| --- |
| license: cc-by-nc-4.0 |
| tags: [vesuvius-challenge, herculaneum, ct, lasagna, ome-zarr] |
| pretty_name: PHercMANBp lasagna field (villa predict3d) |
| --- |
| |
| # PHercMANBp lasagna field |
|
|
| villa's lasagna `predict3d` output for the whole PHercMANBp 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/phercmanbp-lasagna --repo-type dataset --local-dir phercmanbp-lasagna |
| cd phercmanbp-lasagna && sha256sum -c SHA256SUMS |
| for f in parts/*.tar; do tar -xf "$f"; done |
| tar -xf PHercMANBp-lasagna-pyramid-fix.tar # last: the joined PHercMANBp.lasagna.json |
| ``` |
|
|
| You end up with `PHercMANBp.lasagna.json` and `PHercMANBp_{cos,grad_mag,nx,ny}.ome.zarr`, 375 MB in all. |
|
|
| ## Load it |
|
|
| Here the scan is level 2 of the 2.399 um volume (9.60 um voxels), as villa reads its fine scans; every |
| coordinate below is in that grid. |
|
|
| ```python |
| import numpy as np |
| import zarr |
| |
| cos = zarr.open("PHercMANBp_cos.ome.zarr/1", mode="r") # every 2nd scan voxel |
| nx = zarr.open("PHercMANBp_nx.ome.zarr/2", mode="r") # every 4th scan voxel |
| ny = zarr.open("PHercMANBp_ny.ome.zarr/2", mode="r") |
| print("cos", cos.shape, "normals", nx.shape) |
| |
| z, y, x = 1536, 1572, 1572 # 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 this snippet; it was run on the real parts before upload. |
|
|
| ## What it is |
|
|
| - Scan: PHercMANBp, `20251216152116-2.399um-0.2m-78keV-masked.zarr`, level 2, Vesuvius Challenge open data |
| - 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: 5 parts on Hugging Face Jobs (RTX PRO 6000), one 1,024-slice slab 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 across every part edge found no step (worst ratio |
| 1.203 against a 1.5 limit). |
| - 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). |
| - Previews: xy at z 2,144 and xz at y 1,572 (scan voxels of the level read). |
| |
|  |
| |
| ## 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 the level named above with no resampling. |
| |
| ## Related |
| |
| villa lasagna fields for ten more scans are on the [Lasagna Fields](https://huggingface.co/spaces/SharpMeow/lasagna-fields) page. |
| |
| ## 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. |
| |
