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5f9a510
Follow image order from ds_bboxes.attrs["map_image_id_to_filename"]
sfmig Oct 12, 2026
b3b7c1c
Add images array as data variable
sfmig Oct 12, 2026
3235bc6
Save masks as uint16
sfmig Oct 12, 2026
654d576
Add mask array as a data var to ds_bboxes, with a format matching mas…
sfmig Oct 12, 2026
557bebf
Get mask label from bbox id
sfmig Oct 12, 2026
ab41724
Apply smallest wins policy
sfmig Oct 12, 2026
02dbf13
Proposal to compute geom params from predicted masks from bbox annota…
sfmig Oct 12, 2026
e390ae3
Add note on ethology
sfmig Oct 12, 2026
a4fba1c
Import sam2 and ethology inside main and list new script dependencies
sfmig Oct 12, 2026
8f6c17c
Write bboxes and masks to one xarray zarr store
sfmig Oct 12, 2026
a45eca6
Compute mask and ellipse parameters per bbox and add them to the store
sfmig Oct 12, 2026
37f2750
Document the store layout and mask parameters in the script docstring
sfmig Oct 12, 2026
42e8141
Read bboxes, masks and ellipse parameters from one store in the notebook
sfmig Oct 12, 2026
08984e1
Add AI reviewer notes
sfmig Oct 13, 2026
9dd6db0
Cast the space coordinate to object inside create_dataset_store
sfmig Oct 13, 2026
c7533d8
Raise an error when the id slots do not fit in uint16 labels
sfmig Oct 13, 2026
39a9f69
Read image paths from the store with get_image_paths
sfmig Oct 13, 2026
c93ee88
Check that all images have the same size before running SAM2
sfmig Oct 13, 2026
46ea0a0
Test the smallest-wins overlap policy and the eccentricity
sfmig Oct 13, 2026
e713dd6
Select box corners by dimension name, not by transposing
sfmig Oct 13, 2026
1b5862c
Consolidate the store metadata after predicting masks
sfmig Oct 13, 2026
96d4044
Remove metadata attrs that repeat the dataset
sfmig Oct 13, 2026
c1fc4c2
Say why compute_mask_props reads the masks back from the store
sfmig Oct 13, 2026
dd5bd3c
Clarify label_of and theta for near-circular masks in the docstrings
sfmig Oct 13, 2026
1e2b932
Fix path
sfmig Oct 15, 2026
ec420ac
Fix dtype mismatch (to be reviewed)
sfmig Oct 15, 2026
4fc9153
Keep root attributes when appending mask parameters
sfmig Oct 22, 2026
be0821f
Small edit
sfmig Oct 22, 2026
24fdccc
Clarify risk
sfmig Oct 22, 2026
986c715
Upgrade to ethology 0.1.4 (consistent annotation ids and space is obj…
sfmig Oct 26, 2026
b10b01d
Delete Claude proposal and review
sfmig Oct 26, 2026
889f95a
Small edits to docstrings
sfmig Oct 26, 2026
73fe443
Remove import of script on notebook
sfmig Oct 26, 2026
e8f1612
Move returning labels array out of zarr store initialising fn
sfmig Oct 26, 2026
f4c3d82
Add type annotations
sfmig Oct 26, 2026
051e399
Review and add comments
sfmig Oct 26, 2026
178105b
Remove consolidation not needed
sfmig Oct 26, 2026
4cb0961
Review notebook
sfmig Oct 27, 2026
1a80d9d
Review tests
sfmig Oct 27, 2026
929816e
Rename label IDs
sfmig Oct 27, 2026
298e987
Review last tests
sfmig Oct 27, 2026
084941c
Drop libglapi-mesa from CI OpenGL install
sfmig Oct 27, 2026
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4 changes: 2 additions & 2 deletions .github/workflows/test_and_deploy.yml
Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,7 @@ jobs:
shell: bash -l {0}
run: |
sudo apt-get update
sudo apt-get install libglapi-mesa libegl-mesa0 libegl1 libopengl0 libgl1
sudo apt-get install libegl-mesa0 libegl1 libopengl0 libgl1
- name: Run all tests
uses: neuroinformatics-unit/actions/test@v3
with:
Expand All @@ -76,7 +76,7 @@ jobs:
- name: Install OpenGL libraries
run: |
sudo apt-get update
sudo apt-get install libglapi-mesa libegl-mesa0 libegl1 libopengl0 libgl1
sudo apt-get install libegl-mesa0 libegl1 libopengl0 libgl1
# as in bash_scripts/run_mask_array.sh: install torch (and setuptools)
# first, then build SAM2 against them without build isolation
- name: Install crabs, then SAM2
Expand Down
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