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Zarr Tile Sink #1446

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merged 42 commits into from
Mar 21, 2024
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0f537bb
Initial method setup
annehaley Dec 20, 2023
5c6990b
Populate addTile method; tests successful up to 3-D
annehaley Jan 4, 2024
29d8b19
Use test source to copy 5D images to Zarr sink
annehaley Jan 11, 2024
599503f
Remove old TODOs
annehaley Jan 29, 2024
10a1f7e
Refactor __init__ to simplify (split into multiple methods)
annehaley Jan 29, 2024
12946a0
Update Exception class in __del__ method
annehaley Jan 29, 2024
f8fb42e
Merge branch 'master' into zarr-sink
annehaley Jan 31, 2024
d697920
Enable cropping during `write`; does not modify internal data
annehaley Feb 1, 2024
b50ecd9
Merge branch 'master' into zarr-sink
annehaley Feb 9, 2024
f36f1a8
Protect `__del__` method and ensure both `close` operations are called
annehaley Mar 5, 2024
6b6a6a4
Set `_axes`, `_dtype`, `_bandCount`, `sizeX`, `sizeY`, `levels`, and …
annehaley Mar 5, 2024
d6dd5ad
Attempt to improve performance of `addTile`: remove `np.pad` and unne…
annehaley Mar 6, 2024
b7ed234
Merge branch 'master' into zarr-sink
annehaley Mar 6, 2024
df8819f
Fix lint failure: remove trailing whitespace
annehaley Mar 6, 2024
0a832fd
Set `self._levels` to None in `addTile`
annehaley Mar 7, 2024
cd0c715
Avoid creating full mask
annehaley Mar 7, 2024
41ea6b5
Use `np.where` instead of `np.place`
annehaley Mar 8, 2024
eaaf29e
Merge branch 'master' into zarr-sink
annehaley Mar 8, 2024
0414f71
Rename `mask_placement_slices` -> `placement_slices` and avoid mask c…
annehaley Mar 8, 2024
3da02f6
Include statement to add samples axis to mask if necessary
annehaley Mar 11, 2024
d0d6129
Refactor checking of `axes` arg; ensure "s" axis exists
annehaley Mar 13, 2024
07e744f
Use samples axis length in chunking (instead of 32) and rechunk if le…
annehaley Mar 14, 2024
5118fbc
Switch to using DirectoryStore internally (instead of SQLiteStore)
annehaley Mar 18, 2024
e1e9831
Refactor addTile: ensure placement from kwargs is used (including fir…
annehaley Mar 18, 2024
6706f69
Refactor addTile: move attribute changes within `addLock` context
annehaley Mar 18, 2024
b58fcda
style: whitespace changes to fix lint failure
annehaley Mar 18, 2024
756502b
Refactor addTile: expand mask dimensions with tile dimensions
annehaley Mar 18, 2024
58897b3
Merge branch 'master' into zarr-sink
annehaley Mar 18, 2024
a0b3fbc
fix: add NoneType protection to mask axis padding
annehaley Mar 18, 2024
f0e7482
Merge branch 'master' into zarr-sink
annehaley Mar 19, 2024
5317daa
fix: Revert to using SQLiteStore when opening existing Zarr file
annehaley Mar 19, 2024
32c9c58
fix: move start of `self._addLock` context
annehaley Mar 19, 2024
728faee
fix: set dtype of `np.empty` when initializing root
annehaley Mar 19, 2024
14bee28
fix: call `validateZarr` in beginning of `getMetadata` if necessary
annehaley Mar 19, 2024
ce1b1b7
fix: Set `_bandCount` from length of `s` axis if exists
annehaley Mar 19, 2024
5fac3a8
test: enable new algorithm progression tests
annehaley Mar 19, 2024
23b70f7
test: write basic use case tests for zarr sink in `test_sink.py`
annehaley Mar 19, 2024
414ba67
style: fix line too long; use string append
annehaley Mar 19, 2024
f35d06e
style: avoid explicit string concatenation
annehaley Mar 20, 2024
157c731
test: add `testNew` and initialize `_levels`
annehaley Mar 20, 2024
62e6572
fix: unindent mask reshape clause
annehaley Mar 20, 2024
71d1068
test: add `testAddTileWithMask` and fix caching to pass
annehaley Mar 20, 2024
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Merge branch 'master' into zarr-sink
  • Loading branch information
annehaley authored Mar 8, 2024
commit eaaf29eb35d61f24dc86efdc432ff501eadbb24d

This merge commit was added into this branch cleanly.

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