Package gov.nih.mipav.model.algorithms

Class AlgorithmTextureAnalysis

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmTextureAnalysis

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmTextureAnalysis
extends AlgorithmBase

Overview This code contains the texture analysis functions for the paper `Texture Analysis and Segmentation Using Modulation Features, Generative Models, and Weighted Curve Evolution', by I. Kokkinos, G. Evangelopoulos and P. Maragos, appearing in IEEE Transactions on Pattern Analysis and Machine Intelligence, Volume 31, Issue 1, Jan. 2009 Page(s):142 - 157. This toolbox was originally developed in and written for MATLAB, with emphasis on efficient algorithm implementations for multiband image filtering, demodulation in amplitude (AM) and frequency (FM) signals via the regularized 2D discrete energy separation algorithm and probabilistic localization of texture, edge, smooth image regions. Author of the original MATLAB toolbox is Iasonas Kokkinos, currently Assistant Professor at Ecole Centrale Paris, with partial contributions from Georgios Evangelopoulos. The original MATLAB toolbox has been ported from MATLAB to Java by William Gandler. The original MATLAB toolbox can be found at http://cvsp.cs.ntua.gr/software/texture/. Permission to port the original code was generously granted by Iasonas Kokkinos. The provided functions include: multi-scale invalid input: '&' orientation filterbanks for gabors and edges projection on the basis elements of the underlying generative models demodulation with regularized/complex esa channel selection based on the amplitude/teager/mdl criterion texture/edge/smooth classification based on mdl criterion Parameters are primarily related to the filterbank construction and the final classification stage. References: 1.) I. Kokkinos, G. Evangelopoulos and P. Maragos, Texture Analysis and Segmentation using Modulation Features, Generative Models and Weighted Curve Evolution, IEEE Transactions on Pattern Analysis invalid input: '&' Machine Intelligence, vol. 31, no. 1, pp. 142-157, Jan. 2009. 2.) G. Evangelopoulos, I. Kokkinos and P. Maragos, Advances in Variational Image Segmentation using AM-FM Models: Regularized Demodulation and Probabilistic Cue Integration, Proc. Int' l Workshop on Variational and Level Set Methods (VLSM-05), Beijing, China, Oct. 2005, Springer LNCS, vol. 3275, pp. 121-136. 3.) I. Kokkinos, G. Evangelopoulos and P. Maragos, Advances in Texture Analysis: Energy Dominant Component and Multiple Hypothesis Testing, Proc. IEEE Int' l Conf. on Image Processing (ICIP-04), Singapore, Oct. 2004, vol. 3, pp. 1509-1512. 4.) I. Kokkinos, G. Evangelopoulos and P. Maragos, Modulation-Feature Based Textured Image Segmentation Using Curve Evolution, Proc. IEEE Int' l Conf. on Image Processing (ICIP-04), Singapore, Oct. 2004, vol. 2, pp. 1204-1207.

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 ModelImage[]	destImage
private boolean	displayFilters
private ModelImage	edgetd2Image
private ModelImage	edgetd3Image
private final double	epsilon
private ModelImage	gImage
private final boolean	scaleImage
private ModelImage	texttd2Image
private ModelImage	texttd3Image

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

destFlag, 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
AlgorithmTextureAnalysis(ModelImage[] destImage, ModelImage srcImage, boolean scaleImage)

Method Summary

Modifier and Type	Method	Description
private double[]	conv(double[] A, double[] B, double[] Cout)
private void	conv2(double[][] A, double[][] B, double[][] Cout)
private double[][]	deriv_x_left(double[][] buf)
private double[][]	deriv_x_right(double[][] buf)
private double[][]	deriv_y_down(double[][] buf)
private double[][]	deriv_y_up(double[][] buf)
private double[][]	enop2D(double[][] im)
private void	fftshift(double[][] mtx)
private void	filter2(double[][] A, double[][] B, double[][] C)
private void	filterbank_DCA_2D(double[][] omegas, double[][] amplitudes, double[] filterAngle, double[] sigmaX, int nscales, String filterType, int ndirs, double sig2omega, double radianStart, double radianEnd)
private void	freqz2(double[][] hout, double[][] houtImag, double[][] a, int n1, int n2)
private void	ifft2(double[][] buf, double[][] bufI)
private void	ifftshift(double[][] mtx)
private void	rot180(double[][] mtx)
void	runAlgorithm()	Starts the program.
private void	T1_responses(double[][] omegas, double[][] amplitudes, double[] filterAngle, double[] sigmaX, double[][][] td1, double[][][] td2, double[][][] td3, double[][][] td22, double[][][] td23, double[][][] td33, double[][][] fd1, double[][][] fd1Imag, double[][][] fd2, double[][][] fd2Imag, double[][][] fd3, double[][][] fd3Imag, double[][][] fd22, double[][][] fd22Imag, double[][][] fd23, double[][][] fd23Imag, double[][][] fd33, double[][][] fd33Imag, double[] sigmas, int[] ps, int nscales, int ndirs, double sig2omega, double radianStart, double radianEnd, int inputXDim, int inputYDim, String filterType, String[] domain)
private void	T1z2_get_filter_struct(double[][][] td1, double[][][] td2, double[][][] td3, double[][][] td22, double[][][] td23, double[][][] td33, double[][][] fd1, double[][][] fd1Imag, double[][][] fd2, double[][][] fd2Imag, double[][][] fd3, double[][][] fd3Imag, double[][][] fd22, double[][][] fd22Imag, double[][][] fd23, double[][][] fd23Imag, double[][][] fd33, double[][][] fd33Imag, double[] omegas, double[] amplitudes, double filterAngle, double sigmaX, String domain, double[][] xfreq, double[][] yfreq, int index)
private void	T1z2a_convert_filter(double[] omegasOut, double[] amplitudesOut, double[] amplitudesOutImag, double[] omegas, double[] amplitudes, double filterAngle, double sigmaX, int conj)
private double[][]	T1z2b_time_resp(double[] omegas, double[] amplitudes, double[] amplitudesImag, double filterAngle, double sigmaX)
private void	T2z0_projection_terms(double[][][][][] invDes, double[][][] td1, double[][][] td2, double[][][] td3, double[][][] td22, double[][][] td23, double[][][] td33, double[][][] fd1, double[][][] fd1Imag, double[][][] fd2, double[][][] fd2Imag, double[][][] fd3, double[][][] fd3Imag, double[][][] fd22, double[][][] fd22Imag, double[][][] fd23, double[][][] fd23Imag, double[][][] fd33, double[][][] fd33Imag, int[] ps, int nscales, int ndirs, String[] filtDomain, ModelImage inputImage)
private double[][][][]	T2z0a_invert_design(double[][] Sc1, double[][] Sc2, double[][] Sc3, double[][] Sc22, double[][] Sc23, double[][] Sc33)
private void	T2z1_filter(double[][] A, double[][] ph, double[][] Fx, double[][] Fy, int[][] idx, double[][] en, double[][] critDCA, double[][] omegas, double[][] amplitudes, double[] filterAngle, double[] sigmaX, double[][][] td1, double[][][] td2, double[][][] td3, double[][][] fd1, double[][][] fd1Imag, double[][][] fd2, double[][][] fd2Imag, double[][][] fd3, double[][][] fd3Imag, double[][][] fd22, double[][][] fd22Imag, double[][][] fd23, double[][][] fd23Imag, double[][][] fd33, double[][][] fd33Imag, int[] ps, String[] domain, int[] scaleswt, int ndirs, ModelImage inputImage, double[][][][][] invDes, String DCAmethod, String esameth, double[] sgx, double invVariance2, double factorSharpness, double factorMdl)
private void	T2z1a_make_image_structure(double[] fftImagePatch, double[] fftImagePatchImag, double[] fftSupportPatch, double[] fftSupportPatchImag, double[][] input, int patchSize)
private void	T2z1b_get_responses_freq(double[][] preComputedIc1, double[][] preComputedIc2, double[][] preComputedIc3, double[][] preComputedSc1, double[][] preComputedsm, double[][] Sc1, double[][] Sc2, double[][] Sc3, double[][] Sc22, double[][] Sc23, double[][] Sc33, double[] fftSupportPatch, double[] fftSupportPatchImag, int patchSize, double[] fftImagePatch, double[] fftImagePatchImag, double[][] fd1, double[][] fd1Imag, double[][] fd2, double[][] fd2Imag, double[][] fd3, double[][] fd3Imag, double[][] fd22, double[][] fd22Imag, double[][] fd23, double[][] fd23Imag, double[][] fd33, double[][] fd33Imag, int findNorm)
private void	T2z1b_get_responses_time(double[][] preComputedIc1, double[][] preComputedIc2, double[][] preComputedIc3, double[][] preComputedSc1, double[][] preComputedsm, double[][] Sc1, double[][] Sc2, double[][] Sc3, double[][] Sc22, double[][] Sc23, double[][] Sc33, double[][] td1, double[][] td2, double[][] td3, double[][] td22, double[][] td23, double[][] td33, double[][] inputIm, int findNorm)
private void	T2z1d_esa2D(double[][] A, double[][] Wx, double[][] Wy, double[][] freqr, double[][] Anonorm, double[][] Eo, double[][] imInSrc, double[][] imInSrcImag, int signChange, double[] omegas, double[] amplitudes, double filterAngle, double sigmaX, double ct, int diffType)
private void	T2z1dI_get_responses_freq_gabor(double[][] Fx, double[][] FxImag, double[][] Fy, double[][] FyImag, double[][] Fxx, double[][] FxxImag, double[][] Fyy, double[][] FyyImag, double[][] Fxy, double[][] FxyImag, double[][] V2Fx, double[][] V2FxImag, double[][] V2Fy, double[][] V2FyImag, double[][] imIn, double[][] imInImag, double[] omegas, double[] amplitudes, double filterAngle, double sigmaX)
private void	test_T2z0a_invert_design()
private void	testconv2()
private void	testfreqz2()
private void	Tzz_freq_resp(double[][] hout, double[][] omegax, double[][] omegay, double sigmaX, double filterAngle, double[] omegas, double[] amplitudes)

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

destImage

private ModelImage[] destImage

scaleImage

private final boolean scaleImage

epsilon

private final double epsilon

displayFilters

private boolean displayFilters

texttd2Image

private ModelImage texttd2Image

texttd3Image

private ModelImage texttd3Image

edgetd2Image

private ModelImage edgetd2Image

edgetd3Image

private ModelImage edgetd3Image

gImage

private ModelImage gImage

Constructor Details

AlgorithmTextureAnalysis

public AlgorithmTextureAnalysis(ModelImage[] destImage,
 ModelImage srcImage,
 boolean scaleImage)

Method Details

runAlgorithm

public void runAlgorithm()

Starts the program.

Specified by:

runAlgorithm in class AlgorithmBase

T2z1_filter

private void T2z1_filter(double[][] A,
 double[][] ph,
 double[][] Fx,
 double[][] Fy,
 int[][] idx,
 double[][] en,
 double[][] critDCA,
 double[][] omegas,
 double[][] amplitudes,
 double[] filterAngle,
 double[] sigmaX,
 double[][][] td1,
 double[][][] td2,
 double[][][] td3,
 double[][][] fd1,
 double[][][] fd1Imag,
 double[][][] fd2,
 double[][][] fd2Imag,
 double[][][] fd3,
 double[][][] fd3Imag,
 double[][][] fd22,
 double[][][] fd22Imag,
 double[][][] fd23,
 double[][][] fd23Imag,
 double[][][] fd33,
 double[][][] fd33Imag,
 int[] ps,
 String[] domain,
 int[] scaleswt,
 int ndirs,
 ModelImage inputImage,
 double[][][][][] invDes,
 String DCAmethod,
 String esameth,
 double[] sgx,
 double invVariance2,
 double factorSharpness,
 double factorMdl)

T2z1d_esa2D

private void T2z1d_esa2D(double[][] A,
 double[][] Wx,
 double[][] Wy,
 double[][] freqr,
 double[][] Anonorm,
 double[][] Eo,
 double[][] imInSrc,
 double[][] imInSrcImag,
 int signChange,
 double[] omegas,
 double[] amplitudes,
 double filterAngle,
 double sigmaX,
 double ct,
 int diffType)

enop2D

private double[][] enop2D(double[][] im)

deriv_x_right

private double[][] deriv_x_right(double[][] buf)

deriv_x_left

private double[][] deriv_x_left(double[][] buf)

deriv_y_up

private double[][] deriv_y_up(double[][] buf)

deriv_y_down

private double[][] deriv_y_down(double[][] buf)

T2z1dI_get_responses_freq_gabor

private void T2z1dI_get_responses_freq_gabor(double[][] Fx,
 double[][] FxImag,
 double[][] Fy,
 double[][] FyImag,
 double[][] Fxx,
 double[][] FxxImag,
 double[][] Fyy,
 double[][] FyyImag,
 double[][] Fxy,
 double[][] FxyImag,
 double[][] V2Fx,
 double[][] V2FxImag,
 double[][] V2Fy,
 double[][] V2FyImag,
 double[][] imIn,
 double[][] imInImag,
 double[] omegas,
 double[] amplitudes,
 double filterAngle,
 double sigmaX)

ifft2

private void ifft2(double[][] buf,
 double[][] bufI)

T2z0_projection_terms

private void T2z0_projection_terms(double[][][][][] invDes,
 double[][][] td1,
 double[][][] td2,
 double[][][] td3,
 double[][][] td22,
 double[][][] td23,
 double[][][] td33,
 double[][][] fd1,
 double[][][] fd1Imag,
 double[][][] fd2,
 double[][][] fd2Imag,
 double[][][] fd3,
 double[][][] fd3Imag,
 double[][][] fd22,
 double[][][] fd22Imag,
 double[][][] fd23,
 double[][][] fd23Imag,
 double[][][] fd33,
 double[][][] fd33Imag,
 int[] ps,
 int nscales,
 int ndirs,
 String[] filtDomain,
 ModelImage inputImage)

test_T2z0a_invert_design

private void test_T2z0a_invert_design()

T2z0a_invert_design

private double[][][][] T2z0a_invert_design(double[][] Sc1,
 double[][] Sc2,
 double[][] Sc3,
 double[][] Sc22,
 double[][] Sc23,
 double[][] Sc33)

T2z1b_get_responses_time

private void T2z1b_get_responses_time(double[][] preComputedIc1,
 double[][] preComputedIc2,
 double[][] preComputedIc3,
 double[][] preComputedSc1,
 double[][] preComputedsm,
 double[][] Sc1,
 double[][] Sc2,
 double[][] Sc3,
 double[][] Sc22,
 double[][] Sc23,
 double[][] Sc33,
 double[][] td1,
 double[][] td2,
 double[][] td3,
 double[][] td22,
 double[][] td23,
 double[][] td33,
 double[][] inputIm,
 int findNorm)

filter2

private void filter2(double[][] A,
 double[][] B,
 double[][] C)

testconv2

private void testconv2()

conv2

private void conv2(double[][] A,
 double[][] B,
 double[][] Cout)

conv

private double[] conv(double[] A,
 double[] B,
 double[] Cout)

T2z1b_get_responses_freq

private void T2z1b_get_responses_freq(double[][] preComputedIc1,
 double[][] preComputedIc2,
 double[][] preComputedIc3,
 double[][] preComputedSc1,
 double[][] preComputedsm,
 double[][] Sc1,
 double[][] Sc2,
 double[][] Sc3,
 double[][] Sc22,
 double[][] Sc23,
 double[][] Sc33,
 double[] fftSupportPatch,
 double[] fftSupportPatchImag,
 int patchSize,
 double[] fftImagePatch,
 double[] fftImagePatchImag,
 double[][] fd1,
 double[][] fd1Imag,
 double[][] fd2,
 double[][] fd2Imag,
 double[][] fd3,
 double[][] fd3Imag,
 double[][] fd22,
 double[][] fd22Imag,
 double[][] fd23,
 double[][] fd23Imag,
 double[][] fd33,
 double[][] fd33Imag,
 int findNorm)

fftshift

private void fftshift(double[][] mtx)

ifftshift

private void ifftshift(double[][] mtx)

T2z1a_make_image_structure

private void T2z1a_make_image_structure(double[] fftImagePatch,
 double[] fftImagePatchImag,
 double[] fftSupportPatch,
 double[] fftSupportPatchImag,
 double[][] input,
 int patchSize)

T1_responses

private void T1_responses(double[][] omegas,
 double[][] amplitudes,
 double[] filterAngle,
 double[] sigmaX,
 double[][][] td1,
 double[][][] td2,
 double[][][] td3,
 double[][][] td22,
 double[][][] td23,
 double[][][] td33,
 double[][][] fd1,
 double[][][] fd1Imag,
 double[][][] fd2,
 double[][][] fd2Imag,
 double[][][] fd3,
 double[][][] fd3Imag,
 double[][][] fd22,
 double[][][] fd22Imag,
 double[][][] fd23,
 double[][][] fd23Imag,
 double[][][] fd33,
 double[][][] fd33Imag,
 double[] sigmas,
 int[] ps,
 int nscales,
 int ndirs,
 double sig2omega,
 double radianStart,
 double radianEnd,
 int inputXDim,
 int inputYDim,
 String filterType,
 String[] domain)

T1z2_get_filter_struct

private void T1z2_get_filter_struct(double[][][] td1,
 double[][][] td2,
 double[][][] td3,
 double[][][] td22,
 double[][][] td23,
 double[][][] td33,
 double[][][] fd1,
 double[][][] fd1Imag,
 double[][][] fd2,
 double[][][] fd2Imag,
 double[][][] fd3,
 double[][][] fd3Imag,
 double[][][] fd22,
 double[][][] fd22Imag,
 double[][][] fd23,
 double[][][] fd23Imag,
 double[][][] fd33,
 double[][][] fd33Imag,
 double[] omegas,
 double[] amplitudes,
 double filterAngle,
 double sigmaX,
 String domain,
 double[][] xfreq,
 double[][] yfreq,
 int index)

Tzz_freq_resp

private void Tzz_freq_resp(double[][] hout,
 double[][] omegax,
 double[][] omegay,
 double sigmaX,
 double filterAngle,
 double[] omegas,
 double[] amplitudes)

testfreqz2

private void testfreqz2()

freqz2

private void freqz2(double[][] hout,
 double[][] houtImag,
 double[][] a,
 int n1,
 int n2)

rot180

private void rot180(double[][] mtx)

T1z2b_time_resp

private double[][] T1z2b_time_resp(double[] omegas,
 double[] amplitudes,
 double[] amplitudesImag,
 double filterAngle,
 double sigmaX)

T1z2a_convert_filter

private void T1z2a_convert_filter(double[] omegasOut,
 double[] amplitudesOut,
 double[] amplitudesOutImag,
 double[] omegas,
 double[] amplitudes,
 double filterAngle,
 double sigmaX,
 int conj)

filterbank_DCA_2D

private void filterbank_DCA_2D(double[][] omegas,
 double[][] amplitudes,
 double[] filterAngle,
 double[] sigmaX,
 int nscales,
 String filterType,
 int ndirs,
 double sig2omega,
 double radianStart,
 double radianEnd)