org.openscience.nmrshiftdb.util
Class PeakPicker

java.lang.Object
  org.openscience.nmrshiftdb.util.PeakPicker

public class PeakPicker
extends java.lang.Object

Author:

Tobias Helmus

Field Summary

static java.lang.String	GAUSSIAN
static java.lang.String	GAUSSIAN_FIRST_DERIVATIVE
static java.lang.String	GAUSSIAN_SECOND_DERIVATIVE
(package private) double	lowerPeakLimit
private java.lang.String	xAxisLabel
private double[]	xValArray
private java.lang.String	yAxisLabel
private double[]	yValArray

Constructor Summary

PeakPicker(org.xmlcml.cml.element.CMLSpectrumData dataList)

Method Summary

double	absSumAllElements(double[] array) sum of all absolute element values.
double[]	applyFilter(double[] filter, double[] yvals) apply filter.
static double[]	getFilter(int halfWidth, java.lang.String function) creates a filter based on Gaussian and derivatives.
org.xmlcml.cml.element.CMLPeakList	getPeakArray()
org.xmlcml.cml.element.CMLPeakList	makeBars(double[] arr, int windo)
double[]	multiplyBy(double f, double[] peakTemp) array multiplication by a scalar.
(package private) double[]	trimSpectrumBelow(double[] arr, double limit)

Methods inherited from class java.lang.Object

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

Field Detail

lowerPeakLimit

double lowerPeakLimit

xValArray

private double[] xValArray

yValArray

private double[] yValArray

xAxisLabel

private java.lang.String xAxisLabel

yAxisLabel

private java.lang.String yAxisLabel

GAUSSIAN

public static final java.lang.String GAUSSIAN

See Also:

Constant Field Values

GAUSSIAN_FIRST_DERIVATIVE

public static final java.lang.String GAUSSIAN_FIRST_DERIVATIVE

See Also:

Constant Field Values

GAUSSIAN_SECOND_DERIVATIVE

public static final java.lang.String GAUSSIAN_SECOND_DERIVATIVE

See Also:

Constant Field Values

Constructor Detail

PeakPicker

public PeakPicker(org.xmlcml.cml.element.CMLSpectrumData dataList)

Method Detail

getPeakArray

public org.xmlcml.cml.element.CMLPeakList getPeakArray()

applyFilter

public double[] applyFilter(double[] filter,
                            double[] yvals)

apply filter. convolute array with another array. This is 1-D image processing. If filter has <= 1 element, return this unchanged. filter should have an odd number of elements. The filter can be created with a IntArray constructor filter is moved along stepwise

Parameters:

filter - to apply normally smaller than this

yvals -

Returns:

filtered array

getFilter

public static double[] getFilter(int halfWidth,
                                 java.lang.String function)

creates a filter based on Gaussian and derivatives. Scaled so that approximately 2.5 sigma is included (that is value at edge is ca 0.01 of centre

Parameters:

halfWidth -

function -

makeBars

public org.xmlcml.cml.element.CMLPeakList makeBars(double[] arr,
                                                   int windo)

absSumAllElements

public double absSumAllElements(double[] array)

sum of all absolute element values.

Parameters:

filter -

Returns:

sigma(abs(this(i)))

trimSpectrumBelow

double[] trimSpectrumBelow(double[] arr,
                           double limit)

multiplyBy

public double[] multiplyBy(double f,
                           double[] peakTemp)

array multiplication by a scalar. creates new array; does NOT modify 'this'

Parameters:

f - multiplier

peakTemp -

Returns:

the new array