Package sc.fiji.snt.analysis

Class ProfileProcessor<T extends net.imglib2.type.numeric.RealType<T>>

java.lang.Object

sc.fiji.snt.analysis.ProfileProcessor<T>

Type Parameters:

T - pixel type

All Implemented Interfaces:

Callable<double[]>

public class ProfileProcessor<T extends net.imglib2.type.numeric.RealType<T>>
extends Object
implements Callable<double[]>

Profile intensities within local neighborhoods around Path PointInImages

Author:

Cameron Arshadi

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	ProfileProcessor.Metric
static enum	ProfileProcessor.Shape

Constructor Summary

Constructors

Constructor	Description
ProfileProcessor(net.imglib2.RandomAccessibleInterval<T> rai, Path path)

Method Summary

Modifier and Type	Method	Description
double[]	call()	Process and return the profile values.
static ProfileProcessor.Metric[]	getMetrics()	Gets the array of available ProfileProcessor.Metrics
SortedMap<Integer,List<Double>>	getRawValues(int nodeStep)	Gets the raw values for each node at the specified step interval.
static ProfileProcessor.Shape[]	getShapes()	Gets the array of available ProfileProcessor.Shapes
double[]	getValues()	The profile values, or null if they have not been processed yet.
static void	main(String[] args)
void	process()	Processes the profile data by calling the computation.
static <T extends net.imglib2.type.numeric.RealType<T>> double[]	profilePathNodes(net.imglib2.RandomAccessible<T> rai, Path path, double[] values)	Get the intensities for the point coordinates of a Path
void	setMetric(ProfileProcessor.Metric metric)	Sets the metric to be computed for each local neighborhood.
void	setRadius(int radius)	Specify a fixed radius for each ProfileProcessor.Shape region around each PointInImage.
void	setShape(ProfileProcessor.Shape shape)	Sets the shape to be iterated.

Methods inherited from class java.lang.Object

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

Constructor Details

ProfileProcessor

public ProfileProcessor(net.imglib2.RandomAccessibleInterval<T> rai,
 Path path)

Method Details

getMetrics

public static ProfileProcessor.Metric[] getMetrics()

Gets the array of available ProfileProcessor.Metrics

Returns:

the Metric array

getShapes

public static ProfileProcessor.Shape[] getShapes()

Gets the array of available ProfileProcessor.Shapes

Returns:

the Shape array

setMetric

public void setMetric(ProfileProcessor.Metric metric)

Sets the metric to be computed for each local neighborhood. This setting is ignored if using ProfileProcessor.Shape.NONE.

Parameters:

metric -

setShape

public void setShape(ProfileProcessor.Shape shape)

Sets the shape to be iterated.

Parameters:

shape -

setRadius

public void setRadius(int radius)

Specify a fixed radius for each ProfileProcessor.Shape region around each PointInImage. Set to <= 0 to use the actual PointInImage radii.

Parameters:

radius -

getValues

public double[] getValues()

The profile values, or null if they have not been processed yet.

Returns:

the values

getRawValues

public SortedMap<Integer,List<Double>> getRawValues(int nodeStep)

Gets the raw values for each node at the specified step interval.

Parameters:

nodeStep - the step interval between nodes

Returns:

a map of node indices to their raw values

process

public void process()

Processes the profile data by calling the computation.

call

public double[] call()

Process and return the profile values.

Specified by:

call in interface Callable<T extends net.imglib2.type.numeric.RealType<T>>

Returns:

the values.

Throws:

ArrayIndexOutOfBoundsException - if using CENTERLINE shape and any Path nodes are outside the bounds of the image

profilePathNodes

public static <T extends net.imglib2.type.numeric.RealType<T>>
double[] profilePathNodes(net.imglib2.RandomAccessible<T> rai,
 Path path,
 double[] values)

Get the intensities for the point coordinates of a Path

Type Parameters:

T -

Parameters:

rai - the image

path - the Path to profile

values - the array to store the values

Returns:

the value array

Throws:

ArrayIndexOutOfBoundsException - if the Path contains any points outside the image bounds

main

public static void main(String[] args)