Add the Scene class
#220
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Add the Scene class
#220
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jp-dark
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aaronwolen,
johnkerl,
bkmartinjr and
ivirshup
bkmartinjr
approved these changes
Sep 16, 2024
- 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
* Update docstrings * Add ValueError error messages in `SpatialRead` * Rename method `read_level`->`read_region`
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Co-authored-by: nguyenv <[email protected]>
johnkerl
approved these changes
Sep 19, 2024
The individual implementations may find a shared base class useful, but it doesn't need to be included in the abstract specification.
* Create the `Scene` class * Add `spatial` collection of scenes to the `Experiment` class * Add Scene to ephemeral collections and tests
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[sc-55577], [sc-55578], [sc-55579] |
ivirshup
reviewed
Sep 23, 2024
python-spec/src/somacore/scene.py
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| If the subcollection the geometry dataframe is inside of is more than one | ||
| layer deep, the input should be provided as a sequence of names. For example, | ||
| to register a geometry dataframe named "transcripts" in the "var/RNA" | ||
| collection:: | ||
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| scene.register_geometry_dataframe( | ||
| 'transcripts', transform, subcollection=['var', 'RNA'], | ||
| ) |
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Is this a workflow that is being supported? I thought the spec was pretty opinionated about where each kind of thing would be stored.
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The example in the docstring follows the storage guideline and is more than one layer deep.
aaronwolen
approved these changes
Sep 25, 2024
python-spec/src/somacore/scene.py
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| raise NotImplementedError() | ||
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| @abc.abstractmethod | ||
| def get_transformation_to_multiscale_image( |
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Suggested change
| def get_transformation_to_multiscale_image( | |
| def get_transformation_multiscale_image( |
Do we need to here?
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We need something to specify what the transform is going from/to. (Scene to image is different than image to scene). I don't love how verbose the methods are, so I'm open to other suggestions. I did change transformation to match transform (based on one of your suggestion changes on #219).
* Add methods to add new assets to a scene * Rename `register_*` methods to `set_transformation_to_*`
* Rename `_transformation_` methods to `_transform_`. * Add ability to get transforms "from" as well as "to" assets.
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September 26, 2024 16:28
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Sceneclassspatialcollection of scenes to theExperimentclassThis PR is ready for review, but should be merged after PR #219