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Add the Scene class #220

Merged
merged 13 commits into from
Sep 26, 2024
Merged

Add the Scene class #220

merged 13 commits into from
Sep 26, 2024

Commits on Sep 18, 2024

  1. Add new spatial datatypes to SOMA 

    - Add new MultiscaleImage
- Add new SpatialDataframe abstract base class
- Add PointCloud subclass of the SpatialDataFrame
- Add GeometryDataFrame subclass of the SpatialDataFrame
- Add shapely as a dependency
    @jp-dark
    jp-dark committed Sep 18, 2024
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  2. Update MultiscaleImage docstring and other small updates 

    * Update docstrings
* Add ValueError error messages in `SpatialRead`
* Rename method `read_level`->`read_region`
    @jp-dark
    jp-dark committed Sep 18, 2024
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  3. Move docstring updates

    @jp-dark
    jp-dark committed Sep 18, 2024
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Commits on Sep 19, 2024

  1. Update python-spec/src/somacore/spatialdata.py 

    Co-authored-by: nguyenv <[email protected]>
    @jp-dark @nguyenv
    jp-dark and nguyenv authored Sep 19, 2024
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  2. Fix docstring for spatialdata read_region

    @jp-dark
    jp-dark committed Sep 19, 2024
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  3. Remove SpatialDataFrame from spec 

    The individual implementations may find a shared base class useful, but
it doesn't need to be included in the abstract specification.
    @jp-dark
    jp-dark committed Sep 19, 2024
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  4. Add Scene class 

    * Create the `Scene` class
* Add `spatial` collection of scenes to the `Experiment` class
* Add Scene to ephemeral collections and tests
    @jp-dark
    jp-dark committed Sep 19, 2024
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  5. Update docstrings

    @jp-dark
    jp-dark committed Sep 19, 2024
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Commits on Sep 25, 2024

  1. Update the API for adding and setting transforms 

    * Add methods to add new assets to a scene
* Rename `register_*` methods to `set_transformation_to_*`
    @jp-dark
    jp-dark committed Sep 25, 2024
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Commits on Sep 26, 2024

  1. Rename and add transform methods 

    * Rename `_transformation_` methods to `_transform_`.
* Add ability to get transforms "from" as well as "to" assets.
    @jp-dark
    jp-dark committed Sep 26, 2024
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  2. Merge branch 'main' into dark/scene

    @jp-dark
    jp-dark committed Sep 26, 2024
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  3. Fix type hints

    @jp-dark
    jp-dark committed Sep 26, 2024
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  4. Update ephemeral Scene collection for testing

    @jp-dark
    jp-dark committed Sep 26, 2024
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