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Fixups changelog
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JoepVanlier committed Oct 27, 2021
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#### New features

* Add support for axial force detection (i.e. force detection along the Z axis). The high-frequency data can be accessed with `f.force1z` and `f.force2z` while the downsampled low-frequency channels can be accessed with `f.downsampled_force1z` and `f.downsampled_force2z`. The calibrations can be accessed with `f.force1z.calibration` and `f.force2z.calibration`. The Z component is *not* factored in the calculation of the total force `f.downsampled_force1` and `f.downsampled_force2`.
* Added support for axial force detection (i.e. force detection along the Z axis). The high-frequency data can be accessed with `f.force1z` and `f.force2z` while the downsampled low-frequency channels can be accessed with `f.downsampled_force1z` and `f.downsampled_force2z`. The calibrations can be accessed with `f.force1z.calibration` and `f.force2z.calibration`. The Z component is *not* factored in the calculation of the total force `f.downsampled_force1` and `f.downsampled_force2`.
* Added `KymoLineGroup.fit_binding_times()` to allow for dwelltime analysis of bound states found using kymotracker. See [kymotracking](https://lumicks-pylake.readthedocs.io/en/latest/tutorial/kymotracking.html) for more information.
* Allow using data acquired with a fast force sensor by passing `fast_sensor=True` when creating a `PassiveCalibrationModel`.
* Allow using hydrodynamically correct power spectrum when performing force calibration. See [force calibration](https://lumicks-pylake.readthedocs.io/en/latest/tutorial/force_calibration.html) for more information.
* Add ability to crop `CorrelatedStacks`. See [Correlated stacks](https://lumicks-pylake.readthedocs.io/en/latest/tutorial/correlatedstacks.html#correlated-stacks) for more information.
* Added ability to crop `CorrelatedStacks`. See [Correlated stacks](https://lumicks-pylake.readthedocs.io/en/latest/tutorial/correlatedstacks.html#correlated-stacks) for more information.

#### Bug fixes

* Show an error message when user attempts to refine lines before tracking or loading them so the kymotracker widget does not become unresponsive.
* Force calibration models now throw an error when a bead diameter of less than `10^-2` microns is used (rather than produce `NaN` results).
* Fixed bug that prevented export of `CorrelatedStack` if the alignment matrices were missing from the metadata.
* Fixed bug where the exported metadata fields were erroneously exported as `"Applied channel X alignment"` for `CorrelatedStack` where the alignment was not actually applied.
* Fix error in optimal point determination for MSD estimator. Note that this bug led to an error being thrown when the number of points in the trace was exactly 4. Now it results in a more informative error message (`You need at least 5 time points to estimate the number of points to include in the fit.`).
* Fixed error in optimal point determination for MSD estimator. Note that this bug led to an error being thrown when the number of points in the trace was exactly 4. Now it results in a more informative error message (`You need at least 5 time points to estimate the number of points to include in the fit.`).

#### Improvements

* Switch to trust region reflective algorithm for fitting thermal calibration spectrum. This results in fewer optimization failures.
* Make sure that `f_diode` stays below the Nyquist frequency during fitting.
* Switched to trust region reflective algorithm for fitting thermal calibration spectrum. This results in fewer optimization failures.
* Pylake now ensures that `f_diode` stays below the Nyquist frequency during fitting.
* Implemented a bias correction for the thermal calibration. Note that this typically leads to a small correction unless you use a very low number of points per block.

#### Deprecations
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