Deprecated API

Contents

• Classes
• Fields
• Methods
• Constructors
• Enum Constants

Deprecated Classes

Class	Description
sc.fiji.snt.analysis.PeripathDetector	Use PeripathDetector instead. This class is retained for backward compatibility and delegates all calls to the new package.
sc.fiji.snt.analysis.PeripathDetector.Config	Use PeripathDetector.Config instead.
sc.fiji.snt.analysis.PeripathDetector.Detection	Use Detection instead.
sc.fiji.snt.analysis.TreeAnalyzer	Use TreeStatistics instead
sc.fiji.snt.gui.EnhancedGenericDialog
sc.fiji.snt.plugin.AnalyzerCmd	replaced by MeasureUI

Deprecated Fields

Field	Description
sc.fiji.snt.analysis.MultiTreeStatistics.MEAN_RADIUS	use #PATH_MEAN_RADIUS instead
sc.fiji.snt.analysis.TreeStatistics.AVG_SPINE_DENSITY	Use TreeStatistics.PATH_SPINE_DENSITY instead
sc.fiji.snt.analysis.TreeStatistics.CONTRACTION	Use TreeStatistics.BRANCH_CONTRACTION or TreeStatistics.PATH_CONTRACTION instead
sc.fiji.snt.analysis.TreeStatistics.FRACTAL_DIMENSION	Use TreeStatistics.BRANCH_FRACTAL_DIMENSION or TreeStatistics.PATH_FRACTAL_DIMENSION instead
sc.fiji.snt.analysis.TreeStatistics.MEAN_RADIUS	Use TreeStatistics.BRANCH_MEAN_RADIUS or TreeStatistics.PATH_MEAN_RADIUS instead
sc.fiji.snt.Path.noMoreThanOneEvery	Use Path.DEFAULT_SAMPLING_INTERVAL instead
sc.fiji.snt.Path.SWC_END_POINT
sc.fiji.snt.Path.SWC_FORK_POINT

Deprecated Methods

Method	Description
sc.fiji.snt.analysis.graph.GraphUtils.createGraph(Collection<SWCPoint>, boolean)
sc.fiji.snt.analysis.graph.GraphUtils.createGraph(Tree)
sc.fiji.snt.analysis.graph.GraphUtils.createTree(Graph<SWCPoint, ?>)
sc.fiji.snt.analysis.graph.GraphUtils.getSimplifiedGraph(DirectedWeightedGraph)
sc.fiji.snt.analysis.PeripathDetector.createTorusMask(Collection<Path>, ImagePlus, PeripathDetector.Config, double)	Use PeripathDetector.createTorusMask(java.util.Collection<sc.fiji.snt.Path>, net.imglib2.RandomAccessibleInterval<T>, sc.fiji.snt.analysis.detection.PeripathDetector.Config, double) instead.
sc.fiji.snt.analysis.PeripathDetector.createTorusMask(Collection<Path>, RandomAccessibleInterval<T>, PeripathDetector.Config, double)	Use PeripathDetector.createTorusMask(java.util.Collection<sc.fiji.snt.Path>, net.imglib2.RandomAccessibleInterval<T>, sc.fiji.snt.analysis.detection.PeripathDetector.Config, double) instead.
sc.fiji.snt.analysis.PeripathDetector.detect(Collection<Path>, RandomAccessibleInterval<? extends RealType<?>>, PeripathDetector.Config)	Use PeripathDetector.detect(java.util.Collection<sc.fiji.snt.Path>, net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>>, sc.fiji.snt.analysis.detection.PeripathDetector.Config) instead.
sc.fiji.snt.analysis.SNTChart.setVisible(boolean)
sc.fiji.snt.analysis.TreeStatistics.getMetrics()
sc.fiji.snt.gui.EnhancedGenericDialog.menuItemTriggeringResources()
sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas.setCrosshairs(double, double, double, boolean)
sc.fiji.snt.Path.addAsLinesTo3DViewer(Image3DUniverse, Color, ImagePlus)
sc.fiji.snt.Path.addAsLinesTo3DViewer(Image3DUniverse, Color3f, ImagePlus)
sc.fiji.snt.Path.addDiscsTo3DViewer(Image3DUniverse, Color, ImagePlus)
sc.fiji.snt.Path.addDiscsTo3DViewer(Image3DUniverse, Color3f, ImagePlus)
sc.fiji.snt.Path.addTo3DViewer(Image3DUniverse, Color, ImagePlus)	This method is deprecated. Use newer 3D visualization methods instead.
sc.fiji.snt.Path.addTo3DViewer(Image3DUniverse, Color3f, ImagePlus)	This method is deprecated. Use newer 3D visualization methods instead.
sc.fiji.snt.Path.createCircles()	No longer needed - radii and tangents are now stored per-node
sc.fiji.snt.Path.getJunctionNodes()	use Path.getBranchPoints() instead
sc.fiji.snt.Path.getPoint3fList()
sc.fiji.snt.Path.getStartJoins()	use Path.getParentPath() instead
sc.fiji.snt.Path.getStartJoinsPoint()	Use Path.getBranchPoint() instead. NB: Earlier versions of Simple Neurite Tracer allowed paths to connect at either the start point (getStartJoinsPoint()) or end-point (getStartJoinsPoint()). Useful for some applications but a huge headache to handle.
sc.fiji.snt.Path.interpolateMissingRadii(DoublePredicate, boolean)	Use Path.sanitizeRadii(DoublePredicate, boolean) instead
sc.fiji.snt.Path.removeFrom3DViewer(Image3DUniverse)	This method is deprecated. Use newer 3D visualization methods instead.
sc.fiji.snt.Path.setStartJoin(Path, PointInImage)	use Path.setBranchFrom(Path, PointInImage) instead
sc.fiji.snt.Path.unsetStartJoin()
sc.fiji.snt.Path.versionInUse()	Use Path.isActiveVersion() instead
sc.fiji.snt.PathAndFillManager.canvasResized()
sc.fiji.snt.PathAndFillManager.contentAdded(Content)
sc.fiji.snt.PathAndFillManager.contentChanged(Content)
sc.fiji.snt.PathAndFillManager.contentRemoved(Content)
sc.fiji.snt.PathAndFillManager.contentSelected(Content)
sc.fiji.snt.PathAndFillManager.universeClosed()
sc.fiji.snt.plugin.StrahlerCmd.getTable()	Use StrahlerCmd.getSummaryTable() instead
sc.fiji.snt.SNT.get3DUniverse()
sc.fiji.snt.SNT.getPaths3DDisplay()
sc.fiji.snt.SNT.setColorImage(ImagePlus)
sc.fiji.snt.SNT.setPaths3DDisplay(int)
sc.fiji.snt.SNT.showCorrespondencesTo(File, Color, double)
sc.fiji.snt.SNT.startHessian(String, double, double, boolean)
sc.fiji.snt.SNT.updateImageContent(int)
sc.fiji.snt.SNTPrefs.loadStartupPrefs()
sc.fiji.snt.SNTPrefs.saveStartupPrefs()
sc.fiji.snt.SNTService.demoTree()
sc.fiji.snt.SNTService.demoTreeImage()
sc.fiji.snt.SNTService.getAnalyzer(boolean)	Use SNTService.getStatistics(boolean) instead
sc.fiji.snt.SNTService.getPlugin()	use SNTService.getInstance() instead
sc.fiji.snt.SNTUtils.getPluginInstance()	use SNTUtils.getInstance() instead
sc.fiji.snt.tracing.auto.AbstractGWDTTracer.setMinSegmentLength(double)	Use AbstractGWDTTracer.setMinBranchIntensityLength(double) instead. Note: the physical-to-voxel conversion is not meaningful for this parameter since it is an intensity sum, not a distance.
sc.fiji.snt.tracing.auto.AbstractGWDTTracer.setMinSegmentLengthVoxels(double)	Use AbstractGWDTTracer.setMinBranchIntensityLength(double) instead.
sc.fiji.snt.Tree.assignUniqueColors(Collection<Tree>)	use TreeUtils.assignUniqueColors(Collection)
sc.fiji.snt.Tree.assignUniqueColors(Collection<Tree>, String)	use TreeUtils.assignUniqueColors(Collection, String)
sc.fiji.snt.Tree.downSample(double)	Use Tree.downsample(double) instead.
sc.fiji.snt.util.ImgUtils.imgPlusToCalibration(ImgPlus<?>)	Use ImgUtils.getCalibration(ImgPlus) instead
sc.fiji.snt.util.TreeToRaster.rasterizeLabels()	Use TreeToRaster.rasterizePathLabels() instead
sc.fiji.snt.viewer.MultiViewer2D.setLabel(String)
sc.fiji.snt.viewer.OBJMesh.getLabel()	use OBJMesh.label instead
sc.fiji.snt.viewer.Viewer2D.addTree(Tree)	Use Viewer2D.add(Object) instead
sc.fiji.snt.viewer.Viewer2D.addTrees(Collection<Tree>)	use Viewer2D.add(Object) instead
sc.fiji.snt.viewer.Viewer2D.showPlot()	Use Viewer2D.show() instead.
sc.fiji.snt.viewer.Viewer3D.addTrees(Collection<Tree>, boolean)	use Viewer3D.addTrees(Collection, String) instead

Deprecated Constructors

Constructor	Description
sc.fiji.snt.analysis.PathProfiler(Path, ImagePlus)	Use PathProfiler(Path, Dataset)
sc.fiji.snt.analysis.PathProfiler(Tree, ImagePlus)	Use PathProfiler(Tree, Dataset)
sc.fiji.snt.analysis.sholl.parsers.ImageParser(ImagePlus)
sc.fiji.snt.analysis.TreeAnalyzer(Tree)	Use TreeStatistics constructors instead

Deprecated Enum Constants

Enum Constant	Description
sc.fiji.snt.viewer.Viewer3D.ViewMode.SIDE	Use YZ instead
sc.fiji.snt.viewer.Viewer3D.ViewMode.TOP	Use XY instead