prepare low-res tadpole images for template generation #33

niksirbi · 2024-08-19T17:41:28Z

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What is this PR

What does this PR do?

Adds the scripts that worked to generate an initial low-res tadpole atlas

niksirbi · 2024-10-18T15:43:50Z

Had to set explicit_package_bases = true in the mypy config, to force mypy to ignore duplicate python file names in the "examples" folder, see https://mypy.readthedocs.io/en/stable/running_mypy.html#mapping-file-paths-to-modules

We also tried directly excluding the "examples" folder from type checking, but we couldn't make it work.

examples/tadpole/2_prep_lowres.py

alessandrofelder force-pushed the tadpole-prep-lowres branch from 87ea2c9 to 711e87c Compare August 20, 2024 09:54

alessandrofelder changed the title ~~WIP: adapt prep_lowres for tadpoles~~ prepare low-res tadpole images for template generation Aug 22, 2024

alessandrofelder marked this pull request as ready for review August 22, 2024 14:51

niksirbi and others added 6 commits October 18, 2024 14:01

wip adapt prep_lowres for tadpoles

4b16d86

adapt tadpole prep lowres script for manually aligned data

d1792db

draft build_template.sh

8ace178

additionally apply mask when N4 correcting

bb5c040

renamed and cleaned up prep-lowres script for tadpoles

392ea70

renamed tadpole build template script

654b6ad

niksirbi force-pushed the tadpole-prep-lowres branch from 967a2f4 to 654b6ad Compare October 18, 2024 13:41

niksirbi added 2 commits October 18, 2024 15:47

fixe mypy errors

f163a3a

force mypy to only run on the actual package

c59b704

niksirbi requested a review from alessandrofelder October 18, 2024 15:43

alessandrofelder approved these changes Oct 31, 2024

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examples/tadpole/2_prep_lowres.py Outdated Show resolved Hide resolved

Update examples/tadpole/2_prep_lowres.py

ca15d9f

alessandrofelder merged commit 550db3c into main Oct 31, 2024
23 checks passed

alessandrofelder deleted the tadpole-prep-lowres branch October 31, 2024 13:49