Closed alTeska closed 2 months ago
I tested this new regex with the following setup including barrel annotations:
HIERARCHY=/gpfs/bbp.cscs.ch/project/proj100/atlas/mouse/atlas-release-barrels-may2023/hierarchy.json
ANNOTATION=/gpfs/bbp.cscs.ch/project/proj100/atlas/mouse/atlas-release-barrels-may2023/brain_regions.nrrd
DVECTORS=/gpfs/bbp.cscs.ch/project/proj100/atlas/mouse/atlas-release-barrels-may2023/direction_vectors_isocortex_ccfv3.nrrd
OUTPUT=/gpfs/bbp.cscs.ch/project/proj100/atlas/mouse/placement-hints-test
atlas-placement-hints isocortex --hierarchy-path $HIERARCHY --annotation-path $ANNOTATION --direction-vectors-path $DVECTORS --algorithm voxel-based --output-dir $OUTPUT
The newly created placement hints do not have the artefact mentioned in the issue https://github.com/BlueBrain/atlas-placement-hints/issues/12
As discussed with @lecriste, we also checked if the regex is used anywhere else and it seems that direction-vector interpolation uses it here https://github.com/BlueBrain/atlas-direction-vectors/blob/d0b7331f2add43a9a3b185c9bc594f339daab01d/atlas_direction_vectors/app/direction_vectors.py#L212
and this is the metadata that needs to be updated to the regex proposed in this pull request: https://staging.nise.bbp.epfl.ch/nexus/bbp/atlas/resources/https:%2F%2Fbbp.epfl.ch%2Fneurosciencegraph%2Fdata%2F6a593672-9e7d-45aa-8740-19d79da9b3d3#JSON
OK. Can I rerun the Atlas pipeline with this new version of isocortex_metadata.json
?
For me, yes!
Was the pipeline rerun w/ this @lecriste? If so, we can work on getting CI to pass, and get it merged.
Not yet.
@visood it looks like this issue is causing some problems downstream. Was the fix ever implemented/ run?
Vishal and I , had looked at this issue, and what we found was that the issue with the earlier regexes could be potentially be resolved by setting "with_descendants": false
within layers
element in the isocortex_metadata.json
. What is the rationale for "with_descendants": true
in the current code?
Vishal and I , had looked at this issue, and what we found was that the issue with the earlier regexes could be potentially be resolved by setting
"with_descendants": false
withinlayers
element in theisocortex_metadata.json
. What is the rationale for"with_descendants": true
in the current code?
I don't know but are you sure that's enough to fix the issue @alTeska mentioned here?
I tracked the file in the Atlas pipeline repo: https://bbpgitlab.epfl.ch/dke/apps/blue_brain_atlas_pipeline/-/blob/develop/metadata/isocortex_metadata.json Once you agree on the new version, please open an MR there as well and the pipeline will automatically consume the new file. @rai-pranav
Right now, I guess you can update the current pipeline with what @alTeska regex solution. I will test separately , if my solution produces the same result or not.
The placement hints produced with this version of isocortex_metadata.json
and the new CCFv2022 BBPa annotation are here:
/gpfs/bbp.cscs.ch/data/project/proj84/atlas_pipeline_runs/2024-05-26T20:43:55+02:00/placement_hints/
Let me know if they look good. @alTeska @rai-pranav
I had a look at the new [PH]y.nrrd
, there is no artefact in this placement hints, approved.
Was the pipeline rerun w/ this @lecriste? If so, we can work on getting CI to pass, and get it merged.
@mgeplf, it seems we can proceed.
Ok, I also did a release: https://github.com/BlueBrain/atlas-placement-hints/releases/tag/v0.1.3
as discussed: https://github.com/BlueBrain/atlas-commons/pull/5
For layers 6a and 6b the regex still keeps the
6[ab]
part, the rest is removed.Uncertain why the original layer 3 regex had additional symbols:
[^/]3
, am I missing something?