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Subset pixel channel averaging to remove bottleneck #823

Merged
merged 31 commits into from
Dec 7, 2022
Merged

Subset pixel channel averaging to remove bottleneck #823

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6660f25
Initial implementation of pixel subsetting for channel averaging
alex-l-kong Nov 10, 2022
9106b99
Polish up remaining tests that rely on count checks for channel avera…
alex-l-kong Nov 10, 2022
5067dde
Add comment in compute_pixel_cluster_channel_avg documentation to cla…
alex-l-kong Nov 10, 2022
376874c
Merge branch 'main' into subset_channel_avg
alex-l-kong Nov 11, 2022
c360fc9
Merge branch 'main' into subset_channel_avg
alex-l-kong Nov 15, 2022
c3bccd6
Update FOV subset logic
alex-l-kong Nov 15, 2022
2d90461
Merge remote-tracking branch 'origin/subset_channel_avg' into subset_…
alex-l-kong Nov 15, 2022
493b1e1
Include check for fov_subset_proportion too low
alex-l-kong Nov 15, 2022
f4fb94d
Final checks
alex-l-kong Nov 15, 2022
426dbbb
Fix test for remapping
alex-l-kong Nov 15, 2022
f01943f
Increase FOV subset proportion
alex-l-kong Nov 15, 2022
dfb6a99
Add random seed to pytest
alex-l-kong Nov 15, 2022
86dad65
Merge branch 'main' into subset_channel_avg
alex-l-kong Nov 17, 2022
6f36cbd
Update pixel channel average function to take max subset of FOVs and …
alex-l-kong Nov 21, 2022
9ffb268
Add tests for subsetting more FOVs than there exist
alex-l-kong Nov 21, 2022
0120c40
Add test to verify warning is thrown if final number of clusters is l…
alex-l-kong Nov 21, 2022
146dd11
Merge branch 'main' into subset_channel_avg
alex-l-kong Nov 21, 2022
4d89145
Fix fov_subset_proportion to num_fovs_subset
alex-l-kong Nov 21, 2022
ef60b82
Clarify the warning message
alex-l-kong Nov 22, 2022
507748d
Merge branch 'main' into subset_channel_avg
alex-l-kong Nov 28, 2022
5262030
Initial commit of updated notebook process with summary file generati…
alex-l-kong Nov 29, 2022
9481753
Merge branch 'subset_channel_avg' of https://github.com/angelolab/ark…
alex-l-kong Nov 29, 2022
529ab6e
Purge new pipeline of bugs
alex-l-kong Nov 29, 2022
c2f56ea
Define stubs of new functions
alex-l-kong Nov 30, 2022
896b381
Get tests for the broken up pixel clustering functions in
alex-l-kong Nov 30, 2022
1555c89
Adjust existing meta cluster remapping tests so they don't include av…
alex-l-kong Nov 30, 2022
d9c2390
Documentation fix
alex-l-kong Nov 30, 2022
e30bf83
PYCODESTYLE
alex-l-kong Nov 30, 2022
4754b4a
Adjust test in notebooks_test.py for broken up pixel remapping function
alex-l-kong Nov 30, 2022
40b697f
Update error message for lost clusters in channel subsetting
alex-l-kong Dec 6, 2022
60be1a3
Merge branch 'main' into subset_channel_avg
alex-l-kong Dec 6, 2022
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2 changes: 1 addition & 1 deletion .travis.yml
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Expand Up @@ -27,7 +27,7 @@ jobs:
- stage: pytest_run
script:
- python -m pip install --editable .
- python -m pytest --cov=ark --pycodestyle ark
- python -m pytest --cov=ark --pycodestyle ark --randomly-seed=24 --randomly-dont-reorganize
- stage: test_pypi_deploy
if: tag IS present
script:
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