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[python] Update the MultiscaleImage to match somacore API changes #3262

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merged 11 commits into from
Nov 1, 2024

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@jp-dark jp-dark commented Oct 30, 2024

This is the companion TileDB-SOMA changes for single-cell-data/SOMA#238. It consists of major changes to the MultiscaleImage implementation.

Do NOT merge before single-cell-data/SOMA#238.

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@jp-dark jp-dark requested a review from johnkerl October 31, 2024 11:34
@jp-dark jp-dark force-pushed the dark/multiscale-image/sc-57977 branch 2 times, most recently from ab5b3b8 to 497e219 Compare October 31, 2024 13:30
@jp-dark jp-dark changed the base branch from main to dark/somacore-1.0.23 October 31, 2024 13:30
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codecov bot commented Oct 31, 2024

Codecov Report

Attention: Patch coverage is 84.12698% with 20 lines in your changes missing coverage. Please review.

Please upload report for BASE (dark/somacore-1.0.23@714b17b). Learn more about missing BASE report.

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@@                   Coverage Diff                   @@
##             dark/somacore-1.0.23    #3262   +/-   ##
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  Coverage                        ?   83.74%           
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  Files                           ?       51           
  Lines                           ?     5542           
  Branches                        ?        0           
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  Hits                            ?     4641           
  Misses                          ?      901           
  Partials                        ?        0           
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python 83.74% <84.12%> (?)

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Components Coverage Δ
python_api 83.74% <0.00%> (?)
libtiledbsoma ∅ <0.00%> (?)

@jp-dark jp-dark force-pushed the dark/multiscale-image/sc-57977 branch from 1b1e736 to a50d8cf Compare October 31, 2024 20:44
@jp-dark jp-dark marked this pull request as ready for review October 31, 2024 20:55
@jp-dark jp-dark force-pushed the dark/multiscale-image/sc-57977 branch from a50d8cf to b000c29 Compare October 31, 2024 21:10
@jp-dark jp-dark merged commit 99d97c6 into dark/somacore-1.0.23 Nov 1, 2024
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@jp-dark jp-dark deleted the dark/multiscale-image/sc-57977 branch November 1, 2024 14:28
jp-dark added a commit that referenced this pull request Nov 1, 2024
…#3262)

* Directly take the `CoordinateSpace` as a creation parameter.
* Remove confusing `image_type` property/creation parameter. Use `data_axis_order` instead which uses the axis names the user provided.
* Create the first resolution level when creating the `MultiscaleImage`.
* Require the `add_new_level` to only add images smaller than the base (level=0) image.
* Add a `set` method for adding images that exist outside of SOMA.
* Add a property to check the number of channels in the image.
* Replace public facing `ImageProperties` class with internal `_LevelProperties` class.
jp-dark added a commit that referenced this pull request Nov 1, 2024
* Update Scene subcollection API

  - Make subcollection always a positional argument (for consistency).
  - Fix docstrings for `create` methods (no default value for subcollection).

* [python] Update the `MultiscaleImage` to match `somacore` API changes  (#3262)

  - Directly take the `CoordinateSpace` as a creation parameter.
  - Remove confusing `image_type` property/creation parameter. Use `data_axis_order` instead which uses the axis names the user provided.
  - Create the first resolution level when creating the `MultiscaleImage`.
  - Require the `add_new_level` to only add images smaller than the base (level=0) image.
  - Add a `set` method for adding images that exist outside of SOMA.
  - Add a property to check the number of channels in the image.
  - Replace public facing `ImageProperties` class with internal `_LevelProperties` class.
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