Package gov.nih.mipav.model.algorithms.registration

Class ImRegPOC

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.registration.ImRegPOC

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class ImRegPOC
extends AlgorithmBase

Author:

aailb This is a port of the MATLAB code poc_prototype.m by Yoshi Ri at the University of Tokyo updated on 2017/8/11. This code is ported to Java with the 2-clause BSD license: The 2-clause BSD License Copyright (c) 2018, Yoshi Ri All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. The views and conclusions contained in the software and documentation are those of the authors and should not be interpreted as representing official policies, either expressed or implied, of the FreeBSD Project. The warpPolar routine is derived from warpPolar in the Open Source Computer Vision Library with the license: /*M/////////////////////////////////////////////////////////////////////////////////////// // // IMPORTANT: READ BEFORE DOWNLOADING, COPYING, INSTALLING OR USING. // // By downloading, copying, installing or using the software you agree to this license. // If you do not agree to this license, do not download, install, // copy or use the software. // // // License Agreement // For Open Source Computer Vision Library // // Copyright (C) 2000-2008, Intel Corporation, all rights reserved. // Copyright (C) 2009, Willow Garage Inc., all rights reserved. // Copyright (C) 2014-2015, Itseez Inc., all rights reserved. // Third party copyrights are property of their respective owners. // // Redistribution and use in source and binary forms, with or without modification, // are permitted provided that the following conditions are met: // // * Redistribution's of source code must retain the above copyright notice, // this list of conditions and the following disclaimer. // // * Redistribution's in binary form must reproduce the above copyright notice, // this list of conditions and the following disclaimer in the documentation // and/or other materials provided with the distribution. // // * The name of the copyright holders may not be used to endorse or promote products // derived from this software without specific prior written permission. // // This software is provided by the copyright holders and contributors "as is" and // any express or implied warranties, including, but not limited to, the implied // warranties of merchantability and fitness for a particular purpose are disclaimed. // In no event shall the Intel Corporation or contributors be liable for any direct, // indirect, incidental, special, exemplary, or consequential damages // (including, but not limited to, procurement of substitute goods or services; // loss of use, data, or profits; or business interruption) however caused // and on any theory of liability, whether in contract, strict liability, // or tort (including negligence or otherwise) arising in any way out of // the use of this software, even if advised of the possibility of such damage. // //M

Nested Class Summary

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

Thread.Builder, Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
private double	alpha
private double	beta
private double[]	hanw
private int	height
private ModelImage	inputImage	This image is to registered to the reference image.
private boolean	isMATLABVersion
private int	length
private ModelImage	refImage	The inputImage will be registered to this reference image.
private int	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
ImRegPOC(ModelImage dstImage, ModelImage imageA, ModelImage imageB)
ImRegPOC(ModelImage dstImage, ModelImage imageA, ModelImage imageB, double alpha, double beta)

Method Summary

Modifier and Type	Method	Description
private double[]	CenterOfGravity(double[][] mat)
private double[]	createHanningWindow()
private double[][]	fftshift(double[] in, int yDim, int xDim)
private double[][]	ImageRotateScale(double[][] Image, double theta, double scale, int width, int height)
private double[]	imtranslate(double[][] Image, double translateX, double translateY, double outOfBoundsValue)
private double	log2(double input)
private double[][]	PhaseCorrelation(double[] a, double[] b, double[] Diff, double[] peak)
private Jama.Matrix	poc2warp(double cx, double cy, double dx, double dy, double theta, double scale)
void	runAlgorithm()	Actually runs the algorithm.
void	runMATLABVersion()
void	runPythonVersion()
private double[]	Warp_4dof(double[] Img, double dx, double dy, double theta, double scale, double outOfBoundsValue)
private double[]	WeightedCOG(double[][] mat)

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

refImage

private ModelImage refImage

The inputImage will be registered to this reference image.

inputImage

private ModelImage inputImage

This image is to registered to the reference image.

height

private int height

width

private int width

length

private int length

isMATLABVersion

private boolean isMATLABVersion

alpha

private double alpha

beta

private double beta

hanw

private double[] hanw

Constructor Details

ImRegPOC

public ImRegPOC(ModelImage dstImage,
 ModelImage imageA,
 ModelImage imageB)

ImRegPOC

public ImRegPOC(ModelImage dstImage,
 ModelImage imageA,
 ModelImage imageB,
 double alpha,
 double beta)

Method Details

runAlgorithm

public void runAlgorithm()

Description copied from class: AlgorithmBase

Actually runs the algorithm. Implemented by inheriting algorithms.

Specified by:

runAlgorithm in class AlgorithmBase

runPythonVersion

public void runPythonVersion()

Warp_4dof

private double[] Warp_4dof(double[] Img,
 double dx,
 double dy,
 double theta,
 double scale,
 double outOfBoundsValue)

poc2warp

private Jama.Matrix poc2warp(double cx,
 double cy,
 double dx,
 double dy,
 double theta,
 double scale)

PhaseCorrelation

private double[][] PhaseCorrelation(double[] a,
 double[] b,
 double[] Diff,
 double[] peak)

WeightedCOG

private double[] WeightedCOG(double[][] mat)

CenterOfGravity

private double[] CenterOfGravity(double[][] mat)

createHanningWindow

private double[] createHanningWindow()

runMATLABVersion

public void runMATLABVersion()

imtranslate

private double[] imtranslate(double[][] Image,
 double translateX,
 double translateY,
 double outOfBoundsValue)

ImageRotateScale

private double[][] ImageRotateScale(double[][] Image,
 double theta,
 double scale,
 int width,
 int height)

log2

private double log2(double input)

fftshift

private double[][] fftshift(double[] in,
 int yDim,
 int xDim)