Package sc.fiji.snt.plugin

Class StrahlerCmd

java.lang.Object
org.scijava.AbstractContextual
org.scijava.command.ContextCommand
sc.fiji.snt.plugin.StrahlerCmd
All Implemented Interfaces:
Runnable, org.scijava.Cancelable, org.scijava.command.Command, org.scijava.Contextual, org.scijava.plugin.SciJavaPlugin
public class StrahlerCmd extends org.scijava.command.ContextCommand
Command to perform Horton-Strahler analysis on a collection of Trees
Author:
Tiago Ferreira

  • Constructor Details

    • StrahlerCmd

      public StrahlerCmd()
      Instantiates a new StrahlerCmd. Trees to be analyzed expected as input @parameter

    • StrahlerCmd

      public StrahlerCmd(Collection<Tree> trees)
      Instantiates a new StrahlerCmd.
      Parameters:
      trees - the collection of Trees to be analyzed

    • StrahlerCmd

      public StrahlerCmd(Tree tree)
      Instantiates a new StrahlerCmd for a single Tree
      Parameters:
      tree - the single Tree to be analyzed

  • Method Details

    • run

      public void run()

    • getChart

      public SNTChart getChart()
      Returns the 'complete Strahler plot' (e.g., all metrics in a single plot). If multiple trees are being analyzed, returns a multi-panel montage, in which each panel corresponding to each individual plot.
      Returns:
      the Strahler plot

    • getChart

      public SNTChart getChart(String metric)
      Returns a 'Strahler plot' for the specified metric.
      Parameters:
      metric - either "avg contraction", "avg fragmentation", "bifurcation ratio", "branch count", "extension angle", or "length" (default)
      Returns:
      the Strahler plot

    • getHistogram

      public SNTChart getHistogram(String metric)
      Returns a histogram for the specified metric, in which data is grouped by order.
      Parameters:
      metric - either "branch contraction", "branch fragmentation", "branch relative extension angle", or "branch length" (default)
      Returns:
      the Strahler histogram if only a single Tree is being analyzed, or a montage of histograms if multiple trees are being parsed.

    • getBoxPlot

      public SNTChart getBoxPlot(String metric)
      Returns a boxplot for the specified metric, in which data is grouped by order.
      Parameters:
      metric - either "branch contraction", "branch fragmentation", "branch relative extension angle", or "branch length" (default)
      Returns:
      the Strahler boxplot if only a single Tree is being analyzed, or a montage of plots if multiple trees are being parses.

    • getDetailedTable

      public SNTTable getDetailedTable()
      Gets the detailed table listing individual branch properties aggregated by Strahler order.
      Returns:
      the detailed table

    • getSummaryTable

      public SNTTable getSummaryTable()
      Gets the summary table containing the tabular results of the analysis.
      Returns:
      the summary table

    • getTable

      @Deprecated public SNTTable getTable()
      Deprecated.
      Use getSummaryTable() instead

    • validInput

      public boolean validInput()
      Assesses if all trees being analyzed can be parsed (A tree won't be parsed, if topologically invalid, e.g., by containing a loop, or disconnected Paths).
      Returns:
      true, if successful

    • getValidTrees

      public List<Tree> getValidTrees()
      Returns the Tree(s) successfully parsed (i.e., topologically valid)
      Returns:
      the list of parsed trees

    • getInvalidTrees

      public List<Tree> getInvalidTrees()
      Returns the Tree(s) that could not be parsed (i.e., topologically invalid)
      Returns:
      the list of non-parsable trees

    • setDetailedAnalysis

      public void setDetailedAnalysis(boolean detailedAnalysis)
      Whether run calls should output detailed tables and plots
      Parameters:
      detailedAnalysis - if true, subsequent run() calls will include extra outputs

    • main

      public static void main(String[] args)