- A - Variable in class deformablemesh.geometry.Connection3D
-
- abs(double) - Static method in class deformablemesh.util.Vector3DOps
-
- accumulate(RaycastRender.Ray, int) - Method in class deformablemesh.gui.render2d.RaycastRender
-
- accumulate(ImageProcessor) - Method in class deformablemesh.util.KMeansThresholder
-
Creates a set of unsigned short values and collects the px as a short for analysis.
- ActionStack - Class in deformablemesh.util.actions
-
Created by msmith on 12/8/15.
- ActionStack() - Constructor for class deformablemesh.util.actions.ActionStack
-
- activate3DFramePicker() - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- activateSelectMeshMode() - Method in class deformablemesh.gui.RingController
-
- add(double[], double[], double) - Static method in class deformablemesh.util.Vector3DOps
-
Displacing point a by the distance f along vector b.
- addChannel(double[][][], double, double, Color3f) - Method in class deformablemesh.meshview.MultiChannelVolumeTexture
-
- addChannelVolume(ChannelVolume) - Method in class deformablemesh.meshview.MeshFrame3D
-
- addClasses() - Method in class deformablemesh.gui.SwingJSTerm
-
- addCloseListener(Runnable) - Method in class deformablemesh.gui.render2d.RenderFrame2D
-
- addConnection(Connection3D) - Method in class deformablemesh.geometry.ConnectionRemesher
-
- addContrastableListener(IntensityRanges.Contrastable) - Method in class deformablemesh.gui.IntensityRanges
-
- addCursor(ThreeDCursor) - Method in class deformablemesh.gui.meshinitialization.SlicePicker
-
- addCurve(List<double[]>) - Method in class deformablemesh.gui.Slice3DView
-
- addDataObject(DataObject) - Method in class deformablemesh.meshview.MeshFrame3D
-
- addDataObject(DataObject, double, double, double) - Method in class deformablemesh.meshview.MeshFrame3D
-
- addDragListener() - Method in class deformablemesh.gui.meshinitialization.SlicePicker
-
- addDrawable(Drawable) - Method in class deformablemesh.gui.Slice3DView
-
- addDrawables(List<Drawable>) - Method in class deformablemesh.gui.Slice3DView
-
- addExternalEnergy(ExternalEnergy) - Method in class deformablemesh.geometry.DeformableLine3D
-
- addExternalEnergy(ExternalEnergy) - Method in class deformablemesh.geometry.DeformableMesh3D
-
- addFrameListener(FrameListener) - Method in class deformablemesh.gui.RingController
-
- addFrameListener(FrameListener) - Method in class deformablemesh.SegmentationController
-
Adds a new frame listener that gets notified whenever: nextFrame, previousFrame, setFrame, or the backing imageplus is changed.
- addFrameListener(FrameListener) - Method in class deformablemesh.SegmentationModel
-
- addInterceptable(Interceptable) - Method in class deformablemesh.geometry.CompositeInterceptables
-
- additionalControls() - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- addKeyListener(KeyListener) - Method in class deformablemesh.meshview.MeshFrame3D
-
- addLights() - Method in class deformablemesh.meshview.MeshFrame3D
-
- addMesh(DeformableMesh3D) - Method in class deformablemesh.SegmentationController
-
Adds the mesh to the currently selected track.
- addMesh(int, DeformableMesh3D) - Method in class deformablemesh.SegmentationController
-
Adds the provided mesh to the model.
- addMesh(DeformableMesh3D) - Method in class deformablemesh.simulations.GrowingDroplet
-
- addMesh(int, DeformableMesh3D) - Method in class deformablemesh.track.MeshTracker
-
Adds a mesh to the currently selected.
- addMesh(Integer, DeformableMesh3D) - Method in class deformablemesh.track.Track
-
- addMeshFrame3D(MeshFrame3D) - Method in class deformablemesh.gui.ControlFrame
-
- addMeshListener(FrameListener) - Method in class deformablemesh.SegmentationController
-
Adds a listener, that gets notified every time the displayed meshes should change.
- addMeshListener(FrameListener) - Method in class deformablemesh.SegmentationModel
-
- addMeshToTrack(int, DeformableMesh3D, Track) - Method in class deformablemesh.SegmentationModel
-
- addMeshToTrack(int, DeformableMesh3D, Track) - Method in class deformablemesh.track.MeshTracker
-
- addMeshTrack(Track) - Method in class deformablemesh.meshview.MeshViewer
-
- addMeshTrack(Track) - Method in class deformablemesh.SegmentationModel
-
- addMeshTracks(List<Track>) - Method in class deformablemesh.track.MeshTracker
-
- addMouseAdapter(MouseAdapter) - Method in class deformablemesh.gui.Slice3DView
-
- addMouseListener(MouseListener) - Method in class deformablemesh.gui.meshinitialization.SlicePicker
-
- addMouseMotionListener(MouseMotionListener) - Method in class deformablemesh.gui.meshinitialization.SlicePicker
-
- addObject(DataObject) - Method in class deformablemesh.meshview.DataCanvas
-
Adds a "DataObject" which is just an interface for adding a branch group.
- addPickListener(CanvasView) - Method in class deformablemesh.meshview.MeshFrame3D
-
- addPlaneChangeListener(FurrowInput.PlaneChangeListener) - Method in class deformablemesh.gui.FurrowInput
-
- addPoint(T, double, double) - Method in interface deformablemesh.util.astar.PossiblePath
-
- addProjectable(Projectable) - Method in class deformablemesh.gui.meshinitialization.SlicePicker
-
- addProjectable(Projectable, Color) - Method in class deformablemesh.gui.meshinitialization.SlicePicker
-
- addProjectableMesh(ProjectableMesh, DeformableMesh3D) - Method in class deformablemesh.gui.meshinitialization.SlicePicker
-
- addReadyObserver(ReadyObserver) - Method in class deformablemesh.gui.SwingJSTerm
-
- addRegionsToAvoid(List<Box3D>) - Method in class deformablemesh.MeshDetector
-
- addShape(Shape) - Method in class deformablemesh.gui.Slice3DView
-
- addSnakeListener(CanvasView) - Method in class deformablemesh.meshview.DataCanvas
-
Adding a snake listener sets 'picking' events where using the mouse on the 3d view can
cause interactions.
- addStateListener(StateListener) - Method in class deformablemesh.util.actions.ActionStack
-
- addTabbedPanel(Component, String) - Method in class deformablemesh.gui.ControlFrame
-
- addTracer(Track) - Method in class deformablemesh.SegmentationController
-
Addes a line that follows the center of mass of the provided mesh track to the current frame.
- addTrack(Track) - Method in class deformablemesh.track.MeshTracker
-
- addTransientObject(DataObject) - Method in class deformablemesh.meshview.MeshFrame3D
-
- addTransientObject(DataObject) - Method in class deformablemesh.SegmentationController
-
Adds a data object to the current meshframe, the object is "transient" and will be removed
when clear transient objects is called.
- addTriangle(Triangle3D) - Method in class deformablemesh.geometry.ConnectionRemesher
-
- addUndoStateListener(StateListener) - Method in class deformablemesh.SegmentationController
-
Gets notified when the action stack updates the value.
- addViewListener(DataCanvas.ViewListener) - Method in class deformablemesh.meshview.DataCanvas
-
- afterClosing() - Method in class deformablemesh.gui.meshinitialization.CircularMeshInitializationDialog
-
- afterClosing() - Method in class deformablemesh.gui.meshinitialization.FurrowInitializer
-
- ALPHA - Variable in class deformablemesh.geometry.DeformableLine3D
-
- ALPHA - Variable in class deformablemesh.geometry.DeformableMesh3D
-
- ALPHA - Variable in class deformablemesh.ringdetection.ContractileRingDetector
-
- analyzeTimeCourses(File) - Static method in class deformablemesh.util.MeshFaceObscuring
-
- analyzeTimeCourses(List<Track>, String) - Static method in class deformablemesh.util.MeshFaceObscuring
-
- analyzeTracks(List<Track>, MeshImageStack, int, double) - Static method in class deformablemesh.util.MeshFaceObscuring
-
- analyzeTracks(Track, List<Track>, double) - Static method in class deformablemesh.util.MeshFaceObscuring
-
Analyzes the provided tracks.
- AngleGenerator - Class in deformablemesh.geometry
-
Created by melkor on 2/8/16.
- AngleGenerator(int, int) - Constructor for class deformablemesh.geometry.AngleGenerator
-
- appendToDisplay(String) - Method in class deformablemesh.gui.SwingJSTerm
-
- applyMask(ImageStack, ImageStack) - Static method in class deformablemesh.util.MeshImageOps
-
- applyRenderingHints(Graphics2D) - Static method in class deformablemesh.gui.GuiTools
-
For making a g2d that draws nicely.
- applyTracking(List<Track>, MeshImageStack, Path) - Static method in class deformablemesh.io.TrackMateAdapter
-
Takes the provided Tracks for the provided image file and attempts to link them based on associated positions.
- area - Variable in class deformablemesh.geometry.Triangle3D
-
- Arrow - Class in deformablemesh.meshview
-
- Arrow() - Constructor for class deformablemesh.meshview.Arrow
-
Constructs an Arrow with default length of 1, width of 1/3, tip is 0.5 and tail_fraction is 0.4.
- Arrow(double, double) - Constructor for class deformablemesh.meshview.Arrow
-
Uses default values for tip: 0.5 of length and tail_width: 0.4 of width
- Arrow(double, double, double) - Constructor for class deformablemesh.meshview.Arrow
-
Uses default tip tail_width of 0.4 cone width.
- Arrow(double, double, double, double) - Constructor for class deformablemesh.meshview.Arrow
-
Construct an arrow with the supplied geometry
- asJPanel(JFrame) - Method in class deformablemesh.meshview.MeshFrame3D
-
- asJPanel(Window) - Method in class deformablemesh.meshview.MeshFrame3D
-
- AStarBasic<T> - Class in deformablemesh.util.astar
-
A path finding routine.
- AStarBasic(Boundary<T>, BasicHeuristic<T>, BasicCost<T>, ChoiceGenerator<T>, History<T>) - Constructor for class deformablemesh.util.astar.AStarBasic
-
- AStarXY - Class in deformablemesh.util.astar
-
Created by msmith on 10/28/15.
- AStarXY() - Constructor for class deformablemesh.util.astar.AStarXY
-
- autotrackAvailableTracks() - Method in class deformablemesh.SegmentationController
-
- average(double[]...) - Static method in class deformablemesh.util.Vector3DOps
-
- averageRadius(List<double[]>) - Method in class deformablemesh.geometry.Furrow3D
-
Returns the average value of the distance a collection of points is from the
center of this furrow3D.
- Axis3D - Class in deformablemesh.meshview
-
User: msmith
Date: 8/8/13
Time: 7:52 AM
- Axis3D() - Constructor for class deformablemesh.meshview.Axis3D
-
- calculateActinIntensity() - Method in class deformablemesh.SegmentationModel
-
- calculateAllInterfaceTimeScans() - Method in class deformablemesh.SegmentationController
-
Iterates over all of the meshes and calculates intensity.
- calculateAllVolumes(List<Track>, MeshImageStack) - Static method in class deformablemesh.util.MeshAnalysis
-
Generates a text window with the time series for all of the tracks provided.
- calculateAverageCurvature(DeformableMesh3D) - Static method in class deformablemesh.geometry.CurvatureCalculator
-
Calculates the average kappaH value for the whole mesh.
- calculateAverageIntensity(MeshImageStack, List<Triangle3D>, double) - Static method in class deformablemesh.DeformableMesh3DTools
-
- calculateAverageIntensity(int, double) - Method in class deformablemesh.util.MeshAnalysis
-
- calculateCenterOfMass(List<Track>) - Method in class deformablemesh.track.FrameToFrameDisplacement
-
Calculates the center of mass based on the provided tracks.
- calculateCurvature() - Method in class deformablemesh.geometry.CurvatureCalculator
-
Calculates the curvature and normal at each point.
- calculateCurvature() - Method in class deformablemesh.geometry.DeformableMesh3D
-
- calculateCurvatureGradient(int) - Method in class deformablemesh.geometry.CurvatureCalculator
-
Can we calculate a gradient of curvatures.
- calculateIntensity(Box3D, MeshImageStack) - Static method in class deformablemesh.DeformableMesh3DTools
-
- calculateIntensity(MeshImageStack, double) - Method in class deformablemesh.geometry.DeformableMesh3D
-
Thickness is in um.
- calculateInterfaceLineScan(Track) - Method in class deformablemesh.SegmentationModel
-
- calculateInterfaceLineScan(int, List<Track>) - Method in class deformablemesh.SegmentationModel
-
- calculateInterfaceLineScans() - Method in class deformablemesh.SegmentationModel
-
- calculateLineScans() - Method in class deformablemesh.SegmentationController
-
TODO remove
- calculateLineScans() - Method in class deformablemesh.SegmentationModel
-
- calculateLineScans(int, double) - Method in class deformablemesh.util.MeshAnalysis
-
- calculateMeanCurvatureNormal(Node3D, List<Triangle3D>) - Static method in class deformablemesh.geometry.CurvatureCalculator
-
- calculateMeanCurvatureNormalMixedArea(Node3D, List<Triangle3D>) - Static method in class deformablemesh.geometry.CurvatureCalculator
-
This takes a node and calculates the relevant
- calculateMeanNormal(Node3D, List<Triangle3D>) - Static method in class deformablemesh.geometry.CurvatureCalculator
-
Calculates the normal
- calculateMixedArea(Node3D) - Method in class deformablemesh.geometry.CurvatureCalculator
-
- calculateMixedArea(int) - Method in class deformablemesh.geometry.CurvatureCalculator
-
Overload for accessing mixed area via the index.
- calculateMixedArea(Node3D, List<Triangle3D>) - Static method in class deformablemesh.geometry.CurvatureCalculator
-
- calculateNormalScan(MeshImageStack, double) - Method in class deformablemesh.geometry.DeformableMesh3D
-
- calculateObscuringMeshes(double) - Method in class deformablemesh.SegmentationController
-
Calculates the surface area over time, and the surface areas that are obscured by neighboring meshes.
- calculateRadius(List<Connection3D>) - Method in class deformablemesh.geometry.Furrow3D
-
- calculateSelectedInterfaceTimeScans() - Method in class deformablemesh.SegmentationController
-
Calculates the time course for the selected mesh only.
- calculateSlices() - Method in class deformablemesh.util.connectedcomponents.Region
-
- calculateStress() - Method in class deformablemesh.geometry.DeformableMesh3D
-
- calculateSurfaceArea(DeformableMesh3D) - Static method in class deformablemesh.DeformableMesh3DTools
-
- calculateVolume(double[], double[], List<Triangle3D>) - Static method in class deformablemesh.DeformableMesh3DTools
-
normal *dot* direction + |position|*direction
- calculateVolume() - Method in class deformablemesh.geometry.DeformableMesh3D
-
- calculateVolume(double[]) - Method in class deformablemesh.geometry.DeformableMesh3D
-
- calculateVolume() - Method in class deformablemesh.SegmentationModel
-
- calculateVolume() - Method in class deformablemesh.util.connectedcomponents.Region
-
- calculateVolume(ImageStack) - Static method in class deformablemesh.util.MeshImageOps
-
- cancel() - Method in class deformablemesh.gui.RingController
-
- canRedo() - Method in class deformablemesh.SegmentationController
-
Checks if there is an action to be undone.
- canUndo() - Method in class deformablemesh.SegmentationController
-
Checks if there is an action to be undone.
- CanvasController - Class in deformablemesh.meshview
-
Mouse listener class for handling the basic interactions with the DataCanvas interactions.
- CanvasView - Interface in deformablemesh.meshview
-
- center - Variable in class deformablemesh.geometry.Triangle3D
-
- centerAndRadius(List<Node3D>) - Static method in class deformablemesh.DeformableMesh3DTools
-
Calculates the center based on the position of the nodes.
- centerCamera(double[]) - Method in class deformablemesh.meshview.DataCanvas
-
- centerOfMass(List<DeformableMesh3D>) - Static method in class deformablemesh.track.FrameToFrameDisplacement
-
- centerSelectedMesh() - Method in class deformablemesh.SegmentationController
-
- centerView(double[]) - Method in class deformablemesh.meshview.MeshFrame3D
-
- chainActions(UndoableActions, UndoableActions) - Static method in class deformablemesh.util.actions.ActionStack
-
For performing multiple actions such that they are undone, and redone together and in sequence.
- changeBackgroundColor(Color) - Method in class deformablemesh.meshview.DataCanvas
-
- changeVolumeClipping(int, int) - Method in class deformablemesh.meshview.MeshFrame3D
-
- changeVolumeClipping(int, int) - Method in class deformablemesh.SegmentationController
-
Adjust the min/max values for clipping the image.
- ChannelVolume - Class in deformablemesh.meshview
-
For adding a second channel to display.
- ChannelVolume(MeshImageStack, Color) - Constructor for class deformablemesh.meshview.ChannelVolume
-
- checkErrorRate(int) - Static method in class deformablemesh.geometry.ShellMesh
-
- checkNeighbors(int, int, int, ImageStack) - Static method in class deformablemesh.util.MeshImageOps
-
Checks the neighborhood for a zero to see if this point lies on an edge.
- ChoiceGenerator<T> - Interface in deformablemesh.util.astar
-
- chooseToContrastChannelVolume() - Method in class deformablemesh.meshview.MeshFrame3D
-
- chooseToremoveChannelVolume() - Method in class deformablemesh.meshview.MeshFrame3D
-
- CircularMeshInitializationDialog - Class in deformablemesh.gui.meshinitialization
-
Add spheres to create a single shape, then find the center of mass of the spheres and create
a mesh.
- CircularMeshInitializationDialog(SegmentationController) - Constructor for class deformablemesh.gui.meshinitialization.CircularMeshInitializationDialog
-
- clear() - Method in class deformablemesh.gui.meshinitialization.SlicePicker
-
- clear() - Method in class deformablemesh.gui.Slice3DView
-
- clearEnergies() - Method in class deformablemesh.geometry.DeformableLine3D
-
- clearEnergies() - Method in class deformablemesh.geometry.DeformableMesh3D
-
- clearHistory() - Method in class deformablemesh.SegmentationController
-
The history can take up a lot of memory, especially for actions like deformlAllMeshes.
- clearHistory() - Method in class deformablemesh.util.actions.ActionStack
-
- clearMesh(DeformableMesh3D) - Method in class deformablemesh.SegmentationController
-
Least efficient way to clear a mesh.
- clearMeshes() - Method in class deformablemesh.track.MeshTracker
-
- clearMeshFromTrack(Track, int) - Method in class deformablemesh.SegmentationController
-
- clearMeshFromTrack(Track, int, DeformableMesh3D) - Method in class deformablemesh.SegmentationController
-
Clears the mesh specified mesh from the track at the specific time frame.
- clearSelectedMesh() - Method in class deformablemesh.SegmentationController
-
Remove the currently selected mesh, from the current frame only.
- clearTransientObjects() - Method in class deformablemesh.SegmentationController
-
clears all transient objects, objects being displayed in the 3d viewer that were added as transient objects.
- clearTransients() - Method in class deformablemesh.meshview.MeshFrame3D
-
- clicked(MouseEvent) - Method in class deformablemesh.meshview.DataCanvas
-
Gets the 'results' a pick result and send the results on down
the line
- cm - Variable in class deformablemesh.geometry.Furrow3D
-
- cm - Variable in class deformablemesh.util.MeshGroup
-
- ColorInterpolator - Interface in deformablemesh.util
-
- ColorSuggestions - Class in deformablemesh.util
-
Created by msmith on 6/21/16.
- ColorSuggestions() - Constructor for class deformablemesh.util.ColorSuggestions
-
- CompositeInterceptables - Class in deformablemesh.geometry
-
Created by melkor on 3/9/16.
- CompositeInterceptables(Collection<? extends Interceptable>) - Constructor for class deformablemesh.geometry.CompositeInterceptables
-
- CompositeInterceptables(Interceptable...) - Constructor for class deformablemesh.geometry.CompositeInterceptables
-
- confine(Box3D) - Method in class deformablemesh.geometry.DeformableMesh3D
-
- confineMesh(DeformableMesh3D) - Method in class deformablemesh.SegmentationController
-
If a point is outside of the boundary, it is moved to the edge along that axis.
- ConnectedComponents2D - Class in deformablemesh.util.connectedcomponents
-
Connect components for 2D.
- ConnectedComponents2D(ImageProcessor) - Constructor for class deformablemesh.util.connectedcomponents.ConnectedComponents2D
-
Prepares a workspace for performing a connect components routine on the provided image.
- ConnectedComponents3D - Class in deformablemesh.util.connectedcomponents
-
- ConnectedComponents3D() - Constructor for class deformablemesh.util.connectedcomponents.ConnectedComponents3D
-
- Connection3D - Class in deformablemesh.geometry
-
User: msmith
Date: 7/2/13
Time: 7:56 AM
- connection_index - Variable in class deformablemesh.geometry.DeformableLine3D
-
- connection_index - Variable in class deformablemesh.geometry.DeformableMesh3D
-
- connectionRemesh(boolean) - Method in class deformablemesh.gui.ControlFrame
-
- ConnectionRemesher - Class in deformablemesh.geometry
-
This class will remesh based on connection lengths.
- ConnectionRemesher() - Constructor for class deformablemesh.geometry.ConnectionRemesher
-
- connections - Variable in class deformablemesh.geometry.DeformableLine3D
-
- connections - Variable in class deformablemesh.geometry.DeformableMesh3D
-
- contains(double[]) - Method in class deformablemesh.geometry.Box3D
-
- contains(Box3D) - Method in class deformablemesh.geometry.Box3D
-
- contains(double[]) - Method in class deformablemesh.geometry.CompositeInterceptables
-
- contains(double[]) - Method in class deformablemesh.geometry.Furrow3D
-
- contains(double[]) - Method in interface deformablemesh.geometry.Interceptable
-
- contains(double[]) - Method in class deformablemesh.geometry.InterceptingMesh3D
-
- contains(double[]) - Method in class deformablemesh.geometry.Sphere
-
- contains(T) - Method in interface deformablemesh.util.astar.Boundary
-
- containsKey(Integer) - Method in class deformablemesh.track.Track
-
- containsMesh(DeformableMesh3D) - Method in class deformablemesh.track.Track
-
- containsNode(Node3D) - Method in class deformablemesh.geometry.Triangle3D
-
- contentsChanged(ListDataEvent) - Method in class deformablemesh.gui.RingController
-
- continuousPaths(FurrowTransformer) - Method in class deformablemesh.geometry.ProjectableMesh
-
Gets a continuous path version of the projected shape.
- ContractileRingDataObject - Class in deformablemesh.meshview
-
Construct with normalized coordinates.
- ContractileRingDataObject(List<double[]>) - Constructor for class deformablemesh.meshview.ContractileRingDataObject
-
- ContractileRingDetector - Class in deformablemesh.ringdetection
-
This used to be a way to initialize a contractile ring.
- ContractileRingDetector() - Constructor for class deformablemesh.ringdetection.ContractileRingDetector
-
- ControlFrame - Class in deformablemesh.gui
-
GUI commands -> Delegate to segmentation controller.
- ControlFrame(SegmentationController) - Constructor for class deformablemesh.gui.ControlFrame
-
- copyMesh(DeformableMesh3D) - Method in class deformablemesh.SegmentationController
-
Creates a copy of the provided mesh.
- copyOf(DeformableMesh3D) - Static method in class deformablemesh.DeformableMesh3DTools
-
- copyValues() - Method in class deformablemesh.MeshImageStack
-
Copies the image data from the image stack to the double[][] backing the
image data that is used for obtaining values.
- copyValues(ImagePlus) - Method in class deformablemesh.MeshImageStack
-
For creating a backing double array of another ImagePlus that uses the same geometry as the original image
plus.
- create3DObject() - Method in class deformablemesh.geometry.DeformableMesh3D
-
- create3DObject() - Method in class deformablemesh.geometry.Furrow3D
-
- create3DPreviewer(Window) - Method in class deformablemesh.meshview.VolumeContrastSetter
-
- Create3DTrainingDataFromMeshes - Class in deformablemesh.util
-
- Create3DTrainingDataFromMeshes(List<Track>, ImagePlus) - Constructor for class deformablemesh.util.Create3DTrainingDataFromMeshes
-
- createAndShowBinaryImage() - Method in class deformablemesh.gui.meshinitialization.CircularMeshInitializationDialog
-
- createAppearance() - Method in class deformablemesh.meshview.ContractileRingDataObject
-
- createAppearance() - Method in class deformablemesh.meshview.LineDataObject
-
- createAppearance() - Method in class deformablemesh.meshview.PlotSurface
-
- createAppearance() - Method in class deformablemesh.meshview.SphereDataObject
-
- createBinaryImage() - Method in class deformablemesh.SegmentationController
-
Creates an imageplus that is a binary image with pixes values 1 inside a mesh and 0 outside.
- createBinaryImage() - Method in class deformablemesh.SegmentationModel
-
- createBinaryRepresentation(MeshImageStack, ImagePlus, Map<Integer, DeformableMesh3D>) - Static method in class deformablemesh.DeformableMesh3DTools
-
- createBinaryRepresentation(MeshImageStack, DeformableMesh3D) - Static method in class deformablemesh.DeformableMesh3DTools
-
- createBinarySlice() - Method in class deformablemesh.ringdetection.ContractileRingDetector
-
- createButtonAdjustMaximum() - Method in class deformablemesh.gui.ControlFrame
-
- createButtonAdjustMinimum() - Method in class deformablemesh.gui.ControlFrame
-
- createButtonClearMesh() - Method in class deformablemesh.gui.ControlFrame
-
- createButtonClearTransients() - Method in class deformablemesh.gui.ControlFrame
-
- createButtonDeform() - Method in class deformablemesh.gui.ControlFrame
-
- createButtonInitializeMesh2() - Method in class deformablemesh.gui.ControlFrame
-
- createButtonNext() - Method in class deformablemesh.gui.ControlFrame
-
- createButtonPrevious() - Method in class deformablemesh.gui.ControlFrame
-
- createButtonRemesh() - Method in class deformablemesh.gui.ControlFrame
-
- createButtons() - Method in class deformablemesh.meshview.VolumeContrastSetter
-
- createButtonShowForces() - Method in class deformablemesh.gui.ControlFrame
-
- createButtonShowMeshVolume(JPanel) - Method in class deformablemesh.gui.ControlFrame
-
- createButtonShowVolume() - Method in class deformablemesh.gui.ControlFrame
-
- createButtonSnapshot(JPanel) - Method in class deformablemesh.gui.ControlFrame
-
- createCascades() - Method in class deformablemesh.util.DistanceTransformMosaicImage
-
- createComboControl(String, SetValue, int) - Static method in class deformablemesh.gui.GuiTools
-
- createConnectionRemesh() - Method in class deformablemesh.gui.ControlFrame
-
- createCroppedImage(int, int, double[][]) - Method in class Mouse_X
-
Creates the rotated image by mapping the values located in
cnet_map to a new rectangular image.
- createCroppedImageRGB(int, int, double[][]) - Method in class Mouse_X
-
RGB version that interpolates each pixel of the int array
separately, this uses bi-linear interpolation...I hope
- CreateCrossSectionMovies - Class in deformablemesh.examples
-
- createCurvatureHistogram(List<double[]>) - Method in class deformablemesh.geometry.CurvatureCalculator
-
- createCurvatureHistogram() - Method in class deformablemesh.geometry.CurvatureCalculator
-
- createCurvaturePlots() - Method in class deformablemesh.simulations.SphericalCavity
-
- createDataObject() - Method in class deformablemesh.geometry.DeformableLine3D
-
- createDataObject() - Method in class deformablemesh.geometry.Sphere
-
Creates a new data object or re-uses the old one.
- createDataTable() - Method in class deformablemesh.SegmentationController
-
- createDeformingMeshApplication() - Static method in class deformablemesh.Deforming3DMesh_Plugin
-
- createDeformingMeshApplication() - Static method in class DeformingMesh3DApp
-
- createDeformingMeshApplication() - Static method in class DeformingMeshSans3D
-
- createDisplay() - Method in class deformablemesh.simulations.GrowingDroplet
-
- createDisplay() - Method in class deformablemesh.simulations.ManyDrops
-
- createDisplay() - Method in class deformablemesh.simulations.TwoDrops
-
- createDistanceMapImage(ImageStack) - Method in class deformablemesh.util.Create3DTrainingDataFromMeshes
-
- createEnergyImage() - Method in class deformablemesh.SegmentationController
-
Creates an image that is generated by the current image energy.
- createEnergyImage() - Method in class deformablemesh.SegmentationModel
-
- createEnergySelector() - Method in class deformablemesh.gui.ControlFrame
-
- createFurrowInput() - Method in class deformablemesh.gui.RingController
-
Creates a furrow input that is tied to this ring controller.
- createFurrowSlice(int) - Method in class deformablemesh.ringdetection.ContractileRingDetector
-
- createFurrowTransform(double[], double[]) - Method in class deformablemesh.MeshImageStack
-
- createFurrowTransform(double[], double[]) - Method in class deformablemesh.SegmentationController
-
The provided normal and position represent a plane.
- createGrowingCascades() - Method in class deformablemesh.util.DistanceTransformMosaicImage
-
- createHeighMapDataObject() - Method in class deformablemesh.simulations.HeightMapSurface
-
- createInputField(String, SetValue, double, ReadyObserver) - Static method in class deformablemesh.gui.GuiTools
-
- createLabeledImage() - Method in class deformablemesh.util.DistanceTransformMosaicImage
-
- createLabelledImage(List<Track>) - Method in class deformablemesh.SegmentationController
-
Creates a labelled image of the provided tracks.
- createLineAppearance() - Method in class deformablemesh.meshview.DeformableMeshDataObject
-
- createMaskImage(ImageStack) - Method in class deformablemesh.util.Create3DTrainingDataFromMeshes
-
Creates a binary stack (ByteProcessor#threshold(int)) from the provided labelled image.
- createMembraneImage(ImageStack) - Method in class deformablemesh.util.Create3DTrainingDataFromMeshes
-
Creates a "binary" image, 255 or 0, of the membrane by checking neighboring neighboring pixels for either being
background or another blob.
- createMeshFromSpheres(List<Sphere>, int) - Static method in class deformablemesh.gui.meshinitialization.CircularMeshInitializationDialog
-
- createMeshGroup(List<DeformableMesh3D>) - Static method in class deformablemesh.util.GroupDynamics
-
- createMosaicImage() - Method in class deformablemesh.SegmentationController
-
Creates a mosaic image, which is like a binary image, execept each mesh is labelled with it's color instead of
binary.
- createMosaicImage() - Method in class deformablemesh.SegmentationModel
-
- createMosaicRepresentation(MeshImageStack, ImagePlus, List<Track>) - Static method in class deformablemesh.DeformableMesh3DTools
-
- createMouseAdapter(SegmentationController) - Method in class deformablemesh.track.MeshTrackManager
-
- createNewChannelVolume() - Method in class deformablemesh.meshview.MeshFrame3D
-
- createNewMeshTrack(int, DeformableMesh3D) - Method in class deformablemesh.track.MeshTracker
-
Creates a new track, adds the provided mesh, adds it to the tracked tracks,
and selects it.
- createNoImage() - Static method in class deformablemesh.gui.Slice3DView
-
- createNullImage() - Static method in class deformablemesh.gui.Slice3DView
-
- createOffscreenCanvas() - Method in class deformablemesh.meshview.DataCanvas
-
- createOutput(double) - Method in class deformablemesh.util.MeshAnalysis
-
- createOvula() - Method in class Mouse_X
-
This sizes out the rectangle and then gets the pixel values in the image then plots them onto a new image stack
- createRectangleMesh(double, double, double, double) - Static method in class deformablemesh.DeformableMesh3DTools
-
Makes a rectangular prism mesh with triangular elements.
- createRenderingMeshFrame() - Static method in class deformablemesh.gui.render2d.RenderFrame2D
-
- createRhombicDodecahedron(double) - Static method in class deformablemesh.DeformableMesh3DTools
-
- createScaledCascades(int) - Method in class deformablemesh.util.DistanceTransformMosaicImage
-
- createSlice(FurrowTransformer) - Method in class deformablemesh.MeshImageStack
-
- createSlice(double[], double[]) - Method in class deformablemesh.MeshImageStack
-
- createSlice(double[], double[]) - Method in class deformablemesh.SegmentationController
-
Creates an image based on a furrow transformer built using the provided position and normal.
- createSlice(FurrowTransformer) - Method in class deformablemesh.SegmentationController
-
Creates an Image based on slicing the working volume with the plane represented by this transformer.
- createSpotList(Model, MeshImageStack) - Static method in class deformablemesh.io.TrackMateAdapter
-
- createSubMesh(List<Node3D>) - Method in class deformablemesh.geometry.DeformableMesh3D
-
Creates a mesh consisting of all the provided nodes, and their immediate neighbors.
- createSubMesh(DeformableMesh3D, Set<Triangle3D>) - Method in class deformablemesh.SegmentationModel
-
- createSubStack(Box3D) - Method in class deformablemesh.MeshImageStack
-
- createSurface() - Method in class deformablemesh.simulations.WavesOnASheet
-
- createSurfaces(double[]) - Method in class deformablemesh.meshview.Sizeable3DSurface
-
- createTailAppearance() - Method in class deformablemesh.meshview.Arrow
-
- createTestBlock() - Static method in class deformablemesh.DeformableMesh3DTools
-
Creates a 2x2x2 test block.
- createTestBlock(double, double, double) - Static method in class deformablemesh.DeformableMesh3DTools
-
-w/2,-h/2, d/2
0------------------1
/ /|
/ / |
/ | / |
3------------------2 |
| 4- - - - | -5
| / | /
| | /
| |/
7------------------6
w/2,h/2, -d/2
- createTextOuputPane(String) - Static method in class deformablemesh.gui.GuiTools
-
- createTexturedPlane3DObject(MeshImageStack) - Method in class deformablemesh.geometry.Furrow3D
-
- createTipAppearance() - Method in class deformablemesh.meshview.Arrow
-
- createUniqueLabelsRepresentation(MeshImageStack, List<Track>) - Static method in class deformablemesh.DeformableMesh3DTools
-
- createXYAStar(ImageProcessor, int[], int[]) - Static method in class deformablemesh.util.astar.AStarXY
-
- createXYPossiblePath(int[]) - Static method in class deformablemesh.util.astar.AStarXY
-
- cross(double[], double[]) - Static method in class deformablemesh.util.Vector3DOps
-
- CURRENT - Variable in class deformablemesh.MeshImageStack
-
- CurvatureCalculator - Class in deformablemesh.geometry
-
A class used for calculating curvatures based on
"Discrete Differential-Geometry Operators for Triangled 2-Manifolds
Mark Meyer, Mathieu Desbrun, Peter Schroeder, and Alan H.
- CurvatureCalculator(DeformableMesh3D) - Constructor for class deformablemesh.geometry.CurvatureCalculator
-
- curvatureSnapShot() - Method in class deformablemesh.SegmentationController
-
Takes the currently selected mesh and looks for neighbors.
- curvatureSurfacePlot() - Method in class deformablemesh.SegmentationController
-
Creates a 3D plot frame for the currently selected mesh, and plots the curvature on the surface.
- CurvatureSurfacePlot - Class in deformablemesh.util
-
Created by msmith on 05/06/19.
- CurvatureSurfacePlot(DeformableMesh3D) - Constructor for class deformablemesh.util.CurvatureSurfacePlot
-
- GAMMA - Variable in class deformablemesh.geometry.DeformableLine3D
-
- GAMMA - Variable in class deformablemesh.geometry.DeformableMesh3D
-
- GAMMA - Variable in class deformablemesh.ringdetection.ContractileRingDetector
-
- GaussianKernels - Class in deformablemesh.util
-
Created by msmith on 2/1/16.
- GaussianKernels() - Constructor for class deformablemesh.util.GaussianKernels
-
- generateConnectionMap(DeformableMesh3D) - Static method in class deformablemesh.DeformableMesh3DTools
-
- generateGrid() - Static method in class deformablemesh.util.GroupDynamics
-
- generateImageEnergy(DeformableMesh3D) - Method in class deformablemesh.SegmentationModel
-
- generateMosaicImage(List<DeformableMesh3D>) - Static method in class deformablemesh.track.FrameToFrameDisplacement
-
- generateNormals(double[], int[]) - Method in class deformablemesh.meshview.PlotSurface
-
- generateRegion() - Method in class deformablemesh.util.connectedcomponents.ShrinkRegion
-
- generateSurface() - Method in class deformablemesh.simulations.GrowingDroplet
-
- generateTrainingData(int, int) - Method in class deformablemesh.SegmentationController
-
Training data consists of two images.
- generateVoxelPlane(MeshImageStack, int[], double[]) - Static method in class deformablemesh.geometry.BinaryMeshGenerator
-
- get(int, int) - Method in class deformablemesh.util.connectedcomponents.ConnectedComponents2D
-
- get(int) - Method in class deformablemesh.util.connectedcomponents.ConnectedComponents2D
-
- get3DCoordinatesFromFurrowPlane(List<double[]>) - Method in class deformablemesh.ringdetection.ContractileRingDetector
-
- getAbsoluteMinMax(int) - Method in class deformablemesh.meshview.MultiChannelVolumeTexture
-
- getAdjacencyMap(Map<Node3D, List<Connection3D>>) - Method in class deformablemesh.geometry.DeformableMesh3D
-
- getAllMeshTracks() - Method in class deformablemesh.track.MeshTracker
-
- getAllTracks() - Method in class deformablemesh.SegmentationController
-
- getAllTracks() - Method in class deformablemesh.SegmentationModel
-
- getAlpha() - Method in class deformablemesh.SegmentationController
-
- getAlpha() - Method in class deformablemesh.SegmentationModel
-
- getAverageIntensityAtBoundary() - Method in class deformablemesh.util.IntensitySurfacePlot
-
- getAverageIntensityAtNodes() - Method in class deformablemesh.util.IntensitySurfacePlot
-
- getAxisRotation(List<DeformableMesh3D>, List<DeformableMesh3D>) - Static method in class deformablemesh.util.GroupDynamics
-
Consider that a rigid body rotates the group of meshes.
- getBackgroundBlob() - Method in class deformablemesh.util.DistanceTransformMosaicImage
-
- getBackgroundColor() - Method in class deformablemesh.meshview.MeshFrame3D
-
- getBestConfigurationOnSameDevice(Window) - Static method in class deformablemesh.meshview.DataCanvas
-
Gets the best graphics configuration to display on the current device.
- getBeta() - Method in class deformablemesh.SegmentationController
-
- getBeta() - Method in class deformablemesh.SegmentationModel
-
- getBoundingBox() - Method in class deformablemesh.geometry.DeformableMesh3D
-
- getBounds() - Method in class deformablemesh.SegmentationController
-
Bounds of the current image being analyzed.
- getBounds() - Method in class deformablemesh.SegmentationModel
-
- getBranchGroup() - Method in class deformablemesh.meshview.Arrow
-
- getBranchGroup() - Method in class deformablemesh.meshview.Axis3D
-
- getBranchGroup() - Method in class deformablemesh.meshview.ContractileRingDataObject
-
- getBranchGroup() - Method in interface deformablemesh.meshview.DataObject
-
This is required to add to a group
- getBranchGroup() - Method in class deformablemesh.meshview.DeformableMeshDataObject
-
- getBranchGroup() - Method in class deformablemesh.meshview.FurrowPlaneDataObject
-
- getBranchGroup() - Method in class deformablemesh.meshview.LineDataObject
-
- getBranchGroup() - Method in class deformablemesh.meshview.PlotSurface
-
- getBranchGroup() - Method in class deformablemesh.meshview.Sizeable3DSurface
-
- getBranchGroup() - Method in class deformablemesh.meshview.SphereDataObject
-
- getBranchGroup() - Method in class deformablemesh.meshview.TexturedPlaneDataObject
-
- getBranchGroup() - Method in class deformablemesh.meshview.VectorField
-
- getBranchGroup() - Method in class deformablemesh.meshview.VolumeDataObject
-
- getCanvas() - Method in class deformablemesh.meshview.MeshFrame3D
-
- getCanvasBackgroundColor() - Method in class deformablemesh.meshview.DataCanvas
-
- getCanvasView() - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- getCenter() - Method in class deformablemesh.geometry.BinaryInterceptible
-
- getCenter() - Method in class deformablemesh.geometry.Box3D
-
- getCenter() - Method in class deformablemesh.geometry.InterceptingMesh3D
-
- getCenter() - Method in class deformablemesh.geometry.Sphere
-
- getCenter() - Method in class deformablemesh.util.connectedcomponents.Region
-
- getCenter(ImageStack) - Static method in class deformablemesh.util.MeshImageOps
-
- getCenterOfMass() - Method in class deformablemesh.geometry.BinaryMomentsOfInertia
-
center of mass:
c_x = sum_i [x_i m_i] / sum_i [m_i]
c_y = sum_i[ y_i m_i] / sum_i [m_i]
c_z = sum_i[ z_i m_i] / sum_i [m_i]
- getCenterOfMass() - Method in class deformablemesh.MeshImageStack
-
- getCenterOfMass(List<DeformableMesh3D>) - Static method in class deformablemesh.util.GroupDynamics
-
- getCenterRealCoordinates(DeformableMesh3D, MeshImageStack) - Static method in class deformablemesh.io.TrackMateAdapter
-
Uses the same algorithm that is used to get the real coordinates for spot/track generation.
- getCentroids() - Method in class deformablemesh.util.connectedcomponents.ConnectedComponents2D
-
Returns the centroids associated with this connected components.
- getChangeMagnitude(double, double, double, double[]) - Method in class deformablemesh.externalenergies.PerpendicularGradientEnergy
-
- getChangeSquared(double, double, double, double[]) - Method in class deformablemesh.externalenergies.PerpendicularGradientEnergy
-
- getChannelVolumes() - Method in class deformablemesh.meshview.MeshFrame3D
-
- getChoices(T) - Method in interface deformablemesh.util.astar.ChoiceGenerator
-
- getClampedMinMax() - Method in class deformablemesh.meshview.VolumeDataObject
-
- getClipValues() - Method in class deformablemesh.gui.IntensityRanges
-
- getClosableTabComponent(String, ActionListener) - Static method in class deformablemesh.gui.GuiTools
-
- getClosestPointOnPlane(double[]) - Method in class deformablemesh.geometry.Furrow3D
-
- getColor() - Method in class deformablemesh.geometry.DeformableMesh3D
-
- getColor() - Method in class deformablemesh.geometry.ProjectableMesh
-
- getColor() - Method in class deformablemesh.track.Track
-
- getColor(double) - Method in interface deformablemesh.util.ColorInterpolator
-
- getColor() - Method in class deformablemesh.util.connectedcomponents.Region
-
- getColor(double) - Method in class deformablemesh.util.HotAndCold
-
- getColorName(Color) - Static method in class deformablemesh.util.ColorSuggestions
-
- getConnectedNodes() - Method in class deformablemesh.geometry.DeformableMesh3D
-
- getConnections() - Method in class deformablemesh.geometry.DeformableMesh3D
-
- getContainedPixels(MeshImageStack, DeformableMesh3D) - Static method in class deformablemesh.DeformableMesh3DTools
-
Get pixels contained in the mesh.
- getContent() - Method in class deformablemesh.gui.meshinitialization.CircularMeshInitializationDialog
-
- getContentPane(JFrame) - Method in class deformablemesh.gui.RingController
-
- getCoordinates(int) - Method in class deformablemesh.geometry.DeformableMesh3D
-
- getCoordinates() - Method in class deformablemesh.geometry.Node3D
-
Creates a double[] with the position of this node.
- getCoordinates(int) - Method in class deformablemesh.geometry.Triangle3D
-
- getCortexThickness() - Method in class deformablemesh.SegmentationModel
-
- getCost(T) - Method in interface deformablemesh.util.astar.BasicHeuristic
-
An estimate of cost to get from point a to a final destination.
- getCurrent(int) - Method in class deformablemesh.track.MeshTracker
-
- getCurrentChannel() - Method in class deformablemesh.SegmentationController
-
Gets the currently selected channel.
- getCurrentFrame() - Method in class deformablemesh.MeshImageStack
-
Returns a single channel image plus of the current frame.
- getCurrentFrame() - Method in class deformablemesh.SegmentationController
-
Zero based frame number.
- getCurrentFrame() - Method in class deformablemesh.SegmentationModel
-
- getCurrentState() - Method in class deformablemesh.SegmentationController
-
The action stack controls the undo/redo commands.
- getCurrentState() - Method in class deformablemesh.util.actions.ActionStack
-
- getCursor() - Method in class deformablemesh.geometry.modifier.Selector
-
- getCurvatureMap() - Method in class deformablemesh.geometry.DeformableMesh3D
-
- getDataObject() - Method in class deformablemesh.geometry.DeformableLine3D
-
- getDataObject() - Method in class deformablemesh.geometry.Furrow3D
-
- getDataObject(MeshImageStack) - Method in class deformablemesh.util.connectedcomponents.Region
-
- getDeformationCount() - Method in class deformablemesh.SegmentationModel
-
- getDeformationSteps() - Method in class deformablemesh.SegmentationController
-
Gets the current number of deformations that have occurred.
- getDetector() - Method in class deformablemesh.gui.RingController
-
- getDistance(Node3D) - Method in class deformablemesh.geometry.Furrow3D
-
Gets the signed distance to the point, if the value is greater than 0 then the point is infront of the plane,
if it is negative then the point is behind the plane.
- getDistance() - Method in interface deformablemesh.util.astar.PossiblePath
-
- getDivisions() - Method in class deformablemesh.SegmentationController
-
- getDivisions() - Method in class deformablemesh.SegmentationModel
-
- getEffectiveNormal(double[]) - Method in class deformablemesh.externalenergies.SofterStericMesh
-
Finds the normal of the neighbor node nearest to the provided point.
- getEigenVectors() - Method in class deformablemesh.geometry.BinaryMomentsOfInertia
-
Returns the list of eigen vectors, and the eigen values.
- getEmptyStack() - Static method in class deformablemesh.MeshImageStack
-
- getEndPoint() - Method in interface deformablemesh.util.astar.PossiblePath
-
- getEnergy(double[]) - Method in class deformablemesh.externalenergies.BallooningEnergy
-
- getEnergy(double[]) - Method in interface deformablemesh.externalenergies.ExternalEnergy
-
- getEnergy(double[]) - Method in class deformablemesh.externalenergies.GradientEnergy
-
- getEnergy(double[]) - Method in class deformablemesh.externalenergies.IntensityEnergy
-
- getEnergy(double[]) - Method in class deformablemesh.externalenergies.NodeAttractor
-
- getEnergy(double[]) - Method in class deformablemesh.externalenergies.ParabolicSurface
-
- getEnergy(double[]) - Method in class deformablemesh.externalenergies.PerpendicularGradientEnergy
-
- getEnergy(double[]) - Method in class deformablemesh.externalenergies.PerpendicularIntensityEnergy
-
- getEnergy(double[]) - Method in class deformablemesh.externalenergies.PressureForce
-
- getEnergy(double[]) - Method in class deformablemesh.externalenergies.SmoothingForce
-
- getEnergy(double[]) - Method in class deformablemesh.externalenergies.SofterStericMesh
-
- getEnergy(double[]) - Method in class deformablemesh.externalenergies.StericMesh
-
- getEnergy(double[]) - Method in class deformablemesh.externalenergies.TriangleAreaDistributor
-
- getEnergy(double[]) - Method in class deformablemesh.externalenergies.VolumeConservation
-
- getEnergy(double[]) - Method in class deformablemesh.simulations.HeightMapSurface
-
- getExecutionErrors() - Method in class deformablemesh.SegmentationController
-
For the gui to check for errors.
- getExternalEnergies() - Method in class deformablemesh.geometry.DeformableMesh3D
-
- getExternalEnergies(DeformableMesh3D) - Method in class deformablemesh.SegmentationModel
-
- getExternalEnergies() - Method in class deformablemesh.SegmentationModel
-
returns a list of all the external energies, except 'ring energy' affecting the currently selected mesh.
- getFirstFrame() - Method in class deformablemesh.track.Track
-
- getForce(double, double, double, double[]) - Method in class deformablemesh.externalenergies.PerpendicularGradientEnergy
-
- getForce(double, double, double, double[]) - Method in class deformablemesh.externalenergies.PerpendicularIntensityEnergy
-
- getForward() - Method in class deformablemesh.meshview.DataCanvas
-
- getForward() - Method in class deformablemesh.meshview.MeshFrame3D
-
- getFrame() - Method in class deformablemesh.gui.ControlFrame
-
- getFrame(DeformableMesh3D) - Method in class deformablemesh.track.Track
-
- getFrontShape() - Method in class deformablemesh.meshview.FurrowPlaneDataObject
-
- getFurrow() - Method in class deformablemesh.gui.RingController
-
- getFurrow(int) - Method in class deformablemesh.gui.RingController
-
- getFurrow(int) - Method in class deformablemesh.ringdetection.ContractileRingDetector
-
- getFurrow() - Method in class deformablemesh.ringdetection.ContractileRingDetector
-
- getFurrow() - Method in class deformablemesh.ringdetection.FurrowTransformer
-
- getFurrows() - Method in class deformablemesh.gui.RingController
-
- getFurrows() - Method in class deformablemesh.ringdetection.ContractileRingDetector
-
- getFurrowSlice() - Method in class deformablemesh.ringdetection.ContractileRingDetector
-
- getFurrowTransformer() - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- getGamma(double) - Method in class deformablemesh.geometry.Node3D
-
Gamma affects how much the node moves.
- getGamma() - Method in class deformablemesh.SegmentationController
-
- getGamma() - Method in class deformablemesh.SegmentationModel
-
- getHeight() - Method in class deformablemesh.util.connectedcomponents.ConnectedComponents2D
-
- getHeightPx() - Method in class deformablemesh.MeshImageStack
-
- getHeuristic() - Method in interface deformablemesh.util.astar.PossiblePath
-
- getHighColor() - Method in class deformablemesh.util.SurfacePlot
-
- getHighCorner() - Method in class deformablemesh.util.connectedcomponents.Region
-
- getHistControlsPanel() - Method in class deformablemesh.gui.RingController
-
- getIcon() - Static method in class deformablemesh.gui.GuiTools
-
- getImageCoordinates(double[]) - Method in class deformablemesh.MeshImageStack
-
Returns x, y, z in (px, px, slice) indexes of the backing data array.
- getImageWeight() - Method in class deformablemesh.SegmentationController
-
- getImageWeight() - Method in class deformablemesh.SegmentationModel
-
- getIndex() - Method in class deformablemesh.geometry.Node3D
-
- getIndices() - Method in class deformablemesh.geometry.Triangle3D
-
- getIndices(int[]) - Method in class deformablemesh.geometry.Triangle3D
-
- getInertialMatrix() - Method in class deformablemesh.geometry.BinaryMomentsOfInertia
-
Moments of inertia.
- getInputNormal() - Method in class deformablemesh.gui.RingController
-
- getInputPosition() - Method in class deformablemesh.gui.RingController
-
- getIntensityValues() - Method in class deformablemesh.MeshImageStack
-
- getInterpolatedValue(double, double, double) - Method in class deformablemesh.MeshImageStack
-
- getInterpolatedValue(double[]) - Method in class deformablemesh.MeshImageStack
-
- getIntersectingBox(Box3D) - Method in class deformablemesh.geometry.Box3D
-
- getIntersectionConnections(List<Connection3D>) - Method in class deformablemesh.geometry.Furrow3D
-
- getIntersectionPlaneCoordinates(Furrow3D, Connection3D) - Method in class deformablemesh.geometry.ProjectableMesh
-
- getIntersections(double[], double[]) - Method in class deformablemesh.geometry.BinaryInterceptible
-
Assuming the origin is contained within the shape, and and the pixels are points.
- getIntersections(double[], double[]) - Method in class deformablemesh.geometry.Box3D
-
- getIntersections(double[], double[]) - Method in class deformablemesh.geometry.CompositeInterceptables
-
- getIntersections(List<Connection3D>) - Method in class deformablemesh.geometry.Furrow3D
-
- getIntersections(double[], double[]) - Method in class deformablemesh.geometry.Furrow3D
-
- getIntersections(double[], double[]) - Method in class deformablemesh.geometry.InsideOutInterceptable
-
- getIntersections(double[], double[]) - Method in interface deformablemesh.geometry.Interceptable
-
- getIntersections(double[], double[]) - Method in class deformablemesh.geometry.InterceptingMesh3D
-
- getIntersections(double[], double[]) - Method in class deformablemesh.geometry.Sphere
-
- getJFrame() - Method in class deformablemesh.meshview.MeshFrame3D
-
- getLabel() - Method in class deformablemesh.util.connectedcomponents.Region
-
- getLabeledStack() - Method in class deformablemesh.util.Create3DTrainingDataFromMeshes
-
- getLabelledPoints(int) - Method in class deformablemesh.util.connectedcomponents.ConnectedComponents2D
-
- getLabelPixels(int) - Method in class deformablemesh.util.connectedcomponents.RegionGrowing
-
Get the pixels corresponding to slice i.
- getLastFrame() - Method in class deformablemesh.track.Track
-
- getLastSavedFile() - Method in class deformablemesh.SegmentationController
-
For using save without save-as.
- getLastSavedFile() - Method in class deformablemesh.SegmentationModel
-
- getLimits() - Method in class deformablemesh.MeshImageStack
-
- getLowColor() - Method in class deformablemesh.util.SurfacePlot
-
- getLowCorner() - Method in class deformablemesh.util.connectedcomponents.Region
-
- getMarkers() - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- getMass(List<DeformableMesh3D>) - Static method in class deformablemesh.util.GroupDynamics
-
- getMax() - Method in class deformablemesh.util.SurfacePlot
-
- getMaxConnectionLength() - Method in class deformablemesh.SegmentationController
-
- getMaximumSize() - Method in class deformablemesh.gui.FurrowInput
-
- getMaxMixedArea() - Method in class deformablemesh.externalenergies.PressureForce
-
- getMaxRangeMinMax(int) - Method in class deformablemesh.meshview.MultiChannelVolumeTexture
-
- getMaxRangeMinMax() - Method in class deformablemesh.meshview.VolumeDataObject
-
- getMesh() - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- getMesh() - Method in class deformablemesh.geometry.ProjectableMesh
-
- getMesh() - Method in class deformablemesh.SegmentationController
-
- getMesh(Integer) - Method in class deformablemesh.track.Track
-
- getMeshFrame3D() - Method in class deformablemesh.SegmentationController
-
Returns the main 3D view.
- getMeshImageStack() - Method in class deformablemesh.meshview.TexturedPlaneDataObject
-
- getMeshImageStack() - Method in class deformablemesh.SegmentationController
-
Gets the currently selected MeshImageStack.
- getMeshInFrame(List<Track>, int) - Static method in class deformablemesh.util.GroupDynamics
-
- getMeshModified() - Method in class deformablemesh.SegmentationController
-
returns true if the current state of mesh tracks has changed.
- getMin() - Method in class deformablemesh.util.SurfacePlot
-
- getMinConnectionLength() - Method in class deformablemesh.SegmentationController
-
- getMinimumSize() - Method in class deformablemesh.gui.FurrowInput
-
- getMinMax(int) - Method in class deformablemesh.meshview.MultiChannelVolumeTexture
-
- getMinMax() - Method in class deformablemesh.meshview.VolumeDataObject
-
- getMinPx() - Method in class deformablemesh.MeshImageStack
-
Smallest pixel, in the x,y, or z direction from the input image.
- getModel() - Method in class deformablemesh.SegmentationController
-
This is being exposed to create undoable tasks it should not be used if it can be avoided.
- getName() - Method in interface deformablemesh.geometry.modifier.ModificationState
-
- getName() - Method in class deformablemesh.track.Track
-
- getName() - Method in interface deformablemesh.util.actions.UndoableActions
-
- getName() - Method in class deformablemesh.util.connectedcomponents.Region
-
- getNChannels() - Method in class deformablemesh.SegmentationController
-
Get the number of channels of the currently selected image.
- getNChannels() - Method in class deformablemesh.SegmentationModel
-
- getNeighbors(Node3D) - Method in class deformablemesh.geometry.CurvatureCalculator
-
- getNFrames() - Method in class deformablemesh.MeshImageStack
-
- getNFrames() - Method in class deformablemesh.SegmentationController
-
Total number of frames in the movie.
- getNode() - Method in class deformablemesh.meshview.ContractileRingDataObject
-
- getNode() - Method in class deformablemesh.meshview.LineDataObject
-
- getNormal(Integer, double[]) - Method in class deformablemesh.externalenergies.PerpendicularGradientEnergy
-
- getNormal(Integer, double[]) - Method in class deformablemesh.externalenergies.PerpendicularIntensityEnergy
-
- getNormal(Integer) - Method in class deformablemesh.externalenergies.SofterStericMesh
-
- getNormal(Integer, double[]) - Method in class deformablemesh.externalenergies.StericMesh
-
Calculates the normal by averaging the normals of the connecting triangles.
- getNormal(int) - Method in class deformablemesh.geometry.CurvatureCalculator
-
Calculates the normal based on the mean normal.
- getNormal() - Method in class deformablemesh.geometry.Triangle3D
-
- getNormal() - Method in class deformablemesh.gui.meshinitialization.SlicePicker
-
- getNormalAndCurvature(Node3D, List<Triangle3D>) - Static method in class deformablemesh.geometry.CurvatureCalculator
-
- getNormalizedCoordinate(double[]) - Method in class deformablemesh.MeshImageStack
-
Finds the position in normalized coordinates using.
- getNormalizedCoordinates(double, double) - Method in class deformablemesh.gui.meshinitialization.SlicePicker
-
- getNormalizedImageDepth() - Method in class deformablemesh.MeshImageStack
-
Normalized length of the image along the z-axis.
- getNormalizedImageHeight() - Method in class deformablemesh.MeshImageStack
-
Normalized length of the image along the y-axis.
- getNormalizedImageWidth() - Method in class deformablemesh.MeshImageStack
-
Normalized length of the image along the x-axis.
- getNormalizeWeight() - Method in class deformablemesh.SegmentationController
-
- getNormalizeWeight() - Method in class deformablemesh.SegmentationModel
-
- getNSlices() - Method in class deformablemesh.MeshImageStack
-
- getOffset() - Method in class deformablemesh.meshview.Sizeable3DSurface
-
- getOriginalFrame(Integer) - Method in class deformablemesh.util.Create3DTrainingDataFromMeshes
-
- getOriginalMesh() - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- getOriginalPlus() - Method in class deformablemesh.MeshImageStack
-
- getOriginalStackDimensions() - Method in class deformablemesh.SegmentationController
-
- getOriginalStackDimensions() - Method in class deformablemesh.SegmentationModel
-
- getOutterBounds() - Method in class deformablemesh.geometry.DeformableMesh3D
-
- getOverlapArea(DeformableMesh3D) - Method in class deformablemesh.util.MeshFaceObscuring
-
- getPanel() - Method in class deformablemesh.gui.IntensityRanges
-
- getPath() - Method in interface deformablemesh.util.astar.PossiblePath
-
- getPerform() - Method in class deformablemesh.track.FrameToFrameDisplacement
-
Creates an undoable action based on the tracking result.
- getPerpendicularNormalizedVector(double[]) - Static method in class deformablemesh.util.Vector3DOps
-
Finds the shortest component of the input vector, creates a unit vector
along that axis and then uses the cross product to get a mutually exclusive vector.
- getPlaneCoordinates(double[]) - Method in class deformablemesh.ringdetection.FurrowTransformer
-
Using the normalized coordinates, this returns coordinates in the xy plane of the furrow.
- getPlaneNodes(FurrowTransformer) - Method in class deformablemesh.geometry.ProjectableMesh
-
- getPoints() - Method in class deformablemesh.util.connectedcomponents.Region
-
- getPreferredSize() - Method in class deformablemesh.gui.FurrowInput
-
- getPressure() - Method in class deformablemesh.SegmentationController
-
- getPressure() - Method in class deformablemesh.SegmentationModel
-
- getProjection(FurrowTransformer) - Method in interface deformablemesh.geometry.Projectable
-
- getProjection(FurrowTransformer) - Method in class deformablemesh.geometry.ProjectableMesh
-
- getProjection(FurrowTransformer) - Method in class deformablemesh.geometry.Sphere
-
- getProjection(FurrowTransformer) - Method in class deformablemesh.gui.meshinitialization.ThreeDCursor
-
- getQuad(double[], double[], double[]) - Static method in class deformablemesh.geometry.BinaryMeshGenerator
-
- getRadius() - Method in class deformablemesh.geometry.Sphere
-
- getRedoableActionName() - Method in class deformablemesh.util.actions.ActionStack
-
- getRedoName() - Method in class deformablemesh.SegmentationController
-
Returns the name of the next action that can be redone.
- getRegion(Integer) - Method in class deformablemesh.util.connectedcomponents.RegionGrowing
-
- getRegions() - Method in class deformablemesh.util.connectedcomponents.ConnectedComponents2D
-
A map of label -> region for all of the connected components.
- getRegions(ImageStack) - Static method in class deformablemesh.util.connectedcomponents.ConnectedComponents3D
-
Convenience method for getting all of the regions.
- getRingController() - Method in class deformablemesh.SegmentationController
-
Controls the furrow.
- getRingController() - Method in class deformablemesh.SegmentationModel
-
- getScale() - Method in class deformablemesh.gui.meshinitialization.SlicePicker
-
- getScaledLocation(Point2D) - Method in class deformablemesh.gui.Slice3DView
-
- getSelected() - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- getSelectedMesh() - Method in class deformablemesh.SegmentationController
-
- getSelectedMesh(int) - Method in class deformablemesh.SegmentationModel
-
- getSelectedMesh(int) - Method in class deformablemesh.track.MeshTracker
-
- getSelectedMeshName() - Method in class deformablemesh.SegmentationController
-
Gets the name of the currently selected mesh.
- getSelectedMeshTrack() - Method in class deformablemesh.SegmentationController
-
- getSelectedTrack() - Method in class deformablemesh.SegmentationModel
-
- getSelectedTrack() - Method in class deformablemesh.track.MeshTracker
-
- getSelectedTrack() - Method in class deformablemesh.track.MeshTrackManager
-
- getShape() - Method in class deformablemesh.meshview.TexturedPlaneDataObject
-
- getShape3D() - Method in class deformablemesh.geometry.Furrow3D
-
- getShellMesh() - Method in class deformablemesh.geometry.ShellMesh
-
- getShortestConnection() - Method in class deformablemesh.geometry.ConnectionRemesher
-
- getShortestConnection(Set<Connection3D>) - Method in class deformablemesh.geometry.ConnectionRemesher
-
- getShortImageName() - Method in class deformablemesh.SegmentationController
-
Returns the short image name based on the full image title with the image name extension removed.
- getShortImageName() - Method in class deformablemesh.SegmentationModel
-
- getShowSurface() - Method in class deformablemesh.track.Track
-
- getSize() - Method in class deformablemesh.util.connectedcomponents.Region
-
- getSlice() - Method in class deformablemesh.gui.Slice3DView
-
- getSlicedTriangles(FurrowTransformer) - Method in class deformablemesh.geometry.ProjectableMesh
-
- getSliceView() - Method in class deformablemesh.gui.RingController
-
- getSnapShot() - Method in class deformablemesh.gui.Slice3DView
-
- getStericNeighborWeight() - Method in class deformablemesh.SegmentationController
-
- getStericNeighborWeight() - Method in class deformablemesh.SegmentationModel
-
- getSuggestion() - Static method in class deformablemesh.util.ColorSuggestions
-
- getSuggestion(List<Color>) - Static method in class deformablemesh.util.ColorSuggestions
-
Tries to get a color that doesn't exist in the current list.
- getSurfaceOffsets() - Method in class deformablemesh.SegmentationController
-
The origin in the 3d view is in the center of the original image.
- getSurfaceOffsets() - Method in class deformablemesh.SegmentationModel
-
- getTextField() - Method in class deformablemesh.gui.GuiTools.LocaleNumericTextField
-
- getThresh() - Method in class deformablemesh.gui.RingController
-
- getTrack() - Method in class deformablemesh.track.Track
-
Legacy method that returns a duplicate map that represents the time vs.
- getTrackAtColumn(int) - Method in class deformablemesh.track.MeshTrackManager
-
- getTracks() - Method in class deformablemesh.track.MeshTrackManager
-
- getUndoableActionName() - Method in class deformablemesh.util.actions.ActionStack
-
- getUndoName() - Method in class deformablemesh.SegmentationController
-
Gets the name of the next action to be undone, if it has a name.
- getUnits() - Method in class deformablemesh.MeshImageStack
-
- getUp() - Method in class deformablemesh.meshview.DataCanvas
-
The up vector is a vector that would move in the y direction on the current display.
- getValue() - Method in class deformablemesh.gui.GuiTools.LocaleNumericTextField
-
- getValue() - Method in class deformablemesh.gui.ParameterControl
-
- getValue(int, int, int) - Method in class deformablemesh.MeshImageStack
-
Gets the value at the image coordintes x,y,z doesn't perform any sort of check.
- getVectors() - Method in class deformablemesh.meshview.VectorField
-
- getViewParameters() - Method in class deformablemesh.meshview.DataCanvas
-
All of the current view values.
- getViewParameters() - Method in class deformablemesh.meshview.MeshFrame3D
-
All of the values necessary to have the same view.
- getVolume() - Method in class deformablemesh.externalenergies.VolumeConservation
-
- getVolume() - Method in class deformablemesh.geometry.Box3D
-
- getVolumeColor() - Method in class deformablemesh.SegmentationController
-
- getVolumeCoordinates(double[]) - Method in class deformablemesh.ringdetection.FurrowTransformer
-
- getVolumeDataObject() - Method in class deformablemesh.meshview.ChannelVolume
-
- getVolumeDataObject() - Method in class deformablemesh.meshview.MeshFrame3D
-
- getWidth() - Method in class deformablemesh.util.connectedcomponents.ConnectedComponents2D
-
- getWidthPx() - Method in class deformablemesh.MeshImageStack
-
- getWireFrameMesh() - Method in class deformablemesh.geometry.WireframeMesh
-
- getXButton() - Static method in class deformablemesh.gui.GuiTools
-
- getXComponent() - Method in class deformablemesh.gui.FurrowInput
-
- getXCounts() - Method in class deformablemesh.ringdetection.FurrowTransformer
-
- getXIcon(Color) - Static method in class deformablemesh.gui.GuiTools
-
- getXYSlice(int[]) - Method in class deformablemesh.util.connectedcomponents.Region
-
- getXZSlice(int[]) - Method in class deformablemesh.util.connectedcomponents.Region
-
- getYCounts() - Method in class deformablemesh.ringdetection.FurrowTransformer
-
- getZCounts() - Method in class deformablemesh.ringdetection.FurrowTransformer
-
- getZoom() - Method in class deformablemesh.gui.Slice3DView
-
- getZToYScale() - Method in class deformablemesh.SegmentationController
-
- getZToYScale() - Method in class deformablemesh.SegmentationModel
-
- getZYSlice(int[]) - Method in class deformablemesh.util.connectedcomponents.Region
-
- GradientEnergy - Class in deformablemesh.externalenergies
-
Created by msmith on 1/20/16.
- GradientEnergy(MeshImageStack, double) - Constructor for class deformablemesh.externalenergies.GradientEnergy
-
- GroupDynamics - Class in deformablemesh.util
-
- GroupDynamics() - Constructor for class deformablemesh.util.GroupDynamics
-
- GrowingDroplet - Class in deformablemesh.simulations
-
A simulation where the volume increase, when the surface area to volume reaches a certain cutoff, the droplet will
divide by using a projecting remesh +
- GrowingDroplet() - Constructor for class deformablemesh.simulations.GrowingDroplet
-
- guessMeshes(int) - Method in class deformablemesh.SegmentationController
-
Thresholds the current image and places meshes over the individual regions.
- guessMeshes(MeshImageStack) - Method in class deformablemesh.util.connectedcomponents.BoxRegionConnectedComponents
-
- GuiTools - Class in deformablemesh.gui
-
User: msmith
Date: 8/6/13
Time: 9:06 AM
To change this template use File | Settings | File Templates.
- GuiTools() - Constructor for class deformablemesh.gui.GuiTools
-
- GuiTools.LocaleNumericTextField - Class in deformablemesh.gui
-
- mag(double[]) - Static method in class deformablemesh.util.Vector3DOps
-
- main(String[]) - Static method in class deformablemesh.DeformableMesh3DTools
-
- main(String[]) - Static method in class deformablemesh.examples.CreateCrossSectionMovies
-
- main(String[]) - Static method in class deformablemesh.examples.PlotAverageIntensities
-
- main(String[]) - Static method in class deformablemesh.examples.StabilizeMeshes
-
- main(String[]) - Static method in class deformablemesh.externalenergies.BallooningEnergy
-
- main(String[]) - Static method in class deformablemesh.externalenergies.GradientEnergy
-
- main(String[]) - Static method in class deformablemesh.externalenergies.IntensityEnergy
-
- main(String[]) - Static method in class deformablemesh.externalenergies.TriangleAreaDistributor
-
- main(String[]) - Static method in class deformablemesh.geometry.BinaryMomentsOfInertia
-
Create an image and a mesh
- main(String[]) - Static method in class deformablemesh.geometry.ConnectionRemesher
-
- main(String[]) - Static method in class deformablemesh.geometry.CurvatureCalculator
-
- main(String[]) - Static method in class deformablemesh.geometry.Furrow3D
-
- main(String[]) - Static method in class deformablemesh.geometry.modifier.MeshModifier
-
- main(String[]) - Static method in class deformablemesh.geometry.RayCastMesh
-
- main(String[]) - Static method in class deformablemesh.geometry.ShellMesh
-
- main(String[]) - Static method in class deformablemesh.geometry.SpherePathTesting
-
- main(String[]) - Static method in class deformablemesh.geometry.WireframeMesh
-
- main(String[]) - Static method in class deformablemesh.gui.FurrowInput
-
- main(String[]) - Static method in class deformablemesh.gui.IntensityRanges
-
- main(String[]) - Static method in class deformablemesh.gui.meshinitialization.CircularMeshInitializationDialog
-
- main(String[]) - Static method in class deformablemesh.gui.meshinitialization.RectangleMeshInitializingDialog
-
- main(String[]) - Static method in class deformablemesh.gui.render2d.RaycastRender
-
- main(String[]) - Static method in class deformablemesh.gui.render2d.RenderFrame2D
-
- main(String[]) - Static method in class deformablemesh.gui.Slice3DView
-
- main(String[]) - Static method in class deformablemesh.gui.SwingJSTerm
-
- main(String[]) - Static method in class deformablemesh.io.TrackMateAdapter
-
- main(String[]) - Static method in class deformablemesh.meshview.Arrow
-
- main(String[]) - Static method in class deformablemesh.meshview.MeshViewer
-
- main(String[]) - Static method in class deformablemesh.meshview.SphereDataObject
-
- main(String[]) - Static method in class deformablemesh.simulations.FillingBinaryImage
-
- main(String[]) - Static method in class deformablemesh.simulations.GrowingDroplet
-
- main(String[]) - Static method in class deformablemesh.simulations.HeightMapSurface
-
- main(String[]) - Static method in class deformablemesh.simulations.ManyDrops
-
- main(String[]) - Static method in class deformablemesh.simulations.SphericalCavity
-
- main(String[]) - Static method in class deformablemesh.simulations.TwoDrops
-
- main(String[]) - Static method in class deformablemesh.simulations.WavesOnASheet
-
- main(String[]) - Static method in class deformablemesh.track.FrameToFrameDisplacement
-
- main(String[]) - Static method in class deformablemesh.track.MeshTrackManager
-
- main(String[]) - Static method in class deformablemesh.util.astar.AStarBasic
-
- main(String[]) - Static method in class deformablemesh.util.ColorSuggestions
-
- main(String[]) - Static method in class deformablemesh.util.connectedcomponents.BoxRegionConnectedComponents
-
- main(String[]) - Static method in class deformablemesh.util.connectedcomponents.ConnectedComponents2D
-
- main(String[]) - Static method in class deformablemesh.util.connectedcomponents.ConnectedComponents3D
-
- main(String[]) - Static method in class deformablemesh.util.Create3DTrainingDataFromMeshes
-
Creates Cerberus training data.
- main(String[]) - Static method in class deformablemesh.util.DistanceTransformMosaicImage
-
- main(String[]) - Static method in class deformablemesh.util.GroupDynamics
-
- main(String[]) - Static method in class deformablemesh.util.IntensitySurfacePlot
-
- main(String[]) - Static method in class deformablemesh.util.MeshComparisons
-
- main(String[]) - Static method in class DeformingMesh3DApp
-
- main(String[]) - Static method in class DeformingMeshSans3D
-
- main(String[]) - Static method in class Headless3DApp
-
- mainLoop() - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- mainLoop() - Method in class deformablemesh.geometry.SpherePathTesting
-
- manageSegmentationControllerTracks(SegmentationController) - Method in class deformablemesh.track.MeshTrackManager
-
- ManyDrops - Class in deformablemesh.simulations
-
- ManyDrops() - Constructor for class deformablemesh.simulations.ManyDrops
-
- mapTo2D(List<List<double[]>>) - Method in class deformablemesh.ringdetection.ContractileRingDetector
-
- markTo(double, double) - Method in class deformablemesh.gui.FurrowInput
-
Moves the marker to the specified position from image coordinates.
- maskToDistanceTransform() - Method in class deformablemesh.SegmentationController
-
Creates a distance transform with the currently selected image.
- matchesShape(double[][][]) - Method in class deformablemesh.meshview.MultiChannelVolumeTexture
-
- MAX_VALUE - Variable in class deformablemesh.MeshImageStack
-
- measureAllVolumes() - Method in class deformablemesh.SegmentationController
-
Measures the volumes for all of the mesh tracks, creates a text window with the data like.
- measureAllVolumes() - Method in class deformablemesh.SegmentationModel
-
- measureAverageIntensity() - Method in class deformablemesh.geometry.BinaryMomentsOfInertia
-
- measureSelected() - Method in class deformablemesh.SegmentationController
-
Measures the selected track through time and calculates:
c_x, c_y, c_z: centroid position coordinates.
- measureSelectedMesh() - Method in class deformablemesh.SegmentationModel
-
- measureVolume() - Method in class deformablemesh.SegmentationController
-
Opens a window with volume measurements for the currently selected mesh track.
- measureVolume() - Method in class deformablemesh.util.MeshAnalysis
-
- mergeMeshes(List<DeformableMesh3D>) - Static method in class deformablemesh.DeformableMesh3DTools
-
Each mesh is constructed of 3 essential data values: positions, triangles, connections.
- MeshAnalysis - Class in deformablemesh.util
-
Created by msmith on 2/9/16.
- MeshAnalysis(Map<Integer, DeformableMesh3D>, Map<Integer, Furrow3D>, MeshImageStack) - Constructor for class deformablemesh.util.MeshAnalysis
-
- MeshComparisons - Class in deformablemesh.util
-
- MeshComparisons() - Constructor for class deformablemesh.util.MeshComparisons
-
- MeshDetector - Class in deformablemesh
-
- MeshDetector(MeshImageStack) - Constructor for class deformablemesh.MeshDetector
-
- MeshFaceObscuring - Class in deformablemesh.util
-
A class for detecting how much of a mesh is obscured by other meshes.
- MeshFaceObscuring() - Constructor for class deformablemesh.util.MeshFaceObscuring
-
- MeshFrame3D - Class in deformablemesh.meshview
-
Class for creating a frame to view mesh(es).
- MeshFrame3D() - Constructor for class deformablemesh.meshview.MeshFrame3D
-
- MeshFrame3D.HudDisplay - Interface in deformablemesh.meshview
-
- MeshGroup - Class in deformablemesh.util
-
- MeshGroup(List<DeformableMesh3D>) - Constructor for class deformablemesh.util.MeshGroup
-
- MeshImageOps - Class in deformablemesh.util
-
Created by msmith on 2/9/16.
- MeshImageOps() - Constructor for class deformablemesh.util.MeshImageOps
-
- MeshImageStack - Class in deformablemesh
-
This will setup normalized coordinates for an image.
- MeshImageStack() - Constructor for class deformablemesh.MeshImageStack
-
- MeshImageStack(ImagePlus, int, int) - Constructor for class deformablemesh.MeshImageStack
-
- MeshImageStack(ImagePlus) - Constructor for class deformablemesh.MeshImageStack
-
- MeshImageStack(Path) - Constructor for class deformablemesh.MeshImageStack
-
Creates an ImagePlus from the provided path.
- MeshImageSubStack - Class in deformablemesh
-
Created by smithm3 on 20/02/18.
- MeshImageSubStack(Box3D, MeshImageStack, ImagePlus) - Constructor for class deformablemesh.MeshImageSubStack
-
- MeshModifier - Class in deformablemesh.geometry.modifier
-
This needs to be separated into a Controller/Model.
- MeshModifier() - Constructor for class deformablemesh.geometry.modifier.MeshModifier
-
- MeshReader - Class in deformablemesh.io
-
- MeshReader(File) - Constructor for class deformablemesh.io.MeshReader
-
- MeshTracker - Class in deformablemesh.track
-
For keeping track of mesh linking.
- MeshTracker() - Constructor for class deformablemesh.track.MeshTracker
-
- MeshTrackManager - Class in deformablemesh.track
-
A gui/class for organizing a sorting the linking of meshes.
- MeshTrackManager() - Constructor for class deformablemesh.track.MeshTrackManager
-
- MeshViewer - Class in deformablemesh.meshview
-
For loading and viewing meshes.
- MeshViewer() - Constructor for class deformablemesh.meshview.MeshViewer
-
- MeshWriter - Class in deformablemesh.io
-
For writing meshes incrementally.
- MeshWriter(File) - Constructor for class deformablemesh.io.MeshWriter
-
- MIN_VALUE - Variable in class deformablemesh.MeshImageStack
-
- minimumRadiusLocation(List<double[]>) - Method in class deformablemesh.geometry.Furrow3D
-
- minLength(double[]) - Static method in class deformablemesh.util.Vector3DOps
-
- misses - Static variable in class deformablemesh.util.connectedcomponents.Region
-
- model - Variable in class deformablemesh.gui.RingController
-
- ModificationState - Interface in deformablemesh.geometry.modifier
-
- modifyingMesh() - Method in class deformablemesh.gui.RingController
-
- mosaicBinary(MeshImageStack, ImageStack, DeformableMesh3D, int) - Static method in class deformablemesh.DeformableMesh3DTools
-
- Mouse_X - Class in <Unnamed>
-
updated 5/9/2014: Uses the correct dimensions for the image and preserves slice labels.
- Mouse_X() - Constructor for class Mouse_X
-
- mouseClicked(MouseEvent) - Method in class deformablemesh.meshview.CanvasController
-
- mouseClicked(MouseEvent) - Method in class Mouse_X
-
- mouseDragged(MouseEvent) - Method in class deformablemesh.meshview.CanvasController
-
For dragging, when disabled the state of the controller is updated, but the state of the canvas is not modified.
- mouseMoved(MouseEvent) - Method in class deformablemesh.meshview.CanvasController
-
- mouseMoved(MouseEvent) - Method in class Mouse_X
-
During 'state 3' we draw the bounding rectangle
to show the area that will be cropped and rotated.
- mousePressed(MouseEvent) - Method in class deformablemesh.meshview.CanvasController
-
- mouseReleased(MouseEvent) - Method in class deformablemesh.meshview.CanvasController
-
- mouseWheelMoved(MouseWheelEvent) - Method in class deformablemesh.meshview.CanvasController
-
- move(double[]) - Method in class deformablemesh.geometry.Furrow3D
-
- moveBy(double[]) - Method in class deformablemesh.geometry.Sphere
-
- moved(MouseEvent) - Method in class deformablemesh.meshview.DataCanvas
-
- moveTo(double[]) - Method in class deformablemesh.geometry.Furrow3D
-
- moveTo(double[]) - Method in class deformablemesh.geometry.Sphere
-
- moveTo(double, double, double) - Method in class deformablemesh.meshview.Arrow
-
- moveTo(Point3d) - Method in class deformablemesh.meshview.SphereDataObject
-
- moveTo(double, double, double) - Method in class deformablemesh.meshview.SphereDataObject
-
- MultiChannelVolumeTexture - Class in deformablemesh.meshview
-
- MultiChannelVolumeTexture(double[][][], double, double, Color3f) - Constructor for class deformablemesh.meshview.MultiChannelVolumeTexture
-
Creates a MultiChannelVolumeTexture with a single channel.
- paintComponent(Graphics) - Method in class deformablemesh.gui.FurrowInput
-
- panel - Variable in class deformablemesh.gui.Slice3DView
-
- ParabolicSurface - Class in deformablemesh.externalenergies
-
- ParabolicSurface() - Constructor for class deformablemesh.externalenergies.ParabolicSurface
-
- ParameterCombo - Class in deformablemesh.gui
-
- ParameterCombo() - Constructor for class deformablemesh.gui.ParameterCombo
-
- ParameterControl - Class in deformablemesh.gui
-
Created on 31/07/18.
- ParameterControl() - Constructor for class deformablemesh.gui.ParameterControl
-
- parseDouble(String) - Static method in class deformablemesh.gui.GuiTools
-
- partialUpdate() - Method in class deformablemesh.geometry.DeformableMesh3D
-
Performs the bulk of calculations for doing an update.
- pathFinder(List<List<Node3D>>, Node3D) - Static method in class deformablemesh.DeformableMesh3DTools
-
- pause() - Method in class deformablemesh.simulations.SphericalCavity
-
- perform() - Method in interface deformablemesh.util.actions.UndoableActions
-
- PerpendicularGradientEnergy - Class in deformablemesh.externalenergies
-
Created by msmith on 2/10/16.
- PerpendicularGradientEnergy(MeshImageStack, DeformableMesh3D, double) - Constructor for class deformablemesh.externalenergies.PerpendicularGradientEnergy
-
- PerpendicularIntensityEnergy - Class in deformablemesh.externalenergies
-
Created by msmith on 2/10/16.
- PerpendicularIntensityEnergy(MeshImageStack, DeformableMesh3D, double) - Constructor for class deformablemesh.externalenergies.PerpendicularIntensityEnergy
-
- PickSelector - Class in deformablemesh.meshview
-
Created by smithm3 on 24/05/18.
- PickSelector(SegmentationController) - Constructor for class deformablemesh.meshview.PickSelector
-
- ping(double[]) - Method in class deformablemesh.gui.render2d.RaycastRender
-
- pivotAboutCenterOfView(int, int) - Method in class deformablemesh.meshview.DataCanvas
-
Use the original rotation and change the view
- pixel_dimensions - Variable in class deformablemesh.MeshImageStack
-
- PixelSet - Class in deformablemesh.util.connectedcomponents
-
- PlotAverageIntensities - Class in deformablemesh.examples
-
- PlotAverageIntensities() - Constructor for class deformablemesh.examples.PlotAverageIntensities
-
- plotCellCount() - Method in class deformablemesh.SegmentationController
-
Creates a plot of mesh count vs time.
- plotCurvature() - Method in class deformablemesh.simulations.SphericalCavity
-
- plotDisplacementHistogram(List<Track>, MeshImageStack) - Static method in class deformablemesh.util.MeshAnalysis
-
- plotDisplacements() - Method in class deformablemesh.SegmentationController
-
Creates two plots.
- plotDisplacementsVsTime(List<Track>, MeshImageStack) - Static method in class deformablemesh.util.MeshAnalysis
-
- plotElongationsVsTime() - Method in class deformablemesh.SegmentationController
-
Finds the principle moments of Inertia and plots the anisotropy over time.
- plotElongationsVsTime(List<Track>) - Static method in class deformablemesh.util.MeshAnalysis
-
- plotMeshesOverTime(List<Track>, MeshImageStack) - Static method in class deformablemesh.util.MeshAnalysis
-
Plots the number of meshes over time.
- plotNextFrameTrackingResults(List<Track>, int) - Static method in class deformablemesh.util.TrackAnalysis
-
- PlotSurface - Class in deformablemesh.meshview
-
- PlotSurface(double[], int[], float[]) - Constructor for class deformablemesh.meshview.PlotSurface
-
- plotTrackingStatistics() - Method in class deformablemesh.SegmentationController
-
Creates a plot with information about the frame to frame displacement of the current set of meshes.
- plotVolumeAveragedIntensityVsTime() - Method in class deformablemesh.SegmentationController
-
- plotVolumes() - Method in class deformablemesh.SegmentationController
-
Plots the volumes of meshes over time for all of the meshes.
- plotVolumesOverTime(List<Track>, MeshImageStack) - Static method in class deformablemesh.util.MeshAnalysis
-
Creates a plot of the volumes over time.
- pointAlong(double[]) - Method in class deformablemesh.meshview.Arrow
-
- positionFrames(ControlFrame, MeshFrame3D) - Static method in class deformablemesh.gui.PropertySaver
-
For setting up the position of the windows.
- positions - Variable in class deformablemesh.geometry.DeformableLine3D
-
- positions - Variable in class deformablemesh.geometry.DeformableMesh3D
-
- PossiblePath<T> - Interface in deformablemesh.util.astar
-
- post(Runnable) - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- post(Runnable) - Method in class deformablemesh.geometry.SpherePathTesting
-
- postAction(DisplaceNodesAction) - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- postAction(UndoableActions) - Method in class deformablemesh.util.actions.ActionStack
-
- prepareEmptyTrack() - Method in class deformablemesh.track.MeshTracker
-
- prepareEmptyTracks(int) - Method in class deformablemesh.track.MeshTracker
-
Returns n tracks with a name that is not contained in the current set of tracks names.
- prepareEnergies(DeformableMesh3D) - Method in class deformablemesh.simulations.ManyDrops
-
- prepareEnergies() - Method in class deformablemesh.simulations.TwoDrops
-
- prepareMap() - Method in class deformablemesh.geometry.CurvatureCalculator
-
- prepareStericEnergies() - Method in class deformablemesh.simulations.SphericalCavity
-
- prepareValue(JLabel, JComboBox<Integer>) - Method in class deformablemesh.gui.ParameterCombo
-
- prepareValue(JLabel, JTextField) - Method in class deformablemesh.gui.ParameterControl
-
- prepareWorkSpace(DeformableMesh3D) - Method in class deformablemesh.geometry.ConnectionRemesher
-
- pressed(MouseEvent) - Method in class deformablemesh.meshview.DataCanvas
-
- PressureForce - Class in deformablemesh.externalenergies
-
Created by msmith on 2/29/16.
- PressureForce(DeformableMesh3D, double) - Constructor for class deformablemesh.externalenergies.PressureForce
-
- previousCard() - Method in class deformablemesh.gui.meshinitialization.RectangleMeshInitializingDialog
-
- previousFrame() - Method in class deformablemesh.MeshImageStack
-
- previousFrame() - Method in class deformablemesh.SegmentationController
-
Moves to the previous image frame.
- previousFrame() - Method in class deformablemesh.SegmentationModel
-
- previousFrameAction() - Method in class deformablemesh.gui.ControlFrame
-
- print2DMatrix(double[][]) - Static method in class deformablemesh.track.FrameToFrameDisplacement
-
- process() - Method in class deformablemesh.util.connectedcomponents.ConnectedComponents2D
-
This method needs to be called before any of the centroids can be accessed.
- process() - Method in class deformablemesh.util.KMeansThresholder
-
Processes the accumulated images.
- process() - Method in class deformablemesh.util.SurfacePlot
-
Calculates all of the local values at each node.
- processAndShow(boolean) - Method in class deformablemesh.util.SurfacePlot
-
- processAndShow() - Method in class deformablemesh.util.SurfacePlot
-
- processJaccardIndexMap(List<DeformableMesh3D>, List<DeformableMesh3D>) - Method in class deformablemesh.track.FrameToFrameDisplacement
-
- processJaccardIndexMatrix(List<DeformableMesh3D>, List<DeformableMesh3D>) - Method in class deformablemesh.track.FrameToFrameDisplacement
-
- processSlice(ImageProcessor) - Method in class deformablemesh.util.KMeansThresholder
-
Prepares the work space for finding a kmean value.
- progress() - Method in class deformablemesh.io.MeshReader
-
- Projectable - Interface in deformablemesh.geometry
-
Created by msmith on 2/8/16.
- ProjectableMesh - Class in deformablemesh.geometry
-
Created by msmith on 6/23/16.
- ProjectableMesh(DeformableMesh3D) - Constructor for class deformablemesh.geometry.ProjectableMesh
-
- ProjectionSurfacePlot - Class in deformablemesh.util
-
For analyzing a mesh using a 2D projection.
- ProjectionSurfacePlot() - Constructor for class deformablemesh.util.ProjectionSurfacePlot
-
- PropertySaver - Class in deformablemesh.gui
-
For saving constants that the user has entered.
- PropertySaver() - Constructor for class deformablemesh.gui.PropertySaver
-
- proximity(double[], double[], double) - Static method in class deformablemesh.util.Vector3DOps
-
Checks if a and be are within the range of r by summing the square of differences
and squaring r.
- putAll(Map<Integer, DeformableMesh3D>) - Method in class deformablemesh.track.Track
-
- putFurrow(int, Furrow3D) - Method in class deformablemesh.ringdetection.ContractileRingDetector
-
- radius(double, double) - Static method in class deformablemesh.util.MeshAnalysis
-
- RayCastMesh - Class in deformablemesh.geometry
-
Utility class for generating a mesh.
- RayCastMesh() - Constructor for class deformablemesh.geometry.RayCastMesh
-
- rayCastMesh(Interceptable, double[], int) - Static method in class deformablemesh.geometry.RayCastMesh
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- rayCastMesh(List<Interceptable>, double[], int) - Static method in class deformablemesh.geometry.RayCastMesh
-
Checks for interceptsion of all of the included objects.
- RaycastRender - Class in deformablemesh.gui.render2d
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- RaycastRender() - Constructor for class deformablemesh.gui.render2d.RaycastRender
-
- reactangleCheck(String[]) - Static method in class deformablemesh.geometry.BinaryMomentsOfInertia
-
- ReadyObserver - Interface in deformablemesh.gui
-
Created by melkor on 11/18/15.
- recordShot() - Method in class deformablemesh.meshview.MeshFrame3D
-
- recordSnapshots(int, int) - Method in class deformablemesh.SegmentationController
-
Creates an ImagePlus with snapshots from each frame.
- RectangleMeshInitializingDialog - Class in deformablemesh.gui.meshinitialization
-
This will go through, step by reversible step and allow a user to initialize
a 3D mesh.
- RectangleMeshInitializingDialog(JFrame, SegmentationController) - Constructor for class deformablemesh.gui.meshinitialization.RectangleMeshInitializingDialog
-
- redo() - Method in class deformablemesh.SegmentationController
-
moves the action stack forward.
- redo() - Method in class deformablemesh.util.actions.ActionStack
-
- redo() - Method in interface deformablemesh.util.actions.UndoableActions
-
- redoAction() - Method in class deformablemesh.gui.ControlFrame
-
- refineBinary(ImageStack, ImageStack) - Static method in class deformablemesh.util.MeshImageOps
-
- refresh() - Method in class deformablemesh.meshview.MultiChannelVolumeTexture
-
- refreshFurrow() - Method in class deformablemesh.gui.RingController
-
- refreshSlice() - Method in class deformablemesh.gui.meshinitialization.SlicePicker
-
- refreshValues() - Method in class deformablemesh.gui.RingController
-
- Region - Class in deformablemesh.util.connectedcomponents
-
- RegionGrowing - Class in deformablemesh.util.connectedcomponents
-
- RegionGrowing(ImageStack, ImageStack) - Constructor for class deformablemesh.util.connectedcomponents.RegionGrowing
-
- register() - Method in interface deformablemesh.geometry.modifier.ModificationState
-
- register() - Method in class deformablemesh.geometry.modifier.Selector
-
- relateImports(List<Track>) - Method in class deformablemesh.SegmentationController
-
Finds the earliest mesh frame, aligns that to the current frame
- released(MouseEvent) - Method in class deformablemesh.meshview.DataCanvas
-
- remesh(DeformableMesh3D, MeshImageStack) - Static method in class deformablemesh.geometry.BinaryMeshGenerator
-
- remesh(DeformableMesh3D) - Method in class deformablemesh.geometry.ConnectionRemesher
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- reMesh() - Method in class deformablemesh.SegmentationController
-
Remeshes the currently selected mesh by raycasting a sphere.
- remeshAction() - Method in class deformablemesh.gui.ControlFrame
-
- reMeshConnections(Track, int, double, double) - Method in class deformablemesh.SegmentationController
-
Remeshes the current track by using the remesh connection algorithm.
- reMeshConnections(double, double) - Method in class deformablemesh.SegmentationController
-
Remesh the selected mesh to the provided min and max connection lengths.
- reMeshConnectionsAllMeshes(double, double) - Method in class deformablemesh.SegmentationController
-
Applies the connection remesh algorith to all meshes in the current frame.
- remeshMeshes() - Method in class deformablemesh.simulations.SphericalCavity
-
- remove(DeformableMesh3D) - Method in class deformablemesh.track.Track
-
- remove(int[]) - Method in class deformablemesh.util.connectedcomponents.ShrinkRegion
-
- removeChannelVolume(ChannelVolume) - Method in class deformablemesh.meshview.MeshFrame3D
-
- removeConnection(Connection3D) - Method in class deformablemesh.geometry.ConnectionRemesher
-
- removeDataObject() - Method in class deformablemesh.geometry.Furrow3D
-
- removeDataObject(DataObject) - Method in class deformablemesh.meshview.MeshFrame3D
-
- removeDrawable(Drawable) - Method in class deformablemesh.gui.Slice3DView
-
- removeExternalEnergy(ExternalEnergy) - Method in class deformablemesh.geometry.DeformableMesh3D
-
- removeFrameListener(FrameListener) - Method in class deformablemesh.SegmentationController
-
- removeFrameListener(FrameListener) - Method in class deformablemesh.SegmentationModel
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- removeKeyListener(KeyListener) - Method in class deformablemesh.meshview.MeshFrame3D
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- removeLights() - Method in class deformablemesh.meshview.MeshFrame3D
-
- removeMeshFromTrack(int, DeformableMesh3D, Track) - Method in class deformablemesh.SegmentationModel
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- removeMeshFromTrack(int, DeformableMesh3D, Track) - Method in class deformablemesh.track.MeshTracker
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- removeMeshListener(FrameListener) - Method in class deformablemesh.SegmentationController
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- removeMeshListener(FrameListener) - Method in class deformablemesh.SegmentationModel
-
- removeMeshTrack(Track) - Method in class deformablemesh.SegmentationModel
-
- removeMouseAdapter(MouseAdapter) - Method in class deformablemesh.gui.Slice3DView
-
- removeObject(DataObject) - Method in class deformablemesh.meshview.DataCanvas
-
Removes an object if it exists.
- removePickListener(CanvasView) - Method in class deformablemesh.meshview.MeshFrame3D
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- removePlaneChangeListener(FurrowInput.PlaneChangeListener) - Method in class deformablemesh.gui.FurrowInput
-
- removeProjectable(Projectable) - Method in class deformablemesh.gui.meshinitialization.SlicePicker
-
- removeRegion(int) - Method in class deformablemesh.util.connectedcomponents.ConnectedComponents2D
-
Removes a region from this cc2d by removing the label from the map, and setting all of the pixels associated
with the provided label to 0.
- removeShortConnection(Connection3D) - Method in class deformablemesh.geometry.ConnectionRemesher
-
- removeSnakeListener(CanvasView) - Method in class deformablemesh.meshview.DataCanvas
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- removeStateListener(StateListener) - Method in class deformablemesh.util.actions.ActionStack
-
- removeTrack(Track) - Method in class deformablemesh.track.MeshTracker
-
- removeTransient(DataObject) - Method in class deformablemesh.meshview.MeshFrame3D
-
- removeTriangle(Triangle3D) - Method in class deformablemesh.geometry.ConnectionRemesher
-
- removeUndoStateListener(StateListener) - Method in class deformablemesh.SegmentationController
-
- removeViewListener(DataCanvas.ViewListener) - Method in class deformablemesh.meshview.DataCanvas
-
- render() - Method in class deformablemesh.gui.render2d.RenderFrame2D
-
- renderConnections(RenderFrame2D.Camera, List<Connection3D>, Color) - Method in class deformablemesh.gui.render2d.RenderFrame2D
-
- RenderFrame2D - Class in deformablemesh.gui.render2d
-
- RenderFrame2D() - Constructor for class deformablemesh.gui.render2d.RenderFrame2D
-
- renderMeshes(RenderFrame2D.Camera) - Method in class deformablemesh.gui.render2d.RenderFrame2D
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- renderMeshesIn2D() - Method in class deformablemesh.SegmentationController
-
Opens a new window that renders the provided meshes in 2D.
- renderTriangles(RenderFrame2D.Camera, List<Triangle3D>, Color) - Method in class deformablemesh.gui.render2d.RenderFrame2D
-
- repaint() - Method in class deformablemesh.gui.Slice3DView
-
- resetPositions() - Method in class deformablemesh.geometry.DeformableMesh3D
-
- reshape() - Method in class deformablemesh.geometry.DeformableLine3D
-
- reshape() - Method in class deformablemesh.geometry.DeformableMesh3D
-
- reshape() - Method in class deformablemesh.geometry.NewtonMesh3D
-
- resize() - Method in class deformablemesh.gui.Slice3DView
-
- restartMeshes() - Method in class deformablemesh.SegmentationController
-
Clears ALL of the current meshes.
- RingController - Class in deformablemesh.gui
-
Links together the contractile ring detector,
Created by msmith on 4/14/14.
- RingController(SegmentationController) - Constructor for class deformablemesh.gui.RingController
-
- rotate(double[], double[], double) - Method in class deformablemesh.geometry.DeformableMesh3D
-
- rotateMeshes(double[], double[]) - Method in class deformablemesh.util.MeshGroup
-
- rotatePiOver2() - Method in class deformablemesh.ringdetection.FurrowTransformer
-
TODO This should be some sort of general rotation form since the 'image' can be rotated.
- rotatePoint(double[], double[], double[]) - Static method in class deformablemesh.util.Vector3DOps
-
- rotateView() - Method in class deformablemesh.gui.meshinitialization.SlicePicker
-
- rotateView(double[]) - Method in class deformablemesh.meshview.DataCanvas
-
Rotates the view using an axis angle.
- rotateView(int, int) - Method in class deformablemesh.meshview.DataCanvas
-
- rotateView(int, int) - Method in class deformablemesh.meshview.MeshFrame3D
-
rotates the data canvas view.
- rotateViewPhi(double) - Method in class deformablemesh.gui.render2d.RenderFrame2D
-
- rotateViewTheta(double) - Method in class deformablemesh.gui.render2d.RenderFrame2D
-
- run(ImageProcessor) - Method in class deformablemesh.Deforming3DMesh_Plugin
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- run() - Method in class deformablemesh.gui.render2d.RaycastRender
-
- run() - Method in class deformablemesh.simulations.ManyDrops
-
- run(int) - Method in class deformablemesh.util.Create3DTrainingDataFromMeshes
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- run(String) - Method in class DeformingMeshSans3D
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- run(ImageProcessor) - Method in class Mouse_X
-
This will create a new image plus to draw on so that you can
click on the canvas to select the four points necessary
- sameDestination(T) - Method in interface deformablemesh.util.astar.PossiblePath
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- sample(Node3D) - Method in class deformablemesh.util.CurvatureSurfacePlot
-
- sample(Node3D) - Method in class deformablemesh.util.IntensitySurfacePlot
-
- sample(Connection3D) - Method in class deformablemesh.util.IntensitySurfacePlot
-
- sample(Node3D) - Method in class deformablemesh.util.SurfacePlot
-
- samplePlus(Box3D) - Method in class deformablemesh.MeshImageStack
-
- saveAs() - Method in class deformablemesh.gui.ControlFrame
-
- saveAsPLyFile(Path) - Method in class deformablemesh.util.SurfacePlot
-
- saveAsTrackMateFile(MeshImageStack, List<Track>, Path) - Static method in class deformablemesh.io.TrackMateAdapter
-
- saveFurrows(File) - Method in class deformablemesh.SegmentationController
-
Saves the furrow from each plane.
- saveFurrows(File) - Method in class deformablemesh.SegmentationModel
-
- saveMesh(String, DeformableMesh3D) - Static method in class deformablemesh.io.MeshWriter
-
- saveMeshes(File, List<Track>) - Static method in class deformablemesh.io.MeshWriter
-
- saveMeshes(File, MeshTracker) - Static method in class deformablemesh.io.MeshWriter
-
- saveMeshes(File) - Method in class deformablemesh.SegmentationController
-
Saves the current meshes
- saveMeshes(File) - Method in class deformablemesh.SegmentationModel
-
- saveMeshes() - Method in class deformablemesh.simulations.SphericalCavity
-
- saveParameters(File) - Method in class deformablemesh.SegmentationController
-
Saves the current deformation parameters to a file.
- saveProperties(SegmentationController) - Static method in class deformablemesh.gui.PropertySaver
-
Tries to save the currently set properties/constants.
- saveProperties(SegmentationController, File) - Static method in class deformablemesh.gui.PropertySaver
-
- saveStlMesh(File, List<Track>, double[], double, Integer) - Static method in class deformablemesh.io.MeshWriter
-
Saves the current mesh to an ascii
- scale(double, double[]) - Method in class deformablemesh.geometry.DeformableMesh3D
-
- SCALE - Variable in class deformablemesh.MeshImageStack
-
- scale - Variable in class deformablemesh.ringdetection.FurrowTransformer
-
- scale_values - Variable in class deformablemesh.MeshImageStack
-
- scaleToNormalizedLength(double[]) - Method in class deformablemesh.MeshImageStack
-
given a length in px, px, slices this scales the length to normalized
coordinate values.
- scanDirty(List<Intersection>) - Static method in class deformablemesh.DeformableMesh3DTools
-
This puts topographical constraints on the intersections.
- scrollYUnits(double) - Method in class deformablemesh.gui.FurrowInput
-
- sculptClicked(ActionEvent) - Method in class deformablemesh.gui.RingController
-
- secondDerivative1DKernel() - Static method in class deformablemesh.util.GaussianKernels
-
- SegmentationController - Class in deformablemesh
-
This manages the SegmentationModel and provides an interface for interacting with meshes through an action stack
such that changes can be un-done.
- SegmentationController(SegmentationModel) - Constructor for class deformablemesh.SegmentationController
-
Creates a controller for the supplied model.
- SegmentationController.Executable - Interface in deformablemesh
-
Tasks for the exception throwing service.
- SegmentationModel - Class in deformablemesh
-
- SegmentationModel() - Constructor for class deformablemesh.SegmentationModel
-
- selectChannel(int) - Method in class deformablemesh.SegmentationController
-
- selectImports(List<Track>) - Method in class deformablemesh.SegmentationController
-
Reduces the provided meshes to only meshes in the currently selected frame.
- selectMesh(DeformableMesh3D) - Method in class deformablemesh.SegmentationController
-
Attempts to select the track that contains the provided mesh.
- selectMeshTrack(Track) - Method in class deformablemesh.SegmentationController
-
Overload for convenience.
- selectMeshTrack(Track) - Method in class deformablemesh.SegmentationModel
-
- selectMeshTrack(Track) - Method in class deformablemesh.track.MeshTracker
-
- selectNextMeshTrack() - Method in class deformablemesh.SegmentationController
-
Changes the currently selected track to be the next one.
- selectNextTrack() - Method in class deformablemesh.SegmentationModel
-
- selectNextTrack() - Method in class deformablemesh.track.MeshTracker
-
- selectNode(int) - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- selectNode(Node3D) - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- selectNodes(List<Node3D>) - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- selectNodes(ActionEvent) - Method in class deformablemesh.gui.RingController
-
Startes the select nodes activity.
- selectNone() - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- selectNone() - Method in class deformablemesh.SegmentationController
-
Causes no mesh track to be selected.
- selectOpenImage() - Method in class deformablemesh.gui.ControlFrame
-
- selectOpenImage(JFrame) - Static method in class deformablemesh.gui.GuiTools
-
- selectOpenImage(Window, SegmentationController) - Static method in class deformablemesh.gui.GuiTools
-
- Selector - Class in deformablemesh.geometry.modifier
-
- Selector(MeshModifier) - Constructor for class deformablemesh.geometry.modifier.Selector
-
- selectPreviousMeshTrack() - Method in class deformablemesh.SegmentationController
-
Changes to the previously selected track.
- selectPreviousTrack() - Method in class deformablemesh.SegmentationModel
-
- selectPreviousTrack() - Method in class deformablemesh.track.MeshTracker
-
- selectTrackContainingMesh(DeformableMesh3D) - Method in class deformablemesh.track.MeshTracker
-
changes the selected track to the track containing the mesh.
- selectTrackWithMesh(DeformableMesh3D) - Method in class deformablemesh.SegmentationModel
-
- setAlpha(double) - Method in class deformablemesh.SegmentationController
-
Deformation parameter, effectively the spring-like stiffness connections.
- setAlpha(double) - Method in class deformablemesh.SegmentationModel
-
- setAmbientBrightness(float) - Method in class deformablemesh.meshview.MeshFrame3D
-
- setBackgroundColor(Color) - Method in class deformablemesh.meshview.MeshFrame3D
-
- setBackingData(double[]) - Method in class deformablemesh.geometry.Node3D
-
Sets the position array that this node uses to back its data.
- setBeta(double) - Method in class deformablemesh.SegmentationController
-
deformation parameter: represents the bending stiffness.
- setBeta(double) - Method in class deformablemesh.SegmentationModel
-
- setBinary(Image) - Method in class deformablemesh.gui.Slice3DView
-
- setCanvasControllerEnabled(boolean) - Method in class deformablemesh.meshview.MeshFrame3D
-
For enabling and disabling the default controller.
- setCard(int) - Method in class deformablemesh.gui.meshinitialization.RectangleMeshInitializingDialog
-
- setChannel(int) - Method in class deformablemesh.MeshImageStack
-
- setClipValues(double, double) - Method in class deformablemesh.gui.IntensityRanges
-
- setCloseCallback(Runnable) - Method in class deformablemesh.gui.meshinitialization.CircularMeshInitializationDialog
-
- setColor(Color) - Method in class deformablemesh.geometry.DeformableMesh3D
-
- setColor(Color) - Method in class deformablemesh.meshview.Arrow
-
- setColor(int) - Method in class deformablemesh.meshview.ContractileRingDataObject
-
- setColor(Color) - Method in class deformablemesh.meshview.DeformableMeshDataObject
-
- setColor(float, float, float) - Method in class deformablemesh.meshview.LineDataObject
-
- setColor(int, double, double, double) - Method in class deformablemesh.meshview.MultiChannelVolumeTexture
-
- setColor(float, float, float) - Method in class deformablemesh.meshview.SphereDataObject
-
- setColor(Color) - Method in class deformablemesh.meshview.VolumeDataObject
-
- setColor(double, double, double) - Method in class deformablemesh.meshview.VolumeTexture
-
- setColor(Color) - Method in class deformablemesh.track.Track
-
- setCortexThickness(double) - Method in class deformablemesh.SegmentationModel
-
- setCursorRadius(double) - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- setCursorRadius(double) - Method in class deformablemesh.gui.RingController
-
- setCurves(List<List<double[]>>) - Method in class deformablemesh.gui.Slice3DView
-
Sets the currently displayed set of curves.
- setData(Map<Integer, DeformableMesh3D>) - Method in class deformablemesh.track.Track
-
For use when reading data from a file.
- setDefaultControllerEnabled(boolean) - Method in class deformablemesh.meshview.DataCanvas
-
- setDefaultView() - Method in class deformablemesh.gui.render2d.RenderFrame2D
-
- setDirection(double[]) - Method in class deformablemesh.geometry.Furrow3D
-
- setDirectionalBrightness(float) - Method in class deformablemesh.meshview.MeshFrame3D
-
- setDirty(double) - Method in class deformablemesh.geometry.Intersection
-
- setDivisions(int) - Method in class deformablemesh.SegmentationController
-
When a new mesh is created, it is subdivided this number of times.
- setDivisions(int) - Method in class deformablemesh.SegmentationModel
-
- setEnabled(boolean) - Method in class deformablemesh.meshview.CanvasController
-
- setFrame(int) - Method in class deformablemesh.gui.render2d.RenderFrame2D
-
Only meshes existing in the current frame are rendered.
- setFrame(int) - Method in class deformablemesh.gui.RingController
-
- setFrame(int) - Method in class deformablemesh.MeshImageStack
-
- setFrame(int) - Method in class deformablemesh.ringdetection.ContractileRingDetector
-
- setFrame(int) - Method in class deformablemesh.SegmentationModel
-
- setFrame(int) - Method in class deformablemesh.simulations.FillingBinaryImage
-
- setFrameModified(boolean) - Method in class deformablemesh.gui.ControlFrame
-
change the frame title when the meshes get modified.
- setFurrow(Furrow3D) - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- setFurrow(Furrow3D) - Method in class deformablemesh.gui.FurrowInput
-
- setFurrow(int, Furrow3D) - Method in class deformablemesh.gui.RingController
-
- setFurrow(double[], double[]) - Method in class deformablemesh.gui.RingController
-
- setFurrowForCurrentFrame(double[], double[]) - Method in class deformablemesh.SegmentationController
-
Sets the position and normal of the furrow.
- setFurrowValues() - Method in class deformablemesh.gui.RingController
-
- setGamma(double) - Method in class deformablemesh.meshview.VectorField
-
- setGamma(double) - Method in class deformablemesh.SegmentationController
-
Deformation parameter, high values limit the rate of deformation.
- setGamma(double) - Method in class deformablemesh.SegmentationModel
-
- setGammaFactor(double) - Method in class deformablemesh.geometry.Node3D
-
This determines how much this node moves compared to the rest of the mesh.
- setGeometry(double[], double[]) - Method in class deformablemesh.geometry.Furrow3D
-
- setGoal(T) - Method in class deformablemesh.util.astar.AStarBasic
-
- setHardBoundaries(boolean) - Method in class deformablemesh.SegmentationController
-
Hard boundaries cause a mesh to be confined after each step during deformation.
- setHardBoundaries(boolean) - Method in class deformablemesh.SegmentationModel
-
- setHighColor(Color) - Method in class deformablemesh.util.SurfacePlot
-
- setHud(MeshFrame3D.HudDisplay) - Method in class deformablemesh.meshview.MeshFrame3D
-
For drawing graphics on the rendered screen.
- setImage(ImagePlus) - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- setImageEnergyType(ImageEnergyType) - Method in class deformablemesh.SegmentationController
-
The type of image energy that will be used.
- setImageEnergyType(ImageEnergyType) - Method in class deformablemesh.SegmentationModel
-
The energy type will be used to decide which image energy is add during deformations.
- setImageStack(MeshImageStack) - Method in class deformablemesh.ringdetection.ContractileRingDetector
-
- setIntensityExtremes(double, double) - Method in class deformablemesh.gui.IntensityRanges
-
- setLabel(String) - Method in class deformablemesh.gui.meshinitialization.SlicePicker
-
- setLabel(int[], int) - Method in class deformablemesh.util.connectedcomponents.RegionGrowing
-
- setLastSavedFile(File) - Method in class deformablemesh.SegmentationModel
-
- setLength(double) - Method in class deformablemesh.gui.meshinitialization.SlicePicker
-
Sets the limits that this picker can choose, ranging from -l/2 to +l/2.
- setLowColor(Color) - Method in class deformablemesh.util.SurfacePlot
-
- setMarkFromNormal(double[]) - Method in class deformablemesh.gui.FurrowInput
-
- setMax(double) - Method in class deformablemesh.util.SurfacePlot
-
- setMaxConnectionLength(double) - Method in class deformablemesh.SegmentationController
-
Set the maximum connection length that is used when doing a connection remesh.
- setMaxCurvature(double) - Method in class deformablemesh.geometry.CurvatureCalculator
-
- setMaxMixedArea(double) - Method in class deformablemesh.externalenergies.PressureForce
-
- setMesh(DeformableMesh3D) - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- setMesh(DeformableMesh3D) - Method in class deformablemesh.geometry.SpherePathTesting
-
- setMesh(Track, int, DeformableMesh3D) - Method in class deformablemesh.SegmentationController
-
Sets the provided mesh to be the mesh for the provided track at the specified frame.
- setMeshes(List<DeformableMesh3D>) - Method in class deformablemesh.gui.render2d.RaycastRender
-
- setMeshes(List<Track>, int, List<DeformableMesh3D>) - Method in class deformablemesh.SegmentationController
-
Adds all of the provided meshes to the corresponding track.
- setMeshes(List<Track>) - Method in class deformablemesh.SegmentationModel
-
- setMeshFrame3D(MeshFrame3D) - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- setMeshFrame3D(MeshFrame3D) - Method in class deformablemesh.SegmentationController
-
Sets up the provided meshframe3d as the main threed display.
- setMeshTracks(List<Track>) - Method in class deformablemesh.SegmentationController
-
Replaces the current tracks with the provided.
- setMin(double) - Method in class deformablemesh.util.SurfacePlot
-
- setMinAndMaxLengths(double, double) - Method in class deformablemesh.geometry.ConnectionRemesher
-
- setMinConnectionLength(double) - Method in class deformablemesh.SegmentationController
-
Gets the minimum connection length when doing a connection remesh.
- setMinCurvature(double) - Method in class deformablemesh.geometry.CurvatureCalculator
-
- setMinMax(double, double) - Method in interface deformablemesh.gui.IntensityRanges.Contrastable
-
- setMinMax(double, double) - Method in class deformablemesh.util.HotAndCold
-
- setMinMaxRange(double, double) - Method in class deformablemesh.meshview.TexturedPlaneDataObject
-
- setMinMaxRange(double, double) - Method in class deformablemesh.meshview.VolumeDataObject
-
- setName(String) - Method in class deformablemesh.track.Track
-
- setNeighbor(DeformableMesh3D) - Method in class deformablemesh.util.MeshFaceObscuring
-
- setNeighbors(List<DeformableMesh3D>) - Method in class deformablemesh.util.MeshFaceObscuring
-
- setNoHud() - Method in class deformablemesh.meshview.MeshFrame3D
-
- setNormal(double[]) - Method in interface deformablemesh.gui.FurrowInput.PlaneChangeListener
-
- setNormalizerWeight(double) - Method in class deformablemesh.SegmentationController
-
Turns on an external energy that tries to normalize triangle sizes.
- setNormalizerWeight(double) - Method in class deformablemesh.SegmentationModel
-
- setOriginalPlus(ImagePlus) - Method in class deformablemesh.SegmentationController
-
Sets the current image, and sets it on channel 0.
- setOriginalPlus(ImagePlus, int) - Method in class deformablemesh.SegmentationController
-
Causes the provided image to be the main backing image data.
- setOriginalPlus(ImagePlus) - Method in class deformablemesh.SegmentationModel
-
Sets the backing image plus, defaulting the channel to 0 and the frame to the current frame.
- setOriginalPlus(ImagePlus, int) - Method in class deformablemesh.SegmentationModel
-
Sets the current backing image to the provided image at the selected channel and the
current frame.
- setOriginalPlus(ImagePlus, int, int) - Method in class deformablemesh.SegmentationModel
-
- setPanel(JPanel) - Method in class deformablemesh.gui.render2d.RaycastRender
-
- setPosition(double[]) - Method in class deformablemesh.geometry.Node3D
-
Updates the array backing this position.
- setPosition(double, double, double) - Method in class deformablemesh.gui.meshinitialization.ThreeDCursor
-
- setPosition(double, double, double) - Method in class deformablemesh.meshview.VolumeDataObject
-
Sets the position of the lowest corner.
- setPositions(double[]) - Method in class deformablemesh.geometry.DeformableMesh3D
-
- setPressure(double) - Method in class deformablemesh.SegmentationController
-
For shrinking or growing a mesh.
- setPressure(double) - Method in class deformablemesh.SegmentationModel
-
- setPreviewBackgroundColor(Color) - Method in class deformablemesh.meshview.VolumeContrastSetter
-
- setRadius(double) - Method in class deformablemesh.geometry.modifier.Selector
-
- setRadius(double) - Method in class deformablemesh.geometry.Sphere
-
- setRadius(double[]) - Method in class deformablemesh.geometry.Sphere
-
- setRadius(double) - Method in class deformablemesh.meshview.SphereDataObject
-
- setReady(boolean) - Method in class deformablemesh.gui.ControlFrame
-
- setReady(boolean) - Method in interface deformablemesh.gui.ReadyObserver
-
- setRegions(List<Region>) - Method in class deformablemesh.util.connectedcomponents.RegionGrowing
-
- setRigidBoundaries(boolean) - Method in class deformablemesh.SegmentationController
-
When true, deforming meshes are confined at each step.
- setRingController(RingController) - Method in class deformablemesh.SegmentationModel
-
- setScale(double) - Method in class deformablemesh.meshview.Arrow
-
- setScaledClamps(boolean) - Method in class deformablemesh.meshview.VolumeTexture
-
- setSculptMode() - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- setSegmentationController(SegmentationController) - Method in class deformablemesh.meshview.MeshFrame3D
-
- setSelected(boolean) - Method in class deformablemesh.geometry.DeformableMesh3D
-
- setSelected(boolean) - Method in class deformablemesh.track.Track
-
- setSelected(boolean) - Method in class deformablemesh.util.connectedcomponents.Region
-
- setSelectNodesMode() - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- setShowSurface(boolean) - Method in class deformablemesh.geometry.DeformableMesh3D
-
- setShowSurface(boolean) - Method in class deformablemesh.meshview.DeformableMeshDataObject
-
- setShowSurface(boolean) - Method in class deformablemesh.meshview.TexturedPlaneDataObject
-
- setShowSurface(boolean) - Method in class deformablemesh.track.Track
-
- setSlice(Image) - Method in class deformablemesh.gui.Slice3DView
-
- setSliceListener(MouseAdapter) - Method in class deformablemesh.gui.RingController
-
- setSliderValue(int) - Method in class deformablemesh.gui.meshinitialization.SlicePicker
-
- setStack(MeshImageStack) - Method in class deformablemesh.gui.RingController
-
- setStartPoint(Node3D) - Method in class deformablemesh.geometry.SpherePathTesting
-
- setStericNeighborWeight(double) - Method in class deformablemesh.SegmentationController
-
Causes a 'steric' force from neighboring meshes to prevent mesh overlap.
- setStericNeighborWeight(double) - Method in class deformablemesh.SegmentationModel
-
- setSurfaceAppearance(Appearance) - Method in class deformablemesh.meshview.DeformableMeshDataObject
-
- setTexture(Texture3D) - Method in class deformablemesh.meshview.Sizeable3DSurface
-
- setTextureData(MeshImageStack) - Method in class deformablemesh.meshview.TexturedPlaneDataObject
-
- setTextureData(VolumeDataObject, int[], int[]) - Method in class deformablemesh.meshview.VolumeDataObject
-
For creating a volume representing the all of the pixes of the provided mesh image stack.
- setTextureData(MeshImageStack) - Method in class deformablemesh.meshview.VolumeDataObject
-
For creating a volume representing the all of the pixes of the provided mesh image stack.
- setTextureData(MeshImageStack, List<int[]>) - Method in class deformablemesh.meshview.VolumeDataObject
-
For creating a volume that shows part of an image stack.
- setThresh(double) - Method in class deformablemesh.ringdetection.ContractileRingDetector
-
- setThreshold(double) - Method in class deformablemesh.gui.RingController
-
- setTracks(List<Track>) - Method in class deformablemesh.gui.render2d.RenderFrame2D
-
- setTransparencyRange(int, double, double) - Method in class deformablemesh.meshview.MultiChannelVolumeTexture
-
Sets the transparency to the range associated relative to the clamped min and max.
- setTransparencyTrim(double, double) - Method in class deformablemesh.meshview.VolumeDataObject
-
- setup(String, ImagePlus) - Method in class deformablemesh.Deforming3DMesh_Plugin
-
- setup(String, ImagePlus) - Method in class Mouse_X
-
- setValue(double) - Method in class deformablemesh.gui.GuiTools.LocaleNumericTextField
-
- SetValue - Interface in deformablemesh.gui
-
Created by melkor on 11/18/15.
- setValue(double) - Method in interface deformablemesh.gui.SetValue
-
- setView(JComponent) - Method in class deformablemesh.gui.meshinitialization.CircularMeshInitializationDialog
-
- setView(StationaryViews) - Method in class deformablemesh.meshview.DataCanvas
-
- setViewParameters(double[]) - Method in class deformablemesh.meshview.DataCanvas
-
Sets the view based on the parameters.
- setViewParameters(double[]) - Method in class deformablemesh.meshview.MeshFrame3D
-
Restores a previous view.
- setViews(double[], double[]) - Method in class deformablemesh.gui.render2d.RenderFrame2D
-
- setVisible(boolean) - Method in class deformablemesh.gui.meshinitialization.ThreeDCursor
-
- setVisible(boolean) - Method in class deformablemesh.meshview.MeshFrame3D
-
- setVolume(double) - Method in class deformablemesh.externalenergies.VolumeConservation
-
- setVolumeColor(Color) - Method in class deformablemesh.SegmentationController
-
The color the image volume is display as, when the image volume is showing.
- setWeight(double) - Method in class deformablemesh.SegmentationController
-
Sets the magnitude of force the image causes on the mesh.
- setWeight(double) - Method in class deformablemesh.SegmentationModel
-
- setWidth(double) - Method in class deformablemesh.geometry.WireframeMesh
-
- setWireColor(Color) - Method in class deformablemesh.meshview.Axis3D
-
- setWireColor(Color) - Method in class deformablemesh.meshview.DeformableMeshDataObject
-
- setZoom(double) - Method in class deformablemesh.gui.Slice3DView
-
- ShellMesh - Class in deformablemesh.geometry
-
Creates a 'shell' mesh, which is essentially the original mesh + a mesh created by
shifting the nodes along the normal at the node a small displacement.
- ShellMesh(DeformableMesh3D) - Constructor for class deformablemesh.geometry.ShellMesh
-
- shiftViewport(double, double) - Method in class deformablemesh.gui.meshinitialization.SlicePicker
-
- show() - Method in class deformablemesh.util.SurfacePlot
-
- show(boolean) - Method in class deformablemesh.util.SurfacePlot
-
- showAboutWindow(JFrame) - Static method in class deformablemesh.gui.GuiTools
-
- showAxis() - Method in class deformablemesh.meshview.MeshFrame3D
-
- showBinaryBlob() - Method in class deformablemesh.SegmentationController
-
Shows the volume of the currently selected mesh by adding a voxel transient object, similar to the way
show volume works, but the result is binary and colored.
- showCurrent() - Method in class deformablemesh.util.Create3DTrainingDataFromMeshes
-
- showCurvature() - Method in class deformablemesh.SegmentationController
-
TODO remove
- showCurvature() - Method in class deformablemesh.SegmentationModel
-
- showDeformation() - Method in class deformablemesh.simulations.FillingBinaryImage
-
- showDialog(Frame) - Method in class deformablemesh.meshview.VolumeContrastSetter
-
- showEnergy(MeshImageStack, ExternalEnergy) - Method in class deformablemesh.meshview.MeshFrame3D
-
- showForces() - Method in class deformablemesh.SegmentationController
-
Shows forces on the currently selected mesh.
- showForces(DeformableMesh3D) - Method in class deformablemesh.SegmentationController
-
Creates a set of vectors to show how the mesh will deform based on the image energy and
external forces.
- showFrame() - Method in class deformablemesh.gui.ControlFrame
-
- showFrame(boolean) - Method in class deformablemesh.meshview.MeshFrame3D
-
- showFurrow(boolean) - Method in class deformablemesh.gui.RingController
-
- showFurrowValues() - Method in class deformablemesh.SegmentationController
-
Creates a text window with the current furrow values, position in image units and normal.
- showFurrowValues() - Method in class deformablemesh.SegmentationModel
-
Creates a text window with the current furrow values scaled to the image units.
- showInertialVector() - Method in class deformablemesh.SegmentationController
-
Shows a two vectors.
- showStress() - Method in class deformablemesh.SegmentationController
-
TODO remove
- showStress() - Method in class deformablemesh.SegmentationModel
-
- showTerminal() - Method in class deformablemesh.gui.SwingJSTerm
-
- showTexture(boolean) - Method in class deformablemesh.geometry.Furrow3D
-
- showTexturedMeshSurface() - Method in class deformablemesh.SegmentationController
-
Adds a transient data object using a 3D volume texture and a surface with the currently
selected mesh geometry.
- showValuesWindow() - Method in class deformablemesh.util.SurfacePlot
-
- showVolume(MeshImageStack) - Method in class deformablemesh.meshview.MeshFrame3D
-
Backs the volume texture date with the supplied image stack.
- showVolume() - Method in class deformablemesh.SegmentationController
-
Shows the volume data in the meshframe.
- showVolumeAction() - Method in class deformablemesh.gui.ControlFrame
-
- showVolumeClippingDialog() - Method in class deformablemesh.SegmentationController
-
- ShrinkRegion - Class in deformablemesh.util.connectedcomponents
-
- ShrinkRegion(Region) - Constructor for class deformablemesh.util.connectedcomponents.ShrinkRegion
-
- SIGMA - Variable in class deformablemesh.ringdetection.ContractileRingDetector
-
- simulate() - Method in class deformablemesh.simulations.GrowingDroplet
-
- simulate() - Method in class deformablemesh.simulations.SphericalCavity
-
- sixTriangleSphere() - Static method in class deformablemesh.geometry.RayCastMesh
-
- size() - Method in class deformablemesh.track.Track
-
- Sizeable3DSurface - Class in deformablemesh.meshview
-
Recreation of the 3D surface, such that the scale is set.
- Sizeable3DSurface(Texture3D, int[], double[]) - Constructor for class deformablemesh.meshview.Sizeable3DSurface
-
- Slice3DView - Class in deformablemesh.gui
-
For displaying a slice of the 3D image stack, using a uniform scale.
- Slice3DView() - Constructor for class deformablemesh.gui.Slice3DView
-
- SlicePicker - Class in deformablemesh.gui.meshinitialization
-
Created by msmith on 2/5/16.
- SlicePicker(MeshImageStack, double[], double[]) - Constructor for class deformablemesh.gui.meshinitialization.SlicePicker
-
- SmoothingForce - Class in deformablemesh.externalenergies
-
- SmoothingForce(DeformableMesh3D, double) - Constructor for class deformablemesh.externalenergies.SmoothingForce
-
- snapShot() - Method in class deformablemesh.meshview.DataCanvas
-
- snapShot() - Method in class deformablemesh.meshview.MeshFrame3D
-
- SofterStericMesh - Class in deformablemesh.externalenergies
-
- SofterStericMesh(DeformableMesh3D, DeformableMesh3D, double) - Constructor for class deformablemesh.externalenergies.SofterStericMesh
-
- sortPointsByAngle(List<double[]>, double[], double[]) - Static method in class deformablemesh.geometry.ProjectableMesh
-
- Sphere - Class in deformablemesh.geometry
-
For creating new meshes.
- Sphere(double[], double) - Constructor for class deformablemesh.geometry.Sphere
-
- SphereDataObject - Class in deformablemesh.meshview
-
Created by msmith on 2/8/16.
- SphereDataObject(double[], double) - Constructor for class deformablemesh.meshview.SphereDataObject
-
Creates a new moveable sphere at the origin with radius size
- SpherePathTesting - Class in deformablemesh.geometry
-
Created by msmith on 2/17/16.
- SpherePathTesting() - Constructor for class deformablemesh.geometry.SpherePathTesting
-
- sphereRayCastMesh(int) - Static method in class deformablemesh.geometry.RayCastMesh
-
- SphericalCavity - Class in deformablemesh.simulations
-
- SphericalCavity() - Constructor for class deformablemesh.simulations.SphericalCavity
-
- sphericalRayCastBinaryStack(MeshImageStack, int) - Static method in class deformablemesh.geometry.RayCastMesh
-
- split() - Method in class deformablemesh.util.connectedcomponents.Region
-
- splitMesh(List<Triangle3D>) - Method in class deformablemesh.geometry.Furrow3D
-
- splitMesh() - Method in class deformablemesh.SegmentationController
-
- splitMeshTrack() - Method in class deformablemesh.SegmentationController
-
Splits this track into two with all meshes from, and up to the current frame in one
track and all of the subsequent meshes in a new track.
- splitNodes(List<Node3D>) - Method in class deformablemesh.geometry.Furrow3D
-
- sqrt(double) - Static method in class deformablemesh.util.Vector3DOps
-
- square(double) - Static method in class deformablemesh.util.Vector3DOps
-
- StabilizeMeshes - Class in deformablemesh.examples
-
- StabilizeMeshes() - Constructor for class deformablemesh.examples.StabilizeMeshes
-
- start() - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- start() - Method in class deformablemesh.geometry.SpherePathTesting
-
- start() - Method in class deformablemesh.gui.meshinitialization.CircularMeshInitializationDialog
-
- start() - Method in class deformablemesh.gui.meshinitialization.FurrowInitializer
-
- start() - Method in class deformablemesh.gui.meshinitialization.RectangleMeshInitializingDialog
-
- start() - Method in class deformablemesh.simulations.ManyDrops
-
- start() - Method in class deformablemesh.simulations.SphericalCavity
-
- startEmptyTrack() - Method in class deformablemesh.SegmentationModel
-
Starts a track that is not used but has a name unique to the existing tracks.
- startMeshTrack(int, DeformableMesh3D) - Method in class deformablemesh.SegmentationModel
-
- startNewMeshTrack(int, DeformableMesh3D) - Method in class deformablemesh.SegmentationController
-
Starts a new mesh track with one mesh on the specified frame.
- startNewMeshTracks(List<DeformableMesh3D>) - Method in class deformablemesh.SegmentationController
-
Starts a new Track for each of provided meshes.
- StateListener - Interface in deformablemesh.util.actions
-
- stateUpdated(long) - Method in class deformablemesh.track.MeshTrackManager
-
- stateUpdated(long) - Method in interface deformablemesh.util.actions.StateListener
-
- step() - Method in class deformablemesh.simulations.GrowingDroplet
-
- step() - Method in class deformablemesh.simulations.ManyDrops
-
- step() - Method in class deformablemesh.simulations.SphericalCavity
-
- step() - Method in class deformablemesh.simulations.TwoDrops
-
- step(T, T) - Method in interface deformablemesh.util.astar.BasicCost
-
This is used for next step predictions.
- step() - Method in class deformablemesh.util.connectedcomponents.RegionGrowing
-
- step() - Method in class deformablemesh.util.connectedcomponents.ShrinkRegion
-
- step2() - Method in class deformablemesh.simulations.SphericalCavity
-
- steppingMeshes(List<Track>, int) - Static method in class deformablemesh.util.GroupDynamics
-
- StericMesh - Class in deformablemesh.externalenergies
-
Class used for calculating steric forces between meshes.
- StericMesh(DeformableMesh3D, DeformableMesh3D, double) - Constructor for class deformablemesh.externalenergies.StericMesh
-
- stickVertexes(DeformableMesh3D, DeformableMesh3D) - Method in class deformablemesh.simulations.TwoDrops
-
- stickyCell(DeformableMesh3D, DeformableMesh3D) - Method in class deformablemesh.simulations.TwoDrops
-
- stopRunning() - Method in class deformablemesh.gui.render2d.RenderFrame2D
-
- stopRunning() - Method in class deformablemesh.SegmentationController
-
Primarily used to stop deforming a mesh.
- stopRunning() - Method in class deformablemesh.SegmentationModel
-
- subDivideMesh(DeformableMesh3D) - Static method in class deformablemesh.geometry.RayCastMesh
-
Quadruple the number of triangles in a mesh.
- submit(Runnable) - Method in class deformablemesh.gui.RingController
-
- submit() - Method in class deformablemesh.gui.SwingJSTerm
-
- submit(SegmentationController.Executable) - Method in class deformablemesh.SegmentationController
-
Method for submitting jobs to the models main loops.
- surfaceNormal - Variable in class deformablemesh.geometry.Intersection
-
- SurfacePlot - Class in deformablemesh.util
-
For plotting values on the surface of a mesh.
- SurfacePlot() - Constructor for class deformablemesh.util.SurfacePlot
-
- SwingJSTerm - Class in deformablemesh.gui
-
Created by msmith on 4/14/14.
- SwingJSTerm(SegmentationController) - Constructor for class deformablemesh.gui.SwingJSTerm
-
- syncConnectionIndices() - Method in class deformablemesh.geometry.DeformableMesh3D
-
- syncDirectionalLight() - Method in class deformablemesh.meshview.MeshFrame3D
-
- syncFurrowView() - Method in class deformablemesh.geometry.modifier.MeshModifier
-
- syncMesh(int) - Method in class deformablemesh.meshview.MeshFrame3D
-
- syncTriangleIndices() - Method in class deformablemesh.geometry.DeformableMesh3D
-
- takeSnapShot() - Method in class deformablemesh.SegmentationController
-
Creates a snapshot of the current 3d view and creates an image plus window.
- TexturedPlaneDataObject - Class in deformablemesh.meshview
-
A volume
- TexturedPlaneDataObject(DeformableMesh3D, MeshImageStack) - Constructor for class deformablemesh.meshview.TexturedPlaneDataObject
-
- ThreeDCursor - Class in deformablemesh.gui.meshinitialization
-
Created by smithm3 on 24/05/18.
- ThreeDCursor(double, double, double) - Constructor for class deformablemesh.gui.meshinitialization.ThreeDCursor
-
- threeDVersion(List<Track>, List<Track>, int, int) - Method in class deformablemesh.examples.CreateCrossSectionMovies
-
- toFrame(int) - Method in class deformablemesh.SegmentationController
-
Sets the frame.
- toggleAxis() - Method in class deformablemesh.meshview.MeshFrame3D
-
- toggleHud() - Method in class deformablemesh.meshview.HotKeyDelegate
-
- toggleSurface() - Method in class deformablemesh.SegmentationController
-
Toggles displaying the surface of the currently selected mesh track.
- TOL - Static variable in class deformablemesh.util.Vector3DOps
-
- toPosition(double, double[]) - Method in class deformablemesh.gui.meshinitialization.ThreeDCursor
-
Moves to the new normalized coordinates only changing the direction along the normal.
- toSpan(double, double) - Static method in class deformablemesh.util.Vector3DOps
-
How many dr's does it take to fill an l.
- toString() - Method in enum deformablemesh.externalenergies.ImageEnergyType
-
- toString() - Method in class deformablemesh.meshview.ChannelVolume
-
- touchesEdge(List<int[]>, int, int) - Method in class deformablemesh.util.Create3DTrainingDataFromMeshes
-
checks if *any* of the provided pixels touch the edge of the box bound by x ∈ [0, width) and y ∈ [0, height)
- Track - Class in deformablemesh.track
-
Created by msmith on 3/30/16.
- Track(List<Color>) - Constructor for class deformablemesh.track.Track
-
- Track(String, Color) - Constructor for class deformablemesh.track.Track
-
- Track(String) - Constructor for class deformablemesh.track.Track
-
- TrackAnalysis - Class in deformablemesh.util
-
- TrackAnalysis() - Constructor for class deformablemesh.util.TrackAnalysis
-
- trackAvailableFrameForward(SegmentationController) - Static method in class deformablemesh.track.FrameToFrameDisplacement
-
Takes the current set tracks, find tracks that are available in the current frame, and the set of tracks that
are available in the next frame, then attempts to link them.
- TrackMateAdapter - Class in deformablemesh.io
-
A utility class for using TrackMate files.
- TrackMateAdapter() - Constructor for class deformablemesh.io.TrackMateAdapter
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- trackMesh(Track, int) - Method in class deformablemesh.SegmentationController
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Extands the track to (frame + 1) provided by copying the deformable mesh at frame.
- trackMesh() - Method in class deformablemesh.SegmentationController
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Creates a copy of the current mesh, advances a frame and adds it to the current track.
- trackMeshAction() - Method in class deformablemesh.gui.ControlFrame
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- trackMeshBackwards() - Method in class deformablemesh.SegmentationController
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Copies the current mesh, moves to the previous frame and adds the copy to the currently selected track.
- trackMeshBackwardsAction() - Method in class deformablemesh.gui.ControlFrame
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- translate(double[]) - Method in class deformablemesh.geometry.DeformableMesh3D
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Moves all of the nodes in this mesh by the displacement value.
- translate(int, int, int) - Method in class deformablemesh.util.connectedcomponents.Region
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- translate(double[]) - Method in class deformablemesh.util.MeshGroup
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- translateView(int, int) - Method in class deformablemesh.meshview.DataCanvas
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- Triangle3D - Class in deformablemesh.geometry
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An ordered collection of 3 nodes that will be used for calculating geometric properties.
- Triangle3D(Node3D, Node3D, Node3D) - Constructor for class deformablemesh.geometry.Triangle3D
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- triangle_index - Variable in class deformablemesh.geometry.DeformableMesh3D
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- TriangleAreaDistributor - Class in deformablemesh.externalenergies
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Created by msmith on 2/26/16.
- TriangleAreaDistributor(MeshImageStack, DeformableMesh3D, double) - Constructor for class deformablemesh.externalenergies.TriangleAreaDistributor
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- triangles - Variable in class deformablemesh.geometry.DeformableMesh3D
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- twistView(int) - Method in class deformablemesh.meshview.DataCanvas
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- TwoDrops - Class in deformablemesh.simulations
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This class is to test deforming two meshes that are influenced by "gravity", each other and a surface.
- TwoDrops() - Constructor for class deformablemesh.simulations.TwoDrops
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- twoSphereCheck() - Static method in class deformablemesh.geometry.BinaryMomentsOfInertia
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