Package gov.nih.mipav.model.algorithms

Class LocalIntensityOrderPattern

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.LocalIntensityOrderPattern

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class LocalIntensityOrderPattern
extends AlgorithmBase

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	LocalIntensityOrderPattern.tliop
class	LocalIntensityOrderPattern.VlLiopDesc

Nested classes/interfaces inherited from class java.lang.Thread

Thread.Builder, Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
private float	DEFAULT_INTENSITY_THRESHOLD
private int	DEFAULT_NUM_NEIGHBOURS
private int	DEFAULT_NUM_SPATIAL_BINS
private float	DEFAULT_RADIUS
private ModelImage	image

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

destFlag, destImage, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, srcImage, threadStopped

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors

Constructor	Description
LocalIntensityOrderPattern()

Method Summary

Modifier and Type	Method	Description
int	factorial(int num)
int	get_permutation_index(int[] permutation, int size)
float	neigh_cmp(LocalIntensityOrderPattern.VlLiopDesc liop, int i, int j)
void	neigh_sort(LocalIntensityOrderPattern.VlLiopDesc array, int size)
void	neigh_sort_recursive(LocalIntensityOrderPattern.VlLiopDesc array, int begin, int end)
void	neigh_swap(LocalIntensityOrderPattern.VlLiopDesc liop, int i, int j)
float	patch_cmp(LocalIntensityOrderPattern.VlLiopDesc liop, int i, int j)
void	patch_sort(LocalIntensityOrderPattern.VlLiopDesc array, int size)
void	patch_sort_recursive(LocalIntensityOrderPattern.VlLiopDesc array, int begin, int end)
void	patch_swap(LocalIntensityOrderPattern.VlLiopDesc liop, int i, int j)
void	runAlgorithm()	Actually runs the algorithm.
LocalIntensityOrderPattern.tliop	setup()
void	test_basic()
void	test_blob()
void	test_multiple()
void	test_neighbors()
float[][]	vl_liop(float[][][] data, int numNeighbors, int numSpatialBins, float radius, float intensityThreshold)
float[][]	vl_liop(float[][] data, int numNeighbors, int numSpatialBins, float radius, float intensityThreshold)
void	vl_liopdesc_delete(LocalIntensityOrderPattern.VlLiopDesc self)
int	vl_liopdesc_get_dimension(LocalIntensityOrderPattern.VlLiopDesc self)
float	vl_liopdesc_get_intensity_threshold(LocalIntensityOrderPattern.VlLiopDesc self)
double	vl_liopdesc_get_neighbourhood_radius(LocalIntensityOrderPattern.VlLiopDesc self)
int	vl_liopdesc_get_num_neighbours(LocalIntensityOrderPattern.VlLiopDesc self)
int	vl_liopdesc_get_num_spatial_bins(LocalIntensityOrderPattern.VlLiopDesc self)
LocalIntensityOrderPattern.VlLiopDesc	vl_liopdesc_new(int numNeighbours, int numSpatialBins, float radius, int sideLength)
LocalIntensityOrderPattern.VlLiopDesc	vl_liopdesc_new_basic(int sideLength)
void	vl_liopdesc_process(LocalIntensityOrderPattern.VlLiopDesc self, float[] desc, float[] patch)
void	vl_liopdesc_set_intensity_threshold(LocalIntensityOrderPattern.VlLiopDesc self, float x)

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, finalize, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, getSrcImage, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setSrcImage, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Thread

activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, isVirtual, join, join, join, join, ofPlatform, ofVirtual, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, sleep, start, startVirtualThread, stop, suspend, threadId, toString, yield

Methods inherited from class java.lang.Object

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

Field Details

image

private ModelImage image

DEFAULT_INTENSITY_THRESHOLD

private float DEFAULT_INTENSITY_THRESHOLD

DEFAULT_RADIUS

private float DEFAULT_RADIUS

DEFAULT_NUM_SPATIAL_BINS

private int DEFAULT_NUM_SPATIAL_BINS

DEFAULT_NUM_NEIGHBOURS

private int DEFAULT_NUM_NEIGHBOURS

Constructor Details

LocalIntensityOrderPattern

public LocalIntensityOrderPattern()

Method Details

factorial

public int factorial(int num)

get_permutation_index

public int get_permutation_index(int[] permutation,
 int size)

Parameters:

permutation - array containing all values from 0 to (size - 1) (input/output).

size - size of the permutation array.

Returns:

permutation index. Compute the position of @a permutation in the lexycographcial sorting of permutations of the given @a size. For example, in the lexicographical ordering, permutations of four elements are listed as [1 2 3 4], [1 2 4 3], [1 3 2 4], [1 3 4 2], [1 4 2 3], [1 4 3 2], [2 1 3 4], ..., [4 3 2 1]. The index can be computed as follows. First pick the first digit perm[1]. This is either 1,2,...,n. For each choice of the first digits, there are (n-1)! other permutations, separated therefore by (n-1)! elements in lexicographical order. Process then the second digit perm[2]. This can be though as finding the lexycotraphical index of perm[2], ..., perm[n], a permutation of n-1 elements. This can be explicitly obtained by taking out 1 from all elements perm[i] > perm[1].

patch_cmp

public float patch_cmp(LocalIntensityOrderPattern.VlLiopDesc liop,
 int i,
 int j)

patch_swap

public void patch_swap(LocalIntensityOrderPattern.VlLiopDesc liop,
 int i,
 int j)

neigh_cmp

public float neigh_cmp(LocalIntensityOrderPattern.VlLiopDesc liop,
 int i,
 int j)

neigh_swap

public void neigh_swap(LocalIntensityOrderPattern.VlLiopDesc liop,
 int i,
 int j)

vl_liopdesc_new

public LocalIntensityOrderPattern.VlLiopDesc vl_liopdesc_new(int numNeighbours,
 int numSpatialBins,
 float radius,
 int sideLength)

Parameters:

numNeighbours - number of neighbours.

numSpatialBins - number of bins.

radius - radius of the cirucal sample neighbourhoods.

sideLength - width of the input image patch (the patch is square).

Returns:

new object instance. The value of @a radius should be at least less than half the @a sideLength of the patch.

vl_liopdesc_new_basic

public LocalIntensityOrderPattern.VlLiopDesc vl_liopdesc_new_basic(int sideLength)

Parameters:

sideLength - size of the patches to be processed.

Returns:

new object.

vl_liopdesc_delete

public void vl_liopdesc_delete(LocalIntensityOrderPattern.VlLiopDesc self)

Parameters:

self - object instance.

patch_sort

public void patch_sort(LocalIntensityOrderPattern.VlLiopDesc array,
 int size)

Parameters:

array - (in/out) pointer to the array.

size - size of the array. The function sorts the array using quick-sort.

patch_sort_recursive

public void patch_sort_recursive(LocalIntensityOrderPattern.VlLiopDesc array,
 int begin,
 int end)

Parameters:

array - (in/out) pointer to the array.

begin - first element of the array portion.

end - last element of the array portion. The function sorts the array using quick-sort. Note that

neigh_sort

public void neigh_sort(LocalIntensityOrderPattern.VlLiopDesc array,
 int size)

Parameters:

array - (in/out) pointer to the array.

size - size of the array. The function sorts the array using quick-sort.

neigh_sort_recursive

public void neigh_sort_recursive(LocalIntensityOrderPattern.VlLiopDesc array,
 int begin,
 int end)

Parameters:

array - (in/out) pointer to the array.

begin - first element of the array portion.

end - last element of the array portion. The function sorts the array using quick-sort. Note that

vl_liopdesc_process

public void vl_liopdesc_process(LocalIntensityOrderPattern.VlLiopDesc self,
 float[] desc,
 float[] patch)

Parameters:

self - object instance

desc - descriptor to be computed (output).

patch - patch to process Use ::vl_liopdesc_get_dimension to get the size of the descriptor

vl_liopdesc_get_dimension

public int vl_liopdesc_get_dimension(LocalIntensityOrderPattern.VlLiopDesc self)

Parameters:

self - object.

Returns:

dimension.

vl_liopdesc_get_num_neighbours

public int vl_liopdesc_get_num_neighbours(LocalIntensityOrderPattern.VlLiopDesc self)

Parameters:

self - object.

Returns:

number of neighbours.

vl_liopdesc_get_intensity_threshold

public float vl_liopdesc_get_intensity_threshold(LocalIntensityOrderPattern.VlLiopDesc self)

Parameters:

self - object.

Returns:

intensity threshold.

vl_liopdesc_set_intensity_threshold

public void vl_liopdesc_set_intensity_threshold(LocalIntensityOrderPattern.VlLiopDesc self,
 float x)

Parameters:

self - object.

x - intensity threshold. If non-negative, the threshold as is is used when comparing intensities. If negative, the absolute value of the specified number is multipled by the maximum intensity difference inside a patch to obtain the threshold.

vl_liopdesc_get_neighbourhood_radius

public double vl_liopdesc_get_neighbourhood_radius(LocalIntensityOrderPattern.VlLiopDesc self)

Parameters:

self - object.

Returns:

neighbourhood radius.

vl_liopdesc_get_num_spatial_bins

public int vl_liopdesc_get_num_spatial_bins(LocalIntensityOrderPattern.VlLiopDesc self)

Parameters:

self - object.

Returns:

number of spatial bins.

setup

public LocalIntensityOrderPattern.tliop setup()

test_basic

public void test_basic()

test_blob

public void test_blob()

test_neighbors

public void test_neighbors()

test_multiple

public void test_multiple()

vl_liop

public float[][] vl_liop(float[][] data,
 int numNeighbors,
 int numSpatialBins,
 float radius,
 float intensityThreshold)

vl_liop

public float[][] vl_liop(float[][][] data,
 int numNeighbors,
 int numSpatialBins,
 float radius,
 float intensityThreshold)

runAlgorithm

public void runAlgorithm()

Description copied from class: AlgorithmBase

Actually runs the algorithm. Implemented by inheriting algorithms.

Specified by:

runAlgorithm in class AlgorithmBase