Spaces:
Running on Zero
Running on Zero
Every field: Dataset, Manifest, Preview and Copy URL on every field (public Scrolls 0896f42, #293)
Browse files- app.py +6 -3
- fields.json +150 -63
- guide/index.html +46 -26
- make_previews.py +94 -0
- make_thumbs.py +15 -10
app.py
CHANGED
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@@ -209,7 +209,8 @@ def volume_text(vid):
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pub_line = "The open data has villa's field for this scan, so each box is checked against it."
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else:
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listed = [f for f in field_doc().get("fields", []) if f["volume"] == v["volume"] and f.get("dataset")]
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pub_line = ("
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+ (f" Its whole-scan field ({listed[0]['model']}) is on the Every field tab as "
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f"{listed[0]['dataset']}." if listed else ""))
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return (f"{' × '.join(map(str, shape))} voxels (z × y × x) at {v['voxel_um']:g} um. The model reads level "
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@@ -289,10 +290,12 @@ def list_fields(scroll: str = ""):
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villa's own fields in the Vesuvius Challenge open data and the public SharpMeow datasets (made with villa's
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lasagna predict3d or with Lasagnetta 0.1.1, a faster copy of it). Args: scroll, part of a scroll name to keep
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only its fields (empty for all). Returns a list of {scroll, volume, zarr, voxel_um, read_level, model, source,
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made_by, bytes, url, dataset, manifest, stream, note}: stream is
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"""
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keep = ("scroll", "volume", "zarr", "voxel_um", "read_level", "model", "source", "made_by", "bytes", "url",
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"dataset", "manifest", "stream", "note")
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q = str(scroll or "").strip().lower()
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return [{k: f.get(k) for k in keep} for f in field_doc().get("fields", []) if q in f["scroll"].lower()]
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pub_line = "The open data has villa's field for this scan, so each box is checked against it."
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else:
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listed = [f for f in field_doc().get("fields", []) if f["volume"] == v["volume"] and f.get("dataset")]
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+
pub_line = ("Boxes are checked only against the open data's fields and the ten in the Preview tab, so there is "
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+
"nothing to check against for this scan."
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+ (f" Its whole-scan field ({listed[0]['model']}) is on the Every field tab as "
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f"{listed[0]['dataset']}." if listed else ""))
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return (f"{' × '.join(map(str, shape))} voxels (z × y × x) at {v['voxel_um']:g} um. The model reads level "
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villa's own fields in the Vesuvius Challenge open data and the public SharpMeow datasets (made with villa's
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lasagna predict3d or with Lasagnetta 0.1.1, a faster copy of it). Args: scroll, part of a scroll name to keep
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only its fields (empty for all). Returns a list of {scroll, volume, zarr, voxel_um, read_level, model, source,
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+
made_by, bytes, url, dataset, manifest, stream, preview_xy, preview_xz, browse, note}: stream is the run folder
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that zarr reads by URL, manifest its lasagna.json, preview_xy and preview_xz pictures of cos and normals, and
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browse the page to download it from (the dataset, or the open data's file browser).
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"""
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keep = ("scroll", "volume", "zarr", "voxel_um", "read_level", "model", "source", "made_by", "bytes", "url",
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+
"dataset", "manifest", "stream", "preview_xy", "preview_xz", "browse", "note")
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q = str(scroll or "").strip().lower()
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return [{k: f.get(k) for k in keep} for f in field_doc().get("fields", []) if q in f["scroll"].lower()]
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fields.json
CHANGED
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@@ -20,10 +20,13 @@
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"bytes": 7835721663,
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"dataset": "SharpMeow/pherc0009b-lasagnetta",
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"url": "https://huggingface.co/datasets/SharpMeow/pherc0009b-lasagnetta",
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"manifest":
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"stream":
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"gallery": false,
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"note": "the release's self-check kept Lasagnetta on this volume"
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},
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{
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"scroll": "PHerc0009B",
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"bytes": 4397390728,
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"dataset": "SharpMeow/pherc0009b-20250820154339-lasagnetta",
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"url": "https://huggingface.co/datasets/SharpMeow/pherc0009b-20250820154339-lasagnetta",
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"manifest":
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"stream":
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"gallery": false,
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"note": "the release's self-check kept Lasagnetta on this volume"
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},
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{
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"scroll": "PHerc0009B",
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"bytes": 4076425380,
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"dataset": "SharpMeow/pherc0009b-20260319104112-lasagnetta",
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"url": "https://huggingface.co/datasets/SharpMeow/pherc0009b-20260319104112-lasagnetta",
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"manifest":
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"stream":
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"gallery": false,
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"note": "the release's self-check kept Lasagnetta on this volume"
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},
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{
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"scroll": "PHerc0139",
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"manifest": "https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHerc0139/representations/predictions/lasagna/20260102150214-lasagna-20260419180421-L2/PHerc0139-20260102150214-lasagna-20260724.lasagna.json",
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"stream": "https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHerc0139/representations/predictions/lasagna/20260102150214-lasagna-20260419180421-L2",
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"gallery": false,
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"note": "made on 20260102150214, which 20260930100252 replaces in the same voxel frame"
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},
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{
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"scroll": "PHerc0172",
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"bytes": 136447650060,
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"dataset": "SharpMeow/pherc0172-lasagnetta",
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"url": "https://huggingface.co/datasets/SharpMeow/pherc0172-lasagnetta",
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"manifest":
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"stream":
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"gallery": false,
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"note": "the release's self-check pointed to villa's net here: a quick look; use villa's field where exact values matter"
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},
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{
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"scroll": "PHerc0175A",
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"bytes": 48177794159,
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"dataset": "SharpMeow/pherc0175a-lasagna",
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"url": "https://huggingface.co/datasets/SharpMeow/pherc0175a-lasagna",
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"manifest":
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"stream": "https://huggingface.co/buckets/SharpMeow/lasagna-fields/resolve/PHerc0175A/representations/predictions/lasagna/20250521115057-lasagna-de45f011",
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"gallery": true,
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"note": null
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},
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{
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"scroll": "PHerc0175B",
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"bytes": 82186090388,
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"dataset": "SharpMeow/pherc0175b-lasagna",
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"url": "https://huggingface.co/datasets/SharpMeow/pherc0175b-lasagna",
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"manifest":
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"stream": "https://huggingface.co/buckets/SharpMeow/lasagna-fields/resolve/PHerc0175B/representations/predictions/lasagna/20250521125822-lasagna-de45f011",
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"gallery": true,
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"note": null
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},
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{
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"scroll": "PHerc0306B",
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"bytes": 54562105533,
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"dataset": "SharpMeow/pherc0306b-lasagna",
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"url": "https://huggingface.co/datasets/SharpMeow/pherc0306b-lasagna",
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"manifest":
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"stream": "https://huggingface.co/buckets/SharpMeow/lasagna-fields/resolve/PHerc0306B/representations/predictions/lasagna/20250521133212-lasagna-de45f011",
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"gallery": true,
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"note": null
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},
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{
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"scroll": "PHerc0332",
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"manifest": "https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHerc0332/representations/predictions/lasagna/20251211183505-lasagna-20260419180421-L2/PHerc0332-20251211183505-lasagna-20260724.lasagna.json",
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"stream": "https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHerc0332/representations/predictions/lasagna/20251211183505-lasagna-20260419180421-L2",
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"gallery": false,
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"note": null
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},
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{
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"scroll": "PHerc0343",
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"manifest": "https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHerc0343/representations/predictions/lasagna/20250521140437-lasagna-20260419180421/PHerc0343.lasagna.json",
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"stream": "https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHerc0343/representations/predictions/lasagna/20250521140437-lasagna-20260419180421",
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"gallery": false,
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"note": null
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},
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{
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"scroll": "PHerc0343P",
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"bytes": 1849003527,
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"dataset": "SharpMeow/pherc0343p-lasagna",
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"url": "https://huggingface.co/datasets/SharpMeow/pherc0343p-lasagna",
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"manifest":
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"stream":
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"gallery": false,
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"note": null
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},
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{
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"scroll": "PHerc0483A",
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"bytes": 47412439255,
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"dataset": "SharpMeow/pherc0483a-lasagna",
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"url": "https://huggingface.co/datasets/SharpMeow/pherc0483a-lasagna",
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"manifest":
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"stream": "https://huggingface.co/buckets/SharpMeow/lasagna-fields/resolve/PHerc0483A/representations/predictions/lasagna/20250521140913-lasagna-de45f011",
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"gallery": true,
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},
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{
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"scroll": "PHerc0483B",
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"bytes": 41488155807,
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"dataset": "SharpMeow/pherc0483b-lasagna",
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"url": "https://huggingface.co/datasets/SharpMeow/pherc0483b-lasagna",
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"manifest":
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"stream": "https://huggingface.co/buckets/SharpMeow/lasagna-fields/resolve/PHerc0483B/representations/predictions/lasagna/20251124083638-lasagna-de45f011",
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"gallery": true,
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"note": null
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},
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"scroll": "PHerc0490A",
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"bytes": 49710518643,
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"dataset": "SharpMeow/pherc0490a-lasagna",
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"url": "https://huggingface.co/datasets/SharpMeow/pherc0490a-lasagna",
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"manifest":
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"stream": "https://huggingface.co/buckets/SharpMeow/lasagna-fields/resolve/PHerc0490A/representations/predictions/lasagna/20250521151210-lasagna-de45f011",
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"gallery": true,
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"note": null
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},
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{
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"scroll": "PHerc0490B",
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"bytes": 32900441240,
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"dataset": "SharpMeow/pherc0490b-lasagna",
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"url": "https://huggingface.co/datasets/SharpMeow/pherc0490b-lasagna",
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"manifest":
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"stream": "https://huggingface.co/buckets/SharpMeow/lasagna-fields/resolve/PHerc0490B/representations/predictions/lasagna/20250521151215-lasagna-de45f011",
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"gallery": true,
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},
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{
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"scroll": "PHerc0500P2",
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"bytes": 1616067316,
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"dataset": "SharpMeow/pherc0500p2-lasagnetta",
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"url": "https://huggingface.co/datasets/SharpMeow/pherc0500p2-lasagnetta",
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"manifest":
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"stream":
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"gallery": false,
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"note": "the release's self-check has not been run on this whole volume"
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},
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{
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"scroll": "PHerc0814",
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"bytes": 33631289069,
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"dataset": "SharpMeow/pherc0814-20250804134230-lasagnetta",
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"url": "https://huggingface.co/datasets/SharpMeow/pherc0814-20250804134230-lasagnetta",
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"manifest":
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"stream":
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"gallery": false,
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"note": "the release's self-check kept Lasagnetta on this volume"
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},
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"scroll": "PHerc0814",
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"manifest": "https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHerc0814/representations/predictions/lasagna/20260309142202-lasagna-20260419180421-L2/PHerc0814-20260309142202-lasagna-20260724.lasagna.json",
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"stream": "https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHerc0814/representations/predictions/lasagna/20260309142202-lasagna-20260419180421-L2",
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"gallery": false,
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},
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"scroll": "PHerc0814",
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"bytes": 5145709178,
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"dataset": "SharpMeow/pherc0814-20260521123630-lasagnetta",
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"url": "https://huggingface.co/datasets/SharpMeow/pherc0814-20260521123630-lasagnetta",
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-
"manifest":
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"stream":
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"gallery": false,
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"note": "the release's self-check kept Lasagnetta on this volume"
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},
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"scroll": "PHerc0841",
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"bytes": 45944868402,
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"dataset": "SharpMeow/pherc0841-lasagna",
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"url": "https://huggingface.co/datasets/SharpMeow/pherc0841-lasagna",
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"manifest":
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"stream": "https://huggingface.co/buckets/SharpMeow/lasagna-fields/resolve/PHerc0841/representations/predictions/lasagna/20250821151531-lasagna-de45f011",
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"gallery": true,
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},
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"scroll": "PHerc0841",
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"bytes": 8698480358,
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"dataset": "SharpMeow/pherc0841-20260319124803-lasagnetta",
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"url": "https://huggingface.co/datasets/SharpMeow/pherc0841-20260319124803-lasagnetta",
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"manifest":
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"stream":
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"gallery": false,
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"note": "the release's self-check kept Lasagnetta on this volume"
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},
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{
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"scroll": "PHerc0846A",
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"bytes": 32441070754,
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"dataset": "SharpMeow/pherc0846a-lasagna",
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"url": "https://huggingface.co/datasets/SharpMeow/pherc0846a-lasagna",
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"manifest":
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"stream": "https://huggingface.co/buckets/SharpMeow/lasagna-fields/resolve/PHerc0846A/representations/predictions/lasagna/20250728152254-lasagna-de45f011",
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"gallery": true,
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},
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"scroll": "PHerc0846B",
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"bytes": 35033336610,
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"dataset": "SharpMeow/pherc0846b-lasagna",
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"url": "https://huggingface.co/datasets/SharpMeow/pherc0846b-lasagna",
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"manifest":
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"stream": "https://huggingface.co/buckets/SharpMeow/lasagna-fields/resolve/PHerc0846B/representations/predictions/lasagna/20250804142305-lasagna-de45f011",
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"gallery": true,
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},
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"scroll": "PHerc1299",
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"manifest": "https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHerc1299/representations/predictions/lasagna/20260309130042-lasagna-20260419180421-L2/PHerc1299-20260309130042-lasagna-20260724.lasagna.json",
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"stream": "https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHerc1299/representations/predictions/lasagna/20260309130042-lasagna-20260419180421-L2",
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"gallery": false,
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"scroll": "PHerc1667",
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guide/index.html
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@@ -121,9 +121,6 @@ footer .wrap{display:flex;justify-content:space-between;gap:20px;flex-wrap:wrap}
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| 121 |
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@@ -154,6 +151,17 @@ table.flist td.mdl{max-width:300px}
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|
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@@ -221,7 +229,7 @@ table.flist td.mdl{max-width:300px}
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<span>Also: <a href="https://huggingface.co/datasets/SharpMeow/vesuvius-center-lines">center lines</a> · <a href="https://huggingface.co/spaces/SharpMeow/umbilici?mode=lasagna&scan=PHerc0175A&z=6400">PHerc0175A in 3D</a></span>
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|
| 368 |
<script id="fieldlist" type="application/json">null</script>
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@@ -427,35 +440,28 @@ const attr=s=>esc(String(s)).replace(/"/g,'"');
|
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| 427 |
const uniq=a=>a.filter((v,i)=>a.indexOf(v)===i);
|
| 428 |
const um=v=>(+v).toLocaleString('en-US',{maximumFractionDigits:3})+' µm';
|
| 429 |
const lvl=f=>f.read_level?'read at level '+f.read_level+', '+(f.voxel_um*Math.pow(2,f.read_level)).toFixed(1)+' µm':'read at full resolution';
|
| 430 |
-
let fm='',fq='',fw='',fv='cards';
|
|
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|
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|
|
|
|
| 431 |
function fieldRow(f,first,n){
|
| 432 |
-
const
|
| 433 |
-
if(f.dataset)L.push('<a href="'+attr(f.url)+'">Dataset</a>');
|
| 434 |
-
if(f.manifest)L.push('<a href="'+attr(f.manifest)+'">Manifest</a>');
|
| 435 |
-
if(f.gallery)L.push('<button type="button" data-show="'+attr(f.scroll)+'">Preview</button>');
|
| 436 |
-
if(f.stream)L.push('<button type="button" data-url="'+attr(f.stream)+'">Copy URL</button>');
|
| 437 |
-
const where=f.source==='open-data'?'Open data<span class="fnote">villa\'s run, streams by URL</span>':'SharpMeow dataset'+(f.stream?'<span class="fnote">also streams from the bucket</span>':'');
|
| 438 |
return '<tr>'+(first?'<td class="sc" rowspan="'+n+'">'+esc(f.scroll)+'</td>':'')+
|
| 439 |
'<td data-k="Volume"><span class="mono">'+esc(f.volume)+'</span></td>'+
|
| 440 |
'<td data-k="Voxel size" class="num">'+um(f.voxel_um)+'<span class="fnote">'+lvl(f)+'</span></td>'+
|
| 441 |
'<td data-k="Model" class="mdl"><span class="mp '+(f.model.indexOf('Lasagnetta')===0?'lgt':'villa')+'">'+esc(f.model)+'</span>'+(f.note?'<span class="fnote">'+esc(f.note)+'</span>':'')+'</td>'+
|
| 442 |
'<td data-k="Where">'+where+'</td><td data-k="Size" class="num">'+gb(f.bytes)+'</td>'+
|
| 443 |
-
'<td class="get"><div class="flinks">'+
|
| 444 |
-
const
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| 445 |
-
function
|
| 446 |
-
return {src:'assets/thumbs/'+n+'.webp',alt:'https://huggingface.co/datasets/'+f.dataset+'/resolve/main/preview-xy.png',vol:f.volume}}
|
| 447 |
-
function cardLine(f){const L=[];
|
| 448 |
-
if(f.dataset)L.push('<a href="'+attr(f.url)+'">Dataset</a>');
|
| 449 |
-
if(f.manifest)L.push('<a href="'+attr(f.manifest)+'">Manifest</a>');
|
| 450 |
-
if(f.gallery)L.push('<button type="button" data-show="'+attr(f.scroll)+'">Preview</button>');
|
| 451 |
-
if(f.stream)L.push('<button type="button" data-url="'+attr(f.stream)+'">Copy URL</button>');
|
| 452 |
const src=f.source==='open-data'?'open data':'SharpMeow';
|
| 453 |
return '<li><div class="res">'+um(f.voxel_um)+'<span class="mono">'+esc(f.volume)+'</span></div><div class="sz">'+gb(f.bytes)+'</div>'+
|
| 454 |
-
'<div class="row2"><span class="mp '+(f.model.indexOf('Lasagnetta')===0?'lgt':'villa')+'">'+esc(f.model)+'</span><span class="fnote" style="margin:0">'+src+(f.read_level?', level '+f.read_level:'')+'</span><div class="flinks">'+
|
| 455 |
(f.note?'<div class="why">'+esc(f.note)+'</div>':'')+'</li>'}
|
| 456 |
function card(g){const t=thumbOf(g),n=g.length;
|
| 457 |
-
const img=
|
| 458 |
-
:'<div class="ph"><i></i><span>villa field in the open data · stream it by URL</span></div>';
|
| 459 |
return '<article class="sccard"><div class="thumb">'+img+'</div><div class="hd"><h3>'+esc(g[0].scroll)+'</h3><span class="cnt">'+n+(n===1?' field':' fields')+' · '+gb(g.reduce((a,f)=>a+f.bytes,0))+'</span></div><ul>'+g.map(cardLine).join('')+'</ul></article>'}
|
| 460 |
function drawFields(){
|
| 461 |
const t=$('flist');t.querySelectorAll('tbody').forEach(b=>b.remove());
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@@ -463,7 +469,7 @@ function drawFields(){
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| 463 |
if(!F){t.insertAdjacentHTML('beforeend','<tbody><tr><td colspan="7" class="fempty">The list is filled in on the Space: <a href="https://huggingface.co/spaces/SharpMeow/lasagna-fields">huggingface.co/spaces/SharpMeow/lasagna-fields</a>.</td></tr></tbody>');
|
| 464 |
$('fcards').innerHTML='<p class="fempty">The list is filled in on the Space: <a href="https://huggingface.co/spaces/SharpMeow/lasagna-fields">huggingface.co/spaces/SharpMeow/lasagna-fields</a>.</p>';return}
|
| 465 |
const q=fq.trim().toLowerCase();
|
| 466 |
-
const rows=FL.filter(f=>(!fm||f.model===fm)&&(!fw||
|
| 467 |
const groups=uniq(rows.map(f=>f.scroll)).map(s=>rows.filter(f=>f.scroll===s));
|
| 468 |
t.insertAdjacentHTML('beforeend',groups.length?groups.map(g=>'<tbody>'+g.map((f,i)=>fieldRow(f,i===0,g.length)).join('')+'</tbody>').join(''):'<tbody><tr><td colspan="7" class="fempty">No field matches.</td></tr></tbody>');
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| 469 |
$('fcards').innerHTML=groups.length?groups.map(card).join(''):'<p class="fempty">No field matches.</p>';
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document.querySelectorAll('[data-fm]').forEach(b=>b.onclick=()=>{fm=b.dataset.fm;document.querySelectorAll('[data-fm]').forEach(x=>x.setAttribute('aria-pressed',x===b));drawFields()});
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$('fq').oninput=()=>{fq=$('fq').value;drawFields()};
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['flist','fcards'].forEach(id=>$(id).addEventListener('click',e=>{const b=e.target.closest('button');if(!b)return;
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-
if(b.dataset.
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| 477 |
if(b.dataset.url){const t=b.dataset.url,done=()=>{b.textContent='Copied';$('toast').classList.add('on');setTimeout(()=>{b.textContent='Copy URL';$('toast').classList.remove('on')},1200)};
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if(navigator.clipboard&&navigator.clipboard.writeText)navigator.clipboard.writeText(t).then(done,()=>fallback(t,done));else fallback(t,done)}}));
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/* the volumes being made: shown without any link until each is public (fields.json, pending_not_public) */
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if(FP.length){$('pend').hidden=false;
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$('pend').innerHTML='<h3>Being made now, not public yet</h3><p class="sub" style="margin-bottom:14px">Lasagnetta 0.1.1 fields for more volumes of scrolls in the list. None is public yet, so there is nothing to download or stream.</p>'+
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.sccard{background:var(--card);border:1px solid var(--line);border-radius:16px;overflow:hidden;box-shadow:var(--shadow);display:flex;flex-direction:column}
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.sccard .thumb{position:relative;aspect-ratio:2/1;background:#000;overflow:hidden}
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.sccard .thumb img{display:block;width:100%;height:100%;object-fit:cover}
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.sccard .thumb .tag{position:absolute;left:10px;bottom:8px;font-size:11.5px;color:#f1e9dc;background:#000a;padding:2px 8px;border-radius:6px}
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.sccard .hd{display:flex;align-items:baseline;justify-content:space-between;gap:10px;padding:12px 16px 4px}
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.sccard .hd h3{font-size:21px;margin:0}
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.fempty{color:var(--ink3);padding:14px 2px}
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#pend{margin-top:30px}
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#pend table td{color:var(--ink2)}
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.lbox{position:fixed;inset:0;z-index:60;background:color-mix(in srgb,#000 62%,transparent);display:grid;place-items:center;padding:16px}
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.lbox[hidden]{display:none}
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html.lbopen{overflow:hidden}
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.lbpanel{background:var(--card);color:var(--ink);border-radius:16px;box-shadow:var(--shadow);width:min(1100px,100%);max-height:calc(100vh - 32px);display:flex;flex-direction:column;overflow:hidden}
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.lbhead{display:flex;gap:12px;align-items:center;flex-wrap:wrap;padding:12px 16px;border-bottom:1px solid var(--line)}
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.lbhead b{font-size:15px;margin-right:auto}
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#lbslice[hidden]{display:none}
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@media (max-width:600px){.lbhead .seg{order:3;width:100%}.lbhead .seg button{flex:1}}
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.lbx{border:1px solid var(--line);background:var(--bg2);color:var(--ink);border-radius:9px;padding:6px 12px;font:inherit;font-size:13.5px;cursor:pointer}
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#lbimg{display:block;width:100%;min-height:0;flex:1 1 auto;object-fit:contain;background:#0e1117}
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.lbfoot{display:flex;gap:12px;align-items:center;justify-content:space-between;flex-wrap:wrap;padding:10px 16px;font-size:13px;color:var(--ink2)}
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.toast{position:fixed;bottom:20px;left:50%;transform:translateX(-50%) translateY(20px);background:var(--ink);color:var(--bg);padding:8px 14px;border-radius:9px;font-size:14px;opacity:0;transition:.2s;pointer-events:none;z-index:50}
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.toast.on{opacity:1;transform:translateX(-50%)}
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@media (max-width:900px){
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| 229 |
<button type="button" data-fm="" aria-pressed="true">All</button><button type="button" data-fm="villa predict3d" aria-pressed="false">villa predict3d</button><button type="button" data-fm="Lasagnetta 0.1.1" aria-pressed="false">Lasagnetta 0.1.1</button>
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| 230 |
</div>
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| 231 |
<div class="seg" role="group" aria-label="Where">
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| 232 |
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<button type="button" data-fw="" aria-pressed="true">Any source</button><button type="button" data-fw="open-data" aria-pressed="false">Open data</button><button type="button" data-fw="dataset" aria-pressed="false">Made here</button>
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| 233 |
</div>
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<span class="fcount" id="fcount"></span>
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| 235 |
<div class="seg vseg" role="group" aria-label="Layout">
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| 270 |
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| 271 |
<section id="connect"><div class="wrap">
|
| 272 |
<h2>Connect your tool</h2>
|
| 273 |
+
<p class="sub">Every field made here is also in the public bucket <a href="https://huggingface.co/buckets/SharpMeow/lasagna-fields">SharpMeow/lasagna-fields</a>, laid out like the Vesuvius Challenge open data (<code>SCAN/representations/predictions/lasagna/RUN/</code>). Any tool that reads zarr over HTTPS can open it, with no download and no account. The commands here follow the scan you picked above. villa's fields in the open data stream the same way from their run folder: <b>Copy URL</b> in the list gives any field's folder.</p>
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| 274 |
<div class="panel">
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| 275 |
<div style="display:flex;justify-content:space-between;gap:12px;flex-wrap:wrap;align-items:center"><h3 id="cname" style="margin:0"></h3><span style="color:var(--ink3);font-size:13px">Anonymous HTTPS, CORS open, missing chunks read as empty</span></div>
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| 276 |
<div class="codebox"><pre id="curl"></pre><button class="copy" data-copy="curl" type="button">Copy</button></div>
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| 371 |
<span>Also: <a href="https://huggingface.co/datasets/SharpMeow/vesuvius-center-lines">center lines</a> · <a href="https://huggingface.co/spaces/SharpMeow/umbilici?mode=lasagna&scan=PHerc0175A&z=6400">PHerc0175A in 3D</a></span>
|
| 372 |
</div></footer>
|
| 373 |
<div class="toast" id="toast">Copied</div>
|
| 374 |
+
<div class="lbox" id="lbox" hidden role="dialog" aria-modal="true" aria-labelledby="lbtitle"><div class="lbpanel">
|
| 375 |
+
<div class="lbhead"><b id="lbtitle"></b><div class="seg"><button type="button" data-lv="xy" aria-pressed="true">Through the middle</button><button type="button" data-lv="xz" aria-pressed="false">Along the scroll</button></div><button type="button" class="lbx" id="lbclose" aria-label="Close">Close</button></div>
|
| 376 |
+
<img id="lbimg" alt="">
|
| 377 |
+
<div class="lbfoot"><span>Model output: cos (one band per papyrus layer) beside the surface normals as color.</span><button type="button" class="btn" id="lbslice">Open in the slice viewer</button></div>
|
| 378 |
+
</div></div>
|
| 379 |
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| 380 |
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|
| 381 |
<script id="fieldlist" type="application/json">null</script>
|
|
|
|
| 440 |
const uniq=a=>a.filter((v,i)=>a.indexOf(v)===i);
|
| 441 |
const um=v=>(+v).toLocaleString('en-US',{maximumFractionDigits:3})+' µm';
|
| 442 |
const lvl=f=>f.read_level?'read at level '+f.read_level+', '+(f.voxel_um*Math.pow(2,f.read_level)).toFixed(1)+' µm':'read at full resolution';
|
| 443 |
+
let fm='',fq='',fw='',fv='cards',pv=null;
|
| 444 |
+
function links(f){const od=f.source==='open-data';
|
| 445 |
+
return '<a href="'+attr(f.browse||f.url)+'" target="_blank" rel="noopener" title="'+(od?'its run folder in the Vesuvius Challenge open data':'its Hugging Face dataset, to download')+'">Dataset</a>'+
|
| 446 |
+
'<a href="'+attr(f.manifest)+'" target="_blank" rel="noopener" title="the lasagna.json the lasagna fit reads">Manifest</a>'+
|
| 447 |
+
'<button type="button" data-pv="'+FL.indexOf(f)+'" title="cos and normals, through the middle and along the scroll">Preview</button>'+
|
| 448 |
+
'<button type="button" data-url="'+attr(f.stream)+'" title="the run folder, which zarr reads by URL">Copy URL</button>'}
|
| 449 |
function fieldRow(f,first,n){
|
| 450 |
+
const where=f.source==='open-data'?'Open data<span class="fnote">villa\'s run</span>':'SharpMeow dataset<span class="fnote">also in the public bucket</span>';
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|
|
|
|
|
|
|
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|
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|
|
| 451 |
return '<tr>'+(first?'<td class="sc" rowspan="'+n+'">'+esc(f.scroll)+'</td>':'')+
|
| 452 |
'<td data-k="Volume"><span class="mono">'+esc(f.volume)+'</span></td>'+
|
| 453 |
'<td data-k="Voxel size" class="num">'+um(f.voxel_um)+'<span class="fnote">'+lvl(f)+'</span></td>'+
|
| 454 |
'<td data-k="Model" class="mdl"><span class="mp '+(f.model.indexOf('Lasagnetta')===0?'lgt':'villa')+'">'+esc(f.model)+'</span>'+(f.note?'<span class="fnote">'+esc(f.note)+'</span>':'')+'</td>'+
|
| 455 |
'<td data-k="Where">'+where+'</td><td data-k="Size" class="num">'+gb(f.bytes)+'</td>'+
|
| 456 |
+
'<td class="get"><div class="flinks">'+links(f)+'</div></td></tr>'}
|
| 457 |
+
function thumbOf(g){const f=g[0];return {src:'assets/thumbs/'+f.scroll+'-'+f.volume+'.webp',alt:f.preview_xy,vol:f.volume}}
|
| 458 |
+
function cardLine(f){
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|
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|
|
|
|
| 459 |
const src=f.source==='open-data'?'open data':'SharpMeow';
|
| 460 |
return '<li><div class="res">'+um(f.voxel_um)+'<span class="mono">'+esc(f.volume)+'</span></div><div class="sz">'+gb(f.bytes)+'</div>'+
|
| 461 |
+
'<div class="row2"><span class="mp '+(f.model.indexOf('Lasagnetta')===0?'lgt':'villa')+'">'+esc(f.model)+'</span><span class="fnote" style="margin:0">'+src+(f.read_level?', level '+f.read_level:'')+'</span><div class="flinks">'+links(f)+'</div></div>'+
|
| 462 |
(f.note?'<div class="why">'+esc(f.note)+'</div>':'')+'</li>'}
|
| 463 |
function card(g){const t=thumbOf(g),n=g.length;
|
| 464 |
+
const img='<img loading="lazy" src="'+t.src+'" data-alt="'+attr(t.alt)+'" alt="'+attr(g[0].scroll)+' field preview, cos and normals" onerror="if(this.dataset.alt){this.src=this.dataset.alt;this.dataset.alt=\'\'}"><span class="tag">cos | normals · '+esc(t.vol)+'</span>';
|
|
|
|
| 465 |
return '<article class="sccard"><div class="thumb">'+img+'</div><div class="hd"><h3>'+esc(g[0].scroll)+'</h3><span class="cnt">'+n+(n===1?' field':' fields')+' · '+gb(g.reduce((a,f)=>a+f.bytes,0))+'</span></div><ul>'+g.map(cardLine).join('')+'</ul></article>'}
|
| 466 |
function drawFields(){
|
| 467 |
const t=$('flist');t.querySelectorAll('tbody').forEach(b=>b.remove());
|
|
|
|
| 469 |
if(!F){t.insertAdjacentHTML('beforeend','<tbody><tr><td colspan="7" class="fempty">The list is filled in on the Space: <a href="https://huggingface.co/spaces/SharpMeow/lasagna-fields">huggingface.co/spaces/SharpMeow/lasagna-fields</a>.</td></tr></tbody>');
|
| 470 |
$('fcards').innerHTML='<p class="fempty">The list is filled in on the Space: <a href="https://huggingface.co/spaces/SharpMeow/lasagna-fields">huggingface.co/spaces/SharpMeow/lasagna-fields</a>.</p>';return}
|
| 471 |
const q=fq.trim().toLowerCase();
|
| 472 |
+
const rows=FL.filter(f=>(!fm||f.model===fm)&&(!fw||f.source===fw)&&(!q||f.scroll.toLowerCase().indexOf(q)>=0||f.volume.indexOf(q)>=0));
|
| 473 |
const groups=uniq(rows.map(f=>f.scroll)).map(s=>rows.filter(f=>f.scroll===s));
|
| 474 |
t.insertAdjacentHTML('beforeend',groups.length?groups.map(g=>'<tbody>'+g.map((f,i)=>fieldRow(f,i===0,g.length)).join('')+'</tbody>').join(''):'<tbody><tr><td colspan="7" class="fempty">No field matches.</td></tr></tbody>');
|
| 475 |
$('fcards').innerHTML=groups.length?groups.map(card).join(''):'<p class="fempty">No field matches.</p>';
|
|
|
|
| 479 |
document.querySelectorAll('[data-fm]').forEach(b=>b.onclick=()=>{fm=b.dataset.fm;document.querySelectorAll('[data-fm]').forEach(x=>x.setAttribute('aria-pressed',x===b));drawFields()});
|
| 480 |
$('fq').oninput=()=>{fq=$('fq').value;drawFields()};
|
| 481 |
['flist','fcards'].forEach(id=>$(id).addEventListener('click',e=>{const b=e.target.closest('button');if(!b)return;
|
| 482 |
+
if(b.dataset.pv){openPv(FL[+b.dataset.pv],'xy');return}
|
| 483 |
if(b.dataset.url){const t=b.dataset.url,done=()=>{b.textContent='Copied';$('toast').classList.add('on');setTimeout(()=>{b.textContent='Copy URL';$('toast').classList.remove('on')},1200)};
|
| 484 |
if(navigator.clipboard&&navigator.clipboard.writeText)navigator.clipboard.writeText(t).then(done,()=>fallback(t,done));else fallback(t,done)}}));
|
| 485 |
+
/* preview: the field's two pictures in a box over the page (no scrolling of its own) */
|
| 486 |
+
function openPv(f,view){pv=f;const L=$('lbox');
|
| 487 |
+
$('lbimg').src=view==='xz'?f.preview_xz:f.preview_xy;
|
| 488 |
+
$('lbimg').alt=f.scroll+' '+f.volume+' '+view+' preview, cos and normals';
|
| 489 |
+
$('lbtitle').textContent=f.scroll+' · '+um(f.voxel_um)+' · '+f.volume;
|
| 490 |
+
document.querySelectorAll('[data-lv]').forEach(x=>x.setAttribute('aria-pressed',x.dataset.lv===view));
|
| 491 |
+
$('lbslice').hidden=!f.gallery;
|
| 492 |
+
if(L.hidden){L.hidden=false;document.documentElement.classList.add('lbopen');$('lbclose').focus()}}
|
| 493 |
+
function closePv(){$('lbox').hidden=true;document.documentElement.classList.remove('lbopen');$('lbimg').removeAttribute('src');pv=null}
|
| 494 |
+
document.querySelectorAll('[data-lv]').forEach(b=>b.onclick=()=>pv&&openPv(pv,b.dataset.lv));
|
| 495 |
+
$('lbclose').onclick=closePv;
|
| 496 |
+
$('lbox').addEventListener('click',e=>{if(e.target===$('lbox'))closePv()});
|
| 497 |
+
document.addEventListener('keydown',e=>{if(e.key==='Escape'&&!$('lbox').hidden)closePv()});
|
| 498 |
+
$('lbslice').onclick=()=>{const f=pv,i=D.findIndex(s=>s.id===f.scroll);closePv();if(i>=0){pick(i,false);$('scans').scrollIntoView({behavior:'smooth'})}};
|
| 499 |
/* the volumes being made: shown without any link until each is public (fields.json, pending_not_public) */
|
| 500 |
if(FP.length){$('pend').hidden=false;
|
| 501 |
$('pend').innerHTML='<h3>Being made now, not public yet</h3><p class="sub" style="margin-bottom:14px">Lasagnetta 0.1.1 fields for more volumes of scrolls in the list. None is public yet, so there is nothing to download or stream.</p>'+
|
make_previews.py
ADDED
|
@@ -0,0 +1,94 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
"""Preview pictures for the villa fields in the open data, which ship none: a slice through the middle of the scroll
|
| 2 |
+
(xy) and one along it (xz), cos beside the normals as color, read over HTTPS from each field's run folder.
|
| 3 |
+
|
| 4 |
+
python3 spaces/lasagna-fields/make_previews.py OUT_DIR
|
| 5 |
+
|
| 6 |
+
writes OUT_DIR/SCROLL-VOLUME-xy.webp and -xz.webp (at most 1,600 px) for every open-data row of fields.json; upload OUT_DIR as the Space's
|
| 7 |
+
assets/previews/ (pictures stay out of git). Needs numpy, pillow, zarr<3, fsspec and aiohttp. Model output: a
|
| 8 |
+
picture of villa's lasagna field, never a reading.
|
| 9 |
+
"""
|
| 10 |
+
import json
|
| 11 |
+
import os
|
| 12 |
+
import sys
|
| 13 |
+
import urllib.request
|
| 14 |
+
from pathlib import Path
|
| 15 |
+
|
| 16 |
+
import numpy as np
|
| 17 |
+
import zarr
|
| 18 |
+
from PIL import Image, ImageDraw, ImageFont
|
| 19 |
+
|
| 20 |
+
HERE = Path(__file__).resolve().parent
|
| 21 |
+
|
| 22 |
+
|
| 23 |
+
def normals_rgb(nx_u8, ny_u8, cos_u8):
|
| 24 |
+
"""Encoded normals (v * 127 + 128) as color: |x|, |y|, z to red, green, blue; black where cos holds no data
|
| 25 |
+
(villa's open-data fields store 218 in both normals there, not their arrays' fill value)."""
|
| 26 |
+
nx = (nx_u8.astype(np.float32) - 128.0) / 127.0
|
| 27 |
+
ny = (ny_u8.astype(np.float32) - 128.0) / 127.0
|
| 28 |
+
nz = np.sqrt(np.maximum(0.0, 1.0 - nx * nx - ny * ny))
|
| 29 |
+
rgb = np.stack([np.abs(nx), np.abs(ny), nz], -1) * 255.0
|
| 30 |
+
rgb[cos_u8 == 0] = 0
|
| 31 |
+
return np.rint(rgb).clip(0, 255).astype(np.uint8)
|
| 32 |
+
|
| 33 |
+
|
| 34 |
+
def polish(cos, nrm, title, out, min_width=1000, max_width=1600, max_side=1600):
|
| 35 |
+
"""cos and normals side by side, cropped to the data, on a dark ground, with a title and a label over each."""
|
| 36 |
+
occ = (cos > 0) | (nrm.max(-1) > 0)
|
| 37 |
+
ys, xs = np.nonzero(occ)
|
| 38 |
+
pad = max(4, int(0.02 * max(occ.shape)))
|
| 39 |
+
y0, y1 = max(0, ys.min() - pad), min(occ.shape[0], ys.max() + 1 + pad)
|
| 40 |
+
x0, x1 = max(0, xs.min() - pad), min(occ.shape[1], xs.max() + 1 + pad)
|
| 41 |
+
panels = [Image.fromarray(np.ascontiguousarray(np.repeat(cos[y0:y1, x0:x1, None], 3, -1))),
|
| 42 |
+
Image.fromarray(np.ascontiguousarray(nrm[y0:y1, x0:x1]))]
|
| 43 |
+
gap, margin, head, lab = 24, 24, 56, 30
|
| 44 |
+
pw = panels[0].width
|
| 45 |
+
scale = min(max(1.0, min_width / (2 * pw + gap + 2 * margin)), max_width / (2 * pw + gap + 2 * margin))
|
| 46 |
+
if scale != 1.0:
|
| 47 |
+
size = (max(1, round(pw * scale)), max(1, round(panels[0].height * scale)))
|
| 48 |
+
panels = [p.resize(size, Image.NEAREST if scale > 1 else Image.LANCZOS) for p in panels]
|
| 49 |
+
pw, ph = panels[0].size
|
| 50 |
+
font = "/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf"
|
| 51 |
+
big = ImageFont.truetype(font, 22) if os.path.exists(font) else ImageFont.load_default()
|
| 52 |
+
small = ImageFont.truetype(font, 16) if os.path.exists(font) else ImageFont.load_default()
|
| 53 |
+
tw = ImageDraw.Draw(Image.new("RGB", (1, 1))).textlength(title, font=big)
|
| 54 |
+
canvas = Image.new("RGB", (max(2 * pw + gap + 2 * margin, int(tw) + 1 + 2 * margin), head + lab + ph + margin),
|
| 55 |
+
(14, 17, 23))
|
| 56 |
+
draw = ImageDraw.Draw(canvas)
|
| 57 |
+
draw.text((margin, 16), title, fill=(236, 238, 242), font=big)
|
| 58 |
+
for i, (p, text, color) in enumerate(((panels[0], "cos (one band per papyrus layer)", (170, 200, 255)),
|
| 59 |
+
(panels[1], "normals: red x, green y, blue z", (255, 190, 140)))):
|
| 60 |
+
x = margin + i * (pw + gap)
|
| 61 |
+
draw.text((x, head), text, fill=color, font=small)
|
| 62 |
+
canvas.paste(p, (x, head + lab))
|
| 63 |
+
if max(canvas.size) > max_side: # the media rule's 1920 px, with room
|
| 64 |
+
canvas.thumbnail((max_side, max_side), Image.LANCZOS)
|
| 65 |
+
canvas.save(out, quality=86, method=6)
|
| 66 |
+
|
| 67 |
+
|
| 68 |
+
def level_of(root, want=5):
|
| 69 |
+
"""The coarsest level up to want that the array has."""
|
| 70 |
+
attrs = json.load(urllib.request.urlopen(root + "/.zattrs"))
|
| 71 |
+
have = [int(d["path"]) for d in attrs["multiscales"][0]["datasets"]]
|
| 72 |
+
return max(v for v in have if v <= want) if min(have) <= want else min(have)
|
| 73 |
+
|
| 74 |
+
|
| 75 |
+
def main(out):
|
| 76 |
+
out = Path(out)
|
| 77 |
+
out.mkdir(parents=True, exist_ok=True)
|
| 78 |
+
rows = [f for f in json.loads((HERE / "fields.json").read_text())["fields"] if f["source"] == "open-data"]
|
| 79 |
+
for f in rows:
|
| 80 |
+
m = json.load(urllib.request.urlopen(f["manifest"]))
|
| 81 |
+
name = {k: m["groups"][k]["zarr"].split("/")[0] for k in ("cos", "nx", "ny")}
|
| 82 |
+
lv = max(level_of(f"{f['stream']}/{name[k]}") for k in name)
|
| 83 |
+
arr = {k: zarr.open(f"{f['stream']}/{name[k]}/{lv}", mode="r") for k in name}
|
| 84 |
+
zc, yc = arr["cos"].shape[0] // 2, arr["cos"].shape[1] // 2
|
| 85 |
+
views = {"xy": {k: np.asarray(a[zc]) for k, a in arr.items()},
|
| 86 |
+
"xz": {k: np.asarray(a[:, yc, :]) for k, a in arr.items()}}
|
| 87 |
+
for view, v in views.items():
|
| 88 |
+
title = f"{f['scroll']} {f['volume']}, villa predict3d, {'xy at mid z' if view == 'xy' else 'xz at mid y'}"
|
| 89 |
+
polish(v["cos"], normals_rgb(v["nx"], v["ny"], v["cos"]), title, out / f"{f['scroll']}-{f['volume']}-{view}.webp")
|
| 90 |
+
print(f"{f['scroll']} {f['volume']}: level {lv}, {arr['cos'].shape}", flush=True)
|
| 91 |
+
|
| 92 |
+
|
| 93 |
+
if __name__ == "__main__":
|
| 94 |
+
sys.exit(main(sys.argv[1]))
|
make_thumbs.py
CHANGED
|
@@ -1,8 +1,11 @@
|
|
| 1 |
-
"""Card pictures for the Every field tab: each
|
| 2 |
-
|
| 3 |
-
|
|
|
|
| 4 |
|
| 5 |
-
python3 spaces/lasagna-fields/make_thumbs.py OUT_DIR
|
|
|
|
|
|
|
| 6 |
"""
|
| 7 |
import io
|
| 8 |
import json
|
|
@@ -37,15 +40,17 @@ def trim(im):
|
|
| 37 |
|
| 38 |
def main(argv=None):
|
| 39 |
from PIL import Image
|
| 40 |
-
|
|
|
|
|
|
|
| 41 |
out.mkdir(parents=True, exist_ok=True)
|
| 42 |
doc = json.loads((HERE / "fields.json").read_text())
|
| 43 |
for f in doc["fields"]:
|
| 44 |
-
|
| 45 |
-
|
| 46 |
-
|
| 47 |
-
|
| 48 |
-
im = trim(Image.open(io.BytesIO(
|
| 49 |
r = min(W / im.width, H / im.height) # contain, centered on black like the panels
|
| 50 |
im = im.resize((round(im.width * r), round(im.height * r)), Image.LANCZOS)
|
| 51 |
canvas = Image.new("RGB", (W, H))
|
|
|
|
| 1 |
+
"""Card pictures for the Every field tab: each field's xy preview (cos | normals; preview_xy in fields.json, a
|
| 2 |
+
dataset's preview-xy.png or, for villa's fields in the open data, the picture make_previews.py wrote) as a small 2:1
|
| 3 |
+
WebP (fitted whole, on black) under assets/thumbs/SCROLL-VOLUME.webp. The guide falls back to the preview itself when
|
| 4 |
+
a thumb is missing. Like the rest of assets/, the thumbs live on the Space, not in git.
|
| 5 |
|
| 6 |
+
python3 spaces/lasagna-fields/make_thumbs.py OUT_DIR [PREVIEWS_DIR] (then upload OUT_DIR as assets/thumbs/)
|
| 7 |
+
|
| 8 |
+
PREVIEWS_DIR, make_previews.py's output, is read before the Space has the open-data previews.
|
| 9 |
"""
|
| 10 |
import io
|
| 11 |
import json
|
|
|
|
| 40 |
|
| 41 |
def main(argv=None):
|
| 42 |
from PIL import Image
|
| 43 |
+
args = argv or sys.argv[1:]
|
| 44 |
+
out = Path(args[0])
|
| 45 |
+
local = Path(args[1]) if len(args) > 1 else None
|
| 46 |
out.mkdir(parents=True, exist_ok=True)
|
| 47 |
doc = json.loads((HERE / "fields.json").read_text())
|
| 48 |
for f in doc["fields"]:
|
| 49 |
+
name = f"{f['scroll']}-{f['volume']}"
|
| 50 |
+
url = f["preview_xy"]
|
| 51 |
+
here = local / url.rsplit("/", 1)[1] if local else None
|
| 52 |
+
raw = here.read_bytes() if here and here.is_file() else urllib.request.urlopen(url, timeout=120).read()
|
| 53 |
+
im = trim(Image.open(io.BytesIO(raw)).convert("RGB"))
|
| 54 |
r = min(W / im.width, H / im.height) # contain, centered on black like the panels
|
| 55 |
im = im.resize((round(im.width * r), round(im.height * r)), Image.LANCZOS)
|
| 56 |
canvas = Image.new("RGB", (W, H))
|