Package gov.nih.mipav.model.algorithms

Class fMRIBlindDeconvolution

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.fMRIBlindDeconvolution

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class fMRIBlindDeconvolution
extends AlgorithmBase

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	fMRIBlindDeconvolution.ConvAndLinear
(package private) class	fMRIBlindDeconvolution.DiscretInteg
(package private) class	fMRIBlindDeconvolution.Tracker

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

Thread.Builder, Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
private final double	MAX_DELTA
private final double	MIN_DELTA	Reference: Hamza Cherkaoui, Thomas Moreau, Abderrahim Halimi, Philippe Ciuciu.

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
fMRIBlindDeconvolution()

Method Summary

Modifier and Type	Method	Description
double[]	__inf_norm(double[] x)
double[][][]	__inf_norm(double[][][] x)
double[]	_custom_padd(int[] p_total, double[] a, int min_power_of_2, int min_zero_padd, double zero_padd_ratio)
double[][]	_inf_norm(double[][][] arr, int axis)
double[][]	_inf_norm(double[][] arr, int axis)
double[]	_loops_deconv(double[] y, double[] diff_z, double[][] H, double lbda, long nb_iter, boolean early_stopping, long wind, double tol)
double[][]	_padd_assymetric(double[][] arrays, int[] p, double c, String paddtype)
double[]	_padd_assymetric(double[] arrays, int[] p, double c, String paddtype)
double[][]	_padd_symetric(double[][] arrays, int p, double c, String paddtype)
double[]	_padd_symetric(double[] arrays, int p, double c, String paddtype)
void	_test_conv_adj_fourier_hrf(double[] ai_s, double[] hrf, String testname)
void	_test_conv_adj_toeplitz_kernel_hrf(double[] ai_s, double[] hrf, String testname)
void	_test_conv_adj_toeplitz_kernel_signal(double[] ai_s, double[] hrf, String testname)
void	_test_conv_fourier_kernel_hrf(double[] ai_s, double[] hrf, String testname)
void	_test_conv_toeplitz_kernel_hrf(double[] ai_s, double[] hrf, String testname)
void	_test_conv_toeplitz_kernel_signal(double[] ai_s, double[] hrf, String testname)
void	_test_data(double[] noisy_ar_s, double[] ar_s, double[] ai_s, double[] i_s, double[] hrf, double[] noise, double snr, int nb_events, String testnum)
double[][]	_unpadd_assymetric(double[][] arrays, int[] p, String paddtype)
double[]	_unpadd_assymetric(double[] arrays, int[] p, String paddtype)
double[][]	_unpadd_symetric(double[][] arrays, int p, String paddtype)
double[]	_unpadd_symetric(double[] arrays, int p, String paddtype)
void	_yield_data(double[][] noisy_ar_s, double[][] ar_s, double[][] ai_s, double[][] i_s, double[][] hrf, double[][] noise, double[] snr, int[] nb_events)
void	add_gaussian_noise(double[] noisy_signal, double[] noise, double[] signal, double snr, boolean haveSeed, long random_state)
void	bd(Vector<Double> xout, Vector<Double> zout, Vector<Double> diff_zout, Vector<Double> hout, Vector<Double> dr, Vector<Double> dg, Vector<Double> dJ, double[] y, double t_r, double lbda, double theta, double[] z_0, double hrf_dur, double[] bounds, int nb_iter, int nb_sub_iter, int nb_last_iter, int print_period, boolean early_stopping, int wind, double tol, int verbose)
void	blind_deconvolution_example()
double[][]	custom_padd(int[] padd, double[][] arrays, int min_power_of_2, int min_zero_padd, double zero_padd_ratio)
void	data_generation_example()
void	deconv(double[] x, double[] z, double[] diff_z, Vector<Double> J, Vector<Double> R, Vector<Double> G, double[] y, double t_r, double[] hrf, double lbda, boolean early_stopping, double tol, int wind, int nb_iter, int nb_sub_iter, int verbose)
void	deconv_example()
double	fwhm(double[] t_hrf, double[] hrf, int k)
void	gen_regular_ai_s(double[] ai_s, double[] i_s, double[] t, int dur, double tr, double dur_bloc, boolean centered)
void	gen_regular_bloc_bold(double[] noisy_ar_s, double[] ar_s, double[] ai_s, double[] i_s, double[] t, double[] noise, int dur, double tr, double dur_bloc, boolean sourcehrf, double[] hrf, double snr, boolean haveSeed, long random_state)
void	gen_rnd_ai_s(double[] ai_s, double[] i_s, double[] t, double dur, double tr, int nb_events, int avg_dur, double std_dur, boolean middle_spike, boolean overlapping, boolean unitary_block, boolean haveSeed, long random_state, int nb_try, int nb_try_duration, boolean centered)
void	gen_rnd_bloc_bold(double[] noisy_ar_s, double[] ar_s, double[] ai_s, double[] i_s, double[] t, double[] noise, double dur, double tr, boolean sourcehrf, double[] hrf, int nb_events, int avg_dur, double std_dur, boolean middle_spike, boolean overlapping, boolean unitary_block, double snr, int nb_try, int nb_try_duration, boolean centered, boolean haveSeed, long random_state)
void	gen_rnd_event_bold(double[] noisy_ar_s, double[] ar_s, double[] i_s, double[] t, double[] noise, int dur, double tr, boolean sourcehrf, double[] hrf, int nb_events, double avg_ampl, double std_ampl, double snr, boolean haveSeed, long random_state)
void	gen_rnd_i_s(double[] i_s, double[] t, int dur, double tr, int nb_events, double avg_ampl, double std_ampl, boolean haveSeed, long random_state, int nb_try, int nb_try_duration, boolean centered)
void	hrf_estim(double[] h, Vector<Double> J, double[] z, double[] y, double t_r, double dur, int verbose)
double	hrf_fit_err(double theta, double[] z, double[] y, double t_r, double hrf_dur)
private double	inf_norm(double[] x)
private double	inf_norm(Vector<Double> x)
double[]	irfft(double[][] x, boolean isOdd)
double	log2(double x)
double	mad(double[] x, double c)
double	mad_daub_noise_est(double[] x, double c)
double	median(double[] x)
double	norm(double[] x)
Random	random_generator(long random_state)
double[][]	rfft(double[] x)
void	runAlgorithm()	Actually runs the algorithm.
double	sign(double x)
double[]	simple_convolve(double[] k, double[] x, int dim_out)
void	simple_hrf_estimation()
double[]	simple_retro_convolve(double[] k, double[] x, int dim_out)
double[]	spectral_convolve(double[] k, double[] xin)
double[]	spectral_deconvolve(double[] k, double[] x)
double	spectral_radius_est(fMRIBlindDeconvolution.ConvAndLinear L, int x_shape, int nb_iter, double tol, boolean verbose)
double[]	spectral_retro_convolve(double[] k, double[] xin)
double[]	spectral_retro_deconvolve(double[] k, double[] x)
void	spm_hrf(double[] hrf, double[] t_hrf, double delta, double t_r, double dur, boolean normalized_hrf, double dt, double p_delay, double undershoot, double p_disp, double u_disp, double p_u_ratio, double onset)
double	std(double[] x)
void	test_data_gen()
void	test_fourier_adj_convolution_kernel_hrf_on_ai_s()
void	test_fourier_adj_convolution_kernel_hrf_on_dirac()
void	test_fourier_convolution_kernel_hrf_on_ai_s()
void	test_fourier_convolution_kernel_hrf_on_dirac()
void	test_inf_norm()
void	test_integ_adj()
void	test_integ_op()
void	test_power_2_padding_length()
void	test_toeplitz_adj_convolution_kernel_hrf_on_ai_s()
void	test_toeplitz_adj_convolution_kernel_hrf_on_dirac()
void	test_toeplitz_adj_convolution_kernel_signal_on_ai_s()
void	test_toeplitz_adj_convolution_kernel_signal_on_dirac()
void	test_toeplitz_convolution_kernel_hrf_on_ai_s()
void	test_toeplitz_convolution_kernel_hrf_on_dirac()
void	test_toeplitz_convolution_kernel_signal_on_ai_s()
void	test_toeplitz_convolution_kernel_signal_on_dirac()
void	test_zero_mirror_zero_padd_unpadd()
void	test_zero_padd_unpadd()
double[][]	toeplitz_from_kernel(double[] k, int dim_in, int dim_out)
double	tp(double[] t_hrf, double[] hrf)
void	yield_blocks_signal(double[][] ai_s, double[][] hrf, double[][] alpha, double[] tr)
void	yield_diracs_signal(double[][] i_s, double[][] hrf, double[][] alpha, double[] tr)
private double	zabs(double zr, double zi)	zabs computes the absolute value or magnitude of a double precision complex variable zr + j*zi.
private void	zdiv(double ar, double ai, double br, double bi, double[] cr, double[] ci)	complex divide c = a/b.

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

MIN_DELTA

private final double MIN_DELTA

Reference: Hamza Cherkaoui, Thomas Moreau, Abderrahim Halimi, Philippe Ciuciu. Sparsity-based blind deconvolution of neural activation signal in fMRI. IEEE-ICASSP 2019 - International Conference on Acoustics, Speech and Signal Processing, May 2019, Brighton, United Kingdom. ffhal-02085810v2

See Also:

• Constant Field Values

MAX_DELTA

private final double MAX_DELTA

See Also:

• Constant Field Values

Constructor Details

fMRIBlindDeconvolution

public fMRIBlindDeconvolution()

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

spm_hrf

public void spm_hrf(double[] hrf,
 double[] t_hrf,
 double delta,
 double t_r,
 double dur,
 boolean normalized_hrf,
 double dt,
 double p_delay,
 double undershoot,
 double p_disp,
 double u_disp,
 double p_u_ratio,
 double onset)

test_power_2_padding_length

public void test_power_2_padding_length()

test_zero_padd_unpadd

public void test_zero_padd_unpadd()

test_zero_mirror_zero_padd_unpadd

public void test_zero_mirror_zero_padd_unpadd()

_padd_symetric

public double[] _padd_symetric(double[] arrays,
 int p,
 double c,
 String paddtype)

_padd_symetric

public double[][] _padd_symetric(double[][] arrays,
 int p,
 double c,
 String paddtype)

_padd_assymetric

public double[] _padd_assymetric(double[] arrays,
 int[] p,
 double c,
 String paddtype)

_padd_assymetric

public double[][] _padd_assymetric(double[][] arrays,
 int[] p,
 double c,
 String paddtype)

_unpadd_symetric

public double[] _unpadd_symetric(double[] arrays,
 int p,
 String paddtype)

_unpadd_symetric

public double[][] _unpadd_symetric(double[][] arrays,
 int p,
 String paddtype)

_unpadd_assymetric

public double[] _unpadd_assymetric(double[] arrays,
 int[] p,
 String paddtype)

_unpadd_assymetric

public double[][] _unpadd_assymetric(double[][] arrays,
 int[] p,
 String paddtype)

log2

public double log2(double x)

_custom_padd

public double[] _custom_padd(int[] p_total,
 double[] a,
 int min_power_of_2,
 int min_zero_padd,
 double zero_padd_ratio)

custom_padd

public double[][] custom_padd(int[] padd,
 double[][] arrays,
 int min_power_of_2,
 int min_zero_padd,
 double zero_padd_ratio)

rfft

public double[][] rfft(double[] x)

irfft

public double[] irfft(double[][] x,
 boolean isOdd)

spectral_convolve

public double[] spectral_convolve(double[] k,
 double[] xin)

spectral_retro_convolve

public double[] spectral_retro_convolve(double[] k,
 double[] xin)

zabs

private double zabs(double zr,
 double zi)

zabs computes the absolute value or magnitude of a double precision complex variable zr + j*zi.

Parameters:

zr - double

zi - double

Returns:

double

zdiv

private void zdiv(double ar,
 double ai,
 double br,
 double bi,
 double[] cr,
 double[] ci)

complex divide c = a/b.

Parameters:

ar - double

ai - double

br - double

bi - double

cr - double[]

ci - double[]

spectral_deconvolve

public double[] spectral_deconvolve(double[] k,
 double[] x)

spectral_retro_deconvolve

public double[] spectral_retro_deconvolve(double[] k,
 double[] x)

toeplitz_from_kernel

public double[][] toeplitz_from_kernel(double[] k,
 int dim_in,
 int dim_out)

simple_convolve

public double[] simple_convolve(double[] k,
 double[] x,
 int dim_out)

simple_retro_convolve

public double[] simple_retro_convolve(double[] k,
 double[] x,
 int dim_out)

median

public double median(double[] x)

mad

public double mad(double[] x,
 double c)

mad_daub_noise_est

public double mad_daub_noise_est(double[] x,
 double c)

fwhm

public double fwhm(double[] t_hrf,
 double[] hrf,
 int k)

tp

public double tp(double[] t_hrf,
 double[] hrf)

random_generator

public Random random_generator(long random_state)

spectral_radius_est

public double spectral_radius_est(fMRIBlindDeconvolution.ConvAndLinear L,
 int x_shape,
 int nb_iter,
 double tol,
 boolean verbose)

test_inf_norm

public void test_inf_norm()

__inf_norm

public double[] __inf_norm(double[] x)

_inf_norm

public double[][] _inf_norm(double[][] arr,
 int axis)

_inf_norm

public double[][] _inf_norm(double[][][] arr,
 int axis)

__inf_norm

public double[][][] __inf_norm(double[][][] x)

norm

public double norm(double[] x)

add_gaussian_noise

public void add_gaussian_noise(double[] noisy_signal,
 double[] noise,
 double[] signal,
 double snr,
 boolean haveSeed,
 long random_state)

gen_rnd_ai_s

public void gen_rnd_ai_s(double[] ai_s,
 double[] i_s,
 double[] t,
 double dur,
 double tr,
 int nb_events,
 int avg_dur,
 double std_dur,
 boolean middle_spike,
 boolean overlapping,
 boolean unitary_block,
 boolean haveSeed,
 long random_state,
 int nb_try,
 int nb_try_duration,
 boolean centered)

gen_rnd_bloc_bold

public void gen_rnd_bloc_bold(double[] noisy_ar_s,
 double[] ar_s,
 double[] ai_s,
 double[] i_s,
 double[] t,
 double[] noise,
 double dur,
 double tr,
 boolean sourcehrf,
 double[] hrf,
 int nb_events,
 int avg_dur,
 double std_dur,
 boolean middle_spike,
 boolean overlapping,
 boolean unitary_block,
 double snr,
 int nb_try,
 int nb_try_duration,
 boolean centered,
 boolean haveSeed,
 long random_state)

_yield_data

public void _yield_data(double[][] noisy_ar_s,
 double[][] ar_s,
 double[][] ai_s,
 double[][] i_s,
 double[][] hrf,
 double[][] noise,
 double[] snr,
 int[] nb_events)

_test_data

public void _test_data(double[] noisy_ar_s,
 double[] ar_s,
 double[] ai_s,
 double[] i_s,
 double[] hrf,
 double[] noise,
 double snr,
 int nb_events,
 String testnum)

test_data_gen

public void test_data_gen()

gen_regular_ai_s

public void gen_regular_ai_s(double[] ai_s,
 double[] i_s,
 double[] t,
 int dur,
 double tr,
 double dur_bloc,
 boolean centered)

gen_regular_bloc_bold

public void gen_regular_bloc_bold(double[] noisy_ar_s,
 double[] ar_s,
 double[] ai_s,
 double[] i_s,
 double[] t,
 double[] noise,
 int dur,
 double tr,
 double dur_bloc,
 boolean sourcehrf,
 double[] hrf,
 double snr,
 boolean haveSeed,
 long random_state)

gen_rnd_i_s

public void gen_rnd_i_s(double[] i_s,
 double[] t,
 int dur,
 double tr,
 int nb_events,
 double avg_ampl,
 double std_ampl,
 boolean haveSeed,
 long random_state,
 int nb_try,
 int nb_try_duration,
 boolean centered)

gen_rnd_event_bold

public void gen_rnd_event_bold(double[] noisy_ar_s,
 double[] ar_s,
 double[] i_s,
 double[] t,
 double[] noise,
 int dur,
 double tr,
 boolean sourcehrf,
 double[] hrf,
 int nb_events,
 double avg_ampl,
 double std_ampl,
 double snr,
 boolean haveSeed,
 long random_state)

yield_diracs_signal

public void yield_diracs_signal(double[][] i_s,
 double[][] hrf,
 double[][] alpha,
 double[] tr)

yield_blocks_signal

public void yield_blocks_signal(double[][] ai_s,
 double[][] hrf,
 double[][] alpha,
 double[] tr)

_test_conv_toeplitz_kernel_hrf

public void _test_conv_toeplitz_kernel_hrf(double[] ai_s,
 double[] hrf,
 String testname)

test_toeplitz_convolution_kernel_hrf_on_dirac

public void test_toeplitz_convolution_kernel_hrf_on_dirac()

test_toeplitz_convolution_kernel_hrf_on_ai_s

public void test_toeplitz_convolution_kernel_hrf_on_ai_s()

_test_conv_fourier_kernel_hrf

public void _test_conv_fourier_kernel_hrf(double[] ai_s,
 double[] hrf,
 String testname)

test_fourier_convolution_kernel_hrf_on_dirac

public void test_fourier_convolution_kernel_hrf_on_dirac()

test_fourier_convolution_kernel_hrf_on_ai_s

public void test_fourier_convolution_kernel_hrf_on_ai_s()

_test_conv_adj_toeplitz_kernel_hrf

public void _test_conv_adj_toeplitz_kernel_hrf(double[] ai_s,
 double[] hrf,
 String testname)

test_toeplitz_adj_convolution_kernel_hrf_on_dirac

public void test_toeplitz_adj_convolution_kernel_hrf_on_dirac()

test_toeplitz_adj_convolution_kernel_hrf_on_ai_s

public void test_toeplitz_adj_convolution_kernel_hrf_on_ai_s()

_test_conv_adj_fourier_hrf

public void _test_conv_adj_fourier_hrf(double[] ai_s,
 double[] hrf,
 String testname)

test_fourier_adj_convolution_kernel_hrf_on_dirac

public void test_fourier_adj_convolution_kernel_hrf_on_dirac()

test_fourier_adj_convolution_kernel_hrf_on_ai_s

public void test_fourier_adj_convolution_kernel_hrf_on_ai_s()

_test_conv_toeplitz_kernel_signal

public void _test_conv_toeplitz_kernel_signal(double[] ai_s,
 double[] hrf,
 String testname)

test_toeplitz_convolution_kernel_signal_on_dirac

public void test_toeplitz_convolution_kernel_signal_on_dirac()

test_toeplitz_convolution_kernel_signal_on_ai_s

public void test_toeplitz_convolution_kernel_signal_on_ai_s()

_test_conv_adj_toeplitz_kernel_signal

public void _test_conv_adj_toeplitz_kernel_signal(double[] ai_s,
 double[] hrf,
 String testname)

test_toeplitz_adj_convolution_kernel_signal_on_dirac

public void test_toeplitz_adj_convolution_kernel_signal_on_dirac()

test_toeplitz_adj_convolution_kernel_signal_on_ai_s

public void test_toeplitz_adj_convolution_kernel_signal_on_ai_s()

test_integ_op

public void test_integ_op()

test_integ_adj

public void test_integ_adj()

sign

public double sign(double x)

deconv

public void deconv(double[] x,
 double[] z,
 double[] diff_z,
 Vector<Double> J,
 Vector<Double> R,
 Vector<Double> G,
 double[] y,
 double t_r,
 double[] hrf,
 double lbda,
 boolean early_stopping,
 double tol,
 int wind,
 int nb_iter,
 int nb_sub_iter,
 int verbose)

std

public double std(double[] x)

deconv_example

public void deconv_example()

hrf_fit_err

public double hrf_fit_err(double theta,
 double[] z,
 double[] y,
 double t_r,
 double hrf_dur)

hrf_estim

public void hrf_estim(double[] h,
 Vector<Double> J,
 double[] z,
 double[] y,
 double t_r,
 double dur,
 int verbose)

simple_hrf_estimation

public void simple_hrf_estimation()

_loops_deconv

public double[] _loops_deconv(double[] y,
 double[] diff_z,
 double[][] H,
 double lbda,
 long nb_iter,
 boolean early_stopping,
 long wind,
 double tol)

bd

public void bd(Vector<Double> xout,
 Vector<Double> zout,
 Vector<Double> diff_zout,
 Vector<Double> hout,
 Vector<Double> dr,
 Vector<Double> dg,
 Vector<Double> dJ,
 double[] y,
 double t_r,
 double lbda,
 double theta,
 double[] z_0,
 double hrf_dur,
 double[] bounds,
 int nb_iter,
 int nb_sub_iter,
 int nb_last_iter,
 int print_period,
 boolean early_stopping,
 int wind,
 double tol,
 int verbose)

blind_deconvolution_example

public void blind_deconvolution_example()

inf_norm

private double inf_norm(double[] x)

inf_norm

private double inf_norm(Vector<Double> x)

data_generation_example

public void data_generation_example()