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

All Implemented Interfaces:

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

Field Summary

Fields
Modifier and Type Field Description

private double MAX_DELTA

private 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

All Methods Instance Methods Concrete Methods
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, java.lang.String paddtype)`
`double[]`	`_padd_assymetric(double[] arrays, int[] p, double c, java.lang.String paddtype)`
`double[][]`	`_padd_symetric(double[][] arrays, int p, double c, java.lang.String paddtype)`
`double[]`	`_padd_symetric(double[] arrays, int p, double c, java.lang.String paddtype)`
`void`	`_test_conv_adj_fourier_hrf(double[] ai_s, double[] hrf, java.lang.String testname)`
`void`	`_test_conv_adj_toeplitz_kernel_hrf(double[] ai_s, double[] hrf, java.lang.String testname)`
`void`	`_test_conv_adj_toeplitz_kernel_signal(double[] ai_s, double[] hrf, java.lang.String testname)`
`void`	`_test_conv_fourier_kernel_hrf(double[] ai_s, double[] hrf, java.lang.String testname)`
`void`	`_test_conv_toeplitz_kernel_hrf(double[] ai_s, double[] hrf, java.lang.String testname)`
`void`	`_test_conv_toeplitz_kernel_signal(double[] ai_s, double[] hrf, java.lang.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, java.lang.String testnum)`
`double[][]`	`_unpadd_assymetric(double[][] arrays, int[] p, java.lang.String paddtype)`
`double[]`	`_unpadd_assymetric(double[] arrays, int[] p, java.lang.String paddtype)`
`double[][]`	`_unpadd_symetric(double[][] arrays, int p, java.lang.String paddtype)`
`double[]`	`_unpadd_symetric(double[] arrays, int p, java.lang.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(java.util.Vector<java.lang.Double> xout, java.util.Vector<java.lang.Double> zout, java.util.Vector<java.lang.Double> diff_zout, java.util.Vector<java.lang.Double> hout, java.util.Vector<java.lang.Double> dr, java.util.Vector<java.lang.Double> dg, java.util.Vector<java.lang.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, java.util.Vector<java.lang.Double> J, java.util.Vector<java.lang.Double> R, java.util.Vector<java.lang.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, java.util.Vector<java.lang.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(java.util.Vector<java.lang.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)`
`java.util.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, 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
- 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 Detail
- fMRIBlindDeconvolution
```
public fMRIBlindDeconvolution()
```

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

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,
                               java.lang.String paddtype)

_padd_symetric

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

_padd_assymetric

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

_padd_assymetric

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

_unpadd_symetric

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

_unpadd_symetric

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

_unpadd_assymetric

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

_unpadd_assymetric

public double[][] _unpadd_assymetric(double[][] arrays,
                                     int[] p,
                                     java.lang.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 java.util.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,
                       java.lang.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,
                                           java.lang.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,
                                          java.lang.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,
                                               java.lang.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,
                                       java.lang.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,
                                              java.lang.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,
                                                  java.lang.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,
                   java.util.Vector<java.lang.Double> J,
                   java.util.Vector<java.lang.Double> R,
                   java.util.Vector<java.lang.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,
                      java.util.Vector<java.lang.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(java.util.Vector<java.lang.Double> xout,
               java.util.Vector<java.lang.Double> zout,
               java.util.Vector<java.lang.Double> diff_zout,
               java.util.Vector<java.lang.Double> hout,
               java.util.Vector<java.lang.Double> dr,
               java.util.Vector<java.lang.Double> dg,
               java.util.Vector<java.lang.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(java.util.Vector<java.lang.Double> x)

data_generation_example
```
public void data_generation_example()
```

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

Class fMRIBlindDeconvolution

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

MIN_DELTA

MAX_DELTA

Constructor Detail

fMRIBlindDeconvolution

Method Detail

runAlgorithm

spm_hrf

test_power_2_padding_length

test_zero_padd_unpadd

test_zero_mirror_zero_padd_unpadd

_padd_symetric

_padd_symetric

_padd_assymetric

_padd_assymetric

_unpadd_symetric

_unpadd_symetric

_unpadd_assymetric

_unpadd_assymetric

log2

_custom_padd

custom_padd

rfft

irfft

spectral_convolve

spectral_retro_convolve

zabs

zdiv

spectral_deconvolve

spectral_retro_deconvolve

toeplitz_from_kernel

simple_convolve

simple_retro_convolve

median

mad

mad_daub_noise_est

fwhm

tp

random_generator

spectral_radius_est

test_inf_norm

__inf_norm

_inf_norm

_inf_norm

__inf_norm

norm

add_gaussian_noise

gen_rnd_ai_s

gen_rnd_bloc_bold

_yield_data

_test_data

test_data_gen

gen_regular_ai_s

gen_regular_bloc_bold

gen_rnd_i_s

gen_rnd_event_bold

yield_diracs_signal

yield_blocks_signal

_test_conv_toeplitz_kernel_hrf

test_toeplitz_convolution_kernel_hrf_on_dirac

test_toeplitz_convolution_kernel_hrf_on_ai_s

_test_conv_fourier_kernel_hrf

test_fourier_convolution_kernel_hrf_on_dirac

test_fourier_convolution_kernel_hrf_on_ai_s

_test_conv_adj_toeplitz_kernel_hrf

test_toeplitz_adj_convolution_kernel_hrf_on_dirac

test_toeplitz_adj_convolution_kernel_hrf_on_ai_s

_test_conv_adj_fourier_hrf

test_fourier_adj_convolution_kernel_hrf_on_dirac