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remicorne / phd

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allensdk NORMALISATION OF REGIONS #64

Closed jjb-hub closed 1 month ago

jjb-hub commented 7 months ago

The first issue I had with Allensdk was that it updated pandas and broke some things so be mindful.

Here is the reference tree where the atlas names are stored (one place where they are stored) https://allensdk.readthedocs.io/en/latest/reference_space.html

The docs to access this reference space 'tree' structure https://allensdk.readthedocs.io/en/latest/_static/examples/nb/reference_space.html#Constructing-a-structure-tree

jjb-hub commented 7 months ago

temp solution will be to get working phd>module>json>regions_idealy.json dict in jasmine branch

Remi suggests: Maybe you should add a check that len(colname.split('') == 2 ? I surprised i didnt do that

jjb-hub commented 1 month ago

fuck allen SDK too hard but normalised in compounds.json and regions.json