Package sc.fiji.snt.analysis

Class ShollAnalyzer

java.lang.Object
sc.fiji.snt.analysis.ShollAnalyzer
public class ShollAnalyzer extends Object
Class to retrieve Sholl metrics from a Tree.
Author:
Tiago Ferreira

  • Field Details

  • Constructor Details

    • ShollAnalyzer

      public ShollAnalyzer(Tree tree)
      Instantiates a new Sholl analyzer using default settings, i.e., focused on Tree's root; using sampling step size of average inter-node distance; curve fitting enabled; and all other parameters left to defaults/auto-discovery.
      Parameters:
      tree - the Tree to be analyzed

    • ShollAnalyzer

      public ShollAnalyzer(Tree tree, TreeStatistics statistics)

  • Method Details

    • setPolynomialFitRange

      public void setPolynomialFitRange(int fromDegree, int toDegree)
      Sets the polynomial fit range for linear Sholl statistics.
      Parameters:
      fromDegree - the lowest degree to be considered. Set it to -1 to skip polynomial fit
      toDegree - the highest degree to be considered. Set it to -1 to skip polynomial fit

    • setEnableCurveFitting

      public void setEnableCurveFitting(boolean enable)
      Sets whether curve fitting computations should be performed.
      Parameters:
      enable - if true polynomial and linear regression on normalized Sholl data will be performed. Enabling this option may adversely affect performance.

    • getMetrics

      public static List<String> getMetrics()

    • getSingleValueMetrics

      public Map<String,Number> getSingleValueMetrics()

    • getMaximaRadii

      public ArrayList<Double> getMaximaRadii()

    • getSecondaryMaxima

      public ArrayList<double[]> getSecondaryMaxima()

    • getLinearStats

      public LinearProfileStats getLinearStats()
      Gets the LinearProfileStats associated with this analyzer. By default, it is set to determine the polynomial of 'best-fit' (2-20 degree range.)
      Returns:
      the LinearProfileStats instance

    • getNormStats

      public NormalizedProfileStats getNormStats()
      Gets the NormalizedProfileStats associated with this analyzer. By default it is set to determine the regression method of 'best-fit' (log-log or semi-log) using shell volume as normalizer (if Tree has a depth component) or shell area if Tree is 2D.
      Returns:
      the LinearProfileStats instance

    • main

      public static void main(String[] args) throws InterruptedException
      Throws:
      InterruptedException