Package sc.fiji.snt.analysis

Class NodeProfiler

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.NodeProfiler

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 NodeProfiler
extends CommonDynamicCmd

Command to retrieve node profiles (plots of voxel intensities sampled across Path nodes).

Author:

Tiago Ferreira

Field Summary

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
NodeProfiler()	Empty constructor used by CommandService before calling run().
NodeProfiler(net.imagej.Dataset dataset)	Instantiates a new Profiler.

Method Summary

Modifier and Type	Method	Description
ij.gui.Plot	getPlot(Path path)
ij.gui.Plot	getPlot(Path path, int channel)
SNTTable	getTable(Path path)
SNTTable	getTable(Path path, int channel)
<T extends net.imglib2.type.numeric.RealType<T>> SortedMap<Integer,List<Double>>	getValues(Path p)	Gets the profile for the specified path as a map of lists of pixel intensities (profile indices as keys)
<T extends net.imglib2.type.numeric.RealType<T>> SortedMap<Integer,List<Double>>	getValues(Path p, int channel, int frame)	Gets the profile for the specified path as a map of lists of pixel intensities (profile indices as keys)
static void	main(String[] args)
void	run()
void	setNodeStep(int nodeStep)
void	setRadius(int radius)
void	setShape(ProfileProcessor.Shape shape)	Sets the shape of the iterating cursor.

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

Constructor Details

NodeProfiler

public NodeProfiler()

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

NodeProfiler

public NodeProfiler(net.imagej.Dataset dataset)

Instantiates a new Profiler.

Parameters:

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

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 CommonDynamicCmd

getValues

public <T extends net.imglib2.type.numeric.RealType<T>>
SortedMap<Integer,List<Double>> getValues(Path p)

Gets the profile for the specified path as a map of lists of pixel intensities (profile indices as keys)

Parameters:

p - the path to be profiled, using its CT positions in the image

Returns:

The profile

getValues

public <T extends net.imglib2.type.numeric.RealType<T>>
SortedMap<Integer,List<Double>> getValues(Path p,
 int channel,
 int frame)
                                   throws ArrayIndexOutOfBoundsException

Gets the profile for the specified path as a map of lists of pixel intensities (profile indices as keys)

Parameters:

p - the path to be profiled

channel - the channel to be profiled (0-based index)

frame - the frame to be profiled (0-based index)

Returns:

The profile

Throws:

ArrayIndexOutOfBoundsException

getPlot

public ij.gui.Plot getPlot(Path path)

Parameters:

path - the path to be profiled, using its CT positions in the image

Returns:

The profile (Mean±SD of all the profiled data)

getPlot

public ij.gui.Plot getPlot(Path path,
 int channel)

Parameters:

path - the path to be profiled

channel - the channel to be profiled (0-based index)

Returns:

The profile (Mean±SD of all the profiled data)

getTable

public SNTTable getTable(Path path)

Parameters:

path - the path to be profiled, using its CT positions in the image

Returns:

the profiled raw data in tabular form (1 column-per profiled node)

getTable

public SNTTable getTable(Path path,
 int channel)

Parameters:

path - the path to be profiled, using its CT positions in the image

channel - the channel to be profiled (0-based index)

Returns:

the profiled raw data in tabular form (1 column-per profiled node)

setShape

public void setShape(ProfileProcessor.Shape shape)

Sets the shape of the iterating cursor.

Parameters:

shape - A ProfileProcessor.Shape

setRadius

public void setRadius(int radius)

Parameters:

radius - the radius (in pixels) of sampling shape

setNodeStep

public void setNodeStep(int nodeStep)

Parameters:

nodeStep - sets the sampling frequency. I.e., if 10, each 10th node is sampled.

main

public static void main(String[] args)