Package gov.nih.mipav.model.algorithms.filters.OpenCL.filters

Class OpenCLAlgorithmDeconvolution

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.OpenCLAlgorithmBase

gov.nih.mipav.model.algorithms.filters.OpenCL.filters.OpenCLAlgorithmDeconvolution

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener

public class OpenCLAlgorithmDeconvolution
extends OpenCLAlgorithmBase

OpenCL Algorithm computes Deconvolution for a 3D or 4D image.

Nested Class Summary

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

java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
static int	AVERAGE_DECON	Average deconvolution is based on the arithmetical mean of the two estimates from A and B separately
private com.jogamp.opencl.CLBuffer<java.nio.FloatBuffer>	brightnessBuffer	buffer for storing the original maximum of the OpenCL buffer
private int[]	colorMask	Color flags.
private int	iterations	number of iterations in the deconvolution:
static int	JOINT_DECON	Default case
private long	maxWorkSize	Maximum number of work items in a work group on OpenCL.
private int	method
static int	MULTIPLICATION_DECON	Multiplication deconvolution is based on the geometrical mean of the two estimates from A and B separately
private com.jogamp.opencl.CLKernel	reductionKernel	OpenCL reduction kernel, calculates the max of and OpenCL buffer.
private com.jogamp.opencl.CLKernel	scaleKernel	OpenCL scale kernel, multiplies the image by buffer1[0] / buffer2[0], where all buffers are OpenCL buffers on the GPU / CPU.
private float[]	sigmas	Standard deviations of the Gaussian used to calculate the kernels.
private float[]	sigmasB	second sigma values for dual-deconvolution
private ModelImage	srcImageB	second ModelImage for dual-deconvolution
private float[]	sum
private com.jogamp.opencl.CLBuffer<java.nio.FloatBuffer>	sumBuffer	buffer for storing the current max of an OpenCL buffer
private boolean	useConversion	when true, the sigma values are multiplied by: 1.0 / (2*Math.sqrt(2*Math.log(2))) before the gaussian is generated.

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

color, depth, entireImage, height, m_iDeviceType, m_kGL, time, width

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
OpenCLAlgorithmDeconvolution(ModelImage srcImg, int method, float[] sigmas, boolean maskFlag, int iterations, boolean conversion)	New Deconvolution algorithm, applies the deconvolution based on the sigma values and iterations to the input image.
OpenCLAlgorithmDeconvolution(ModelImage destImg, ModelImage srcImg, int method, float[] sigmas, boolean maskFlag, int iterations, boolean conversion)	New Deconvolution algorithm, applies the deconvolution based on the sigma values and iterations to the input image.
OpenCLAlgorithmDeconvolution(ModelImage destImg, ModelImage srcImg, int method, float[] sigmas, boolean maskFlag, int iterations, boolean conversion, long deviceType)	New Deconvolution algorithm, applies the deconvolution based on the sigma values and iterations to the input image.
OpenCLAlgorithmDeconvolution(ModelImage srcImgA, ModelImage srcImgB, int method, float[] sigmasA, float[] sigmasB, boolean maskFlag, int iterations, boolean conversion)	New Dual image Deconvolution algorithm, applies the deconvolution based on the sigma values and iterations to the input image.
OpenCLAlgorithmDeconvolution(ModelImage destImg, ModelImage srcImgA, ModelImage srcImgB, int method, float[] sigmasA, float[] sigmasB, boolean maskFlag, int iterations, boolean conversion)	New Dual image Deconvolution algorithm, applies the deconvolution based on the sigma values and iterations to the input image.
OpenCLAlgorithmDeconvolution(ModelImage destImg, ModelImage srcImgA, ModelImage srcImgB, int method, float[] sigmasA, float[] sigmasB, boolean maskFlag, int iterations, boolean conversion, long deviceType)	New Dual image Deconvolution algorithm, applies the deconvolution based on the sigma values and iterations to the input image.

Method Summary

Modifier and Type	Method	Description
private void	deconvolution4D()	Calls Deconvolution for each volume in the time series image.
private void	deconvolutionSep3D_2(int time)	Single - Image deconvolution
private void	deconvolutionSep3D_Dual(int time)	Dual image deconvolution.
void	finalize()	Prepares this class for destruction.
private float[]	getKernel(float sigma)	Computes a 1D Gaussian kernel for the given sigma value.
private long	getMaxMemoryUsed(float[] sigmas)	Determines the amount of memory used for the OpenCL buffers required for the gaussian kernels for the given sigmas.
void	runAlgorithm()	Starts the program.

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

fillBuffer, fillBuffer, fillBuffer, fillBuffer, getMaxMemoryUsed, initCL, isOCLAvailable, readBuffer, readBuffer, readKernelFile, roundUp, roundUp, saveImage, saveImage, setBlue, setGreen, setRed, setTime

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

actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, 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, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, suspend, toString, yield

Methods inherited from class java.lang.Object

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

Field Detail

colorMask

private int[] colorMask

Color flags.

sigmas

private float[] sigmas

Standard deviations of the Gaussian used to calculate the kernels.

iterations

private int iterations

number of iterations in the deconvolution:

useConversion

private boolean useConversion

when true, the sigma values are multiplied by: 1.0 / (2*Math.sqrt(2*Math.log(2))) before the gaussian is generated.

reductionKernel

private com.jogamp.opencl.CLKernel reductionKernel

OpenCL reduction kernel, calculates the max of and OpenCL buffer.

scaleKernel

private com.jogamp.opencl.CLKernel scaleKernel

OpenCL scale kernel, multiplies the image by buffer1[0] / buffer2[0], where all buffers are OpenCL buffers on the GPU / CPU.

sumBuffer

private com.jogamp.opencl.CLBuffer<java.nio.FloatBuffer> sumBuffer

buffer for storing the current max of an OpenCL buffer

brightnessBuffer

private com.jogamp.opencl.CLBuffer<java.nio.FloatBuffer> brightnessBuffer

buffer for storing the original maximum of the OpenCL buffer

sum

private float[] sum

srcImageB

private ModelImage srcImageB

second ModelImage for dual-deconvolution

sigmasB

private float[] sigmasB

second sigma values for dual-deconvolution

maxWorkSize

private long maxWorkSize

Maximum number of work items in a work group on OpenCL.

JOINT_DECON

public static final int JOINT_DECON

Default case

See Also:

Constant Field Values

AVERAGE_DECON

public static final int AVERAGE_DECON

Average deconvolution is based on the arithmetical mean of the two estimates from A and B separately

See Also:

Constant Field Values

MULTIPLICATION_DECON

public static final int MULTIPLICATION_DECON

Multiplication deconvolution is based on the geometrical mean of the two estimates from A and B separately

See Also:

Constant Field Values

method

private int method

Constructor Detail

OpenCLAlgorithmDeconvolution

public OpenCLAlgorithmDeconvolution(ModelImage srcImg,
                                    int method,
                                    float[] sigmas,
                                    boolean maskFlag,
                                    int iterations,
                                    boolean conversion)

New Deconvolution algorithm, applies the deconvolution based on the sigma values and iterations to the input image. Overwrites the input image.

Parameters:

srcImg -

method -

sigmas -

maskFlag -

iterations -

conversion -

OpenCLAlgorithmDeconvolution

public OpenCLAlgorithmDeconvolution(ModelImage destImg,
                                    ModelImage srcImg,
                                    int method,
                                    float[] sigmas,
                                    boolean maskFlag,
                                    int iterations,
                                    boolean conversion)

New Deconvolution algorithm, applies the deconvolution based on the sigma values and iterations to the input image. Stores the output in the destImage.

Parameters:

destImg -

srcImg -

method -

sigmas -

maskFlag -

iterations -

conversion -

OpenCLAlgorithmDeconvolution

public OpenCLAlgorithmDeconvolution(ModelImage destImg,
                                    ModelImage srcImg,
                                    int method,
                                    float[] sigmas,
                                    boolean maskFlag,
                                    int iterations,
                                    boolean conversion,
                                    long deviceType)

New Deconvolution algorithm, applies the deconvolution based on the sigma values and iterations to the input image. Stores the output in the destImage. Enables the user to specify the device type (CL.CL_DEVICE_TYPE_GPU or CL.CL_DEVICE_TYPE_CPU)

Parameters:

destImg -

srcImg -

method -

sigmas -

maskFlag -

iterations -

conversion -

deviceType -

OpenCLAlgorithmDeconvolution

public OpenCLAlgorithmDeconvolution(ModelImage srcImgA,
                                    ModelImage srcImgB,
                                    int method,
                                    float[] sigmasA,
                                    float[] sigmasB,
                                    boolean maskFlag,
                                    int iterations,
                                    boolean conversion)

New Dual image Deconvolution algorithm, applies the deconvolution based on the sigma values and iterations to the input image. Overwrites the input imageA as output.

Parameters:

srcImgA -

srcImgB -

method -

sigmasA -

sigmasB -

maskFlag -

iterations -

conversion -

OpenCLAlgorithmDeconvolution

public OpenCLAlgorithmDeconvolution(ModelImage destImg,
                                    ModelImage srcImgA,
                                    ModelImage srcImgB,
                                    int method,
                                    float[] sigmasA,
                                    float[] sigmasB,
                                    boolean maskFlag,
                                    int iterations,
                                    boolean conversion)

New Dual image Deconvolution algorithm, applies the deconvolution based on the sigma values and iterations to the input image.

Parameters:

destImg -

srcImgA -

srcImgB -

method -

sigmasA -

sigmasB -

maskFlag -

iterations -

conversion -

OpenCLAlgorithmDeconvolution

public OpenCLAlgorithmDeconvolution(ModelImage destImg,
                                    ModelImage srcImgA,
                                    ModelImage srcImgB,
                                    int method,
                                    float[] sigmasA,
                                    float[] sigmasB,
                                    boolean maskFlag,
                                    int iterations,
                                    boolean conversion,
                                    long deviceType)

New Dual image Deconvolution algorithm, applies the deconvolution based on the sigma values and iterations to the input image. Stores the output in the destImage. Enables the user to specify the device type (CL.CL_DEVICE_TYPE_GPU or CL.CL_DEVICE_TYPE_CPU)

Parameters:

destImg -

srcImgA -

srcImgB -

method -

sigmasA -

sigmasB -

maskFlag -

iterations -

conversion -

deviceType -

Method Detail

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class OpenCLAlgorithmBase

runAlgorithm

public void runAlgorithm()

Starts the program.

Specified by:

runAlgorithm in class AlgorithmBase

deconvolution4D

private void deconvolution4D()

Calls Deconvolution for each volume in the time series image.

deconvolutionSep3D_2

private void deconvolutionSep3D_2(int time)

Single - Image deconvolution

Parameters:

time -

deconvolutionSep3D_Dual

private void deconvolutionSep3D_Dual(int time)

Dual image deconvolution.

Parameters:

time -

getKernel

private float[] getKernel(float sigma)

Computes a 1D Gaussian kernel for the given sigma value.

Parameters:

sigma -

Returns:

getMaxMemoryUsed

private long getMaxMemoryUsed(float[] sigmas)

Determines the amount of memory used for the OpenCL buffers required for the gaussian kernels for the given sigmas.

Parameters:

sigmas -

Returns: