Field Detail

• showPartsNearby

  protected JCheckBox showPartsNearby

• useSnapWindow

  protected JCheckBox useSnapWindow

• snapWindowXYsizeSpinner

  protected JSpinner snapWindowXYsizeSpinner

• snapWindowZsizeSpinner

  protected JSpinner snapWindowZsizeSpinner

• nearbyFieldSpinner

  protected JSpinner nearbyFieldSpinner

• guiUtils

  protected final GuiUtils guiUtils

• recViewer

  protected Viewer3D recViewer

• recViewerFrame

  protected Frame recViewerFrame

• sciViewSNT

  protected SciViewSNT sciViewSNT

• listener

  protected final sc.fiji.snt.SNTUI.GuiListener listener

• READY

  public static final int READY

  Flag specifying that image data is available and the UI is not waiting on any pending operations, thus 'ready to trace'

  See Also:

  Constant Field Values

• RUNNING_CMD

  public static final int RUNNING_CMD

  See Also:

  Constant Field Values

• WAITING_FOR_SIGMA_POINT_I

  public static final int WAITING_FOR_SIGMA_POINT_I

  See Also:

  Constant Field Values

• LOADING

  public static final int LOADING

  Flag specifying UI is currently waiting for I/0 operations to conclude

  See Also:

  Constant Field Values

• FITTING_PATHS

  public static final int FITTING_PATHS

  Flag specifying UI is currently waiting for fitting operations to conclude

  See Also:

  Constant Field Values

• EDITING

  public static final int EDITING

  Flag specifying UI is currently waiting for user to edit a selected Path

  See Also:

  Constant Field Values

• SNT_PAUSED

  public static final int SNT_PAUSED

  Flag specifying all SNT are temporarily disabled (all user interactions are waived back to ImageJ)

  See Also:

  Constant Field Values

• TRACING_PAUSED

  public static final int TRACING_PAUSED

  Flag specifying tracing functions are (currently) disabled. Tracing is disabled when the user chooses so or when no valid image data is available (e.g., when no image has been loaded and a placeholder display canvas is being used)

  See Also:

  Constant Field Values

• confirmTemporarySegments

  protected boolean confirmTemporarySegments

• finishOnDoubleConfimation

  protected boolean finishOnDoubleConfimation

• discardOnDoubleCancellation

  protected boolean discardOnDoubleCancellation

• askUserConfirmation

  protected boolean askUserConfirmation

Constructor Detail

• SNTUI

  public SNTUI(SNT plugin)

  Instantiates SNT's main UI and associated PathManagerUI and FillManagerUI instances.

  Parameters:

  plugin - the SNT instance associated with this UI

Method Detail

• getState

  public int getState()

  Gets the current UI state.

  Returns:

  the current UI state, e.g., READY, RUNNING_CMD, etc.

• isReady

  public boolean isReady()

  Assesses whether the UI is blocked.

  Returns:

  true if the UI is currently unblocked, i.e., ready for tracing/editing/analysis *

• setEnableDebugMode

  public void setEnableDebugMode(boolean enable)

  Enables/disables debug mode

  Parameters:

  enable - true to enable debug mode, otherwise false

• runCommand

  public void runCommand(String cmd)
                  throws IllegalArgumentException

  Runs a menu command (as listed in the menu bar hierarchy).

  Parameters:

  cmd - The command to be run, exactly as listed in its menu (either in the this dialog, or PathManagerUI)

  Throws:

  IllegalArgumentException - if cmd was not found.

• runCommand

  protected static void runCommand(JMenuBar menuBar,
                                   String cmd)
                            throws IllegalArgumentException

  Throws:

  IllegalArgumentException

• gaussianCalculated

  protected void gaussianCalculated(boolean succeeded)

• refresh

  public void refresh()

• updateSettingsString

  protected void updateSettingsString()

• exitRequested

  protected void exitRequested()

• disableImageDependentComponents

  protected void disableImageDependentComponents()

• changeState

  public void changeState(int newState)

  Changes this UI to a new state. Does nothing if newState is the current UI state

  Parameters:

  newState - the new state, e.g., READY, TRACING_PAUSED, etc.

• resetState

  protected void resetState()

• error

  public void error(String msg)

• showMessage

  public void showMessage(String msg,
                          String title)

• loadImagefromGUI

  protected void loadImagefromGUI(int newC,
                                  int newT)

• buttonPanel

  protected static JPanel buttonPanel(JButton... buttons)

• openFile

  protected File openFile(String promptMsg,
                          String extension)

• openFile

  protected File openFile(String promptMsg,
                          File suggestedFile)

• saveFile

  protected File saveFile(String promptMsg,
                          String suggestedFileName,
                          String fallbackExtension)

• updateExternalImgWidgets

  protected void updateExternalImgWidgets()

• showStatus

  public void showStatus(String msg,
                         boolean temporary)

  Updates the status bar.

  Parameters:

  msg - the text to displayed. Set it to null (or empty String) to reset the status bar.

  temporary - if true and msg is valid, text is displayed transiently for a couple of seconds

• setLookAndFeel

  public void setLookAndFeel(String lookAndFeelName)

• displayOnStarting

  protected void displayOnStarting()

• setFillListVisible

  protected void setFillListVisible(boolean makeVisible)

• nearbySlices

  protected boolean nearbySlices()

• setSigmaPaletteListener

  public void setSigmaPaletteListener(SigmaPaletteListener listener)

• getPathManager

  public PathManagerUI getPathManager()

  Gets the Path Manager dialog.

  Returns:

  the PathManagerUI associated with this UI

• getFillManager

  public FillManagerUI getFillManager()

  Gets the Fill Manager dialog.

  Returns:

  the FillManagerUI associated with this UI

• getReconstructionViewer

  public Viewer3D getReconstructionViewer(boolean initializeIfNull)

  Gets the Reconstruction Viewer.

  Parameters:

  initializeIfNull - it true, initializes the Viewer if it has not yet been initialized

  Returns:

  the reconstruction viewer

• getSciViewSNT

  public SciViewSNT getSciViewSNT(boolean initializeIfNull)

  Gets the active getSciViewSNT (SciView<>SNT bridge) instance.

  Parameters:

  initializeIfNull - it true, initializes SciView if it has not yet been initialized

  Returns:

  the SciView viewer

• setReconstructionViewer

  protected void setReconstructionViewer(Viewer3D recViewer)

• setSciViewSNT

  protected void setSciViewSNT(SciViewSNT sciViewSNT)

• reset

  protected void reset()

• inputImageChanged

  protected void inputImageChanged()

• abortCurrentOperation

  protected void abortCurrentOperation()

• launchSigmaPaletteAround

  protected void launchSigmaPaletteAround(int x,
                                          int y)

• togglePathsChoice

  protected void togglePathsChoice()

• setSecondaryLayerTracingSelected

  protected void setSecondaryLayerTracingSelected(boolean enable)

• toggleSecondaryLayerTracing

  protected void toggleSecondaryLayerTracing()

• toggleSecondaryLayerBuiltin

  protected void toggleSecondaryLayerBuiltin()

• toggleSecondaryLayerExternal

  protected void toggleSecondaryLayerExternal()

• enableSecondaryLayerBuiltin

  protected void enableSecondaryLayerBuiltin(boolean enable)

• enableSecondaryLayerExternal

  protected void enableSecondaryLayerExternal(boolean enable)

• enableAStarGUI

  protected void enableAStarGUI(boolean enable)

  Should only be called by SNT.enableAstar(boolean)

• togglePartsChoice

  protected void togglePartsChoice()

• toggleChannelAndFrameChoice

  protected void toggleChannelAndFrameChoice()

• noValidImageDataError

  protected void noValidImageDataError()

• saveToXML

  protected boolean saveToXML(File file)

• saveAllPathsToSwc

  protected boolean saveAllPathsToSwc(String filePath)