sc.fiji.snt.analysis

Class PathProfiler

java.lang.Object

org.scijava.AbstractContextual

org.scijava.command.ContextCommand

sc.fiji.snt.analysis.PathProfiler

All Implemented Interfaces:

java.lang.Runnable, org.scijava.Cancelable, org.scijava.command.Command, org.scijava.Contextual, org.scijava.plugin.SciJavaPlugin

public class PathProfiler
extends org.scijava.command.ContextCommand

Command to retrieve Profile plots (plots of voxel intensities values along a Path) from reconstructions.

Author:

Tiago Ferreira

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	X_VALUES Flag for retrieving distances from getValues(Path)
static java.lang.String	Y_VALUES Flag for retrieving intensities from getValues(Path)

Constructor Summary

Constructors

Constructor and Description
PathProfiler(Path path, ij.ImagePlus imp) Instantiates a new Profiler from a single path
PathProfiler(Tree tree, ij.ImagePlus imp) Instantiates a new Profiler

Method Summary

Modifier and Type	Method and Description
void	assignValues() Calls assignValues(Path) on the Paths of the profiled Tree
void	assignValues(Path p) Retrieves pixel intensities at each node of the Path storing them as Path values
ij.gui.Plot	getPlot() Gets the plot profile as an IJ1 Plot.
java.util.Map<java.lang.String,java.util.List<java.lang.Double>>	getValues(Path p) Gets the profile for the specified path as a map of lists, with distances stored under X_VALUES ("x-values") and intensities under Y_VALUES ("y-values").
net.imagej.plot.XYPlot	getXYPlot() Gets the plot profile as an PlotService plot.
static void	main(java.lang.String[] args)
void	run()
void	setNodeIndicesAsDistances(boolean nodeIndices) Sets whether the profile abscissae should be reported in real-word units (the default) or node indices (zero-based).
boolean	validImage() Checks whether the specified image contains all the nodes of the profiled Tree/Path.

Methods inherited from class org.scijava.command.ContextCommand

cancel, getCancelReason, isCanceled

Methods inherited from class org.scijava.AbstractContextual

context, getContext

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.scijava.Contextual

setContext

Field Detail

X_VALUES

public static final java.lang.String X_VALUES

Flag for retrieving distances from getValues(Path)

See Also:

Constant Field Values

Y_VALUES

public static final java.lang.String Y_VALUES

Flag for retrieving intensities from getValues(Path)

See Also:

Constant Field Values

Constructor Detail

PathProfiler

public PathProfiler(Tree tree,
                    ij.ImagePlus imp)

Instantiates a new Profiler

Parameters:

tree - the Tree to be profiled

imp - the image from which pixel intensities will be retrieved. Note that no effort is made to ensure that the image is suitable for profiling, if Tree nodes lay outside the image dimensions, pixels intensities will be retrieved as Float#NaN

PathProfiler

public PathProfiler(Path path,
                    ij.ImagePlus imp)

Instantiates a new Profiler from a single path

Parameters:

path - the path to be profiled

imp - the image from which pixel intensities will be retrieved. Note that no effort is made to ensure that the image is suitable for profiling, if Tree nodes lay outside the image dimensions, pixels intensities will be retrieved as Float#NaN

Method Detail

run

public void run()

validImage

public boolean validImage()

Checks whether the specified image contains all the nodes of the profiled Tree/Path.

Returns:

true, if successful, false if Tree has nodes outside the image boundaries.

assignValues

public void assignValues()

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

assignValues

public void assignValues(Path p)

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

Parameters:

p - the Path to be profiled

See Also:

Path.setNodeValues(double[])

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 java.util.Map<java.lang.String,java.util.List<java.lang.Double>> getValues(Path p)

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

Parameters:

p - the path to be profiled

Returns:

the profile

getPlot

public ij.gui.Plot getPlot()

Gets the plot profile as an IJ1 Plot.

Returns:

the plot

getXYPlot

public net.imagej.plot.XYPlot getXYPlot()

Gets the plot profile as an PlotService plot. Requires Contextual.setContext(org.scijava.Context) to be called beforehand.

Returns:

the plot

main

public static void main(java.lang.String[] args)