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Restructure the README for new users - #29
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The scripts and their configs only worked from a clone. They now live in the package (deepaneseg/cli, deepaneseg/configs) and are installed as commands: deepaneseg-remove-skull, -extract-points, -preprocess, -train, -predict and -evaluate. `pip install git+<repo>` is enough to run them from any folder. configs/ is a package so that Hydra finds it once installed. Existing tests now run the modules instead of the script paths; the Docker image and CI use the commands.
deepaneseg-prepare converts a dataset of scans and aneurysm label
masks, by default in the ADAM challenge layout, to the P????/F.csv/
config.json layout the pipeline reads. Scans and masks are found
with {case} patterns, each mask component becomes a two-point
diameter annotation (the sphere fit used by the evaluation code), and
cases.csv maps patients back to the original cases. Cases with an
empty mask become patients without aneurysm.
Reorders the README around first use: a short overview and method summary (the abstract is folded), a quick start with every command, installation (uv, pip, Docker), the data layout and dataset conversion, usage, configuration, outputs, hardware requirements and development. List overrides are quoted so they also work in zsh.
youssefassis
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Sep 30, 2026
Restructure the README for new users
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Based on #28 (merge that first).
Reorganizes the README around first use: overview and method summary (the abstract is folded), a quick start, installation (uv, pip, Docker), data layout and conversion, usage, configuration, outputs, hardware requirements and development. The GitLab note stays at the top.
I ran the quick start as written on a small synthetic ADAM-style dataset. It needs #30 for the patient without aneurysm.