Package sc.fiji.snt.plugin

Class ShollAnalysisPrefsCmd

java.lang.Object
org.scijava.module.AbstractModule
org.scijava.module.DefaultMutableModule
org.scijava.command.DynamicCommand
org.scijava.options.OptionsPlugin
sc.fiji.snt.plugin.ShollAnalysisPrefsCmd
All Implemented Interfaces:
Runnable, org.scijava.Cancelable, org.scijava.command.Command, org.scijava.Contextual, org.scijava.module.Module, org.scijava.module.MutableModule, org.scijava.plugin.SciJavaPlugin, org.scijava.plugin.SingletonPlugin
public class ShollAnalysisPrefsCmd extends org.scijava.options.OptionsPlugin
Implements the "Sholl Options" command
Author:
Tiago Ferreira

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
    ALLOWED_MAX_DEGREE
     
    static final int
    ALLOWED_MIN_DEGREE
     
    static final int
    DEF_ANGLE_STEP_SIZE
    Default angle step size for Polar analyses
    static final boolean
    DEF_DEBUG_MODE
     
    static final boolean
    DEF_DETAILED_METRICS
     
    static final int
    DEF_ENCLOSING_RADIUS_CUTOFF
    Default cutoff value for enclosing radius
    static final boolean
    DEF_INCLUDE_ZERO_COUNTS
    Default setting for including zero counts in analysis
    static final boolean
    DEF_KS_TESTING
     
    static final int
    DEF_MAX_DEGREE
    Default maximum degree for polynomial fitting
    static final int
    DEF_MIN_DEGREE
    Default minimum degree for polynomial fitting
    static final String
    DEF_ROI_SIZE
     
    static final double
    DEF_RSQUARED
     
    static final boolean
    DEF_SKIP_SINGLE_VOXELS
    Default setting for skipping single voxel intersections
    static final boolean
    DEF_SKIP_SOMATIC_SEGMENTS
    Default setting for skipping somatic segments
    protected static final String
    DESCRIPTION_HTML
     
    protected static final String
    HEADER_HTML
     

    Fields inherited from class org.scijava.options.OptionsPlugin

    eventService

    Fields inherited from class org.scijava.command.DynamicCommand

    moduleService, pluginService

  • Constructor Summary

    Constructors
    Constructor
    Description
    ShollAnalysisPrefsCmd()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    reset()
     
    void
    run()
     

    Methods inherited from class org.scijava.options.OptionsPlugin

    cancel, load, save

    Methods inherited from class org.scijava.command.DynamicCommand

    cancel, context, getCancelReason, getContext, getInfo, getInput, getOutput, isCanceled, saveInputs, setContext, setInput, setOutput, uncancel

    Methods inherited from class org.scijava.module.AbstractModule

    getDelegateObject, getInputs, getOutputs, initialize, isInputResolved, isOutputResolved, preview, resolveInput, resolveOutput, setInputs, setOutputs, unresolveInput, unresolveOutput

    Methods inherited from class java.lang.Object

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

    Methods inherited from interface org.scijava.module.Module

    getDelegateObject, getInputs, getOutputs, initialize, isInputResolved, isOutputResolved, isResolved, preview, resolveInput, resolveOutput, setInputs, setOutputs, setResolved, unresolveInput, unresolveOutput

    Methods inherited from interface org.scijava.module.MutableModule

    addInput, addInput, addOutput, addOutput, removeInput, removeOutput

  • Field Details

    • DEF_SKIP_SINGLE_VOXELS

      public static final boolean DEF_SKIP_SINGLE_VOXELS
      Default setting for skipping single voxel intersections
      See Also:

    • DEF_INCLUDE_ZERO_COUNTS

      public static final boolean DEF_INCLUDE_ZERO_COUNTS
      Default setting for including zero counts in analysis
      See Also:

    • DEF_SKIP_SOMATIC_SEGMENTS

      public static final boolean DEF_SKIP_SOMATIC_SEGMENTS
      Default setting for skipping somatic segments
      See Also:

    • DEF_ENCLOSING_RADIUS_CUTOFF

      public static final int DEF_ENCLOSING_RADIUS_CUTOFF
      Default cutoff value for enclosing radius
      See Also:

    • DEF_MIN_DEGREE

      public static final int DEF_MIN_DEGREE
      Default minimum degree for polynomial fitting
      See Also:

    • DEF_MAX_DEGREE

      public static final int DEF_MAX_DEGREE
      Default maximum degree for polynomial fitting
      See Also:

    • DEF_ANGLE_STEP_SIZE

      public static final int DEF_ANGLE_STEP_SIZE
      Default angle step size for Polar analyses
      See Also:

    • ALLOWED_MAX_DEGREE

      public static final int ALLOWED_MAX_DEGREE
      See Also:

    • ALLOWED_MIN_DEGREE

      public static final int ALLOWED_MIN_DEGREE
      See Also:

    • DEF_RSQUARED

      public static final double DEF_RSQUARED
      See Also:

    • DEF_KS_TESTING

      public static final boolean DEF_KS_TESTING
      See Also:

    • DEF_DEBUG_MODE

      public static final boolean DEF_DEBUG_MODE
      See Also:

    • DEF_DETAILED_METRICS

      public static final boolean DEF_DETAILED_METRICS
      See Also:

    • DEF_ROI_SIZE

      public static final String DEF_ROI_SIZE
      See Also:

    • HEADER_HTML

      protected static final String HEADER_HTML
      See Also:

    • DESCRIPTION_HTML

      protected static final String DESCRIPTION_HTML
      See Also:

  • Constructor Details

    • ShollAnalysisPrefsCmd

      public ShollAnalysisPrefsCmd()

  • Method Details

    • run

      public void run()
      Specified by:
      run in interface org.scijava.module.MutableModule
      Specified by:
      run in interface Runnable
      Overrides:
      run in class org.scijava.options.OptionsPlugin

    • reset

      public void reset()
      Overrides:
      reset in class org.scijava.options.OptionsPlugin