Locan

=================

New Features
------------

locan.data
^^^^^^^^^^^^^^^
- Modified Polygon.contains function to increase performance.
- Implemented randomize function for all hull types.

locan.io
^^^^^^^^^^^^^^^
- Added methods to load DECODE and SMAP files.

locan.render
^^^^^^^^^^^^^^^
- Added rendering functions for 3D
- Added rendering functions for RGB image (multi-color overlay)

API Changes
-----------

locan.io
^^^^^^^^^^^^^^^
- Extended load_txt_files to convert property names to locan standard property names.

locan.render
^^^^^^^^^^^^^^^
- Refactored intensity rescaling by introducing standard normalization procedures.

Bug Fixes
---------

locan.data
^^^^^^^^^^^^^^^
- Fixed bunwarp transformation

locan.io
^^^^^^^^^^^^^^^
- Fixed lineterminator in load_rapidstorm_track_file

Other Changes and Additions
---------------------------
- Ensured support of locan and all optional dependencies for Python 3.9
- Ensured support of locan (without optional dependencies) for Python 3.10
- Turned hdbscan into optional dependency

=================

New Features
------------

locan.io
^^^^^^^^^^^^^^^
- Add function to load rapidSTORM file with tracked data.
- Add function to load and save SMLM file.

Other Changes and Additions
---------------------------
- Locan went public.
- Readthedocs was set up.
- Zenodo DOI was generated.

================

API Changes
-----------

locan.analysis
^^^^^^^^^^^^^^^
- Refactor computation of blinking_statistics

locan.data
^^^^^^^^^^^^^^^
- Restructured Region management introducing new classes in locan.data.region
- Rename function to computer inertia moments

locan.render
^^^^^^^^^^^^^^^
- Change image orientation in render_2d_napari to be consistent with points coordinates.

locan.simulation
^^^^^^^^^^^^^^^^^^^
- Refactored simulation functions to make use of numpy random number generator.
- Refactored simulation functions to generate Neyman-Scott point processes in expanded regions.
- Add function to simulate dSTORM data as localization clusters
with normal-distributed coordinates and geometric-distributed number of localizations.

Other Changes and Additions
---------------------------
- Added or modified tutorials on mutiprocessing, regions and simulation.
- Introduce pytest markers for test functions that are excluded from test run per default.

================

API Changes
-----------

locan.scripts
^^^^^^^^^^^^^^^
- Default values for verbose and extra flags in script show_versions were changed.

Bug Fixes
---------

locan.analysis
^^^^^^^^^^^^^^^
- Fit procedure was fixed for NearestNeighborDistances.

Other Changes and Additions
---------------------------
- Library was renamed to LOCAN
- Documentation and tutorials were modified accordingly
- Test coverage was improved and use of coverage.py introduced
- _future module was deprecated

================

API Changes
------------

locan.analysis
^^^^^^^^^^^^^^^
- Added new keyword parameters in LocData.from_chunks and Drift.
- Extended class for blinking analysis.

Other Changes and Additions
---------------------------
- Turn warning into log for file io.
- Restructured documentation, added tutorials, and changed html-scheme to furo.

================

New Features
------------
- Introduced logging capability.
- Added script for running tests from command line interface.

locan.analysis
^^^^^^^^^^^^^^^
- Make all analysis classes pickleable.
- Refactored Pipeline class
- Enabled and tested multiprocessing based on multiprocessing or ray.
- Added more processing bars.
- Added drift analysis and correction based on imagecorrelation and iterative closest point registration.

locan.data
^^^^^^^^^^^^^^^
- Made LocData class pickleable.
- Added computation of inertia moments.
- Added orientation property based on oriented bounding box and inertia moments.
- Added elongation property based on oriented bounding box.
- Add transformation method to overlay LocData objects.

locan.io
^^^^^^^^^^^^^^^
- Added loading function for Nanoimager data.

locan.render
^^^^^^^^^^^^^^^
- Added windowing function for image data.

API Changes
-----------

locan.analysis
^^^^^^^^^^^^^^^
- Fixed and extended methods for Drift analysis and correction.

locan.data
^^^^^^^^^^^^^^^
- Implemented copy and deepcopy for LocData.
- Changed noise output in clustering methods. Removed noise parameter.

locan.datasets
^^^^^^^^^^^^^^^
- Added dataset for microtubules

locan.io
^^^^^^^^^^^^^^^
- Added option for file-like objects in io_locdata functions.
- Added Bins class, introduced use of boost-histogram package, and restructured binning.
- Introduced use of napari.run.
- Changed default value in render_2d_mpl to interpolation='nearest'.

locan.scripts
^^^^^^^^^^^^^^^
- Added arguments for locan napari and locan rois.

locan.simulation
^^^^^^^^^^^^^^^^^^^
- Added simulation of frame values.

Bug Fixes
---------

locan.data
^^^^^^^^^^^^^^^
- Fixed treatment of empty LocData in clustering and hull functions.

locan.gui
^^^^^^^^^^^^^^^
- Use PySide2 as default QT backend depending on QT_API setting.

locan.io
^^^^^^^^^^^^^^^
- Fixed enconding issues for loading Elyra data.

Other Changes and Additions
---------------------------
- Test data is included in distribution.
- New dockerfiles for test and deployment.
- Included pyproject.toml file