PeakDetect — Peak detection of peaks and valleys.

This module defines a peak detection utility that looks for local maxima and minima. It is based on code by Marcos Duarte, https://github.com/demotu/BMC.

class admit.util.peakfinder.PeakDetect.PeakDetect(spec, x=None, **kwarg)

Detect peaks in data based on their amplitude and other features.

Parameters:

spec : 1D array_like

The input spectra to search for peaks.

x : 1D array_like

The x co-ordinates for the spectrum (optional). Default: None.

kwarg : Dict

Any additional arguments, see the Attributes list for a complete listing.

Examples

from admit.util.peakfinder.PeakDetect import PeakDetect
import numpy as np
x = np.random.randn(100)
x[60:81] = np.nan
# detect all peaks
pd = PeakDetect(x)
ind = pd.find()
print(ind)

x = np.sin(2*np.pi*5*np.linspace(0, 1, 200)) + np.random.randn(200)/5
# set minimum peak height = 0 and minimum peak distance = 20
pd = PeakDetect(x, min_sep=20, thresh=0)
ind = pd.find()

x = [0, 1, 0, 2, 0, 3, 0, 2, 0, 1, 0]
# set minimum peak distance = 2
pd = PeakDetect(x, min_sep=2)
ind = pd.find()

x = [0, 1, 1, 0, 1, 1, 0]
# detect both edges
pd = PeakDetect(x, edge='both')
ind = pd.find()

Attributes

spec	(1D array_like) The input spectra to search for peaks.
x	(1D array_like) The x co-ordinates for the spectrum (optional) Default: None.
thresh	(float) Detect peaks that are greater than minimum peak height. Default: 0.0.
min_sep	(int) Detect peaks that are at least separated by minimum peak distance, in number of channels. Default : 5.
edge	(str) One of ‘rising’, ‘falling’, or ‘both’, optional. For a flat peak, keep only the rising edge (‘rising’), only the falling edge (‘falling’), both edges (‘both’). Default : ‘rising’.
kpsh	(bool) Keep peaks with same height even if they are closer than min_sep, optional. Default: False.

Methods

detect_peaks(spec[, valley])	Detects peaks.
find()	Method to locate peaks in an input spectrum

detect_peaks(spec, valley=False)

Detects peaks.

Parameters:

spec : 1D array

The specrum to analyze.

valley : bool

Whether to search for peaks (positive) or valleys (negative). Default: False

Returns:

1D array_like

indeces of the peaks in spec.

Notes

The detection of valleys instead of peaks is performed internally by simply negating the data: ind_valleys = detect_peaks(-x)

The function can handle NaN’s

See this IPython Notebook [R5].

References

[R5]	(1, 2) http://nbviewer.ipython.org/github/demotu/BMC/blob/master/notebooks/DetectPeaks.ipynb

edge = 'rising'

find()

Method to locate peaks in an input spectrum

Parameters:None Returns:Numpy array containing the located peaks

kpsh = False

min_sep = 5

thresh = 0.0