Comments (9)
This isn't a bug in the atlasapi, the validation script explicitly updates the atlas. Maybe the validation script should have some logic to deal specifically with atlas versions that are newer than those on GIN?
from brainglobe-atlasapi.
You can keep it open, just maybe change the title so we know what the actual issue is.
As an aside, I've actually just disabled Discussions. We decided a while back to not use that feature (in favour of issues, Zulip & image.sc), and I didn't know we still had it enabled on this repo.
from brainglobe-atlasapi.
Detect the difference but don't replace the atlases automatically.
What was done automatically? Nothing in BrainGlobe should update the atlases without specific user interaction.
from brainglobe-atlasapi.
It started to download the atlases without me running the brainglobe update -a kim_mouse_25um
(or any other) command.
from brainglobe-atlasapi.
What started to? What process was running?
from brainglobe-atlasapi.
I ran the validation.py
function. This is the output:
(bg-atlasapi) vplattner@hpc-gw1:~/_projects/validation/brainglobe-atlasapi$ python brainglobe_atlasapi/atlas_generation/validate_atlases.py
example_mouse_100um 1.2
allen_mouse_10um 1.2
allen_mouse_25um 1.2
allen_mouse_50um 1.2
allen_mouse_100um 1.2
mpin_zfish_1um 1.0
allen_human_500um 0.1
/nfs/nhome/live/vplattner/_projects/validation/brainglobe-atlasapi/brainglobe_atlasapi/core.py:65: UserWarning: This atlas seems to be outdated as no additional_references list is found in metadata!
warnings.warn(
kim_mouse_10um 1.0
brainglobe_atlasapi: kim_mouse_10um not found locally. Downloading...
Downloading... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.0% • 645.2/645.2 MB • speed: 1.8 MB/s • ETA: 0:00:00
kim_mouse_25um 1.0
brainglobe_atlasapi: kim_mouse_25um version 1.1is not the latest available (1.0). To update the atlas run in the terminal:
brainglobe update -a kim_mouse_25um
brainglobe_atlasapi: kim_mouse_25um version 1.1is not the latest available (1.0). To update the atlas run in the terminal:
brainglobe update -a kim_mouse_25um
brainglobe_atlasapi: kim_mouse_25um version 1.1is not the latest available (1.0). To update the atlas run in the terminal:
brainglobe update -a kim_mouse_25um
brainglobe_atlasapi: updating kim_mouse_25um
Downloading... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.0% • 226.7/226.7 MB • speed: 1.1 MB/s • ETA: 0:00:00
brainglobe_atlasapi: kim_mouse_25um updated to version: 1.0
kim_mouse_50um 1.0
brainglobe_atlasapi: kim_mouse_50um version 1.1is not the latest available (1.0). To update the atlas run in the terminal:
brainglobe update -a kim_mouse_50um
brainglobe_atlasapi: kim_mouse_50um version 1.1is not the latest available (1.0). To update the atlas run in the terminal:
brainglobe update -a kim_mouse_50um
brainglobe_atlasapi: kim_mouse_50um version 1.1is not the latest available (1.0). To update the atlas run in the terminal:
brainglobe update -a kim_mouse_50um
brainglobe_atlasapi: updating kim_mouse_50um
Downloading... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╺━━━━━━━━ 87.8% • 167.2/190.5 MB • speed: 1.1 MB/s • ETA: 0:00:21
from brainglobe-atlasapi.
Can you link to that file?
from brainglobe-atlasapi.
from brainglobe-atlasapi.
Should I convert this into a discussion or close it?
from brainglobe-atlasapi.
Related Issues (20)
- validate_atlases.py additional_references error HOT 5
- Add updated version of the kim atlas HOT 1
- [Feature] flexibly generate atlases with different resolutions
- perens_atlas alignment trouble with new version [BUG] HOT 4
- perens_lsfm_mouse_20um_v1.1 is oriented incorrectly HOT 1
- Use pooch to download data
- User is informed (twice) that the atlas is not the latest when they're updating it
- The warning that an atlas is not the latest is missing a space
- Standardise the axial resolution of the allen spinal cord atlas HOT 1
- Save atlases to `.brainglobe/atlases`
- Atlases should be returned by `brainglobe list` in alphabetical order
- Enforce standardised orientation
- Atlas resolution as an attribute, not a name.
- Move atlas generation code out of the `brainglobe-atlasapi` package
- Ensure all tests are run
- Ensure tests do not affect local system when run locally.
- [BUG] Kim developmental atlases fail validation
- [Feature] Smooth Kim meshes HOT 1
- [Feature] Just one Kim dev top-level mesh
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from brainglobe-atlasapi.