io.github.msdk.featuredetection.adap3d.algorithms

Class SignalToNoise

java.lang.Object

io.github.msdk.featuredetection.adap3d.algorithms.SignalToNoise

public class SignalToNoise
extends Object

SignalToNoise class.

Author:

owenmyers Modified by Dharak Shah to include in MSDK

Constructor Summary

Constructors

Constructor and Description
SignalToNoise()

Method Summary

Modifier and Type	Method and Description
static double	filterBySNRandWindowSelect(double[] intensities, int peakLeft, int peakRight) filterBySNRandWindowSelect.
static double	filterBySNStaticWindowSweep(double[] intensities, int peakLeft, int peakRight) filterBySNStaticWindowSweep.
static double	filterBySNWindowInOutSweep(double[] intensities, int peakLeft, int peakRight) filterBySNWindowInOutSweep.
static double	filterBySNWindowSweep(double[] intensities, int peakLeft, int peakRight) filterBySNWindowSweep.
static double	findSNUsingWaveletCoefficents(double[][] allCoefficients, double bestCoeff, int peakLeft, int peakRight, double windowSizeMult, boolean absWaveCoeffs) findSNUsingWaveletCoefficents.
static double	getQuantile(List<Double> values, double probability) Estimate quantile of the list of values Estimation is equivalent to the default quantile estimate in R: if x[j] and x[j+1] are two values adjacent to the quantile, than Q[p] = (gamma - 1) * x[j] + gamma * x[j+1] where gamma = (size - 1) * p + 1 - j and j starts from 1

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SignalToNoise

public SignalToNoise()

Method Detail

findSNUsingWaveletCoefficents

public static double findSNUsingWaveletCoefficents(double[][] allCoefficients,
                                                   double bestCoeff,
                                                   int peakLeft,
                                                   int peakRight,
                                                   double windowSizeMult,
                                                   boolean absWaveCoeffs)

findSNUsingWaveletCoefficents.

Parameters:

allCoefficients - an array of double.

bestCoeff - a double.

peakLeft - a int.

peakRight - a int.

windowSizeMult - a double.

absWaveCoeffs - a boolean.

Returns:

a double.

getQuantile

public static double getQuantile(List<Double> values,
                                 double probability)

Estimate quantile of the list of values Estimation is equivalent to the default quantile estimate in R: if x[j] and x[j+1] are two values adjacent to the quantile, than Q[p] = (gamma - 1) * x[j] + gamma * x[j+1] where gamma = (size - 1) * p + 1 - j and j starts from 1

Parameters:

values - list of doubles

probability - value between 0.0 and 1.0

Returns:

quantile

filterBySNRandWindowSelect

public static double filterBySNRandWindowSelect(double[] intensities,
                                                int peakLeft,
                                                int peakRight)

filterBySNRandWindowSelect.

Parameters:

intensities - an array of double.

peakLeft - a int.

peakRight - a int.

Returns:

a double.

filterBySNWindowSweep

public static double filterBySNWindowSweep(double[] intensities,
                                           int peakLeft,
                                           int peakRight)

filterBySNWindowSweep.

Parameters:

intensities - an array of double.

peakLeft - a int.

peakRight - a int.

Returns:

a double.

filterBySNWindowInOutSweep

public static double filterBySNWindowInOutSweep(double[] intensities,
                                                int peakLeft,
                                                int peakRight)

filterBySNWindowInOutSweep.

Parameters:

intensities - an array of double.

peakLeft - a int.

peakRight - a int.

Returns:

a double.

filterBySNStaticWindowSweep

public static double filterBySNStaticWindowSweep(double[] intensities,
                                                 int peakLeft,
                                                 int peakRight)

filterBySNStaticWindowSweep.

Parameters:

intensities - an array of double.

peakLeft - a int.

peakRight - a int.

Returns:

a double.