Locan

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

New Features
------------
- Add analysis routine for `SubpixelBias`
- Add function `merge_metadata` to merge metadata from class instance or file
- Add class `Files` for managing file selections to be used in batch processing
- Add `utilities/statistics` module with helper function to compute
`WeightedMeanVariance`
- Add `locdata.utilities.statistics.ratio_fwhm_to_sigma` function
- Add `locdata.utilities.statistics.biased_variance` function
- Add analysis routine for `ConvexHullExpectation`,
`GroupedPropertyExpectation` and `PositionVarianceExpectation`.
- Add function to standardize locdata.
- add `Locdata.update_properties_in_references` method
- add analysis class `locdata.analysis.ConvexHullExpectationBatch`.

API Changes
-----------
- Change `find_pattern_upstream` into `find_file_upstream`
- Add analysis class `LocalizationUncertainty` and
deprecate `LocalizationUncertaintyFromIntensity`
- Refactor `LocData.properties` to include weighted coordinate averages
and properties for frame and intensity
- Refactor `locan.simulation.simulate_locdata.resample`
- Change `LoData.coordinate_properties` to `LocData.coordinate_keys` and
add `LocData.uncertainty_keys` and corresponding functions in
`locan.constants.PropertyKeys`

Bug Fixes
---------
- Fix use of callables in `LocalizationUncertainty`
- Adapt to to bug fixes in lmfit 1.2.0

Other Changes and Additions
---------------------------
- Use ruff for linting
- Use pyproject.toml for all specifications and deprecate use of setup.cfg
- Use import open3d-cpu instead of open3d
- docs: add tutorial for analysis of grouped cluster properties

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

New Features
------------
- Add CLI for --info and --version
- Add overlay function to transform locdatas
- Add function to standardize locdata.
- Add function load_metadata_from_toml to read metadata from toml file
- Add function find_pattern_upstream.
- Add function transform_counts_to_photons.

API Changes
-----------
- Add boost_histogram_axes property to Bins

Bug Fixes
---------
- Fix intensity transform with nan
- Fix simulation on region being a rotated rectangle
- Fix Roi.from_yaml for rotated rectangular rois
- Fix Roi.from_yaml to work with Polygon regions
- Fix bug in localization_property_2d.
- Fix bug in localizations_per_frame concerning the time units
- Fix histogram with bins=Bins_instance as input
- Fix conversion of bin_edges to bin_size for float numbers
- Fix tests by excluding shapely 2.0.0 and 2.0.1
- Use np.random.default_rng for random number generation in simulate_drift.py

Other Changes and Additions
---------------------------
- Use of pre-commit
- Adapt to isort, black, flake8, bandit
- Integrate qtpy
- Add benchmark setup for Airspeed Velocity
- Modify dockerfiles to run with slim-bullseye
- Add conditional import of tomllib to replace tomli for python>=3.11
- Add CITATION.cff file
- Add some type hints

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

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

locan.configuration
^^^^^^^^^^^^^^^^^^^^^
- Introduced module locan.configuration to hold user-specific configuration values

locan.constants
^^^^^^^^^^^^^^^^^
- Introduced enum `PropertyKey` that holds `PropertyDescription` dataclasses
with information on name, type, units and description

locan.data
^^^^^^^^^^^^^^^
- Provided new scheme for metadata
- Added tutorial about metadata for LocData
- Introduced use of protobuf Timestamp and Duration types in metadata messages
- Added function in `locan.data.metadata_utils` to provide scheme of default metadata
- Added function in `locan.data.metadata_utils` to read metadata from toml file

locan.io
^^^^^^^^^^^^^^^
- Refactored locan_io.locdata module structure

locan.render
^^^^^^^^^^^^^^^
- Changed default value for n_bins in HistogramEqualization to increase intensity resolution.
Note: This modification changes the visual presentation of localization data with a large dynamic range.

Bug Fixes
---------

locan.utils.system_information
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- Fixed `show_version` to read out all dependency versions

locan.data
^^^^^^^^^^^^^^^
- Fixed bug in cluster functions such that setting the region of empty collections does not raise a TypeError anymore
- Fixed protobuf issues related to protobuf 4.21

Other Changes and Additions
---------------------------
- Dropped support for python 3.7
- Various minor changes of documentation and code
- Removed numba as dependency
- Based conda-related dockerfiles on mambaforge
- Introduced use of fixture from pytest-qt for testing QT interfaces

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

Bug Fixes
---------

locan.scripts
^^^^^^^^^^^^^^^
- Fix a bug introduced in 0.11 in napari and rois script.

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

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.