Serialized Form (SNT 5.0.12-SNAPSHOT API)

Package sc.fiji.snt

Class sc.fiji.snt.FillManagerUI

class FillManagerUI extends JDialog implements Serializable

serialVersionUID:: 1L

Serialized Fields

actions

List<sc.fiji.snt.FillManagerUI.FillAction> actions

currentState
```
FillManagerUI.State currentState
```
currentThresholdLabel
```
JLabel currentThresholdLabel
```
cursorPositionLabel
```
JLabel cursorPositionLabel
```
cursorThresholdChoice
```
JRadioButton cursorThresholdChoice
```
exploredThresholdApplyButton
```
JButton exploredThresholdApplyButton
```
exploredThresholdChoice
```
JRadioButton exploredThresholdChoice
```
exportFillsMenu
```
JPopupMenu exportFillsMenu
```
fillList
```
JList<Fill> fillList
```
fillTypeLabel
```
JLabel fillTypeLabel
```
gUtils
```
GuiUtils gUtils
```
listModel
```
DefaultListModel<Fill> listModel
```
manualThresholdApplyButton
```
JButton manualThresholdApplyButton
```
manualThresholdChoice
```
JRadioButton manualThresholdChoice
```
manualThresholdInputField
```
JTextField manualThresholdInputField
```
maxThresholdLabel
```
JLabel maxThresholdLabel
```
maxThresholdValue
```
double maxThresholdValue
```
pathAndFillManager
```
PathAndFillManager pathAndFillManager
```
plugin
```
SNT plugin
```
reloadFill
```
JButton reloadFill
```
saveFill
```
JButton saveFill
```
splitFillsCheckbox
```
JCheckBox splitFillsCheckbox
```
startFill
```
JButton startFill
```
statusText
```
JLabel statusText
```
stopFill
```
JButton stopFill
```
storeExtraNodesCheckbox
```
JCheckBox storeExtraNodesCheckbox
```
transparentCheckbox
```
JCheckBox transparentCheckbox
```

Class sc.fiji.snt.MultiPathTracerCanvas

class MultiPathTracerCanvas extends TracerCanvas implements Serializable

serialVersionUID:

1L
- Serialized Fields
  - dimmedAlpha
    
    int dimmedAlpha
  - dimmedOOBAlpha
    
    int dimmedOOBAlpha
  - entries
    
    List<MultiPathTracerCanvas.Entry> entries
  - highlightedAlpha
    
    int highlightedAlpha
    
    Per-entry transparencies (percent).
  - highlightedOOBAlpha
    
    int highlightedOOBAlpha
    
    Out-of-band transparencies (percent).

Class sc.fiji.snt.PathManagerUI

class PathManagerUI extends JDialog implements Serializable

serialVersionUID:: 1L

Serialized Fields

colorMenu
```
ColorMenu colorMenu
```

fittingHelper

sc.fiji.snt.PathManagerUI.FitHelper fittingHelper

fitVolumeMenuItem
```
JMenuItem fitVolumeMenuItem
```

fullTreeModel

sc.fiji.snt.PathManagerUI.HelpfulTreeModel fullTreeModel

guiUtils
```
GuiUtils guiUtils
```
measureUI
```
MeasureUI measureUI
```
menuBar
```
JMenuBar menuBar
```

multiSpectralRefineHelper

sc.fiji.snt.PathManagerUI.MultiSpectralRefineHelper multiSpectralRefineHelper

navToolbar

sc.fiji.snt.PathManagerUI.NavigationToolBar navToolbar

pathAndFillManager
```
PathAndFillManager pathAndFillManager
```
plugin
```
SNT plugin
```

proofReadingToolBar

sc.fiji.snt.PathManagerUI.ProofReadingTagsToolBar proofReadingToolBar

searchableBar

PathManagerUISearchableBar searchableBar

swcTypeButtonGroup
```
ButtonGroup swcTypeButtonGroup
```
swcTypeMenu
```
JMenu swcTypeMenu
```
table
```
SNTTable table
```
tagsMenu
```
JMenu tagsMenu
```

tree

sc.fiji.snt.PathManagerUI.HelpfulJTree tree

Class sc.fiji.snt.SeedManager

class SeedManager extends JPanel implements Serializable

serialVersionUID:

1L
- Serialized Fields
  - colorModeCombo
    
    JComboBox<SeedOverlay.ColorMode> colorModeCombo
  - countLabel
    
    JLabel countLabel
  - lowerSlider
    
    JSlider lowerSlider
  - lowerSpinner
    
    JSpinner lowerSpinner
  - lutRamp
    
    sc.fiji.snt.SeedManager.LutRamp lutRamp
  - overlay
    
    SeedOverlay overlay
  - overlayListener
    
    SeedOverlay.SeedOverlayListener overlayListener
  - seedTable
    
    JTable seedTable
  - snt
    
    SNT snt
  - sntui
    
    SNTUI sntui
  - swatchCacheBuilt
    
    int swatchCacheBuilt
    
    Generation observed at last cache rebuild; rebuild when generations diverge.
  - swatchCacheGeneration
    
    int swatchCacheGeneration
    
    Monotonic counter bumped whenever the swatch caches need rebuilding.
  - swatchCacheMode
    
    SeedOverlay.ColorMode swatchCacheMode
    
    Color mode observed at last cache rebuild; rebuild on mode change.
  - swatchCategoryOrdinals
    
    Map<String,Integer> swatchCategoryOrdinals
    
    Companion to SeedManager.swatchIndexMap for TYPE / SOURCE color modes.
  - swatchHostModelIndex
    
    int swatchHostModelIndex
    
    Model index of the column currently hosting SeedManager.swatchRenderer, or -1 if the renderer hasn't been installed yet. Tracked so that SeedManager.installSwatchOnEncodingColumn() can detach the renderer from the previous host before re-installing on the new one (without this, switching color modes would leave a stale chip column alongside the new one).
  - swatchIndexMap
    
    Map<SeedPoint,Integer> swatchIndexMap
    
    Cached per-render-pass color-map state, owned by the SeedManager.SwatchCellRenderer. Built lazily on the first cell paint after an overlay change (which bumps SeedManager.swatchCacheGeneration) and reused for the rest of the pass.
  - swatchRenderer
    
    sc.fiji.snt.SeedManager.SwatchCellRenderer swatchRenderer
    
    Cached singleton renderer reused as the chip is moved between columns.
  - tableDetacher
    
    GuiUtils.JTables.DetachableTable tableDetacher
  - tableModel
    
    SeedTableModel tableModel
  - tableScroll
    
    JScrollPane tableScroll
  - tableScrollGbc
    
    GridBagConstraints tableScrollGbc
  - tableSorter
    
    TableRowSorter<SeedTableModel> tableSorter
  - toggleVisibilityAction
    
    Action toggleVisibilityAction
  - updatingFromOverlay
    
    boolean updatingFromOverlay
    
    Guards against feedback loops between widget listeners and overlay fires.
  - upperSlider
    
    JSlider upperSlider
  - upperSpinner
    
    JSpinner upperSpinner
  - visitingZoom
    
    GuiUtils.JTables.VisitingZoom visitingZoom
    
    Zoom level applied when navigating to a seed by double-clicking a table row. Initialised to roughly two zoom steps above the current canvas magnification (see GuiUtils.JTables.VisitingZoom.resetFor(ij.ImagePlus)).

Class sc.fiji.snt.SNTUI

class SNTUI extends JDialog implements Serializable

Serialized Fields

activeWorker

sc.fiji.snt.SNTUI.ActiveWorker activeWorker

askUserConfirmation
```
boolean askUserConfirmation
```
assignDiameterSpinner
```
JSpinner assignDiameterSpinner
```
aStarCheckBox
```
JCheckBox aStarCheckBox
```
aStarPanel
```
JPanel aStarPanel
```
autoRbmi
```
JRadioButtonMenuItem autoRbmi
```
bookmarkManager
```
BookmarkManager bookmarkManager
```
bvvSNT
```
Bvv bvvSNT
```
commandFinder
```
SNTCommandFinder commandFinder
```
completePath
```
JButton completePath
```
confirmTemporarySegments
```
boolean confirmTemporarySegments
```

confirmTemporarySegmentsCheckbox

JCheckBox confirmTemporarySegmentsCheckbox

curationManager
```
CurationManager curationManager
```
currentState
```
int currentState
```
debugCheckBox
```
JCheckBox debugCheckBox
```
delineationsManager
```
DelineationsManager delineationsManager
```
diametersCheckBox
```
JCheckBox diametersCheckBox
```
discardOnDoubleCancellation
```
boolean discardOnDoubleCancellation
```
finishOnDoubleConfimation
```
boolean finishOnDoubleConfimation
```
fmUI
```
FillManagerUI fmUI
```
guiUtils
```
GuiUtils guiUtils
```
junkSegment
```
JButton junkSegment
```
keepSegment
```
JButton keepSegment
```
listener
```
sc.fiji.snt.SNTUI.GuiListener listener
```
notesui
```
NotesUI notesui
```
onlyActiveCTposition
```
JCheckBox onlyActiveCTposition
```
ontologyBrowserDialog
```
JDialog ontologyBrowserDialog
```
openRecViewer
```
JButton openRecViewer
```
openSciView
```
JButton openSciView
```
partsNearbyCSpinner
```
CheckboxSpinner partsNearbyCSpinner
```
pathAndFillManager
```
PathAndFillManager pathAndFillManager
```
plausibilityMonitor
```
PlausibilityMonitor plausibilityMonitor
```
plugin
```
SNT plugin
```
pmUI
```
PathManagerUI pmUI
```
quitMenuItem
```
JMenuItem quitMenuItem
```
rebuildCanvasButton
```
JButton rebuildCanvasButton
```
recorder
```
ScriptRecorder recorder
```
recViewer
```
Viewer3D recViewer
```
recViewerFrame
```
Frame recViewerFrame
```
sciViewSNT
```
SciViewSNT sciViewSNT
```
searchAlgoChoice
```
JComboBox<String> searchAlgoChoice
```
secLayerActivateCheckbox
```
JCheckBox secLayerActivateCheckbox
```

secLayerImgOverlayCSpinner

CheckboxSpinner secLayerImgOverlayCSpinner

seedManager
```
SeedManager seedManager
```
settingsArea
```
JTextArea settingsArea
```
showOrHideFillList
```
JButton showOrHideFillList
```
showOrHidePathList
```
JButton showOrHidePathList
```
showPathsSelected
```
JCheckBox showPathsSelected
```
sigmaPalette
```
SigmaPalette sigmaPalette
```

sigmaPaletteListener

SigmaPaletteListener sigmaPaletteListener

snapWindowXYsizeSpinner
```
JSpinner snapWindowXYsizeSpinner
```
snapWindowZsizeSpinner
```
JSpinner snapWindowZsizeSpinner
```
sourcePanel
```
JPanel sourcePanel
```

standardTracingRbmi

JRadioButtonMenuItem standardTracingRbmi

states

Map<Integer,sc.fiji.snt.SNTUI.UIState> states

statusBarText
```
JLabel statusBarText
```
statusText
```
JLabel statusText
```
svSyncPathManager
```
JButton svSyncPathManager
```
useSnapWindow
```
JCheckBox useSnapWindow
```
workspaceIndicator
```
JButton workspaceIndicator
```

Class sc.fiji.snt.TracerCanvas

class TracerCanvas extends MultiDThreePanesCanvas implements Serializable

serialVersionUID:

3620108290844138287L
- Serialized Fields
  - backBufferGraphics
    
    Graphics2D backBufferGraphics
  - backBufferHeight
    
    int backBufferHeight
  - backBufferImage
    
    Image backBufferImage
  - backBufferWidth
    
    int backBufferWidth
  - eitherSide
    
    int eitherSide
  - just_near_slices
    
    boolean just_near_slices
  - nodeSize
    
    double nodeSize
  - pathAndFillManager
    
    PathAndFillManager pathAndFillManager
  - searchArtists
    
    Set<SearchArtist> searchArtists
  - transparencies
    
    int[] transparencies

Package sc.fiji.snt.analysis
- Class sc.fiji.snt.analysis.SNTChart
  
  class SNTChart extends org.jfree.chart.ChartPanel implements Serializable
  
  serialVersionUID:
  
  5245298401153759551L
  - Serialized Fields
    
    equalizedXY
    
    boolean equalizedXY
    
    frame
    
    JFrame frame
    
    otherCombinedCharts
    
    List<SNTChart> otherCombinedCharts
    
    title
    
    String title
- Class sc.fiji.snt.analysis.SNTTable
  
  class SNTTable extends org.scijava.table.DefaultGenericTable implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    displayService
    
    org.scijava.display.DisplayService displayService
    
    hasUnsavedData
    
    boolean hasUnsavedData
    
    tableIO
    
    org.scijava.table.io.DefaultTableIOPlugin tableIO
    
    title
    
    String title
- Exception Class sc.fiji.snt.analysis.UnknownMetricException
  
  class UnknownMetricException extends IllegalArgumentException implements Serializable
  
  serialVersionUID:
  
  1L
Package sc.fiji.snt.analysis.graph
- Class sc.fiji.snt.analysis.graph.AnnotationGraph
  
  class AnnotationGraph extends SNTGraph<BrainAnnotation,AnnotationWeightedEdge> implements Serializable
  
  serialVersionUID:
  
  6826816297520498404L
  - Serialized Fields
    
    maxOntologyDepth
    
    int maxOntologyDepth
    
    metric
    
    String metric
    
    threshold
    
    double threshold
    
    treeCollection
    
    Collection<Tree> treeCollection
- Class sc.fiji.snt.analysis.graph.AnnotationWeightedEdge
  
  class AnnotationWeightedEdge extends org.jgrapht.graph.DefaultWeightedEdge implements Serializable
  
  serialVersionUID:
  
  1L
- Class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
  
  class DirectedWeightedGraph extends SNTGraph<SWCPoint,SWCWeightedEdge> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    tree
    
    Tree tree
- Class sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph
  
  class DirectedWeightedSubgraph extends org.jgrapht.graph.AsSubgraph<SWCPoint,SWCWeightedEdge> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    graph
    
    DirectedWeightedGraph graph
    
    label
    
    String label
- Class sc.fiji.snt.analysis.graph.SNTGraph
  
  class SNTGraph extends org.jgrapht.graph.AbstractBaseGraph<V,E extends org.jgrapht.graph.DefaultWeightedEdge> implements Serializable
  
  serialVersionUID:
  
  8458292348918037500L
  - Serialized Fields
    
    edgeColorRGBMap
    
    Map<E extends org.jgrapht.graph.DefaultWeightedEdge,org.scijava.util.ColorRGB> edgeColorRGBMap
    
    vertexColorRGBMap
    
    Map<V,org.scijava.util.ColorRGB> vertexColorRGBMap
    
    vertexValueMap
    
    Map<V,Double> vertexValueMap
- Class sc.fiji.snt.analysis.graph.SNTPseudograph
  
  class SNTPseudograph extends SNTGraph<V,E extends org.jgrapht.graph.DefaultWeightedEdge> implements Serializable
  
  serialVersionUID:
  
  4375953050236896508L
- Class sc.fiji.snt.analysis.graph.SparseDirectedWeightedGraph
  
  class SparseDirectedWeightedGraph extends DirectedWeightedGraph implements Serializable
  
  serialVersionUID:
  
  1L
- Class sc.fiji.snt.analysis.graph.SWCWeightedEdge
  
  class SWCWeightedEdge extends org.jgrapht.graph.DefaultWeightedEdge implements Serializable
  
  serialVersionUID:
  
  1L
Package sc.fiji.snt.analysis.sholl.gui
- Class sc.fiji.snt.analysis.sholl.gui.ShollTable
  
  class ShollTable extends SNTTable implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    detailedSummary
    
    boolean detailedSummary
    
    prefService
    
    org.scijava.prefs.PrefService prefService
    
    profile
    
    Profile profile
    
    stats
    
    ShollStats[] stats
    
    title
    
    String title
Package sc.fiji.snt.gui
- Class sc.fiji.snt.gui.CheckboxSpinner
  
  class CheckboxSpinner extends JPanel implements Serializable
  
  serialVersionUID:
  
  937359242995500492L
  - Serialized Fields
    
    checkbox
    
    JCheckBox checkbox
    
    label
    
    JLabel label
    
    spinner
    
    JSpinner spinner
- Class sc.fiji.snt.gui.CollapsiblePanel
  
  class CollapsiblePanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    checkbox
    
    JCheckBox checkbox
    
    contents
    
    Component contents
- Class sc.fiji.snt.gui.ColorChooserButton
  
  class ColorChooserButton extends JButton implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    current
    
    Color current
    
    listener
    
    ColorChangedListener listener
- Class sc.fiji.snt.gui.ColorMenu
  
  class ColorMenu extends JMenu implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    _activeBorder
    
    Border _activeBorder
    
    _colorPanes
    
    Map<SNTColor,sc.fiji.snt.gui.ColorMenu.ColorPane> _colorPanes
    
    _selectedBorder
    
    Border _selectedBorder
    
    _selectedColorPane
    
    sc.fiji.snt.gui.ColorMenu.ColorPane _selectedColorPane
    
    _unselectedBorder
    
    Border _unselectedBorder
- Class sc.fiji.snt.gui.EnhancedGenericDialog
  
  class EnhancedGenericDialog extends fiji.util.gui.GenericDialogPlus implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    helpActionButtonListener
    
    ActionListener helpActionButtonListener
    
    Deprecated.
    
    helpActionMouseListener
    
    MouseAdapter helpActionMouseListener
    
    Deprecated.
    
    labelOfHelpActionButton
    
    String labelOfHelpActionButton
    
    Deprecated.
- Class sc.fiji.snt.gui.FileChooser
  
  class FileChooser extends JFileChooser implements Serializable
  
  serialVersionUID:
  
  9398079702362074L
  - Serialized Fields
    
    detailsTable
    
    JTable detailsTable
    
    toggleFilterPatternButton
    
    JToggleButton toggleFilterPatternButton
    
    toggleHiddenFilesButton
    
    JToggleButton toggleHiddenFilesButton
- Class sc.fiji.snt.gui.FilePicker
  
  class FilePicker extends JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    fallbackFile
    
    File fallbackFile
    
    fileChooser
    
    FileChooser fileChooser
    
    fileChooserType
    
    int fileChooserType
    
    label
    
    String label
    
    textField
    
    JTextField textField
    
    title
    
    String title
- Class sc.fiji.snt.gui.GuiUtils.Buttons.OptionsButton
  
  class OptionsButton extends JButton implements Serializable
  - Serialized Fields
    
    popupMenu
    
    JPopupMenu popupMenu
- Class sc.fiji.snt.gui.MeasureUI
  
  class MeasureUI extends JFrame implements Serializable
  
  serialVersionUID:
  
  6565638887510865592L
  - Serialized Fields
    
    backgroundTask
    
    sc.fiji.snt.gui.MeasureUI.GenerateTableAction.BackgroundTask backgroundTask
    
    bar
    
    JProgressBar bar
    
    distinguishCompartments
    
    boolean distinguishCompartments
    
    guiUtils
    
    GuiUtils guiUtils
    
    lastDirPath
    
    String lastDirPath
    
    panel
    
    sc.fiji.snt.gui.MeasureUI.MeasurePanel panel
    
    plugin
    
    SNT plugin
    
    prefService
    
    org.scijava.prefs.PrefService prefService
    
    table
    
    SNTTable table
- Class sc.fiji.snt.gui.OntologyBrowser
  
  class OntologyBrowser extends JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    pathFormatter
    
    Function<TreePath,String> pathFormatter
    
    selectionListeners
    
    List<Consumer<List<String>>> selectionListeners
    
    singleSelection
    
    boolean singleSelection
    
    tabbedPane
    
    JTabbedPane tabbedPane
    
    tabs
    
    List<OntologyBrowser.OntologyTab> tabs
- Class sc.fiji.snt.gui.OntologyBrowser.AllenCCFRenderer
  
  class AllenCCFRenderer extends DefaultTreeCellRenderer implements Serializable
  
  serialVersionUID:
  
  1L
- Class sc.fiji.snt.gui.OntologyBrowser.OntologyTab
  
  class OntologyTab extends JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    searchableBar
    
    SNTSearchableBar searchableBar
    
    tree
    
    sc.fiji.snt.gui.OntologyBrowser.BrowserTree tree
- Class sc.fiji.snt.gui.PathManagerUISearchableBar
  
  class PathManagerUISearchableBar extends SNTSearchableBar implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    guiUtils
    
    GuiUtils guiUtils
    
    pmui
    
    PathManagerUI pmui
- Class sc.fiji.snt.gui.ScriptRecorder
  
  class ScriptRecorder extends JDialog implements Serializable
  
  serialVersionUID:
  
  -5275540638446494067L
  - Serialized Fields
    
    combo
    
    JComboBox<sc.fiji.snt.gui.ScriptRecorder.LANG> combo
    
    currentLang
    
    sc.fiji.snt.gui.ScriptRecorder.LANG currentLang
    
    editor
    
    SNTEditorPane editor
    
    pauseButton
    
    JToggleButton pauseButton
    
    paused
    
    boolean paused
- Class sc.fiji.snt.gui.SearchField
  
  class SearchField extends com.formdev.flatlaf.extras.components.FlatTextField implements Serializable
  - Serialized Fields
    
    caseButton
    
    JToggleButton caseButton
    
    optionsButton
    
    JButton optionsButton
    
    regexButton
    
    JToggleButton regexButton
    
    wordButton
    
    JToggleButton wordButton
- Class sc.fiji.snt.gui.SNTEditorPane
  
  class SNTEditorPane extends org.scijava.ui.swing.script.EditorPane implements Serializable
  - Serialized Fields
    
    scrollPane
    
    org.fife.ui.rtextarea.RTextScrollPane scrollPane
- Class sc.fiji.snt.gui.SNTInterpreterWindow
  
  class SNTInterpreterWindow extends JFrame implements Serializable
  - Serialized Fields
    
    pane
    
    SNTInterpreterPane pane
- Class sc.fiji.snt.gui.SNTREPL
  
  class SNTREPL extends SNTInterpreterWindow implements Serializable
- Class sc.fiji.snt.gui.SNTSearchableBar
  
  class SNTSearchableBar extends com.jidesoft.swing.SearchableBar implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    _extraButtons
    
    List<AbstractButton> _extraButtons
    
    builtinSearchHistory
    
    List<String> builtinSearchHistory
    
    guiUtils
    
    GuiUtils guiUtils
    
    historyMenu
    
    JMenu historyMenu
    
    objectDescription
    
    String objectDescription
    
    optionsMenu
    
    JPopupMenu optionsMenu
    
    statusLabelPlaceholder
    
    String statusLabelPlaceholder
    
    subFilteringEnabled
    
    boolean subFilteringEnabled
    
    subFilteringStatusIcon
    
    Icon subFilteringStatusIcon
- Class sc.fiji.snt.gui.SWCExportDialog
  
  class SWCExportDialog extends JDialog implements Serializable
  - Serialized Fields
    
    collapseFileHeader
    
    boolean collapseFileHeader
    
    collapseWarning
    
    boolean collapseWarning
    
    filePicker
    
    FilePicker filePicker
    
    imp
    
    ij.ImagePlus imp
    
    metadataTable
    
    JTable metadataTable
    
    succeeded
    
    boolean succeeded
- Class sc.fiji.snt.gui.SWCImportDialog
  
  class SWCImportDialog extends JDialog implements Serializable
  - Serialized Fields
    
    assumePixelCoordinates
    
    boolean assumePixelCoordinates
    
    cancelButton
    
    JButton cancelButton
    
    filePicker
    
    FilePicker filePicker
    
    lastPreviewedFile
    
    File lastPreviewedFile
    
    offsetPanel
    
    sc.fiji.snt.gui.SWCImportDialog.BoxPanel offsetPanel
    
    okButton
    
    JButton okButton
    
    previewArea
    
    sc.fiji.snt.gui.SWCImportDialog.PreviewArea previewArea
    
    replaceExistingPaths
    
    boolean replaceExistingPaths
    
    replaceExistingPathsCheckbox
    
    JCheckBox replaceExistingPathsCheckbox
    
    scalingPanel
    
    sc.fiji.snt.gui.SWCImportDialog.BoxPanel scalingPanel
    
    succeeded
    
    boolean succeeded
Package sc.fiji.snt.gui.cmds
- Class sc.fiji.snt.gui.cmds.AutoTraceConfigDialog
  
  class AutoTraceConfigDialog extends JDialog implements Serializable
  - Serialized Fields
    
    applyCallback
    
    Consumer<AutoTraceConfig> applyCallback
    
    config
    
    AutoTraceConfig config
    
    tableModel
    
    sc.fiji.snt.gui.cmds.AutoTraceConfigDialog.ParamTableModel tableModel
Package sc.fiji.snt.hyperpanes
- Class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas
  
  class MultiDThreePanesCanvas extends ij.gui.ImageCanvas implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    annotationsColor
    
    Color annotationsColor
    
    canvasText
    
    String canvasText
    
    canvasTextBackground
    
    Color canvasTextBackground
    
    current_x
    
    double current_x
    
    current_y
    
    double current_y
    
    current_z
    
    double current_z
    
    cursorLocked
    
    boolean cursorLocked
    
    cursorText
    
    String cursorText
    
    draw_crosshairs
    
    boolean draw_crosshairs
    
    owner
    
    PaneOwner owner
    
    plane
    
    int plane
    
    waitingForRoiDrawing
    
    boolean waitingForRoiDrawing
    
    waveInteractionsToIJ
    
    boolean waveInteractionsToIJ
Package sc.fiji.snt.io
- Exception Class sc.fiji.snt.io.SWCExportException
  
  class SWCExportException extends IOException implements Serializable
- Exception Class sc.fiji.snt.io.TracesFileFormatException
  
  class TracesFileFormatException extends SAXException implements Serializable
Package sc.fiji.snt.seed
- Class sc.fiji.snt.seed.SeedTableModel
  
  class SeedTableModel extends AbstractTableModel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    cachedStatuses
    
    String[] cachedStatuses
    
    Cached coverage state, parallel to SeedOverlay.list(). Built lazily; invalidated whenever the overlay fires (any add/remove/clear/ threshold change). Path-only changes don't trigger invalidation: user actions on the seed table will see a slightly stale Status until the overlay listener fires again.
    
    includeStatus
    
    boolean includeStatus
    
    lastKnownRowCount
    
    int lastKnownRowCount
    
    Row count observed at the previous listener fire. Used to decide whether to emit a AbstractTableModel.fireTableDataChanged() or a AbstractTableModel.fireTableRowsUpdated(int, int) (values may have changed but row identities are stable).
    
    listener
    
    SeedOverlay.SeedOverlayListener listener
    
    overlay
    
    SeedOverlay overlay
    
    snt
    
    SNT snt
    
    Optional, for Status compute. null → no Status column.
Package sc.fiji.snt.viewer
- Class sc.fiji.snt.viewer.Viewer3D.ManagerPanel
  
  class ManagerPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    debugCheckBox
    
    JCheckBoxMenuItem debugCheckBox
    
    debugger
    
    sc.fiji.snt.viewer.Viewer3D.Debugger debugger
    
    disableActions
    
    boolean disableActions
    
    mgrGuiUtils
    
    GuiUtils mgrGuiUtils
    
    progressBar
    
    sc.fiji.snt.viewer.Viewer3D.ManagerPanel.ProgressBar progressBar
    
    searchableBar
    
    SNTSearchableBar searchableBar
    
    table
    
    SNTTable table
Package sc.fiji.snt.viewer.geditor
- Class sc.fiji.snt.viewer.geditor.AnnotationGraphComponent
  
  class AnnotationGraphComponent extends SNTGraphComponent implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    forceConstant
    
    double forceConstant
    
    initialTemp
    
    double initialTemp
    
    maxDistance
    
    double maxDistance
    
    maxIterations
    
    double maxIterations
    
    minDistance
    
    double minDistance
    
    radius
    
    double radius
- Class sc.fiji.snt.viewer.geditor.GraphEditor
  
  class GraphEditor extends JPanel implements Serializable
  
  serialVersionUID:
  
  -6561623072112577140L
  - Serialized Fields
    
    animateLayoutChange
    
    boolean animateLayoutChange
    
    annotationDepthField
    
    JFormattedTextField annotationDepthField
    
    annotationMetricJCombo
    
    JComboBox<String> annotationMetricJCombo
    
    annotationThresholdField
    
    JFormattedTextField annotationThresholdField
    
    appTitle
    
    String appTitle
    
    bottomPanel
    
    JSplitPane bottomPanel
    
    changeTracker
    
    com.mxgraph.util.mxEventSource.mxIEventListener changeTracker
    
    context
    
    org.scijava.Context context
    
    currentFile
    
    File currentFile
    
    editorConsole
    
    sc.fiji.snt.viewer.geditor.EditorConsole editorConsole
    
    graphComponent
    
    com.mxgraph.swing.mxGraphComponent graphComponent
    
    graphOutline
    
    com.mxgraph.swing.mxGraphOutline graphOutline
    
    keyboardHandler
    
    com.mxgraph.swing.handler.mxKeyboardHandler keyboardHandler
    
    legendPanel
    
    JPanel legendPanel
    
    libraryPane
    
    JTabbedPane libraryPane
    
    mainPanel
    
    JSplitPane mainPanel
    
    modified
    
    boolean modified
    
    Flag indicating whether the current graph has been modified
    
    popupMenu
    
    sc.fiji.snt.viewer.geditor.EditorPopupMenu popupMenu
    
    prefService
    
    org.scijava.prefs.PrefService prefService
    
    rubberband
    
    com.mxgraph.swing.handler.mxRubberband rubberband
    
    statusBar
    
    JLabel statusBar
    
    toolbar
    
    sc.fiji.snt.viewer.geditor.EditorToolBar toolbar
    
    undoHandler
    
    com.mxgraph.util.mxEventSource.mxIEventListener undoHandler
    
    undoManager
    
    com.mxgraph.util.mxUndoManager undoManager
- Class sc.fiji.snt.viewer.geditor.SNTGraphComponent
  
  class SNTGraphComponent extends com.mxgraph.swing.mxGraphComponent implements Serializable
  
  serialVersionUID:
  
  -341155071963647372L
  - Serialized Fields
    
    adapter
    
    SNTGraphAdapter<?,? extends org.jgrapht.graph.DefaultWeightedEdge> adapter
    
    cmdService
    
    org.scijava.command.CommandService cmdService
    
    editor
    
    GraphEditor editor
    
    saveDir
    
    File saveDir
    
    spaceDown
    
    boolean spaceDown
- Class sc.fiji.snt.viewer.geditor.SNTPseudographComponent
  
  class SNTPseudographComponent extends SNTGraphComponent implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    layout
    
    com.mxgraph.layout.mxGraphLayout layout
- Class sc.fiji.snt.viewer.geditor.TreeGraphComponent
  
  class TreeGraphComponent extends SNTGraphComponent implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    layout
    
    com.mxgraph.layout.mxCompactTreeLayout layout

Serialized Form

Package sc.fiji.snt

Class sc.fiji.snt.FillManagerUI

Serialized Fields

actions

currentState

currentThresholdLabel

cursorPositionLabel

cursorThresholdChoice

exploredThresholdApplyButton

exploredThresholdChoice

exportFillsMenu

fillList

fillTypeLabel

gUtils

listModel

manualThresholdApplyButton

manualThresholdChoice

manualThresholdInputField

maxThresholdLabel

maxThresholdValue

pathAndFillManager

plugin

reloadFill

saveFill

splitFillsCheckbox

startFill

statusText

stopFill

storeExtraNodesCheckbox

transparentCheckbox

Class sc.fiji.snt.MultiPathTracerCanvas

Serialized Fields

dimmedAlpha

dimmedOOBAlpha

entries

highlightedAlpha

highlightedOOBAlpha

Class sc.fiji.snt.PathManagerUI

Serialized Fields

colorMenu

fittingHelper

fitVolumeMenuItem

fullTreeModel

guiUtils

measureUI

menuBar

multiSpectralRefineHelper

navToolbar

pathAndFillManager

plugin

proofReadingToolBar

searchableBar

swcTypeButtonGroup

swcTypeMenu

table

tagsMenu

tree

Class sc.fiji.snt.SeedManager

Serialized Fields

colorModeCombo

countLabel

lowerSlider

lowerSpinner

lutRamp

overlay

overlayListener

seedTable

snt

sntui

swatchCacheBuilt

swatchCacheGeneration

swatchCacheMode

swatchCategoryOrdinals

swatchHostModelIndex

swatchIndexMap

swatchRenderer

tableDetacher

tableModel

tableScroll