PyDDM.ddm_calc

PyDDM.ddm_calcΒΆ

This module contains the code for calculating and fitting the DDM matrix. The module PyDDM.ddm_analysis_and_fitting defines classes which interface with the functions here.

Functions

computeDDMMatrix

Calculates DDM matrix

determining_A_and_B

Used to assist in determining the parameters \(A\) and \(B\) in the expression for the DDM matrix \(D(q,\Delta t) = A(q) [1 - f(q, \Delta t)] + B(q)\).

execute_LSQ_fit

Performs least_squares fit.

execute_ScipyCurveFit_fit

Performs curve_fit fit.

find_radial_average

Computes the radial average of a single 2D matrix.

fit_ddm

Function to fit the DDM matrix or ISF for one wavevector.

fit_ddm_all_qs

Function to fit the DDM matrix or ISF for all wavevectors.

generateLogDistributionOfTimeLags

This function will generate a logarithmically spaced set of numbers.

generate_mask

Generates a mask of the same size as im to avoid radially averaging the whole DDM matrix.

get_FF_DDM_matrix

This code calculates the far-field DDM matrix for the series of images in imageFile at the lag times specified in dts.

get_MSD_from_DDM_data

Finds the mean squared displacement (MSD) from the DDM matrix as well as values for the amplitude (A) and background (B).

newt

radial_avg_ddm_matrix

Radially averages DDM matrix.

temporalVarianceDDMMatrix

Calculates DDM matrix as a function of time at given lag time

window_function

Applies windowing function to images.

Classes

IPythonStreamHandler

A StreamHandler for logging that clears output between entries.

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