[c++,python] Fix default reads on unwritten dense arrays #3136
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
johnkerl
approved these changes
Oct 4, 2024
| int32_t is_empty; | ||
| T ned[2]; | ||
|
|
||
| // TODO currently we need to use the TileDB C API in order to check |
There was a problem hiding this comment.
Do we have a tracking task with @teo-tsirpanis ? If not please open one! :)
* Found issue while working on spatial's `MultiscaleImage` and erroring out when applying `read_spatial_region` to a level that had not been written to yet * Add new `non_empty_domain_slot_opt` alongside `non_empty_domain_slot` that returns `std::nullopt` if it is empty rather than (0, 0) * Fix logic in C++ `ManagedQuery::setup_read` to check if the array has been written to yet. If it hasn't, set the subarray to use soma_dim_0's full domain. Otherwise, use the non-empty domain as before * Also fix logic in Python `DenseNDArray.read` to use the new `non_empty_domain_slot_opt` and correctly set the `data_shape` to the full domain if the array has not been written to yet * Add unit test in pytest
nguyenv
force-pushed
the
viviannguyen/fix-dense-array-default-on-unwritten-arrays
branch
from
600d1bb
to
bae0b64
Compare
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #3136 +/- ##
==========================================
+ Coverage 82.41% 82.54% +0.13%
==========================================
Files 50 50
Lines 5203 5209 +6
==========================================
+ Hits 4288 4300 +12
+ Misses 915 909 -6
Flags with carried forward coverage won't be shown. Click here to find out more.
|
nguyenv
deleted the
viviannguyen/fix-dense-array-default-on-unwritten-arrays
branch
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Issue and/or context:
Found issue while working on spatial's
MultiscaleImageand erroring out when applyingread_spatial_regionto a level that had not been written to yet.Changes:
non_empty_domain_slot_optalongsidenon_empty_domain_slotthat returnsstd::nulloptif it is empty rather than (0, 0)ManagedQuery::setup_readto check if the array has been written to yet. If it hasn't, set the subarray to use soma_dim_0's full domain. Otherwise, use the non-empty domain as beforeDenseNDArray.readto use the newnon_empty_domain_slot_optand correctly set thedata_shapeto the full domain if the array has not been written to yet