java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.registration.ImRegPOC

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.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
  java.lang.Thread.State, java.lang.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

All Methods Instance Methods Concrete Methods
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, 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

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 Detail

ImRegPOC

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

ImRegPOC

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

Method Detail

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)

Class ImRegPOC

Nested Class Summary

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

Field Summary

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

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

refImage

inputImage

height

width

length

isMATLABVersion

alpha

beta

hanw

Constructor Detail

ImRegPOC

ImRegPOC

Method Detail

runAlgorithm

runPythonVersion

Warp_4dof

poc2warp

PhaseCorrelation

WeightedCOG

CenterOfGravity

createHanningWindow

runMATLABVersion

imtranslate

ImageRotateScale

log2

fftshift