| --- |
| license: cc-by-nc-4.0 |
| tags: [vesuvius-challenge, herculaneum, ct, lasagna, ome-zarr] |
| pretty_name: PHerc0490A lasagna field (villa predict3d) |
| --- |
| |
| # PHerc0490A lasagna field |
|
|
| villa's lasagna `predict3d` output for the whole PHerc0490A scan, in villa's own layout, so you can point lasagna or the |
| spiral fit at it without running the model yourself. The open data has no lasagna field for this scan. |
|
|
|  |
|
|
| ## Get it |
|
|
| ```bash |
| hf download SharpMeow/pherc0490a-lasagna --repo-type dataset --local-dir pherc0490a-lasagna |
| cd pherc0490a-lasagna && sha256sum -c SHA256SUMS |
| for f in parts/*.tar; do tar -xf "$f"; done |
| tar -xf PHerc0490A-lasagna-pyramid-fix.tar # last: the joined PHerc0490A.lasagna.json |
| ``` |
|
|
| You end up with `PHerc0490A.lasagna.json` and `PHerc0490A_{cos,grad_mag,nx,ny}.ome.zarr`. |
|
|
| ## Load it |
|
|
| ```python |
| import numpy as np |
| import zarr |
| |
| cos = zarr.open("PHerc0490A_cos.ome.zarr/1", mode="r") # every 2nd scan voxel |
| nx = zarr.open("PHerc0490A_nx.ome.zarr/2", mode="r") # every 4th scan voxel |
| ny = zarr.open("PHerc0490A_ny.ome.zarr/2", mode="r") |
| print("cos", cos.shape, "normals", nx.shape) |
| |
| z, y, x = 1536, 4550, 4550 # a point in full-resolution scan voxels |
| patch = cos[z // 2, y // 2 - 256:y // 2 + 256, x // 2 - 256:x // 2 + 256] |
| a = (float(nx[z // 4, y // 4, x // 4]) - 128) / 127 |
| b = (float(ny[z // 4, y // 4, x // 4]) - 128) / 127 |
| print("cos patch", patch.shape, "mean", round(float(patch.mean()), 1)) |
| print("normal", round(a, 3), round(b, 3), round(float(np.sqrt(max(0.0, 1 - a * a - b * b))), 3)) |
| ``` |
|
|
| `load_example.py` is a runnable version of this snippet; it was run on the real parts before upload. |
|
|
| ## Stream it, no download |
|
|
| The same field, unpacked, is in the public bucket |
| [SharpMeow/lasagna-fields](https://huggingface.co/buckets/SharpMeow/lasagna-fields) under `PHerc0490A/representations/predictions/lasagna/20250521151210-lasagna-de45f011/`, so any zarr reader |
| can open it by URL: |
|
|
| ```python |
| import zarr # zarr 3, with fsspec and aiohttp |
| |
| base = "https://huggingface.co/buckets/SharpMeow/lasagna-fields/resolve/PHerc0490A/representations/predictions/lasagna/20250521151210-lasagna-de45f011" |
| cos = zarr.open_array(base + "/PHerc0490A_cos.ome.zarr/1", mode="r", zarr_format=2) |
| ``` |
|
|
| Region downloads, a Neuroglancer link and the methods for all ten fields are on the |
| [Lasagna Fields](https://huggingface.co/spaces/SharpMeow/lasagna-fields) page. |
|
|
| ## What it is |
|
|
| - Scan: PHerc0490A, `20250521151210-8.640um-1.2m-116keV-masked.zarr`, level 0, Vesuvius Challenge open data (8.64 um) |
| - Model: `scrollprize/lasagna` `model_current.pt` at revision de45f011 (sha256 4cc0c40a...) |
| - Code: ScrollPrize/villa lasagna at db3dbea2, `lasagna-preprocess predict3d --tile-size 192`, default chunks and levels |
| - Channels: cos at OME-Zarr level 1 (2x down); grad_mag, nx, ny at level 2 (4x down); each with its pyramid |
| - Run: 25 parts on Hugging Face Jobs (RTX PRO 6000), one x, y, z box each. Every part edge sits on a multiple of |
| 1,024 scan voxels, so every chunk of every level, level 4 included, was written by exactly one part, and the parts |
| together are the whole field. A seam check on level 2 found no step at any part edge (worst ratio 1.18 against a |
| 1.5 limit; 1.0 means no step). |
| - Settings check: the same code and settings reproduce villa's published PHerc0343 lasagna field on a test crop |
| (cos within 2 of 255 at every voxel compared). |
| |
| ## Notes |
| |
| Raw model output; nobody has checked it by eye. Regions the masked scan leaves empty are absent (fill 0). The model |
| ran on the scan at its native resolution with no resampling. |
| |
| ## Related |
| |
| A center line (umbilicus) for PHerc0490A is in [SharpMeow/vesuvius-center-lines](https://huggingface.co/datasets/SharpMeow/vesuvius-center-lines). |
| The same kind of field for PHerc0175A is in |
| [SharpMeow/pherc0175a-lasagna](https://huggingface.co/datasets/SharpMeow/pherc0175a-lasagna). |
| |
| ## Credit and terms |
| |
| The scan is Vesuvius Challenge open data, CC BY-NC 4.0; this derived field is shared under the same terms. Model and |
| code are ScrollPrize/villa's lasagna, credit to its authors. Shared by Chase Hendrick. |
| |
