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:

• Constant Field Values

DEF_INCLUDE_ZERO_COUNTS

public static final boolean DEF_INCLUDE_ZERO_COUNTS

Default setting for including zero counts in analysis

See Also:

• Constant Field Values

DEF_SKIP_SOMATIC_SEGMENTS

public static final boolean DEF_SKIP_SOMATIC_SEGMENTS

Default setting for skipping somatic segments

See Also:

• Constant Field Values

DEF_ENCLOSING_RADIUS_CUTOFF

public static final int DEF_ENCLOSING_RADIUS_CUTOFF

Default cutoff value for enclosing radius

See Also:

• Constant Field Values

DEF_MIN_DEGREE

public static final int DEF_MIN_DEGREE

Default minimum degree for polynomial fitting

See Also:

• Constant Field Values

DEF_MAX_DEGREE

public static final int DEF_MAX_DEGREE

Default maximum degree for polynomial fitting

See Also:

• Constant Field Values

DEF_ANGLE_STEP_SIZE

public static final int DEF_ANGLE_STEP_SIZE

Default angle step size for Polar analyses

See Also:

• Constant Field Values

ALLOWED_MAX_DEGREE

public static final int ALLOWED_MAX_DEGREE

See Also:

• Constant Field Values

ALLOWED_MIN_DEGREE

public static final int ALLOWED_MIN_DEGREE

See Also:

• Constant Field Values

DEF_RSQUARED

public static final double DEF_RSQUARED

See Also:

• Constant Field Values

DEF_KS_TESTING

public static final boolean DEF_KS_TESTING

See Also:

• Constant Field Values

DEF_DEBUG_MODE

public static final boolean DEF_DEBUG_MODE

See Also:

• Constant Field Values

DEF_DETAILED_METRICS

public static final boolean DEF_DETAILED_METRICS

See Also:

• Constant Field Values

DEF_ROI_SIZE

public static final String DEF_ROI_SIZE

See Also:

• Constant Field Values

HEADER_HTML

protected static final String HEADER_HTML

See Also:

• Constant Field Values

DESCRIPTION_HTML

protected static final String DESCRIPTION_HTML

See Also:

• Constant Field Values

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