API Reference
=============

This detailed reference lists all the classes and functions contained in the package.
If you are just looking to get started, read the :doc:`/tutorial/index` first.

.. currentmodule:: lumicks.pylake

.. autosummary::
    :toctree: _api
    :template: class.rst

    File
    channel.Slice
    fdcurve.FdCurve
    fdensemble.FdEnsemble
    kymo.Kymo
    scan.Scan
    point_scan.PointScan
    ImageStack
    ColorAdjustment
    ScaleBar

    :template: instance.rst

    colormaps

    :template: function.rst

    download_from_doi

Force calibration
-----------------

.. autosummary::
    :toctree: _api
    :template: class.rst

    PassiveCalibrationModel
    ActiveCalibrationModel
    force_calibration.power_spectrum.PowerSpectrum
    force_calibration.power_spectrum_calibration.CalibrationResults

    :template: function.rst

    calibrate_force
    calculate_power_spectrum
    fit_power_spectrum
    viscosity_of_water
    density_of_water


FD Fitting
----------

.. autosummary::
    :toctree: _api
    :template: class.rst

    fitting.model.Model
    FdFit
    fitting.parameters.Params
    fitting.parameters.Parameter

    :template: function.rst
    parameter_trace

.. _fd_models:
.. rubric:: Available models

.. autosummary::
    :toctree: _api
    :template: function.rst

    force_offset
    distance_offset
    wlc_marko_siggia_force
    wlc_marko_siggia_distance
    ewlc_marko_siggia_force
    ewlc_marko_siggia_distance
    ewlc_odijk_force
    ewlc_odijk_distance
    dsdna_ewlc_odijk_distance
    twlc_force
    twlc_distance
    efjc_force
    efjc_distance
    ssdna_efjc_distance


Kymotracking
------------

.. autosummary::
    :toctree: _api
    :template: class.rst

    kymotracker.kymotrack.KymoTrack
    kymotracker.kymotrack.KymoTrackGroup
    kymotracker.detail.msd_estimation.DiffusionEstimate
    kymotracker.detail.msd_estimation.EnsembleMSD
    KymoWidgetGreedy

    :template: function.rst

    track_greedy
    track_lines
    filter_tracks
    refine_tracks_centroid
    refine_tracks_gaussian

Notebook widgets
----------------

.. autosummary::
    :toctree: _api
    :template: class.rst

    KymoWidgetGreedy
    lumicks.pylake.nb_widgets.range_selector.SliceRangeSelectorWidget
    FdRangeSelector
    FdDistanceRangeSelector
    lumicks.pylake.nb_widgets.image_editing.ImageEditorWidget

Population Dynamics
-------------------

.. autosummary::
    :toctree: _api
    :template: class.rst

    HiddenMarkovModel
    GaussianMixtureModel
    DwelltimeModel
    population.dwelltime.DwelltimeBootstrap
    population.dwelltime.DwelltimeProfiles
    population.detail.fit_info.PopulationFitInfo

Piezo tracking
--------------

.. autosummary::
    :toctree: _api
    :template: class.rst

    DistanceCalibration
    ForceBaseLine
    PiezoTrackingCalibration
    PiezoForceDistance

Simulation
----------

.. autosummary::
    :toctree: _api
    :template: function.rst

    simulation.simulate_diffusive_tracks