API Reference#

Classes

Model

Represents a model.

Parameter

Represents a model parameter or a single parameter vector.

Penalty

Represents a penalty term of the objective function.

FitResult

Represents the results of a fit.

UQResult

Represents the uncertainty quantification of fit results.

Functions

fit

Fit the model(s) to the dataset(s)

merge

Create a multi-response model from multiple individual models.

link

Create equality relationships between parameters

lincombine

Create model whose response is a linear combination of multiple individual model responses.

relate

Create functional relationships between model parameters.

regoperator

Computes the discrete approximation to the derivative operators used as regularization operators.

selregparam

Selection of optimal regularization parameter based on a selection criterion.

noiselevel

Estimate the noise level in a dataset.

whitegaussnoise

Generates a vector of white Gaussian (normal) noise

diststats

Computes statistical quantities for the location, spread, and shape of a distance distribution, with or without their corresponding uncertainties.

correctphase

Phase correction of complex-valued data.

bootstrap_analysis

Bootstrap analysis for uncertainty quantification

profile_analysis

Profile likelihood analysis for uncertainty quantification

snlls

Separable non-linear least squares (SNLLS) solver

fnnls

Fast non-negative least-squares (NNLS) solver.

cvxnnls

Non-negative least-squares (NNLS) via the CVXOPT package.

Dipolar EPR functions

dipolarmodel

Generate a dipolar EPR signal model.

dipolarpenalty

Construct penalties based on the distance distribution.

deerload

Load file in BES3T format (Bruker EPR Standard for Spectrum Storage and Transfer)

dipolarkernel

Compute the (multi-pathway) dipolar kernel operator which enables the linear transformation from distance-domain to time-domain data.

dipolarbackground

Calculate multi-pathway dipolar background decays.

fftspec

Fast-Fourier transform spectrum

distancerange

Empirical distance range given a DEER time axis

Utility functions

All functions in deerlab.utils are private functions used internally by other functions. Stable functionality is not guaranteed.

store_pickle

Save/export an object to a .pkl file serialized as bytes.

read_pickle

Load a pickled object file .pkl and deserialize the bytes into a Python object.

hccm

Heteroscedasticity Consistent Covariance Matrix (HCCM)

Jacobian

Finite difference Jacobian estimation

nearest_psd

Find the nearest positive semi-definite matrix

movmean

Moving mean filter

ovl

Overlap index

der_snr

DER-SNR noise estimation