SNT

java.lang.Object
- sc.fiji.snt.hyperpanes.MultiDThreePanes
- - sc.fiji.snt.SNT

All Implemented Interfaces:

features.GaussianGenerationCallback, PaneOwner, SearchProgressCallback
```
public class SNT
extends MultiDThreePanes
implements SearchProgressCallback, features.GaussianGenerationCallback
```
Implements the SNT plugin.

Author:

Tiago Ferreira

Field Summary
- Fields inherited from class sc.fiji.snt.hyperpanes.MultiDThreePanes
  XY_PLANE, XZ_PLANE, ZY_PLANE

Constructor Summary

Constructors
Constructor and Description
`SNT(org.scijava.Context context, ij.ImagePlus sourceImage)` Instantiates SNT in 'Tracing Mode'.
`SNT(org.scijava.Context context, PathAndFillManager pathAndFillManager)` Instantiates SNT in 'Analysis Mode'

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`boolean`	`accessToValidImageData()`
`void`	`addListener(SNTListener listener)`
`Path`	`autoTrace(java.util.List<PointInImage> pointList, PointInImage forkPoint)` Automatically traces a path from a list of points and adds it to the active `PathAndFillManager` instance.
`Path`	`autoTrace(PointInImage start, PointInImage end, PointInImage forkPoint)` Automatically traces a path from a point A to a point B.
`void`	`cancelPath()` Cancels the temporary path.
`void`	`cancelSearch(boolean cancelFillToo)`
`void`	`cancelTemporary()`
`void`	`changeUIState(int newState)`
`void`	`closeAndResetAllPanes()`
`void`	`confirmTemporary()`
`sc.fiji.snt.InteractiveTracerCanvas`	`createCanvas(ij.ImagePlus imagePlus, int plane)`
`void`	`discardFill()`
`boolean`	`editModeAllowed()` Assesses if activation of 'Edit Mode' is possible.
`void`	`enableAstar(boolean enable)` Toggles the A* search algorithm (enabled by default)
`void`	`enableAutoActivation(boolean enable)`
`void`	`enableHessian(boolean enable)`
`void`	`enableSnapCursor(boolean enable)` Enables SNT's XYZ snap cursor feature.
`void`	`finished(SearchInterface source, boolean success)`
`org.scijava.Context`	`getContext()`
`Path`	`getCurrentPath()`
`boolean`	`getDrawDiametersXY()`
`ij.ImagePlus`	`getFilledVolume(boolean asMask)`
`HessianCaller`	`getHessianCaller(java.lang.String image)`
`double`	`getHessianSigma(java.lang.String image, boolean physicalUnits)`
`ij.ImagePlus`	`getImagePlus()`
`ij.ImagePlus`	`getImagePlus(int pane)` Gets the Image associated with a view pane.
`ij.ImagePlus`	`getLoadedDataAsImp()` Retrieves the pixel data of the main image currently loaded in memory as an ImagePlus object.
`double`	`getMinimumSeparation()`
`PathAndFillManager`	`getPathAndFillManager()`
`SNTPrefs`	`getPrefs()`
`ij.ImagePlus`	`getSecondaryDataAsImp()` Retrieves the 'secondary image' data currently loaded in memory as an ImagePlus object.
`float[]`	`getSecondaryImageMinMax()`
`java.util.Collection<Path>`	`getSelectedPaths()`
`SNTUI`	`getUI()` Gets the main UI.
`void`	`initialize(boolean singlePane, int channel, int frame)` Initializes the plugin by assembling all the required tracing views
`void`	`initialize(ij.ImagePlus imp)`
`boolean`	`is2D()`
`boolean`	`isAstarEnabled()` Checks if A* search is enabled
`boolean`	`isHessianEnabled(java.lang.String image)` Checks if Hessian analysis is enabled
`boolean`	`isOnlySelectedPathsVisible()`
`boolean`	`isSecondaryImageLoaded()` Assesses if the 'secondary image' has been loaded into memory.
`boolean`	`isTubenessImageCached(java.lang.String image)`
`void`	`justDisplayNearSlices(boolean value, int eitherSide)`
`void`	`loadLabelsFile(java.lang.String path)`
`void`	`loadSecondaryImage(java.io.File file)` Loads the 'secondary image' specified by `setSecondaryImage(File)` into memory as 32-bit data.
`void`	`loadSecondaryImage(ij.ImagePlus imp)`
`void`	`loadTracings(java.io.File file)`
`void`	`loadTubenessImage(java.lang.String type, java.io.File file)`
`void`	`loadTubenessImage(java.lang.String type, ij.ImagePlus imp)`
`ij.ImagePlus`	`makePathVolume()`
`ij.ImagePlus`	`makePathVolume(java.util.Collection<Path> paths)`
`void`	`mouseMovedTo(double x_in_pane, double y_in_pane, int in_plane, boolean sync_panes_modifier_down, boolean join_modifier_down)`
`void`	`notifyListeners(SNTEvent event)`
`void`	`pauseOrRestartFilling()`
`void`	`pointsInSearch(SearchInterface source, int inOpen, int inClosed)`
`void`	`proportionDone(double proportion)`
`void`	`rebuildDisplayCanvases()` Rebuilds display canvases, i.e., the placeholder canvases used when no valid image data exists (a single-canvas is rebuilt if only the XY view is active).
`void`	`rebuildZYXZpanes()`
`void`	`reloadImage(int channel, int frame)`
`void`	`saveFill()`
`void`	`selectPath(Path p, boolean addToExistingSelection)`
`void`	`setCurrentPath(Path path)`
`void`	`setDrawDiametersXY(boolean draw)`
`void`	`setFillList(java.lang.String[] newList)`
`void`	`setFillThreshold(double distance)`
`void`	`setFillThresholdFrom(double world_x, double world_y, double world_z)`
`void`	`setPathList(java.lang.String[] newList, Path justAdded, boolean expandAll)`
`void`	`setSecondaryImage(java.io.File file)` Specifies the 'secondary image' to be used during a tracing session.
`void`	`setSecondaryImageMinMax(float min, float max)`
`void`	`setSelectedPaths(java.util.HashSet<Path> selectedPathsSet, java.lang.Object source)`
`void`	`setShowOnlySelectedPaths(boolean showOnlySelectedPaths)`
`void`	`setTemporaryPath(Path path)`
`void`	`showCorrespondencesTo(java.io.File tracesFile, java.awt.Color c, double maxDistance)` Deprecated.
`void`	`showMIPOverlays(double opacity)` Overlays a semi-transparent MIP (8-bit scaled) of the data being traced over the tracing canvas(es).
`void`	`showStatus(int progress, int maximum, java.lang.String status)`
`void`	`startFillerThread(FillerThread filler)`
`void`	`startFillingPaths(java.util.Set<Path> fromPaths)`
`void`	`startHessian(java.lang.String image, double sigma, double max, boolean wait)`
`void`	`startUI()`
`void`	`threadStatus(SearchInterface source, int status)`
`void`	`updateAllViewers()`
`void`	`updateDisplayCanvases()` Rebuilds display canvas(es) to ensure all paths are contained in the image.

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - SNT
```
public SNT(org.scijava.Context context,
           ij.ImagePlus sourceImage)
    throws java.lang.IllegalArgumentException
```
    Instantiates SNT in 'Tracing Mode'.
    
    Parameters:
    
    context - the SciJava application context providing the services required by the class
    
    sourceImage - the source image
    
    Throws:
    
    java.lang.IllegalArgumentException - If sourceImage is of type 'RGB'
  - SNT
```
public SNT(org.scijava.Context context,
           PathAndFillManager pathAndFillManager)
```
    Instantiates SNT in 'Analysis Mode'
    
    Parameters:
    
    context - the SciJava application context providing the services required by the class
    
    pathAndFillManager - The PathAndFillManager instance to be associated with the plugin
- Method Detail
  - rebuildDisplayCanvases
```
public void rebuildDisplayCanvases()
                            throws java.lang.IllegalArgumentException
```
    Rebuilds display canvases, i.e., the placeholder canvases used when no valid image data exists (a single-canvas is rebuilt if only the XY view is active).
    Useful when multiple files are imported and imported paths 'fall off' the dimensions of current canvas(es). If there is not enough memory to accommodate enlarged dimensions, the resulting canvas will be a 2D image.
    
    Throws:
    
    java.lang.IllegalArgumentException - if valid image data exists
  - updateDisplayCanvases
```
public void updateDisplayCanvases()
```
    Rebuilds display canvas(es) to ensure all paths are contained in the image. Does nothing if placeholder canvas(es) are not being used.
    
    See Also:
    
    rebuildDisplayCanvases()
  - accessToValidImageData
```
public boolean accessToValidImageData()
```
  - initialize
```
public void initialize(ij.ImagePlus imp)
```
    Overrides:
    
    initialize in class MultiDThreePanes
  - initialize
```
public void initialize(boolean singlePane,
                       int channel,
                       int frame)
```
    Initializes the plugin by assembling all the required tracing views
    
    Parameters:
    
    singlePane - if true only the XY view will be generated, if false XY, ZY, XZ views are created
    
    channel - the channel to be traced. Ignored when no valid image data exists.
    
    frame - the frame to be traced. Ignored when no valid image data exists.
  - reloadImage
```
public void reloadImage(int channel,
                        int frame)
```
  - rebuildZYXZpanes
```
public void rebuildZYXZpanes()
```
  - startUI
```
public void startUI()
```
  - loadTracings
```
public void loadTracings(java.io.File file)
```
  - getPathAndFillManager
```
public PathAndFillManager getPathAndFillManager()
```
  - getImagePlus
```
public ij.ImagePlus getImagePlus()
```
  - createCanvas
```
public sc.fiji.snt.InteractiveTracerCanvas createCanvas(ij.ImagePlus imagePlus,
                                                        int plane)
```
    Overrides:
    
    createCanvas in class MultiDThreePanes
  - cancelSearch
```
public void cancelSearch(boolean cancelFillToo)
```
  - threadStatus
```
public void threadStatus(SearchInterface source,
                         int status)
```
    Specified by:
    
    threadStatus in interface SearchProgressCallback
  - changeUIState
```
public void changeUIState(int newState)
```
  - saveFill
```
public void saveFill()
```
  - discardFill
```
public void discardFill()
```
  - pauseOrRestartFilling
```
public void pauseOrRestartFilling()
```
  - addListener
```
public void addListener(SNTListener listener)
```
  - notifyListeners
```
public void notifyListeners(SNTEvent event)
```
  - finished
```
public void finished(SearchInterface source,
                     boolean success)
```
    Specified by:
    
    finished in interface SearchProgressCallback
  - pointsInSearch
```
public void pointsInSearch(SearchInterface source,
                           int inOpen,
                           int inClosed)
```
    Specified by:
    
    pointsInSearch in interface SearchProgressCallback
  - justDisplayNearSlices
```
public void justDisplayNearSlices(boolean value,
                                  int eitherSide)
```
  - editModeAllowed
```
public boolean editModeAllowed()
```
    Assesses if activation of 'Edit Mode' is possible.
    
    Returns:
    
    true, if possible, false otherwise
  - loadLabelsFile
```
public void loadLabelsFile(java.lang.String path)
```
  - mouseMovedTo
```
public void mouseMovedTo(double x_in_pane,
                         double y_in_pane,
                         int in_plane,
                         boolean sync_panes_modifier_down,
                         boolean join_modifier_down)
```
  - setTemporaryPath
```
public void setTemporaryPath(Path path)
```
  - setCurrentPath
```
public void setCurrentPath(Path path)
```
  - getCurrentPath
```
public Path getCurrentPath()
```
  - makePathVolume
```
public ij.ImagePlus makePathVolume(java.util.Collection<Path> paths)
```
  - makePathVolume
```
public ij.ImagePlus makePathVolume()
```
  - confirmTemporary
```
public void confirmTemporary()
```
  - cancelTemporary
```
public void cancelTemporary()
```
  - cancelPath
```
public void cancelPath()
```
    Cancels the temporary path.
  - autoTrace
```
public Path autoTrace(PointInImage start,
                      PointInImage end,
                      PointInImage forkPoint)
```
    Automatically traces a path from a point A to a point B. See autoTrace(List, PointInImage) for details.
    
    Parameters:
    
    start - the PointInImage the starting point of the path
    
    end - the PointInImage the terminal point of the path
    
    forkPoint - the PointInImage fork point of the parent Path from which the searched path should branch off, or null if the the path should not have any parent.
    
    Returns:
    
    the path a reference to the computed path.
    
    See Also:
    
    autoTrace(List, PointInImage)
  - autoTrace
```
public Path autoTrace(java.util.List<PointInImage> pointList,
                      PointInImage forkPoint)
```
    Automatically traces a path from a list of points and adds it to the active PathAndFillManager instance. Note that this method still requires SNT's UI. For headless auto-tracing have a look at TracerThread.
    SNT's UI will remain blocked in "search mode" until the Path computation completes. Tracing occurs through the active SearchInterface selected in the UI, i.e., TracerThread (the default A* search), TubularGeodesicsTracer, etc.
    All input PointInImage must be specified in real world coordinates.
    
    Parameters:
    
    pointList - the list of PointInImage containing the nodes to be used as target goals during the search. If the search cannot converge into a target point, such point is omitted from path, if Successful, target point will be included in the final path. the final path. The first point in the list is the start of the path, the last its terminus. Null objects not allowed.
    
    forkPoint - the PointInImage fork point of the parent Path from which the searched path should branch off, or null if the the path should not have any parent.
    
    Returns:
    
    the path a reference to the computed path. It is added to the Path Manager list.If a path cannot be fully computed from the specified list of points, a single-point path is generated.
  - setFillThresholdFrom
```
public void setFillThresholdFrom(double world_x,
                                 double world_y,
                                 double world_z)
```
  - setFillThreshold
```
public void setFillThreshold(double distance)
```
  - getFilledVolume
```
public ij.ImagePlus getFilledVolume(boolean asMask)
```
  - startFillerThread
```
public void startFillerThread(FillerThread filler)
```
  - startFillingPaths
```
public void startFillingPaths(java.util.Set<Path> fromPaths)
```
  - getMinimumSeparation
```
public double getMinimumSeparation()
```
  - getLoadedDataAsImp
```
public ij.ImagePlus getLoadedDataAsImp()
```
    Retrieves the pixel data of the main image currently loaded in memory as an ImagePlus object. Returned image is always a single channel image.
    
    Returns:
    
    the loaded data corresponding to the C,T position currently being traced, or null if no image data has been loaded into memory.
  - startHessian
```
public void startHessian(java.lang.String image,
                         double sigma,
                         double max,
                         boolean wait)
```
  - isSecondaryImageLoaded
```
public boolean isSecondaryImageLoaded()
```
    Assesses if the 'secondary image' has been loaded into memory. Note that while some tracer Threads will load the image into memory, others may waive the loading to third party libraries
    
    Returns:
    
    true, if image has been loaded into memory.
  - setSecondaryImage
```
public void setSecondaryImage(java.io.File file)
```
    Specifies the 'secondary image' to be used during a tracing session.
    
    Parameters:
    
    file - The file containing the 'secondary image'
  - loadSecondaryImage
```
public void loadSecondaryImage(java.io.File file)
                        throws java.io.IOException,
                               java.lang.IllegalArgumentException
```
    Loads the 'secondary image' specified by setSecondaryImage(File) into memory as 32-bit data.
    
    Parameters:
    
    file - The file to be loaded
    
    Throws:
    
    java.io.IOException - If image could not be loaded
    
    java.lang.IllegalArgumentException - if dimensions are unexpected, or image type is not supported
    
    See Also:
    
    isSecondaryImageLoaded(), getSecondaryDataAsImp()
  - loadSecondaryImage
```
public void loadSecondaryImage(ij.ImagePlus imp)
                        throws java.lang.IllegalArgumentException
```
    Throws:
    
    java.lang.IllegalArgumentException
  - setSecondaryImageMinMax
```
public void setSecondaryImageMinMax(float min,
                                    float max)
```
  - getSecondaryImageMinMax
```
public float[] getSecondaryImageMinMax()
```
  - loadTubenessImage
```
public void loadTubenessImage(java.lang.String type,
                              java.io.File file)
                       throws java.io.IOException,
                              java.lang.IllegalArgumentException
```
    Throws:
    
    java.io.IOException
    
    java.lang.IllegalArgumentException
  - loadTubenessImage
```
public void loadTubenessImage(java.lang.String type,
                              ij.ImagePlus imp)
                       throws java.lang.IllegalArgumentException
```
    Throws:
    
    java.lang.IllegalArgumentException
  - getSecondaryDataAsImp
```
public ij.ImagePlus getSecondaryDataAsImp()
```
    Retrieves the 'secondary image' data currently loaded in memory as an ImagePlus object. Returned image is always of 32-bit type.
    
    Returns:
    
    the loaded data or null if no image has been loaded.
    
    See Also:
    
    isSecondaryImageLoaded(), loadSecondaryImage(ImagePlus), loadSecondaryImage(File)
  - enableHessian
```
public void enableHessian(boolean enable)
```
  - getPrefs
```
public SNTPrefs getPrefs()
```
  - proportionDone
```
public void proportionDone(double proportion)
```
    Specified by:
    
    proportionDone in interface features.GaussianGenerationCallback
  - showCorrespondencesTo
```
@Deprecated
public void showCorrespondencesTo(java.io.File tracesFile,
                                              java.awt.Color c,
                                              double maxDistance)
```
    Deprecated.
  - setShowOnlySelectedPaths
```
public void setShowOnlySelectedPaths(boolean showOnlySelectedPaths)
```
  - getImagePlus
```
public ij.ImagePlus getImagePlus(int pane)
```
    Gets the Image associated with a view pane.
    
    Parameters:
    
    pane - the flag specifying the view either MultiDThreePanes.XY_PLANE, MultiDThreePanes.XZ_PLANE or MultiDThreePanes.ZY_PLANE.
    
    Returns:
    
    the image associate with the specified view, or null if the view is not available
  - isOnlySelectedPathsVisible
```
public boolean isOnlySelectedPathsVisible()
```
  - updateAllViewers
```
public void updateAllViewers()
```
  - selectPath
```
public void selectPath(Path p,
                       boolean addToExistingSelection)
```
  - getSelectedPaths
```
public java.util.Collection<Path> getSelectedPaths()
```
  - setPathList
```
public void setPathList(java.lang.String[] newList,
                        Path justAdded,
                        boolean expandAll)
```
  - setFillList
```
public void setFillList(java.lang.String[] newList)
```
  - setSelectedPaths
```
public void setSelectedPaths(java.util.HashSet<Path> selectedPathsSet,
                             java.lang.Object source)
```
  - showMIPOverlays
```
public void showMIPOverlays(double opacity)
```
    Overlays a semi-transparent MIP (8-bit scaled) of the data being traced over the tracing canvas(es). Does nothing if image is 2D. Note that with multidimensional images, only the C,T position being traced is projected.
    
    Parameters:
    
    opacity - (alpha), in the range 0.0-1.0, where 0.0 is none (fully transparent) and 1.0 is fully opaque. Setting opacity to zero clears previous MIPs.
  - enableSnapCursor
```
public void enableSnapCursor(boolean enable)
```
    Enables SNT's XYZ snap cursor feature. Does nothing if no image data is available
    
    Parameters:
    
    enable - whether cursor snapping should be enabled
  - enableAutoActivation
```
public void enableAutoActivation(boolean enable)
```
  - enableAstar
```
public void enableAstar(boolean enable)
```
    Toggles the A* search algorithm (enabled by default)
    
    Parameters:
    
    enable - true to enable A* search, false otherwise
  - isAstarEnabled
```
public boolean isAstarEnabled()
```
    Checks if A* search is enabled
    
    Returns:
    
    true, if A* search is enabled, otherwise false
  - isHessianEnabled
```
public boolean isHessianEnabled(java.lang.String image)
```
    Checks if Hessian analysis is enabled
    
    Returns:
    
    true, if Hessian analysis is enabled, otherwise false
  - getHessianSigma
```
public double getHessianSigma(java.lang.String image,
                              boolean physicalUnits)
```
  - isTubenessImageCached
```
public boolean isTubenessImageCached(java.lang.String image)
```
  - is2D
```
public boolean is2D()
```
    Returns:
    
    true if the image currently loaded does not have a depth (Z) dimension
  - setDrawDiametersXY
```
public void setDrawDiametersXY(boolean draw)
```
  - getDrawDiametersXY
```
public boolean getDrawDiametersXY()
```
  - closeAndResetAllPanes
```
public void closeAndResetAllPanes()
```
    Overrides:
    
    closeAndResetAllPanes in class MultiDThreePanes
  - getContext
```
public org.scijava.Context getContext()
```
  - getUI
```
public SNTUI getUI()
```
    Gets the main UI.
    
    Returns:
    
    the main dialog of SNT's UI
  - showStatus
```
public void showStatus(int progress,
                       int maximum,
                       java.lang.String status)
```
    Specified by:
    
    showStatus in interface PaneOwner
    
    Overrides:
    
    showStatus in class MultiDThreePanes
  - getHessianCaller
```
public HessianCaller getHessianCaller(java.lang.String image)
```

Class SNT

Field Summary

Fields inherited from class sc.fiji.snt.hyperpanes.MultiDThreePanes

Constructor Summary

Method Summary

Methods inherited from class sc.fiji.snt.hyperpanes.MultiDThreePanes

Methods inherited from class java.lang.Object

Constructor Detail

SNT

SNT

Method Detail

rebuildDisplayCanvases

updateDisplayCanvases

accessToValidImageData

initialize

initialize

reloadImage

rebuildZYXZpanes

startUI

loadTracings

getPathAndFillManager

getImagePlus

createCanvas

cancelSearch

threadStatus

changeUIState

saveFill

discardFill

pauseOrRestartFilling

addListener

notifyListeners

finished

pointsInSearch

justDisplayNearSlices

editModeAllowed

loadLabelsFile

mouseMovedTo

setTemporaryPath

setCurrentPath

getCurrentPath

makePathVolume

makePathVolume

confirmTemporary

cancelTemporary

cancelPath

autoTrace

autoTrace

setFillThresholdFrom

setFillThreshold

getFilledVolume

startFillerThread

startFillingPaths

getMinimumSeparation

getLoadedDataAsImp

startHessian

isSecondaryImageLoaded

setSecondaryImage

loadSecondaryImage

loadSecondaryImage

setSecondaryImageMinMax

getSecondaryImageMinMax

loadTubenessImage

loadTubenessImage

getSecondaryDataAsImp

enableHessian

getPrefs

proportionDone

showCorrespondencesTo

setShowOnlySelectedPaths

getImagePlus

isOnlySelectedPathsVisible

updateAllViewers

selectPath

getSelectedPaths

setPathList

setFillList

setSelectedPaths

showMIPOverlays

enableSnapCursor

enableAutoActivation