Package sc.fiji.snt.analysis

Class PCAnalyzer.PrincipalAxis

java.lang.Object
sc.fiji.snt.analysis.PCAnalyzer.PrincipalAxis
Enclosing class:
PCAnalyzer
public static class PCAnalyzer.PrincipalAxis extends Object
Represents a principal axis containing the direction vector and associated variance (eigenvalue) from Principal Component Analysis.

Each principal axis represents a direction of variance in the analyzed data, with the primary axis having the highest variance, secondary axis the second highest, and tertiary axis the lowest.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    final double
    eigenvalue
    The eigenvalue associated with this axis
    final double
    x
    The X component of the axis direction
    final double
    y
    The Y component of the axis direction
    final double
    z
    The Z component of the axis direction

  • Method Summary

    Modifier and Type
    Method
    Description
    double
    getAngleWith(double[] directionComponents)
    Computes the acute angle between this principal axis and a direction vector.
    double
    getAngleWith(double dirX, double dirY, double dirZ)
    Computes the acute angle between this principal axis and a direction vector.
    double
    getEigenvalue()
     
    double
    getVariance()
     
    double
    getVariancePercentage(double totalVariance)
    Computes the percentage of total variance explained by this principal axis.
    static double[]
    getVariancePercentages(PCAnalyzer.PrincipalAxis[] axes)
    Computes the variance percentages for an array of principal axes.
    double
    getX()
     
    double
    getY()
     
    double
    getZ()
     
    String
    toString()
     

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

  • Field Details

    • x

      public final double x
      The X component of the axis direction

    • y

      public final double y
      The Y component of the axis direction

    • z

      public final double z
      The Z component of the axis direction

    • eigenvalue

      public final double eigenvalue
      The eigenvalue associated with this axis

  • Method Details

    • 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, which is useful for understanding the overall shape variation along each 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

    • getX

      public double getX()
      Returns:
      the X component of the axis direction

    • getY

      public double getY()
      Returns:
      the Y component of the axis direction

    • getZ

      public double getZ()
      Returns:
      the Z component of the axis direction

    • getEigenvalue

      public double getEigenvalue()
      Returns:
      the eigenvalue (variance) associated with this axis

    • getVariance

      public double getVariance()
      Returns:
      the absolute variance along this axis

    • getVariancePercentage

      public double getVariancePercentage(double totalVariance)
      Computes the percentage of total variance explained by this principal axis.
      Parameters:
      totalVariance - the sum of all eigenvalues (total variance)
      Returns:
      the percentage of total variance explained by this axis (0-100%)

    • getAngleWith

      public double getAngleWith(double[] directionComponents)
      Computes the acute angle between this principal axis and a direction vector.
      Parameters:
      directionComponents - the 3-element array of the (X,Y,Z) components of the direction vector
      Returns:
      the acute angle in degrees (0-90°), or NaN if the direction vector has zero magnitude

    • getAngleWith

      public double getAngleWith(double dirX, double dirY, double dirZ)
      Computes the acute angle between this principal axis and a direction vector.
      Parameters:
      dirX - the X component of the direction vector
      dirY - the Y component of the direction vector
      dirZ - the Z component of the direction vector
      Returns:
      the acute angle in degrees (0-90°), or NaN if the direction vector has zero magnitude

    • toString

      public String toString()
      Overrides:
      toString in class Object