PeakUtils — A peak finding algorithm.

A version of the PyPi PeakUtils, converted from Python3.4 to Python2.7.

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

PeakUtils peak finding algorithm

Parameters:

spec : List or numpy array

The spectrum to be analyzed.

x : List or numpy array, optional

The x co-ordinates for the spectrum. Default = None.

kwarg : Dict

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

Attributes

spec	(numpy array) The spectrum to be analyzed.
x	(numpy array) The x co-ordinates of the spectrum.
thres	(float) Threshold for detecting a peak/valley. The absolute value of the intensity must be above this value. Default: 0.0.
min_dist	(int) The minimum distance between peaks in channels. Deafult: 5.
profile	(str) The spectral line profile to use when refining the fits. Choices are “gaussian” and “lorentzian”. Default: “gaussian”.
width	(int) The number of channels on either side of a peak to use when refining the fit. Default: 10.
basedeg	(int) Degree of the polynomial that will estimate the data baseline. Default: 3.
baseiter	(int) The maximum number of iterations to perform when trying to fit the baseline. Default: 100.
basetol	(float) Tolerance to use when comparing the difference between the current fit coefficient and the ones from the last iteration. Default: 1e-3.
dobase	(boolean) Whether or not to do baseline/continuum subtraction. Default: False.

Methods

baseline([deg, max_it, tol])	Computes the baseline of a given data.
centroid([chans])	Computes the centroid for the specified data.
find()	Method to find any peaks in the spectrum.
gaussian(x, ampl, center, dev)	Computes the Gaussian function.
gaussian_fit([chans])	Performs a Gaussian fitting of the specified data.
indexes([thres, min_dist])	Peak detection routine.
interpolate([ind, width, func])	Tries to enhance the resolution of the peak detection by using Gaussian fitting, centroid computation or an arbitrary function on the neighborhood of each previously detected peak index.
laurentzian_fit([chans])	Performs a Lorentzian fitting of the specified data.
lorentzian(x, ampl, center, width)	Computes the Lorentzian function.
scale(x[, new_range, eps])	Changes the scale of an array

basedeg = 3

baseiter = 100

baseline(deg=3, max_it=100, tol=0.001)

Computes the baseline of a given data.

Iteratively performs a polynomial fitting in the data to detect its baseline. At every iteration, the fitting weights on the regions with peaks is reduced to identify the baseline only.

Parameters:

deg : int

Degree of the polynomial that will estimate the data baseline. A low degree may fail to detect all the baseline present, while a high degree may make the data too oscillatory, especially at the edges.

max_it : int

Maximum number of iterations to perform.

tol : float

Tolerance to use when comparing the difference between the current fit coefficient and the ones from the last iteration. The iteration procedure will stop when the difference between them is lower than tol.

Returns:

ndarray

Array with the baseline amplitude for every original point in y

basetol = 0.001

centroid(chans=[0, -1])

Computes the centroid for the specified data.

Parameters:

chans : list

The indexes to start and end at. Default: [0,-1]

Returns:

float

Centroid of the data.

dobase = False

find()

Method to find any peaks in the spectrum. A baseline will be subtracted first if requested.

Parameters:

None

Returns:

numpy array of floats

containing the locations of the peaks

gaussian(x, ampl, center, dev)

Computes the Gaussian function.

Parameters:

x : float

Point to evaluate the Gaussian for.

ampl : float

Amplitude.

center : float

Center.

dev : float

Width.

Returns:

float

Value of the specified Gaussian at x

gaussian_fit(chans=[0, -1])

Performs a Gaussian fitting of the specified data.

Parameters:

chans : list

The indexes to start and end at. Default: [0,-1]

Returns:

ndarray

Parameters of the Gaussian that fits the specified data

indexes(thres=0.0, min_dist=5)

Peak detection routine.

Finds the peaks in y by taking its first order difference. By using thres and min_dist parameters, it is possible to reduce the number of detected peaks.

Parameters:

thres : float

Threshold for detecting a peak/valley. The absolute value of the intensity must be above this value. Default: 0.0

min_dist : int

Minimum distance between each detected peak. The peak with the highest amplitude is preferred to satisfy this constraint.

Returns:

ndarray

Array containing the indexes of the peaks that were detected

interpolate(ind=None, width=10, func='gaussian_fit')

Tries to enhance the resolution of the peak detection by using Gaussian fitting, centroid computation or an arbitrary function on the neighborhood of each previously detected peak index.

Parameters:

ind : ndarray

Indexes of the previously detected peaks. If None, indexes() will be called with the default parameters.

width : int

Number of points (before and after) each peak index to pass to func in order to increase the resolution in x.

func : function(x,y)

Function that will be called to detect an unique peak in the x,y data.

Returns:

ndarray :

Array with the adjusted peak positions (in x)

laurentzian_fit(chans=[0, -1])

Performs a Lorentzian fitting of the specified data.

Parameters:

chans : list

The indexes to start and end at. Default: [0,-1]

Returns:

ndarray

Parameters of the Lorentzian that fits the specified data

lorentzian(x, ampl, center, width)

Computes the Lorentzian function.

Parameters:

x : float

Point to evaluate the Gaussian for.

ampl : float

Amplitude.

center : float

Center.

width : float

Width.

Returns:

float

Value of the specified Gaussian at x

min_dist = 1

profile = 'gaussian'

scale(x, new_range=(0.0, 1.0), eps=1e-09)

Changes the scale of an array

Parameters:

x : ndarray

1D array to change the scale (remains unchanged)

new_range : tuple (float, float)

Desired range of the array

eps: float

Numerical precision, to detect degenerate cases (for example, when every value of x is equal)

Returns:

ndarray

Scaled array

tuple (float, float)

Previous data range, allowing a rescale to the old range

thres = 0.0

width = 10