FindPeaks.accessory.classes

Class FindPeaksTools

java.lang.Object

FindPeaks.accessory.classes.FindPeaksTools

public class FindPeaksTools
extends java.lang.Object

Generic methods for peak detection in a one-dimensional array of values Based on the Octave findPeak method (https://searchcode.com/codesearch/view/64213481/) Also, invokes methods from the ArraySortTools class, which is based on snippets from https://stackoverflow.com/questions/4859261/get-the-indices-of-an-array-after-sorting See license at the beginning of this file

Author:

thomasbraschler

Constructor Summary

Constructors

Constructor and Description
FindPeaksTools()

Method Summary

Modifier and Type	Method and Description
static int[]	filterPeaks(int[] idx, double[] vals, double minD, double minW, double maxW, double minH, double fitMin) This is the second part of the Java implementation of the Octave findPeaks function (see https://searchcode.com/codesearch/view/64213481/) We estimate widths of peaks remove peaks that have quality issues: width smaller than given minal width or larger than maximal width.
static int[]	findPeaks(double[] vals, double threshold, double minD, boolean doFiltering, double minW, double maxW, double minH) Main function to identify peaks an array of double values.
static int[]	identifyPeaksAtMinimalDistance(double[] vals, double threshold, double minD) This function identifies peaks above a threshold, and with a minimal distance between them.

Methods inherited from class java.lang.Object

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

Constructor Detail

FindPeaksTools

public FindPeaksTools()

Method Detail

findPeaks

public static int[] findPeaks(double[] vals,
                              double threshold,
                              double minD,
                              boolean doFiltering,
                              double minW,
                              double maxW,
                              double minH)

Main function to identify peaks an array of double values. Parameters as defined for the corresponding findPeaks function in Octave (https://searchcode.com/codesearch/view/64213481/) However, currently, double-sided peak evaluation is not implemented, if you wish to so, follow the instructions for the Octave function (i.e. subtract the mean and take the absolute value before passing the array to this function, https://searchcode.com/codesearch/view/64213481/)

Parameters:

vals - Array of values in which we search for peaks

threshold - Threshold above which the values need to lie to be considered peak candidates

minD - Minimal distance between peaks (unit spacing between individual values is assumed)

doFiltering - Should we do filtering for width and height or just accept the peaks found in the primary search?

minW - Minimal width (if filtering)

maxW - Maximal width (if filtering)

minH - Minimal height (above threshold for fitted parabola, effective only when filtering)

Returns:

Ordered array of indices of the peaks

identifyPeaksAtMinimalDistance

public static int[] identifyPeaksAtMinimalDistance(double[] vals,
                                                   double threshold,
                                                   double minD)

This function identifies peaks above a threshold, and with a minimal distance between them. The function is a bit rough and therefore needs some cleanup afterwards, but it gives suitable primary candidates. This is the first part of the findPeak implementation in Octave (https://searchcode.com/codesearch/view/64213481/)

Parameters:

vals - Values of the function for which peaks should be found. Unit spacing between sequential values is assumed

threshold - Threshold above which a value need to lie to be considered as a candidate for being peak

minD - Minimal distance between neighboring peaks

Returns:

Array of indices indicating the peaks

filterPeaks

public static int[] filterPeaks(int[] idx,
                                double[] vals,
                                double minD,
                                double minW,
                                double maxW,
                                double minH,
                                double fitMin)

This is the second part of the Java implementation of the Octave findPeaks function (see https://searchcode.com/codesearch/view/64213481/) We estimate widths of peaks remove peaks that have quality issues: width smaller than given minal width or larger than maximal width. wrong concavity. not high enough data at peak is lower than parabola by 1% position of extrema minus center is bigger equal than minD/2

Parameters:

idx - the pre-filtered peak candidates,typicaly obtained from the method identifyPeaksAtMinimalDistance

vals - Underlying values (complete dataset)

minD - distance required between the peaks (minD)

minW - Minimal fitting width

maxW - Maximal fitting width

minH - Minimal fitting height

fitMin - Minimal environment around peak for parabola fitting

Returns:

Indices point to peaks passing quality criteria