lightly-studio 0.4.0__py3-none-any.whl → 0.4.1__py3-none-any.whl
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- lightly_studio/__init__.py +1 -2
- lightly_studio/api/db_tables.py +3 -0
- lightly_studio/api/routes/api/dataset.py +5 -3
- lightly_studio/api/routes/api/embeddings2d.py +4 -16
- lightly_studio/core/dataset_query/dataset_query.py +98 -2
- lightly_studio/core/dataset_query/sample_field.py +11 -2
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/assets/0.B-Bn8V7R.css +1 -0
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/assets/Samples.CTl60pQb.css +1 -0
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/assets/_layout.CxuTMeYy.css +1 -0
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/assets/transform.Bte-FZ4V.css +1 -0
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/{ChlxSwqI.js → 7XnHnNk_.js} +1 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/{DthpwYR_.js → BDE1kT04.js} +2 -2
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/{D8ZGoCPm.js → BHoO7UL_.js} +2 -2
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/{BiGQqqJP.js → BTpMiPuk.js} +1 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/BbG6fgnL.js +1 -0
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/Bip0vTKl.js +1 -0
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/{BrNKoXwc.js → BzYRexN9.js} +1 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/{CP9M7pei.js → C5oezL0m.js} +1 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/CEPpkZIV.js +1 -0
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/ChO13USc.js +96 -0
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/{ClzkJBWk.js → CmNXvs5e.js} +1 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/{DUtlYNuP.js → D9WxTSWa.js} +1 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/DELrRF6e.js +4 -0
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/{BtXGzlpP.js → DFib3GIP.js} +1 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/{DMJzr1NB.js → DeAqvaPB.js} +1 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/DgCXCApo.js +438 -0
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/DqhovIS0.js +1 -0
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/entry/{app.Y-sSoz5q.js → app.CED-eiXl.js} +2 -2
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/entry/start.D6UcpqyO.js +1 -0
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/nodes/{0.0Fm6E-5B.js → 0.waSqEGqm.js} +2 -2
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/nodes/{1.DB-0vkHb.js → 1.Bb_sKkYl.js} +1 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/nodes/{10.vaUePh5k.js → 10.D9Uicmfq.js} +1 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/nodes/{11.7i7ljNVT.js → 11.DKnK0EcJ.js} +1 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/nodes/13.D7dGgxYC.js +1 -0
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/nodes/{2.Drwwdm7A.js → 2.BzK1sjoM.js} +138 -100
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/nodes/{3.D3X_-Wan.js → 3.B08UPFst.js} +1 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/nodes/{4.C9TqY3tA.js → 4.C19_Nx95.js} +1 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/nodes/5.B2cR7brs.js +39 -0
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/nodes/{6.fqfYR7dB.js → 6.C9Y2LZxG.js} +1 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/nodes/{7.C7gMM-gk.js → 7.CEbWmgIF.js} +1 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/nodes/8.Con-GcPz.js +20 -0
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/nodes/{9.DbHcSiMn.js → 9.DW7FBNNH.js} +1 -1
- lightly_studio/dist_lightly_studio_view_app/_app/version.json +1 -1
- lightly_studio/dist_lightly_studio_view_app/index.html +7 -8
- lightly_studio/models/annotation/annotation_base.py +9 -0
- lightly_studio/models/dataset.py +6 -0
- lightly_studio/models/sample.py +1 -1
- lightly_studio/models/two_dim_embedding.py +16 -0
- lightly_studio/resolvers/annotation_resolver/get_all.py +3 -1
- lightly_studio/resolvers/dataset_resolver.py +18 -1
- lightly_studio/resolvers/sample_embedding_resolver.py +44 -2
- lightly_studio/resolvers/sample_resolver.py +1 -3
- lightly_studio/resolvers/twodim_embedding_resolver.py +93 -3
- lightly_studio/selection/select.py +70 -1
- lightly_studio/selection/selection_config.py +1 -1
- {lightly_studio-0.4.0.dist-info → lightly_studio-0.4.1.dist-info}/METADATA +1 -1
- {lightly_studio-0.4.0.dist-info → lightly_studio-0.4.1.dist-info}/RECORD +58 -58
- lightly_studio/dataset/loader.py +0 -581
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/assets/0.CN4hnTks.css +0 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/assets/Samples.C0_eo9eP.css +0 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/assets/_layout.kFFGI0zL.css +0 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/assets/transform.sLzR40om.css +0 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/BOmrKuMn.js +0 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/BPpOWbDa.js +0 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/BaFFwDFr.js +0 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/BsaJCCG_.js +0 -96
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/CWuDkrMZ.js +0 -436
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/DyIcJj6J.js +0 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/chunks/WEyXQRi6.js +0 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/entry/start.CvxVp0Cu.js +0 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/nodes/13.9qy3WtZv.js +0 -1
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/nodes/5.iRw6HCWX.js +0 -39
- lightly_studio/dist_lightly_studio_view_app/_app/immutable/nodes/8.C4v1w-oS.js +0 -20
- {lightly_studio-0.4.0.dist-info → lightly_studio-0.4.1.dist-info}/WHEEL +0 -0
lightly_studio/dist_lightly_studio_view_app/_app/immutable/nodes/{3.D3X_-Wan.js → 3.B08UPFst.js}
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import{u as a}from"../chunks/
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import{u as a}from"../chunks/DeAqvaPB.js";import{L as d}from"../chunks/DVxjPOJB.js";const s=async({parent:t,params:{dataset_id:e}})=>{const{globalStorage:o}=await t(),{tagsSelected:n}=a({dataset_id:e,kind:["annotation"]});return{annotationsSelectedTagsIds:n,annotationsSelectedAnnotationLabelsIds:o.selectedAnnotationFilterIds}},r=Object.freeze(Object.defineProperty({__proto__:null,load:s},Symbol.toStringTag,{value:"Module"}));export{d as component,r as universal};
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lightly_studio/dist_lightly_studio_view_app/_app/immutable/nodes/{4.C9TqY3tA.js → 4.C19_Nx95.js}
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import{u as a}from"../chunks/CmNXvs5e.js";import{u as l}from"../chunks/DeAqvaPB.js";import{u as m}from"../chunks/Bip0vTKl.js";import{L as b}from"../chunks/DVxjPOJB.js";const r=async({params:{dataset_id:e}})=>{const{selectedAnnotationFilterIds:s,textEmbedding:o}=m(),{tagsSelected:t}=l({dataset_id:e,kind:["sample"]}),{dimensionsValues:n}=a();return{samplesSelectedTagsIds:t,samplesDimensions:n,samplesTextEmbedding:o,samplesSelectedAnnotationLabelsIds:s}},c=Object.freeze(Object.defineProperty({__proto__:null,load:r},Symbol.toStringTag,{value:"Module"}));export{b as component,c as universal};
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t.sample}}),p(K),i(Q,K)},$$slots:{default:!0}})},$$slots:{default:!0}}),ve(),c()}var tn=Z('<div class="flex h-full w-full space-x-4 px-4 pb-4" data-testid="sample-details"><div class="h-full w-full space-y-6 rounded-[1vw] bg-card p-4"><!></div></div>');function An(m,t){ge(t,!0);const g=o(()=>xe.params.sampleId),d=xe.data.dataset,n=o(()=>Number(xe.params.sampleIndex));var c=tn(),l=x(c),h=x(l);ja(h,{get sampleId(){return e(g)},get dataset(){return d},get sampleIndex(){return e(n)},children:(ne,de)=>{var T=ie(),y=I(T);{var G=_=>{var P=ie(),Q=I(P);Be(Q,()=>t.children),i(_,P)};O(y,_=>{t.children&&_(G)})}i(ne,T)},$$slots:{default:!0}}),p(l),p(c),i(m,c),ve()}export{An as component};
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lightly_studio/dist_lightly_studio_view_app/_app/immutable/nodes/{6.fqfYR7dB.js → 6.C9Y2LZxG.js}
RENAMED
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import{r as s}from"../chunks/
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import{r as s}from"../chunks/7XnHnNk_.js";import{r as d}from"../chunks/CEPpkZIV.js";import{r as n}from"../chunks/B90CZVMX.js";const i=async()=>{const{data:t}=await d();if(!t||t.length===0)throw new Error("No datasets found");const e=t.toSorted((r,o)=>new Date(o.created_at||0).getTime()-new Date(r.created_at||0).getTime())[0],a=e==null?void 0:e.dataset_id;if(!a)throw new Error("No valid dataset ID found");n(307,s.toSamples(a))},m=Object.freeze(Object.defineProperty({__proto__:null,load:i},Symbol.toStringTag,{value:"Module"}));export{m as universal};
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lightly_studio/dist_lightly_studio_view_app/_app/immutable/nodes/{7.C7gMM-gk.js → 7.CEbWmgIF.js}
RENAMED
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@@ -1 +1 @@
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import"../chunks/CWj6FrbW.js";import{p as f,u as $,g as a,a as _,b as o}from"../chunks/C3xJX0nD.js";import{s as i,a as h}from"../chunks/DmGM9V9Q.js";import{A as S}from"../chunks/
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import"../chunks/CWj6FrbW.js";import{p as f,u as $,g as a,a as _,b as o}from"../chunks/C3xJX0nD.js";import{s as i,a as h}from"../chunks/DmGM9V9Q.js";import{A as S}from"../chunks/DgCXCApo.js";import{u as T}from"../chunks/Bip0vTKl.js";import"../chunks/BDE1kT04.js";import"../chunks/CmNXvs5e.js";import"../chunks/CEPpkZIV.js";import"../chunks/D9WxTSWa.js";import"../chunks/69_IOA4Y.js";import"../chunks/BHoO7UL_.js";import{u as G}from"../chunks/DeAqvaPB.js";import"../chunks/gBp1tBnA.js";function q(n,t){f(t,!0);const p=()=>i(c,"$lastGridType",s),e=()=>i(d,"$sampleSize",s),[s,m]=h(),{datasetId:r,sampleSize:d,selectedAnnotationFilterIds:l}=t.data,{lastGridType:c}=T(),u=o(()=>G({dataset_id:r})),g=o(()=>a(u).clearTagsSelected);$(()=>{p()!=="annotations"&&a(g)()}),S(n,{get itemHeight(){return e().height},get itemWidth(){return e().width},get dataset_id(){return r},get selectedAnnotationFilterIds(){return l}}),_(),m()}export{q as component};
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* Copyright (c) for portions of Lucide are held by Cole Bemis 2013-2022 as part of Feather (MIT). All other copyright (c) for Lucide are held by Lucide Contributors 2022.
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lightly_studio/dist_lightly_studio_view_app/_app/immutable/nodes/{9.DbHcSiMn.js → 9.DW7FBNNH.js}
RENAMED
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+
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"""Database table storing cached 2D embeddings."""
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col(SampleTable.file_path_abs).asc(),
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def get_dataset_details(session: Session, dataset: DatasetTable) -> DatasetViewWithCount:
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"""Convert a DatasetTable to DatasetViewWithCount with computed sample count."""
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sample_count = (
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session.exec(
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or 0
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return DatasetViewWithCount(
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dataset_id=dataset.dataset_id,
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name=dataset.name,
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created_at=dataset.created_at,
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)
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def update(session: Session, dataset_id: UUID, dataset_data: DatasetCreate) -> DatasetTable:
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"""Update an existing dataset."""
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dataset = get_by_id(session=session, dataset_id=dataset_id)
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@@ -2,9 +2,10 @@
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from __future__ import annotations
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import hashlib
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from uuid import UUID
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from sqlalchemy import String, cast
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from sqlalchemy import String, cast, func
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from sqlmodel import Session, col, select
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from lightly_studio.models.sample import SampleTable
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@@ -81,6 +82,47 @@ def get_all_by_dataset_id(
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.where(SampleEmbeddingTable.sample_id == SampleTable.sample_id)
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.where(SampleTable.dataset_id == dataset_id)
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.where(SampleEmbeddingTable.embedding_model_id == embedding_model_id)
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.order_by(col(SampleTable.
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.order_by(col(SampleTable.file_path_abs).asc())
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)
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return list(session.exec(query).all())
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def get_hash_by_sample_ids(
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session: Session,
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sample_ids_ordered: list[UUID],
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embedding_model_id: UUID,
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) -> tuple[str, list[UUID]]:
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"""Return a combined hash and the ordered sample IDs with stored embeddings.
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Args:
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session: Database session.
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sample_ids_ordered: Sample IDs to consider, order defines deterministic hash.
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embedding_model_id: Embedding model identifier.
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Returns:
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Tuple of (combined hash, ordered sample IDs that have stored embeddings).
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"""
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if not sample_ids_ordered:
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return "empty", []
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rows = session.exec(
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select(
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SampleEmbeddingTable.sample_id,
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func.hash(SampleEmbeddingTable.embedding).label("hash_column"),
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)
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.where(col(SampleEmbeddingTable.sample_id).in_(set(sample_ids_ordered)))
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.where(SampleEmbeddingTable.embedding_model_id == embedding_model_id)
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).all()
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# Mypy does not get that 'hash_column' is an attribute of the returned rows
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sample_id_to_hash = {row.sample_id: row.hash_column for row in rows} # type: ignore[attr-defined]
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sample_ids_of_samples_with_embeddings = [
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sample_id for sample_id in sample_ids_ordered if sample_id in sample_id_to_hash
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]
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hashes_ordered = [
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sample_id_to_hash[sample_id] for sample_id in sample_ids_of_samples_with_embeddings
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]
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hasher = hashlib.sha256()
|
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hasher.update("".join(str(h) for h in hashes_ordered).encode("utf-8"))
|
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128
|
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return hasher.hexdigest(), sample_ids_of_samples_with_embeddings
|
|
@@ -156,9 +156,7 @@ def get_all_by_dataset_id( # noqa: PLR0913
|
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156
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col(SampleTable.sample_id) == col(SampleEmbeddingTable.sample_id),
|
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).where(SampleEmbeddingTable.embedding_model_id == embedding_model_id)
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else:
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-
samples_query = samples_query.order_by(
|
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col(SampleTable.created_at).asc(), col(SampleTable.sample_id).asc()
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-
)
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159
|
+
samples_query = samples_query.order_by(col(SampleTable.file_path_abs).asc())
|
|
162
160
|
|
|
163
161
|
# Apply pagination if provided
|
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if pagination is not None:
|
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@@ -1,14 +1,104 @@
|
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1
|
-
"""Handler for getting 2D embeddings from high-dimensional embeddings."""
|
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1
|
+
"""Handler for getting cached 2D embeddings from high-dimensional embeddings."""
|
|
2
2
|
|
|
3
3
|
from __future__ import annotations
|
|
4
4
|
|
|
5
|
+
from uuid import UUID
|
|
6
|
+
|
|
7
|
+
import numpy as np
|
|
5
8
|
from lightly_mundig import TwoDimEmbedding # type: ignore[import-untyped]
|
|
9
|
+
from numpy.typing import NDArray
|
|
10
|
+
from sqlmodel import Session, col, select
|
|
6
11
|
|
|
7
12
|
from lightly_studio.dataset.env import LIGHTLY_STUDIO_LICENSE_KEY
|
|
13
|
+
from lightly_studio.models.embedding_model import EmbeddingModelTable
|
|
14
|
+
from lightly_studio.models.sample import SampleTable
|
|
15
|
+
from lightly_studio.models.two_dim_embedding import TwoDimEmbeddingTable
|
|
16
|
+
from lightly_studio.resolvers import sample_embedding_resolver
|
|
17
|
+
|
|
18
|
+
|
|
19
|
+
def get_twodim_embeddings(
|
|
20
|
+
session: Session,
|
|
21
|
+
dataset_id: UUID,
|
|
22
|
+
embedding_model_id: UUID,
|
|
23
|
+
) -> tuple[NDArray[np.float32], NDArray[np.float32], list[UUID]]:
|
|
24
|
+
"""Return cached 2D embeddings together with their sample identifiers.
|
|
25
|
+
|
|
26
|
+
Uses a cache to avoid recomputing the 2D embeddings. The cache key combines the sorted
|
|
27
|
+
sample identifiers with a deterministic 64-bit hash over the stored high-dimensional
|
|
28
|
+
embeddings.
|
|
29
|
+
|
|
30
|
+
Args:
|
|
31
|
+
session: Database session.
|
|
32
|
+
dataset_id: Dataset identifier.
|
|
33
|
+
embedding_model_id: Embedding model identifier.
|
|
34
|
+
|
|
35
|
+
Returns:
|
|
36
|
+
Tuple of (x coordinates, y coordinates, ordered sample IDs).
|
|
37
|
+
"""
|
|
38
|
+
embedding_model = session.get(EmbeddingModelTable, embedding_model_id)
|
|
39
|
+
if embedding_model is None:
|
|
40
|
+
raise ValueError(f"Embedding model {embedding_model_id} not found.")
|
|
41
|
+
|
|
42
|
+
# Define a fixed order of sample IDs for the cache key.
|
|
43
|
+
sample_ids_ordered = list(
|
|
44
|
+
session.exec(
|
|
45
|
+
select(SampleTable.sample_id)
|
|
46
|
+
.where(SampleTable.dataset_id == dataset_id)
|
|
47
|
+
.order_by(col(SampleTable.sample_id).asc())
|
|
48
|
+
).all()
|
|
49
|
+
)
|
|
50
|
+
|
|
51
|
+
# Check if we have a cached 2D embedding for the given samples and embedding model.
|
|
52
|
+
# The order is defined by sample_ids_ordered.
|
|
53
|
+
cache_key, sample_ids_of_samples_with_embeddings = (
|
|
54
|
+
sample_embedding_resolver.get_hash_by_sample_ids(
|
|
55
|
+
session=session,
|
|
56
|
+
sample_ids_ordered=sample_ids_ordered,
|
|
57
|
+
embedding_model_id=embedding_model_id,
|
|
58
|
+
)
|
|
59
|
+
)
|
|
60
|
+
|
|
61
|
+
if not sample_ids_of_samples_with_embeddings:
|
|
62
|
+
empty = np.array([], dtype=np.float32)
|
|
63
|
+
return empty, empty, []
|
|
64
|
+
|
|
65
|
+
# If there is a cached entry, return it.
|
|
66
|
+
cached = session.get(TwoDimEmbeddingTable, cache_key)
|
|
67
|
+
if cached is not None:
|
|
68
|
+
x_values = np.array(cached.x, dtype=np.float32)
|
|
69
|
+
y_values = np.array(cached.y, dtype=np.float32)
|
|
70
|
+
return x_values, y_values, sample_ids_of_samples_with_embeddings
|
|
71
|
+
|
|
72
|
+
# No cached entry found - load the high-dimensional embeddings.
|
|
73
|
+
# The order is defined by sample_ids_of_samples_with_embeddings.
|
|
74
|
+
sample_embeddings = sample_embedding_resolver.get_by_sample_ids(
|
|
75
|
+
session=session,
|
|
76
|
+
sample_ids=sample_ids_of_samples_with_embeddings,
|
|
77
|
+
embedding_model_id=embedding_model_id,
|
|
78
|
+
)
|
|
79
|
+
|
|
80
|
+
# If there are no embeddings, return empty arrays.
|
|
81
|
+
if not sample_embeddings:
|
|
82
|
+
empty = np.array([], dtype=np.float32)
|
|
83
|
+
return empty, empty, []
|
|
84
|
+
|
|
85
|
+
# Compute the 2D embedding from the high-dimensional embeddings.
|
|
86
|
+
# The order is now defined by sample_embeddings. They are the ordered subset of the
|
|
87
|
+
# sample_ids_of_samples_with_embeddings that have embeddings.
|
|
88
|
+
sample_ids_of_samples_with_embeddings = [embedding.sample_id for embedding in sample_embeddings]
|
|
89
|
+
embedding_values = [embedding.embedding for embedding in sample_embeddings]
|
|
90
|
+
planar_embeddings = _calculate_2d_embeddings(embedding_values)
|
|
91
|
+
embeddings_2d = np.asarray(planar_embeddings, dtype=np.float32)
|
|
92
|
+
x_values, y_values = embeddings_2d[:, 0], embeddings_2d[:, 1]
|
|
93
|
+
|
|
94
|
+
# Write the computed 2D embeddings to the cache.
|
|
95
|
+
cache_entry = TwoDimEmbeddingTable(hash=cache_key, x=list(x_values), y=list(y_values))
|
|
96
|
+
session.add(cache_entry)
|
|
97
|
+
session.commit()
|
|
98
|
+
|
|
99
|
+
return x_values, y_values, sample_ids_of_samples_with_embeddings
|
|
8
100
|
|
|
9
101
|
|
|
10
|
-
# TODO(Malte, 10/2025): Add the get_twodim_embeddings function here that handles the
|
|
11
|
-
# caching in the DB and calls _calculate_2d_embeddings when needed.
|
|
12
102
|
def _calculate_2d_embeddings(embedding_values: list[list[float]]) -> list[tuple[float, float]]:
|
|
13
103
|
n_samples = len(embedding_values)
|
|
14
104
|
# For 0, 1 or 2 samples we hard-code deterministic coordinates.
|