Spaces:
Running on Zero
Running on Zero
Make normals easy to find and share by scroll
Browse files- README.md +19 -9
- app.py +51 -26
- coverage.json +2518 -0
- fields.json +0 -0
- guide/index.html +276 -9
- lasfield.py +24 -4
README.md
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@@ -11,7 +11,7 @@ pinned: false
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license: apache-2.0
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suggested_hardware: zero-a10g
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startup_duration_timeout: 1h
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short_description:
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models:
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- scrollprize/lasagna
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datasets:
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# Lasagna Fields
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- **
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are
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also stream from a bucket (PHerc0175A, PHerc0175B, PHerc0306B, PHerc0483A, PHerc0483B, PHerc0490A, PHerc0490B,
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PHerc0841, PHerc0846A and PHerc0846B), and twenty-two with [Lasagnetta](https://huggingface.co/SharpMeow/lasagnetta)
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0.1.1, a faster copy of it.
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- **Make a field** for any box of any public scan: pick a scan and a point, and the Space runs villa's own lasagna
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model there on ZeroGPU, checks the result against the field the open data already publishes for that scan, and
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hands you a download in villa's own layout.
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per papyrus layer), its gradient size **grad_mag**, and the surface normal (**nx**, **ny**). It is model output:
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geometry inputs, not a reading of any text.
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## Make a field: what runs
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`lasagna/preprocess_cos_omezarr.py predict3d` from [ScrollPrize/villa](https://github.com/ScrollPrize/villa) at commit
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## For agents
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The page is also an API and an MCP server (`https://sharpmeow-lasagna-fields.hf.space/gradio_api/mcp/`):
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`list_fields`, `list_scans`, `list_models`, `example_points`, `plan_field` and `make_field`.
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A field uses the caller's ZeroGPU time.
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## Credit and licenses
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license: apache-2.0
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suggested_hardware: zero-a10g
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startup_duration_timeout: 1h
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short_description: Explore scroll layers, previews, and published sources
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models:
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- scrollprize/lasagna
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datasets:
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# Lasagna Fields
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Explore published layer fields for Herculaneum scroll scans:
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- **Browse fields**: choose a scroll and scan, view a preview where one is available, then open its published
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dataset or manifest. Each field identifies its scan, voxel size and model. Fields from
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[Lasagnetta](https://huggingface.co/SharpMeow/lasagnetta) are labeled separately from villa's Lasagna fields.
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- **Make a field** for any box of any public scan: pick a scan and a point, and the Space runs villa's own lasagna
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model there on ZeroGPU, checks the result against the field the open data already publishes for that scan, and
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hands you a download in villa's own layout.
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per papyrus layer), its gradient size **grad_mag**, and the surface normal (**nx**, **ny**). It is model output:
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geometry inputs, not a reading of any text.
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The catalog records source links, model provenance and coverage status. A listed field or preview does not prove
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whole-volume completeness. An unknown coverage status means completeness has not been verified. A missing preview
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or size estimate means it is unavailable.
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## Reference fields
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The original ten hosted reference fields use the same villa commit and checkpoint as Make a field:
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PHerc0175A, PHerc0175B, PHerc0306B, PHerc0483A, PHerc0483B, PHerc0490A, PHerc0490B, PHerc0841,
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PHerc0846A and PHerc0846B. Their published datasets remain available through the scroll selector and
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the dataset links above. The current catalog also lists fields from other runs and models.
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## Make a field: what runs
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`lasagna/preprocess_cos_omezarr.py predict3d` from [ScrollPrize/villa](https://github.com/ScrollPrize/villa) at commit
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## For agents
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The page is also an API and an MCP server (`https://sharpmeow-lasagna-fields.hf.space/gradio_api/mcp/`):
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`list_fields`, `list_coverage`, `list_scans`, `list_models`, `example_points`, `plan_field` and `make_field`.
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`list_coverage` reports catalog entries and volumes separately, including missing fields and unknown completeness.
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See the page's **Agents and API** tab.
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A field uses the caller's ZeroGPU time.
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## Credit and licenses
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app.py
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@@ -267,7 +267,7 @@ def result_text(r):
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def list_scans():
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"""List the scans this Space can make a lasagna field for.
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Every volume of the Vesuvius Challenge open data (its metadata.json)
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shape, and the CT level the model reads. Returns a list of {volume, sample, voxel_um, shape_zyx, level, url}.
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"""
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return [{k: v[k] for k in ("volume", "sample", "voxel_um", "shape_zyx", "level", "url")}
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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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def field_counts():
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rows = field_doc().get("fields", [])
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return {"scrolls": len({f["scroll"] for f in rows}), "fields": len(rows),
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# ---------------------------------------------------------------- the page
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INTRO = """\
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-
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layout. New here? Start with the example and press **Make the field**.
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"""
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ABOUT_MODEL = """\
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**villa lasagna (exact)** runs villa's own code, `lasagna/preprocess_cos_omezarr.py predict3d` at commit
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`{commit}`, with the `scrollprize/lasagna` checkpoint (SHA-256 `{sha}`), both MIT. Nothing is reimplemented: the
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CSS = """
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:root, .dark { --lf-accent:#c2462b; }
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.gradio-container { width: 100% !important; max-width:
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.lf-head { display:flex; align-items:center; gap:14px; padding:6px 2px 2px; }
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.lf-head .layers { width:30px; height:24px; border-radius:5px; flex:none;
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background:repeating-linear-gradient(180deg,#c2462b 0 4px,#e07a3f 4px 7px,#f3e2bf 7px 10px,#4f7a3a 10px 11px,#f3e2bf 11px 12px); }
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.lf-head h1 { white-space:nowrap; font-family: Fraunces, Georgia, serif; font-weight:650; font-size:30px; margin:0; letter-spacing:-.01em; }
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.lf-head span { color: var(--body-text-color-subdued); font-size:15px; }
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/* no fixed height: onescroll.html fits the guide's frame to the guide, so the page scrolls and the frame does not;
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min-height only holds the place until it has */
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.lf-guide iframe { width:100%; min-height:640px; border:0; border-radius:12px; background:#f7f2ea; }
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.lf-note p { font-size:13px; color: var(--body-text-color-subdued); margin:0; }
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.lf-est p { font-size:13.5px; color: var(--body-text-color-subdued); }
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.lf-point { flex-wrap:
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.lf-credit { text-align:center; font-size:13px; color: var(--body-text-color-subdued); padding:18px 0 6px; }
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.lf-credit a { color: var(--lf-accent) !important; padding:0 !important; margin:0 !important; }
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.lf-howto img { border-radius:10px; border:1px solid var(--border-color-primary); max-width:min(100%, 760px); display:block; margin:8px 0; }
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# one page scroll bar: fits the guide's frame to its content (written by python -m kit spaceconnect render)
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ONESCROLL = HERE / "onescroll.html"
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HEAD += ONESCROLL.read_text() if ONESCROLL.is_file() else ""
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def theme():
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data = json.dumps(field_doc(), ensure_ascii=False).replace("</", "<\\/")
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page = page.replace('<script id="fieldlist" type="application/json">null</script>',
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f'<script id="fieldlist" type="application/json">{data}</script>', 1)
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return f'<iframe title="Every lasagna field" srcdoc="{html.escape(page, quote=True)}"></iframe>'
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with gr.Blocks(title="Lasagna Fields", delete_cache=(1800, 3600)) as demo:
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n = field_counts()
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gr.HTML('<div class="lf-head"><div class="layers"></div>
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'</span></div>')
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with gr.Tabs(elem_id="lf-tabs"):
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with gr.Tab("Every field", id="scans"):
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gr.HTML(guide_html(), elem_classes="lf-guide")
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with gr.Row(equal_height=False):
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with gr.Column(scale=2, min_width=300):
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ex = gr.Dropdown([(e["label"], i) for i, e in enumerate(EXAMPLES)], value=0,
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label="
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vid = gr.Dropdown(choices, value=first["volume"], label="Scan
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filterable=True)
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est = gr.Markdown(estimate_text(first["volume"], first["z"], first["y"], first["x"], 256),
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elem_classes="lf-est")
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with gr.Column(scale=3, min_width=320):
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example = MEDIA / "example-result.png"
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pic = gr.Image(str(example) if example.is_file() else None,
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"the model (about a minute).")
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dl = gr.File(label="Download: villa output folder, field.npz, receipt.json", height=88,
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elem_id="lf-dl")
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with gr.Accordion("
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receipt = gr.JSON(max_height=None, elem_id="lf-receipt")
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with gr.Accordion("About the model", open=False):
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gr.Markdown(ABOUT_MODEL.format(commit=L.VILLA["commit"][:12],
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gr.Markdown(HOW_TO, elem_classes="lf-howto")
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with gr.Tab("Agents and API", id="agents"):
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gr.Markdown(AGENTS.format(host=host))
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with gr.Accordion("Connect your tool: the fields and scans by URL", open=
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# the data's URLs and ready snippets, made by python -m kit spaceconnect render from connect.json
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gr.HTML(CONNECT_HTML.read_text() if CONNECT_HTML.exists() else "")
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gr.HTML('<footer class="lf-credit">Made by <a href="https://github.com/ChaseHendrick">Chase Hendrick</a> · '
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a_size = gr.Number(256, precision=0, label="size")
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a_json, a_img, a_file = gr.JSON(), gr.Image(type="numpy", format="png"), gr.File()
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a_scroll = gr.Textbox("", label="scroll")
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a_btns = [gr.Button() for _ in range(
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hidden = dict(api_visibility="private")
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vid.change(volume_text, vid, vinfo, **hidden)
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(a_btns[2], example_points, [], a_json, "example_points"),
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(a_btns[3], plan_field, ins, a_json, "plan_field"),
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(a_btns[4], make_field, ins, [a_img, a_json, a_file], "make_field"),
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(a_btns[5], list_fields, [a_scroll], a_json, "list_fields")
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heavy = name == "make_field"
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btn.click(guard(fn), i, o, api_name=name, api_description=fn.__doc__.split("\n\n")[0],
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concurrency_id="model" if heavy else None, concurrency_limit=2 if heavy else 8)
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def list_scans():
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"""List the scans this Space can make a lasagna field for.
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Every volume of the Vesuvius Challenge open data (its metadata.json), with its voxel size,
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shape, and the CT level the model reads. Returns a list of {volume, sample, voxel_um, shape_zyx, level, url}.
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"""
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return [{k: v[k] for k in ("volume", "sample", "voxel_um", "shape_zyx", "level", "url")}
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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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"normal_source", "availability", "provenance", "normals_access")
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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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def list_coverage(scroll: str = ""):
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"""List coverage for every catalog sample and volume, with metadata-only limits.
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Lasagna and Lasagnetta count as available fields. m7-derived normals and fiber
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predictions do not. whole_volume_complete=null means not verified. Existing
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fields list and make-field endpoints keep their current arguments.
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"""
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doc = json.loads((HERE / "coverage.json").read_text(encoding="utf-8"))
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query = str(scroll or "").strip().lower()
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return {**doc, "samples": [s for s in doc["samples"] if query in s["scroll"].lower()]}
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+
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def field_counts():
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rows = field_doc().get("fields", [])
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return {"scrolls": len({f["scroll"] for f in rows}), "fields": len(rows),
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# ---------------------------------------------------------------- the page
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INTRO = """\
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Make a small field from a scan. Start with an example, or choose your own acquisition and location.
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This runs villa's model using your Hugging Face GPU quota. The result is model output, not a reading.
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"""
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ABOUT_MODEL = """\
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**villa lasagna (exact)** runs villa's own code, `lasagna/preprocess_cos_omezarr.py predict3d` at commit
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`{commit}`, with the `scrollprize/lasagna` checkpoint (SHA-256 `{sha}`), both MIT. Nothing is reimplemented: the
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CSS = """
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:root, .dark { --lf-accent:#c2462b; }
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.gradio-container { width: 100% !important; max-width: 1200px !important; margin: 0 auto !important; }
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.lf-head { display:flex; align-items:center; gap:14px; padding:6px 2px 2px; }
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.lf-head .layers { width:30px; height:24px; border-radius:5px; flex:none;
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background:repeating-linear-gradient(180deg,#c2462b 0 4px,#e07a3f 4px 7px,#f3e2bf 7px 10px,#4f7a3a 10px 11px,#f3e2bf 11px 12px); }
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.lf-head h1 { white-space:nowrap; font-family: Fraunces, Georgia, serif; font-weight:650; font-size:30px; margin:0; letter-spacing:-.01em; }
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.lf-head { padding:14px 6px 16px; }
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.lf-head span { color: var(--body-text-color-subdued); font-size:15px; }
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/* no fixed height: onescroll.html fits the guide's frame to the guide, so the page scrolls and the frame does not;
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min-height only holds the place until it has */
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.lf-guide iframe { width:100%; min-height:640px; border:0; border-radius:12px; background:#f7f2ea; }
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.lf-note p { font-size:13px; color: var(--body-text-color-subdued); margin:0; }
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.lf-est p { font-size:13.5px; color: var(--body-text-color-subdued); }
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.lf-point { flex-wrap: wrap !important; }
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.lf-credit { text-align:center; font-size:13px; color: var(--body-text-color-subdued); padding:18px 0 6px; }
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.lf-credit a { color: var(--lf-accent) !important; padding:0 !important; margin:0 !important; }
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.lf-howto img { border-radius:10px; border:1px solid var(--border-color-primary); max-width:min(100%, 760px); display:block; margin:8px 0; }
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# one page scroll bar: fits the guide's frame to its content (written by python -m kit spaceconnect render)
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ONESCROLL = HERE / "onescroll.html"
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HEAD += ONESCROLL.read_text() if ONESCROLL.is_file() else ""
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HEAD += '<style>@media (max-width:640px){.app{padding:12px 8px!important}.lf-guide,.lf-guide .html-container{padding:0!important;border:0!important}#lf-tabs .tabitem,#lf-tabs [role="tabpanel"]{padding:0!important}}</style>'
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def theme():
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data = json.dumps(field_doc(), ensure_ascii=False).replace("</", "<\\/")
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page = page.replace('<script id="fieldlist" type="application/json">null</script>',
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f'<script id="fieldlist" type="application/json">{data}</script>', 1)
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# UI metadata only: retain the coverage worker's acquisition list and its uncertainty.
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try:
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| 627 |
+
coverage = json.loads((HERE / "coverage.json").read_text(encoding="utf-8"))
|
| 628 |
+
except (OSError, ValueError):
|
| 629 |
+
coverage = {}
|
| 630 |
+
coverage_data = json.dumps(coverage, ensure_ascii=False).replace("</", "<\\/")
|
| 631 |
+
page = page.replace('<script id="coverage-list" type="application/json">null</script>',
|
| 632 |
+
f'<script id="coverage-list" type="application/json">{coverage_data}</script>', 1)
|
| 633 |
return f'<iframe title="Every lasagna field" srcdoc="{html.escape(page, quote=True)}"></iframe>'
|
| 634 |
|
| 635 |
|
|
|
|
| 681 |
|
| 682 |
with gr.Blocks(title="Lasagna Fields", delete_cache=(1800, 3600)) as demo:
|
| 683 |
n = field_counts()
|
| 684 |
+
gr.HTML('<div class="lf-head"><div class="layers" aria-hidden="true"></div>'
|
| 685 |
+
'<h1>Lasagna Fields</h1><span>Explore the layers of Herculaneum scrolls</span></div>')
|
|
|
|
| 686 |
with gr.Tabs(elem_id="lf-tabs"):
|
| 687 |
with gr.Tab("Every field", id="scans"):
|
| 688 |
gr.HTML(guide_html(), elem_classes="lf-guide")
|
|
|
|
| 691 |
with gr.Row(equal_height=False):
|
| 692 |
with gr.Column(scale=2, min_width=300):
|
| 693 |
ex = gr.Dropdown([(e["label"], i) for i, e in enumerate(EXAMPLES)], value=0,
|
| 694 |
+
label="Start with an example")
|
| 695 |
+
vid = gr.Dropdown(choices, value=first["volume"], label="Scan acquisition",
|
| 696 |
filterable=True)
|
| 697 |
+
with gr.Accordion("Location, box size and model", open=True):
|
| 698 |
+
with gr.Accordion("Scan details", open=False):
|
| 699 |
+
vinfo = gr.Markdown(volume_text(first["volume"]), elem_classes="lf-note")
|
| 700 |
+
with gr.Row(elem_classes="lf-point"):
|
| 701 |
+
z = gr.Number(first["z"], label="Depth (z)", precision=0, minimum=0, min_width=80)
|
| 702 |
+
y = gr.Number(first["y"], label="Row (y)", precision=0, minimum=0, min_width=80)
|
| 703 |
+
x = gr.Number(first["x"], label="Column (x)", precision=0, minimum=0, min_width=80)
|
| 704 |
+
gr.Markdown("Point in full-resolution (level 0) voxels, as the data browser and VC3D show "
|
| 705 |
+
"them.", elem_classes="lf-note")
|
| 706 |
+
size = gr.Radio([("256 voxels", 256), ("512 voxels", 512)], value=256, label="Box side")
|
| 707 |
+
model = gr.Radio(offered, value="lasagna", label="Model")
|
| 708 |
est = gr.Markdown(estimate_text(first["volume"], first["z"], first["y"], first["x"], 256),
|
| 709 |
elem_classes="lf-est")
|
| 710 |
+
go = gr.Button("Make the field", variant="primary", size="lg")
|
| 711 |
with gr.Column(scale=3, min_width=320):
|
| 712 |
example = MEDIA / "example-result.png"
|
| 713 |
pic = gr.Image(str(example) if example.is_file() else None,
|
|
|
|
| 718 |
"the model (about a minute).")
|
| 719 |
dl = gr.File(label="Download: villa output folder, field.npz, receipt.json", height=88,
|
| 720 |
elem_id="lf-dl")
|
| 721 |
+
with gr.Accordion("Technical receipt", open=False):
|
| 722 |
receipt = gr.JSON(max_height=None, elem_id="lf-receipt")
|
| 723 |
with gr.Accordion("About the model", open=False):
|
| 724 |
gr.Markdown(ABOUT_MODEL.format(commit=L.VILLA["commit"][:12],
|
|
|
|
| 727 |
gr.Markdown(HOW_TO, elem_classes="lf-howto")
|
| 728 |
with gr.Tab("Agents and API", id="agents"):
|
| 729 |
gr.Markdown(AGENTS.format(host=host))
|
| 730 |
+
with gr.Accordion("Connect your tool: the fields and scans by URL", open=False):
|
| 731 |
# the data's URLs and ready snippets, made by python -m kit spaceconnect render from connect.json
|
| 732 |
gr.HTML(CONNECT_HTML.read_text() if CONNECT_HTML.exists() else "")
|
| 733 |
gr.HTML('<footer class="lf-credit">Made by <a href="https://github.com/ChaseHendrick">Chase Hendrick</a> · '
|
|
|
|
| 742 |
a_size = gr.Number(256, precision=0, label="size")
|
| 743 |
a_json, a_img, a_file = gr.JSON(), gr.Image(type="numpy", format="png"), gr.File()
|
| 744 |
a_scroll = gr.Textbox("", label="scroll")
|
| 745 |
+
a_btns = [gr.Button() for _ in range(7)]
|
| 746 |
|
| 747 |
hidden = dict(api_visibility="private")
|
| 748 |
vid.change(volume_text, vid, vinfo, **hidden)
|
|
|
|
| 757 |
(a_btns[2], example_points, [], a_json, "example_points"),
|
| 758 |
(a_btns[3], plan_field, ins, a_json, "plan_field"),
|
| 759 |
(a_btns[4], make_field, ins, [a_img, a_json, a_file], "make_field"),
|
| 760 |
+
(a_btns[5], list_fields, [a_scroll], a_json, "list_fields"),
|
| 761 |
+
(a_btns[6], list_coverage, [a_scroll], a_json, "list_coverage")):
|
| 762 |
heavy = name == "make_field"
|
| 763 |
btn.click(guard(fn), i, o, api_name=name, api_description=fn.__doc__.split("\n\n")[0],
|
| 764 |
concurrency_id="model" if heavy else None, concurrency_limit=2 if heavy else 8)
|
coverage.json
ADDED
|
@@ -0,0 +1,2518 @@
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"ct_url": "https://data.aws.ash2txt.org/samples/PHercParis4/volumes/20230206171837-7.910um-54keV-masked.zarr/",
|
| 2383 |
+
"input_shape_zyx": [
|
| 2384 |
+
10529,
|
| 2385 |
+
7812,
|
| 2386 |
+
8316
|
| 2387 |
+
],
|
| 2388 |
+
"exposed_in_live_space": false,
|
| 2389 |
+
"available_models": [],
|
| 2390 |
+
"manifests": [],
|
| 2391 |
+
"status": "no_lasagna_or_lasagnetta_field_found",
|
| 2392 |
+
"whole_volume_complete": null,
|
| 2393 |
+
"chunks_checked": "not applicable"
|
| 2394 |
+
},
|
| 2395 |
+
{
|
| 2396 |
+
"scroll": "PHercParis4",
|
| 2397 |
+
"sample_type": "scroll",
|
| 2398 |
+
"volume": "20260310170716",
|
| 2399 |
+
"scan_id": "20260310152857",
|
| 2400 |
+
"zarr": "20260310170716-45.532um-11.0m-74keV-masked.zarr",
|
| 2401 |
+
"voxel_um": 45.532,
|
| 2402 |
+
"superseded_by": null,
|
| 2403 |
+
"read_level": 0,
|
| 2404 |
+
"ct_url": "https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHercParis4/volumes/20260310170716-45.532um-11.0m-74keV-masked.zarr/",
|
| 2405 |
+
"input_shape_zyx": [
|
| 2406 |
+
4071,
|
| 2407 |
+
2264,
|
| 2408 |
+
2264
|
| 2409 |
+
],
|
| 2410 |
+
"exposed_in_live_space": false,
|
| 2411 |
+
"available_models": [],
|
| 2412 |
+
"manifests": [],
|
| 2413 |
+
"status": "no_lasagna_or_lasagnetta_field_found",
|
| 2414 |
+
"whole_volume_complete": null,
|
| 2415 |
+
"chunks_checked": "not applicable"
|
| 2416 |
+
},
|
| 2417 |
+
{
|
| 2418 |
+
"scroll": "PHercParis4",
|
| 2419 |
+
"sample_type": "scroll",
|
| 2420 |
+
"volume": "20260310173927",
|
| 2421 |
+
"scan_id": "20260310160232",
|
| 2422 |
+
"zarr": "20260310173927-45.532um-11.0m-110keV-masked.zarr",
|
| 2423 |
+
"voxel_um": 45.532,
|
| 2424 |
+
"superseded_by": null,
|
| 2425 |
+
"read_level": 0,
|
| 2426 |
+
"ct_url": "https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHercParis4/volumes/20260310173927-45.532um-11.0m-110keV-masked.zarr/",
|
| 2427 |
+
"input_shape_zyx": [
|
| 2428 |
+
4066,
|
| 2429 |
+
2264,
|
| 2430 |
+
2264
|
| 2431 |
+
],
|
| 2432 |
+
"exposed_in_live_space": false,
|
| 2433 |
+
"available_models": [],
|
| 2434 |
+
"manifests": [],
|
| 2435 |
+
"status": "no_lasagna_or_lasagnetta_field_found",
|
| 2436 |
+
"whole_volume_complete": null,
|
| 2437 |
+
"chunks_checked": "not applicable"
|
| 2438 |
+
},
|
| 2439 |
+
{
|
| 2440 |
+
"scroll": "PHercParis4",
|
| 2441 |
+
"sample_type": "scroll",
|
| 2442 |
+
"volume": "20260323153942",
|
| 2443 |
+
"scan_id": "20260315072529",
|
| 2444 |
+
"zarr": "20260323153942-2.400um-0.2m-137keV-masked.zarr",
|
| 2445 |
+
"voxel_um": 2.4,
|
| 2446 |
+
"superseded_by": null,
|
| 2447 |
+
"read_level": 2,
|
| 2448 |
+
"ct_url": "https://data.aws.ash2txt.org/samples/PHercParis4/volumes/20260323153942-2.400um-0.2m-137keV-masked.zarr/",
|
| 2449 |
+
"input_shape_zyx": [
|
| 2450 |
+
1657,
|
| 2451 |
+
2108,
|
| 2452 |
+
2108
|
| 2453 |
+
],
|
| 2454 |
+
"exposed_in_live_space": false,
|
| 2455 |
+
"available_models": [],
|
| 2456 |
+
"manifests": [],
|
| 2457 |
+
"status": "no_lasagna_or_lasagnetta_field_found",
|
| 2458 |
+
"whole_volume_complete": null,
|
| 2459 |
+
"chunks_checked": "not applicable"
|
| 2460 |
+
},
|
| 2461 |
+
{
|
| 2462 |
+
"scroll": "PHercParis4",
|
| 2463 |
+
"sample_type": "scroll",
|
| 2464 |
+
"volume": "20260411134726",
|
| 2465 |
+
"scan_id": "20260311024914",
|
| 2466 |
+
"zarr": "20260411134726-2.400um-0.2m-78keV-masked.zarr",
|
| 2467 |
+
"voxel_um": 2.4,
|
| 2468 |
+
"superseded_by": null,
|
| 2469 |
+
"read_level": 2,
|
| 2470 |
+
"ct_url": "https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHercParis4/volumes/20260411134726-2.400um-0.2m-78keV-masked.zarr/",
|
| 2471 |
+
"input_shape_zyx": [
|
| 2472 |
+
18946,
|
| 2473 |
+
8174,
|
| 2474 |
+
8174
|
| 2475 |
+
],
|
| 2476 |
+
"exposed_in_live_space": false,
|
| 2477 |
+
"available_models": [
|
| 2478 |
+
"lasagna"
|
| 2479 |
+
],
|
| 2480 |
+
"manifests": [
|
| 2481 |
+
"https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHercParis4/representations/predictions/lasagna/20260411134726-lasagna-20260419180421-L2/PHercParis4-20260411134726-las-sd2-5b17ff6c.lasagna.json"
|
| 2482 |
+
],
|
| 2483 |
+
"status": "field_metadata_available",
|
| 2484 |
+
"whole_volume_complete": null,
|
| 2485 |
+
"chunks_checked": "sample presence only"
|
| 2486 |
+
},
|
| 2487 |
+
{
|
| 2488 |
+
"scroll": "PHercParis4",
|
| 2489 |
+
"sample_type": "scroll",
|
| 2490 |
+
"volume": "20260608103018",
|
| 2491 |
+
"scan_id": "20260315102010",
|
| 2492 |
+
"zarr": "20260608103018-1.129um-0.2m-78keV-masked.zarr",
|
| 2493 |
+
"voxel_um": 1.129,
|
| 2494 |
+
"superseded_by": null,
|
| 2495 |
+
"read_level": 3,
|
| 2496 |
+
"ct_url": "https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHercParis4/volumes/20260608103018-1.129um-0.2m-78keV-masked.zarr/",
|
| 2497 |
+
"input_shape_zyx": [
|
| 2498 |
+
7497,
|
| 2499 |
+
4501,
|
| 2500 |
+
4045
|
| 2501 |
+
],
|
| 2502 |
+
"exposed_in_live_space": false,
|
| 2503 |
+
"available_models": [],
|
| 2504 |
+
"manifests": [],
|
| 2505 |
+
"status": "no_lasagna_or_lasagnetta_field_found",
|
| 2506 |
+
"whole_volume_complete": null,
|
| 2507 |
+
"chunks_checked": "not applicable"
|
| 2508 |
+
}
|
| 2509 |
+
]
|
| 2510 |
+
}
|
| 2511 |
+
],
|
| 2512 |
+
"limitations": [
|
| 2513 |
+
"Metadata and sampled chunk presence only. No scan or prediction values read.",
|
| 2514 |
+
"A Zarr fill value, manifest or one chunk does not establish full coverage.",
|
| 2515 |
+
"Fiber predictions tagged lasagna in the source catalog are excluded by origin path and channel schema.",
|
| 2516 |
+
"m7-derived normals do not count as Lasagna or Lasagnetta."
|
| 2517 |
+
]
|
| 2518 |
+
}
|
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|
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guide/index.html
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@@ -264,9 +264,125 @@ html.lbopen{overflow:hidden}
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|
| 264 |
if(t!=='light'&&t!=='dark'){try{t=new URLSearchParams(parent.location.search).get('__theme')}catch(e){t=null}}
|
| 265 |
if(t==='light'||t==='dark')document.documentElement.dataset.theme=t;})();
|
| 266 |
</script>
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| 267 |
</head>
|
| 268 |
<body>
|
| 269 |
-
<
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<svg class="fields" id="fields" viewBox="0 0 1600 900" preserveAspectRatio="xMidYMax slice" aria-hidden="true"></svg>
|
| 271 |
<button class="tbtn" id="theme" type="button" aria-label="Switch light or dark">Theme</button>
|
| 272 |
<div class="wrap">
|
|
@@ -283,6 +399,7 @@ html.lbopen{overflow:hidden}
|
|
| 283 |
</div>
|
| 284 |
</header>
|
| 285 |
|
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|
| 286 |
<section id="all"><div class="wrap">
|
| 287 |
<h2>Every field, by scroll</h2>
|
| 288 |
<p class="sub">One card per scroll. <span class="mp villa">villa predict3d</span> is the villa lasagna model itself, the reference. <span class="mp lgt">Lasagnetta 0.1.1</span> copies it and runs about 5 times faster: use its fields as a preview, and villa's where exact values matter.</p>
|
|
@@ -306,6 +423,8 @@ html.lbopen{overflow:hidden}
|
|
| 306 |
<div id="pend" hidden></div>
|
| 307 |
</div></section>
|
| 308 |
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|
| 309 |
<section id="use"><div class="wrap">
|
| 310 |
<h2>Stream, download and load</h2>
|
| 311 |
<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>, so any tool that reads zarr over HTTPS opens it with no download and no account. Pick one of the first ten fields made here, with the villa lasagna model, to see its field, its numbers and the commands to get it; for any other field, <b>Copy URL</b> in the list gives its folder.</p>
|
|
@@ -402,6 +521,8 @@ html.lbopen{overflow:hidden}
|
|
| 402 |
</div>
|
| 403 |
</div></section>
|
| 404 |
|
|
|
|
|
|
|
| 405 |
<section id="about"><div class="wrap"><div class="about">
|
| 406 |
<h2>About these fields</h2>
|
| 407 |
<p class="sub">A lasagna field is the input that the lasagna surface fit in villa reads. These are public so that nobody has to spend a GPU day before trying an idea on these scrolls: use them, compare against them, and tell us if you find a problem.</p>
|
|
@@ -432,6 +553,7 @@ and with Lasagnetta 0.1.1 (SharpMeow/lasagnetta), on Vesuvius Challenge open dat
|
|
| 432 |
</details>
|
| 433 |
</div></div></section>
|
| 434 |
|
|
|
|
| 435 |
<footer><div class="wrap">
|
| 436 |
<span>Lasagna Fields, by Chase Hendrick · <a href="https://huggingface.co/SharpMeow">huggingface.co/SharpMeow</a> · <a href="https://github.com/ChaseHendrick">github.com/ChaseHendrick</a></span>
|
| 437 |
<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>
|
|
@@ -445,11 +567,13 @@ and with Lasagnetta 0.1.1 (SharpMeow/lasagnetta), on Vesuvius Challenge open dat
|
|
| 445 |
|
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<script id="data" 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|
| 447 |
<script id="fieldlist" type="application/json">null</script>
|
|
|
|
| 448 |
<script>
|
| 449 |
const D=JSON.parse(document.getElementById('data').textContent);
|
| 450 |
const $=id=>document.getElementById(id);
|
| 451 |
const fmt=n=>n.toLocaleString('en-US');
|
| 452 |
-
const gb=b=>(b/1e9).toFixed(1)+' GB';
|
|
|
|
| 453 |
const esc=s=>s.replace(/&/g,'&').replace(/</g,'<');
|
| 454 |
let cur=0,view='xy',ut='connect';
|
| 455 |
|
|
@@ -511,7 +635,7 @@ const openSc=new Set();
|
|
| 511 |
function links(f){const od=f.source==='open-data';
|
| 512 |
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>'+
|
| 513 |
'<a href="'+attr(f.manifest)+'" target="_blank" rel="noopener" title="the lasagna.json the lasagna fit reads">Manifest</a>'+
|
| 514 |
-
'<button type="button" data-pv="'+FL.indexOf(f)+'" title="cos and normals, through the middle and along the scroll">Preview</button>'+
|
| 515 |
'<button type="button" data-url="'+attr(f.stream)+'" title="the run folder, which zarr reads by URL">Copy URL</button>'}
|
| 516 |
function fieldRow(f,first,n){
|
| 517 |
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>';
|
|
@@ -521,7 +645,7 @@ function fieldRow(f,first,n){
|
|
| 521 |
'<td data-k="Model" class="mdl">'+chip(f.model)+(f.note?'<span class="fnote">'+esc(f.note)+'</span>':'')+'</td>'+
|
| 522 |
'<td data-k="Where">'+where+'</td><td data-k="Size" class="num">'+gb(f.bytes)+'</td>'+
|
| 523 |
'<td class="get"><div class="flinks">'+links(f)+'</div></td></tr>'}
|
| 524 |
-
function thumbOf(g){const f=g[0];return {src:'assets/thumbs/'+f.scroll+'-'+f.volume+'.webp',alt:f.preview_xy,vol:f.volume}}
|
| 525 |
const srcOf=f=>f.source==='open-data'?'open data':'SharpMeow';
|
| 526 |
/* one field of a card: its voxel size and volume, model and source, the four links, and its note */
|
| 527 |
function cardLine(f,size){
|
|
@@ -536,11 +660,11 @@ function summary(g){
|
|
| 536 |
const vs=(v.length>2?v[0]+' to '+v[v.length-1]:v.join(' and '))+' µm';
|
| 537 |
return '<div class="sum">'+ms+'<span class="dim">'+vs+' · '+uniq(g.map(srcOf)).join(' and ')+'</span></div>'}
|
| 538 |
function card(g){const t=thumbOf(g),n=g.length,sc=g[0].scroll;
|
| 539 |
-
const img='<img loading="lazy" src="'+t.src+'" data-alt="'+attr(t.alt)+'" alt="'+attr(sc)+' field preview, cos and normals" onerror="if(this.dataset.alt){this.src=this.dataset.alt;this.dataset.alt=\'\'}"><span class="tag">cos | normals</span>';
|
| 540 |
const open=openSc.has(sc)||(fq.trim()!=='');
|
| 541 |
const foot=n===1?'<div class="foot one"><ul>'+cardLine(g[0],false)+'</ul></div>'
|
| 542 |
:'<details class="foot more" data-sc="'+attr(sc)+'"'+(open?' open':'')+'><summary>Show the '+n+' fields and their links</summary><ul>'+g.map(f=>cardLine(f,true)).join('')+'</ul></details>';
|
| 543 |
-
return '<article class="sccard"><div class="thumb">'+img+'</div><div class="body"><div class="hd"><h3>'+esc(sc)+'</h3><span class="cnt">'+n+(n===1?' field':' fields')+' · '+
|
| 544 |
function drawFields(){
|
| 545 |
const t=$('flist');t.querySelectorAll('tbody').forEach(b=>b.remove());
|
| 546 |
$('fcards').hidden=fv!=='cards';$('ftable').hidden=fv!=='table';
|
|
@@ -572,11 +696,11 @@ function placeLb(){const L=$('lbox'),v=onScreen();if(!v)return;
|
|
| 572 |
L.querySelector('.lbpanel').style.maxHeight=(v.h-32)+'px'}
|
| 573 |
function toastOn(){const T=$('toast'),v=onScreen();if(v){T.style.position='absolute';T.style.bottom='auto';T.style.top=(v.top+v.h-64)+'px'}T.classList.add('on')}
|
| 574 |
try{parent.addEventListener('scroll',()=>{if(!$('lbox').hidden)placeLb()},{passive:true})}catch(e){}
|
| 575 |
-
function openPv(f,view){pv=f;const L=$('lbox');
|
| 576 |
$('lbimg').src=view==='xz'?f.preview_xz:f.preview_xy;
|
| 577 |
$('lbimg').alt=f.scroll+' '+f.volume+' '+view+' preview, cos and normals';
|
| 578 |
$('lbtitle').textContent=f.scroll+' · '+um(f.voxel_um)+' · '+f.volume;
|
| 579 |
-
document.querySelectorAll('[data-lv]').forEach(x=>x.setAttribute('aria-pressed',x.dataset.lv===view));
|
| 580 |
$('lbslice').hidden=!f.gallery;
|
| 581 |
if(L.hidden){L.hidden=false;placeLb();document.documentElement.classList.add('lbopen');$('lbclose').focus({preventScroll:true})}}
|
| 582 |
function closePv(){$('lbox').hidden=true;document.documentElement.classList.remove('lbopen');$('lbimg').removeAttribute('src');pv=null}
|
|
@@ -595,7 +719,7 @@ drawFields();
|
|
| 595 |
/* stats */
|
| 596 |
const totB=D.reduce((a,s)=>a+s.bytes,0),totP=D.reduce((a,s)=>a+s.parts.length,0);
|
| 597 |
const ours=FL.filter(f=>f.source==='dataset'),nsc=uniq(FL.map(f=>f.scroll)).length;
|
| 598 |
-
$('stats').innerHTML=(FL.length?[[nsc,'scrolls'],[FL.length-ours.length,'villa fields in the open data'],[ours.length,'fields made here'],[
|
| 599 |
:[[D.length,'scans'],[Math.round(totB/1e9)+' GB','to download'],[fmt(totP),'GPU parts'],['4','channels each']])
|
| 600 |
.map(([b,s])=>'<div class="stat"><b>'+b+'</b><span>'+s+'</span></div>').join('');
|
| 601 |
$('nscrolls').textContent=FL.length?nsc:D.length;
|
|
@@ -692,6 +816,149 @@ document.addEventListener('click',e=>{const b=e.target.closest('.copy');if(!b)re
|
|
| 692 |
function fallback(t,done){const a=document.createElement('textarea');a.value=t;document.body.appendChild(a);a.select();try{document.execCommand('copy');done()}catch(e){}a.remove()}
|
| 693 |
|
| 694 |
pick(0,false);
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|
| 695 |
</script>
|
| 696 |
</body>
|
| 697 |
</html>
|
|
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|
| 264 |
if(t!=='light'&&t!=='dark'){try{t=new URLSearchParams(parent.location.search).get('__theme')}catch(e){t=null}}
|
| 265 |
if(t==='light'||t==='dark')document.documentElement.dataset.theme=t;})();
|
| 266 |
</script>
|
| 267 |
+
<style>
|
| 268 |
+
/* The human view uses the same catalog and leaves the existing guide hooks intact. */
|
| 269 |
+
[hidden]{display:none!important}
|
| 270 |
+
.human{max-width:1120px;margin:auto;padding:30px 28px 12px}
|
| 271 |
+
.human-intro{display:flex;justify-content:space-between;align-items:flex-start;gap:20px;margin-bottom:28px}
|
| 272 |
+
.human-kicker{font-size:12px;font-weight:650;letter-spacing:.12em;text-transform:uppercase;color:var(--accent);margin-bottom:10px}
|
| 273 |
+
.human-intro h2{font-size:clamp(28px,3.5vw,40px);margin-bottom:10px}
|
| 274 |
+
.human-intro p:not(.human-kicker){color:var(--ink2);margin:0}
|
| 275 |
+
.human button,.human select,.human input,.human a.human-primary{min-height:44px;font:inherit;border:1px solid var(--line);border-radius:9px;background:var(--card);color:var(--ink);padding:9px 12px}
|
| 276 |
+
.human button{cursor:pointer}.human button:disabled{opacity:.5;cursor:default}
|
| 277 |
+
.human :focus-visible,.human-fold summary:focus-visible{outline:3px solid #5081ae;outline-offset:3px}
|
| 278 |
+
.human .human-quiet{font-size:13px;white-space:nowrap;background:transparent}
|
| 279 |
+
.human-browser{display:grid;grid-template-columns:minmax(240px,300px) minmax(0,1fr);gap:32px;align-items:start}
|
| 280 |
+
.human-choices{min-width:0}.human label{display:block;font-size:14px;font-weight:650;margin:0 0 7px}
|
| 281 |
+
.human select,.human input{width:100%;margin:0 0 16px;max-width:100%;text-overflow:ellipsis}
|
| 282 |
+
.human-help{font-size:13px;color:var(--ink2);line-height:1.5;margin:-8px 0 20px}
|
| 283 |
+
.human-status{padding:15px 0;border-top:1px solid var(--line);margin-top:4px}
|
| 284 |
+
#human-availability{display:block;font-size:14px;font-weight:650;color:var(--ink)}
|
| 285 |
+
#human-completeness{font-size:12px;color:var(--ink2);line-height:1.5;margin:5px 0 0}
|
| 286 |
+
.human-actions{display:grid;gap:10px;margin:8px 0 18px}
|
| 287 |
+
.human .human-primary{background:var(--accent);color:var(--card);text-align:center;font-weight:650;border-color:transparent;text-decoration:none}
|
| 288 |
+
:root[data-theme="dark"] .human .human-primary{color:#141210}
|
| 289 |
+
@media(prefers-color-scheme:dark){:root:not([data-theme="light"]) .human .human-primary{color:#141210}}
|
| 290 |
+
.human-normals{padding:16px;border:1px solid var(--line);border-radius:10px;background:var(--card);margin:12px 0;min-width:0}
|
| 291 |
+
.human-normals h3{font-size:18px;margin-bottom:12px}.human-normals p{font-size:13px;line-height:1.6;margin:12px 0}
|
| 292 |
+
.human-channel{display:grid;grid-template-columns:minmax(0,1fr) auto;align-items:center;gap:6px;margin:12px 0}
|
| 293 |
+
.human-channel label{margin:0;font-size:13px}.human .human-channel button{font-size:12px;padding:5px 9px;min-height:36px;width:auto}
|
| 294 |
+
.human .human-channel input{grid-column:1 / -1;min-width:0;width:100%;font:12px/1.5 ui-monospace,monospace;margin:0;min-height:36px;padding:7px 9px;text-overflow:clip}
|
| 295 |
+
.human-normals>button{width:100%;font-size:13px}
|
| 296 |
+
.human-normal-links{display:flex;flex-wrap:wrap;gap:8px 18px;margin:14px 0;font-size:13px}
|
| 297 |
+
#human-using{border-top:1px solid var(--line);font-size:13px}#human-using summary{cursor:pointer;padding:12px 0;min-height:44px}
|
| 298 |
+
.human-normals .human-smallprint{font-size:11px;line-height:1.5;color:var(--ink2);margin:4px 0 0}
|
| 299 |
+
.human-make{font-size:14px;display:inline-block;padding:4px 0}
|
| 300 |
+
.human-preview{margin:0;border:1px solid var(--line);border-radius:14px;background:var(--card);overflow:hidden;min-width:0}
|
| 301 |
+
.human-preview-head{display:flex;gap:12px;align-items:center;justify-content:space-between;padding:15px 18px;border-bottom:1px solid var(--line)}
|
| 302 |
+
.human-preview-head h3{font:650 15px/1.4 Inter,system-ui,sans-serif;margin:0}
|
| 303 |
+
.human-preview-head>div{display:flex;gap:4px}.human-preview-head button{font-size:13px;padding:7px 10px;min-height:40px;border-color:transparent}
|
| 304 |
+
.human-preview-head button[aria-pressed="true"]{background:var(--bg2);border-color:var(--line)}
|
| 305 |
+
.human-image{min-height:300px;display:flex;align-items:center;justify-content:center;background:var(--bg2);padding:16px}
|
| 306 |
+
.human-image img{display:block;width:100%;max-height:420px;object-fit:contain}
|
| 307 |
+
.human-image p{max-width:28em;text-align:center;color:var(--ink2);font-size:14px;padding:24px;margin:0}
|
| 308 |
+
.human-preview figcaption{padding:14px 18px;color:var(--ink2);font-size:12px;line-height:1.6}
|
| 309 |
+
.human-details,.human-fold{border-top:1px solid var(--line);margin:24px auto 0;max-width:1064px}
|
| 310 |
+
.human-details summary,.human-fold>summary{cursor:pointer;padding:16px 0;font-size:14px;font-weight:650;color:var(--ink2);min-height:48px}
|
| 311 |
+
.human-details dl{display:grid;grid-template-columns:140px minmax(0,1fr);gap:8px 20px;font-size:13px;margin:8px 0 16px}
|
| 312 |
+
.human-details dt{color:var(--ink2)}.human-details dd{margin:0;overflow-wrap:anywhere}
|
| 313 |
+
.human-details p,.human-details>a{font-size:13px;overflow-wrap:anywhere}.human-explainer{font-size:13px;color:var(--ink2);margin:10px 0 16px}
|
| 314 |
+
.human-fold{margin-top:0}.human-fold section{padding:18px 0 32px}.human-fold .wrap{padding:0}
|
| 315 |
+
.human-fold[open]>summary{color:var(--ink)}.human-fold:last-of-type{margin-bottom:24px}
|
| 316 |
+
footer .wrap{max-width:1120px}#top[hidden]{display:none!important}
|
| 317 |
+
.human-no-preview{display:flex;align-items:center;justify-content:center;min-height:140px;width:100%;color:var(--ink2);font-size:13px;background:var(--bg2)}
|
| 318 |
+
@media(max-width:700px){
|
| 319 |
+
.human{padding:12px 8px 4px}.human-intro{gap:12px;margin-bottom:18px}.human-intro h2{font-size:27px}
|
| 320 |
+
.human-intro p:not(.human-kicker){font-size:14px}.human .human-quiet{font-size:12px;padding:7px}
|
| 321 |
+
.human-browser{display:flex;flex-direction:column;gap:12px}.human-choices{display:contents}
|
| 322 |
+
.human-inputs{order:0;width:100%}.human-preview{order:1;width:100%}
|
| 323 |
+
.human-status,.human-actions,#human-copy-status,.human-make,.human-normals{order:2;width:100%;margin:0}
|
| 324 |
+
.human-actions{margin-bottom:8px}.human-image{min-height:180px;padding:8px}
|
| 325 |
+
.human-image img{max-height:250px}.human select,.human input{margin-bottom:10px}.human-help{margin:0 0 10px}
|
| 326 |
+
.human-inputs>.human-help:not(#human-link-note){font-size:12px;margin-bottom:4px}
|
| 327 |
+
.human-preview-head{padding:12px;flex-wrap:wrap}.human-preview-head>div{margin-left:auto}
|
| 328 |
+
.human-fold{margin-left:8px;margin-right:8px}.human-details dl{grid-template-columns:1fr;gap:3px}.human-details dd{margin-bottom:10px}
|
| 329 |
+
.human-intro{position:relative;padding-right:76px}.human .human-quiet{position:absolute;right:0;top:0;max-width:70px;white-space:normal}
|
| 330 |
+
}
|
| 331 |
+
@media(prefers-reduced-motion:reduce){html{scroll-behavior:auto!important}*{animation:none!important;transition:none!important}}
|
| 332 |
+
|
| 333 |
+
</style>
|
| 334 |
</head>
|
| 335 |
<body>
|
| 336 |
+
<main class="human" id="human-browser">
|
| 337 |
+
<div class="human-intro">
|
| 338 |
+
<div><p class="human-kicker">Published fields</p><h2>Explore scroll layers</h2>
|
| 339 |
+
<p>Choose a scroll, preview a field, and open its source.</p></div>
|
| 340 |
+
<button type="button" id="human-theme" class="human-quiet">Light / dark</button>
|
| 341 |
+
</div>
|
| 342 |
+
<div class="human-browser">
|
| 343 |
+
<div class="human-choices">
|
| 344 |
+
<div class="human-inputs">
|
| 345 |
+
<label for="human-search">Find a scroll</label><input id="human-search" type="search" placeholder="1447, PHerc1447, 175..." autocomplete="off">
|
| 346 |
+
<p id="human-link-note" class="human-help" role="status" hidden></p>
|
| 347 |
+
<label for="human-scroll">Scroll</label><select id="human-scroll"></select>
|
| 348 |
+
<label for="human-volume">Scan acquisition</label><select id="human-volume"></select>
|
| 349 |
+
<p class="human-help">A scroll can have several scans. Pick the acquisition you need.</p>
|
| 350 |
+
<div id="human-field-choice" hidden><label for="human-field">Field</label><select id="human-field"></select></div>
|
| 351 |
+
</div>
|
| 352 |
+
<div class="human-status" aria-live="polite"><span id="human-availability"></span></div>
|
| 353 |
+
<div class="human-actions"><button id="human-normals-toggle" class="human-primary" type="button" aria-controls="human-normals-panel" aria-expanded="false">Get normals</button>
|
| 354 |
+
<button id="human-share" type="button">Copy link to this field</button></div>
|
| 355 |
+
<div id="human-normals-panel" class="human-normals" hidden>
|
| 356 |
+
<h3>Surface normals</h3><p id="human-normals-description"></p>
|
| 357 |
+
<p class="human-help">Use these chunked Zarr array URLs in a compatible reader.</p>
|
| 358 |
+
<div class="human-channel"><label for="human-nx">nx array</label><button id="human-copy-nx" type="button">Copy nx</button>
|
| 359 |
+
<input id="human-nx" type="text" readonly spellcheck="false" aria-label="Exact nx Zarr array URL"></div>
|
| 360 |
+
<div class="human-channel"><label for="human-ny">ny array</label><button id="human-copy-ny" type="button">Copy ny</button>
|
| 361 |
+
<input id="human-ny" type="text" readonly spellcheck="false" aria-label="Exact ny Zarr array URL"></div>
|
| 362 |
+
<button id="human-copy" type="button">Copy both with scan details</button>
|
| 363 |
+
<div class="human-normal-links"><a id="human-source" target="_blank" rel="noopener">Open published source</a>
|
| 364 |
+
<a id="human-normals-manifest" target="_blank" rel="noopener">Manifest</a></div>
|
| 365 |
+
<details id="human-using"><summary>Using these files</summary><p id="human-coordinates" class="human-help"></p></details>
|
| 366 |
+
<p id="human-completeness" class="human-smallprint">Whole-volume completeness is not verified here.</p>
|
| 367 |
+
</div>
|
| 368 |
+
<p id="human-copy-status" class="human-help" role="status"></p>
|
| 369 |
+
<a class="human-make" href="?tab=make">Need a new field? Make a small box</a>
|
| 370 |
+
</div>
|
| 371 |
+
<figure class="human-preview">
|
| 372 |
+
<div class="human-preview-head"><h3>Field preview</h3><div role="group" aria-label="Preview direction">
|
| 373 |
+
<button type="button" id="human-xy" aria-pressed="true">Top view</button>
|
| 374 |
+
<button type="button" id="human-xz" aria-pressed="false">Side view</button></div></div>
|
| 375 |
+
<div class="human-image"><img id="human-image" alt="" hidden><p id="human-empty">Choose a scroll to see its preview.</p></div>
|
| 376 |
+
<figcaption id="human-caption">The layer signal and surface directions are model output, not a reading.</figcaption>
|
| 377 |
+
</figure>
|
| 378 |
+
</div>
|
| 379 |
+
<details class="human-details" id="human-provenance"><summary>Field details and provenance</summary>
|
| 380 |
+
<dl id="human-facts"></dl><p id="human-note"></p><a id="human-manifest" target="_blank" rel="noopener">Open field manifest</a>
|
| 381 |
+
</details>
|
| 382 |
+
<p class="human-explainer">A field describes the shape of papyrus layers. It helps surface-fitting tools follow them.</p>
|
| 383 |
+
</main>
|
| 384 |
+
|
| 385 |
+
<header class="hero" id="top" hidden>
|
| 386 |
<svg class="fields" id="fields" viewBox="0 0 1600 900" preserveAspectRatio="xMidYMax slice" aria-hidden="true"></svg>
|
| 387 |
<button class="tbtn" id="theme" type="button" aria-label="Switch light or dark">Theme</button>
|
| 388 |
<div class="wrap">
|
|
|
|
| 399 |
</div>
|
| 400 |
</header>
|
| 401 |
|
| 402 |
+
<details class="human-fold" id="human-all"><summary>All fields, filters and tables</summary>
|
| 403 |
<section id="all"><div class="wrap">
|
| 404 |
<h2>Every field, by scroll</h2>
|
| 405 |
<p class="sub">One card per scroll. <span class="mp villa">villa predict3d</span> is the villa lasagna model itself, the reference. <span class="mp lgt">Lasagnetta 0.1.1</span> copies it and runs about 5 times faster: use its fields as a preview, and villa's where exact values matter.</p>
|
|
|
|
| 423 |
<div id="pend" hidden></div>
|
| 424 |
</div></section>
|
| 425 |
|
| 426 |
+
</details>
|
| 427 |
+
<details class="human-fold" id="human-use"><summary>Download and developer recipes</summary>
|
| 428 |
<section id="use"><div class="wrap">
|
| 429 |
<h2>Stream, download and load</h2>
|
| 430 |
<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>, so any tool that reads zarr over HTTPS opens it with no download and no account. Pick one of the first ten fields made here, with the villa lasagna model, to see its field, its numbers and the commands to get it; for any other field, <b>Copy URL</b> in the list gives its folder.</p>
|
|
|
|
| 521 |
</div>
|
| 522 |
</div></section>
|
| 523 |
|
| 524 |
+
</details>
|
| 525 |
+
<details class="human-fold" id="human-about"><summary>About these fields and credits</summary>
|
| 526 |
<section id="about"><div class="wrap"><div class="about">
|
| 527 |
<h2>About these fields</h2>
|
| 528 |
<p class="sub">A lasagna field is the input that the lasagna surface fit in villa reads. These are public so that nobody has to spend a GPU day before trying an idea on these scrolls: use them, compare against them, and tell us if you find a problem.</p>
|
|
|
|
| 553 |
</details>
|
| 554 |
</div></div></section>
|
| 555 |
|
| 556 |
+
</details>
|
| 557 |
<footer><div class="wrap">
|
| 558 |
<span>Lasagna Fields, by Chase Hendrick · <a href="https://huggingface.co/SharpMeow">huggingface.co/SharpMeow</a> · <a href="https://github.com/ChaseHendrick">github.com/ChaseHendrick</a></span>
|
| 559 |
<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>
|
|
|
|
| 567 |
|
| 568 |
<script id="data" 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| 569 |
<script id="fieldlist" type="application/json">null</script>
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| 570 |
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| 571 |
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| 572 |
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| 573 |
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| 574 |
const fmt=n=>n.toLocaleString('en-US');
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| 575 |
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const gb=b=>Number.isFinite(b)&&b>=0?(b/1e9).toFixed(1)+' GB':'Size not listed';
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| 638 |
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| 660 |
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| 661 |
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| 662 |
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| 663 |
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| 665 |
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| 666 |
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| 667 |
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| 699 |
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|
| 703 |
+
document.querySelectorAll('[data-lv]').forEach(x=>{x.setAttribute('aria-pressed',x.dataset.lv===view);x.disabled=!f['preview_'+x.dataset.lv]});
|
| 704 |
$('lbslice').hidden=!f.gallery;
|
| 705 |
if(L.hidden){L.hidden=false;placeLb();document.documentElement.classList.add('lbopen');$('lbclose').focus({preventScroll:true})}}
|
| 706 |
function closePv(){$('lbox').hidden=true;document.documentElement.classList.remove('lbopen');$('lbimg').removeAttribute('src');pv=null}
|
|
|
|
| 719 |
/* stats */
|
| 720 |
const totB=D.reduce((a,s)=>a+s.bytes,0),totP=D.reduce((a,s)=>a+s.parts.length,0);
|
| 721 |
const ours=FL.filter(f=>f.source==='dataset'),nsc=uniq(FL.map(f=>f.scroll)).length;
|
| 722 |
+
$('stats').innerHTML=(FL.length?[[nsc,'scrolls'],[FL.length-ours.length,'villa fields in the open data'],[ours.length,'fields made here'],[sizeLabel(ours),'listed download size']]
|
| 723 |
:[[D.length,'scans'],[Math.round(totB/1e9)+' GB','to download'],[fmt(totP),'GPU parts'],['4','channels each']])
|
| 724 |
.map(([b,s])=>'<div class="stat"><b>'+b+'</b><span>'+s+'</span></div>').join('');
|
| 725 |
$('nscrolls').textContent=FL.length?nsc:D.length;
|
|
|
|
| 816 |
function fallback(t,done){const a=document.createElement('textarea');a.value=t;document.body.appendChild(a);a.select();try{document.execCommand('copy');done()}catch(e){}a.remove()}
|
| 817 |
|
| 818 |
pick(0,false);
|
| 819 |
+
</script>
|
| 820 |
+
<script>
|
| 821 |
+
/* Presentation only. Catalog browsing and link copying never call scientific endpoints. */
|
| 822 |
+
(() => {
|
| 823 |
+
let coverage = {};
|
| 824 |
+
try { coverage = JSON.parse(document.getElementById('coverage-list').textContent) || {}; } catch (_) {}
|
| 825 |
+
const samples = coverage.samples || [];
|
| 826 |
+
const names = [...new Set([...FL.map(f => f.scroll), ...samples.map(s => s.scroll)])].sort();
|
| 827 |
+
const el = id => document.getElementById('human-' + id);
|
| 828 |
+
const normalize = value => String(value || '').trim().toUpperCase().replace(/^PHERC[.\s_-]*/, '').replace(/[\s_.-]+/g, '').replace(/^0+(?=\d)/, '');
|
| 829 |
+
let selected = null, direction = 'xy';
|
| 830 |
+
const url = value => { try { const u = new URL(value); return u.protocol === 'https:' ? u.href : null; } catch (_) { return null; } };
|
| 831 |
+
const manifestOf = f => f && url(f.normals_access?.manifest_url || f.manifest);
|
| 832 |
+
const fieldId = f => manifestOf(f) || '';
|
| 833 |
+
const rowsFor = () => FL.filter(f => f.scroll === el('scroll').value && f.volume === el('volume').value);
|
| 834 |
+
function options(node, values, placeholder = null) {
|
| 835 |
+
const items = placeholder === null ? values : [['',placeholder], ...values];
|
| 836 |
+
node.replaceChildren(...items.map(([value,label]) => { const o = document.createElement('option'); o.value = value; o.textContent = label; return o; }));
|
| 837 |
+
node.disabled = !values.length;
|
| 838 |
+
}
|
| 839 |
+
function notice(message = '') { el('link-note').textContent = message; el('link-note').hidden = !message; }
|
| 840 |
+
function link(node, value) { const href = url(value); node.hidden = !href; if (href) node.href = href; else node.removeAttribute('href'); }
|
| 841 |
+
function normals(f) {
|
| 842 |
+
const a = f?.normals_access;
|
| 843 |
+
if (a) return {nx:url(a.channels?.nx?.array_url), ny:url(a.channels?.ny?.array_url)};
|
| 844 |
+
const arrays = f?.availability?.arrays;
|
| 845 |
+
return {nx:url(arrays?.nx?.url), ny:url(arrays?.ny?.url)};
|
| 846 |
+
}
|
| 847 |
+
function shareURL() {
|
| 848 |
+
if (!selected || !fieldId(selected)) return null;
|
| 849 |
+
const u = new URL('https://sharpmeow-lasagna-fields.hf.space/');
|
| 850 |
+
u.searchParams.set('scroll', selected.scroll); u.searchParams.set('volume', selected.volume);
|
| 851 |
+
u.searchParams.set('field', fieldId(selected));
|
| 852 |
+
return u.href;
|
| 853 |
+
}
|
| 854 |
+
function normalContext() {
|
| 855 |
+
const n = normals(selected), manifest = manifestOf(selected);
|
| 856 |
+
if (!selected || !n.nx || !n.ny || !manifest) return null;
|
| 857 |
+
return ['Lasagna Fields: surface normals', 'Scroll: ' + selected.scroll, 'Acquisition: ' + selected.volume,
|
| 858 |
+
'Model: ' + selected.model, 'Two encoded direction channels, nx and ny (chunked Zarr).',
|
| 859 |
+
'nx: ' + n.nx, 'ny: ' + n.ny, 'Manifest: ' + manifest,
|
| 860 |
+
selected.normals_access?.coordinate_note || '', 'View: ' + shareURL()].filter(Boolean).join('\n');
|
| 861 |
+
}
|
| 862 |
+
async function copy(value, success) {
|
| 863 |
+
if (!value) return;
|
| 864 |
+
try { await navigator.clipboard.writeText(value); el('copy-status').textContent = success; }
|
| 865 |
+
catch (_) { el('copy-status').textContent = 'Clipboard unavailable. Select the links in Surface normals to copy them.'; }
|
| 866 |
+
}
|
| 867 |
+
function preview() {
|
| 868 |
+
const image = el('image'), empty = el('empty');
|
| 869 |
+
const source = selected && url(selected['preview_' + direction]);
|
| 870 |
+
for (const view of ['xy','xz']) { el(view).disabled = !(selected && url(selected['preview_' + view])); el(view).setAttribute('aria-pressed', String(view === direction)); }
|
| 871 |
+
image.hidden = true; image.removeAttribute('src'); empty.hidden = false;
|
| 872 |
+
empty.textContent = selected ? 'No preview image is listed for this view. You can still use the published normals links.' : 'Choose a listed scroll, acquisition and field to see its preview.';
|
| 873 |
+
if (source) {
|
| 874 |
+
image.alt = selected.scroll + ', acquisition ' + selected.volume + ': ' + (direction === 'xy' ? 'top' : 'side') + ' view of the model field';
|
| 875 |
+
empty.textContent = 'Loading the published preview...';
|
| 876 |
+
image.onload = () => { image.hidden = false; empty.hidden = true; };
|
| 877 |
+
image.onerror = () => { image.hidden = true; empty.hidden = false; empty.textContent = 'This preview could not load. Published access links remain available under Get normals.'; };
|
| 878 |
+
image.src = source;
|
| 879 |
+
}
|
| 880 |
+
el('caption').textContent = selected ? 'Grayscale shows the layer pattern; color shows surface direction. ' + (selected.model || 'Published model') + '. Model output, not a reading.' : 'Field availability is specific to the selected scan acquisition.';
|
| 881 |
+
}
|
| 882 |
+
function showField() {
|
| 883 |
+
const rows = rowsFor(), matching = rows.filter(f => fieldId(f) === el('field').value);
|
| 884 |
+
selected = matching.length === 1 ? matching[0] : null;
|
| 885 |
+
el('completeness').textContent = selected && selected.availability?.whole_volume_complete === true ? 'Catalog reports whole-volume completeness; see provenance.' : 'Whole-volume completeness is not verified here.';
|
| 886 |
+
const f = selected || {}, a = f.normals_access || {}, p = f.provenance || {}, n = normals(selected);
|
| 887 |
+
const source = a.download?.page_url || f.browse || f.url;
|
| 888 |
+
link(el('source'), source); link(el('manifest'), manifestOf(selected));
|
| 889 |
+
link(el('normals-manifest'), manifestOf(selected));
|
| 890 |
+
el('source').textContent = source && source.includes('/tree/') ? 'Open file browser' : a.download?.kind === 'hf_dataset_bundle' ? 'Open field bundle source' : 'Open published source';
|
| 891 |
+
el('normals-panel').hidden = true; el('normals-toggle').setAttribute('aria-expanded','false');
|
| 892 |
+
const accessible = Boolean(n.nx && n.ny && manifestOf(selected));
|
| 893 |
+
el('availability').textContent = accessible ? 'Normals links available' : selected ? 'Normals links not listed' : 'No published field selected';
|
| 894 |
+
el('normals-toggle').disabled = !accessible; el('copy').disabled = !accessible;
|
| 895 |
+
el('normals-toggle').textContent = selected && !accessible ? 'Normals links not listed' : 'Get normals';
|
| 896 |
+
for (const channel of ['nx','ny']) { el(channel).value = n[channel] || ''; el('copy-'+channel).disabled = !n[channel]; }
|
| 897 |
+
el('using').open = false;
|
| 898 |
+
el('normals-description').textContent = selected ? selected.model + '. Two encoded surface-direction channels, nx and ny.' : '';
|
| 899 |
+
el('coordinates').textContent = a.coordinate_note || 'Use the manifest for coordinate scales and decoding.';
|
| 900 |
+
el('share').disabled = !shareURL(); el('copy-status').textContent = '';
|
| 901 |
+
const facts = [['Scroll',el('scroll').value],['Acquisition',el('volume').value],['Model',f.model],['Source',f.source],['Made by',f.made_by],['Voxel size',f.voxel_um != null ? f.voxel_um+' µm' : null],['CT input level',f.read_level],['Normal source',f.normal_source],['Checkpoint',p.checkpoint_revision],['Published size',f.bytes != null ? gb(f.bytes) : null],['Availability status',f.availability?.status]];
|
| 902 |
+
el('facts').replaceChildren(...facts.filter(([,v]) => v !== undefined && v !== null && v !== '').flatMap(([k,v]) => { const dt = document.createElement('dt'), dd = document.createElement('dd'); dt.textContent = k; dd.textContent = String(v); return [dt,dd]; }));
|
| 903 |
+
el('note').textContent = f.note || '';
|
| 904 |
+
direction = f.preview_xy ? 'xy' : 'xz'; preview();
|
| 905 |
+
}
|
| 906 |
+
function acquisition(requestedField = null) {
|
| 907 |
+
const rows = rowsFor(), invalid = requestedField !== null && !rows.some(f => fieldId(f) === requestedField);
|
| 908 |
+
options(el('field'), rows.map(f => [fieldId(f),(f.model || 'Field')+' · '+(f.source || 'published source')]), invalid ? 'Choose a listed field' : null);
|
| 909 |
+
if (requestedField !== null && !invalid) el('field').value = requestedField;
|
| 910 |
+
el('field-choice').hidden = rows.length < 2 && !invalid;
|
| 911 |
+
showField();
|
| 912 |
+
if (invalid) notice('The field in this link is not listed for this acquisition. Choose a listed field.');
|
| 913 |
+
else if (el('volume').value && !rows.length) { el('availability').textContent = 'No published field listed'; el('empty').textContent = 'No published field is listed for this acquisition. Choose another acquisition or make a small box.'; }
|
| 914 |
+
}
|
| 915 |
+
function scroll(requestedVolume = null, requestedField = null) {
|
| 916 |
+
const name = el('scroll').value, volumes = new Map();
|
| 917 |
+
for (const v of (samples.find(s => s.scroll === name)?.volumes || [])) volumes.set(v.volume,v);
|
| 918 |
+
for (const f of FL.filter(f => f.scroll === name)) if (!volumes.has(f.volume)) volumes.set(f.volume,f);
|
| 919 |
+
const invalid = requestedVolume !== null && !volumes.has(requestedVolume);
|
| 920 |
+
options(el('volume'), [...volumes.values()].sort((a,b) => a.volume.localeCompare(b.volume)).map(v => [v.volume,v.volume+(v.voxel_um != null ? ' · '+v.voxel_um+' µm' : '')+(v.superseded_by ? ' (superseded)' : '')]), invalid ? 'Choose a listed acquisition' : null);
|
| 921 |
+
if (requestedVolume !== null && !invalid) el('volume').value = requestedVolume;
|
| 922 |
+
acquisition(invalid ? null : requestedField);
|
| 923 |
+
if (invalid) notice('The acquisition in this link is not listed for this scroll. Choose a listed acquisition.');
|
| 924 |
+
}
|
| 925 |
+
function search() {
|
| 926 |
+
const q = normalize(el('search').value), matches = names.filter(n => normalize(n).includes(q));
|
| 927 |
+
const exact = matches.filter(n => normalize(n) === q), previous = el('scroll').value;
|
| 928 |
+
const chosen = exact.length === 1 ? exact[0] : matches.length === 1 ? matches[0] : !q && matches.includes(previous) ? previous : null;
|
| 929 |
+
options(el('scroll'), matches.map(s => [s,s]), chosen ? null : matches.length ? 'Choose a scroll or variant' : 'No matching scroll');
|
| 930 |
+
if (chosen) el('scroll').value = chosen;
|
| 931 |
+
notice(chosen ? '' : matches.length ? 'Choose a specific scroll or variant from the matches.' : 'No scroll matches this search.');
|
| 932 |
+
scroll();
|
| 933 |
+
}
|
| 934 |
+
options(el('scroll'),names.map(s => [s,s]));
|
| 935 |
+
if (names.includes('PHerc0139')) el('scroll').value = 'PHerc0139';
|
| 936 |
+
el('search').oninput = search;
|
| 937 |
+
el('scroll').onchange = () => { notice(); scroll(); };
|
| 938 |
+
el('volume').onchange = () => { notice(); acquisition(); };
|
| 939 |
+
el('field').onchange = () => { notice(); showField(); };
|
| 940 |
+
for (const view of ['xy','xz']) el(view).onclick = () => { direction=view; preview(); };
|
| 941 |
+
el('theme').onclick = () => document.getElementById('theme').click();
|
| 942 |
+
el('normals-toggle').onclick = () => { const panel=el('normals-panel'); panel.hidden=!panel.hidden; el('normals-toggle').setAttribute('aria-expanded',String(!panel.hidden)); };
|
| 943 |
+
el('copy').onclick = () => copy(normalContext(),'Both normals links, manifest and field context copied.');
|
| 944 |
+
for (const channel of ['nx','ny']) el('copy-'+channel).onclick = () => copy(normals(selected)[channel],channel+' array URL copied.');
|
| 945 |
+
el('share').onclick = () => copy(shareURL(),'Link to this exact field copied.');
|
| 946 |
+
function reveal(target) { for (let n=target;n;n=n.parentElement) if (n.tagName==='DETAILS') n.open=true; }
|
| 947 |
+
document.addEventListener('click',e => { const a=e.target.closest('a[href^="#"]'); if(a)reveal(document.getElementById(a.getAttribute('href').slice(1))); if(e.target.closest('#lbslice'))reveal(document.getElementById('use')); },true);
|
| 948 |
+
window.addEventListener('hashchange',() => reveal(document.getElementById(location.hash.slice(1))));
|
| 949 |
+
reveal(document.getElementById(location.hash.slice(1)));
|
| 950 |
+
let params;
|
| 951 |
+
try { params=new URLSearchParams(window.parent.location.search); } catch (_) { params=new URLSearchParams(); }
|
| 952 |
+
if (params.has('scroll')) {
|
| 953 |
+
const requested=params.get('scroll'), exact=names.filter(n => normalize(n)===normalize(requested));
|
| 954 |
+
if (exact.length===1) { el('scroll').value=exact[0]; scroll(params.get('volume'),params.get('field')); }
|
| 955 |
+
else { el('search').value=requested; search(); if(el('scroll').value) { options(el('scroll'),names.map(s=>[s,s]),'Choose a listed scroll'); scroll(); } notice('This link needs a specific listed scroll or variant. Choose one below.'); }
|
| 956 |
+
} else if (params.has('volume') || params.has('field')) {
|
| 957 |
+
options(el('scroll'),names.map(s=>[s,s]),'Choose a listed scroll'); scroll(); notice('This link is missing its scroll. Choose a scroll and acquisition.');
|
| 958 |
+
} else if (names.length) scroll();
|
| 959 |
+
else { scroll(); notice('No published field metadata loaded.'); }
|
| 960 |
+
})();
|
| 961 |
+
|
| 962 |
</script>
|
| 963 |
</body>
|
| 964 |
</html>
|
lasfield.py
CHANGED
|
@@ -37,8 +37,8 @@ import numpy as np
|
|
| 37 |
BUCKET = "https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com"
|
| 38 |
METADATA = BUCKET + "/metadata.json"
|
| 39 |
USER_AGENT = "lasagna-fields-space (huggingface.co/spaces/SharpMeow/lasagna-fields)"
|
| 40 |
-
#
|
| 41 |
-
REFUSED_SAMPLES =
|
| 42 |
CACHE = Path(os.environ.get("LASFIELD_CACHE") or Path(tempfile.gettempdir()) / "lasagna-fields")
|
| 43 |
|
| 44 |
# villa's lasagna at the commit the ten whole-scan fields of this Space were made with (docs/tools/lasagna-fields.md);
|
|
@@ -109,6 +109,26 @@ def level_for(um):
|
|
| 109 |
return max(0, int(round(math.log2(TARGET_UM / float(um))))) if um else 0
|
| 110 |
|
| 111 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 112 |
def catalog(refresh_s=6 * 3600):
|
| 113 |
"""Every volume of the open data's metadata.json this Space may read, by volume id."""
|
| 114 |
with _LOCK:
|
|
@@ -127,7 +147,7 @@ def catalog(refresh_s=6 * 3600):
|
|
| 127 |
vols[vid] = {"volume": vid, "sample": sid, "long_id": v["long_id"], "voxel_um": float(um),
|
| 128 |
"shape_zyx": shape, "level": level_for(um),
|
| 129 |
"superseded_by": pr.get("superseded_by"),
|
| 130 |
-
"url": f"{BUCKET}/{sid}/volumes/{v['long_id']}/"}
|
| 131 |
_CATALOG.update(at=time.time(), volumes=vols)
|
| 132 |
return vols
|
| 133 |
|
|
@@ -142,7 +162,7 @@ def volume(vid):
|
|
| 142 |
if v["long_id"] == vid or v["long_id"].startswith(vid + "-"):
|
| 143 |
return v
|
| 144 |
if any(vid.lower().startswith(s) for s in REFUSED_SAMPLES):
|
| 145 |
-
raise FieldError("this
|
| 146 |
raise FieldError(f"{vid!r} is not a volume in the Vesuvius Challenge open data (metadata.json); "
|
| 147 |
"give its 14-digit volume id, such as 20260102150214")
|
| 148 |
|
|
|
|
| 37 |
BUCKET = "https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com"
|
| 38 |
METADATA = BUCKET + "/metadata.json"
|
| 39 |
USER_AGENT = "lasagna-fields-space (huggingface.co/spaces/SharpMeow/lasagna-fields)"
|
| 40 |
+
# Public geometry coverage includes every catalog scroll.
|
| 41 |
+
REFUSED_SAMPLES = set()
|
| 42 |
CACHE = Path(os.environ.get("LASFIELD_CACHE") or Path(tempfile.gettempdir()) / "lasagna-fields")
|
| 43 |
|
| 44 |
# villa's lasagna at the commit the ten whole-scan fields of this Space were made with (docs/tools/lasagna-fields.md);
|
|
|
|
| 109 |
return max(0, int(round(math.log2(TARGET_UM / float(um))))) if um else 0
|
| 110 |
|
| 111 |
|
| 112 |
+
def public_ct_urls(v):
|
| 113 |
+
"""Declared public ordinary OME-Zarr origins; compressed formats need their own reader."""
|
| 114 |
+
urls = []
|
| 115 |
+
for item in v.get("data", []):
|
| 116 |
+
if item.get("type") != "ome-zarr":
|
| 117 |
+
continue
|
| 118 |
+
for origin in item.get("origins", []):
|
| 119 |
+
for root in origin.get("access_roots", []):
|
| 120 |
+
if root.get("usage") != "public-read":
|
| 121 |
+
continue
|
| 122 |
+
base = root.get("url", "")
|
| 123 |
+
if base == "s3://vesuvius-challenge-open-data":
|
| 124 |
+
base = BUCKET
|
| 125 |
+
if base.startswith("https://"):
|
| 126 |
+
url = base.rstrip("/") + "/" + origin["path"].strip("/") + "/"
|
| 127 |
+
if url not in urls:
|
| 128 |
+
urls.append(url)
|
| 129 |
+
return urls
|
| 130 |
+
|
| 131 |
+
|
| 132 |
def catalog(refresh_s=6 * 3600):
|
| 133 |
"""Every volume of the open data's metadata.json this Space may read, by volume id."""
|
| 134 |
with _LOCK:
|
|
|
|
| 147 |
vols[vid] = {"volume": vid, "sample": sid, "long_id": v["long_id"], "voxel_um": float(um),
|
| 148 |
"shape_zyx": shape, "level": level_for(um),
|
| 149 |
"superseded_by": pr.get("superseded_by"),
|
| 150 |
+
"url": (public_ct_urls(v) or [f"{BUCKET}/{sid}/volumes/{v['long_id']}/"])[0]}
|
| 151 |
_CATALOG.update(at=time.time(), volumes=vols)
|
| 152 |
return vols
|
| 153 |
|
|
|
|
| 162 |
if v["long_id"] == vid or v["long_id"].startswith(vid + "-"):
|
| 163 |
return v
|
| 164 |
if any(vid.lower().startswith(s) for s in REFUSED_SAMPLES):
|
| 165 |
+
raise FieldError("this sample is not enabled")
|
| 166 |
raise FieldError(f"{vid!r} is not a volume in the Vesuvius Challenge open data (metadata.json); "
|
| 167 |
"give its 14-digit volume id, such as 20260102150214")
|
| 168 |
|