Package sc.fiji.snt.analysis

Class PathProfiler

java.lang.Object

org.scijava.module.AbstractModule

org.scijava.module.DefaultMutableModule

org.scijava.command.DynamicCommand

sc.fiji.snt.gui.cmds.CommonDynamicCmd

sc.fiji.snt.analysis.PathProfiler

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

public class PathProfiler
extends CommonDynamicCmd

Command to retrieve Path profiles (plots of voxel intensities values along a Path)

Author:

Tiago Ferreira, Cameron Arshadi

Field Summary

Fields

Modifier and Type	Field	Description
protected static final String	CIRCLE2D
protected static final String	CIRCLE3D
protected static final String	DISK2D
protected static final String	DISK3D
protected static final String	LINE2D
protected static final String	LINE3D
protected static final String	NONE
protected static final String	SPHERE
static final String	X_VALUES	Key for retrieving distances from getValues(Path)
static final String	Y_VALUES	Key for retrieving intensities from getValues(Path)

Fields inherited from class sc.fiji.snt.gui.cmds.CommonDynamicCmd

EMPTY_LABEL, HEADER_HTML, snt, sntService, statusService, ui, uiService

Fields inherited from class org.scijava.command.DynamicCommand

moduleService, pluginService

Constructor Summary

Constructors

Constructor	Description
PathProfiler()	Empty constructor used by CommandService before calling run().
PathProfiler(Path path, ij.ImagePlus imp)	Deprecated. Use PathProfiler(Path, Dataset)
PathProfiler(Path path, net.imagej.Dataset dataset)	Instantiates a new Profiler from a single path.
PathProfiler(Tree tree, ij.ImagePlus imp)	Deprecated. Use PathProfiler(Tree, Dataset)
PathProfiler(Tree tree, net.imagej.Dataset dataset)	Instantiates a new Profiler.

Method Summary

Modifier and Type	Method	Description
void	assignValues()	Calls assignValues(Path) on the Paths of the profiled Tree
void	assignValues(int channel)	Retrieves pixel intensities at each node of the Path storing them as Path values
void	assignValues(Path p)	Retrieves pixel intensities at each node of the Path storing them as Path values
<T extends net.imglib2.type.numeric.RealType<T>> void	assignValues(Path p, int channel)	Retrieves pixel intensities at each node of the Path storing them as Path values
int[]	findMaxima(Path path, int channel)	Finds the maxima in the profile of the specified path.
int[]	findMinima(Path path, int channel)	Finds the minima in the profile of the specified path.
ij.gui.Plot	getPlot()	Gets the plot profile as an ImageJ Plot (all channels).
ij.gui.Plot	getPlot(int channel)	Gets the plot profile as an ImageJ plot (single-channel).
ij.gui.Plot	getPlot(Path path)	Gets the plot profile as an ImageJ plot (all channels included).
Map<String,List<Double>>	getValues(Path p)	Gets the profile for the specified path as a map of lists, with distances (or indices) stored under X_VALUES ("x-values") and intensities under Y_VALUES ("y-values").
Map<String,List<Double>>	getValues(Path p, int channel)	Gets the profile for the specified path as a map of lists, with distances (or indices) stored under X_VALUES ("x-values") and intensities under Y_VALUES ("y-values").
org.scijava.plot.XYPlot	getXYPlot()	Gets the plot profile as an PlotService plot.
org.scijava.plot.XYPlot	getXYPlot(int channel)	Gets the plot profile as an PlotService plot.
static void	main(String[] args)
void	run()
void	setMetric(ProfileProcessor.Metric metric)
void	setNodeIndicesAsDistances(boolean nodeIndices)	Sets whether the profile abscissae should be reported in real-word units (the default) or node indices (zero-based).
void	setRadius(int radius)
void	setShape(ProfileProcessor.Shape shape)

Methods inherited from class sc.fiji.snt.gui.cmds.CommonDynamicCmd

cancel, cancel, error, getPromptWithCloseHandler, getPromptWithCloseHandler, init, isCanceled, msg, notifyExternalDataLoaded, notifyLoadingEnd, notifyLoadingStart, resetUI, resetUI, resetUI, status

Methods inherited from class org.scijava.command.DynamicCommand

context, getCancelReason, getContext, getInfo, getInput, getOutput, 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

CIRCLE2D

protected static final String CIRCLE2D

See Also:

• Constant Field Values

CIRCLE3D

protected static final String CIRCLE3D

See Also:

• Constant Field Values

DISK2D

protected static final String DISK2D

See Also:

• Constant Field Values

DISK3D

protected static final String DISK3D

See Also:

• Constant Field Values

SPHERE

protected static final String SPHERE

See Also:

• Constant Field Values

LINE2D

protected static final String LINE2D

See Also:

• Constant Field Values

LINE3D

protected static final String LINE3D

See Also:

• Constant Field Values

NONE

protected static final String NONE

See Also:

• Constant Field Values

X_VALUES

public static final String X_VALUES

Key for retrieving distances from getValues(Path)

See Also:

• Constant Field Values

Y_VALUES

public static final String Y_VALUES

Key for retrieving intensities from getValues(Path)

See Also:

• Constant Field Values

Constructor Details

PathProfiler

public PathProfiler()

Empty constructor used by CommandService before calling run(). Should not be called directly.

PathProfiler

@Deprecated
public PathProfiler(Tree tree,
 ij.ImagePlus imp)

Deprecated.

Use PathProfiler(Tree, Dataset)

PathProfiler

@Deprecated
public PathProfiler(Path path,
 ij.ImagePlus imp)

Deprecated.

Use PathProfiler(Path, Dataset)

PathProfiler

public PathProfiler(Tree tree,
 net.imagej.Dataset dataset)

Instantiates a new Profiler.

Parameters:

tree - the Tree to be profiled

dataset - the dataset from which pixel intensities will be retrieved. Note that no effort is made to ensure that the image is suitable for profiling.

PathProfiler

public PathProfiler(Path path,
 net.imagej.Dataset dataset)

Instantiates a new Profiler from a single path.

Parameters:

path - the path to be profiled

dataset - the dataset from which pixel intensities will be retrieved.Note that no effort is made to ensure that the image is suitable for profiling

Method Details

setShape

public void setShape(ProfileProcessor.Shape shape)

Parameters:

shape - Either ProfileProcessor.Shape

setMetric

public void setMetric(ProfileProcessor.Metric metric)

setRadius

public void setRadius(int radius)

run

public void run()

Specified by:

run in interface org.scijava.module.MutableModule

Specified by:

run in interface Runnable

Overrides:

run in class CommonDynamicCmd

assignValues

public void assignValues()
                  throws IllegalArgumentException

Calls assignValues(Path) on the Paths of the profiled Tree

Throws:

IllegalArgumentException

assignValues

public void assignValues(int channel)
                  throws IllegalArgumentException,
ArrayIndexOutOfBoundsException

Retrieves pixel intensities at each node of the Path storing them as Path values

Parameters:

channel - the channel to be parsed (base-0 index)

Throws:

IllegalArgumentException - if image does not contain the path's channel

ArrayIndexOutOfBoundsException

assignValues

public void assignValues(Path p)
                  throws IllegalArgumentException

Retrieves pixel intensities at each node of the Path storing them as Path values

Parameters:

p - the Path to be profiled

Throws:

IllegalArgumentException - if image does not contain the path's channel

See Also:

• Path.setNodeValues(double[])

assignValues

public <T extends net.imglib2.type.numeric.RealType<T>>
void assignValues(Path p,
 int channel)
           throws ArrayIndexOutOfBoundsException

Retrieves pixel intensities at each node of the Path storing them as Path values

Parameters:

p - the Path to be profiled

channel - the channel to be parsed (base-0 index)

Throws:

IllegalArgumentException - if image does not contain the path's channel

ArrayIndexOutOfBoundsException

See Also:

• Path.setNodeValues(double[])

findMaxima

public int[] findMaxima(Path path,
 int channel)

Finds the maxima in the profile of the specified path.

A maxima (peak) will only be considered if protruding more than the profile's standard deviation from the ridge to a higher maximum

Parameters:

channel - the channel to be parsed (base-0 index)

Returns:

the indices of the maxima

findMinima

public int[] findMinima(Path path,
 int channel)

Finds the minima in the profile of the specified path.

A maxima (peak) will only be considered if protruding less than the profile's standard deviation from the ridge to a lower minimum

Parameters:

channel - the channel to be parsed (base-0 index)

Returns:

the indices of the minima

setNodeIndicesAsDistances

public void setNodeIndicesAsDistances(boolean nodeIndices)

Sets whether the profile abscissae should be reported in real-word units (the default) or node indices (zero-based). Must be called before calling getValues(Path), getPlot() or getXYPlot().

Parameters:

nodeIndices - If true, distances will be reported as indices.

getValues

public Map<String,List<Double>> getValues(Path p)

Gets the profile for the specified path as a map of lists, with distances (or indices) stored under X_VALUES ("x-values") and intensities under Y_VALUES ("y-values").

Parameters:

p - the path to be profiled

Returns:

the profile

getValues

public Map<String,List<Double>> getValues(Path p,
 int channel)

Gets the profile for the specified path as a map of lists, with distances (or indices) stored under X_VALUES ("x-values") and intensities under Y_VALUES ("y-values").

Parameters:

p - the path to be profiled

channel - the channel to be parsed (base-0 index)

Returns:

the profile map

getPlot

public ij.gui.Plot getPlot()
                    throws IllegalArgumentException,
ArrayIndexOutOfBoundsException

Gets the plot profile as an ImageJ Plot (all channels).

Returns:

the plot

Throws:

IllegalArgumentException

ArrayIndexOutOfBoundsException

getPlot

public ij.gui.Plot getPlot(int channel)
                    throws IllegalArgumentException,
ArrayIndexOutOfBoundsException

Gets the plot profile as an ImageJ plot (single-channel).

Parameters:

channel - the channel to be parsed (base-0 index)

Returns:

the plot

Throws:

IllegalArgumentException

ArrayIndexOutOfBoundsException

getPlot

public ij.gui.Plot getPlot(Path path)

Gets the plot profile as an ImageJ plot (all channels included).

Returns:

the plot

getXYPlot

public org.scijava.plot.XYPlot getXYPlot()

Gets the plot profile as an PlotService plot. It is recommended to call DynamicCommand.setContext(org.scijava.Context) beforehand.

Returns:

the plot

getXYPlot

public org.scijava.plot.XYPlot getXYPlot(int channel)
                                  throws IllegalArgumentException

Gets the plot profile as an PlotService plot. It is recommended to call DynamicCommand.setContext(org.scijava.Context) beforehand.

Parameters:

channel - the channel to be parsed (base-0 index)

Returns:

the plot

Throws:

IllegalArgumentException

main

public static void main(String[] args)