Serve low-res volumes from a writable root; fix make_lowres for real dataset layout

[aperson30]

Why

?res=low has been silently serving full-res because the low-res files never got generated. Two reasons make_lowres.py couldn't run on the server:

1. Read-only mount — it wrote *_lowres.nii.gz next to the originals under PANTS_PATH, which is a read-only NFS mount. nib.save fails there (same class as the uint8-mask issue).
2. Wrong input glob — it globbed PANTS_PATH/data/ImageTr|ImageTe/*/ct.nii.gz, which finds zero cases. The real layout is PANTS_PATH/image_only/<case>/ct.nii.gz + PANTS_PATH/mask_only/<case>/combined_labels.nii.gz.

(Server discovery: 9,901 cases, ~32 MB/CT; factor 2 ≈ 40–45 GB, factor 4 ≈ 5–6 GB; /home has 1.2 TB free.)

Changes

• make_lowres.py: glob image_only/*/ct.nii.gz; write under --out-root (default /home/visitor/pants_lowres, or $PANTS_LOWRES_PATH), mirroring image_only/<case>/ + mask_only/<case>/; makedirs the output dirs; refresh docstring + conda interpreter.
• api_blueprint.py: get-main-nifti / get-segmentations ?res=low now read from LOWRES_ROOT (same default/env) instead of the read-only mount.

Read and write paths use the identical convention, so they line up by construction.

Additive / safe

If the low-res files don't exist, both endpoints fall through to full-res exactly as today — a no-op until the batch runs. Nothing writes into the read-only image_only/ / mask_only/.

Deploy (after merge, on the server)

PYBIN=/home/visitor/.conda/envs/PanTS_backend/bin/python3.11
cd /home/visitor/PanTS-Viewer/flask-server
$PYBIN scripts/make_lowres.py --factor 2 --limit 5   # trial
nohup $PYBIN scripts/make_lowres.py --factor 2 > /tmp/make_lowres.log 2>&1 &   # full batch

No .env change needed (default matches). Restart the backend after the batch so ?res=low starts serving the new files.

Test plan

• py_compile clean on both files
• Trial run (--limit 5) writes to /home/visitor/pants_lowres/{image_only,mask_only}/<case>/…
• After batch + restart: curl ".../api/get-main-nifti/<id>.nii.gz?res=low" returns the smaller file