FdEnsemble

lumicks.pylake.fdensemble.FdEnsemble

class FdEnsemble(fd_curves)

An ensemble of F,d curves exported from Bluelake.

This class provides a way to handle an ensemble of force distance curves and perform procedures such as curve alignment on them.

Parameters:

fd_curves (dict of FdCurve) – Dictionary of unprocessed FdCurve.

fd_curves

Dictionary of unprocessed F,d curves.

Type:

dict of FdCurve

fd_curves_processed

Dictionary of F,d curves that were processed by the ensemble.

Type:

dict of FdCurve

Examples

import lumicks.pylake as lk

file = lk.File("example.h5")
fd_ensemble = lk.FdEnsemble(file.fdcurves)  # Create the ensemble

# Use the first 0.02 and last 0.04 um of data to align the data
fd_ensemble.align_linear(distance_range_low=0.02, distance_range_low=0.04)

# Plot the aligned Fd curves
for fd in fd_ensemble.values():
    fd.plot_scatter()

align_linear(distance_range_low, distance_range_high)

Aligns F,d curves to the first F,d curve in the ensemble.

Force is aligned by taking the mean of the lowest distances. Distance is aligned by considering the last segment of each F,d curve. This method regresses a line to the last segment of each F,d curve and aligns the curves based on this regressed line. Note that this requires the ends of the aligned F,d curves to be in a comparably folded state and obtained in the elastic range of the force, distance curve. If any of these assumptions are not met, this method should not be applied.

Parameters:

• distance_range_low (float) – Range of distances to use for the force alignment. Distances in the range [smallest_distance, smallest_distance + distance_range_low] are used to determine the force offsets.

• distance_range_high (float) – Upper range of distances to use. Distances in the range [largest_distance - distance_range_high, largest_distance] are used for the distance alignment.