Arcos4py

Fixed
- Bug where trackCollev would overwrite the inputdata in the ARCOS object, preventing repeat tracking of collective events.
- Spelling mistake in \__init__.py

Changed
- None detrending now rescales measurements to 0,1 range on a global scale and not on a track-by-track basis.
- Added the parameter epsPrev by separating it from eps.
epsPrev is the maximum distance cells within collective events can be separated from each other when linking them from one frame to the next.
If set to 'None', as default, the same value as for eps is used.

Added
- New function estimate_eps (import from tools) to estimate the eps paramter used for DBSCAN clustering based on the nearest neighbour distribution. Three methods are supported, either mean of NN, median of NN or kneepoint of the sorted NN distribution.
- Functions to perform resampling and bootstrapping to perform validation of arcos output.
- Unittests for added functionallity.

Changed
- Changed running median for global smoothing of trajectories from scipy running_median
to pandas running.median, since this allows a different endrule mode
- Changed running median endrule for local smoothing of trajectories from constant to nearest

Fixed
- Fix for lm detrending
- Fix for none detrending
- Fix grouping failure when object id was a string in rescale data method in binarization class

Changed
- Binarization Thresholding value now sets everything to be active for >=, as opposed to > like it was before

Fixed
- Bug where if object id was a string, splitting arrays into groups would fail.
- Hardcoded collective id name in stats module
- Wrong example in main module

Added
- More examples for plots in plotting module
- mkdocstrings-python-legacy extension (required for building docs)

Added
- NoodlePlot for collective events

Changed
- binarize_detrend: converted pandas operations to numpy for performance improvements
- detect_events: converted pandas operations to numpy for performance imporovements
- stats: converted pandas operations to numpy for performance improvements
- various small changes
- updated docstrings to match changes

Fixed
- numpy warning caused by stats module

Added
- More plotting functionallity to the plotting module.
- Measurment density plot
- Tracklength histogram
- Position/T plot
- Collective event statistcs plot

Changed
- Interpolation class in tools now uses pandas.interpolate to interpolate missing values.
- Interpolation now interpolates all values in all columns of the dataframe.
- Improved usage section in the documentation.

Fixed
- Bug in trackCollev class that would lead to an error message in some cases.
- Spelling in docstrings.