Cellseg-gsontools

Fixes
Fix a bug `gdf_to_file`. Failed when qupath data fields were added to gdf.

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Features

- Add support for querying a WSI with bbox coords.
- Add support for rasterizing a gdf into a instance or semantic segmentation mask
- add support for intensity features

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Docs

- Add cell clustering example
- Add cell regionalization example
- Add medial line extraction example

Features

- Add medial line extraction funtion `cellseg_gsontools.geometry.medial_lines`. Extracts the medial lines using voronoi diagram.
- Add perpendicular line extraction funtion `cellseg_gsontools.geometry.perpendicular_lines`. Extracts the perpendicular lines from a given line gdf.
- Add `num_processes` arguments in `local_character`, `local_distances`, `local_diversity` and `shape_metric` functions.

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Breaking changes

- The SpatialContext API now takes params: `parallel` and `num_processes` in the class constructor instead of the `fit()`-method.

Features

- Added support for new backends (python libraries) to compute the spatial joins in the `SpatialContext`-classes. This allows for more efficient computation of the spatial joins especially for very large tissue areas.
- Backends:
- dask-geopandas
- spatialpandas

- Add `h3` hexgrid support in grid fitting for spatial context classes

Performance
- sjoin operations replaced with sindex ops. This makes subsetting 10-100x faster.

Docs
New documentation website: https://okunator.github.io/cellseg_gsontools/

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Deprecated

- the `Pipeline` class was removed.

Features

- Add `local_distances` function to compute the mean/median/sum of the distances between nodes in local neighborhoods

- Add `weights2gdf` function to convert `libpysal.weights.W` into a `gpd.GeoDataFrame` with `geometry` column consisting of `shapely.geometry.LineStrings`
- Add grid fitting to `_SpatialContext` classes. Allows a grid of patches to be overlayed on top of different context areas. The patch sizes and strides can be user defined.
- Better looking links in `_SpatialContext.plot()`. Different link classes now represented with different colors.
- Add `grid_classify` method to classify grids based on heuristics.

Performance
- Support for parallel spatial context fitting: `_SpatialContext.fit(parallel=True)`

Fixes

- Drop duplicates in `context2gdf`-class method

- clarify the `apply_gdf` function api.
- clarify the `_SpatialContext` api.

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Features

- Add join predicate param for `sjoin` operation in `get_objs_within` function

Performance

- Optimize spatial subsetting operations by getting rid of redundant operations in spatial context classes.

Perf

- Parallelize and memory optimize `AreaMerger`.

Fixes

- Simplify `border_network` computation and return only the node-node links that go accross the border.
- Simplify weights plotting interfacee

- Fix bug in interface and roi network fitting.

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