Package sc.fiji.snt.analysis

Class PCAnalyzer

java.lang.Object
sc.fiji.snt.analysis.PCAnalyzer
public class PCAnalyzer extends Object
Utility class for performing Principal Component Analysis (PCA) on various SNT data structures including Trees, Paths, and collections of SNTPoints.

This class provides methods to compute the principal axes of 3D point data, which represent the directions of maximum variance in the data. This is useful for analyzing the overall orientation and shape characteristics of neuronal structures, meshes, and other 3D geometries.

  • Constructor Details

    • PCAnalyzer

      public PCAnalyzer()

  • Method Details

    • getPrincipalAxes

      public static PCAnalyzer.PrincipalAxis[] getPrincipalAxes(Tree tree)
      Computes the principal axes for a Tree structure.
      Parameters:
      tree - the Tree to analyze
      Returns:
      array of three PrincipalAxis objects ordered by decreasing variance (primary, secondary, tertiary), or null if computation fails

    • getPrincipalAxes

      public static PCAnalyzer.PrincipalAxis[] getPrincipalAxes(Tree tree, boolean excludeRoot)
      Computes the principal axes for a Tree structure with option to exclude root.
      Parameters:
      tree - the Tree to analyze
      excludeRoot - if true, excludes the root node from the analysis
      Returns:
      array of three PrincipalAxis objects ordered by decreasing variance (primary, secondary, tertiary), or null if computation fails

    • getPrincipalAxes

      public static PCAnalyzer.PrincipalAxis[] getPrincipalAxes(Path path)
      Computes the principal axes for a Path structure.
      Parameters:
      path - the Path to analyze
      Returns:
      array of three PrincipalAxis objects ordered by decreasing variance (primary, secondary, tertiary), or null if computation fails

    • getPrincipalAxes

      public static PCAnalyzer.PrincipalAxis[] getPrincipalAxes(net.imagej.mesh.Vertices vertices)
      Computes the principal axes from the vertices of a mesh
      Parameters:
      vertices - the collection of vertices to analyze
      Returns:
      array of three PrincipalAxis objects ordered by decreasing variance (primary, secondary, tertiary), or null if computation fails

    • getPrincipalAxes

      public static PCAnalyzer.PrincipalAxis[] getPrincipalAxes(Collection<? extends SNTPoint> points)
      Computes the principal axes for a collection of SNTPoints.
      Parameters:
      points - the collection of points to analyze
      Returns:
      array of three PrincipalAxis objects ordered by decreasing variance (primary, secondary, tertiary), or null if computation fails

    • getVariancePercentages

      public static double[] getVariancePercentages(PCAnalyzer.PrincipalAxis[] axes)
      Computes the variance percentages for an array of principal axes. This is a convenience method that returns the percentage of total variance explained by each principal axis.
      Parameters:
      axes - the array of three PrincipalAxis objects (primary, secondary, tertiary)
      Returns:
      array of three percentages (primary, secondary, tertiary) that sum to 100%, or null if axes is null

    • orientTowardTips

      public static PCAnalyzer.PrincipalAxis[] orientTowardTips(PCAnalyzer.PrincipalAxis[] axes, Tree tree)
      Convenience method to orient existing principal axes toward a tree's tips centroid. For several topologies, this orients the primary axis is so it aligns with the general growth direction of the arbor.
      Parameters:
      axes - the principal axes to orient
      tree - the tree to get tips centroid from (orientation reference)
      Returns:
      oriented principal axes

    • orientTowardDirection

      public static PCAnalyzer.PrincipalAxis[] orientTowardDirection(PCAnalyzer.PrincipalAxis[] axes, double[] referenceDirection)
      Orients principal axes so the primary axis points toward a reference direction, i.e., the primary axis is oriented to minimize the angle with the reference direction. If the primary axis points away from the reference (dot product < 0), it's flipped.\
      Parameters:
      axes - the principal axes to orient
      referenceDirection - the reference direction vector [x, y, z]
      Returns:
      oriented principal axes