DwelltimeModel

lumicks.pylake.DwelltimeModel

class DwelltimeModel(dwelltimes, n_components=1, *, min_observation_time=0, max_observation_time=inf, tol=None, max_iter=None)

Exponential mixture model optimization for dwelltime analysis.

Parameters

  • dwelltimes (numpy.ndarray) – observations on which the model was trained. Note: the units of the optimized lifetime will be in the units of the dwelltime data. If the dwelltimes are calculated as the number of frames, these then need to be multiplied by the frame time in order to obtain the physically relevant parameter.

  • n_components (int) – number of components in the model.

  • min_observation_time (float) – minimum experimental observation time

  • max_observation_time (float) – maximum experimental observation time.

  • tol (float) – The tolerance for optimization convergence. This parameter is forwarded as the ftol argument to scipy.optimize.minimize(method="SLSQP").

  • max_iter (int) – The maximum number of iterations to perform. This parameter is forwarded as the maxiter argument to scipy.optimize.minimize(method="SLSQP").

calculate_bootstrap(iterations=500)

Calculate a bootstrap distribution for the model.

Parameters

iterations (int) – Number of iterations to sample for the distribution.

hist(n_bins=25, bin_spacing='linear', hist_kwargs=None, component_kwargs=None, fit_kwargs=None, xscale=None, yscale=None)

Plot the dwelltime distribution histogram and overlayed model density.

Parameters

  • n_bins (int) – number of bins in the histogram

  • bin_spacing ({"log", "linear"}) – determines how bin edges are spaced apart

  • hist_kwargs (Optional[dict]) – dictionary of plotting kwargs applied to histogram

  • component_kwargs (Optional[dict]) – dictionary of plotting kwargs applied to the line plot for each component

  • fit_kwargs (Optional[dict]) – dictionary of plotting kwargs applied to line plot for the total fit

  • xscale ({"log", "linear", None}) – scaling for the x-axis; when None default is “linear”

  • yscale ({"log", "linear", None}) – scaling for the y-axis; when None default is same as bin_spacing

pdf(x)

Probability Distribution Function (states as rows).

Parameters

x (np.array) – array of independent variable values at which to calculate the PDF.

plot(n_bins=25, bin_spacing='linear', hist_kwargs=None, component_kwargs=None, fit_kwargs=None, xscale=None, yscale=None)

Deprecated since version 0.12.0: This method has been renamed to more closely match its behavior. Use DwelltimeModel.hist() instead.

property aic

Akaike Information Criterion.

property amplitudes

Fractional amplitude of each model component.

property bic

Bayesian Information Criterion.

property bootstrap

Bootstrap distribution.

Deprecated since version 0.13.3: This property will be removed in a future release. Use the class population.dwelltime.DwelltimeBootstrap returned from calculate_bootstrap() instead.

property lifetimes

Lifetime parameter (in time units) of each model component.

property rate_constants

First order rate constant (units of per time) of each model component.