsNumber: Main constructor.
ActionUpdateOptionsRadio - Class in com.github.celldynamics.quimp.plugin.protanalysis: Update option from Radio Button (grouped).
ActionUpdateOptionsRadio(String, String, ProtAnalysisUi, MutableInt, int) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ActionUpdateOptionsRadio: Action creator.
addBgController(ActionListener) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Assign listener to BG button.
addCancelController(ActionListener) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Assign listener to Cancel button.
addCloneController(ActionListener) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Assign listener to Clone button.
addEntry(String, BOAState) - Method in class com.github.celldynamics.quimp.HistoryLogger: Deprecated.

Add entry to log.
addF_total(ExtendedVector2d) - Method in class com.github.celldynamics.quimp.Node: Update total force for Node.
addFgController(ActionListener) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Assign listener to FG button.
addFluosToResultTable(ResultsTable, int) - Method in class com.github.celldynamics.quimp.CellStats: Add results stored in FrameStatistics object to ResultTable for all frames.
addFluoToResultTable(ResultsTable, int) - Method in class com.github.celldynamics.quimp.FrameStatistics: Add channel statistic to given ResultsTable.
addHandler(Roi, int) - Method in class com.github.celldynamics.quimp.Nest: Add roi to Nest - convert them to Snake and store in SnakeHandler.
addHandlers(ArrayList<ArrayList<SegmentedShapeRoi>>) - Method in class com.github.celldynamics.quimp.Nest: Convert array of SegmentedShapeRoi to SnakeHandlers.
addHandlers(Roi[], int) - Method in class com.github.celldynamics.quimp.Nest: Add rois to Nest - convert them to Snake and store in SnakeHandler.
addHelpController(ActionListener) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Assign listener to Help button.
addImageController(ActionListener) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Assign listener to original image selector.
addLoadQconfController(ActionListener) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Assign listener to Load Qconf button.
addOutlinehandler(OutlineHandler) - Method in class com.github.celldynamics.quimp.Nest: Store OutlineHandler as finalSnake.
addPair(Polygon, Polygon) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.TrackCollection: Add pair of tracks to collection backwardTrack,forwardTrack.
addPair(List<Point>, List<Point>) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.TrackCollection: Add pair of tracks to collection.
addPoint(T) - Method in class com.github.celldynamics.quimp.Shape: Add node before head node assuring that list is a closed loop.
addQconfShowSeedImageController(ActionListener) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Assign listener to Show loaded Qconfbutton.
addRunActiveController(ActionListener) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Assign listener to Run selected slice button.
addRunController(ActionListener) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Assign listener to Run button.
addSeedController(ActionListener) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Assign listener to all seed selectors.
addSeedRoiController(ActionListener) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Assign listener to Seed ROI button.
addStatsToResultTable(ResultsTable) - Method in class com.github.celldynamics.quimp.CellStats: Add statistics for all frames to table.
addStatToResultTable(ResultsTable) - Method in class com.github.celldynamics.quimp.FrameStatistics: Add statistics for this frame to resutl table.
addVec(ExtendedVector2d) - Method in class com.github.celldynamics.quimp.geom.ExtendedVector2d: Add vector to this.
addVel(ExtendedVector2d) - Method in class com.github.celldynamics.quimp.Node: Update velocity for Node.
addWindowController(WindowFocusListener) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Assign listener to whole window.
afterSerialize() - Method in class com.github.celldynamics.quimp.BOAState
afterSerialize() - Method in class com.github.celldynamics.quimp.filesystem.ANAParamCollection
afterSerialize() - Method in class com.github.celldynamics.quimp.filesystem.DataContainer: Called after serialization.
afterSerialize() - Method in interface com.github.celldynamics.quimp.filesystem.IQuimpSerialize: This method is called after restoring object from JSON but before returning the object.
afterSerialize() - Method in class com.github.celldynamics.quimp.filesystem.OutlinesCollection: Rebuild every Outline from temporary array.
afterSerialize() - Method in class com.github.celldynamics.quimp.filesystem.StatsCollection
afterSerialize() - Method in class com.github.celldynamics.quimp.Nest
afterSerialize() - Method in class com.github.celldynamics.quimp.Outline
afterSerialize() - Method in class com.github.celldynamics.quimp.OutlineHandler: Call afterSerialzie() for other objects and restore transient fields where possible.
afterSerialize() - Method in class com.github.celldynamics.quimp.plugin.AbstractPluginOptions
afterSerialize() - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions
afterSerialize() - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ProtStat
afterSerialize() - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap
afterSerialize() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel
afterSerialize() - Method in class com.github.celldynamics.quimp.Shape
afterSerialize() - Method in class com.github.celldynamics.quimp.Snake: Call super and then oo Snake related actions
afterSerialize() - Method in class com.github.celldynamics.quimp.SnakeHandler: Prepare all Snake stored in this SnakeHandler for loading.
afterSerialize() - Method in class com.github.celldynamics.quimp.SnakePluginList
alev - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: alev parameter.
algOptions - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Parameters of Random Walk algorithm itself.
alive - Variable in class com.github.celldynamics.quimp.Snake: true if snake is alive Changed during segmentation and user interaction.
ALL - Static variable in class com.github.celldynamics.quimp.geom.filters.HatSnakeFilter: Algorithm will look for cavities and protrusions.
allDead() - Method in class com.github.celldynamics.quimp.Nest: Check if there is live Snake in Nest.
ALLFLU - Static variable in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Combine all FLU maps.
allFrozen() - Method in class com.github.celldynamics.quimp.Nest: Return true is all snake handlers are froze by user.
ALLMAPS - Static variable in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Combine all maps.
alpha - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkOptions: Alpha penalises pixels whose intensities are far away from the mean seed intensity.
amplificationFactor(double, double, double) - Method in class com.github.celldynamics.quimp.geom.filters.OutlineProcessor: Return amplification factor dependent on curvature.
ANA - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The ana.
ANA_ - Class in com.github.celldynamics.quimp.plugin.ana: Main ANA class implementing IJ PlugInFilter.
ANA_() - Constructor for class com.github.celldynamics.quimp.plugin.ana.ANA_: Default constructor called always.
ANA_RUN - Static variable in class com.github.celldynamics.quimp.filesystem.DataContainer: Indicate that ANA module is not null (it has been run already on those data).
ANA_Runner - Class in <Unnamed>: Compatibility layer for ImageJ.
ANA_Runner() - Constructor for class ANA_Runner
analyse(ImagePlus, boolean) - Method in class com.github.celldynamics.quimp.Nest: Write stQP file using current Snakes
anaMigDist - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The ana mig dist.
AnaOptions - Class in com.github.celldynamics.quimp.plugin.ana: Hold ANA options.
AnaOptions() - Constructor for class com.github.celldynamics.quimp.plugin.ana.AnaOptions: Default constructor.
ANAp - Class in com.github.celldynamics.quimp.plugin.ana: Container class for parameters concerned with ANA analysis.
ANAp() - Constructor for class com.github.celldynamics.quimp.plugin.ana.ANAp: Default constructor.
ANAp(ANAp) - Constructor for class com.github.celldynamics.quimp.plugin.ana.ANAp: Copy constructor.
ANAParamCollection - Class in com.github.celldynamics.quimp.filesystem: Serialization container for ANAp.
ANAParamCollection() - Constructor for class com.github.celldynamics.quimp.filesystem.ANAParamCollection: Default constructor.
ANAParamCollection(int) - Constructor for class com.github.celldynamics.quimp.filesystem.ANAParamCollection: Create size elements in store for ANAp configurations.
ANAState - Variable in class com.github.celldynamics.quimp.filesystem.DataContainer: Hold ANA state.
angle(ExtendedVector2d, ExtendedVector2d) - Static method in class com.github.celldynamics.quimp.geom.ExtendedVector2d: Calculate angle between 2 vectors.
angleLabel - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.QPolarAxes: Show angle labels.
angleNonRelative(ExtendedVector2d, ExtendedVector2d) - Static method in class com.github.celldynamics.quimp.geom.ExtendedVector2d: Calculate non relative angle between 2 vectors.
angleTh - Variable in class com.github.celldynamics.quimp.plugin.ana.ANAp: Angle threshold.
apiCall - Variable in class com.github.celldynamics.quimp.plugin.AbstractOptionsParser: If true plugin is run from parametrised constructor what usually means API.
appendDelim() - Method in class com.github.celldynamics.quimp.utils.CsvWritter: Add current delimiter to line.
appendDistance() - Method in class com.github.celldynamics.quimp.AboutDialog: Add line of length of window.
appendLine(String) - Method in class com.github.celldynamics.quimp.AboutDialog: Add line of text to window TextArea.
appendLine(String) - Method in class com.github.celldynamics.quimp.utils.CsvWritter: Write line to file.
appendLine(Double...) - Method in class com.github.celldynamics.quimp.utils.CsvWritter: Write series of Doubles using defined precision and default delimiter.
applyB - Variable in class com.github.celldynamics.quimp.plugin.utils.QWindowBuilder: The apply B.
area - Variable in class com.github.celldynamics.quimp.FrameStatistics: Area of outline.
areAllPointOutside(List<? extends Tuple2d>, List<? extends Tuple2d>) - Method in class com.github.celldynamics.quimp.geom.BasicPolygons: Test if all points from Ptest are outside of P.
areAllPointsInside(List<? extends Tuple2d>, List<? extends Tuple2d>) - Method in class com.github.celldynamics.quimp.geom.BasicPolygons: Test if all points Ptest are inside polygon P.
areaToScale(double, double) - Static method in class com.github.celldynamics.quimp.utils.QuimpToolsCollection: Area to scale.
areMultipleFiles - Variable in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterModel: Save one file with all snakes or many files with one snake.
array2dMax(double[][]) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Array max.
array2dMin(double[][]) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Array min.
arrayMax(int[]) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Array max.
arrayMax(double[]) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Array max.
arrayMin(double[]) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Array min.
arrayToFile(double[][], String, File) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Array to file.
aS - Variable in class com.github.celldynamics.quimp.filesystem.ANAParamCollection: Array of configuration options for every cell present in the image.
asFloatRoi() - Method in class com.github.celldynamics.quimp.Shape: Return current Shape as ImageJ float number polygon.
asIntRoi() - Method in class com.github.celldynamics.quimp.Shape: Return current Shape as ImageJ ROI object.
asList() - Method in class com.github.celldynamics.quimp.Shape: Returns current Shape as list of points (copy).
asPolygon() - Method in class com.github.celldynamics.quimp.Shape: Return current Shape as Java polygon.
attachContext(ViewUpdater) - Method in class com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentation_
attachContext(ViewUpdater) - Method in interface com.github.celldynamics.quimp.plugin.IQuimpPluginSynchro: Pass to plugin ViewUpdater object which is accessor to selected methods from QuimP interface.
attachData(List<Point2d>) - Method in interface com.github.celldynamics.quimp.plugin.snakes.IQuimpBOAPoint2dFilter: Attach processed data to plugin.
attachData(Snake) - Method in interface com.github.celldynamics.quimp.plugin.snakes.IQuimpBOASnakeFilter: Attach processed data to plugin.
attachFile(File) - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverter: Attach file for conversion.
attachImage(ImageProcessor) - Method in class com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentation_
attachImage(ImageProcessor) - Method in interface com.github.celldynamics.quimp.plugin.IQuimpPluginAttachImage: Attach image to filter.
attachImagePlus(ImagePlus) - Method in class com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentation_
attachImagePlus(ImagePlus) - Method in interface com.github.celldynamics.quimp.plugin.IQuimpPluginAttachImagePlus: Attach image plus to filter.
attachNest(Nest) - Method in class com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentation_
attachNest(Nest) - Method in interface com.github.celldynamics.quimp.plugin.IQuimpPluginAttachNest: Attach processed data to plugin.
averageCurvature(double) - Method in class com.github.celldynamics.quimp.geom.filters.OutlineProcessor: Compute average curvature of Outline.
averageCurvDist - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds.Contour: Distance to average curvature over.
averageNormalsDist - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds.Contour: Distance to set normals equal.
avgCov - Variable in class com.github.celldynamics.quimp.plugin.qanalysis.Qp: The avg cov.

B

background - Variable in class com.github.celldynamics.quimp.geom.TrackOutline: The background color.
backupLiveSnake(int) - Method in class com.github.celldynamics.quimp.SnakeHandler: Stores liveSnake (currently processed) in segSnakes array.
backupThisSnake(Snake, int) - Method in class com.github.celldynamics.quimp.SnakeHandler: Makes copy of snake and store it as segmented snake.
BAD_HEAD - Static variable in class com.github.celldynamics.quimp.Shape: List contains node marked as head but without proper flag or null.
BAD_INDEX - Static variable in class com.github.celldynamics.quimp.geom.MapTracker: Denote bad index.
BAD_LINKING - Static variable in class com.github.celldynamics.quimp.Shape: List is not closed.
BAD_NUM_POINTS - Static variable in class com.github.celldynamics.quimp.Shape: Number of list elements does match to the number stored in Shape.POINTS.
BasicPolygons - Class in com.github.celldynamics.quimp.geom: Calculates basic geometry on polygons defined as list of point in specified direction.
BasicPolygons() - Constructor for class com.github.celldynamics.quimp.geom.BasicPolygons: Default constructor.
beforeSerialize() - Method in class com.github.celldynamics.quimp.BOAState: Should be called before serialization.
beforeSerialize() - Method in class com.github.celldynamics.quimp.filesystem.ANAParamCollection
beforeSerialize() - Method in class com.github.celldynamics.quimp.filesystem.DataContainer: Called before serialization.
beforeSerialize() - Method in interface com.github.celldynamics.quimp.filesystem.IQuimpSerialize: This method is called just before JSON is generated.
beforeSerialize() - Method in class com.github.celldynamics.quimp.filesystem.OutlinesCollection: Prepare Outlines for serialization.
beforeSerialize() - Method in class com.github.celldynamics.quimp.filesystem.StatsCollection
beforeSerialize() - Method in class com.github.celldynamics.quimp.Nest
beforeSerialize() - Method in class com.github.celldynamics.quimp.Outline
beforeSerialize() - Method in class com.github.celldynamics.quimp.OutlineHandler: Prepare all Outline stored in this OutlineHandler for loading.
beforeSerialize() - Method in class com.github.celldynamics.quimp.plugin.AbstractPluginOptions
beforeSerialize() - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions
beforeSerialize() - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ProtStat
beforeSerialize() - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap
beforeSerialize() - Method in class com.github.celldynamics.quimp.Shape
beforeSerialize() - Method in class com.github.celldynamics.quimp.Snake: Call super and then oo Snake related actions
beforeSerialize() - Method in class com.github.celldynamics.quimp.SnakeHandler: Prepare all Snake stored in this SnakeHandler for saving.
beforeSerialize() - Method in class com.github.celldynamics.quimp.SnakePluginList: Fills fields in Plugin class related to configuration and version.
beta - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkOptions: Beta penalises pixels located at an edge, i.e.
BgController() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_.BgController
bgName - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.SeedPicker: Prefix for background ROI.
binary - Variable in class com.github.celldynamics.quimp.plugin.generatemask.GenerateMaskOptions: If true generate binary image, grayscales otherwise (each separated object at different shade starting from 1).
BinaryFilters - Class in com.github.celldynamics.quimp.plugin.randomwalk: Provide sets of binary filters.
BinaryFilters() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.BinaryFilters
BinaryFilters.EmptyMorpho - Class in com.github.celldynamics.quimp.plugin.randomwalk: Dummy filter that does nothing.
BinaryFilters.Filters - Enum in com.github.celldynamics.quimp.plugin.randomwalk: Filters available in this class.
BinaryFilters.MedianMorpho - Class in com.github.celldynamics.quimp.plugin.randomwalk: Perform median filtering with radius 2 on image.
BinaryFilters.MorphoOperations - Enum in com.github.celldynamics.quimp.plugin.randomwalk: Available binary operations.
BinaryFilters.SimpleMorpho - Class in com.github.celldynamics.quimp.plugin.randomwalk: Filter image using 1 iteration opening.
BinarySegmentation - Class in com.github.celldynamics.quimp.plugin.binaryseg: Run Binary segmentation converting grayscale masks to ordered ROIs.
BinarySegmentation(ImagePlus) - Constructor for class com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentation: Constructor for segmentation of stack.
BinarySegmentation_ - Class in com.github.celldynamics.quimp.plugin.binaryseg: Binary segmentation plugin called from Fiji.
BinarySegmentation_() - Constructor for class com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentation_: Default constructor.
BinarySegmentation_(AbstractPluginOptions) - Constructor for class com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentation_: Constructor for API calls.
BinarySegmentation_Runner - Class in <Unnamed>: Compatibility layer for ImageJ.
BinarySegmentation_Runner() - Constructor for class BinarySegmentation_Runner
BinarySegmentationOptions - Class in com.github.celldynamics.quimp.plugin.binaryseg: Hold options for Binary Segmentation.
BinarySegmentationOptions() - Constructor for class com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentationOptions
binarySegmentationPlugin - Variable in class com.github.celldynamics.quimp.BOAState: Instance of binary segmentation plugin that converts BW masks into snakes.
BinarySegmentationView - Class in com.github.celldynamics.quimp.plugin.binaryseg: Show UI for segmentation from masks and run it.
BinarySegmentationView() - Constructor for class com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentationView: Construct object.
blowup() - Method in class com.github.celldynamics.quimp.Snake: Deprecated.
blue - Variable in class com.github.celldynamics.quimp.QColor: Color component.
bnGradientPickActive - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Indicate that pick point mode is on.
BOA_ - Class in com.github.celldynamics.quimp: Main class implementing BOA plugin.
BOA_() - Constructor for class com.github.celldynamics.quimp.BOA_: Main constructor.
BOA_RUN - Static variable in class com.github.celldynamics.quimp.filesystem.DataContainer: Indicate that BOAState module is not null.
BOA_Runner - Class in <Unnamed>: Compatibility layer for ImageJ.
BOA_Runner() - Constructor for class BOA_Runner
BoaException - Exception in com.github.celldynamics.quimp: Exception thrown by BOA class.
BoaException(String, int, int) - Constructor for exception com.github.celldynamics.quimp.BoaException: Create exception object for given frame and type.
BoaException(String) - Constructor for exception com.github.celldynamics.quimp.BoaException: Create exception object.
BoaException() - Constructor for exception com.github.celldynamics.quimp.BoaException: BoaException.
BoaException(String, Throwable, boolean, boolean) - Constructor for exception com.github.celldynamics.quimp.BoaException: BoaException.
BoaException(String, Throwable) - Constructor for exception com.github.celldynamics.quimp.BoaException: BoaException.
BoaException(Throwable) - Constructor for exception com.github.celldynamics.quimp.BoaException: BoaException.
boap - Variable in class com.github.celldynamics.quimp.BOAState: Reference to old BOAp class, keeps internal state of BOA.
BOAp() - Constructor for class com.github.celldynamics.quimp.BOAState.BOAp: Default constructor.
BOAState - Class in com.github.celldynamics.quimp: Hold current BOA state that can be serialized.
BOAState() - Constructor for class com.github.celldynamics.quimp.BOAState: Default constructor.
BOAState(ImagePlus) - Constructor for class com.github.celldynamics.quimp.BOAState: Construct BOAState object for given stack size.
BOAState(ImagePlus, PluginFactory, ViewUpdater) - Constructor for class com.github.celldynamics.quimp.BOAState: Construct full base object filling snapshots with default but valid objects.
BOAState - Variable in class com.github.celldynamics.quimp.filesystem.DataContainer: Object to store all BOA state.
BOAState.BOAp - Class in com.github.celldynamics.quimp: Holds parameters defining snake and controlling contour matching algorithm.
BOTTOM - Static variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentation: Direction of circshift coded as in Matlab.
build(String, boolean) - Method in class com.github.celldynamics.quimp.registration.Registration: Construct and display window.
buildWindow(ParamList) - Method in class com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentationView
buildWindow(ParamList) - Method in class com.github.celldynamics.quimp.plugin.utils.QWindowBuilder: Main window builder.
bwScale(double, int, double, double) - Static method in class com.github.celldynamics.quimp.QColor: Bw scale.

C

calcArea() - Method in class com.github.celldynamics.quimp.Outline: calcArea.
calcCentroid() - Method in class com.github.celldynamics.quimp.Shape: Calculate centroid of Shape.
calculateRank(List<Point2d>, ImageProcessor) - Method in class com.github.celldynamics.quimp.geom.filters.HatSnakeFilter: Evaluate rank for given outline.
calcVolume() - Method in class com.github.celldynamics.quimp.Outline: calcVolume.
cancelB - Variable in class com.github.celldynamics.quimp.plugin.utils.QWindowBuilder: The cancel B.
CancelBtnController() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_.CancelBtnController
castToNumber(ImageProcessor) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Convert ImageProcessor pixel data to array of objects.
CAVITIES - Static variable in class com.github.celldynamics.quimp.geom.filters.HatSnakeFilter: Algorithm will look for cavities.
cellStatistics - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtStat: Hold cell shape based statistics.
CellStats - Class in com.github.celldynamics.quimp: Keep statistics (outline and fluoro) for one cell along frames.
CellStats() - Constructor for class com.github.celldynamics.quimp.CellStats: Initialises empty container.
CellStats(ArrayList<FrameStatistics>) - Constructor for class com.github.celldynamics.quimp.CellStats: Initialises container.
CellStatsEval - Class in com.github.celldynamics.quimp: Calculate statistics for whole stack (all cells).
CellStatsEval(OutlineHandler, ImagePlus, File, double, double) - Constructor for class com.github.celldynamics.quimp.CellStatsEval: Create and run the object.
CellStatsEval(OutlineHandler, ImagePlus, double, double) - Constructor for class com.github.celldynamics.quimp.CellStatsEval: Only create the object.
cellStatSuffix - Static variable in class com.github.celldynamics.quimp.filesystem.FileExtensions: Suffix for cell stats given by ProtAnalyis.
centroid - Variable in class com.github.celldynamics.quimp.FrameStatistics: Centroid of outline.
centroid - Variable in class com.github.celldynamics.quimp.Shape: Centroid point of the Shape.
CH1 - Static variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Channel for tables.
CH2 - Static variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Channel for tables.
CH3 - Static variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Channel for tables.
CHANGE_SIZE - Static variable in interface com.github.celldynamics.quimp.plugin.IQuimpCorePlugin: Plugin change size of input data.
channel - Variable in class com.github.celldynamics.quimp.plugin.ana.AnaOptions: The channel.
channel - Variable in class com.github.celldynamics.quimp.plugin.qanalysis.Qp: The channel.
channels - Variable in class com.github.celldynamics.quimp.FrameStatistics: Fluorescence stats added by ANA module.
ChannelStat - Class in com.github.celldynamics.quimp.plugin.ana: Hold statistic of fluorescence for one channel.
ChannelStat() - Constructor for class com.github.celldynamics.quimp.plugin.ana.ChannelStat: Default constructor.
charge - Variable in class com.github.celldynamics.quimp.Vert: Charge on the vertex.
chargeDensity - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: field complexity (set to -1 to leave as marker density).
chbAreaPlot - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Plot map.
chbCircPlot - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Plot map.
chbCortexAreaPlot - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Plot 2D.
chbCortexWidthPlot - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Plot 2D.
chbCytoAreaPlot - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Plot 2D.
chbDisplPlot - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Plot map.
chbDistPlot - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Plot map.
chbElongPlot - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Plot map.
chbFlattenStaticTrackImage - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Whether to flatten static track.
chbManCtfPlot - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Plot 2D.
chbMeanCtfPlot - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Plot 2D.
chbMeanCytoPlot - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Plot 2D.
chbMeanFluPlot - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Plot 2D.
chbNewImage - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Whether to show tracks in new plot or in embedded in GUI.
chbPerimPlot - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Plot map.
chbPersistencePlot - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Plot map.
chbShowPoint - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Show tracked point on dynamic track.
chbShowTrack - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Show track on dynamic track.
chbShowTrackMotility - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Show tracks on motility map.
chbSmoothTracks - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Apply track smoothing.
chbSpeedPlot - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Plot map.
chbTotalCtf2Plot - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Plot 2D.
chbTotalCytoPlot - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Plot 2D.
chbTotFluPlot - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Plot 2D.
chbXcentrPlot - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Plot map.
chbYcentrPlot - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Plot map.
checkCoordErrors() - Method in class com.github.celldynamics.quimp.Outline: checkCoordErrors.
checkIsHead() - Method in class com.github.celldynamics.quimp.Shape: Check if there is a head node.
circleRadius - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Radius of circles plotted by tool.
circleRadius - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.TrackVisualisation: Radius of circles plotted.
circularity - Variable in class com.github.celldynamics.quimp.FrameStatistics: Circularity of outline.
CIRCULARPAD - Static variable in interface com.github.celldynamics.quimp.plugin.utils.IPadArray: defines circular padding.
className - Variable in class com.github.celldynamics.quimp.Serializer: Name of wrapped class, decoded from object.
cleanNest() - Method in class com.github.celldynamics.quimp.Nest: Remove all handlers from Nest.
clear() - Method in class com.github.celldynamics.quimp.plugin.protanalysis.TrackVisualisation: Clear overlay.
clear() - Method in class com.github.celldynamics.quimp.SnakePluginList: Deletes all plugins from list and closes theirs windows.
clearElements() - Method in class com.github.celldynamics.quimp.Shape: Clear Elements array that stores list of {Node, Snake} in ArrayList form.
clearFlu - Variable in class com.github.celldynamics.quimp.plugin.ana.AnaOptions: Whether to clear Fluo stats before.
clearFluo() - Method in class com.github.celldynamics.quimp.FrameStatistics: Clear channel statistics.
clearFluores() - Method in class com.github.celldynamics.quimp.Outline: clearFluores.
clone() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterModel
clone() - Method in class com.github.celldynamics.quimp.Outline: Deprecated.
Change to copy constructor
clone() - Method in class com.github.celldynamics.quimp.plugin.ana.AnaOptions
clone() - Method in class com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentationOptions
clone() - Method in class com.github.celldynamics.quimp.plugin.ecmm.EcmmOptions
clone() - Method in class com.github.celldynamics.quimp.plugin.generatemask.GenerateMaskOptions
clone() - Method in class com.github.celldynamics.quimp.plugin.qanalysis.Qp
CloneController() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_.CloneController
close() - Method in class com.github.celldynamics.quimp.omero.OmeroBrowser
close() - Method in class com.github.celldynamics.quimp.utils.CsvWritter: Close stream.
closeAllImages() - Static method in class com.github.celldynamics.quimp.utils.IJTools: Close all images without saving.
closeAllWindows() - Method in class com.github.celldynamics.quimp.SnakePluginList: Close all opened plugins windows.
closeHistory() - Method in class com.github.celldynamics.quimp.HistoryLogger: Deprecated.

Close window and call windowClosing() and windowClosed() methods.
closestFloor(Outline, double) - Static method in class com.github.celldynamics.quimp.utils.QuimpToolsCollection: Closest floor.
color - Static variable in class com.github.celldynamics.quimp.plugin.protanalysis.TrackVisualisation: Definition of colors used to plot tracks.
color - Variable in class com.github.celldynamics.quimp.Vert: Color of Vert.
colorInt23f(int) - Static method in class com.github.celldynamics.quimp.QColor: Color int 23 f.
colors - Variable in class com.github.celldynamics.quimp.geom.TrackOutline: List of colors of objects that were used to produce SegmentedShapeRoi.
colorScaling - Static variable in class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds: Scale color values in composite preview.
colour - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qcircle: The colour.
colour - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qline: The colour.
colour - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.QPolarAxes: The colour.
colour - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.QScaleBar: Text colour.
colour - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qtext: The colour.
colourMap(String, int) - Static method in class com.github.celldynamics.quimp.QColor: Create a color map.
colourMaps - Static variable in class com.github.celldynamics.quimp.QColor: The colour maps.
com.github.celldynamics.quimp - package com.github.celldynamics.quimp: This is the main package.
com.github.celldynamics.quimp.filesystem - package com.github.celldynamics.quimp.filesystem
com.github.celldynamics.quimp.filesystem.converter - package com.github.celldynamics.quimp.filesystem.converter: Contain tools for conversion between old and new files.
com.github.celldynamics.quimp.filesystem.versions - package com.github.celldynamics.quimp.filesystem.versions: Contain converters of QCONF files from older to current format.
com.github.celldynamics.quimp.geom - package com.github.celldynamics.quimp.geom
com.github.celldynamics.quimp.geom.filters - package com.github.celldynamics.quimp.geom.filters: This package contains methods for processing vector contours.
com.github.celldynamics.quimp.omero - package com.github.celldynamics.quimp.omero: Omero reader/writer.
com.github.celldynamics.quimp.plugin - package com.github.celldynamics.quimp.plugin: This package contains interfaces that define QuimP plugins.
com.github.celldynamics.quimp.plugin.ana - package com.github.celldynamics.quimp.plugin.ana: About
com.github.celldynamics.quimp.plugin.bar - package com.github.celldynamics.quimp.plugin.bar
com.github.celldynamics.quimp.plugin.binaryseg - package com.github.celldynamics.quimp.plugin.binaryseg: Binary segmentation plugin.
com.github.celldynamics.quimp.plugin.dic - package com.github.celldynamics.quimp.plugin.dic
com.github.celldynamics.quimp.plugin.ecmm - package com.github.celldynamics.quimp.plugin.ecmm: About
com.github.celldynamics.quimp.plugin.engine - package com.github.celldynamics.quimp.plugin.engine: This package contains engine for loading BOA plugins.
com.github.celldynamics.quimp.plugin.generatemask - package com.github.celldynamics.quimp.plugin.generatemask: Convert snakes to binary masks.
com.github.celldynamics.quimp.plugin.protanalysis - package com.github.celldynamics.quimp.plugin.protanalysis: Demo of node tracking.
com.github.celldynamics.quimp.plugin.qanalysis - package com.github.celldynamics.quimp.plugin.qanalysis: About
com.github.celldynamics.quimp.plugin.randomwalk - package com.github.celldynamics.quimp.plugin.randomwalk: Random Walk solver and QuimP plugin.
com.github.celldynamics.quimp.plugin.snakes - package com.github.celldynamics.quimp.plugin.snakes
com.github.celldynamics.quimp.plugin.utils - package com.github.celldynamics.quimp.plugin.utils
com.github.celldynamics.quimp.registration - package com.github.celldynamics.quimp.registration
com.github.celldynamics.quimp.utils - package com.github.celldynamics.quimp.utils
com.github.celldynamics.quimp.utils.graphics - package com.github.celldynamics.quimp.utils.graphics
com.github.celldynamics.quimp.utils.graphics.svg - package com.github.celldynamics.quimp.utils.graphics.svg
com.github.celldynamics.quimp.utils.graphics.vrml - package com.github.celldynamics.quimp.utils.graphics.vrml
com.github.celldynamics.quimp.utils.test - package com.github.celldynamics.quimp.utils.test: Collection of tools used in tests.
ComponentList() - Constructor for class com.github.celldynamics.quimp.plugin.utils.QWindowBuilder.ComponentList
computeMaximaIJ(double) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.MaximaFinder: Compute maxima using ImageJ procedure.
computeMaximaImage(ImageProcessor) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.MaximaFinder: Compute maxima from image where points different from background stand for location of maxima in ip.
configFileExt - Static variable in class com.github.celldynamics.quimp.filesystem.FileExtensions: Extension for old file format.
connect() - Method in class com.github.celldynamics.quimp.omero.OmeroBrowser: Connect to Omero.
connectSnakeObject(Snake) - Method in class com.github.celldynamics.quimp.ViewUpdater: Connect current snake (on current frame) to this object.
constrict(Snake, ImageProcessor) - Method in class com.github.celldynamics.quimp.Constrictor: Compute force power and moves nodes by predefined step.
Constrictor - Class in com.github.celldynamics.quimp: Calculate forces that affect the snake.
Constrictor() - Constructor for class com.github.celldynamics.quimp.Constrictor: Default constructor.
constrictWrite(Snake, ImageProcessor) - Method in class com.github.celldynamics.quimp.Constrictor: Deprecated.
Strictly related to absolute paths on disk. Probably for testing only.
containsKey(String) - Method in class com.github.celldynamics.quimp.plugin.utils.LinkedStringMap: containsKey.
Contour() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds.Contour: Default constructor without storing seed history.
Contour(boolean, AutoThresholder.Method) - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds.Contour: Allow to store seed history that can be later presented in form of composite image.
Contour(boolean, AutoThresholder.Method, double, double, double, double) - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds.Contour: Allow additionally to set power of shrinking curved parts of the outline and window for equalising normals.
Converter170202<T extends IQuimpSerialize> - Class in com.github.celldynamics.quimp.filesystem.versions: Converts QCONF files saved in versions lower than 17.02.02.
Converter170202(QuimpVersion) - Constructor for class com.github.celldynamics.quimp.filesystem.versions.Converter170202
convertTo3dMatrix(Object) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.ProbabilityMaps: Convert list of maps under specified key to 3d array of doubles.
convertToImageStack(Object) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.ProbabilityMaps: Convert probability maps to ImageStack.
convertToList(RandomWalkSegmentation.SeedTypes) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.Seeds: Convert binary maps representing foregrounds and background seeds to lists of coordinates (format accepted by RandomWalkSegmentation.solver(Seeds, RealMatrix[])).
convertToStack(RandomWalkSegmentation.SeedTypes) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.Seeds: Convert seeds to ImageStack.
CONVEXITY - Static variable in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Convexity map code.
convimageFileExt - Static variable in class com.github.celldynamics.quimp.filesystem.FileExtensions: Extension for file containing convexity image map.
convmapFileExt - Static variable in class com.github.celldynamics.quimp.filesystem.FileExtensions: Extension for file containing convexity map.
COORD - Static variable in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Coordinates map code.
coord - Variable in class com.github.celldynamics.quimp.Vert: coord relative to head node on current frame.
coordmapFileExt - Static variable in class com.github.celldynamics.quimp.filesystem.FileExtensions: Extension for file containing coordinates map.
coordReset() - Method in class com.github.celldynamics.quimp.Outline: Set head node coord to zero.
copy2darray(double[][], double[][]) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Make deep copy of 2D array.
copyFromCellStat(List<CellStatsEval>) - Method in class com.github.celldynamics.quimp.filesystem.StatsCollection: Bridge method to maintain compatibility with old code.
copyFromFinalToLive(int) - Method in class com.github.celldynamics.quimp.SnakeHandler: Copy final snake from frame to liveSnake.
copyFromFinalToSeg() - Method in class com.github.celldynamics.quimp.SnakeHandler: Copy all finalSnakes to segSnakes.
copyFromSegToFinal() - Method in class com.github.celldynamics.quimp.SnakeHandler: Copy all segSnakes to finalSnakes.
copyPluginListFromSnapshot(int) - Method in class com.github.celldynamics.quimp.BOAState: Copy SnakePluginList data from given snapshot to current frame.
copySegParamFromSnapshot(int) - Method in class com.github.celldynamics.quimp.BOAState: Copy SegParam data from given snapshot to current frame.
correctDensity(double, double) - Method in class com.github.celldynamics.quimp.Outline: Insert or remove nodes according to criteria.
correctDistance(boolean) - Method in class com.github.celldynamics.quimp.Snake: Ensure nodes are between maxDist and minDist apart, add remove nodes as required.
cortexArea - Variable in class com.github.celldynamics.quimp.plugin.ana.ChannelStat: Scaled outer area - scaled inner area.
cortexWidth - Variable in class com.github.celldynamics.quimp.plugin.ana.ChannelStat: Scaled width of the cortex.
cortexWidth - Variable in class com.github.celldynamics.quimp.QParams: The cortex width.
countPoints() - Method in class com.github.celldynamics.quimp.Shape: Count number of Points in Shape.
createdOn - Variable in class com.github.celldynamics.quimp.Serializer: Date when file has been created.
createInstance(Type) - Method in class com.github.celldynamics.quimp.filesystem.DataContainerInstanceCreator
createJCheckBox(String, FormatConverterModel) - Static method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi: Build checkbox with link to model.
crop(ImageProcessor, int, int, int, int) - Method in class com.github.celldynamics.quimp.plugin.utils.ImageProcessorPlus: Crop image.
cropImageAfterRotation(ImageProcessor, int, int) - Method in class com.github.celldynamics.quimp.plugin.utils.ImageProcessorPlus: Crop image.
CsvWritter - Class in com.github.celldynamics.quimp.utils: Write csv filed line by line.
CsvWritter() - Constructor for class com.github.celldynamics.quimp.utils.CsvWritter: Create empty file with random name in temporary folder.
CsvWritter(Path, String...) - Constructor for class com.github.celldynamics.quimp.utils.CsvWritter: Create file and fill first line with header.
curvatureLocal - Variable in class com.github.celldynamics.quimp.Vert: curvature local to a node.
curvatureSmoothed - Variable in class com.github.celldynamics.quimp.Vert: Smoothed curvature.
curvatureSum - Variable in class com.github.celldynamics.quimp.Vert: summed curvature over x microns this is the value recorded into maps.
curvLimits - Variable in class com.github.celldynamics.quimp.OutlineHandler: The curv limits.
cutIntersects() - Method in class com.github.celldynamics.quimp.Snake: Cut out intersects.
cutLoops() - Method in class com.github.celldynamics.quimp.Snake: Cut out a loop Insert a new node at cut point.
cutSelfIntersects() - Method in class com.github.celldynamics.quimp.Outline: Done once at the end of each frame to cut out any parts of the contour that self intersect.

D

d - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: threshold distance to stop.
darkBackground - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds: Default setting.
DataContainer - Class in com.github.celldynamics.quimp.filesystem: Integrate outputs from every module of QuimP.
DataContainer() - Constructor for class com.github.celldynamics.quimp.filesystem.DataContainer: Default constructor.
DataContainer(PluginFactory, ViewUpdater) - Constructor for class com.github.celldynamics.quimp.filesystem.DataContainer: Create DataContainer with attached PluginFactory and ViewUpdater.
DataContainerInstanceCreator - Class in com.github.celldynamics.quimp.filesystem: Object builder for GSon and DataContainer class.
DataContainerInstanceCreator(PluginFactory, ViewUpdater) - Constructor for class com.github.celldynamics.quimp.filesystem.DataContainerInstanceCreator: Assign additional fields to DataContainer after serialization.
dateAsString() - Static method in class com.github.celldynamics.quimp.utils.QuimpToolsCollection: Date as string.
decide(ILoggingEvent) - Method in class com.github.celldynamics.quimp.LogbackFilter
decodeSeedsfromGrayscaleImage(ImageProcessor) - Static method in class com.github.celldynamics.quimp.plugin.randomwalk.SeedProcessor: Convert grayscale image to Seeds.
decodeSeedsfromRgb(ImageProcessor, List<Color>, Color) - Static method in class com.github.celldynamics.quimp.plugin.randomwalk.SeedProcessor: Decode RGB seed images to separate binary images.
decodeSeedsfromRgb(ImagePlus, List<Color>, Color) - Static method in class com.github.celldynamics.quimp.plugin.randomwalk.SeedProcessor: Decode RGB seed images to separate binary images.
decodeSeedsfromRoi(List<Roi>, String, String, int, int) - Static method in class com.github.celldynamics.quimp.plugin.randomwalk.SeedProcessor: Decode seeds from list of ROIs objects.
decodeSeedsfromRoiStack(List<Roi>, String, String, int, int, int) - Static method in class com.github.celldynamics.quimp.plugin.randomwalk.SeedProcessor: Convert list of ROIs to binary images separately for each ROI.
decPlaces - Variable in class com.github.celldynamics.quimp.utils.CsvWritter: Decimal places.
deductFilterFileName() - Method in class com.github.celldynamics.quimp.BOAState.BOAp: Generate main filter config file name.
deductNewParamFileName() - Method in class com.github.celldynamics.quimp.BOAState.BOAp: Generate main param file (new) name.
deductParamFileName(int) - Method in class com.github.celldynamics.quimp.BOAState.BOAp: Generate main param file (old) name basing on ID.
deductSnakeFileName(int) - Method in class com.github.celldynamics.quimp.BOAState.BOAp: Generate Snake file name basing on ID.
deductStatsFileName(int) - Method in class com.github.celldynamics.quimp.BOAState.BOAp: Generate stats file name basing on ID.
defNote - Static variable in class com.github.celldynamics.quimp.utils.QuimpToolsCollection: Message returned by QuimpToolsCollection.getQuimPBuildInfo() if info is not found in jar.
deletePlugin(int) - Method in class com.github.celldynamics.quimp.SnakePluginList: Deletes plugin from memory.
DELIMITER - Static variable in class com.github.celldynamics.quimp.plugin.utils.QWindowBuilder: Delimiter used in UI definition strings.
delimiter - Variable in class com.github.celldynamics.quimp.utils.CsvWritter: Column delimiter.
deserialize(String, T) - Static method in class com.github.celldynamics.quimp.plugin.AbstractPluginOptions: Create AbstractPluginOptions reference from JSon.
deserialize2Macro(String, T) - Static method in class com.github.celldynamics.quimp.plugin.AbstractPluginOptions: Deserialize JSon produced by AbstractPluginOptions.serialize2Macro(), that is json without quotations.
dialogItemChanged(GenericDialog, AWTEvent) - Method in class com.github.celldynamics.quimp.plugin.ana.ANA_
DicException - Exception in com.github.celldynamics.quimp.plugin.dic: Basic class derived from Exception for purposes of DICReconstruction module.
DicException(String) - Constructor for exception com.github.celldynamics.quimp.plugin.dic.DicException: Main constructor.
DicLidReconstruction_ - Class in com.github.celldynamics.quimp.plugin.dic: Main implementation of ImageJ plugin.
DicLidReconstruction_() - Constructor for class com.github.celldynamics.quimp.plugin.dic.DicLidReconstruction_
DicLidReconstruction_Runner - Class in <Unnamed>: Compatibility layer for ImageJ.
DicLidReconstruction_Runner() - Constructor for class DicLidReconstruction_Runner
disableDensityCorrections - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The disable density corrections.
dispersion - Variable in class com.github.celldynamics.quimp.FrameStatistics: Deprecated.
Not used
displacement - Variable in class com.github.celldynamics.quimp.FrameStatistics: Displacement of outline.
dist - Variable in class com.github.celldynamics.quimp.FrameStatistics: Cumulated distance that cell moved from the first recorded frame.
distance - Variable in class com.github.celldynamics.quimp.Vert: distance vert migrated (actually converted to speed by Tool.speedToScale.
distanceFromScale(double, double) - Static method in class com.github.celldynamics.quimp.utils.QuimpToolsCollection: Distance from scale.
distanceToScale(double, double) - Static method in class com.github.celldynamics.quimp.utils.QuimpToolsCollection: Distance to scale.
distanceToScale(int, double) - Static method in class com.github.celldynamics.quimp.utils.QuimpToolsCollection: Distance to scale.
distBetweenInts(Vert, Vert) - Static method in class com.github.celldynamics.quimp.Outline: distBetweenInts.
distPoinToInfLine(ExtendedVector2d, ExtendedVector2d, ExtendedVector2d) - Static method in class com.github.celldynamics.quimp.geom.ExtendedVector2d: Calculate distance of point to line given as two points.
distPointToSegment(ExtendedVector2d, ExtendedVector2d, ExtendedVector2d) - Static method in class com.github.celldynamics.quimp.geom.ExtendedVector2d: Compute distance between closest point and segment.
doAfterSerialize - Variable in class com.github.celldynamics.quimp.Serializer: Indicates if afterSerialze should be called.
doBeforeSerialize - Variable in class com.github.celldynamics.quimp.Serializer: Indicates if IQuimpSerialize.beforeSerialize() should be called.
doConversion() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverter: Perform conversion depending on which file has been loaded.
DOES_SNAKES - Static variable in interface com.github.celldynamics.quimp.plugin.IQuimpCorePlugin: Plugin process snakes only.
dot(ExtendedVector2d, ExtendedVector2d) - Static method in class com.github.celldynamics.quimp.geom.ExtendedVector2d: Compute scalar dot.
double2dfloat(double[][]) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Convert 2D double array to float.
double2float(double[]) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Convert 1d double array to float.
download(ImageData, Path) - Method in class com.github.celldynamics.quimp.omero.OmeroBrowser: Download image and attachment.
download(String) - Method in class com.github.celldynamics.quimp.omero.OmeroClient_: Downloads image.
downloadPluginsConfig() - Method in class com.github.celldynamics.quimp.SnakePluginList: Download configuration from all opened plugins into internal structure.
draw(PrintWriter) - Method in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter: Write to file svg definition of frawn object.
draw(PrintWriter) - Method in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qcircle
draw(PrintWriter) - Method in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qline
draw(PrintWriter) - Method in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.QPolarAxes
draw(PrintWriter) - Method in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.QScaleBar
draw(PrintWriter) - Method in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qtext
dropValue - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Percentage of drop from maximum of motility map to consider point in tracking line.
dt - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkOptions: Timestep, if dt=1 we are at the limit of CFL stability.
Dummy() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds.Dummy: Default constructor without storing seed history.
Dummy(boolean) - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds.Dummy: Allow to store seed history that can be later presented in form of composite image.
dydt(ExtendedVector2d, Sector) - Static method in class com.github.celldynamics.quimp.plugin.ecmm.ODEsolver: Get first derivative.

E

ECMM_Mapping - Class in com.github.celldynamics.quimp.plugin.ecmm: Main ECMM implementation class.
ECMM_Mapping() - Constructor for class com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping: Default constructor called on plugin run from IJ GUI.
ECMM_Mapping(int) - Constructor for class com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping: Constructor called by ANA.
ECMM_Mapping(String) - Constructor for class com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping: Constructor that allows to provide own parameters.
ECMM_Mapping(File) - Constructor for class com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping: Create object and fill options with specified file.
ECMM_MappingRunner - Class in <Unnamed>: Compatibility layer for ImageJ.
ECMM_MappingRunner() - Constructor for class ECMM_MappingRunner
ECMM_RUN - Static variable in class com.github.celldynamics.quimp.filesystem.DataContainer: Indicate that ECMM module is not null (it has been run already on those data).
EcmmOptions - Class in com.github.celldynamics.quimp.plugin.ecmm: Hold ECMM options, currently only file name to process.
EcmmOptions(File) - Constructor for class com.github.celldynamics.quimp.plugin.ecmm.EcmmOptions: Allow to add file name to options.
EcmmOptions() - Constructor for class com.github.celldynamics.quimp.plugin.ecmm.EcmmOptions: Default constructor.
ECMMState - Variable in class com.github.celldynamics.quimp.filesystem.DataContainer: Object to store ECCM output.
ECMp - Class in com.github.celldynamics.quimp.plugin.ecmm: Container class holding parameters related to ECMM analysis.
ECMp() - Constructor for class com.github.celldynamics.quimp.plugin.ecmm.ECMp: Default constructor.
editSnake() - Method in class com.github.celldynamics.quimp.Snake: Edits the snake.
elongation - Variable in class com.github.celldynamics.quimp.FrameStatistics: Elongation of outline.
EmptyMorpho() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.BinaryFilters.EmptyMorpho
enableUI(boolean) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Enables/disables UI.
endFrame - Variable in class com.github.celldynamics.quimp.plugin.ana.ANAp: Frame range.
endFrame - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The end frame.
endFrame - Variable in class com.github.celldynamics.quimp.ShapeHandler: Last frame of Outline.
equals(Object) - Method in class com.github.celldynamics.quimp.FluoMeasurement
equals(Object) - Method in class com.github.celldynamics.quimp.Node
equals(Object) - Method in class com.github.celldynamics.quimp.Outline
equals(Object) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.Point
equals(Object) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel
equals(Object) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkOptions
equals(Object) - Method in class com.github.celldynamics.quimp.PointsList
equals(Object) - Method in class com.github.celldynamics.quimp.QColor
equals(Object) - Method in class com.github.celldynamics.quimp.QuimpVersion
equals(Object) - Method in class com.github.celldynamics.quimp.Shape
equals(Object) - Method in class com.github.celldynamics.quimp.Snake
equals(Object) - Method in class com.github.celldynamics.quimp.Vert
erColorMap2(String, double, double, double) - Static method in class com.github.celldynamics.quimp.QColor: ER color map 2.
errorSink - Variable in class com.github.celldynamics.quimp.plugin.AbstractOptionsParser: Indicate that plugin is run as macro from script.
EscapedPath - Annotation Type in com.github.celldynamics.quimp.plugin: This annotation denotes that annotated field will be escaped by specified symbols.
escapeJsonMacro(String) - Method in class com.github.celldynamics.quimp.plugin.AbstractPluginOptions: Remove quotes and white characters from JSon file.
estimateBackground - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Estimate background if true.
euler(Vert, Sector) - Static method in class com.github.celldynamics.quimp.plugin.ecmm.ODEsolver: Euler solver.
executeForLowerThan() - Method in class com.github.celldynamics.quimp.filesystem.versions.Converter170202
executeForLowerThan() - Method in interface com.github.celldynamics.quimp.filesystem.versions.IQconfOlderConverter: Threshold to execture converter.
executer() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterController
executer() - Method in class com.github.celldynamics.quimp.plugin.AbstractPluginBase: Executed if AbstractPluginBase.run(String) got parsable parameter string.
executer() - Method in class com.github.celldynamics.quimp.plugin.AbstractPluginQconf
executer() - Method in class com.github.celldynamics.quimp.plugin.AbstractPluginTemplate
executer() - Method in class com.github.celldynamics.quimp.plugin.ana.ANA_
executer() - Method in class com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping
executer() - Method in class com.github.celldynamics.quimp.plugin.qanalysis.Q_Analysis
exitIj(ImageJ) - Static method in class com.github.celldynamics.quimp.utils.IJTools: Exit IJ and wait time to accomplish.
expandPower - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: ExpandPower parameter.
ExtendedVector2d - Class in com.github.celldynamics.quimp.geom: Defines 2D vector and performs operations on vectors and lines.
ExtendedVector2d(double[]) - Constructor for class com.github.celldynamics.quimp.geom.ExtendedVector2d: Constructs and initializes a Vector2d from the specified array.
ExtendedVector2d(Tuple2d) - Constructor for class com.github.celldynamics.quimp.geom.ExtendedVector2d: Constructs and initializes a Vector2d from the specified Tuple.
ExtendedVector2d(Tuple2f) - Constructor for class com.github.celldynamics.quimp.geom.ExtendedVector2d: Constructs and initializes a Vector2d from the specified Tuple.
ExtendedVector2d(Vector2d) - Constructor for class com.github.celldynamics.quimp.geom.ExtendedVector2d: Constructs and initializes a Vector2d from the specified Vector.
ExtendedVector2d(Vector2f) - Constructor for class com.github.celldynamics.quimp.geom.ExtendedVector2d: Constructs and initializes a Vector2d from the specified Vector.
ExtendedVector2d() - Constructor for class com.github.celldynamics.quimp.geom.ExtendedVector2d: Constructs and initializes a Vector2d to (0,0).
ExtendedVector2d(double, double) - Constructor for class com.github.celldynamics.quimp.geom.ExtendedVector2d: Simple constructor.
extendImageBeforeRotation(ImageProcessor, double) - Method in class com.github.celldynamics.quimp.plugin.utils.ImageProcessorPlus: Add borders around image to prevent cropping during rotating.
extension - Variable in class com.github.celldynamics.quimp.FrameStatistics: Deprecated.
Not used

F

fCoord - Variable in class com.github.celldynamics.quimp.Vert: coord relative to coord on previous frame.
FgController() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_.FgController
fgName - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.SeedPicker: Prefix for foreground ROIs.
file2Array(String, File) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Load map file produced by arrayToFile.
FileDialogEx - Class in com.github.celldynamics.quimp.filesystem: Implements file dialog with file filtering.
FileDialogEx(Dialog, String, int) - Constructor for class com.github.celldynamics.quimp.filesystem.FileDialogEx: Construct object with default file filtering.
FileDialogEx(Dialog, String) - Constructor for class com.github.celldynamics.quimp.filesystem.FileDialogEx: Construct object with default file filtering.
FileDialogEx(Dialog) - Constructor for class com.github.celldynamics.quimp.filesystem.FileDialogEx: Construct object with default file filtering.
FileDialogEx(Frame, String, int) - Constructor for class com.github.celldynamics.quimp.filesystem.FileDialogEx: Construct object with default file filtering.
FileDialogEx(Frame, String) - Constructor for class com.github.celldynamics.quimp.filesystem.FileDialogEx: Construct object with default file filtering.
FileDialogEx(Frame) - Constructor for class com.github.celldynamics.quimp.filesystem.FileDialogEx: Construct object with default file filtering.
FileDialogEx(Frame, String...) - Constructor for class com.github.celldynamics.quimp.filesystem.FileDialogEx: Construct object with given file extension filtering.
fileExt - Variable in class com.github.celldynamics.quimp.plugin.AbstractPluginQconf: Extension of file plugin asks for after execution in IJ mode.
FileExtensions - Class in com.github.celldynamics.quimp.filesystem: Contain list of all extensions supported by QuimP.
FileExtensions() - Constructor for class com.github.celldynamics.quimp.filesystem.FileExtensions
filename - Variable in class com.github.celldynamics.quimp.plugin.qanalysis.Qp: The core of filename.
fill(int, int, int, double, double) - Method in class com.github.celldynamics.quimp.plugin.qanalysis.FluoMap: Put value to fluoromap calculating correct color.
fill2Darray(double[][], double) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Fill 2D array with given value.
fill2Darray(int[][], int) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Fill 2D array with given value.
fillRegForm() - Method in class com.github.celldynamics.quimp.registration.Registration: Read registration details from IJ and fills the registration window.
finalFilter - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkOptions: Reference to filter used on final processing.
finalShrink - Variable in class com.github.celldynamics.quimp.QParams: Shrink value.
findClosestTo(int, int, int, double) - Method in class com.github.celldynamics.quimp.Nest: Find Snake that distance of its centroid to given point is smaller than given value.
findCoordEdge(double) - Method in class com.github.celldynamics.quimp.Outline: findCoordEdge.
findDataset(String) - Method in class com.github.celldynamics.quimp.omero.OmeroBrowser: Find dataset of specified name.
findDataset(Long) - Method in class com.github.celldynamics.quimp.omero.OmeroBrowser: Find dataset of specified id.
findFirstNode(char) - Method in class com.github.celldynamics.quimp.Outline: Find the first node in terms of coord (c) or fcoord (f) ie closest to zero.
findImage(String, DatasetData, boolean) - Method in class com.github.celldynamics.quimp.omero.OmeroBrowser: Find image of specified name in the dataset.
findImage(Long, DatasetData) - Method in class com.github.celldynamics.quimp.omero.OmeroBrowser: Find image of specified id in dataset.
findIndex(double[], double, double) - Static method in class com.github.celldynamics.quimp.geom.MapCoordConverter: Find index of element val in array with tolerance.
findIntersect(Vert, int) - Static method in class com.github.celldynamics.quimp.Outline: findIntersect.
findNumPeaks(double[], int) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Find num peaks.
findParamFiles() - Method in class com.github.celldynamics.quimp.QParams: Traverse through current directory looking for paQP files.
findParamFiles() - Method in class com.github.celldynamics.quimp.QParamsQconf: For new file format it redirects call to super class searching for old files (paQP).
findPointIndex(double[], double[], double, double, double) - Static method in class com.github.celldynamics.quimp.geom.MapCoordConverter: Find point defined by xmap and ymap for given frame which is closest to another point (x;y) within tolerance.
fLandCoord - Variable in class com.github.celldynamics.quimp.Vert: landing relative to previous frame.
flatten(int, boolean) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.TrackVisualisation: Flatten stack according to given type.
flatten(Seeds, RandomWalkSegmentation.SeedTypes, int) - Static method in class com.github.celldynamics.quimp.plugin.randomwalk.SeedProcessor: Flatten seeds of specified type and output grayscale image.
float2ddouble(float[][]) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Convert 2D float array to double.
float2double(float[]) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Deprecated.
Use ij.Tools.toDouble
FLU1 - Static variable in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Fluorescence channel 1 map code.
FLU2 - Static variable in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Fluorescence channel 2 map code.
FLU3 - Static variable in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Fluorescence channel 3 map code.
fluLims - Variable in class com.github.celldynamics.quimp.OutlineHandler: The flu lims.
FluoMap - Class in com.github.celldynamics.quimp.plugin.qanalysis: Hold fluorescence map for given channel together with indexed colors.
FluoMap(FluoMap) - Constructor for class com.github.celldynamics.quimp.plugin.qanalysis.FluoMap: Copy constructor.
FluoMap(int, int, int) - Constructor for class com.github.celldynamics.quimp.plugin.qanalysis.FluoMap: Constructor.
fluomapFileExt - Static variable in class com.github.celldynamics.quimp.filesystem.FileExtensions: Extension for file containing fluoromap map.
fluoMaps - Variable in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Fluoroscence maps for channels.
FluoMeasurement - Class in com.github.celldynamics.quimp: Hold fluorescence value for pixel.
FluoMeasurement(double, double, double) - Constructor for class com.github.celldynamics.quimp.FluoMeasurement: Constructor of the fluoro pixel.
FluoMeasurement(FluoMeasurement) - Constructor for class com.github.celldynamics.quimp.FluoMeasurement: Copy constructor.
fluores - Variable in class com.github.celldynamics.quimp.Vert: fluorescence channels 1-3.
fluoResultTable - Variable in class com.github.celldynamics.quimp.plugin.ana.AnaOptions: UI setting.
fluoResultTableAppend - Variable in class com.github.celldynamics.quimp.plugin.ana.AnaOptions: UI setting.
fluTiffs - Variable in class com.github.celldynamics.quimp.plugin.ana.ANAp: Array of fluorescent channels.
fluTiffs - Variable in class com.github.celldynamics.quimp.QParams: This field is set by direct call from ANA.
font - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qtext: The font.
fontSize - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.QPolarAxes: Font size.
forceBackwardMapping - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The force backward mapping.
forceForwardMapping - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The force forward mapping.
forceNoSectors - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The force no sectors.
Format_ConverterRunner - Class in <Unnamed>: Compatibility layer for ImageJ.
Format_ConverterRunner() - Constructor for class Format_ConverterRunner
FormatConverter - Class in com.github.celldynamics.quimp.filesystem.converter: This class allows for converting between paQP and QCONF and vice versa.
FormatConverter() - Constructor for class com.github.celldynamics.quimp.filesystem.converter.FormatConverter: Do nothing.
FormatConverter(File) - Constructor for class com.github.celldynamics.quimp.filesystem.converter.FormatConverter: Construct FormatConverter from provided file.
FormatConverter(QconfLoader) - Constructor for class com.github.celldynamics.quimp.filesystem.converter.FormatConverter: Construct conversion object from QconfLoader.
FormatConverterController - Class in com.github.celldynamics.quimp.filesystem.converter: Performs conversion actions.
FormatConverterController() - Constructor for class com.github.celldynamics.quimp.filesystem.converter.FormatConverterController: Default constructor.
FormatConverterController(Path) - Constructor for class com.github.celldynamics.quimp.filesystem.converter.FormatConverterController: Constructor allowing passing file to process.
FormatConverterModel - Class in com.github.celldynamics.quimp.filesystem.converter: Keep status of FormatConverterUi checkboxes in List.
FormatConverterModel() - Constructor for class com.github.celldynamics.quimp.filesystem.converter.FormatConverterModel: Default constructor.
FormatConverterUi - Class in com.github.celldynamics.quimp.filesystem.converter: Build format converter view.
FormatConverterUi() - Constructor for class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi: Default constructor - for tests and WindowCreator.
FormatConverterUi(FormatConverterModel) - Constructor for class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi: Create the dialog.
fps - Variable in class com.github.celldynamics.quimp.plugin.qanalysis.Qp: Frames per second.
frame - Variable in class com.github.celldynamics.quimp.BOAState.BOAp: Current frame, CustomStackWindow.updateSliceSelector().
frame - Variable in class com.github.celldynamics.quimp.FrameStatistics: Frame number.
frame - Variable in class com.github.celldynamics.quimp.geom.SegmentedShapeRoi: Frame number where this outline was found.
frameInterval - Variable in class com.github.celldynamics.quimp.plugin.ana.ANAp: Frame interval.
frameInterval - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The frame interval.
frameInterval - Variable in class com.github.celldynamics.quimp.plugin.qanalysis.Qp: The frame interval.
framestat - Variable in class com.github.celldynamics.quimp.CellStats: List of statistic calculated for subsequent frames for the same object.
FrameStatistics - Class in com.github.celldynamics.quimp: Hold statistic evaluated for one frame and one outline, both geometric and fluorescence.
FrameStatistics() - Constructor for class com.github.celldynamics.quimp.FrameStatistics: Default constructor, create empty container.
freeze() - Method in class com.github.celldynamics.quimp.PointsList: Freeze Point.
freezeAll() - Method in class com.github.celldynamics.quimp.Shape: Freeze all nodes in Shape.
freezeHandler() - Method in class com.github.celldynamics.quimp.SnakeHandler: Prevent this handler from segmentation.
freezeNode(Node) - Method in class com.github.celldynamics.quimp.Snake: Freeze a specific node.
freezeProx(double, double) - Method in class com.github.celldynamics.quimp.Outline: Freeze a node and corresponding edge if its to close && close to parallel.
freezeProxSnakes(Nest, int) - Method in class com.github.celldynamics.quimp.Constrictor: Freeze snakes which are close to each other in nest.
freezeTh - Variable in class com.github.celldynamics.quimp.plugin.ana.ANAp: Angle to freeze neighbouring vertexes.
fromReader(Reader) - Method in class com.github.celldynamics.quimp.Serializer: Restore wrapped object from JSON string.
fromString(String) - Method in class com.github.celldynamics.quimp.Serializer: Restore wrapped object from JSON string.

G

gamma - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkOptions: Gamma is the strength of competition between foreground and background.
gCoord - Variable in class com.github.celldynamics.quimp.Vert: global coord relative to head node on frame 1.
GENERAL - Static variable in interface com.github.celldynamics.quimp.plugin.IQuimpCorePlugin: Type of plugin not defined.
GenerateMask_ - Class in com.github.celldynamics.quimp.plugin.generatemask: Convert QCONF files to BW masks.
GenerateMask_() - Constructor for class com.github.celldynamics.quimp.plugin.generatemask.GenerateMask_: Executed if plugin is run from IJ.
GenerateMask_(String) - Constructor for class com.github.celldynamics.quimp.plugin.generatemask.GenerateMask_: Constructor that allows to provide own parameters.
GenerateMask_Runner - Class in <Unnamed>: Compatibility layer for ImageJ.
GenerateMask_Runner() - Constructor for class GenerateMask_Runner
GenerateMaskOptions - Class in com.github.celldynamics.quimp.plugin.generatemask: Keep parameters for GenerateMask_ plugin.
GenerateMaskOptions() - Constructor for class com.github.celldynamics.quimp.plugin.generatemask.GenerateMaskOptions
generateMaskSuffix - Static variable in class com.github.celldynamics.quimp.filesystem.FileExtensions: Mask generated by GenerateMask plugin.
generatePlot(String) - Method in class com.github.celldynamics.quimp.utils.graphics.PolarPlot: Polar plot of mean of motility along frames.
generatePlotFrame(String, int) - Method in class com.github.celldynamics.quimp.utils.graphics.PolarPlot: Polar plot of one frame.
get(RandomWalkSegmentation.SeedTypes, int) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.Seeds: Retrieve specified seed map from specified key.
get(String) - Method in class com.github.celldynamics.quimp.plugin.utils.LinkedStringMap: Get the value of key.
getActiveHandler() - Method in class com.github.celldynamics.quimp.QParamsQconf: Gets the active handler.
getActualTypeArguments() - Method in class com.github.celldynamics.quimp.Serializer
getANA() - Method in class com.github.celldynamics.quimp.filesystem.QconfLoader: Query for ANA object.
getANAState() - Method in class com.github.celldynamics.quimp.filesystem.DataContainer: getANAState.
getArraySize(Object) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Get size of array across all dimensions.
getBackupSnake(int) - Method in class com.github.celldynamics.quimp.SnakeHandler: Gets the backup snake.
getBackwardFrames(int, int) - Method in class com.github.celldynamics.quimp.geom.MapTracker: Deprecated.
Use MapTracker.trackBackwardValid(int, int, int) instead
getBf() - Method in class com.github.celldynamics.quimp.plugin.protanalysis.TrackCollection: Get unmodifiable list of all tracks.
getBinaryProcessor(ImageProcessor) - Static method in class com.github.celldynamics.quimp.plugin.randomwalk.BinaryFilters: Converts input image to BinaryProcessor duplicating it.
getBlowup() - Method in class com.github.celldynamics.quimp.QParams: getBlowup.
getBlowup() - Method in class com.github.celldynamics.quimp.QParamsQconf
getBlue() - Method in class com.github.celldynamics.quimp.QColor: Gets the blue.
getBlue(int) - Method in class com.github.celldynamics.quimp.QColor: Gets the blue.
getBnBack() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get BG button ref.
getBnFore() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get FG button ref.
getBOA() - Method in class com.github.celldynamics.quimp.filesystem.QconfLoader: Query for BOA object.
getBOAState() - Method in class com.github.celldynamics.quimp.filesystem.DataContainer: getBOAState.
getBooleanFromUI(String) - Method in class com.github.celldynamics.quimp.plugin.utils.QWindowBuilder: Return value related to given key.
getBooleanValue(String) - Method in class com.github.celldynamics.quimp.plugin.ParamList: Get Boolean value from list associated with \c key.
getBounds() - Method in class com.github.celldynamics.quimp.Snake: Gets bounds of snake.
getBtnBoa() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getBtnEcmm() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getBtnMaps() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getBtnQ11Stats() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getBtnRawStats() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getBuildstamp() - Method in class com.github.celldynamics.quimp.QuimpVersion: Get time and date.
getCancelButton() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getCbCreatedSeedImage() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get seed image selected in dynamic created mask panel.
getCbMaskSeedImage() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get seed image selected in dynamic binary mask panel.
getCbOrginalImage() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get name of selected original image.
getCbRgbSeedImage() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get seed image selected in dynamic rgb panel.
getCentroid() - Method in class com.github.celldynamics.quimp.Shape: Getter for centroid.
getChains() - Method in class com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentation: Compose chains of object related to each others along frames.
getChannel() - Method in class com.github.celldynamics.quimp.plugin.qanalysis.FluoMap: getChannel.
getChckbxCentroid() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getChckbxCentroidEcmm() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getChckbxConvexity() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getChckbxCoord() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getChckbxFluo() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getChckbxFluoresStat() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getChckbxGeometric() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getChckbxMotility() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getChckbxMultiFileOutput() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getChckbxOrigin() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getChckbxOutlinesEcmm() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getChckbxQ11Stat() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getChckbxSnakes() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getChckbxStoreCred() - Method in class com.github.celldynamics.quimp.omero.OmeroLoginDialog
getChckbxX() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getChckbxY() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getChHatFilter() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get status of HatSnake filter.
getChInterFrameFilter() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get status of chInterFrameFilter.
getChLocalMean() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get status of Local mean.
getChMaskCut() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get status of mask cut filter.
getChShowPreview() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get status of show preview.
getChShowProbMaps() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get status of show prob maps.
getChShowSeed() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get status of show seed.
getChTrueBackground() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get status of True Background.
getCircle(Point2d, float) - Static method in class com.github.celldynamics.quimp.utils.graphics.GraphicsElements: Return circle.
getCircle(double, double, Color, double) - Static method in class com.github.celldynamics.quimp.utils.graphics.GraphicsElements: Generate filled circle.
getClassName() - Method in class com.github.celldynamics.quimp.plugin.engine.PluginProperties: getClassName.
getColor(Track) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.TrackVisualisation: Helper method.
getColorBW(int) - Method in class com.github.celldynamics.quimp.QColor: Gets the color BW.
getColorInt() - Method in class com.github.celldynamics.quimp.QColor: Gets the color int.
getColors() - Method in class com.github.celldynamics.quimp.geom.TrackOutline: Get colors of pixels that outlines were produced from.
getColorSVG() - Method in class com.github.celldynamics.quimp.QColor: Convert color to SVG codes.
getColours() - Method in class com.github.celldynamics.quimp.plugin.qanalysis.FluoMap: getColours.
getCommonPoints() - Method in class com.github.celldynamics.quimp.plugin.protanalysis.TrackMapAnalyser: getCommonPoints.
getComposite(ImagePlus, ImagePlus, ImagePlus) - Static method in class com.github.celldynamics.quimp.utils.IJTools: Return composite image created from background cell image and FG and BG pixels.
getCompositeSeed(ImagePlus, int) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds.Dummy
getCompositeSeed(ImagePlus, int) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds: Produce composite image containing seeds generated during segmentation of particular frames.
getConfig(int) - Method in class com.github.celldynamics.quimp.SnakePluginList: Return i-th plugin configuration.
getContentPanel() - Method in class com.github.celldynamics.quimp.omero.OmeroLoginDialog
getConvertButton() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getConvexFile() - Method in class com.github.celldynamics.quimp.QParams: getConvexFile name.
getConvMap() - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: getConvMap.
getCoordFile() - Method in class com.github.celldynamics.quimp.QParams: getCoordFile name.
getCoordMap() - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Get coordinates map.
getCopyofShapes() - Method in class com.github.celldynamics.quimp.geom.TrackOutline: Return deep copy of Shapes.
getCortexWidthPixel() - Method in class com.github.celldynamics.quimp.plugin.ana.ANAp: Get cortex width in pixels.
getCortexWidthScale() - Method in class com.github.celldynamics.quimp.plugin.ana.ANAp: Get cortex scale.
getCurrentDate() - Method in class com.github.celldynamics.quimp.Serializer: Get current date included in saved file.
getCurvatureLocal() - Method in class com.github.celldynamics.quimp.PointsList: Evaluate local curvature of T related to previous, this and next T.
getDataConverterInstance() - Method in class com.github.celldynamics.quimp.geom.filters.PointListProcessor: Return underlying DataConverter instance.
getDeepCopy() - Method in class com.github.celldynamics.quimp.SnakePluginList: Copy method.
getDoubleBounds() - Method in class com.github.celldynamics.quimp.Shape: Get bounds of Shape.
getDoubleFromUI(String) - Method in class com.github.celldynamics.quimp.plugin.utils.QWindowBuilder: Return value related to given key.
getDoubleValue(String) - Method in class com.github.celldynamics.quimp.plugin.ParamList: Get Double value from list associated with \c key.
getEcmm() - Method in class com.github.celldynamics.quimp.filesystem.QconfLoader: Query for ECMM object.
getEcmmState() - Method in class com.github.celldynamics.quimp.filesystem.DataContainer: getECMMState.
getEndFrame() - Method in class com.github.celldynamics.quimp.OutlineHandler: Gets the end frame.
getEndFrame() - Method in class com.github.celldynamics.quimp.QParams: getEndFrame.
getEndFrame() - Method in class com.github.celldynamics.quimp.QParamsQconf
getEndFrame() - Method in class com.github.celldynamics.quimp.ShapeHandler: Gets the end frame.
getExceptionMessageChain(Throwable) - Static method in exception com.github.celldynamics.quimp.QuimpException: Get messages from exception stack.
getF_total() - Method in class com.github.celldynamics.quimp.Node: Setter to F_total field.
getFile() - Method in class com.github.celldynamics.quimp.plugin.engine.PluginProperties: File getter.
getFileExtension(String) - Static method in class com.github.celldynamics.quimp.utils.QuimpToolsCollection: Get file extension.
getFileName() - Method in class com.github.celldynamics.quimp.BOAState.BOAp: Get fileName.
getFileName() - Method in class com.github.celldynamics.quimp.QParams: Get the name of parameter file but without extension.
getFileName() - Method in class com.github.celldynamics.quimp.QParamsQconf: Get name of configuration file.
getFileVersion() - Method in class com.github.celldynamics.quimp.QParamsQconf: Return file creation date and other parameters.
getFilter(BinaryFilters.Filters) - Static method in class com.github.celldynamics.quimp.plugin.randomwalk.BinaryFilters: Factory of filters supported by this class.
getFilteringMethod() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: cbFilteringMethod getter.
getFilteringMethods() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Get filtering methods supported by BinaryFilters class in form of String[].
getFilteringPostMethod() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: cbFilteringMethod getter.
getFloatX() - Method in class com.github.celldynamics.quimp.plugin.utils.QuimpDataConverter: Data accessor.
getFloatY() - Method in class com.github.celldynamics.quimp.plugin.utils.QuimpDataConverter: Data accessor.
getFluFiles() - Method in class com.github.celldynamics.quimp.QParams: Get names of flu files.
getFluMaps() - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: getFluMaps.
getFormattedQuimPversion(QuimpVersion) - Static method in class com.github.celldynamics.quimp.utils.QuimpToolsCollection: Prepare info plate for QuimP.
getForwardFrames(int, int) - Method in class com.github.celldynamics.quimp.geom.MapTracker: Deprecated.
Use MapTracker.trackForwardValid(int, int, int) instead
getFrame() - Method in exception com.github.celldynamics.quimp.BoaException: Get frame.
getFrame() - Method in class com.github.celldynamics.quimp.geom.SegmentedShapeRoi: Get Roi frame.
getFrameInterval() - Method in class com.github.celldynamics.quimp.QParams: getFrameInterval.
getFrameInterval() - Method in class com.github.celldynamics.quimp.QParamsQconf
getFrames() - Method in class com.github.celldynamics.quimp.BOAState.BOAp: Get FRAMES.
getFramestat() - Method in class com.github.celldynamics.quimp.CellStats: Return list of statistic calculated for subsequent frames for the same object.
getGrayLut() - Static method in class com.github.celldynamics.quimp.utils.IJTools: Convert LUT to grayscale.
getGreen() - Method in class com.github.celldynamics.quimp.QColor: Gets the green.
getGreen(int) - Method in class com.github.celldynamics.quimp.QColor: Gets the green.
getHandler(int) - Method in class com.github.celldynamics.quimp.Nest: Gets SnakeHandler.
getHandlerofId(int) - Method in class com.github.celldynamics.quimp.Nest: Get SnakeHandler of given id.
getHandlers() - Method in class com.github.celldynamics.quimp.Nest: Return list of handlers stored in Nest.
getHead() - Method in class com.github.celldynamics.quimp.Shape: Get head of current Shape.
getHeight() - Method in class com.github.celldynamics.quimp.BOAState.BOAp: Get HEIGHT.
getId() - Method in class com.github.celldynamics.quimp.geom.SegmentedShapeRoi: Get id.
getID() - Method in class com.github.celldynamics.quimp.SnakeHandler: Gets the id of handler.
getImage() - Method in class com.github.celldynamics.quimp.filesystem.QconfLoader: Try to load image associated with QCONF or paQP file.
getImageFrameInterval() - Method in class com.github.celldynamics.quimp.BOAState.BOAp: Get imageFrameInterval.
getImageScale() - Method in class com.github.celldynamics.quimp.BOAState.BOAp: Get scale of the image.
getImageScale() - Method in class com.github.celldynamics.quimp.QParams: getImageScale.
getImageScale() - Method in class com.github.celldynamics.quimp.QParamsQconf
getIndex() - Method in enum com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentation.SeedTypes: Convert enum to int.
getIndex(int, int, int) - Static method in interface com.github.celldynamics.quimp.plugin.utils.IPadArray: Helper method to pick values from X, Y arrays.
getInfoText() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getInstance(String) - Method in class com.github.celldynamics.quimp.plugin.engine.PluginFactory: Return instance of named plugin.
getInstance() - Static method in class com.github.celldynamics.quimp.PluginFactoryFactory: Get instance of PluginFactory.
getInstance(int) - Method in class com.github.celldynamics.quimp.SnakePluginList: Return i-th instance of plugin.
getIntegerFromUI(String) - Method in class com.github.celldynamics.quimp.plugin.utils.QWindowBuilder: Return value related to given key.
getIntersectionParents(List<Polygon>, int) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.TrackMapAnalyser: Find common points among polygons.
getIntersectionPoints(List<Polygon>) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.TrackMapAnalyser: Find common points among polygons.
getIntersectionPoints(Polygon, Polygon) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.TrackMapAnalyser: Check if p1 and p2 have common vertexes.
getIntValue(String) - Method in class com.github.celldynamics.quimp.plugin.ParamList: Get Integer value from list associated with \c key.
getLength() - Method in class com.github.celldynamics.quimp.Shape: Add up lengths between all verts.
getLine(Polygon, int, Color) - Static method in class com.github.celldynamics.quimp.utils.graphics.GraphicsElements: Generate line.
getLine(Polygon, Color) - Static method in class com.github.celldynamics.quimp.utils.graphics.GraphicsElements: Generate line.
getLine(Polygon, Color, int) - Static method in class com.github.celldynamics.quimp.utils.graphics.GraphicsElements: Generate line on frame f.
getLine(float[], float[], int, Color) - Static method in class com.github.celldynamics.quimp.utils.graphics.GraphicsElements: Generate line.
getList() - Method in class com.github.celldynamics.quimp.geom.filters.PointListProcessor: Return modified list.
getList() - Method in class com.github.celldynamics.quimp.plugin.utils.QuimpDataConverter: Data accessor.
getList() - Method in class com.github.celldynamics.quimp.SnakePluginList: Returns unmodifiable list of plugins.
getListAwtDouble() - Method in class com.github.celldynamics.quimp.geom.filters.PointListProcessor: Return modified awt double list.
getListAwtInt() - Method in class com.github.celldynamics.quimp.geom.filters.PointListProcessor: Return modified awt int list.
getListDatasetsDownload() - Method in class com.github.celldynamics.quimp.omero.OmeroLoginDialog
getListDatasetsUpload() - Method in class com.github.celldynamics.quimp.omero.OmeroLoginDialog
getListofDoublePoints() - Method in class com.github.celldynamics.quimp.plugin.utils.QuimpDataConverter: Data accessor.
getListofIntPoints() - Method in class com.github.celldynamics.quimp.plugin.utils.QuimpDataConverter: Data accessor.
getLiveSnake() - Method in class com.github.celldynamics.quimp.SnakeHandler: Gets the live snake.
getLoadButton() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi
getLoadedDataContainer() - Method in class com.github.celldynamics.quimp.QParamsQconf: Extract DataContainer from Serializer super class.
getMap() - Method in class com.github.celldynamics.quimp.plugin.qanalysis.FluoMap: getMap.
getMax(RealMatrix) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Find maximum in 2D RealMatrix.
getMaxima() - Method in class com.github.celldynamics.quimp.plugin.protanalysis.MaximaFinder: getMaxima.
getMaximaNumber() - Method in class com.github.celldynamics.quimp.plugin.protanalysis.MaximaFinder: Number of points found.
getMaxValues() - Method in class com.github.celldynamics.quimp.plugin.protanalysis.MaximaFinder: Return values corresponding to indexes returned by getMaxima.
getMeanC(double[][]) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Calculate mean of map for every column.
getMeanR(double[][]) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Calculate mean of map for every row.
getMeanSeedGlobal(List<Point>) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentation: Compute mean value from image only seeded pixels.
getMeanSeedLocal(ImageProcessor, int) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentation: Calculate local mean intensity for input image but only for areas masked by specified mask.
getMessageSinkType() - Method in exception com.github.celldynamics.quimp.QuimpException: Get message sink.
getMin(RealMatrix) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Find minimum in 2D RealMatrix.
getModel() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterController: Get model and allow to set own configuration in no-gui mode.
getMotilityFile() - Method in class com.github.celldynamics.quimp.QParams: getMotilityFile name.
getMotMap() - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: getMotMap.
getName() - Method in class com.github.celldynamics.quimp.QuimpVersion: Get software name.
getName(int) - Method in class com.github.celldynamics.quimp.SnakePluginList: Return i-th plugin name.
getNest() - Method in class com.github.celldynamics.quimp.QParamsQconf: Return Nest object.
getNext(int, int) - Method in class com.github.celldynamics.quimp.geom.MapTracker: Get position of membraneIndex on frame currentFrame+1.
getNext() - Method in class com.github.celldynamics.quimp.PointsList: Get next node in chain (previous if not clockwise).
getNextIntersect(Vert) - Static method in class com.github.celldynamics.quimp.Outline: getNextIntersect.
getNodeRes() - Method in class com.github.celldynamics.quimp.QParams: getNodeRes.
getNodeRes() - Method in class com.github.celldynamics.quimp.QParamsQconf
getNormal() - Method in class com.github.celldynamics.quimp.PointsList: Gets the normal.
getNumberOfLinesinFile(File) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Return number of lines in file.
getNumofParam(String, char) - Static method in class com.github.celldynamics.quimp.plugin.utils.StringParser: Get number of parameters in input string.
getNumPoints() - Method in class com.github.celldynamics.quimp.Shape: Get number of points in Shape.
getNumStoredFrames() - Method in class com.github.celldynamics.quimp.CellStats: Get number of frames.
getO() - Method in class com.github.celldynamics.quimp.geom.filters.OutlineProcessor: Outline getter.
getOkButton() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterUi: Get reference to OK button.
getOptions() - Method in class com.github.celldynamics.quimp.plugin.AbstractOptionsParser: Return AbstractOptionsParser.options.
getOrgFile() - Method in class com.github.celldynamics.quimp.BOAState.BOAp: Get orgFile - image opened in BOA.
getOriginalImage() - Method in class com.github.celldynamics.quimp.plugin.protanalysis.TrackVisualisation: getOriginalImage.
getOriginalImage() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Get original image from this object.
getOriginFile() - Method in class com.github.celldynamics.quimp.QParams: getOriginFile name.
getOriginMap() - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Get origin map.
getOutline() - Method in class com.github.celldynamics.quimp.plugin.utils.QuimpDataConverter: Return Outline created from stored data.
getOutlineAndColors(ImageProcessor, boolean) - Static method in class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds.Contour: Convert mask to outline.
getOutlineasPoints() - Method in class com.github.celldynamics.quimp.geom.SegmentedShapeRoi: Convert this ROI to list of points using smoothing and step.
getOutlineasRawPoints() - Method in class com.github.celldynamics.quimp.geom.SegmentedShapeRoi: Convert this ROI to list of points without any interpolation.
getOutlineasRawPoints() - Method in class com.github.celldynamics.quimp.geom.TrackOutline: Convert found outlines to List without any interpolation.
getOutlines(double, boolean) - Method in class com.github.celldynamics.quimp.geom.TrackOutline: Convert found outlines to Outline.
getOutlinesasPoints(double, boolean) - Method in class com.github.celldynamics.quimp.geom.TrackOutline: Convert found outlines to List.
getOutlinesColors(double, boolean) - Method in class com.github.celldynamics.quimp.geom.TrackOutline: Convert found outlines to Outline.
getOutputFileCore() - Method in class com.github.celldynamics.quimp.BOAState.BOAp: Get outputFileCore.
getOwnerType() - Method in class com.github.celldynamics.quimp.Serializer
getPairs(double, boolean) - Method in class com.github.celldynamics.quimp.geom.TrackOutline: Reformat collected outlines and Colors to list of pairs.
getPairsOutlineAndColors(ImageProcessor, boolean) - Static method in class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds.Contour: Convert mask to outline.
getPanelDownload() - Method in class com.github.celldynamics.quimp.omero.OmeroLoginDialog
getPanelSetup() - Method in class com.github.celldynamics.quimp.omero.OmeroLoginDialog
getPanelUpload() - Method in class com.github.celldynamics.quimp.omero.OmeroLoginDialog
getParamFile() - Method in class com.github.celldynamics.quimp.QParams: Get name of parameter file with extension (paQP).
getParamFile() - Method in class com.github.celldynamics.quimp.QParamsQconf: Get configuration file (with path).
getParamFormat() - Method in class com.github.celldynamics.quimp.QParams: Return loaded format.
getParams(String, char) - Static method in class com.github.celldynamics.quimp.plugin.utils.StringParser: Split input string into separate substrings using defined separator.
getParsed(String, char) - Method in class com.github.celldynamics.quimp.plugin.ParamList: Get string associated with key and parse it to split according to delimiter.
getPath() - Method in class com.github.celldynamics.quimp.filesystem.FileDialogEx: Get path to selected file.
getPath() - Method in class com.github.celldynamics.quimp.QParams: getPath.
getPath() - Method in class com.github.celldynamics.quimp.utils.CsvWritter: Return file path.
getPathasPath() - Method in class com.github.celldynamics.quimp.QParams: getPathasPath.
getPluginConfig() - Method in class com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentation_
getPluginConfig() - Method in class com.github.celldynamics.quimp.plugin.dic.DicLidReconstruction_
getPluginConfig() - Method in interface com.github.celldynamics.quimp.plugin.IQuimpPluginExchangeData: Retrieve plugin configuration data as pairs (key,value>=).
getPluginFactory(String) - Static method in class com.github.celldynamics.quimp.PluginFactoryFactory: Provide mocked PluginFactory object that uses sources of plugins available on path.
getPluginNames(int) - Method in class com.github.celldynamics.quimp.plugin.engine.PluginFactory: Return list of plugins of given types.
getPluginNames(int) - Method in class com.github.celldynamics.quimp.SnakePluginList: Return names of plugins of given type registered in PluginFactory associated with this object.
getPoint() - Method in class com.github.celldynamics.quimp.PointsList: Gets the point.
getPoint(double, double, Color) - Static method in class com.github.celldynamics.quimp.utils.graphics.GraphicsElements: Generate point roi.
getPoint(int[], int[], Color) - Static method in class com.github.celldynamics.quimp.utils.graphics.GraphicsElements: Generate points roi.
getPoint(Polygon, Color) - Static method in class com.github.celldynamics.quimp.utils.graphics.GraphicsElements: Generate points roi.
getPolyArea(List<? extends Tuple2d>) - Method in class com.github.celldynamics.quimp.geom.BasicPolygons: Calculates area of polygon.
getPolyPerim(List<? extends Tuple2d>) - Method in class com.github.celldynamics.quimp.geom.BasicPolygons: Calculates perimeter of polygon.
getPosition() - Method in class com.github.celldynamics.quimp.PointsList: Get normalised position of node.
getPrev(int, int) - Method in class com.github.celldynamics.quimp.geom.MapTracker: Get position of membraneIndex on frame currentFrame-1.
getPrev() - Method in class com.github.celldynamics.quimp.PointsList: Get previous node in chain (next if not clockwise).
getProbabilityMaps() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentation: Return probability maps for each object (foreground is last).
getPropagator(PropagateSeeds.Propagators, boolean, AutoThresholder.Method) - Static method in class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds: Return demanded propagator.
getPw() - Method in class com.github.celldynamics.quimp.utils.CsvWritter: Return PrintWritter object.
getQ() - Method in class com.github.celldynamics.quimp.filesystem.QconfLoader: Query for Q object.
getQconfFile() - Method in class com.github.celldynamics.quimp.filesystem.QconfLoader: Return path to loaded configuration file.
getQconfFile() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Get qconffile field.
getQconfLoader() - Method in class com.github.celldynamics.quimp.plugin.AbstractPluginQconf: Return QconfLoader object.
getQconfVersion(Reader) - Method in class com.github.celldynamics.quimp.Serializer: Read QuimP version from QCONF file.
getQp() - Method in class com.github.celldynamics.quimp.filesystem.QconfLoader: Return QParams object.
getQState() - Method in class com.github.celldynamics.quimp.filesystem.DataContainer: getQState.
getQuimPBuildInfo() - Method in class com.github.celldynamics.quimp.utils.QuimpToolsCollection: Get build info read from jar file.
getQuimPversion() - Method in class com.github.celldynamics.quimp.utils.QuimpToolsCollection: Prepare info plate for QuimP.
getRawType() - Method in class com.github.celldynamics.quimp.Serializer
getRed() - Method in class com.github.celldynamics.quimp.QColor: Gets the red.
getRed(int) - Method in class com.github.celldynamics.quimp.QColor: Gets the red.
getRef() - Method in class com.github.celldynamics.quimp.plugin.engine.PluginProperties: Return reference of loaded plugin or null if plugin is not used.
getRegisterdPlugins() - Method in class com.github.celldynamics.quimp.plugin.engine.PluginFactory: Accessor to internal database of loaded plugins.
getRes() - Method in class com.github.celldynamics.quimp.plugin.generatemask.GenerateMask_: Return image generated by plugin.
getRes() - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Return resolution of the map.
getResult() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_: Retrieve result of segmentation.
getRGB(ImagePlus, ImagePlus, ImagePlus) - Static method in class com.github.celldynamics.quimp.utils.IJTools: Return RGB image created from R, G, B 8-bit images.
getRGB(ImageProcessor, ImageProcessor, ImageProcessor) - Static method in class com.github.celldynamics.quimp.utils.IJTools: Return RGB image created from R, G, B 8-bit images.
getSeedImage() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Get seed image.
getSeedSource() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: cbFilteringMethod getter.
getSeedSources() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Get seed sources defined in RandomWalkModel.SeedSource.
getSegImageFile() - Method in class com.github.celldynamics.quimp.QParams: Get name of BOA loaded image.
getSelectedFilteringMethod() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Filtering getter.
getSelectedFilteringPostMethod() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Post filtering getter.
getSelectedSeedSource() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: SeedSource getter.
getselectedShrinkMethod() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Shrink method getter.
getShallowCopy() - Method in class com.github.celldynamics.quimp.SnakePluginList: Copy method.
getShapes() - Method in class com.github.celldynamics.quimp.geom.TrackOutline: Return shallow copy of Shapes.
getShrinkMethod() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: cbShrinkMethod getter.
getShrinkMethods() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Get shrink methods supported by PropagateSeeds class in form of String[].
getSize() - Method in class com.github.celldynamics.quimp.OutlineHandler: Gets the size.
getSnake(int) - Method in class com.github.celldynamics.quimp.plugin.utils.QuimpDataConverter: Return Snake created from stored data.
getSnakeasPoints() - Method in class com.github.celldynamics.quimp.ViewUpdater: Request copy of connected snake for previewing purposes.
getSnakeasSnake() - Method in class com.github.celldynamics.quimp.ViewUpdater: Request copy of connected snake for previewing purposes.
getSnakeID() - Method in class com.github.celldynamics.quimp.Snake: Get ID of Snake.
getSnakeQP() - Method in class com.github.celldynamics.quimp.QParams: Get snQP file name.
getSnakeQP() - Method in class com.github.celldynamics.quimp.QParamsQconf: Create fake snQP name, for compatibility reasons.
getSnakesforFrame(int) - Method in class com.github.celldynamics.quimp.Nest: Get list of snakes (its IDs) that are on frame frame.
getSrAlev() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get value of alev parameter.
getSrAlpha() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get RW alpha parameter.
getSrBeta() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get RW beta parameter.
getSrExpandPower() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get expand power.
getSrGamma0() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get RW gamma 0 parameter.
getSrGamma1() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get RW gamma 1 parameter.
getSrIter() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get RW number of iterations.
getSrLocalMeanWindow() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get value of window parameter for local mean.
getSrNum() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get value of num parameter.
getSrRelerr() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get RW number of iterations.
getSrScaleCurvDistDist() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get distance.
getSrScaleEqNormalsDist() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get distance.
getSrScaleMagn() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get magnitude.
getSrScaleSigma() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get sigma.
getSrShrinkPower() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get shrink power.
getSrWindow() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get value of window parameter.
getStartFrame() - Method in class com.github.celldynamics.quimp.OutlineHandler: Gets the start frame.
getStartFrame() - Method in class com.github.celldynamics.quimp.QParams: getStartFrame.
getStartFrame() - Method in class com.github.celldynamics.quimp.QParamsQconf
getStartFrame() - Method in class com.github.celldynamics.quimp.ShapeHandler: Gets the start frame.
getStatCollection() - Method in class com.github.celldynamics.quimp.filesystem.StatsCollection: Get stats collection object wrapped by this class.
getStatH() - Method in class com.github.celldynamics.quimp.CellStatsEval: Return statistics in new format for one cell along all frames it appears in.
getStats() - Method in class com.github.celldynamics.quimp.filesystem.converter.StatFileParser: CellStat getter.
getStats() - Method in class com.github.celldynamics.quimp.filesystem.DataContainer: getStats.
getStats() - Method in class com.github.celldynamics.quimp.filesystem.QconfLoader: Query for Stats object.
getStatsQP() - Method in class com.github.celldynamics.quimp.QParams: Get stats file name.
getStatsQP() - Method in class com.github.celldynamics.quimp.QParamsQconf
getStatus() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterModel: Return status map.
getStoredOutline(int) - Method in class com.github.celldynamics.quimp.OutlineHandler: Return Outline stored for frame f.
getStoredSnake(int) - Method in class com.github.celldynamics.quimp.SnakeHandler: Return final Snake (after plugins) stored for frame f.
getStringFromUI(String) - Method in class com.github.celldynamics.quimp.plugin.utils.QWindowBuilder: Return value related to given key.
getStringValue(String) - Method in class com.github.celldynamics.quimp.plugin.ParamList: .
getSystemClassPath() - Static method in class com.github.celldynamics.quimp.plugin.engine.PluginFactory: Prints system classpath.
getT() - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Return number of outline points.
getTabbedPane() - Method in class com.github.celldynamics.quimp.omero.OmeroLoginDialog
getTableImagesDownload() - Method in class com.github.celldynamics.quimp.omero.OmeroLoginDialog
getTableImagesUpload() - Method in class com.github.celldynamics.quimp.omero.OmeroLoginDialog
getTangent() - Method in class com.github.celldynamics.quimp.PointsList: Gets the tangent.
getToolTipString(String) - Static method in class com.github.celldynamics.quimp.utils.UiTools: Get tooltip string wrapped.
getTpInfo() - Method in class com.github.celldynamics.quimp.omero.OmeroLoginDialog
getTrackCollection() - Method in class com.github.celldynamics.quimp.plugin.protanalysis.TrackMapAnalyser: getTrackCollection.
getTrackNum() - Method in class com.github.celldynamics.quimp.PointsList: Gets the track num.
getTracks(STmap[], Integer, MaximaFinder) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ActionTrackPoints: Get tracks.
getType() - Method in exception com.github.celldynamics.quimp.BoaException: Get type.
getType() - Method in class com.github.celldynamics.quimp.plugin.engine.PluginProperties: Type getter.
getValues() - Method in class com.github.celldynamics.quimp.plugin.utils.QWindowBuilder: Receives parameters related to UI elements as Map.
getVarR(double[][]) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Calculate variance of map for every row.
getVel() - Method in class com.github.celldynamics.quimp.Node: Setter to vel field.
getVer(int) - Method in class com.github.celldynamics.quimp.SnakePluginList: Return i-th plugin version.
getVersion() - Method in class com.github.celldynamics.quimp.plugin.dic.DicLidReconstruction_
getVersion() - Method in class com.github.celldynamics.quimp.plugin.engine.PluginProperties: Version getter.
getVersion() - Method in interface com.github.celldynamics.quimp.plugin.IQuimpCorePlugin: Get version of plugin.
getVersion() - Method in class com.github.celldynamics.quimp.QuimpVersion: Get Version.
getVerticalResolution() - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Compute vertical resolution tiff image generated from map.
getWidth() - Method in class com.github.celldynamics.quimp.BOAState.BOAp: Get WIDTH.
getWnd() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Get window reference.
getX() - Method in class com.github.celldynamics.quimp.plugin.utils.QuimpDataConverter: Data accessor.
getX() - Method in class com.github.celldynamics.quimp.PointsList: point getter.
getxMap() - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: getxMap.
getxmapFile() - Method in class com.github.celldynamics.quimp.QParams: Get x coord map file.
getY() - Method in class com.github.celldynamics.quimp.plugin.utils.QuimpDataConverter: Data accessor.
getY() - Method in class com.github.celldynamics.quimp.PointsList: point getter.
getyMap() - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: getyMap.
getymapFile() - Method in class com.github.celldynamics.quimp.QParams: Get y coord map file.
gLandCoord - Variable in class com.github.celldynamics.quimp.Vert: landing coord relative to head node on frame 1.
gradientPoint - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Gradient point for polar plot.
GraphicsElements - Class in com.github.celldynamics.quimp.utils.graphics: This class contains static methods for creating simple graphics elements using IJ Roi API.
GraphicsElements() - Constructor for class com.github.celldynamics.quimp.utils.graphics.GraphicsElements
green - Variable in class com.github.celldynamics.quimp.QColor: Color component.
gsonBuilder - Variable in class com.github.celldynamics.quimp.Serializer: The gson builder.
guessOtherFileNames() - Method in class com.github.celldynamics.quimp.QParams: Generate names and handles of files associated with paQP that will be created in result of analysis.

H

h - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: Euler time step, was 0.6.
handleException(Frame, String) - Method in exception com.github.celldynamics.quimp.QuimpException: Handle this exception displaying it and logging depending on QuimpException.messageSinkType.
hashCode() - Method in class com.github.celldynamics.quimp.FluoMeasurement
hashCode() - Method in class com.github.celldynamics.quimp.Node: (non-Javadoc) Compare only current Node, no neighbours.
hashCode() - Method in class com.github.celldynamics.quimp.Outline
hashCode() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.Point
hashCode() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel
hashCode() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkOptions
hashCode() - Method in class com.github.celldynamics.quimp.PointsList
hashCode() - Method in class com.github.celldynamics.quimp.QColor
hashCode() - Method in class com.github.celldynamics.quimp.QuimpVersion
hashCode() - Method in class com.github.celldynamics.quimp.Shape
hashCode() - Method in class com.github.celldynamics.quimp.Snake
hashCode() - Method in class com.github.celldynamics.quimp.Vert: (non-Javadoc)
hatFilter - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: true for HatFilter active.
HatSnakeFilter - Class in com.github.celldynamics.quimp.geom.filters: Implementation of HatFilter for removing convexes from polygon.
HatSnakeFilter() - Constructor for class com.github.celldynamics.quimp.geom.filters.HatSnakeFilter: Construct HatFilter Input array with data is virtually circularly padded.
HatSnakeFilter(int, int, double) - Constructor for class com.github.celldynamics.quimp.geom.filters.HatSnakeFilter: Constructor passing algorithm parameters.
head - Variable in class com.github.celldynamics.quimp.PointsList: Indicate if this point is head.
head - Variable in class com.github.celldynamics.quimp.Shape: first node in double linked list, always maintained, initialised in constructor.
headerEcmmOutline - Static variable in class com.github.celldynamics.quimp.filesystem.converter.FormatConverter: Order of parameters saved by FormatConverter.saveOutline(Outline, CsvWritter).
HistoryLogger - Class in com.github.celldynamics.quimp: Deprecated.
No longer in use
HistoryLogger() - Constructor for class com.github.celldynamics.quimp.HistoryLogger: Deprecated.

Construct main window.

I

id - Variable in class com.github.celldynamics.quimp.geom.SegmentedShapeRoi: The id of the shape.
IJTools - Class in com.github.celldynamics.quimp.utils: Contain IJ based procedures.
IJTools() - Constructor for class com.github.celldynamics.quimp.utils.IJTools
image - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The image.
image - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ActionTrackPoints
image - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.SeedPicker: Image used for seeding.
imageProcessor2RealMatrix(ImageProcessor) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Create RealMatrix 2D from image.
ImageProcessorPlus - Class in com.github.celldynamics.quimp.plugin.utils: Class implementing extra functionalities for ij.ImageProcessor
ImageProcessorPlus() - Constructor for class com.github.celldynamics.quimp.plugin.utils.ImageProcessorPlus: Main constructor.
imp - Variable in class com.github.celldynamics.quimp.geom.TrackOutline: Original image.
implementationDateConverter(String) - Static method in class com.github.celldynamics.quimp.utils.QuimpToolsCollection: Reformat date from jar (put there by Maven).
implode(Nest, int) - Method in class com.github.celldynamics.quimp.Constrictor: Implode nest.
implode() - Method in class com.github.celldynamics.quimp.Snake: Implode.
importStQp() - Method in class com.github.celldynamics.quimp.filesystem.converter.StatFileParser: Read all files along given path and prefix used for constructing the object and convert them to CellStat objects.
includeFirst - Variable in class com.github.celldynamics.quimp.geom.MapTracker: Decides whether include starting point in tracking.
increment - Variable in class com.github.celldynamics.quimp.plugin.qanalysis.Qp: The increment.
indexGetOutline(int) - Method in class com.github.celldynamics.quimp.OutlineHandler: Index get outline.
inFile - Variable in class com.github.celldynamics.quimp.plugin.ana.ANAp: Input file reference.
INFILE - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The infile.
initDouble2dArray(int, int) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Create 2D array of doubles.
initInteger2dArray(int, int) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Create 2D array of integers.
innerArea - Variable in class com.github.celldynamics.quimp.plugin.ana.ChannelStat: Area of inner contour - scaled.
insertInterpolatedVert(Vert) - Method in class com.github.celldynamics.quimp.Outline: Insert a vertex in-between v and v.next with interpolated values
insertNode(Node) - Method in class com.github.celldynamics.quimp.Snake: Insert default Node after Node v.
insertPoint(T, T) - Method in class com.github.celldynamics.quimp.Shape: Insert point ne after point n.
insertVert(Vert) - Method in class com.github.celldynamics.quimp.Outline: Insert default Vert after Vert v.
int2short(int[]) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Convert integer array to short.
intensity - Variable in class com.github.celldynamics.quimp.FluoMeasurement: Pixel intensity.
interFrameFilter - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: If true add extra filtering during applying PropagateSeeds.Propagators.CONTOUR shrink method.
intermediateFilter - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkOptions: Reference to filter used for filtering results between sweeps.
interpLinear(double[], double[], double[]) - Static method in class com.github.celldynamics.quimp.utils.graphics.PolarPlot: http://www.java2s.com/Code/Java/Collections-Data-Structure/LinearInterpolation.htm
interpolateCoord(double, double) - Method in class com.github.celldynamics.quimp.Outline: interpolate between co-ordinates (that run 0-1).
intsectID - Variable in class com.github.celldynamics.quimp.Vert: intsectID.
intState - Variable in class com.github.celldynamics.quimp.Vert: Internal state of the vert.
invertsBetween(Vert, Vert) - Static method in class com.github.celldynamics.quimp.Outline: invertsBetween.
IPadArray - Interface in com.github.celldynamics.quimp.plugin.utils: Basic interface for all family of filters based on moving window.
IQconfOlderConverter<T extends IQuimpSerialize> - Interface in com.github.celldynamics.quimp.filesystem.versions: This interface provides method that is run on loaded class reference when current tool version is higher than version of loaded object.
IQuimpBOAPoint2dFilter - Interface in com.github.celldynamics.quimp.plugin.snakes: General interface that defines filter run on points in euclidean space.
IQuimpBOASnakeFilter - Interface in com.github.celldynamics.quimp.plugin.snakes: General interface that defines filter run on Snakes directly.
IQuimpCorePlugin - Interface in com.github.celldynamics.quimp.plugin: General definition of plugin interface for QuimP.
IQuimpFilter - Interface in com.github.celldynamics.quimp.plugin: Interface for plugin filter used in QuimP Bar.
IQuimpNestPlugin - Interface in com.github.celldynamics.quimp.plugin: This core plugin accepts Nest as input and can modify it.
IQuimpPlugin - Interface in com.github.celldynamics.quimp.plugin: Interface for plugins used in QuimP Bar.
IQuimpPluginAttachImage - Interface in com.github.celldynamics.quimp.plugin: Allow to attach image to filter.
IQuimpPluginAttachImagePlus - Interface in com.github.celldynamics.quimp.plugin: Allow to attach image plus to filter.
IQuimpPluginAttachNest - Interface in com.github.celldynamics.quimp.plugin: Allow to attach Nest to filter.
IQuimpPluginExchangeData - Interface in com.github.celldynamics.quimp.plugin: Allow to attach upload and download configuration from plugin.
IQuimpPluginFilter - Interface in com.github.celldynamics.quimp.plugin: This interface supports plugins used in QuimP Bar.
IQuimpPluginSynchro - Interface in com.github.celldynamics.quimp.plugin: The interface that add synchronisation between plugin and QuimP.
IQuimpSerialize - Interface in com.github.celldynamics.quimp.filesystem: Interface that is required by Serializer class.
isActive(int) - Method in class com.github.celldynamics.quimp.SnakePluginList: Check if plugin is active.
isANAPresent() - Method in class com.github.celldynamics.quimp.filesystem.QconfLoader: Just decoder of DataContainer.validateDataContainer().
isBOAPresent() - Method in class com.github.celldynamics.quimp.filesystem.QconfLoader: Just decoder of DataContainer.validateDataContainer().
isEcmmHasRun() - Method in class com.github.celldynamics.quimp.QParams: Check if ECMM was run.
isECMMPresent() - Method in class com.github.celldynamics.quimp.filesystem.QconfLoader: Just decoder of DataContainer.validateDataContainer().
isEnabled() - Method in class com.github.celldynamics.quimp.plugin.qanalysis.FluoMap: Check if enabled.
isfIAdjusted() - Method in class com.github.celldynamics.quimp.BOAState.BOAp: Get fIAdjusted.
isFileLoaded() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverter: Return type of loaded file or 0 if not loaded yet.
isFileLoaded() - Method in class com.github.celldynamics.quimp.filesystem.QconfLoader: Return type of loaded file or 0 if not loaded yet.
isFrameEdited - Variable in class com.github.celldynamics.quimp.BOAState: Store information whether for current frame button Edit was used.
isFrozen() - Method in class com.github.celldynamics.quimp.PointsList: Getter to frozen field.
isFrozen() - Method in class com.github.celldynamics.quimp.Snake: Check if all nodes are frozen.
isHead() - Method in class com.github.celldynamics.quimp.PointsList: Checks if is head.
isInitialPointIncluded() - Method in class com.github.celldynamics.quimp.plugin.protanalysis.TrackCollection: Check if initial point is included in tracking.
isIntPoint() - Method in class com.github.celldynamics.quimp.Vert: isIntPoint.
isLive() - Method in class com.github.celldynamics.quimp.SnakeHandler: Checks if is live snake is live.
isOpened() - Method in class com.github.celldynamics.quimp.HistoryLogger: Deprecated.

Check if window is opened.
isOutlineAt(int) - Method in class com.github.celldynamics.quimp.OutlineHandler: Checks if is outline at.
isPointInside(List<? extends Tuple2d>, Tuple2d) - Method in class com.github.celldynamics.quimp.geom.BasicPolygons: Test whether Ptest is inside polygon P
isQPresent() - Method in class com.github.celldynamics.quimp.filesystem.QconfLoader: Just decoder of DataContainer.validateDataContainer().
isRefListEmpty() - Method in class com.github.celldynamics.quimp.SnakePluginList: Check if list of references contains all null elements.
isScaleAdjusted() - Method in class com.github.celldynamics.quimp.BOAState.BOAp: Get scaleAdjusted.
isSnakeHandlerFrozen() - Method in class com.github.celldynamics.quimp.SnakeHandler: Return true if this handler is frozen.
isStatsPresent() - Method in class com.github.celldynamics.quimp.filesystem.QconfLoader: Just decoder of DataContainer.validateDataContainer().
isVacant() - Method in class com.github.celldynamics.quimp.Nest: Check if Nest is empty.
isWindowVisible() - Method in class com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentation_: Return true if window is visible.
isWindowVisible() - Method in class com.github.celldynamics.quimp.plugin.utils.QWindowBuilder: Check if window is visible.
itemStateChanged(ItemEvent) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set enable/disabled controls depending on hatsnake checkbox.
iter - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkOptions: Maximum number of Euler iterations.
iterateMorphological(ImageProcessor, BinaryFilters.MorphoOperations, double) - Static method in class com.github.celldynamics.quimp.plugin.randomwalk.BinaryFilters: Run morphological operation on input image.
iterator() - Method in class com.github.celldynamics.quimp.plugin.protanalysis.TrackCollection: Get iterator over pairs of tracks (related to one starting point).
iterator() - Method in class com.github.celldynamics.quimp.Shape
iteratorTrack() - Method in class com.github.celldynamics.quimp.plugin.protanalysis.TrackCollection: Get iterator over all tracks in collection.
its - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: total euler iterations.

K

k - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The k.
KEY - Static variable in class com.github.celldynamics.quimp.plugin.AbstractPluginOptions: Default key used to denote options string in IJ macro recorder.
kill(SnakeHandler) - Method in class com.github.celldynamics.quimp.Nest: Remove SnakeHandler from Nest.
kill() - Method in class com.github.celldynamics.quimp.SnakeHandler: Kill.
kscale - Variable in class com.github.celldynamics.quimp.utils.graphics.PolarPlot: Distance of polar plot from 0.

L

labels - Variable in class com.github.celldynamics.quimp.utils.graphics.PolarPlot: Whether to plot rho and theta labels.
LEFT - Static variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentation: Direction of circshift coded as in Matlab.
length() - Method in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qline: Length.
length() - Method in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qtext: Length.
lengthP2P(ExtendedVector2d, ExtendedVector2d) - Static method in class com.github.celldynamics.quimp.geom.ExtendedVector2d: Get length of the vector between points.
letterSpacing - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qtext: If letters overlap, set it to half of font size.
LidReconstructor - Class in com.github.celldynamics.quimp.plugin.dic: Implementation of Line Integration and Deconvolution algorithm proposed by Kam.
LidReconstructor(ImagePlus, double, double) - Constructor for class com.github.celldynamics.quimp.plugin.dic.LidReconstructor: Default constructor that accepts ImagePlus.
LidReconstructor(ImageProcessor, double, double) - Constructor for class com.github.celldynamics.quimp.plugin.dic.LidReconstructor: Default constructor that accepts ImageProcessor.
LidReconstructor(ImageProcessor, double, double, String, int) - Constructor for class com.github.celldynamics.quimp.plugin.dic.LidReconstructor: Default constructor.
lightColor() - Static method in class com.github.celldynamics.quimp.QColor: Get a random light color.
LINE_WRAP - Static variable in class com.github.celldynamics.quimp.QuimP: Desired length of line in message box.
lineCharges - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The line charges.
lineIntersectionOLD(ExtendedVector2d, ExtendedVector2d, ExtendedVector2d, ExtendedVector2d) - Static method in class com.github.celldynamics.quimp.geom.ExtendedVector2d: Deprecated.
Actually not used in this version of QuimP
lineIntersectionOLD2(ExtendedVector2d, ExtendedVector2d, ExtendedVector2d, ExtendedVector2d) - Static method in class com.github.celldynamics.quimp.geom.ExtendedVector2d: Deprecated.
Actually not used in this version of QuimP
LinkedStringMap<V> - Class in com.github.celldynamics.quimp.plugin.utils: Extension of LinkedHashMap that assumes that Key is String and it is case insensitive.
LinkedStringMap() - Constructor for class com.github.celldynamics.quimp.plugin.utils.LinkedStringMap: Default constructor.
LinkedStringMap(int) - Constructor for class com.github.celldynamics.quimp.plugin.utils.LinkedStringMap: LinkedStringMap.
linspace(double, double, int) - Static method in class com.github.celldynamics.quimp.geom.ExtendedVector2d: Generate linearly distributed doubles between a;b including a and b.
LIST_OK - Static variable in class com.github.celldynamics.quimp.Shape: List is correct: has head, looped.
listDatasets() - Method in class com.github.celldynamics.quimp.omero.OmeroBrowser: List datasets.
ListMap<T> - Class in com.github.celldynamics.quimp.plugin.randomwalk: Store objects (maps) under specified key.
ListMap() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.ListMap: Default constructor.
ListMap(int) - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.ListMap: Constructor with initial capacity.
listProjects() - Method in class com.github.celldynamics.quimp.omero.OmeroBrowser: List projects.
load(String) - Method in class com.github.celldynamics.quimp.Serializer: Load GSon file.
load(File) - Method in class com.github.celldynamics.quimp.Serializer: Load wrapped object from JSON file.
loadFile(String) - Method in class com.github.celldynamics.quimp.plugin.AbstractPluginQconf: Load specified configuration file and execute plugin depending on file type.
loadFile(String) - Method in class com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping
loadFile(String) - Method in class com.github.celldynamics.quimp.plugin.qanalysis.Q_Analysis
loadParams(QParams) - Method in class com.github.celldynamics.quimp.BOAState: Build internal boa state from QParams object.
LoadQconfController() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_.LoadQconfController
localMeanMaskSize - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkOptions: Size of mask for local mean algorithm (odd).
LogbackFilter - Class in com.github.celldynamics.quimp: Filter that filters out packages that not belong to QuimP.
LogbackFilter() - Constructor for class com.github.celldynamics.quimp.LogbackFilter: Main constructor.
logger - Static variable in class com.github.celldynamics.quimp.filesystem.converter.FormatConverter
logger - Variable in class com.github.celldynamics.quimp.plugin.AbstractOptionsParser: The Constant logger.
LOGGER - Static variable in class com.github.celldynamics.quimp.plugin.AbstractPluginOptions: The Constant logger.
logger - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisAbstractAction
LOGGER - Static variable in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: The Constant LOGGER.
logger - Variable in exception com.github.celldynamics.quimp.QuimpException: The LOGGER.
loosen(Nest, int) - Method in class com.github.celldynamics.quimp.Constrictor: Expand all snakes while preventing overlaps adequately to blowup parameter.

M

main(String[]) - Static method in class com.github.celldynamics.quimp.omero.OmeroBrowser: Dummy tests.
makeAntiClockwise() - Method in class com.github.celldynamics.quimp.Shape: Make Shape anti-clockwise.
makeNavigationButton(String, String, String, String) - Method in class com.github.celldynamics.quimp.plugin.bar.QuimP_Bar: Make navigation button.
makeUnit() - Method in class com.github.celldynamics.quimp.geom.ExtendedVector2d: Make versor from vector.
map2ColorImagePlus(String, String, double[][], double, double) - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Convert raw map to colorscale.
map2ImagePlus(String, ImageProcessor) - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Convert ImageProcessor created from Map to ImagePlus.
MAP_MISSING - Static variable in class com.github.celldynamics.quimp.filesystem.QconfLoader: Stand for missing file in experiment.
MapCoordConverter - Class in com.github.celldynamics.quimp.geom: Convert between map coordinates (frame;outline pos) and image coordinates (x;y).
MapCoordConverter() - Constructor for class com.github.celldynamics.quimp.geom.MapCoordConverter
mapRes - Variable in class com.github.celldynamics.quimp.plugin.qanalysis.Qp: The map resolution.
MapTracker - Class in com.github.celldynamics.quimp.geom: Compute forward and backward tracking maps from origin and coordinates maps.
MapTracker(double[][], double[][]) - Constructor for class com.github.celldynamics.quimp.geom.MapTracker: Construct tracking maps.
markerRes - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: resolution of outlines.
maskFileName - Variable in class com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentationOptions: Keep file name of mask if loaded by Load button.
maskLimit - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkOptions: If true, RW mask will be cut by AC mask.
MAX_NODES - Static variable in class com.github.celldynamics.quimp.Shape: Max number of nodes allowed in Shape.
maxCellSize - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The max cell size.
maxCoor - Variable in class com.github.celldynamics.quimp.OutlineHandler: The max coor.
MAXIMA_COLOR - Static variable in class com.github.celldynamics.quimp.plugin.protanalysis.TrackVisualisation: Color for maxima points.
MaximaFinder - Class in com.github.celldynamics.quimp.plugin.protanalysis: Calculate maxima for image.
MaximaFinder(ImageProcessor) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.MaximaFinder: Construct MaximaFinder object.
MAXITER - Static variable in class com.github.celldynamics.quimp.plugin.AbstractPluginOptions: Maximal length of parameter string.
maxIter - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The max iter.
maxLength - Variable in class com.github.celldynamics.quimp.OutlineHandler: longest outline in outlines.
maxVertF - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: max force allowed on a marker (0.06).
meanCorFluo - Variable in class com.github.celldynamics.quimp.plugin.ana.ChannelStat: totalCorFluo / (outer contour area (not scaled) - inner contour area (not scaled)).
meanFluor - Variable in class com.github.celldynamics.quimp.plugin.ana.ChannelStat: Mean intensity within outer contour.
meanInnerFluor - Variable in class com.github.celldynamics.quimp.plugin.ana.ChannelStat: Mean intensity of inner contour.
MedianMorpho() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.BinaryFilters.MedianMorpho
messageSinkType - Variable in exception com.github.celldynamics.quimp.QuimpException: Message sinks - where they will appear.
migLimits - Variable in class com.github.celldynamics.quimp.OutlineHandler: The mig limits.
migPower - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The mig power.
migQ - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The mig Q.
minArrayIndex(double[]) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Find index of minimal element.
minArrayIndexElement(double[]) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Find index of minimal element and the element itself.
minCoor - Variable in class com.github.celldynamics.quimp.OutlineHandler: The min coor.
minListIndex(List<T>) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Find index of minimal element in Collection.
mobileQ - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The mobile Q.
model - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisAbstractAction
MODIFY_INPUT - Static variable in interface com.github.celldynamics.quimp.plugin.IQuimpCorePlugin: Plugin modify input data in place.
Morphological() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds.Morphological: Default constructor without storing seed history.
Morphological(boolean, AutoThresholder.Method) - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds.Morphological: Allow to store seed history that can be later presented in form of composite image.
MOTILITY - Static variable in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Motility map code.
motimageFileExt - Static variable in class com.github.celldynamics.quimp.filesystem.FileExtensions: Extension for file containing motility image map.
motmapFileExt - Static variable in class com.github.celldynamics.quimp.filesystem.FileExtensions: Extension for file containing motility map.
motvecimageFileExt - Static variable in class com.github.celldynamics.quimp.filesystem.FileExtensions: Extension for file containing motility vector plot.
mouseSensitivity - Static variable in class com.github.celldynamics.quimp.QuimP: Maximum distance from snake centroid that triggers action on mouse click.
multiply(double) - Method in class com.github.celldynamics.quimp.geom.ExtendedVector2d: Multiply this vector.

N

nest - Variable in class com.github.celldynamics.quimp.BOAState: Reference to Nest, which is serializable as well.
Nest - Class in com.github.celldynamics.quimp: Represent collection of SnakeHandlers.
Nest() - Constructor for class com.github.celldynamics.quimp.Nest: Default constructor.
NEW_QUIMP - Static variable in class com.github.celldynamics.quimp.QParams: The Constant NEW_QUIMP.
newConfigFileExt - Static variable in class com.github.celldynamics.quimp.filesystem.FileExtensions: Extension for new file format.
newFileFormat - Static variable in class com.github.celldynamics.quimp.QuimP: This field is used for sharing information between bar and other plugins.
next - Variable in class com.github.celldynamics.quimp.PointsList: Next point in list, null if no other point.
nextTrackNumber - Variable in class com.github.celldynamics.quimp.Shape: Next node ID's.
NO_HEAD - Static variable in class com.github.celldynamics.quimp.Shape: No head found among first 10000.
Node - Class in com.github.celldynamics.quimp: Represents a node in the snake - its basic component In fact this class stands for bidirectional list containing Nodes.
Node() - Constructor for class com.github.celldynamics.quimp.Node: Default constructor.
Node(int) - Constructor for class com.github.celldynamics.quimp.Node: Create Node with given id.
Node(Node) - Constructor for class com.github.celldynamics.quimp.Node: Copy constructor.
Node(double, double, int) - Constructor for class com.github.celldynamics.quimp.Node: Create Node from coordinates.
noiseTolerance - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Sensitivity of maximum detection.
NONE - Static variable in class com.github.celldynamics.quimp.BOA_: Reserved word that stands for plugin that is not selected.
normal - Variable in class com.github.celldynamics.quimp.PointsList: Normal vector.
normalise - Variable in class com.github.celldynamics.quimp.plugin.ana.AnaOptions: The normalise.
NOT_COUNTED - Static variable in class com.github.celldynamics.quimp.geom.SegmentedShapeRoi: The Constant NOT_COUNTED.
num - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: num parameter.
NUM_SNAKE_PLUGINS - Static variable in class com.github.celldynamics.quimp.BOA_: Number of Snake plugins available.
numINTS - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The num INTS.
numofIntCircles - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.QPolarAxes: Number of circles in polar plot.

O

obj - Variable in class com.github.celldynamics.quimp.Serializer: Wrapped object being serialized.
object2double(Number[]) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Convert 1d double array to Double.
ODEsolver - Class in com.github.celldynamics.quimp.plugin.ecmm: ODE Solver.
ODEsolver() - Constructor for class com.github.celldynamics.quimp.plugin.ecmm.ODEsolver: Default constructor.
oHs - Variable in class com.github.celldynamics.quimp.filesystem.OutlinesCollection: Contain OutlineHandler objects.
OLD_QUIMP - Static variable in class com.github.celldynamics.quimp.QParams: The Constant OLD_QUIMP.
OmeroBrowser - Class in com.github.celldynamics.quimp.omero: Provide access to Omero.
OmeroBrowser(String, String, String, int) - Constructor for class com.github.celldynamics.quimp.omero.OmeroBrowser: Initialise browser.
OmeroClient_ - Class in com.github.celldynamics.quimp.omero: QuimP module for Omero integration.
OmeroClient_() - Constructor for class com.github.celldynamics.quimp.omero.OmeroClient_: Create all instances of UI and API.
OmeroClient_Runner - Class in <Unnamed>: Compatibility layer for ImageJ.
OmeroClient_Runner() - Constructor for class OmeroClient_Runner
OmeroLoginDialog - Class in com.github.celldynamics.quimp.omero: Dialog by WindowsBuilder.
OmeroLoginDialog() - Constructor for class com.github.celldynamics.quimp.omero.OmeroLoginDialog: Default constructor.
OmeroLoginDialog(OmeroClient_) - Constructor for class com.github.celldynamics.quimp.omero.OmeroLoginDialog: Create the dialog and update fields.
oneFrameRes - Variable in class com.github.celldynamics.quimp.plugin.ana.ANAp: Frame resolution.
openDataset(DatasetData) - Method in class com.github.celldynamics.quimp.omero.OmeroBrowser: Open dataset.
openHistory() - Method in class com.github.celldynamics.quimp.HistoryLogger: Deprecated.

Make window visible.
options - Variable in class com.github.celldynamics.quimp.plugin.AbstractOptionsParser
options - Variable in class com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentationOptions: Plugin options in format of QWindowBuilder.
options - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisAbstractAction
ORIGIN - Static variable in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Origin map code.
originalImage - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.TrackVisualisation: The original image.
originmapFileExt - Static variable in class com.github.celldynamics.quimp.filesystem.FileExtensions: Extension for file containing origins map.
outFile - Variable in class com.github.celldynamics.quimp.plugin.ana.ANAp: Output snQP file reference (the same as ANAp.inFile.
OUTFILE - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The outfile.
outFile - Variable in class com.github.celldynamics.quimp.plugin.qanalysis.Qp: Full path to output file.
Outline - Class in com.github.celldynamics.quimp: Represent Outline object used as Snake representation after ECMM mapping.
Outline() - Constructor for class com.github.celldynamics.quimp.Outline: Default constructor.
Outline(Vert, int) - Constructor for class com.github.celldynamics.quimp.Outline: Create a Outline from existing linked list
Outline(Vert) - Constructor for class com.github.celldynamics.quimp.Outline: Blank outline.
Outline(Outline) - Constructor for class com.github.celldynamics.quimp.Outline: Copy constructor.
Outline(Snake) - Constructor for class com.github.celldynamics.quimp.Outline: Conversion constructor.
Outline(Roi) - Constructor for class com.github.celldynamics.quimp.Outline: Create an outline from an Roi.
Outline(List<? extends Tuple2d>) - Constructor for class com.github.celldynamics.quimp.Outline: Construct Outline object from list of nodes.
Outline(double[], double[]) - Constructor for class com.github.celldynamics.quimp.Outline: Construct Outline object from X and Y arrays.
OutlineHandler - Class in com.github.celldynamics.quimp: Collection of outlines for subsequent frames (f1 and f2) for one cell.
OutlineHandler(QParams) - Constructor for class com.github.celldynamics.quimp.OutlineHandler: Instantiates a new outline handler.
OutlineHandler(OutlineHandler) - Constructor for class com.github.celldynamics.quimp.OutlineHandler: Copy constructor.
OutlineHandler(SnakeHandler) - Constructor for class com.github.celldynamics.quimp.OutlineHandler: Conversion constructor.
OutlineHandler(int, int) - Constructor for class com.github.celldynamics.quimp.OutlineHandler: Instantiates a new outline handler.
OutlineHandler() - Constructor for class com.github.celldynamics.quimp.OutlineHandler: Default constructor.
outlinePlot - Variable in class com.github.celldynamics.quimp.plugin.qanalysis.Qp: The outline plot.
outlinePlots - Variable in class com.github.celldynamics.quimp.plugin.qanalysis.Qp: The outline plots.
OutlineProcessor<T extends Shape<?>> - Class in com.github.celldynamics.quimp.geom.filters: Support algorithms for processing outlines using their specific properties.
OutlineProcessor(T) - Constructor for class com.github.celldynamics.quimp.geom.filters.OutlineProcessor: Assign outline to be processed to object.
outlines - Variable in class com.github.celldynamics.quimp.geom.TrackOutline: List of found outlines as ROIs.
OutlinesCollection - Class in com.github.celldynamics.quimp.filesystem: Represent collection of OutlineHandlers for cells.
OutlinesCollection(int) - Constructor for class com.github.celldynamics.quimp.filesystem.OutlinesCollection: Instantiates a new outlines collection.
OutlinesCollection() - Constructor for class com.github.celldynamics.quimp.filesystem.OutlinesCollection: Instantiates a new outlines collection.
overlay - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.TrackVisualisation: The overlay.

P

PAQP_INVALID - Static variable in class com.github.celldynamics.quimp.filesystem.QconfLoader: Stand for bad paQP experiment that has some files missing.
PAQP_VALID - Static variable in class com.github.celldynamics.quimp.filesystem.QconfLoader: Stand for good paQP experiment that has all files.
paramFile - Variable in class com.github.celldynamics.quimp.plugin.AbstractPluginOptions: Name and path of QCONF file.
paramFormat - Variable in class com.github.celldynamics.quimp.QParams: Indicates format of data file.
ParamList - Class in com.github.celldynamics.quimp.plugin: List of parameters in [key,value] HashList, where both key and value are java.lang.String and key is case insensitive.
ParamList(ParamList) - Constructor for class com.github.celldynamics.quimp.plugin.ParamList: Copy constructor.
ParamList() - Constructor for class com.github.celldynamics.quimp.plugin.ParamList: Default constructor.
parseArgumentString(String) - Method in class com.github.celldynamics.quimp.plugin.AbstractOptionsParser: Analyse and parse parameter string passed from IJ, macro or API.
parseArgumentString(String) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.Prot_Analysis
percCortexFluo - Variable in class com.github.celldynamics.quimp.plugin.ana.ChannelStat: totalCorFluo / totalFluor * 100.
perimiter - Variable in class com.github.celldynamics.quimp.FrameStatistics: Perimeter of outline.
persistance - Variable in class com.github.celldynamics.quimp.FrameStatistics: Persistence of outline.
persistanceToSource - Variable in class com.github.celldynamics.quimp.FrameStatistics: Deprecated.
Not used
persistent - Variable in exception com.github.celldynamics.quimp.QuimpException: If true sink type will not be changed in QuimpException.setMessageSinkType(MessageSinkTypes...) and QuimpException.setMessageSinkType(Set).
plot - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping: The plot.
plot - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The plot.
PLOT_DYNAMIC - Static variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Vale for dynamic plot.
PLOT_STATIC - Static variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Vale for static plot.
plotArea - Variable in class com.github.celldynamics.quimp.utils.graphics.PolarPlot: Size and position of left upper corner of plot area.
plotArrow(Vector2d, Point2d, float, float) - Static method in class com.github.celldynamics.quimp.utils.graphics.GraphicsElements: Create an arrow.
plotCentroidParamVsFrame(String, CellStats, String) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ActionPlot2d: Plot geometric feature versus frame number for specified cell.
plotCircle(double, double, Color, double) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.TrackVisualisation: Plot filled circle on overlay.
plotFluoParamVsFrame(String, CellStats, int) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ActionPlot2d: Plot fluorescence feature versus frame number for specified cell.
plotGeomParamVsFrame(String, CellStats) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ActionPlot2d: Plot geometric feature versus frame number for specified cell.
plotOnRoi(ImageProcessor, List<Point2d>, Color) - Static method in class com.github.celldynamics.quimp.utils.test.RoiSaver: Plot ROI on image.
plotOutlines - Variable in class com.github.celldynamics.quimp.plugin.ana.AnaOptions: UI setting.
plotStaticDynamic - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Plot dynamic or static plots.
plotTrack(String, int) - Method in class com.github.celldynamics.quimp.utils.graphics.svg.SVGplotter: Plot track.
plotTrackAnim() - Method in class com.github.celldynamics.quimp.utils.graphics.svg.SVGplotter: Deprecated.
plotTrackER(String) - Method in class com.github.celldynamics.quimp.utils.graphics.svg.SVGplotter: Plot track ER.
PLUGIN_DIR - Static variable in class com.github.celldynamics.quimp.QuimP: This field keeps localisation of -quimp plugins.
PluginFactory - Class in com.github.celldynamics.quimp.plugin.engine: Plugin jar loader.
PluginFactory(Path) - Constructor for class com.github.celldynamics.quimp.plugin.engine.PluginFactory: Build object connected to plugin directory.
PluginFactoryFactory - Class in com.github.celldynamics.quimp: This class create instance of PluginFactory.
PluginFactoryFactory() - Constructor for class com.github.celldynamics.quimp.PluginFactoryFactory: Main constructor.
pluginFileExt - Static variable in class com.github.celldynamics.quimp.filesystem.FileExtensions: Extension for file produced by BOA containing plugin configuration.
pluginPanel - Variable in class com.github.celldynamics.quimp.plugin.utils.QWindowBuilder: The plugin panel.
PluginProperties - Class in com.github.celldynamics.quimp.plugin.engine: Store basic plugin properties read from jar file and jar instance.
PluginProperties(File, String, int, String) - Constructor for class com.github.celldynamics.quimp.plugin.engine.PluginProperties: Construct plugin properties object.
pluginWnd - Variable in class com.github.celldynamics.quimp.plugin.utils.QWindowBuilder: The plugin wnd.
Point - Class in com.github.celldynamics.quimp.plugin.randomwalk: Basic class for storing point in Cartesian system.
Point(int, int) - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.Point: Declare point.
point - Variable in class com.github.celldynamics.quimp.PointsList: x,y co-ordinates of the point.
point2i2Polygon(List<Point>) - Static method in class com.github.celldynamics.quimp.plugin.protanalysis.TrackMapAnalyser: Convert list of Points to list of Polygons.
pointColor - Static variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Color of selected point on the outline when hoover the mouse.
PointListProcessor - Class in com.github.celldynamics.quimp.geom.filters: Perform filtering on basic list of coordinates.
PointListProcessor(List<? extends Tuple2d>) - Constructor for class com.github.celldynamics.quimp.geom.filters.PointListProcessor: Initialize object with list of points.
PointListProcessor(Collection<? extends Point2D>) - Constructor for class com.github.celldynamics.quimp.geom.filters.PointListProcessor: Initialize object with list of points.
POINTS - Variable in class com.github.celldynamics.quimp.Shape: number of points.
pointSize - Static variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Size of the point when hoover.
PointsList<T extends PointsList<T>> - Class in com.github.celldynamics.quimp: Represents node of bidirectional list of points in Cartesian coordinates.
PointsList() - Constructor for class com.github.celldynamics.quimp.PointsList: Default constructor, assumes that first point is created on list with ID = 1.
PointsList(int) - Constructor for class com.github.celldynamics.quimp.PointsList: Create point with given ID.
PointsList(PointsList<?>) - Constructor for class com.github.celldynamics.quimp.PointsList: Copy constructor.
PointsList(double, double, int) - Constructor for class com.github.celldynamics.quimp.PointsList: Creates point with given ID and coordinates.
pointToSegment(ExtendedVector2d, ExtendedVector2d, ExtendedVector2d) - Static method in class com.github.celldynamics.quimp.geom.ExtendedVector2d: Calculate the closest point on a segment to point P.
PolarPlot - Class in com.github.celldynamics.quimp.utils.graphics: Generate polar plots of motility speed along cell perimeter.
PolarPlot(STmap, Point2d) - Constructor for class com.github.celldynamics.quimp.utils.graphics.PolarPlot: Create PolarPlot object with default plot size.
polarPlotSuffix - Static variable in class com.github.celldynamics.quimp.filesystem.FileExtensions: Polar plot suffix given by ProtAnalyis.
polygon2Point2i(List<Polygon>) - Static method in class com.github.celldynamics.quimp.plugin.protanalysis.TrackMapAnalyser: Convert list of Polygons to list of Points.
polygonCenterOfMass(List<? extends Tuple2d>) - Method in class com.github.celldynamics.quimp.geom.BasicPolygons: Get center of mass of polygon.
pos - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qtext: Position of text.
position - Variable in class com.github.celldynamics.quimp.PointsList: Normalized position on list.
power(double) - Method in class com.github.celldynamics.quimp.geom.ExtendedVector2d: Power this vector.
prepare() - Method in class com.github.celldynamics.quimp.geom.TrackOutline: Filter input image to remove single pixels.
prepareMessage(Exception, String) - Static method in exception com.github.celldynamics.quimp.QuimpException: Prepare formatted message to show.
prev - Variable in class com.github.celldynamics.quimp.PointsList: Previous point in list, null if no other point.
print() - Method in class com.github.celldynamics.quimp.Outline: Old toString.
print() - Method in class com.github.celldynamics.quimp.QColor: Prints the.
print(double[]) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Prints the.
print(double[][]) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Prints the.
print(String) - Method in class com.github.celldynamics.quimp.Vert: Deprecated.
This is old part of code
printSnake() - Method in class com.github.celldynamics.quimp.Snake: Prints the snake.
ProbabilityMaps - Class in com.github.celldynamics.quimp.plugin.randomwalk: Store probability maps computed for foreground and background objects.
ProbabilityMaps() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.ProbabilityMaps: Default constructor.
propagateSeed(ImageProcessor, ImageProcessor, double, double) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds.Contour: Generate seeds for next frame using provided mask.
propagateSeed(ImageProcessor, ImageProcessor, double, double) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds.Dummy
propagateSeed(ImageProcessor, ImageProcessor, double, double) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds.Morphological: Generate new seeds using segmented image.
propagateSeed(ImageProcessor, ImageProcessor, double, double) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds: Propagate seed.
PropagateSeeds - Class in com.github.celldynamics.quimp.plugin.randomwalk: Generate new seeds for n+1 frame in stack using previous results of segmentation.
PropagateSeeds() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds: Default constructor.
PropagateSeeds(boolean, AutoThresholder.Method) - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds: Allow to store seed history that can be later presented in form of composite image.
PropagateSeeds.Contour - Class in com.github.celldynamics.quimp.plugin.randomwalk: Contain methods for propagating seeds to the next frame using contour shrinking operations.
PropagateSeeds.Dummy - Class in com.github.celldynamics.quimp.plugin.randomwalk: Empty propagator.
PropagateSeeds.Morphological - Class in com.github.celldynamics.quimp.plugin.randomwalk: Contain methods for propagating seeds to next frame using morphological operations.
PropagateSeeds.Propagators - Enum in com.github.celldynamics.quimp.plugin.randomwalk: Seed propagators available in this class.
PropertyReader - Class in com.github.celldynamics.quimp: Read properties from resources.
PropertyReader() - Constructor for class com.github.celldynamics.quimp.PropertyReader: Default constructor.
Prot_Analysis - Class in com.github.celldynamics.quimp.plugin.protanalysis: Main class for Protrusion Analysis module.
Prot_Analysis() - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.Prot_Analysis: Default constructor.
Prot_Analysis(String) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.Prot_Analysis: Constructor that allows to provide own configuration parameters.
Prot_AnalysisRunner - Class in <Unnamed>: Compatibility layer for ImageJ.
Prot_AnalysisRunner() - Constructor for class Prot_AnalysisRunner
ProtAnalysisAbstractAction - Class in com.github.celldynamics.quimp.plugin.protanalysis: Abstract actions for Prot_Analysis UI.
ProtAnalysisAbstractAction(ProtAnalysisUi) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisAbstractAction: Constructor for calling actions without AbstractAction (as Listener but not Action).
ProtAnalysisAbstractAction(String, String, ProtAnalysisUi) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisAbstractAction: Default action.
ProtAnalysisOptions - Class in com.github.celldynamics.quimp.plugin.protanalysis: Hold all configuration for Protrusion Analysis Module.
ProtAnalysisOptions() - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Instantiates a new prot analysis config.
ProtAnalysisOptions.GradientType - Enum in com.github.celldynamics.quimp.plugin.protanalysis: Types of gradient points.
ProtAnalysisOptions.OutlinePlotTypes - Enum in com.github.celldynamics.quimp.plugin.protanalysis: Plot types supported by TrackVisualisation.Stack.addOutlinesToImage(STmap, ProtAnalysisOptions).
PROTRUSIONS - Static variable in class com.github.celldynamics.quimp.geom.filters.HatSnakeFilter: Algorithm will look for protrusions.
ProtStat - Class in com.github.celldynamics.quimp.plugin.protanalysis: Compute statistics for one cell.
ProtStat(MaximaFinder, TrackCollection, CellStats, STmap) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.ProtStat: Construct the object using various data containers.
protStatistics - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtStat: Hold protrusion statistics.
protStatSuffix - Static variable in class com.github.celldynamics.quimp.filesystem.FileExtensions: Protrusion statistics file suffix given by ProtAnalyis.
proximity(ExtendedVector2d, Sector) - Static method in class com.github.celldynamics.quimp.plugin.ecmm.ODEsolver: Proximity.
publishMacroString(String) - Method in class com.github.celldynamics.quimp.plugin.AbstractOptionsParser: Helper, show macro parameters string if recorder is active.
put(RandomWalkSegmentation.SeedTypes, T) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.ListMap: Store specified map in this structure.
put(String, V) - Method in class com.github.celldynamics.quimp.plugin.utils.LinkedStringMap
putAll(Map<? extends String, ? extends V>) - Method in class com.github.celldynamics.quimp.plugin.utils.LinkedStringMap
putIfAbsent(String, V) - Method in class com.github.celldynamics.quimp.plugin.utils.LinkedStringMap

Q

Q_Analysis - Class in com.github.celldynamics.quimp.plugin.qanalysis: Run Q analysis for ECMM data.
Q_Analysis() - Constructor for class com.github.celldynamics.quimp.plugin.qanalysis.Q_Analysis: Main constructor and runner - class entry point.
Q_Analysis(File) - Constructor for class com.github.celldynamics.quimp.plugin.qanalysis.Q_Analysis: Parameterised constructor for tests.
Q_AnalysisRunner - Class in <Unnamed>: Compatibility layer for ImageJ.
Q_AnalysisRunner() - Constructor for class Q_AnalysisRunner
Q_Explorer - Class in com.github.celldynamics.quimp
Q_Explorer() - Constructor for class com.github.celldynamics.quimp.Q_Explorer
Q_RUN - Static variable in class com.github.celldynamics.quimp.filesystem.DataContainer: Indicate that Q module is not null (it has been run already on those data).
Qcircle(double, double, double) - Constructor for class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qcircle: Instantiates a new circle.
QColor - Class in com.github.celldynamics.quimp: Just a class for colors, that does not use stupid floats represented as RGB in the range 0->1.
QColor(QColor) - Constructor for class com.github.celldynamics.quimp.QColor: Copy constructor.
QColor(double, double, double) - Constructor for class com.github.celldynamics.quimp.QColor: Instantiates a new q color.
QCONF_INVALID - Static variable in class com.github.celldynamics.quimp.filesystem.QconfLoader: Stand for bad QCONF file that can not be loaded.
QconfLoader - Class in com.github.celldynamics.quimp.filesystem: Load QCONF or paQP file and initiate proper instance of QParams class.
QconfLoader() - Constructor for class com.github.celldynamics.quimp.filesystem.QconfLoader: Default constructor.
QconfLoader(File, String) - Constructor for class com.github.celldynamics.quimp.filesystem.QconfLoader: Parametrised constructor.
QconfLoader(File) - Constructor for class com.github.celldynamics.quimp.filesystem.QconfLoader: Parameterised constructor.
qconfLoader - Variable in class com.github.celldynamics.quimp.plugin.AbstractPluginQconf: Loaded configuration file.
QconfShowSeedImageController() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_.QconfShowSeedImageController
Qline(double, double, double, double) - Constructor for class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qline: Instantiates a new qline.
Qp - Class in com.github.celldynamics.quimp.plugin.qanalysis: Configuration class for Q_Analysis.
Qp() - Constructor for class com.github.celldynamics.quimp.plugin.qanalysis.Qp: Instantiates a new qp.
Qp(File) - Constructor for class com.github.celldynamics.quimp.plugin.qanalysis.Qp: Allow to add file name to options.
QParams - Class in com.github.celldynamics.quimp: Container class for parameters defining the whole process of analysis in QuimP.
QParams() - Constructor for class com.github.celldynamics.quimp.QParams: Instantiates a new q params.
QParams(File) - Constructor for class com.github.celldynamics.quimp.QParams: Read basic information from paQP file such as its name and path.
QParamsQconf - Class in com.github.celldynamics.quimp: This class override most of methods from super class QParams.
QParamsQconf() - Constructor for class com.github.celldynamics.quimp.QParamsQconf: Instantiates a new q params qconf.
QParamsQconf(File) - Constructor for class com.github.celldynamics.quimp.QParamsQconf: Set default values for superclass, also prefix and path for files.
QPolarAxes(Rectangle) - Constructor for class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.QPolarAxes: Create polar axes.
QScaleBar(ExtendedVector2d, String, int, double) - Constructor for class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.QScaleBar: Constructor.
qState - Static variable in class com.github.celldynamics.quimp.BOA_: Configuration object, available from all modules.
QState - Variable in class com.github.celldynamics.quimp.filesystem.DataContainer: Store maps generated by Q Analysis plugin for every OutlineHandler from ECMMState.
Qtext(String, double, String, ExtendedVector2d) - Constructor for class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qtext: Instantiates a new qtext.
QuimP - Class in com.github.celldynamics.quimp: Static configuration definitions.
QuimP() - Constructor for class com.github.celldynamics.quimp.QuimP
QUIMP_11 - Static variable in class com.github.celldynamics.quimp.QParams: The Constant QUIMP_11.
QuimP_Bar - Class in com.github.celldynamics.quimp.plugin.bar: Create QuimP bar with icons to QuimP plugins.
QuimP_Bar() - Constructor for class com.github.celldynamics.quimp.plugin.bar.QuimP_Bar
QuimP_BarRunner - Class in <Unnamed>: Compatibility layer for ImageJ.
QuimP_BarRunner() - Constructor for class QuimP_BarRunner
QUIMP_PREFS_SUFFIX - Static variable in class com.github.celldynamics.quimp.QuimP: Suffix added to every preference entry.
QuimPArrayUtils - Class in com.github.celldynamics.quimp.utils: Deliver simple methods operating on arrays.
QuimPArrayUtils() - Constructor for class com.github.celldynamics.quimp.utils.QuimPArrayUtils
QuimpDataConverter - Class in com.github.celldynamics.quimp.plugin.utils: Perform conversions among Snake, List and xc, yc arrays.
QuimpDataConverter() - Constructor for class com.github.celldynamics.quimp.plugin.utils.QuimpDataConverter: Default constructor.
QuimpDataConverter(List<? extends Tuple2d>) - Constructor for class com.github.celldynamics.quimp.plugin.utils.QuimpDataConverter: Default constructor if Node list is in form of List.
QuimpDataConverter(Collection<? extends Point2D>) - Constructor for class com.github.celldynamics.quimp.plugin.utils.QuimpDataConverter: Default constructor collection of awt.Point.
QuimpDataConverter(double[], double[]) - Constructor for class com.github.celldynamics.quimp.plugin.utils.QuimpDataConverter: Default if Node list is in form of two arrays with coordinates.
QuimpDataConverter(float[], float[]) - Constructor for class com.github.celldynamics.quimp.plugin.utils.QuimpDataConverter: Default if Node list is in form of two arrays with coordinates.
QuimpDataConverter(Shape<?>) - Constructor for class com.github.celldynamics.quimp.plugin.utils.QuimpDataConverter: Default constructor if Node list is in form of Snake object.
QuimpException - Exception in com.github.celldynamics.quimp: Template of exceptions thrown by QuimP API.
QuimpException() - Constructor for exception com.github.celldynamics.quimp.QuimpException: Default constructor, set message sink to console.
QuimpException(QuimpException.MessageSinkTypes...) - Constructor for exception com.github.celldynamics.quimp.QuimpException: Allow to set type of message, where it should be displayed.
QuimpException(QuimpException.MessageSinkTypes) - Constructor for exception com.github.celldynamics.quimp.QuimpException: Allow to set type of message, where it should be displayed.
QuimpException(String) - Constructor for exception com.github.celldynamics.quimp.QuimpException: Default exception with message.
QuimpException(String, QuimpException.MessageSinkTypes) - Constructor for exception com.github.celldynamics.quimp.QuimpException: Exception with message.
QuimpException(String, QuimpException.MessageSinkTypes, boolean) - Constructor for exception com.github.celldynamics.quimp.QuimpException: Exception with message.
QuimpException(String, QuimpException.MessageSinkTypes...) - Constructor for exception com.github.celldynamics.quimp.QuimpException: Exception with message.
QuimpException(Throwable) - Constructor for exception com.github.celldynamics.quimp.QuimpException: QuimpException.
QuimpException(Throwable, QuimpException.MessageSinkTypes) - Constructor for exception com.github.celldynamics.quimp.QuimpException: QuimpException.
QuimpException(Throwable, QuimpException.MessageSinkTypes...) - Constructor for exception com.github.celldynamics.quimp.QuimpException: QuimpException.
QuimpException(String, Throwable) - Constructor for exception com.github.celldynamics.quimp.QuimpException: QuimpException.
QuimpException(String, Throwable, boolean, boolean) - Constructor for exception com.github.celldynamics.quimp.QuimpException: QuimpException.
QuimpException(String, Throwable, QuimpException.MessageSinkTypes) - Constructor for exception com.github.celldynamics.quimp.QuimpException: QuimpException.
QuimpException(String, Throwable, QuimpException.MessageSinkTypes...) - Constructor for exception com.github.celldynamics.quimp.QuimpException: QuimpException.
QuimpException.MessageSinkTypes - Enum in com.github.celldynamics.quimp: Define where the message should be displayed.
quimpInfo - Static variable in class com.github.celldynamics.quimp.BOA_: Keep data from getQuimPBuildInfo().
QuimpPluginException - Exception in com.github.celldynamics.quimp.plugin: Basic class derived from Exception for purposes of QuimP plugins.
QuimpPluginException(QuimpException.MessageSinkTypes) - Constructor for exception com.github.celldynamics.quimp.plugin.QuimpPluginException: Exception constructor for given sink type (GUI or Text).
QuimpPluginException(String, QuimpException.MessageSinkTypes) - Constructor for exception com.github.celldynamics.quimp.plugin.QuimpPluginException: Exception constructor for given sink type (GUI or Text).
QuimpPluginException(String, QuimpException.MessageSinkTypes, boolean) - Constructor for exception com.github.celldynamics.quimp.plugin.QuimpPluginException: Exception constructor for given sink type (GUI or Text).
QuimpPluginException(String, Throwable, QuimpException.MessageSinkTypes) - Constructor for exception com.github.celldynamics.quimp.plugin.QuimpPluginException: Exception constructor for given sink type (GUI or Text).
QuimpPluginException(Throwable, QuimpException.MessageSinkTypes) - Constructor for exception com.github.celldynamics.quimp.plugin.QuimpPluginException: Exception constructor for given sink type (GUI or Text).
QuimpPluginException() - Constructor for exception com.github.celldynamics.quimp.plugin.QuimpPluginException: Default constructor for text sink type.
QuimpPluginException(String, Throwable, boolean, boolean) - Constructor for exception com.github.celldynamics.quimp.plugin.QuimpPluginException: Constructor for text sink type.
QuimpPluginException(String, Throwable) - Constructor for exception com.github.celldynamics.quimp.plugin.QuimpPluginException: Constructor for text sink type.
QuimpPluginException(String) - Constructor for exception com.github.celldynamics.quimp.plugin.QuimpPluginException: Constructor for text sink type.
QuimpPluginException(Throwable) - Constructor for exception com.github.celldynamics.quimp.plugin.QuimpPluginException: Constructor for text sink type.
QuimpToolsCollection - Class in com.github.celldynamics.quimp.utils: Collection of tools used across QuimP.
QuimpToolsCollection() - Constructor for class com.github.celldynamics.quimp.utils.QuimpToolsCollection
QuimpVersion - Class in com.github.celldynamics.quimp: Holds version and build information.
QuimpVersion() - Constructor for class com.github.celldynamics.quimp.QuimpVersion: Default constructor.
QuimpVersion(String, String, String) - Constructor for class com.github.celldynamics.quimp.QuimpVersion: Set version data.
QWindowBuilder - Class in com.github.celldynamics.quimp.plugin.utils: Simple window builder for QuimP plugins
QWindowBuilder() - Constructor for class com.github.celldynamics.quimp.plugin.utils.QWindowBuilder: Default constructor.
QWindowBuilder.ComponentList - Class in com.github.celldynamics.quimp.plugin.utils: Stores components under Keys that are not case insensitive.

R

radius - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qcircle: The radius.
radiusLabels - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.QPolarAxes: Labels for radius.
randDirection() - Static method in class com.github.celldynamics.quimp.PointsList: Set direction of list.
RandomWalkException - Exception in com.github.celldynamics.quimp.plugin.randomwalk: Exception class for Random Walker plugin.
RandomWalkException(QuimpException.MessageSinkTypes) - Constructor for exception com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkException: Construct exception with given sink type.
RandomWalkException(String, QuimpException.MessageSinkTypes) - Constructor for exception com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkException: Construct exception with given sink type and message.
RandomWalkException(String, Throwable, QuimpException.MessageSinkTypes) - Constructor for exception com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkException: Construct exception with given sink type, message and cause.
RandomWalkException(Throwable, QuimpException.MessageSinkTypes) - Constructor for exception com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkException: Construct exception with given sink type and cause.
RandomWalkException() - Constructor for exception com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkException: Default exception with sink set to GUI.
RandomWalkException(String, Throwable, boolean, boolean) - Constructor for exception com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkException: Construct exception.
RandomWalkException(String, Throwable) - Constructor for exception com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkException: Construct exception with default sin set to GUI.
RandomWalkException(String) - Constructor for exception com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkException: Construct exception with default sin set to GUI.
RandomWalkException(Throwable) - Constructor for exception com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkException: Construct exception with default sin set to GUI.
RandomWalkModel - Class in com.github.celldynamics.quimp.plugin.randomwalk: This class holds all possible RW parameters.
RandomWalkModel() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Default constructor setting default parameters.
RandomWalkModel.SeedSource - Enum in com.github.celldynamics.quimp.plugin.randomwalk: Possible sources of seeds.
RandomWalkOptions - Class in com.github.celldynamics.quimp.plugin.randomwalk: Hold algorithm parameters.
RandomWalkOptions() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkOptions: Set default values.
RandomWalkOptions(Double, Double, Double, Double, Integer, Double, Double[], Boolean, Integer) - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkOptions: Set user values.
RandomWalkSegmentation - Class in com.github.celldynamics.quimp.plugin.randomwalk: This is implementation of Matlab version of Random Walk segmentation algorithm.
RandomWalkSegmentation(ImageProcessor, RandomWalkOptions) - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentation: Construct segmentation object from ImageProcessor.
RandomWalkSegmentation(RealMatrix, RandomWalkOptions) - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentation: Construct segmentation object from 2D RealMatrix representing image.
RandomWalkSegmentation.SeedTypes - Enum in com.github.celldynamics.quimp.plugin.randomwalk: Define foreground and background indexes enums with numerical indexes.
RandomWalkSegmentationPlugin_ - Class in com.github.celldynamics.quimp.plugin.randomwalk: Run RandomWalkSegmentation in IJ environment.
RandomWalkSegmentationPlugin_() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_: Default constructor.
RandomWalkSegmentationPlugin_(String) - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_: Constructor that allows to provide own configuration parameters.
RandomWalkSegmentationPlugin_(AbstractPluginOptions) - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_: This constructor allows to provide user configuration.
RandomWalkSegmentationPlugin_.BgController - Class in com.github.celldynamics.quimp.plugin.randomwalk: Handle BG button.
RandomWalkSegmentationPlugin_.CancelBtnController - Class in com.github.celldynamics.quimp.plugin.randomwalk: Handle Cancel button.
RandomWalkSegmentationPlugin_.CloneController - Class in com.github.celldynamics.quimp.plugin.randomwalk: Handle Clone button.
RandomWalkSegmentationPlugin_.FgController - Class in com.github.celldynamics.quimp.plugin.randomwalk: Handle FG button.
RandomWalkSegmentationPlugin_.LoadQconfController - Class in com.github.celldynamics.quimp.plugin.randomwalk: Handle Load qconf button.
RandomWalkSegmentationPlugin_.QconfShowSeedImageController - Class in com.github.celldynamics.quimp.plugin.randomwalk: Handle show loaded qconf file mask button.
RandomWalkSegmentationPlugin_.SeedRoiController - Class in com.github.celldynamics.quimp.plugin.randomwalk: Handle seed ROI button.
RandomWalkSegmentationPlugin_Runner - Class in <Unnamed>: Compatibility layer for ImageJ.
RandomWalkSegmentationPlugin_Runner() - Constructor for class RandomWalkSegmentationPlugin_Runner
RandomWalkView - Class in com.github.celldynamics.quimp.plugin.randomwalk: UI for Random Walk algorithm.
RandomWalkView() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Build View but not show it.
read(File) - Static method in class com.github.celldynamics.quimp.FrameStatistics: Load statistics from old file format.
readParams(File) - Method in class com.github.celldynamics.quimp.BOAState: Read set of snake parameters from disk.
readParams() - Method in class com.github.celldynamics.quimp.QParams: Read the paQP file specified by paramFile
readParams() - Method in class com.github.celldynamics.quimp.QParamsQconf: Read composite QCONF file.
readProperty(String, String) - Method in class com.github.celldynamics.quimp.PropertyReader: Read property from property file for QuimP package.
readProperty(Class<?>, String, String, String) - Static method in class com.github.celldynamics.quimp.PropertyReader: Read property from jar file.
readRegInfo() - Method in class com.github.celldynamics.quimp.registration.Registration: Read info from IJ container.
readSuccess - Variable in class com.github.celldynamics.quimp.OutlineHandler: The read success.
readUI() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_: Updates model from view.
realMatrix2D2File(RealMatrix, String) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Save RelaMatrix 2D to file.
realMatrix2ImageProcessor(RealMatrix) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Create FloatProcessor 2D from RealMatrix.
recalculateColorScale(double) - Method in class com.github.celldynamics.quimp.plugin.qanalysis.FluoMap: Recalculate colors for map array.
reconstructionDicLid() - Method in class com.github.celldynamics.quimp.plugin.dic.LidReconstructor: Reconstruct DIC image by LID method.
red - Variable in class com.github.celldynamics.quimp.QColor: Color component.
registerConverter(IQconfOlderConverter<T>) - Method in class com.github.celldynamics.quimp.Serializer: This method register format converter on list of converters.
registerInstanceCreator(Class<T>, Object) - Method in class com.github.celldynamics.quimp.Serializer: Register constructor for wrapped class.
Registration - Class in com.github.celldynamics.quimp.registration: Support registration checking.
Registration(Window, String) - Constructor for class com.github.celldynamics.quimp.registration.Registration: Create and display registration window if necessary.
Registration(Window) - Constructor for class com.github.celldynamics.quimp.registration.Registration: Construct object but does not display window.
relim - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkOptions: Upper relative error limit used as stopping criterion.
remove(String) - Method in class com.github.celldynamics.quimp.plugin.utils.LinkedStringMap: Remove key.
remove(String, Object) - Method in class com.github.celldynamics.quimp.plugin.utils.LinkedStringMap: Remove key.
removeDuplicates(List<T>) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Remove duplicated elements from input list.
removeExtension(String) - Static method in class com.github.celldynamics.quimp.utils.QuimpToolsCollection: Get file name without extension.
removeHandler(SnakeHandler) - Method in class com.github.celldynamics.quimp.Nest: Remove SnakeHandler from Nest.
removeNanoEdges() - Method in class com.github.celldynamics.quimp.Outline: Remove really small edges that cause numerical inaccuracy when checking for self intersects.
removeNode(Node) - Method in class com.github.celldynamics.quimp.Snake: Remove selected node from list.
removePoint(T, boolean) - Method in class com.github.celldynamics.quimp.Shape: Remove selected point from list.
removeProx(double, double) - Method in class com.github.celldynamics.quimp.Outline: Remove close vertexes.
removeSelfRepeatings(List<Pair<Point, Point>>, List<Polygon>) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.TrackMapAnalyser: Removes the self repeatings.
removeSpaces(String) - Static method in class com.github.celldynamics.quimp.plugin.utils.StringParser: Remove spaces from beginning and end of string.
removeSpacesMacro(String) - Static method in class com.github.celldynamics.quimp.plugin.AbstractPluginOptions: Remove white characters from string except those enclosed in ().
removeVert(Vert) - Method in class com.github.celldynamics.quimp.Outline: Remove selected Vert from list.
replace(String, V, V) - Method in class com.github.celldynamics.quimp.plugin.utils.LinkedStringMap
replace(String, V) - Method in class com.github.celldynamics.quimp.plugin.utils.LinkedStringMap
replaceAll(BiFunction<? super String, ? super V, ? extends V>) - Method in class com.github.celldynamics.quimp.plugin.utils.LinkedStringMap: This method is not supported.
requiredVersion - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping: Required version of IJ1.
reset(ImagePlus, PluginFactory, ViewUpdater) - Method in class com.github.celldynamics.quimp.BOAState: Reset BOAState class.
reset() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.SeedPicker: Prepare for new ROI selection.
reset() - Method in class com.github.celldynamics.quimp.SnakeHandler: Reset snakes in handler.
resetAllCoords() - Method in class com.github.celldynamics.quimp.Outline: Reset all linear coordinates related to node Vert.coord, Vert.gCoord, Vert.fCoord.
resetNest() - Method in class com.github.celldynamics.quimp.Nest: Reset live snakes to ROI's.
resize(ImagePlus) - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Resize image to size of this map.
restore(int) - Method in class com.github.celldynamics.quimp.BOAState: Restore from snapshots data to current one.
reverseIntArray(int[]) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: reverse the given array in place.
reverseShape() - Method in class com.github.celldynamics.quimp.Shape: Turn Shape back anti clockwise.
revive() - Method in class com.github.celldynamics.quimp.SnakeHandler: Revive.
reviveNest() - Method in class com.github.celldynamics.quimp.Nest: Make all Snakes live in nest.
RIGHT - Static variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentation: Direction of circshift coded as in Matlab.
roiPrefix - Static variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Prefix added to Roi in ROI Manager.
RoiSaver - Class in com.github.celldynamics.quimp.utils.test: Helper class to export shapes as *.tif images
RoiSaver() - Constructor for class com.github.celldynamics.quimp.utils.test.RoiSaver: Dummy constructor.
rotate(ImageProcessor, double, boolean) - Method in class com.github.celldynamics.quimp.plugin.utils.ImageProcessorPlus: Rotate image by specified angle keeping correct rotation direction.
run(String) - Method in class com.github.celldynamics.quimp.BOA_: Main method called from Fiji.
run(String) - Method in class com.github.celldynamics.quimp.plugin.AbstractPluginBase: Called on plugin run by ImageJ or from API.
run(String) - Method in class com.github.celldynamics.quimp.plugin.ana.ANA_
run(String) - Method in class com.github.celldynamics.quimp.plugin.bar.QuimP_Bar
run(ImageProcessor) - Method in class com.github.celldynamics.quimp.plugin.dic.DicLidReconstruction_: This method is run when current image was accepted and input data were correct.
run(String) - Method in class com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping
run(String) - Method in class com.github.celldynamics.quimp.plugin.generatemask.GenerateMask_
run(String) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.Prot_Analysis
run(String) - Method in class com.github.celldynamics.quimp.plugin.qanalysis.Q_Analysis
run(Seeds) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentation: Main runner, does segmentation.
run(String) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_
run(String) - Method in class com.github.celldynamics.quimp.Q_Explorer
run(String) - Method in class com.github.celldynamics.quimp.Test_QuimP: Deprecated.
runBoa(int, int) - Method in class com.github.celldynamics.quimp.BOA_: Start segmentation process on range of frames.
runByANA(OutlineHandler, ImageProcessor, double) - Method in class com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping: Called by ANA if no ECCM results are in file (old path).
runFromPaqp() - Method in class com.github.celldynamics.quimp.plugin.AbstractPluginQconf: Called if loaded file is paQP.
runFromPaqp() - Method in class com.github.celldynamics.quimp.plugin.ana.ANA_
runFromPaqp() - Method in class com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping
runFromPaqp() - Method in class com.github.celldynamics.quimp.plugin.generatemask.GenerateMask_
runFromPaqp() - Method in class com.github.celldynamics.quimp.plugin.protanalysis.Prot_Analysis
runFromPaqp() - Method in class com.github.celldynamics.quimp.plugin.qanalysis.Q_Analysis
runFromQconf() - Method in class com.github.celldynamics.quimp.plugin.AbstractPluginQconf: Called if loaded file is QCONF.
runFromQconf() - Method in class com.github.celldynamics.quimp.plugin.ana.ANA_
runFromQconf() - Method in class com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping
runFromQconf() - Method in class com.github.celldynamics.quimp.plugin.generatemask.GenerateMask_
runFromQconf() - Method in class com.github.celldynamics.quimp.plugin.protanalysis.Prot_Analysis
runFromQconf() - Method in class com.github.celldynamics.quimp.plugin.qanalysis.Q_Analysis
runningAverageSmooth - Variable in class com.github.celldynamics.quimp.geom.SegmentedShapeRoi: true for using running average for smoothing.
runningMean(int, int) - Method in class com.github.celldynamics.quimp.geom.filters.OutlineProcessor: Apply running mean filter to Shape.
runningMean(double[], int) - Static method in class com.github.celldynamics.quimp.geom.filters.PointListProcessor: Running mean on input array.
runningMean(ImageProcessor, String, int) - Method in class com.github.celldynamics.quimp.plugin.utils.ImageProcessorPlus: Perform running mean on image using convolution.
runningMedian(int, int) - Method in class com.github.celldynamics.quimp.geom.filters.OutlineProcessor: Apply running median filter to Shape.
runningMedian(double[], int) - Static method in class com.github.celldynamics.quimp.geom.filters.PointListProcessor: Running median on input array.
runPlugin() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterController
runPlugin(List<Point2d>) - Method in class com.github.celldynamics.quimp.geom.filters.HatSnakeFilter: In contrary to HatSnakeFilter.runPlugin(List, ImageProcessor, Pair) this method does not use intensity weighting nor externally calculated ranks.
runPlugin(List<Point2d>, ImageProcessor) - Method in class com.github.celldynamics.quimp.geom.filters.HatSnakeFilter: In contrary to HatSnakeFilter.runPlugin(List, ImageProcessor, Pair) this method does not use externally calculated ranks.
runPlugin(List<Point2d>, ImageProcessor, Pair<ArrayList<Double>, ArrayList<Boolean>>) - Method in class com.github.celldynamics.quimp.geom.filters.HatSnakeFilter: Main filter runner.
runPlugin() - Method in class com.github.celldynamics.quimp.plugin.AbstractPluginTemplate: Main plugin logic.
runPlugin() - Method in class com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentation_: Main plugin logic.
runPlugin() - Method in interface com.github.celldynamics.quimp.plugin.IQuimpNestPlugin: Runs filter and modify Nest object.
runPlugin() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_: Run segmentation.
runPlugin() - Method in interface com.github.celldynamics.quimp.plugin.snakes.IQuimpBOAPoint2dFilter: Runs filter and return filtered points in the same order as input points.
runPlugin() - Method in interface com.github.celldynamics.quimp.plugin.snakes.IQuimpBOASnakeFilter: Runs filter and return filtered points in the same order as input points.
rwbMap(double, double, double) - Static method in class com.github.celldynamics.quimp.QColor: RWB map.

S

s2d(String) - Static method in class com.github.celldynamics.quimp.utils.QuimpToolsCollection: S 2 d.
sampleAtSame - Variable in class com.github.celldynamics.quimp.plugin.ana.AnaOptions: The sample at same.
sampleFluo(ImageProcessor, int, int) - Static method in class com.github.celldynamics.quimp.plugin.ecmm.ODEsolver: Get intensity value for given coordinates.
save(Outline, int) - Method in class com.github.celldynamics.quimp.OutlineHandler: Copy Outline into internal outlines array on correct position.
save(String) - Method in class com.github.celldynamics.quimp.Serializer: Save wrapped object passed in constructor as JSON file.
saveBoaCentroids() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverter: Save each snake centroid for each frame.
saveBoaSnakes(boolean) - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverter: Save all data associated with BOA analysis.
saveDataFiles() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterController: Save data selected in FormatConverterModel.
saveEcmmCentroids() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverter: Save each outline centroid for each frame.
saveEcmmOutlines(boolean) - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverter: Save all data associated with ECMM and ANA analysis.
saveMaps(int) - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverter: Save selected maps to files.
saveMaps(int) - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Save map files (maQP) on disk.
saveOutline(Outline, CsvWritter) - Static method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverter: Save specified outline to CsvWritter.
saveRoi(String, List<Point2d>) - Static method in class com.github.celldynamics.quimp.utils.test.RoiSaver: Save ROI as image
saveRoi(String, Roi) - Static method in class com.github.celldynamics.quimp.utils.test.RoiSaver: Save ROI as image.
saveRois(String, int, int, List<Point2d>, Color, List<Point2d>, Color, List<Point2d>, Color) - Static method in class com.github.celldynamics.quimp.utils.test.RoiSaver: Save ROIs as image
saveRois(ImagePlus, String, ArrayList<ArrayList<SegmentedShapeRoi>>) - Static method in class com.github.celldynamics.quimp.utils.test.RoiSaver: Create stack from List of Rois.
saveStatFluores() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverter: Save statistic data associated with ANA analysis for all three channels.
saveStatGeom() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverter: Save statistic data associated with ECMM analysis for all three channels.
saveStats() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverter: Create stQP file using internally stored Stats from QCONF.
saveTracks - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Save tracks to csv file.
saveTracks(Writer) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.TrackCollection: Save tracks to csv file.
scale - Variable in class com.github.celldynamics.quimp.plugin.ana.ANAp: Image scale.
scale - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The scale.
scale - Variable in class com.github.celldynamics.quimp.plugin.qanalysis.Qp: Pixel size in microns.
scale(double) - Method in class com.github.celldynamics.quimp.Shape: Scale current Shape by stepSize.
scale(float) - Method in class com.github.celldynamics.quimp.utils.graphics.vrml.VRMLobject: Scale.
scaleCurvDistDist - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Range of averaging of curvature.
scaleEqNormalsDist - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: If non zero, normals are set to direction of normal of node with smallest curvature (negative).
scaleMagn - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds.Contour: Scale magnification.
scaleMagn - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Maximal magnitude of scaling for regions with smallest curvature.
scaleOutline(double, double, double, double) - Method in class com.github.celldynamics.quimp.Outline: Scale the outline proportionally.
scaleSigma - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds.Contour: Sigma.
scaleSigma - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Scale sigma parameter.
scaleSnake(double, double, boolean) - Method in class com.github.celldynamics.quimp.Snake: Scale current Snake by amount in increments of stepSize.
SeedPicker - Class in com.github.celldynamics.quimp.plugin.randomwalk: Simple seed picker by means of ROIs.
SeedPicker() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.SeedPicker: Default constructor.
SeedPicker(ImagePlus, boolean) - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.SeedPicker: Allow to provide image to process and disable UI.
SeedPicker(ImagePlus) - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.SeedPicker: Allow to provide image to work with.
SeedPicker(boolean) - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.SeedPicker: Create the frame.
SeedProcessor - Class in com.github.celldynamics.quimp.plugin.randomwalk: Contain various methods for converting labelled images to Seeds.
SeedProcessor() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.SeedProcessor
SeedRoiController() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_.SeedRoiController
seeds - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds: Container for FG and BG seeds pixels used for seed visualisation.
Seeds - Class in com.github.celldynamics.quimp.plugin.randomwalk: Keep information about seeds for different Seed types.
Seeds() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.Seeds: Default constructor.
Seeds(int) - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.Seeds: Allow to set initial capacity.
seedsRoi - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.SeedPicker: Converted seeds available after Finish.
seedsToGrayscaleImage(Seeds) - Static method in class com.github.celldynamics.quimp.plugin.randomwalk.SeedProcessor: Convert the whole Seeds object into one-slice grayscale image.
SegmentedShapeRoi - Class in com.github.celldynamics.quimp.geom: Add some fields indicating that this Shape has been included already in any Snake chain.
SegmentedShapeRoi(Roi) - Constructor for class com.github.celldynamics.quimp.geom.SegmentedShapeRoi: Construct object from ij.gui.Roi.
SegmentedShapeRoi(Shape) - Constructor for class com.github.celldynamics.quimp.geom.SegmentedShapeRoi: Construct object from java.awt.Shape.
SegmentedShapeRoi(float[]) - Constructor for class com.github.celldynamics.quimp.geom.SegmentedShapeRoi: Construct object from array.
SegmentedShapeRoi(int, int, Shape) - Constructor for class com.github.celldynamics.quimp.geom.SegmentedShapeRoi: Constructs a ShapeRoi from a Shape.
segmentIntersection(double, double, double, double, double, double, double, double, double[]) - Static method in class com.github.celldynamics.quimp.geom.ExtendedVector2d: Compute the intersection between two line segments, or two lines of infinite length.
segParam - Variable in class com.github.celldynamics.quimp.BOAState: Reference to segmentation parameters.
selActiveCellMap - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Cell used for generating maps.
selActiveCellPlot - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Cell used for generating plots.
selActiveChannel - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Active channel for plotting maps.
selectedShrinkMethod - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Selected shrink algorithm.
selOutlineColoring - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Hold configuration for plotting outlines of cells on stack of images.
SEPARATOR - Static variable in class com.github.celldynamics.quimp.filesystem.QconfLoader: Separator for error messages.
serialize() - Method in class com.github.celldynamics.quimp.plugin.AbstractPluginOptions: Create JSon string from this object.
serialize2Macro() - Method in class com.github.celldynamics.quimp.plugin.AbstractPluginOptions: Serialize this class and produce JSon without spaces (except escaped strings) and without quotes.
Serializer<T extends IQuimpSerialize> - Class in com.github.celldynamics.quimp: Support saving and loading wrapped class to/from JSON file or string.
Serializer(Type, QuimpVersion) - Constructor for class com.github.celldynamics.quimp.Serializer: Default constructor used for restoring object.
Serializer(T, QuimpVersion) - Constructor for class com.github.celldynamics.quimp.Serializer: Constructor used for saving wrapped class.
setActive(int, boolean) - Method in class com.github.celldynamics.quimp.SnakePluginList: Activate or deactivate plugin.
setActiveHandler(int) - Method in class com.github.celldynamics.quimp.QParamsQconf: Sets the active handler.
setBlowup(int) - Method in class com.github.celldynamics.quimp.QParams: setBlowup.
setBlowup(int) - Method in class com.github.celldynamics.quimp.QParamsQconf
setBooleanValue(String, boolean) - Method in class com.github.celldynamics.quimp.plugin.ParamList: Store Boolean value in List.
setCalibration(ImagePlus) - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Calibrate image for sizes of this maps.
setCancelLabel(String) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set text on cancel button.
setCbCreatedSeedImage(String[], String) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set seed image in dynamic created mask panel.
setCbMaskSeedImage(String[], String) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set seed image in dynamic binary mask panel.
setCbOrginalImage(String[], String) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set names of original images and select one.
setCbRgbSeedImage(String[], String) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set seed image in dynamic rgb panel.
setChHatFilter(boolean) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set status of HatSnake filter.
setChInterFrameFilter(boolean) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set status of chInterFrameFilter.
setChLocalMean(boolean) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set status of local mean.
setChMaskCut(boolean) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set status of mask cut filter.
setChShowPreview(boolean) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set status of show preview.
setChShowProbMaps(boolean) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set status of show prob maps.
setChShowSeed(boolean) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set status of show seed.
setChTrueBackground(boolean) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set status of True Background.
setClockwise(boolean) - Static method in class com.github.celldynamics.quimp.PointsList: Sets the clockwise.
setColors() - Method in class com.github.celldynamics.quimp.geom.TrackOutline: Set Roi.setStrokeColor(Color) of each found Roi to color of pixels it was produced from.
setConvexFile(File) - Method in class com.github.celldynamics.quimp.QParams: setConvexFile name.
setConvMap(double[][]) - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Set map.
setCoordFile(File) - Method in class com.github.celldynamics.quimp.QParams: setCoordFile name.
setCoordMap(double[][]) - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Set map.
setCortextWidthScale(double) - Method in class com.github.celldynamics.quimp.plugin.ana.ANAp: Set cortex scale.
setCortexWidthPixel(double) - Method in class com.github.celldynamics.quimp.plugin.ana.ANAp: Set cortex widh in pixels.
setCurvatureLocal() - Method in class com.github.celldynamics.quimp.Vert: Calculate and set local field Vert.curvatureLocal.
setDoubleValue(String, double) - Method in class com.github.celldynamics.quimp.plugin.ParamList: Store Double value in List.
setEnabled(boolean) - Method in class com.github.celldynamics.quimp.plugin.qanalysis.FluoMap: Enables this map.
setEndFrame(int) - Method in class com.github.celldynamics.quimp.QParams: setEndFrame.
setEndFrame(int) - Method in class com.github.celldynamics.quimp.QParamsQconf
setExtension(String...) - Method in class com.github.celldynamics.quimp.filesystem.FileDialogEx: Set extensions to filter.
setF_total(ExtendedVector2d) - Method in class com.github.celldynamics.quimp.Node: Set total force for Node.
setFilteringMethod(String[], String) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Initialiser of cbFilteringMethod.
setFilteringPostMethod(String[], String) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Initialiser of cbFilteringPostMethod.
setFluores(FluoMeasurement[]) - Method in class com.github.celldynamics.quimp.Vert: setFluores.
setFluoresChannel(FluoMeasurement, int) - Method in class com.github.celldynamics.quimp.Vert: setFluoresChannel.
setFluoresChannel(int, int, int, int) - Method in class com.github.celldynamics.quimp.Vert: setFluoresChannel.
setFrame(int) - Method in exception com.github.celldynamics.quimp.BoaException: Set frame.
setFrame(int) - Method in class com.github.celldynamics.quimp.geom.SegmentedShapeRoi: Set Roi frame.
setFrameInterval(double) - Method in class com.github.celldynamics.quimp.QParams: setFrameInterval.
setFrameInterval(double) - Method in class com.github.celldynamics.quimp.QParamsQconf
setHead(boolean) - Method in class com.github.celldynamics.quimp.PointsList: Set head marker to current node.
setHead(T) - Method in class com.github.celldynamics.quimp.Shape: Set head of the shape to given element of the list.
setHead(int) - Method in class com.github.celldynamics.quimp.Shape: Assign head to node nodeIndex.
setHeadClosestTo(ExtendedVector2d) - Method in class com.github.celldynamics.quimp.Shape: Set head to element closest to given coordinates.
setId(int) - Method in class com.github.celldynamics.quimp.geom.SegmentedShapeRoi: Set Roi id.
setImageFrameInterval(double) - Method in class com.github.celldynamics.quimp.BOAState.BOAp: Set imageFrameInterval.
setImageScale(double) - Method in class com.github.celldynamics.quimp.BOAState.BOAp: Set scale of teh image.
setImageScale(double) - Method in class com.github.celldynamics.quimp.QParams: setImageScale.
setImageScale(double) - Method in class com.github.celldynamics.quimp.QParamsQconf
setInstance(int, String, boolean) - Method in class com.github.celldynamics.quimp.SnakePluginList: Sets instance of plugin on slot i.
setInterpolationParameters(double, boolean) - Method in class com.github.celldynamics.quimp.geom.SegmentedShapeRoi: Allow to set non-standard parameters used during conversion from outline (ROI) to list of points.
setInterpolationParameters(double, boolean, boolean) - Method in class com.github.celldynamics.quimp.geom.SegmentedShapeRoi: Allow to set non-standard parameters used during conversion from outline (ROI) to list of points.
setIntPoint(boolean, int) - Method in class com.github.celldynamics.quimp.Vert: setIntPoint.
setIntValue(String, int) - Method in class com.github.celldynamics.quimp.plugin.ParamList: Store Integer value in List.
setIp(ImageProcessor) - Method in class com.github.celldynamics.quimp.plugin.dic.LidReconstructor: Assigns ImageProcessor for reconstruction to current object.
setLandingCoord(ExtendedVector2d, Vert) - Method in class com.github.celldynamics.quimp.Vert: setLandingCoord.
setLimitsEqual(double[]) - Static method in class com.github.celldynamics.quimp.utils.QuimpToolsCollection: Sets the limits equal.
setLqconfFile(String) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set name of loaded qconf.
setLroiSeedsInfo(String) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set ROP info.
setMap(double[][]) - Method in class com.github.celldynamics.quimp.plugin.qanalysis.FluoMap: Set new fluorescence map calculating also adequate colorscale.
setMaxima(Collection<? extends Point2D>) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.MaximaFinder: Set maxima for this object.
setMaximad(Collection<Point2d>) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.MaximaFinder: Set maxima for this object.
setMessageSinkType(QuimpException.MessageSinkTypes...) - Method in exception com.github.celldynamics.quimp.QuimpException: Set message sink.
setMessageSinkType(Set<QuimpException.MessageSinkTypes>) - Method in exception com.github.celldynamics.quimp.QuimpException: Set message sink.
setMode(int) - Method in class com.github.celldynamics.quimp.geom.filters.HatSnakeFilter: Set detection mode.
setMotilityFile(File) - Method in class com.github.celldynamics.quimp.QParams: setMotilityFile name.
setMotMap(double[][]) - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Set map.
setNext(T) - Method in class com.github.celldynamics.quimp.PointsList: Adds next (or previous if not clockwise) Node to list.
setNodeRes(double) - Method in class com.github.celldynamics.quimp.QParams: setNodeRes.
setNodeRes(double) - Method in class com.github.celldynamics.quimp.QParamsQconf
setNormal(double, double) - Method in class com.github.celldynamics.quimp.PointsList: Sets the normal.
setOrgFile(File) - Method in class com.github.celldynamics.quimp.BOAState.BOAp: Set orgFile.
setOriginalImage(ImagePlus) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Set original image and update name field for serialisation.
setOriginFile(File) - Method in class com.github.celldynamics.quimp.QParams: setOriginFile name.
setOriginMap(double[][]) - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Set map.
setOutline(int, Outline) - Method in class com.github.celldynamics.quimp.OutlineHandler: Sets the outline.
setOutputFileCore(String) - Method in class com.github.celldynamics.quimp.BOAState.BOAp: Set setOutputFileCore.
setParamFile(File) - Method in class com.github.celldynamics.quimp.QParams: Set name of parameter file.
setParams(double, double) - Method in class com.github.celldynamics.quimp.plugin.dic.LidReconstructor: Sets new reconstruction parameters for current object.
setParams(double) - Static method in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: Defines default values for ECMM algorithm.
setParams(Qp) - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Attach other than default configuration object.
setPluginConfig(ParamList) - Method in class com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentation_
setPluginConfig(ParamList) - Method in class com.github.celldynamics.quimp.plugin.dic.DicLidReconstruction_
setPluginConfig(ParamList) - Method in interface com.github.celldynamics.quimp.plugin.IQuimpPluginExchangeData: Pass to plugin its configuration data as pairs (key,value).
setPluginName(String) - Method in class com.github.celldynamics.quimp.plugin.AbstractPluginBase: Set plugin name, should be that recognisable by IJ, usually plugins.config.
setPosition(double) - Method in class com.github.celldynamics.quimp.PointsList: Set normalised position of node.
setPositions() - Method in class com.github.celldynamics.quimp.Shape: Calculate position of Shape element expressed as distance of element on Shape perimeter from head.
setPrelim(ExtendedVector2d) - Method in class com.github.celldynamics.quimp.Node: Set preliminary point for Node.
setPretty() - Method in class com.github.celldynamics.quimp.Serializer: Sets pretty JSON formatting on save operation.
setPrev(T) - Method in class com.github.celldynamics.quimp.PointsList: Adds previous (or next if not clockwise) Node to list.
setQconfFile(String) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Setter of qconffile filed.
setRef(IQuimpCorePlugin) - Method in class com.github.celldynamics.quimp.plugin.engine.PluginProperties: Set reference to plugin.
setResolution(double) - Method in class com.github.celldynamics.quimp.Outline: Evenly spaces a new vertices around the outline by following vectors between verts.
setResolutionN(double) - Method in class com.github.celldynamics.quimp.Outline: Evenly spaces a new vertices around the outline by following vectors between verts.
setRGB(double, double, double) - Method in class com.github.celldynamics.quimp.QColor: Sets the RGB.
setScale(double) - Method in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.QScaleBar: Set scale.
setSeedImage(ImagePlus) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Set seed image and update name for serialisation.
setSeedSource(String[], String) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Initialiser of cbSeedSource.
setSegImageFile(File) - Method in class com.github.celldynamics.quimp.QParams: Set name of BOA loaded image.
setSelectedFilteringMethod(BinaryFilters.Filters) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Filtering setter.
setSelectedFilteringMethod(int) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Post filtering setter.
setSelectedFilteringPostMethod(BinaryFilters.Filters) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Post filtering setter.
setSelectedFilteringPostMethod(int) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Post filtering setter.
setSelectedSeedSource(RandomWalkModel.SeedSource) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: SeedSource setter.
setSelectedSeedSource(int) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: SeedSource setter.
setselectedShrinkMethod(PropagateSeeds.Propagators) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Seed propagator setter.
setselectedShrinkMethod(int) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: Seed propagator setter.
setShrinkMethod(String[], String) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Initialiser of cbShrinkMethod.
setSnakeID(int) - Method in class com.github.celldynamics.quimp.Snake: Change current snakeID.
setSnakeQP(File) - Method in class com.github.celldynamics.quimp.QParams: Set snQP file name.
setSrAlev(double) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set value of alev parameter.
setSrAlpha(double) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set RW alpha parameter.
setSrBeta(double) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set RW beta parameter.
setSrExpandPower(double) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set expand power.
setSrGamma0(double) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set RW gamma 0 parameter.
setSrGamma1(double) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set RW gamma 1 parameter.
setSrIter(int) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set RW number of iterations.
setSrLocalMeanWindow(int) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set value of local mean window parameter.
setSrNum(int) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set value of num parameter.
setSrRelerr(double) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set RW number of iterations.
setSrScaleCurvDistDist(double) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set distance.
setSrScaleEqNormalsDist(double) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set distance.
setSrScaleMagn(double) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set magnitude power.
setSrScaleSigma(double) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set sigma power.
setSrShrinkPower(double) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set shrink power.
setSrWindow(int) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Set value of window parameter.
setStartFrame(int) - Method in class com.github.celldynamics.quimp.QParams: setStartFrame.
setStartFrame(int) - Method in class com.github.celldynamics.quimp.QParamsQconf
setStatCollection(ArrayList<CellStats>) - Method in class com.github.celldynamics.quimp.filesystem.StatsCollection: Set stats collection object wrapped by this class.
setStatsQP(File) - Method in class com.github.celldynamics.quimp.QParams: Set stats file name.
setStringValue(String, String) - Method in class com.github.celldynamics.quimp.plugin.ParamList: Store String value in List.
setToolTip(JComponent, String) - Static method in class com.github.celldynamics.quimp.utils.UiTools: Set tooltip to component with line breaking.
setTrackNum(int) - Method in class com.github.celldynamics.quimp.PointsList: Sets the track num.
setTrueBackgroundProcessing(AutoThresholder.Method) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds: Turn on processing background before using it as seed.
setup(ImagePlus) - Method in class com.github.celldynamics.quimp.BOAState.BOAp: Initialize internal parameters of BOA plugin from ImagePlus.
setup(String, ImagePlus) - Method in class com.github.celldynamics.quimp.plugin.dic.DicLidReconstruction_
setup() - Method in class com.github.celldynamics.quimp.plugin.dic.DicLidReconstruction_
setup() - Method in interface com.github.celldynamics.quimp.plugin.IQuimpCorePlugin: Provide basic information to QuimP about plugin.
setup(QParams) - Method in class com.github.celldynamics.quimp.plugin.qanalysis.Qp: Copies selected data from QParams to this object.
setValues(ParamList) - Method in class com.github.celldynamics.quimp.plugin.utils.QWindowBuilder: Set plugin parameters.
setVel(ExtendedVector2d) - Method in class com.github.celldynamics.quimp.Node: Set velocity for Node.
setVisible(boolean) - Method in class com.github.celldynamics.quimp.AboutDialog: Show or hide main window.
setX(double) - Method in class com.github.celldynamics.quimp.PointsList: Set X space co-ordinate.
setxMap(double[][]) - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Set map.
setxmapFile(File) - Method in class com.github.celldynamics.quimp.QParams: Set x coord map file.
setXY(double, double) - Method in class com.github.celldynamics.quimp.geom.ExtendedVector2d: Set vector coordinates.
setY(double) - Method in class com.github.celldynamics.quimp.PointsList: Set Y space co-ordinate.
setyMap(double[][]) - Method in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Set map.
setymapFile(File) - Method in class com.github.celldynamics.quimp.QParams: Set y coord map file.
Shape<T extends PointsList<T>> - Class in com.github.celldynamics.quimp: Form abstract shape from bidirectional list of points.
Shape() - Constructor for class com.github.celldynamics.quimp.Shape: Default constructor, creates empty Shape.
Shape(T, int) - Constructor for class com.github.celldynamics.quimp.Shape: Create Shape from existing list of points (can be one point as well).
Shape(T) - Constructor for class com.github.celldynamics.quimp.Shape: Create Shape from one point, created Shape will be looped.
Shape(Shape<T>) - Constructor for class com.github.celldynamics.quimp.Shape: Copy constructor.
Shape(Shape<T>, T) - Constructor for class com.github.celldynamics.quimp.Shape: Conversion and copy constructor.
Shape(List<? extends Tuple2d>, T, boolean) - Constructor for class com.github.celldynamics.quimp.Shape: Create Shape of elements elInst with coordinates p.
Shape(double[], double[], T, boolean) - Constructor for class com.github.celldynamics.quimp.Shape: Create Shape of elements elInst with coordinates x and y.
ShapeHandler<T extends Shape<?>> - Class in com.github.celldynamics.quimp: Base class for Shape holders.
show() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkView: Show the window.
showConversionCapabilities(Frame) - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverter: Show message with conversion capabilities.
showGuiWithMessage(Frame, String) - Static method in exception com.github.celldynamics.quimp.QuimpException: Show UI with message.
showOpenDialog() - Method in class com.github.celldynamics.quimp.filesystem.FileDialogEx: Show dialog and wait for user action.
showPreview - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: true for showing preview.
showProbMaps - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: true for showing probability maps.
showSeeds - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: true for showing seeds.
showUi(boolean) - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterController
showUi(boolean) - Method in class com.github.celldynamics.quimp.plugin.AbstractPluginBase: Open plugin UI.
showUi(boolean) - Method in class com.github.celldynamics.quimp.plugin.ana.ANA_
showUi(boolean) - Method in class com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentation_
showUi(boolean) - Method in class com.github.celldynamics.quimp.plugin.dic.DicLidReconstruction_: Shows user dialog and check conditions.
showUi(boolean) - Method in class com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping
showUi(boolean) - Method in class com.github.celldynamics.quimp.plugin.generatemask.GenerateMask_
showUi(boolean) - Method in interface com.github.celldynamics.quimp.plugin.IQuimpCorePlugin: Show or hide plugin UI.
showUi(boolean) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.Prot_Analysis
showUi(boolean) - Method in class com.github.celldynamics.quimp.plugin.qanalysis.Q_Analysis
showUi(boolean) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_: Build main dialog.
showWindow(boolean) - Method in class com.github.celldynamics.quimp.plugin.utils.QWindowBuilder: Show or hide window.
shrinkAmount - Variable in class com.github.celldynamics.quimp.geom.filters.HatSnakeFilter: Number of steps used for outline shrinking for intensity sampling.
shrinkLin(double, double, double, double) - Method in class com.github.celldynamics.quimp.geom.filters.OutlineProcessor: Shrink outline linearly.
shrinknl(double, double, double, double, double, double, double, double) - Method in class com.github.celldynamics.quimp.geom.filters.OutlineProcessor: Shrink the outline nonlinearly.
shrinkPower - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: ShrinkPower parameter.
sHs - Variable in class com.github.celldynamics.quimp.filesystem.StatsCollection: List of statistic objects for separate cells.
silentClose() - Method in class com.github.celldynamics.quimp.omero.OmeroBrowser: Close Omero without exception.
SimpleMorpho() - Constructor for class com.github.celldynamics.quimp.plugin.randomwalk.BinaryFilters.SimpleMorpho
size() - Method in class com.github.celldynamics.quimp.Nest: Get NEst size.
size() - Method in class com.github.celldynamics.quimp.plugin.utils.QuimpDataConverter: Data accessor.
size - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qtext: The size.
smoothMean(int, int) - Method in class com.github.celldynamics.quimp.geom.filters.PointListProcessor: Apply mean filter to list.
smoothMedian(int, int) - Method in class com.github.celldynamics.quimp.geom.filters.PointListProcessor: Apply median filter to list.
Snake - Class in com.github.celldynamics.quimp: Low level snake definition.
Snake(Node, int, int) - Constructor for class com.github.celldynamics.quimp.Snake: Create a snake from existing linked list (at least one head node).
Snake(Snake, int) - Constructor for class com.github.celldynamics.quimp.Snake: Copy constructor with new ID.
Snake(Snake) - Constructor for class com.github.celldynamics.quimp.Snake: Copy constructor.
Snake(Roi, int, boolean) - Constructor for class com.github.celldynamics.quimp.Snake: Create snake from ROI
Snake(PolygonRoi, int) - Constructor for class com.github.celldynamics.quimp.Snake: Initialises snake from PolyginRoi.
Snake(List<? extends Tuple2d>, int) - Constructor for class com.github.celldynamics.quimp.Snake: Construct Snake object from list of nodes.
Snake(double[], double[], int) - Constructor for class com.github.celldynamics.quimp.Snake: Construct Snake object from X and Y arrays.
Snake() - Constructor for class com.github.celldynamics.quimp.Snake: Construct empty Snake object.
snakeFileExt - Static variable in class com.github.celldynamics.quimp.filesystem.FileExtensions: Extension for file produced by BOA containing snake nodes.
SnakeHandler - Class in com.github.celldynamics.quimp: Store all the snakes computed for one cell across frames and it is responsible for writing them to file.
SnakeHandler() - Constructor for class com.github.celldynamics.quimp.SnakeHandler: Instantiates a new snake handler.
SnakeHandler(Roi, int, int) - Constructor for class com.github.celldynamics.quimp.SnakeHandler: Constructor of SnakeHandler.
SnakeHandler(List<SegmentedShapeRoi>, int) - Constructor for class com.github.celldynamics.quimp.SnakeHandler: Copy constructor.
snakePluginList - Variable in class com.github.celldynamics.quimp.BOAState: List of plugins selected in plugin stack and information if they are active or not.
SnakePluginList - Class in com.github.celldynamics.quimp: Ordered list of plugins related to snake processing for one frame.
SnakePluginList() - Constructor for class com.github.celldynamics.quimp.SnakePluginList: Default constructor.
SnakePluginList(int, PluginFactory, ViewUpdater) - Constructor for class com.github.celldynamics.quimp.SnakePluginList: Main constructor.
snakePluginListSnapshots - Variable in class com.github.celldynamics.quimp.BOAState: Keep snapshots of SnakePluginList objects for every frame separately.
snakeReader(File) - Method in class com.github.celldynamics.quimp.SnakeHandler: Deprecated.
snakeToZoom - Variable in class com.github.celldynamics.quimp.BOAState.BOAp: Snake selected in zoom selector, negative value if 100% view.
snapped - Variable in class com.github.celldynamics.quimp.Vert: The vert has been snapped to an edge.
SNQP_MISSING - Static variable in class com.github.celldynamics.quimp.filesystem.QconfLoader: Stand for missing file in experiment.
snQPfile - Variable in class com.github.celldynamics.quimp.plugin.qanalysis.Qp: snQP file.
solver(Seeds, RealMatrix[]) - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentation: Run Random Walk segmentation.
speed - Variable in class com.github.celldynamics.quimp.FrameStatistics: Speed at which the centroid moved between the current and previous frame.
speedToScale(double, double, double) - Static method in class com.github.celldynamics.quimp.utils.QuimpToolsCollection: Speed to scale.
speedToScale(int, double, double) - Static method in class com.github.celldynamics.quimp.utils.QuimpToolsCollection: Speed to scale.
splineSmooth - Variable in class com.github.celldynamics.quimp.geom.SegmentedShapeRoi: true for using spline smoothing during interpolation.
startFrame - Variable in class com.github.celldynamics.quimp.plugin.ana.ANAp: Frame range.
startFrame - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The start frame.
startFrame - Variable in class com.github.celldynamics.quimp.ShapeHandler: First frame of Outline.
startingNnodes - Variable in class com.github.celldynamics.quimp.Snake: how many nodes at start of segmentation.
statFile - Variable in class com.github.celldynamics.quimp.plugin.ana.ANAp: Reference to Stats file.
StatFileParser - Class in com.github.celldynamics.quimp.filesystem.converter: Parse stQP files and convert it to StatsCollection.
StatFileParser(String) - Constructor for class com.github.celldynamics.quimp.filesystem.converter.StatFileParser: Construct object.
staticPointColor - Static variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Color of selected point.
staticPointSize - Static variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions: Size of the point when selected.
Stats - Variable in class com.github.celldynamics.quimp.filesystem.DataContainer: Store statistics for cells computed for outlines and fluorescence data.
STATS_AVAIL - Static variable in class com.github.celldynamics.quimp.filesystem.DataContainer: Indicate that QCONF contains statistics.
StatsCollection - Class in com.github.celldynamics.quimp.filesystem: Keep statistics for cells.
StatsCollection(int) - Constructor for class com.github.celldynamics.quimp.filesystem.StatsCollection: Create size elements in store for CellStats objects.
StatsCollection() - Constructor for class com.github.celldynamics.quimp.filesystem.StatsCollection: Default constructor.
statsFileExt - Static variable in class com.github.celldynamics.quimp.filesystem.FileExtensions: Extension for file containing excel stats.
statsQP - Variable in class com.github.celldynamics.quimp.QParams: The stats QP.
step - Variable in class com.github.celldynamics.quimp.geom.SegmentedShapeRoi: Step during conversion outline to points.
stepRes - Variable in class com.github.celldynamics.quimp.plugin.ana.ANAp: Atomic step during contour shrinking.
STEPS - Static variable in class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds: Default resolution used during outlining objects.
stepSize - Static variable in class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds.Contour: Step size during object outline shrinking.
STmap - Class in com.github.celldynamics.quimp.plugin.qanalysis: Create spatial temporal maps from ECMM and ANA data.
STmap() - Constructor for class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Default constructor to satisfy GSon builder.
STmap(STmap) - Constructor for class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Copy constructor.
STmap(OutlineHandler, int, Qp) - Constructor for class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Build object for given.
STMap3D - Class in com.github.celldynamics.quimp.plugin.qanalysis
STMap3D(double[][], double[][], int[]) - Constructor for class com.github.celldynamics.quimp.plugin.qanalysis.STMap3D: Instantiates a new ST map 3 D.
store(int) - Method in class com.github.celldynamics.quimp.BOAState: Make snapshot of current objects state.
storeLiveSnake(int) - Method in class com.github.celldynamics.quimp.SnakeHandler: Make copy of liveSnake into final snakes array.
storeLocation() - Method in class com.github.celldynamics.quimp.plugin.bar.QuimP_Bar: Store location.
storeOnlyEdited(int) - Method in class com.github.celldynamics.quimp.BOAState: Store information whether frame was edited only.
storeSeeds - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds: By default seed history is not stored.
storeThisSnake(Snake, int) - Method in class com.github.celldynamics.quimp.SnakeHandler: Makes copy of snake and store it as final snake.
STQP_MISSING - Static variable in class com.github.celldynamics.quimp.filesystem.QconfLoader: Stand for missing file in experiment.
stQPfile - Variable in class com.github.celldynamics.quimp.plugin.qanalysis.Qp: stQP file.
StringParser - Class in com.github.celldynamics.quimp.plugin.utils: Class for parsing parameter strings.
StringParser() - Constructor for class com.github.celldynamics.quimp.plugin.utils.StringParser
stringWrap(String, int) - Static method in class com.github.celldynamics.quimp.utils.QuimpToolsCollection: Insert \n character after given number of chars trying to not break words.
stringWrap(String) - Static method in class com.github.celldynamics.quimp.utils.QuimpToolsCollection: Insert \n character after default number of chars trying to not break words.
stringWrap(String, int, String) - Static method in class com.github.celldynamics.quimp.utils.QuimpToolsCollection: Insert any symbol after given number of chars trying to not break words.
strokecolour - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qcircle: The strokecolour.
sumArray(int[]) - Static method in class com.github.celldynamics.quimp.utils.QuimPArrayUtils: Sum array.
sumCov - Variable in class com.github.celldynamics.quimp.plugin.qanalysis.Qp: The sum cov.
sumCurvature(double) - Method in class com.github.celldynamics.quimp.geom.filters.OutlineProcessor: Sum smoothed curvature over a region of the membrane.
SUPER_DEBUG - Static variable in class com.github.celldynamics.quimp.QuimP: Switch on/off additional debug.
SVGplotter - Class in com.github.celldynamics.quimp.utils.graphics.svg: SVG plotter used in QuimP.
SVGplotter(OutlineHandler, double, double, int, File) - Constructor for class com.github.celldynamics.quimp.utils.graphics.svg.SVGplotter: Instantiates a new SV gplotter.
SVGwritter - Class in com.github.celldynamics.quimp.utils.graphics.svg: Plot primitives on SVG image.
SVGwritter() - Constructor for class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter
SVGwritter.Qcircle - Class in com.github.celldynamics.quimp.utils.graphics.svg: Represent circle on SVG image.
SVGwritter.Qline - Class in com.github.celldynamics.quimp.utils.graphics.svg: Represent line on SVG image.
SVGwritter.QPolarAxes - Class in com.github.celldynamics.quimp.utils.graphics.svg: Create axes in polar coordinates.
SVGwritter.QScaleBar - Class in com.github.celldynamics.quimp.utils.graphics.svg: Plot scale bar on svg.
SVGwritter.Qtext - Class in com.github.celldynamics.quimp.utils.graphics.svg: Represent text on SVG image.
SYMMETRICPAD - Static variable in interface com.github.celldynamics.quimp.plugin.utils.IPadArray: defines symmetric padding.

T

tan - Variable in class com.github.celldynamics.quimp.PointsList: tangent vector.
tarLandingCoord - Variable in class com.github.celldynamics.quimp.Vert: tarLandingCoord.
tarPower - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The tar power.
tarQ - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The tar Q.
Test_QuimP - Class in com.github.celldynamics.quimp: Deprecated.
Test_QuimP() - Constructor for class com.github.celldynamics.quimp.Test_QuimP: Deprecated.
text - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qtext: The text.
textAnchor - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qtext: Text anchor.
thickness - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qcircle: The thickness.
thickness - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qline: The thickness.
thickness - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.QPolarAxes: The thickness.
thickness - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.QScaleBar: Line thickness.
timeStamp - Variable in class com.github.celldynamics.quimp.Serializer: Version and other information passed to serializer.
toCartesian(STmap, int, double, double) - Static method in class com.github.celldynamics.quimp.geom.MapCoordConverter: Convert (Frame;Outline) to Cartesian (x;y).
toggleWindow(boolean) - Method in class com.github.celldynamics.quimp.plugin.utils.QWindowBuilder: Toggle window visibility if input is \c true.
toMap(STmap, int, double, double, double) - Static method in class com.github.celldynamics.quimp.geom.MapCoordConverter: Convert Cartesian coordinates for given frame to map coordinates (frame;outlinePos).
TOOL_VERSION - Static variable in class com.github.celldynamics.quimp.QuimP: Quimp package version taken from jar.
TOOLTIPDELAY - Static variable in class com.github.celldynamics.quimp.utils.UiTools: Tootltip delay for this window in ms.
toolTipLength - Static variable in class com.github.celldynamics.quimp.utils.UiTools: Length of tool tip text.
TOP - Static variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentation: Direction of circshift coded as in Matlab.
toScale(double, double) - Method in class com.github.celldynamics.quimp.FrameStatistics: Rescale scalable parameters (area, perimeter,etc) to SI units.
toString() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverter
toString() - Method in class com.github.celldynamics.quimp.filesystem.converter.FormatConverterModel
toString() - Method in class com.github.celldynamics.quimp.FluoMeasurement
toString() - Method in class com.github.celldynamics.quimp.geom.TrackOutline
toString() - Method in class com.github.celldynamics.quimp.Nest
toString() - Method in class com.github.celldynamics.quimp.Node
toString() - Method in class com.github.celldynamics.quimp.Outline
toString() - Method in class com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentationOptions
toString() - Method in class com.github.celldynamics.quimp.plugin.engine.PluginProperties
toString() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.Point
toString() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel
toString() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkOptions
toString() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.Seeds
toString() - Method in class com.github.celldynamics.quimp.PointsList
toString() - Method in class com.github.celldynamics.quimp.QColor
toString() - Method in class com.github.celldynamics.quimp.QuimpVersion
toString() - Method in class com.github.celldynamics.quimp.Serializer: Convert wrapped class to JSON representation together with Serializer wrapper
toString() - Method in class com.github.celldynamics.quimp.Shape: Print Shape nodes.
toString() - Method in class com.github.celldynamics.quimp.Snake
toString() - Method in class com.github.celldynamics.quimp.SnakeHandler
toString() - Method in class com.github.celldynamics.quimp.Vert
totalCorFluo - Variable in class com.github.celldynamics.quimp.plugin.ana.ChannelStat: Mean intensity in outer contour - mean intensity within inner contour.
totalFluor - Variable in class com.github.celldynamics.quimp.plugin.ana.ChannelStat: Mean intensity in outer contour * outer contour area.
totalInnerFluor - Variable in class com.github.celldynamics.quimp.plugin.ana.ChannelStat: Mean intensity within inner contour * unscaled area of inner contour.
trackBackward(int, int, int) - Method in class com.github.celldynamics.quimp.geom.MapTracker: Deprecated.
Use trackBackwardValid(int, int, int) instead
trackBackwardValid(int, int, int) - Method in class com.github.celldynamics.quimp.geom.MapTracker: Track given point backward.
TrackCollection - Class in com.github.celldynamics.quimp.plugin.protanalysis: Represent collection of tracks.
TrackCollection(boolean) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.TrackCollection: Instantiates a new track collection.
trackColor - Variable in class com.github.celldynamics.quimp.plugin.qanalysis.Qp: The track color.
trackForward(int, int, int) - Method in class com.github.celldynamics.quimp.geom.MapTracker: Deprecated.
Use trackForwardValid(int, int, int) instead
trackForwardValid(int, int, int) - Method in class com.github.celldynamics.quimp.geom.MapTracker: Track given point forward.
TrackMapAnalyser - Class in com.github.celldynamics.quimp.plugin.protanalysis: Track point using tracking map generated by MapTracker.
TrackMapAnalyser() - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.TrackMapAnalyser: Instantiates a new track map analyser.
trackMaxima(STmap, double, MaximaFinder) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.TrackMapAnalyser: Track maxima across motility map as long as they fulfil criterion of amplitude.
tracknumber - Variable in class com.github.celldynamics.quimp.PointsList: ID number of point, unique across list.
trackObjects() - Method in class com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentation: Main runner for tracking.
TrackOutline - Class in com.github.celldynamics.quimp.geom: Convert grayscale masks into list of vertices in correct order.
TrackOutline(ImageProcessor, int, int) - Constructor for class com.github.celldynamics.quimp.geom.TrackOutline: Constructor from ImageProcessor.
TrackOutline(ImageProcessor, int) - Constructor for class com.github.celldynamics.quimp.geom.TrackOutline: Constructor from ImageProcessor for single images.
TrackOutline(ImagePlus, int) - Constructor for class com.github.celldynamics.quimp.geom.TrackOutline: Default constructor.
trackvecimageFileExt - Static variable in class com.github.celldynamics.quimp.filesystem.FileExtensions: Extension for file containing track vector plot.
TrackVisualisation - Class in com.github.celldynamics.quimp.plugin.protanalysis: Support various methods of visualising protrusion data.
TrackVisualisation(ImagePlus) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.TrackVisualisation: Create correct object.
TrackVisualisation(String, ImageProcessor) - Constructor for class com.github.celldynamics.quimp.plugin.protanalysis.TrackVisualisation: Construct object from raw ImageProcessor.
transform(float, float, float) - Method in class com.github.celldynamics.quimp.utils.graphics.vrml.VRMLobject: Transform.
triangleArea(ExtendedVector2d, ExtendedVector2d, ExtendedVector2d) - Static method in class com.github.celldynamics.quimp.geom.ExtendedVector2d: Compute area of triangle (can be negative).
trigger - Variable in class com.github.celldynamics.quimp.filesystem.versions.Converter170202: Version below the Converter170202.upgradeFromOld(Serializer) will be executed.

U

ui - Variable in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisAbstractAction
ui - Variable in class com.github.celldynamics.quimp.plugin.utils.QWindowBuilder: The ui.
UiTools - Class in com.github.celldynamics.quimp.utils: Contain UI related tools.
UiTools() - Constructor for class com.github.celldynamics.quimp.utils.UiTools
unescapeJsonMacro(String) - Static method in class com.github.celldynamics.quimp.plugin.AbstractPluginOptions: Reverse AbstractPluginOptions.escapeJsonMacro(String).
unfreeze() - Method in class com.github.celldynamics.quimp.PointsList: Unfreeze Point.
unfreezeAll() - Method in class com.github.celldynamics.quimp.Shape: Unfreeze all nodes in Shape.
unfreezeAll() - Method in class com.github.celldynamics.quimp.Snake: Unfreeze all nodes.
unfreezeHandler() - Method in class com.github.celldynamics.quimp.SnakeHandler: Unlock handler.
unfreezeNode(Node) - Method in class com.github.celldynamics.quimp.Snake: Unfreeze a specific node.
unitVector(ExtendedVector2d, ExtendedVector2d) - Static method in class com.github.celldynamics.quimp.geom.ExtendedVector2d: Unit vector to target.
unload() - Method in class com.github.celldynamics.quimp.plugin.AbstractPluginQconf: Remove loaded QCONF file and allows to load new one.
unSnapped - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: number of nodes that failed to snap.
update() - Method in class com.github.celldynamics.quimp.Node: Update point and force with preliminary values, and reset.
updateCurrentView() - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisAbstractAction: Helper for updating current frame.
updateCurvature() - Method in class com.github.celldynamics.quimp.Outline: Update curvature for all Vert in Outline.
updateNormale(boolean) - Method in class com.github.celldynamics.quimp.PointsList: Updates the normal (must point inwards).
updateNormals(boolean) - Method in class com.github.celldynamics.quimp.Shape: Update all node normals.
updateRefs(PluginFactory, ViewUpdater) - Method in class com.github.celldynamics.quimp.SnakePluginList: Updates references of external object connected in constructor.
updateView() - Method in class com.github.celldynamics.quimp.ViewUpdater: Calls updateView method from object ob.
upgradeFromOld(Serializer<T>) - Method in class com.github.celldynamics.quimp.filesystem.versions.Converter170202
upgradeFromOld(Serializer<T>) - Method in interface com.github.celldynamics.quimp.filesystem.versions.IQconfOlderConverter: This method is run when deserialised class is in version lower that version of loader.
upload(String[], DatasetData) - Method in class com.github.celldynamics.quimp.omero.OmeroBrowser: Upload specified image to dataset.
upload(String, String, DatasetData) - Method in class com.github.celldynamics.quimp.omero.OmeroBrowser: Upload attachment and attach it to image from dataset.
upload() - Method in class com.github.celldynamics.quimp.omero.OmeroClient_: Upload qconf and related image to currently selected dataset.
uploadPluginsConfig() - Method in class com.github.celldynamics.quimp.SnakePluginList: Transfer locally stored config to plugins instance for current list of plugin.
uscale - Variable in class com.github.celldynamics.quimp.utils.graphics.PolarPlot: Distance of plot from edge.
useFiltering - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds.Contour: Use or not extra filtering defined in TrackOutline.
useLocalMean - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkOptions: true if local mean algorithm is used.
userScale - Variable in class com.github.celldynamics.quimp.plugin.ana.AnaOptions: Scale typed in UI.

V

validate() - Method in class com.github.celldynamics.quimp.plugin.AbstractPluginQconf: Override this method to pass your own validation of QCONF structure.
validate() - Method in class com.github.celldynamics.quimp.plugin.ana.ANA_
validate() - Method in class com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping
validate() - Method in class com.github.celldynamics.quimp.plugin.protanalysis.Prot_Analysis
validate() - Method in class com.github.celldynamics.quimp.plugin.qanalysis.Q_Analysis
validateDataContainer() - Method in class com.github.celldynamics.quimp.filesystem.DataContainer: Get information about available modules in object.
validatePaqp(Path) - Static method in class com.github.celldynamics.quimp.filesystem.QconfLoader: Perform blind validation of accessible files without reading them.
validateQconf() - Method in class com.github.celldynamics.quimp.filesystem.QconfLoader: Validate loaded QCONF file in accordance to modules run on it.
validateSeeds(Seeds, RandomWalkSegmentation.SeedTypes) - Static method in class com.github.celldynamics.quimp.plugin.randomwalk.SeedProcessor: Validate if at least one map in specified seed type contains non-zero pixel.
validateShape() - Method in class com.github.celldynamics.quimp.Shape: Validate correctness of the Shape.
valueOf(String) - Static method in enum com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions.GradientType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions.OutlinePlotTypes: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.celldynamics.quimp.plugin.randomwalk.BinaryFilters.Filters: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.celldynamics.quimp.plugin.randomwalk.BinaryFilters.MorphoOperations: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds.Propagators: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel.SeedSource: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentation.SeedTypes: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.celldynamics.quimp.QuimpException.MessageSinkTypes: Returns the enum constant of this type with the specified name.
values() - Static method in enum com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions.GradientType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions.OutlinePlotTypes: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.celldynamics.quimp.plugin.randomwalk.BinaryFilters.Filters: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.celldynamics.quimp.plugin.randomwalk.BinaryFilters.MorphoOperations: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds.Propagators: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel.SeedSource: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentation.SeedTypes: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.celldynamics.quimp.QuimpException.MessageSinkTypes: Returns an array containing the constants of this enum type, in the order they are declared.
vecP2P(ExtendedVector2d, ExtendedVector2d) - Static method in class com.github.celldynamics.quimp.geom.ExtendedVector2d: Create vector between points.
verifyEcmminpsnQP() - Method in class com.github.celldynamics.quimp.QParams: Verify if ECMM was run on snQP file.
Vert - Class in com.github.celldynamics.quimp: Represents a vertex in the outline.
Vert() - Constructor for class com.github.celldynamics.quimp.Vert: Default constructor, creates Vert element with ID=1.
Vert(int) - Constructor for class com.github.celldynamics.quimp.Vert: Create Vert element with given ID.
Vert(double, double, int) - Constructor for class com.github.celldynamics.quimp.Vert: Create Vert from {x,y} coordinates.
Vert(Vert) - Constructor for class com.github.celldynamics.quimp.Vert: Copy constructor.
Vert(Node) - Constructor for class com.github.celldynamics.quimp.Vert: Conversion constructor.
viewUpdater - Static variable in class com.github.celldynamics.quimp.BOA_: Hold current BOA object and provide access to only selected methods from plugin.
ViewUpdater - Class in com.github.celldynamics.quimp: Accessor that masks all public methods from object it holds except those manually exposed.
ViewUpdater(Object) - Constructor for class com.github.celldynamics.quimp.ViewUpdater: Connect object to accessor.
visualRes - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: The visual res.
VRMLobject - Class in com.github.celldynamics.quimp.utils.graphics.vrml
VRMLobject(Point3f[], Color3f[], int[]) - Constructor for class com.github.celldynamics.quimp.utils.graphics.vrml.VRMLobject: Instantiates a new VRM lobject.

W

w - Static variable in class com.github.celldynamics.quimp.plugin.ecmm.ECMp: size of displacment of mig edge charges.
WAIT_TIME - Static variable in class com.github.celldynamics.quimp.utils.IJTools: Time to wait after exit.
waited - Variable in class com.github.celldynamics.quimp.registration.Registration: Flag that indicates that user has waited already.
window - Variable in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel: window parameter.
windowActivated(WindowEvent) - Method in class com.github.celldynamics.quimp.HistoryLogger: Deprecated.
windowClosed(WindowEvent) - Method in class com.github.celldynamics.quimp.HistoryLogger: Deprecated.
windowClosing(WindowEvent) - Method in class com.github.celldynamics.quimp.HistoryLogger: Deprecated.
windowDeactivated(WindowEvent) - Method in class com.github.celldynamics.quimp.HistoryLogger: Deprecated.
windowDeiconified(WindowEvent) - Method in class com.github.celldynamics.quimp.HistoryLogger: Deprecated.
windowIconified(WindowEvent) - Method in class com.github.celldynamics.quimp.HistoryLogger: Deprecated.
windowOpened(WindowEvent) - Method in class com.github.celldynamics.quimp.HistoryLogger: Deprecated.
windowState - Variable in class com.github.celldynamics.quimp.plugin.utils.QWindowBuilder: The window state.
WITH_SELFCROSSING - Static variable in class com.github.celldynamics.quimp.plugin.protanalysis.TrackMapAnalyser: Allow detection common points in backward and forward tracks generated for the same starting point.
WITHOUT_SELFCROSSING - Static variable in class com.github.celldynamics.quimp.plugin.protanalysis.TrackMapAnalyser: Disallow detection common points in backward and forward tracks generated for the same starting point.
write(FrameStatistics[], File, double, double) - Static method in class com.github.celldynamics.quimp.FrameStatistics: Write stat file in old format (stQP.csv).
write(File) - Method in class com.github.celldynamics.quimp.utils.graphics.vrml.VRMLobject: Write.
writeCell(PrintWriter, int) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ProtStat: Add stats for this cell to output.
writeHeader(PrintWriter, Rectangle) - Static method in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter: Generate typical header.
writeLine(String) - Method in class com.github.celldynamics.quimp.utils.CsvWritter: Write line to file.
writeLine(Double...) - Method in class com.github.celldynamics.quimp.utils.CsvWritter: Write series of Doubles using defined precision and default delimiter.
writeOldParams() - Method in class com.github.celldynamics.quimp.QParamsQconf: Write parameter file paQP in old format (QuimP11).
writeOutlines(File, boolean) - Method in class com.github.celldynamics.quimp.OutlineHandler: Write this outline to disk.
writeParams(int, int, int) - Method in class com.github.celldynamics.quimp.BOAState: Write set of snake parameters to disk.
writeParams() - Method in class com.github.celldynamics.quimp.QParams: Write params.
writeParams() - Method in class com.github.celldynamics.quimp.QParamsQconf: Write all parameters in new format.
writeProtrusion(PrintWriter, int) - Method in class com.github.celldynamics.quimp.plugin.protanalysis.ProtStat: Write stats for protrusions for this cell.
writeSnakes() - Method in class com.github.celldynamics.quimp.Nest: Write all Snakes to file.
writeSnakes() - Method in class com.github.celldynamics.quimp.SnakeHandler: Write Snakes from this handler to *.snPQ file.
writeUI() - Method in class com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_: Updates view from model.

X

x - Variable in class com.github.celldynamics.quimp.FluoMeasurement: Pixel x coordinate.
x1 - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qcircle: x coordinate of center.
x1 - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qline: x coordinate of first point of section.
x2 - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qline: x coordinate of last point of section.
XMAP - Static variable in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: X coordinates map code.
xmapFileExt - Static variable in class com.github.celldynamics.quimp.filesystem.FileExtensions: Extension for file containing x map.
xtoArr() - Method in class com.github.celldynamics.quimp.Shape: Convert coordinate of Shape to array.

Y

y - Variable in class com.github.celldynamics.quimp.FluoMeasurement: Pixel y coordinate.
y1 - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qcircle: y coordinate of center.
y1 - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qline: y coordinate of first point of section.
y2 - Variable in class com.github.celldynamics.quimp.utils.graphics.svg.SVGwritter.Qline: y coordinate of last point of section.
YMAP - Static variable in class com.github.celldynamics.quimp.plugin.qanalysis.STmap: Y coordinates map code.
ymapFileExt - Static variable in class com.github.celldynamics.quimp.filesystem.FileExtensions: Extension for file containing y map.
ytoArr() - Method in class com.github.celldynamics.quimp.Shape: Convert coordinate of Shape to array.

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