nmr-processing 22.15.0 → 22.16.0

package/dist/nmr-processing.js

@@ -1,2 +1,2 @@
-var Dr=Object.defineProperty;var yt=(e,n)=>{for(var t in n)Dr(e,t,{get:n[t],enumerable:!0})};export*from"gyromagnetic-ratio";import{xEnsureFloat64 as Hr}from"ml-spectra-processing";function z(e,n){let{windowData:t,output:s=new Float64Array(e)}=n,i=s.length;if(i!==t.length)throw new RangeError("window function and data should have the same length");for(let o=0;o<i;o++)s[o]*=t[o];return Hr(s)}import{xDivide as xr,xMaxValue as Or}from"ml-spectra-processing";function on(e,n){let t=new Float64Array(n);for(let s=0;s<n;s++)t[s]=e(s);return t}function an(e,n){let{dw:t}=n,{lineBroadening:s}=e,i=-s*Math.PI*t;return o=>Math.exp(i*o)}function rn(e,n){let{dw:t,length:s}=n,{lineBroadening:i,lineBroadeningCenter:o}=e;if(o>1||o<0)throw new Error("The lineBroadeningCenter of gaussian shape should be inside of the window function: 0 - 1");let a=Math.PI*i*t,r=o*(s-1);return m=>Math.exp(-1*((r-m)*a)**2)}function ln(e,n){return bt({exponent:1,...e},n)}function bt(e,n){let{length:t}=n,{exponent:s,offset:i}=e;if(t===void 0)throw new Error("length options should exists for sineBell shape");let o=Math.PI*i,a=Math.PI*(1-i)/(t-1);return r=>Math.sin(o+a*r)**s}function mn(e,n){return bt({...e,exponent:2},n)}function cn(e,n){let{length:t,dw:s}=n,i=-s/e.lineBroadening;return o=>{let a=Math.exp(i*o);return a/(a**2+Math.exp(-i*(o-t))**2)}}function gn(e,n){let{kind:t,options:s}=e;switch(t){case"exponential":return an(s,n);case"gaussian":return rn(s,n);case"sineBell":return ln(s,n);case"sineSquare":return mn(s,n);case"traf":return cn(s,n);default:throw new Error(`Unknown distribution ${t}`)}}function ne(e){let{shapes:n,windowOptions:t}=e,s=new Float64Array(t.length).fill(1);for(let[i,o]of Object.entries(n)){let{options:a,apply:r=!0}=o;if(!r)continue;let m=on(gn({kind:i,options:a},t),t.length);z(s,{windowData:m,output:s})}return xr(s,Or(s),{output:s})}import{TopicMolecule as Ir}from"openchemlib-utils";import{Molecule as Nr}from"openchemlib";import{agnes as vr}from"ml-hclust";import{Matrix as Pr}from"ml-matrix";import{Molecule as fn}from"openchemlib";function dn(e,n={}){let t=n.output||structuredClone(e);for(let s of t)s.id=crypto.randomUUID();return t}var Sr={h:"1H",c:"13C"};function un(e){return Object.values(e).map(n=>Sr[n.toLowerCase()])}function Fr(e){if(!e.from||!e.to)throw new Error("options from and to are mandatory")}async function se(e,n){Fr(n);let{from:t,to:s,minLength:i=0,maxLength:o,predictions:a,includeDiagonal:r=!1}=n,m={...n.joinDistance,H:.05,C:.5},{correlationPaths:l=jr(e,{fromLabel:t,toLabel:s,minLength:i,maxLength:o})}=n,c=e.getGroupedDiastereotopicAtomIDs()||[],d=[];for(let D of c||[])d.push({...D,pathInfo:structuredClone(l[D.atoms[0]])});let g=a[s],u=a[t];if(!u||!g)throw new Error("predictions are not availaible");let p={x:u,y:g},C={x:{},y:{}};for(let D in C)for(let b of p[D].joinedSignals){if(!b.diaIDs)throw new Error("Signal has not diaIDs");C[D][b.diaIDs[0]]=b}let y={};for(let D of d){let b=D.pathInfo;if(b.paths.length===0||!C.x[b.oclID])continue;let x=b.paths;for(let v of x){if(!C.y[l[v.to].oclID])continue;let S={x:b,y:l[v.to]},H=`${S.x.oclID}-${S.y.oclID}`;if(H===`${b.oclID}-${b.oclID}`||y[H])continue;let O={id:crypto.randomUUID(),x:0,y:0,z:100},P={id:crypto.randomUUID(),x:{delta:0,diaIDs:[],atoms:[]},y:{delta:0,diaIDs:[],atoms:[]},peaks:[]};for(let j of["x","y"]){let F=S[j].oclID;O[j]=C[j][F].delta,P[j].delta=C[j][F].delta,P[j].diaIDs=[F];let{atoms:R}=C[j][F];R&&(P[j].atoms=R)}P.peaks=[O],y[H]=P}}r&&Rr(y,{paths:l,signalsByDiaID:C});let f=Object.values(y),h=wr(f,{joinDistance:m,from:t,to:s});return{nuclei:un({from:t,to:s}),joinedSignals:f,signals:Mr(f),zones:h}}function jr(e,n){let{fromLabel:t,toLabel:s,minLength:i,maxLength:o=Number.MAX_SAFE_INTEGER}=n,a=e.diaIDs,r=e.moleculeWithH,m=e.distanceMatrix,l=fn.getAtomicNoFromLabel(t),c=fn.getAtomicNoFromLabel(s),d=[];for(let g=0;g<r.getAllAtoms();g++){let u={oclID:a[g],paths:[]};for(let p=0;p<r.getAllAtoms();p++){if(g===p||r.getAtomicNo(p)!==c||r.getAtomicNo(g)!==l)continue;let C=m[g][p];C>=i&&C<=o&&u.paths.push({from:g,to:p})}d.push(u)}return d}function Mr(e){let n=[];for(let t of e)for(let s of t.x.atoms||[])for(let i of t.y.atoms||[]){let o=structuredClone(t);o.x.atoms=[s],o.y.atoms=[i],n.push(o)}return dn(n)}function Rr(e,n){let{paths:t=[],signalsByDiaID:s}=n;for(let i of t){let o=i.oclID;if(!s.x[o]||e[`${o}-${o}`])continue;let a=s.x[o].delta,r=s.y[o].delta,m={id:crypto.randomUUID(),x:{delta:a,diaIDs:[o],atoms:s.x[o].atoms},y:{delta:r,diaIDs:[o],atoms:s.y[o].atoms},peaks:[{id:crypto.randomUUID(),x:a,y:r,z:1,minX:a,maxX:a,minY:r,maxY:r}]};e[`${i.oclID}-${i.oclID}`]=m}}function wr(e,n){if(e.length===0)return[];let{joinDistance:t,from:s,to:i}=n,o=new Pr(e.map(p=>[p.x.delta,p.y.delta])),a=o.minColumn(0),r=o.maxColumn(0),m=o.minColumn(1),l=o.maxColumn(1);o.mulColumn(0,1/(r-a)),o.mulColumn(1,1/(l-m));let c=Math.hypot(t[s]/(r-a),t[i]/(l-m)),d=vr(o.to2DArray(),{method:"centroid"}),g=pn([d],c),u=[];for(let p of g){let C=[];p.isLeaf&&C.push(e[p.index]);for(let y of p.children)for(let f of y.indices())C.push(e[f]);u.push({id:crypto.randomUUID(),...Ar(C,{joinDistance:t,from:s,to:i}),signals:C})}return u}function Ar(e,n){let{joinDistance:t,from:s,to:i}=n,o=Number.MAX_SAFE_INTEGER,a=Number.MAX_SAFE_INTEGER,r=Number.MIN_SAFE_INTEGER,m=Number.MIN_SAFE_INTEGER;for(let l of e)l.x.delta<o&&(o=l.x.delta),l.x.delta>r&&(r=l.x.delta),l.y.delta<a&&(a=l.y.delta),l.y.delta>m&&(m=l.y.delta);return{x:{from:o-t[s],to:r+t[s]},y:{from:a-t[i],to:m+t[i]}}}function pn(e,n){let t=e.length;for(let s=0;s<e.length;s++){let i=e[s];i.height>n&&(e.push(...i.children),e.splice(s--,1))}return e.length<t?pn(e,n):e}async function Cn(e,n){let{minLength:t,maxLength:s,predictions:{H:i},includeDiagonal:o=!0,minCoupling:a=1.5}=n;if(!i)throw new Error("prediction is not availaible");let r={...n,from:"H",to:"H",includeDiagonal:o};return(!t||!s)&&(r.correlationPaths=kr(e,i,a)),se(e,r)}function kr(e,n,t){let s=e.diaIDs,i=[],o={},a=n.signals;for(let l of a){let c=l.diaIDs[0];o[c]??={};for(let d of l.js){if(!d.diaIDs||d.diaIDs.length===0)throw new Error("should contains assigned coupling by atoms");let g=d.diaIDs[0];o[c][g]=Math.max(d.coupling,o[c][g]??Number.MIN_SAFE_INTEGER)}}let r=e.moleculeWithH,m=Nr.getAtomicNoFromLabel("H");for(let l=0;l<r.getAllAtoms();l++){let c={oclID:s[l],paths:[]};for(let d=0;d<r.getAllAtoms();d++)l!==d&&r.getAtomicNo(d)===m&&r.getAtomicNo(l)===m&&o[s[l]]?.[s[d]]>=t&&c.paths.push({from:l,to:d});i.push(c)}return i}function yn(e,n){async function t(s){let i=await fetch(n,{headers:{accept:"application/json","content-type":"application/json"},method:"POST",body:JSON.stringify({molfile:s.toMolfile({version:3})})});if(i.status!==200){let a=await i.text();throw new Error(`${i.statusText}: ${a}`)}let{data:o}=await i.json();return{nucleus:o.nucleus,joinedSignals:o.joinedSignals??[],signals:o.signals??[],ranges:o.ranges??[]}}return Object.defineProperty(t,"name",{value:`default${e[0].toUpperCase()}${e.slice(1)}Predictor`}),t}var bn=yn("proton","https://nmr-prediction.service.zakodium.com/v1/predict/proton"),hn=yn("carbon","https://nmr-prediction.service.zakodium.com/v1/predict/carbon");async function Ae(e,n,t){let{cache:s,predictorOptions:i}=t;if(typeof s=="function"){let a=await s(e);if(a)return a}let o=await n(e,i);return typeof s=="function"&&await s(e,o),o}async function Dn(e,n={}){let{predictor:t=hn,predictorOptions:s={},cache:i}=n;return e.molecule.getAllAtoms()===0?{nucleus:"13C",joinedSignals:[],signals:[],ranges:[]}:Ae(e,t,{cache:i,predictorOptions:s})}async function Hn(e,n){let{minLength:t=2,maxLength:s=3,joinDistance:i}=n;return se(e,{...n,from:"H",to:"C",minLength:t,maxLength:s,joinDistance:i})}async function xn(e,n){let{minLength:t=1,maxLength:s=1,joinDistance:i}=n;return se(e,{...n,from:"H",to:"C",minLength:t,maxLength:s,joinDistance:i})}async function On(e,n={}){let{predictor:t=bn,cache:s,predictorOptions:i={}}=n;return e.molecule.getAllAtoms()===0?{nucleus:"1H",joinedSignals:[],signals:[],ranges:[]}:Ae(e,t,{cache:s,predictorOptions:i})}function ht(e,n){if(e in n)return!0;let t="hsqc"in n||"hmbc"in n;return e==="C"?t:e==="H"?t||"cosy"in n:!1}var Tr={cosy:{predictor:Cn,required:["H"],message:"Proton prediction is missing so COSY could not be generated."},hsqc:{predictor:xn,required:["H","C"],message:"Carbon and / or proton prediction is missing so HSQC could not be generated."},hmbc:{predictor:Hn,required:["H","C"],message:"Carbon and / or proton prediction is missing so HMBC could not be generated."}};async function Y(e,n={}){let{logger:t,joinDistance:s={H:.05,C:.5},predictOptions:i={H:{},C:{},hsqc:{},hmbc:{},cosy:{}}}=n,o=new Ir(e),a=ht("H",i)?await On(o,{...i?.H}):void 0,r=ht("C",i)?await Dn(o,i?.C):void 0,m={},l=o.diaIDs,c={};Sn(a,l)&&(c.H=a,"H"in i&&(m.proton=a)),Sn(r,l)&&(c.C=r,"C"in i&&(m.carbon=r));let g=["cosy","hsqc","hmbc"].filter(p=>p in i).map(async p=>{let{predictor:C,required:y,message:f}=Tr[p];if(y.every(h=>h in c)){let h=await C(o,{predictions:c,...i[p],joinDistance:s});return{key:p,result:h}}else t&&t.warn(f);return{key:p,result:void 0}}),u=await Promise.all(g);for(let{key:p,result:C}of u)C&&(m[p]=C);return{diaIDs:o.diaIDs,hoses:o.hoseCodes,distanceMatrix:o.distanceMatrix,moleculeWithHydrogens:o.moleculeWithH,groupedDiaIDs:o.getGroupedDiastereotopicAtomIDs()||[],molfile:o.toMolfile(),molfileWithH:o.toMolfileWithH(),spectra:m}}function Sn(e,n=[]){if(!e||e.ranges.length===0)return!1;let{signals:t}=e;for(let s of t)if(!s.diaIDs?.every(o=>n.includes(o)))return!1;return!0}import{xIsMonotonic as ml,xRescale as cl,xSequentialFillFromTo as gl}from"ml-spectra-processing";var _=[{label:"singlet",value:"s",multiplicity:1,names:[]},{label:"doublet",value:"d",multiplicity:2,names:[]},{label:"triplet",value:"t",multiplicity:3,names:[]},{label:"quartet",value:"q",multiplicity:4,names:[]},{label:"quintet",value:"i",acs:"quint",multiplicity:5,names:["quint","qui","qnt","pentet","pnt","pent"]},{label:"sextet",value:"h",multiplicity:6,names:["x","sxt","sext","hexuplet","hex"]},{label:"septet",value:"p",acs:"sept",multiplicity:7,names:["sept","spt","heptet","hpt","hept"]},{label:"octet",value:"o",multiplicity:8,names:["oct"]},{label:"nonet",value:"n",multiplicity:9,names:["non"]},{label:"multiplet",value:"m",multiplicity:null,names:["massive"]}];var Dt={};for(let{value:e,multiplicity:n,names:t}of _){n&&(Dt[e]=n-1);for(let s of t)n&&(Dt[s]=n-1)}var X=Dt;function ie(e){let n=structuredClone(e),t=e.reduce((s,i)=>{let{atoms:o=[]}=i;return Math.max(...o,s)},0)+1;for(let[s,i]of e.entries()){let{js:o=[],atoms:a=[t++]}=i,{newCouplings:r,tempSignals:m}=Er(o,a,t+e.length);m.length>0&&n.push(...m),n[s].js=r,n[s].atoms=a}return n.sort((s,i)=>s.delta-i.delta),n}function Er(e,n,t){let s=[];return{newCouplings:e.reduce((o,a)=>{let{atoms:r=[],multiplicity:m,coupling:l}=a;if(r.length===0&&l&&m){let c=[],d=X[m];for(let g=0;g<d;g++)t++,c.push({coupling:l,multiplicity:"d",atoms:[t]}),s.push(zr(l,[t],n));o.push(...c)}else o.push(a);return o},[]),tempSignals:s}}function zr(e,n,t){return{delta:1e5,atoms:n,js:[{coupling:e,atoms:t}]}}import{Matrix as Lr}from"ml-matrix";import{Matrix as Ht}from"ml-matrix";import{simpleClustering as Br}from"ml-simple-clustering";function L(e){let{couplingConstants:n,connectivity:t}=e,s=Ht.checkMatrix(n),i=t?Ht.checkMatrix(t):Xr(s),{levels:o=Array.from({length:i.rows},()=>2),clusters:a=Br(i.to2DArray(),{out:"indexes"})}=e;return{...e,levels:o,clusters:a,connectivity:i,couplingConstants:s}}function Xr(e){let n=Ht.ones(e.rows,e.rows);for(let t=0;t<e.rows;t++)for(let s=t;s<e.columns;s++)e.get(t,s)===0&&(n.set(t,s,0),n.set(s,t,0));return n}function qr(e){for(let n of e){if(!n.js)throw new Error("there is not js");if(!n.atoms)throw new Error("there is not atoms");for(let t of n.js)if(!t.atoms)throw new Error("there is not atoms")}}function W(e){qr(e);let n=e.length,t=[],s=Lr.zeros(n,n),i={};for(let o=0;o<n;o++){t.push(e[o].delta);let a=e[o].atoms[0];i[a]=o}for(let o=0;o<n;o++){let{atoms:a,js:r}=e[o],m=a[0];for(let l of r){let{coupling:c,atoms:d}=l,g=d[0];s.set(i[m],i[g],c),s.set(i[g],i[m],c)}}return L({couplingConstants:s,chemicalShifts:t})}import{generateSpectrum as il}from"spectrum-generator";import Vr from"binary-search";import{EVD as Gr,Matrix as Jr}from"ml-matrix";import{SparseMatrix as ke}from"ml-sparse-matrix";import{SparseMatrix as Yr}from"ml-sparse-matrix";function vn(e,n){let t=2*e*n,s=new Yr(t,t,{initialCapacity:2*e*n});for(let i=0;i<e;i++){let o=2*i*n,a=2*i*n;for(let r=0;r<n;r++)s.set(o+n+r,a+r,1)}return s}import{SparseMatrix as Wr}from"ml-sparse-matrix";function xt(e,n){let t=2*e*n,s=new Wr(t,t,{initialCapacity:2*e*n});for(let i=0;i<e;i++){let o=2*i*n,a=2*i*n;for(let r=0;r<n;r++)s.set(o+r,a+n+r,.5),s.set(o+n+r,a+r,.5)}return s}import{SparseMatrix as Zr}from"ml-sparse-matrix";function Ot(e,n){let t=2*e*n,s=new Zr(t,t,{initialCapacity:2*e*n});for(let i=0;i<e;i++){let o=2*i*n,a=2*i*n;for(let r=0;r<n;r++)s.set(o+r,a+n+r,-.5),s.set(o+n+r,a+r,.5)}return s}import{SparseMatrix as Ur}from"ml-sparse-matrix";function Ne(e,n){let t=2*e*n,s=new Ur(t,t,{initialCapacity:2*e*n});for(let i=0;i<e;i++){let o=2*i*n,a=o+n;for(let r=0;r<n;r++)s.set(o+r,o+r,.5),s.set(a+r,a+r,-.5)}return s}var St=.01;function Pn(e,n={}){let{lineWidth:t=1,maxClusterSize:s=8,frequency:i=400}=n,o=L(e),a=o.chemicalShifts.slice();for(let l=0;l<a.length;l++)a[l]=a[l]*i;let r=o.levels,m=[];for(let l of o.clusters){let c=l.map(y=>y<0?-y-1:y),d=1,g=0,u=[],p=[];if(l.length>s){let y=0;for(;l[y++]<0;);y=l[y-1],u.push(-a[y]);for(let f=0;f<l.length;f++)if(l[f]<0){let h=o.couplingConstants.get(y,c[f])/2,D=u.length;for(let b=0;b<D;b++)u.push(u[b]+h),u[b]-=h}u.sort((f,h)=>f-h),g=u.length,d=1;for(let f=0;f<g;f++)p.push(1)}else{let y=_r(a,o.couplingConstants,r,o.connectivity,c),f=y.rows,h=new Gr(y),D=h.eigenvectorMatrix,b=h.realEigenvalues,x=new ke(f,f),v=l.length;d=0;for(let F=0;F<v;F++){let R={rows:2**F},w={rows:2**(v-F-1)},M=vn(R.rows,w.rows);l[F]>=0?(x.add(M.mul(l[F]+1)),d++):x.add(M.mul(l[F]))}let S=Jr.zeros(f,f);x.forEachNonZero((F,R,w)=>{if(w>0)for(let M=0;M<D.columns;M++){let A=D.get(R,M);A!==0&&S.set(F,M,S.get(F,M)+A)}return w});let H=S.clone();x.forEachNonZero((F,R,w)=>{if(w<0)for(let M=0;M<D.columns;M++){let A=D.get(R,M);A!==0&&H.set(F,M,H.get(F,M)+A)}return w});let O=D.transpose();S=O.mmul(S);let P=new ke(S.to2DArray(),{threshold:St});H=O.mmul(H);let j=new ke(H.to2DArray(),{threshold:St});j.forEachNonZero((F,R,w)=>w),$r(j,St),j.forEachNonZero((F,R,w)=>{let M=P.get(F,R);M=Math.min(Math.abs(M),Math.abs(w)),M*=M,g+=M;let A=b[F]-b[R],N=Vr(u,A,(k,De)=>k-De);return N<0?(u.splice(-1-N,0,A),p.splice(-1-N,0,M)):p[N]+=M,w})}let C=u.length;if(C>0){d/=g;let y=t/64,f=u[0],h=p[0],D=1;for(let b=1;b<C;b++)Math.abs(u[b]-f/D)<y?(h+=p[b],f+=u[b],D++):(m.push({x:-f/D/i,y:h*d}),f=u[b],h=p[b],D=1);m.push({x:-f/D/i,y:h*d})}}return m.filter(l=>l.x<1e3)}function $r(e,n){e.forEachNonZero((t,s,i)=>Math.abs(i)<=n?0:i)}function _r(e,n,t,s,i){let o=1;for(let r of i)o*=t[r];let a=new ke(o,o);for(let r=0;r<i.length;r++){let m=i[r],l={rows:2**r},c={rows:2**(i.length-r-1)},d=e[m],g=Ne(l.rows,c.rows);a.add(g.mul(d));for(let u=0;u<i.length;u++){let p=i[u];if(s.get(m,p)===1){let C={rows:2**u},y={rows:2**(i.length-u-1)},f=xt(l.rows,c.rows).mmul(xt(C.rows,y.rows));f.add(Ot(l.rows,c.rows).mul(-1).mmul(Ot(C.rows,y.rows))),f.add(Ne(l.rows,c.rows).mmul(Ne(C.rows,y.rows))),a.add(f.mul(n.get(m,p)/2))}}}return a}import el from"binary-search";import{EVD as tl,Matrix as nl}from"ml-matrix";import{SparseMatrix as q}from"ml-sparse-matrix";import{SparseMatrix as Kr}from"ml-sparse-matrix";function Fn(e){let n=(e-1)/2,t=[],s=[];for(let l=0;l<e;l++)t.push(e-1-l-n),s.push(Math.sqrt(n*(n+1)-t[l]*(t[l]+1)));let i=vt(s,1,e,e);for(let l=0;l<e;l++)s[l]=Math.sqrt(n*(n+1)-t[l]*(t[l]-1));let o=vt(s,-1,e,e),a=i.clone().add(o).mul(.5),r=o.clone().mul(-1).add(i).mul(-.5),m=vt(t,0,e,e);return{x:a,y:r,z:m,m:o,p:i}}function vt(e,n,t,s){let i=new Kr(t,s,{initialCapacity:20});for(let o=0;o<e.length;o++)o-n>=0&&o-n<t&&o<s&&i.set(o-n,o,e[o]);return i}var Qr=Fn(2);function Oe(e){return e===2?Qr:Fn(e)}var Ie=.01;function Z(e,n={}){let{lineWidth:t=1,maxClusterSize:s=8,frequency:i=400}=n,o=L(e),a=o.chemicalShifts.slice();for(let l=0;l<a.length;l++)a[l]=a[l]*i;let r=o.levels,m=[];for(let l of o.clusters){let c=l.map(y=>y<0?-y-1:y),d=1,g=0,u=[],p=[];if(l.length>s){let y=0;for(;l[y++]<0;);y=l[y-1],u.push(-a[y]);for(let f=0;f<l.length;f++)if(l[f]<0){let h=o.couplingConstants.get(y,c[f])/2,D=u.length;for(let b=0;b<D;b++)u.push(u[b]+h),u[b]-=h}u.sort((f,h)=>f-h),g=u.length,d=1;for(let f=0;f<g;f++)p.push(1)}else{let y=sl(a,o.couplingConstants,r,o.connectivity,c),f=y.rows,h=new tl(y),D=h.eigenvectorMatrix,b=h.realEigenvalues,x=new q(f,f),v=l.length;d=0;for(let F=0;F<v;F++){let R=Oe(r[c[F]]),w=1;for(let k=0;k<F;k++)w*=r[c[k]];let M=q.eye(w);w=1;for(let k=F+1;k<v;k++)w*=r[c[k]];let A=q.eye(w),N=M.kroneckerProduct(R.m).kroneckerProduct(A);l[F]>=0?(x.add(N.mul(l[F]+1)),d++):x.add(N.mul(l[F]))}let S=nl.zeros(f,f);x.forEachNonZero((F,R,w)=>{if(w>0)for(let M=0;M<D.columns;M++){let A=D.get(R,M);A!==0&&S.set(F,M,S.get(F,M)+A)}return w});let H=S.clone();x.forEachNonZero((F,R,w)=>{if(w<0)for(let M=0;M<D.columns;M++){let A=D.get(R,M);A!==0&&H.set(F,M,H.get(F,M)+A)}return w});let O=D.transpose();S=O.mmul(S);let P=new q(S.to2DArray(),{threshold:Ie});jn(P,Ie),H=O.mmul(H);let j=new q(H.to2DArray(),{threshold:Ie});j.forEachNonZero((F,R,w)=>w),jn(j,Ie),j.forEachNonZero((F,R,w)=>{let M=S.get(F,R);M=Math.min(Math.abs(M),Math.abs(w)),M*=M,g+=M;let A=b[F]-b[R],N=el(u,A,(k,De)=>k-De);return N<0?(u.splice(-1-N,0,A),p.splice(-1-N,0,M)):p[N]+=M,w})}let C=u.length;if(C>0){d/=g;let y=t/64,f=u[0],h=p[0],D=1;for(let b=1;b<C;b++)Math.abs(u[b]-f/D)<y?(h+=p[b],f+=u[b],D++):(m.push({x:-f/D/i,y:h*d}),f=u[b],h=p[b],D=1);m.push({x:-f/D/i,y:h*d})}}return m.filter(l=>l.x<1e3)}function jn(e,n){e.forEachNonZero((t,s,i)=>Math.abs(i)<=n?0:i)}function sl(e,n,t,s,i){let o=1;for(let r of i)o*=t[r];let a=new q(o,o);for(let r=0;r<i.length;r++){let m=i[r],l=Oe(t[m]),c=1;for(let C=0;C<r;C++)c*=t[i[C]];let d=q.eye(c);c=1;for(let C=r+1;C<i.length;C++)c*=t[i[C]];let g=q.eye(c),u=e[m],p=d.kroneckerProduct(l.z).kroneckerProduct(g);a.add(p.mul(u));for(let C=0;C<i.length;C++){let y=i[C];if(s.get(m,y)===1){let f=Oe(t[y]),h=1;for(let v=0;v<C;v++)h*=t[i[v]];let D=q.eye(h);h=1;for(let v=C+1;v<i.length;v++)h*=t[i[v]];let b=q.eye(h),x=d.kroneckerProduct(l.x).kroneckerProduct(g).mmul(D.kroneckerProduct(f.x).kroneckerProduct(b));x.add(d.kroneckerProduct(l.y).kroneckerProduct(g).mul(-1).mmul(D.kroneckerProduct(f.y).kroneckerProduct(b))),x.add(d.kroneckerProduct(l.z).kroneckerProduct(g).mmul(D.kroneckerProduct(f.z).kroneckerProduct(b))),a.add(x.mul(n.get(m,y)/2))}}}return a}function Mn(e,n={}){let t=L(e),{lineWidth:s=1,frequency:i=400,from:o=0,to:a=10,nbPoints:r=16*1024,noise:m,baseline:l,shape:c={kind:"gaussian"},isProton:d=t.levels.every(u=>u===2)}=n,g=d?Pn(t,n):Z(t,n);return il(g,{generator:{from:o,to:a,nbPoints:r},peakOptions:{shape:c,width:s/i},noise:m,baseline:l})}import{agnes as ol}from"ml-hclust";import{Matrix as al}from"ml-matrix";function U(e,n={}){let t=L(e),{chemicalShifts:s,couplingConstants:i,connectivity:o}=t,{frequency:a=400,maxClusterSize:r=8}=n,m=rl(s,i,a),l=ol(m,{method:"single",isDistanceMatrix:!0}),c=[],d=s.length;Pt(l,c,{maxClusterSize:r,force:!1,nSpins:d,connectivity:o});let g=ll(c,r),u=g.length,p=[];for(let C=0;C<u;C++){let y=[];for(let f=0;f<d;f++){let h=g[C][f];h!==0&&y.push(h<0?-(f+1):f)}p.push(y)}return p}function Pt(e,n,t){let{maxClusterSize:s,force:i,nSpins:o,connectivity:a}=t;if(!i&&e.size<=s)n.push(Rn(e.indices(),o));else for(let r of e.children)if(r.size<=s){let m=Rn(r.indices(),o),l=0;for(let c=0;c<o;c++)if(m[c]===1){for(let d=0;d<o;d++)a.get(c,d)===1&&m[d]===0&&(m[d]=-1,l++);l++}l<=s?n.push(m):r.index<0?Pt(r,n,{maxClusterSize:s,force:!0,nSpins:o,connectivity:a}):(m[r.index]=2,n.push(m))}else Pt(r,n,{maxClusterSize:s,force:!1,nSpins:o,connectivity:a})}function rl(e,n,t){let s=n.rows,i=n.columns,o=al.zeros(s,s);for(let a=0;a<s;a++)for(let r=a;r<i;r++){let m=n.get(a,r);if(e[a]-e[r]!==0){let l=1-Math.abs(m/((e[a]-e[r])*t));o.set(a,r,l),o.set(r,a,l)}else a===r||m!==0||(o.set(a,r,1),o.set(r,a,1))}return o.to2DArray()}function ll(e,n){for(let t=e.length-1;t>=0;t--){let s=e[t],i=s.length,o=0;for(;o<i&&s[o++]!==-1;);if(!(o>=i))for(let a=e.length-1;a>=t+1;a--){let r=e[a],m=0,l=0;for(let c=0;c<i;c++)s[c]*r[c]===-1&&l++,(s[c]!==0||r[c]!==0)&&m++;if(l>0&&m<=n){for(let c=0;c<i;c++)r[c]===1?s[c]=1:r[c]===-1&&s[c]!==1&&(s[c]=-1);e.splice(a,1)}}}return e}function Rn(e,n){let t=new Int16Array(n);for(let s of e)t[s]=1;return t}function dl(e){for(let n of e){if(!n.js)throw new Error("There is not js");if(!n.atoms)throw new Error("There is not atoms");for(let t of n.js)if(!t.atoms)throw new Error("There is not atoms")}}function Te(e,n={}){let t=ie(e);dl(t);let{frequency:s=400,shape:i={kind:"gaussian"},from:o=0,to:a=10,lineWidth:r=1,nbPoints:m=16*1024,maxValue:l=1e8,maxClusterSize:c=8,...d}=n;if(t.length===0)return{x:gl({from:o,to:a,size:m}),y:new Float64Array(m)};let g=W(t);g.clusters=U(g,{frequency:s,maxClusterSize:c});let u=Mn(g,{frequency:s,from:o,to:a,nbPoints:m,lineWidth:r,shape:i,maxClusterSize:c,...d});return l&&ml(u.y)===0&&(u.y=cl(u.y,{max:l})),u}import{getGyromagneticRatio as wn}from"gyromagnetic-ratio";function Se(e,n){let{nucleus:t,frequency:s}=n,i=wn(e),o=wn(t);if(!o||!i)throw new Error(`${e} or ${t} is not supported`);return s*i/o}var i1=Se;function An(e,n){let{nbPoints:t,lineWidth:s,frequency:i}=n,o=[];for(let a in e)if(a==="proton"||a==="carbon"){let r=e[a];if(!r)continue;o.push(ul(r,{nbPoints:t,lineWidth:s,...n[a],experiment:a,frequency:i}))}return o}function ul(e,n){let{frequency:t=400,experiment:s}=n,i=Se(e.nucleus,{nucleus:"1H",frequency:t}),{x:o,y:a}=Te(e.signals,{...n,frequency:i});return{data:{x:o,re:a,im:null},info:{nucleus:e.nucleus,dimension:1,isComplex:!1,originFrequency:i,baseFrequency:i,pulseSequence:"prediction",experiment:s,isFt:!0},ranges:{values:e.ranges}}}import{xEnsureFloat64 as fl}from"ml-spectra-processing";import{generateSpectrum2D as pl}from"spectrum-generator";function K(e){return typeof e!="object"?{x:e,y:e}:{...e}}function Nn(e,n={}){let{from:t=-1,to:s=12,nbPoints:i=512,factor:o=3}=n,{width:a=.02}=n,r={x:[],y:[],z:[]};for(let c of e)r.x.push(c.x.delta),r.y.push(c.y.delta),r.z.push(1e6);let{z:m,...l}=pl(Cl(r),{generator:{from:K(t),to:K(s),nbPoints:K(i)},peaks:{width:K(a),factor:o}});return{z:m.map(fl),...l}}function Cl(e){let n=structuredClone(e);for(let t=0;t<n.x.length;t++)for(let s=t+1;s<n.x.length;s++)n.x[t]===n.x[s]&&n.y[t]===n.y[s]&&(n.z[t]+=n.z[s],n.x.splice(s,1),n.y.splice(s,1),n.z.splice(s,1),s--);return n}function kn(e,n){let t=Se(e[1],{nucleus:e[0],frequency:n});return[n,t]}function Tn(e,n){let t=[];for(let s in e){if(!bl(s)||!e[s])continue;let i=e[s];t.push(yl(i,{experiment:s,...n}))}return t}function yl(e,n){let{signals:t,zones:s,nuclei:i}=e,{experiment:o,frequency:a,width:r=hl(i),nbPoints:m,fromTo:l}=n,c=kn(i,a),d=l[In(i[0])],g=l[In(i[1])],u=Dl(r,c),p=Nn(t,{from:{x:d.from,y:g.from},to:{x:d.to,y:g.to},nbPoints:m,factor:3,width:u}),C=c.join(",");return{data:{rr:{...p,noise:.01}},info:{nucleus:i,originFrequency:C,baseFrequency:C,pulseSequence:o,experiment:"2d"},zones:{values:s}}}function bl(e){return["cosy","hsqc","hmbc"].includes(e)}function hl(e){return{x:8,y:e[0]===e[1]?8:24}}function Dl(e,n){let t=K(e);return{x:t.x/n[0],y:t.y/n[1]}}function In(e){return e.includes("H")?"proton":"carbon"}async function O1(e,n={}){let{logger:t,simulation:s={oneD:{},twoD:{}},prediction:i={}}=n,{spectra:o}=await Y(e,{logger:t,...i});!("frequency"in s)&&t&&t.warn("Frequency is settled to 400 MHz");let{frequency:a=400,oneD:r,twoD:m}=s,l={proton:{from:-1,to:12},carbon:{from:-10,to:220},nbPoints:65536,lineWidth:1,...r},c={frequency:a,fromTo:{proton:l.proton,carbon:l.carbon},nbPoints:{x:1024,y:1024},...m},d=An(o,{frequency:a,...l}),g=Tn(o,c);return{spectra:[...d,...g],molecules:[{molfile:e.toMolfile()}]}}import{TreeSet as Sl}from"ml-tree-set";function En(e){let{restrictionByCS:n,predictions:t,targets:s,useIntegrationRestriction:i}=e,{tolerance:o,chemicalShiftRestriction:a}=n,r=Math.abs(o),m={};for(let l in t){let c=t[l];if(c.error&&(c.error=Math.abs(c.error)),m[l]=[],s)for(let d in s){let g=s[d];if(i&&g.integration>0?c.nbAtoms-g.integration<1:!0)if(!a||c.delta===void 0)m[l].push(d);else{let p=r;c.error&&(p=Math.max(p,c.error));let C=g.signals&&g.signals.length>0?g.signals[0].delta:(g.to+g.from)/2;Math.abs(c.delta-C-r)<4*r&&m[l].push(d)}}m[l].push("*")}return m}function zn(e,n){let{useIntegrationRestriction:t,diaIDPeerPossibleAssignment:s,nbAllowedUnAssigned:i,restrictionByCS:o,predictions:a,targets:r}=n,{useChemicalShiftScore:m}=o,l=0,c=e.length,d={},g=[];for(let y=0;y<e.length;y++){let f=e[y];f&&f!=="*"&&(g.push(y),d[f]||(d[f]=[]),d[f].push(s[y])),f==="*"&&l++}if(l>i)return 0;let u=Object.keys(d);if(u.length===0)return 0;if(t)for(let y of u){let f=d[y],h=0;for(let b of f){let x=a[b];h+=x.allHydrogens}let{integration:D}=r[y];if(h-D>=.5)return 0}let p=m?Hl(e,n):1,C=l/c;return p-C}function Hl(e,n){let{tolerance:t}=n.restrictionByCS,{diaIDPeerPossibleAssignment:s,predictions:i,targets:o}=n,a=0,r=0;for(let m=0;m<e.length;m++){let l=e[m];if(l&&l!=="*"){r++;let c=s[m],d=i[c],g=o[l],u=t;if(d.error&&(u=Math.max(d.error,t)),d.delta===void 0)a+=1;else{let p=g.signals&&g.signals.length>0?g.signals[0].delta:(g.to+g.from)/2,C=Math.abs(d.delta-p);C<u?a+=1:(C=Math.abs(C-u),a+=-.25/u*C+1)}}}return r>0&&(a/=r),a}function Ft(e,n,t,s){let{nSources:i,restrictionByCS:o,timeout:a,timeStart:r,maxSolutions:m,targets:l,predictions:c,lowerBoundScore:d,nbAllowedUnAssigned:g,possibleAssignmentMap:u,useIntegrationRestriction:p,diaIDPeerPossibleAssignment:C}=e;if(Date.now()-r>a)return;let y=C[n],f=u[y];for(let h of f){t[n]=h;let D=zn(t,{useIntegrationRestriction:p,diaIDPeerPossibleAssignment:C,nbAllowedUnAssigned:g,restrictionByCS:o,predictions:c,targets:l});if(D===0){h==="*"&&(t[n]=null);continue}n===i-1&&D>=d?xl(s,{predictions:c,partial:t,score:D,maxSolutions:m}):n<i-1&&Ft({nSources:i,restrictionByCS:o,timeout:a,timeStart:r,maxSolutions:m,targets:l,predictions:c,lowerBoundScore:d,nbAllowedUnAssigned:g,possibleAssignmentMap:u,useIntegrationRestriction:p,diaIDPeerPossibleAssignment:C},n+1,structuredClone(t),s)}}function xl(e,n){let{score:t,maxSolutions:s,partial:i,predictions:o}=n;e.nSolutions++;let a={assignment:structuredClone(i),score:t/Ol(i,o)};if(e.nSolutions>=s){let r=e.solutions.last();a.score>r.score&&(e.solutions.pollLast(),e.solutions.add(a))}else e.solutions.add(a),e.nSolutions++}function Ol(e,n){let t=Object.keys(n).length,s=new Set(e),i=t-s.size;return i>0?2*i:1}var vl=(e,n)=>n.score-e.score;async function Ee(e){let{restrictionByCS:n={},useIntegrationRestriction:t,timeout:s,minScore:i,nbAllowedUnAssigned:o,maxSolutions:a,targets:r,joinedSignals:m}=e,{tolerance:l=1,useChemicalShiftScore:c=!1,chemicalShiftRestriction:d=!0}=n,g=m.length,u={};for(let b of m){let x=b.diaIDs[0],v=b.atoms[0];u[x]={...b,diaIDIndex:v,allHydrogens:b.nbAtoms}}let p=En({restrictionByCS:{tolerance:l,useChemicalShiftScore:c,chemicalShiftRestriction:d},useIntegrationRestriction:t,predictions:u,targets:r}),C=Object.keys(p),y=new Array(g).fill(null),f={solutions:new Sl(vl),nSolutions:0},h=Date.now();Ft({nSources:g,restrictionByCS:{tolerance:l,useChemicalShiftScore:c,chemicalShiftRestriction:d},timeout:s,timeStart:h,targets:r,predictions:u,maxSolutions:a,lowerBoundScore:i,nbAllowedUnAssigned:o,possibleAssignmentMap:p,diaIDPeerPossibleAssignment:C,useIntegrationRestriction:t},0,y,f);let D=[];for(let b of f.solutions.elements){let{assignment:x,score:v}=b,S=structuredClone(r);for(let H=0;H<x.length;H++){let O=x[H];if(typeof O!="string")continue;let P=S[O];(!P.signals||P.signals.length===0)&&(P.signals=[{delta:(P.to+P.from)/2}]);let j=P.signals[0];j.diaIDs||(j.diaIDs=[]),O&&j.diaIDs.push(C[H])}D.push({score:v,assignment:Object.values(S)})}return D}function Pl(e){for(let n of e){if(!n.atoms)throw new Error("signal has not atoms property");if(!n.diaIDs)throw new Error("signal has not diaIDs property");if(!n.nbAtoms)throw new Error("signal has not nbAtoms property")}}function Fl(e){for(let n of e)if(n.integration===void 0)throw new Error("ranges has not integration property")}async function X1(e,n,t={}){let{restrictionByCS:s,minScore:i=1,maxSolutions:o=10,nbAllowedUnAssigned:a=0,timeout:r=6e3,predictionOptions:m={}}=t;if(!n)throw new Error("It is needed a OCL molecule instance to assign");let{spectra:l}=await Y(n,{predictOptions:{H:m}}),c=l.proton?.joinedSignals||[];Fl(e),Pl(c);let d={};for(let g of e){let{id:u=crypto.randomUUID()}=g;d[u]=structuredClone(g)}return Ee({restrictionByCS:s,timeout:r,minScore:i,nbAllowedUnAssigned:a,maxSolutions:o,targets:d,joinedSignals:c,useIntegrationRestriction:!0})}function jl(e){for(let n of e){if(!n.atoms)throw new Error("signal has not atoms property");if(!n.diaIDs)throw new Error("signal has not diaIDs property");if(!n.nbAtoms)throw new Error("signal has not nbAtoms property")}}function Ml(e){let n=structuredClone(e);for(let t of n)t.integration===void 0&&(t.integration=0);return n}async function W1(e,n,t={}){let{restrictionByCS:s={},minScore:i=1,maxSolutions:o=10,nbAllowedUnAssigned:a=0,timeout:r=6e3,predictionOptions:m={}}=t,{spectra:l}=await Y(n,{predictOptions:{C:m}}),c=l.carbon?.joinedSignals||[];jl(c);let d=Ml(e),g={};for(let u of d){let{id:p=crypto.randomUUID()}=u;g[p]=structuredClone(u)}return Ee({restrictionByCS:s,timeout:r,minScore:i,nbAllowedUnAssigned:a,maxSolutions:o,targets:g,joinedSignals:c,useIntegrationRestriction:!1})}import{ensureHeterotopicChiralBonds as _l}from"openchemlib-utils";import{TreeSet as Yn}from"ml-tree-set";import{getConnectivityMatrix as Bl}from"openchemlib-utils";import{getCorrelationDelta as Rl}from"nmr-correlation";function Bn(e,n){let{restrictionByCS:t,predictions:s,targets:i}=n,{tolerance:o,chemicalShiftRestriction:a}=t,r=Object.keys(s);for(let m of r){let l=o[m],c=s[m],d=i[m];e[m]||(e[m]={});for(let g in c){let u=c[g];if(e[m][g]=[],d)for(let p in d){let C=d[p],{integration:y,protonsCount:f}=C;if(y?m==="H"?u.nbAtoms-y<1:f.length>0?f.includes(u.protonsCount):!0:!0)if(!a||u.delta===void 0)e[m][g].push(p);else{let D=Rl(C);if(D===void 0)throw new Error("Correlation has not delta");Math.abs(u.delta-D-l)<4*l&&e[m][g].push(p)}}e[m][g].push("*")}}return e}import{getCorrelationDelta as Al}from"nmr-correlation";function wl(e,n,t){let s=e[0],{H:i=[]}=n[s].attachment,o=[{targetIDs:[s],attachments:new Set(i)}];for(let a=1;a<e.length;a++){let r=e[a],m=n[r],{H:l=[]}=m.attachment,c=!0;for(let d of o)if(l.some(u=>d.attachments.has(u))){c=!1,d.targetIDs.push(r);for(let u of l)d.attachments.add(u);break}c&&o.push({targetIDs:[r],attachments:new Set(l)})}return o.map(a=>({atomType:"C",targetIDs:a.targetIDs,integration:t?Array.from(a.attachments).reduce((r,m)=>t[m].integration+r,0):0}))}var Xn=wl;function Ln(e,n){let{diaIDPeerPossibleAssignment:t,infoByAtomTypes:s,restrictionByCS:i,predictions:o,targets:a,correlations:r}=n,{tolerance:m,useChemicalShiftScore:l}=i,c=0,d=0,g={},u={},p=Object.keys(e);for(let S of p){let H=0,{nbAllowedUnAssigned:O}=s[S],P={},j=e[S]||[];g[S]=P,u[S]=[],d+=j.length;for(let F=0;F<j.length;F++){let R=j[F];R&&R!=="*"&&(u[S].push(F),P[R]||(P[R]=[]),P[R].push(t[S][F])),R==="*"&&H++}if(H>O)return 0;c+=H}let C={};for(let S in g)C[S]=Object.keys(g[S]);if(Object.values(C).every(S=>S.length===0))return 0;let f=kl.bind({},o),h=[];for(let S in e)if(S==="C"&&C[S].length>0)h.push(...Xn(C[S],a[S],r));else for(let H of C[S])h.push({atomType:S,targetIDs:[H],integration:a.H[H].integration});for(let S of h){let{integration:H,atomType:O,targetIDs:P}=S;if(H===void 0||Number.isNaN(H))continue;let j=0;for(let F of P){let R=g[O][F];for(let w of R){let{prediction:M,atomType:A}=f(w);O===A&&(j+=M.allHydrogens)}}if(j-H>=5)return 0}let D=1,b=1;if(l){b=0,D=0;for(let S of Object.keys(e)){let H=e[S],O=a[S];for(let P=0;P<H.length;P++){let j=H[P];if(j&&j!=="*"){D++;let F=t[S][P],R=o[S][F],w=O[j],M=m[S];if(R.delta===void 0)b+=1;else{let A=Al(w);if(A===void 0)throw new Error("correlation has not delta");let N=Math.abs(R.delta-A);N<M?b+=1:(N=Math.abs(N-M),b+=-.25/M*N+1)}}}}D>0&&(b/=D)}let x=0;if(Il(C)>1){let S={},H=[];for(let P of Object.keys(u))H=H.concat(u[P].map(j=>({index:j,atomType:P})));for(let P=0;P<H.length;P++){let{atomType:j,index:F}=H[P],R=o[j][t[j][F]];for(let w=P+1;w<H.length;w++){let{atomType:M,index:A}=H[w],N=o[M][t[M][A]],De=R.pathLength[N.diaIDIndex]<5,He=e[j][F],xe=e[M][A];if(!He||!xe)continue;let Ct=He>xe?`${xe} ${He}`:`${He} ${xe}`,nn=Nl({from:{targetID:He,atomType:j},to:{targetID:xe,atomType:M}},a),sn=De?nn?1:0:nn?0:1;S[Ct]=S[Ct]?Math.max(S[Ct],sn):sn}}let O=0;for(let P in S)O+=S[P];x=O/(H.length*(H.length-1)/2)}let v=c/d;return b===0?x-v:x===0?b-v:(b+x)/2-v}function Nl(e,n){let{from:t,to:s}=e;if(t.targetID===s.targetID)return!0;let 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f[S])f[S][F].allHydrogens*=100/j;y[S]={nSources:P.length,currentIndex:0,nbAllowedUnAssigned:a[S]||0}}h=Bn(h,{restrictionByCS:s,predictions:f,targets:g}),D={};for(let S in h)D[S]=Object.keys(h[S]);let x=Yl(p,y,b);p={solutions:new Yn(Wn),nSolutions:0};let v=Date.now();for(let S of x)jt({currentAtomTypes:b,restrictionByCS:s,timeout:i,timeStart:v,targets:g,predictions:f,correlations:m,maxSolutions:r,lowerBoundScore:u,possibleAssignmentMap:h,diaIDPeerPossibleAssignment:D},y,S,p)}return ql({store:p,spectra:n,diaIDPeerPossibleAssignment:D,targets:g})}function ql(e){let{store:n,spectra:t,diaIDPeerPossibleAssignment:s,targets:i}=e,{solutions:o}=n,a={},r=Object.keys(i);for(let l of r){let c=i[l];for(let d in c){let g=c[d];for(let u of g.link){let p=u.signal.id;a[p]||(a[u.signal.id]=qn(p,t))}}}let m=[];for(let l of o.elements){let c=structuredClone(t),{assignment:d,score:g}=l,u=Object.keys(d);for(let p of u){let C=i[p],y=d[p];for(let f=0;f<y.length;f++){let h=y[f];if(h==="*"||!h)continue;let D=C[h],b=s[p][f];for(let x of D.link){let{spectrumIndex:v,elementIndex:S,signalIndex:H}=a[x.signal.id],O=c[v];if(V(O)){let{ranges:P}=O,F=P[S].signals[H];if(F.diaIDs||(F.diaIDs=[]),F.diaIDs.includes(b))continue;F.diaIDs.push(b)}else{let P=x.axis,j=O.zones[S].signals[H];if(j[P].diaIDs||(j[P].diaIDs=[]),j[P].diaIDs?.includes(b))continue;j[P].diaIDs?.push(b)}}}}m.push({score:g,assignment:c})}return m}function Yl(e,n,t){return e.nSolutions>0?e.solutions.elements.map(s=>{let i=s.assignment;for(let o of t)i[o]=Un(n[o].nSources);return i}):Wl(n,t)}function Wl(e,n){let t={},s=Object.keys(e);for(let i of s){let o=n.includes(i)?null:"*";t[i]=Un(e[i].nSources,o)}return[t]}function Un(e,n=null){let t=new Array(e);for(let s=0;s<e;s++)t[s]=n;return t}async function Zl(e){let{molecule:n,predictedSignals:t,options:s,atomType:i}=e;if(t)return t;let{spectra:o}=await Y(n,{predictOptions:s});return o[i==="C"?"carbon":"proton"]?.joinedSignals||[]}function Vn(e=[]){let n=structuredClone(e),t=[];for(let s of n){if(!("info"in s))throw new Error("each spectrum should contain info properties with nucleus information");if(V(s)){let{info:i,id:o}=s,a=ze(s.ranges);t.push({id:o,info:i,ranges:a})}else{let{info:i,id:o,zones:a}=s,r=ze(a);t.push({id:o,info:i,zones:r})}}return t}function Ul(e){for(let n of e){if(!n.id)throw new Error("A range/zone has not an ID");for(let t of n.signals||[])if(!t.id)throw new Error("A signal has not an ID")}}function ze(e){for(let n of e){n.id||(n.id=crypto.randomUUID());for(let t of n.signals||[])t.id||(t.id=crypto.randomUUID())}return Ul(e),e}import{buildCorrelationData as Gl}from"nmr-correlation";function Gn(e=[]){let n=structuredClone(e),t=[];for(let s of n)if(V(s)){let{id:i,info:o}=s,a=Vl({id:i,info:o,ranges:s.ranges});t.push({id:i,info:o,ranges:{values:a}})}else{let{id:i,info:o,zones:a}=s;t.push({id:i,info:o,zones:{values:a}})}return t}function Vl(e){if(e.info.nucleus!=="1H")return e.ranges;let n=e.ranges.reduce((t,s)=>t+(s.integration??0),0);for(let t of e.ranges)if(t.integration&&(t.integration*=100/n,t.signals)){let s=t.signals.reduce((i,o)=>i+(o.integration??0),0);for(let i of t.signals)i.integration?i.integration*=t.integration/s:i.integration=t.integration}return e.ranges}function Jn(e,n){let{H:t=[]}=e,s=0;for(let i of t){let o=n[i];s+=Number(o.link[0].signal.integration)}return s}function $n(e,n={}){let{tolerance:t={C:.25,H:.05}}=n,s=Gn(e),o=Gl(s,{tolerance:t}).values.map(r=>({...r,integration:0})),a={H:{},C:{}};for(let r of o){if(r.pseudo)continue;let{id:m,atomType:l,link:c,attachment:d}=r;(l==="H"||l==="C")&&(a[l][m]=r,l==="H"?a[l][m].integration=c[0].signal.integration||0:a[l][m].integration=Jn(d,o),a[l][m]=r)}return{targets:a,correlations:o}}function Jl(e,n=[]){let t=$l(e),{hasHSQC:s,types:i}=t;if(n.length>0)return{assignmentOrder:n,experimentTypes:t};let o=[];return s?o.push(["C"],["H"]):o.push(i.filter(a=>a==="H"||a==="C")),{assignmentOrder:o,experimentTypes:t}}var _n=Jl;function $l(e){let n=new Set;for(let t of e)for(let s of t.link){let i=s.experimentType;i==="1d"&&(i=s.atomType[0].toUpperCase()),n.add(i)}return{types:Array.from(n),hasProton:n.has("H"),hasCarbon:n.has("C"),hasHSQC:n.has("hsqc")}}async function PC(e,n={}){let{restrictionByCS:t={},justAssign:s,minScore:i=.01,maxSolutions:o=10,nbAllowedUnAssigned:a,timeout:r=6e3,predictionOptions:m={},predictions:l={},correlation:c={}}=n,{tolerance:d={H:.2,C:1},useChemicalShiftScore:g=!1,chemicalShiftRestriction:u=!0}=t,p=e.molecule;if(!p)throw new Error("It is needed a molecule to assign");p.addImplicitHydrogens(),_l(p);let C=Vn(e.spectra),{targets:y,correlations:f}=$n(C,c),{assignmentOrder:h}=_n(f,s);return await Zn({restrictionByCS:{tolerance:d,useChemicalShiftScore:g,chemicalShiftRestriction:u},spectra:C,molecule:p,timeout:r,minScore:i,maxSolutions:o,assignmentOrder:h,nbAllowedUnAssigned:a,correlations:f,targets:y,predictionOptions:m,predictions:l})}var Kl={unspecified:"Unspecified",unknown:"Unknown",signal:"Signal",residualSolvent:"Residual solvent",reference:"Reference",nmrSolvent:"NMR Solvent",impurity:"Impurity",standard:"Standard",artifact:"Artifact",p1:"Product 1",p2:"Product 2",p3:"Product 3"};function Ql(e){return typeof e=="string"&&Kl[e]!==void 0}function Q(e){return e===void 0?"signal":Ql(e)?e:"unspecified"}var Be=new Set(["signal"]);var Kn=_.toSorted((e,n)=>e.multiplicity===null&&n.multiplicity===null?0:e.multiplicity===null?1:n.multiplicity===null?-1:e.multiplicity-n.multiplicity),Mt=Kn.map(e=>e.value),Xe=Kn.map(e=>e.acs||e.value);import{Molecule as em}from"openchemlib";import{TopicMolecule as tm}from"openchemlib-utils";function ve(e,n,t){let{name:s}=e,i=t[s],{idCode:o}=n[i];if(i===void 0)throw new Error("atom map does not exists");return{...e,idCode:o,atom:i}}function Qn(e,n,t){let s=[];for(let i of e){let{from:o,to:a}=i;s.push({...i,from:o.map(r=>ve(r,n,t)),to:a.map(r=>ve(r,n,t))})}return s}function es(e,n,t){let s=[];for(let i of e){let{atoms:o}=i;s.push({...i,atoms:o.map(a=>ve(a,n,t))})}return s}function ns(e,n){let t=[],s=Rt(n),i=n[0].nucleusType.atomicNumber;for(let o of e){let a=Rt(o.from),r=ts(s,a),l=o[r?"to":"from"],c=r?a:Rt(o.to),{nucleusType:{atomicNumber:d},idCode:g}=l[0];!ts(s,c)||d!==i||t.push({coupling:o.value,atoms:l.map(u=>u.atom),diaIDs:[g]})}return t}function ts(e,n){for(let t of e)if(n.has(t))return!0;return!1}function Rt(e){let n=e.filter(t=>t.shift!==null).map(t=>t.shift);return new Set(n)}function ss(e,n,t){let s=new Set,i=[];for(let o of e){let{name:a}=o,r=n[a],{idCode:m}=t[r];if(!r)throw new Error("atom mapping does not exists");s.add(m),i.push(r)}return{diaIDs:Array.from(s),atoms:i}}function is(e){let n=[];for(let t of e){let{atoms:s=[],...i}=t;if(s.length>1)for(let o of s)n.push({...i,atoms:[o]});else n.push(t)}return n}function os(e){let n=[];for(let t of e){let s=is(t.js);for(let i of t.atoms){let o={...t,atoms:[i],nbAtoms:1,js:s};n.push(o)}}return n}function as(e,n){let{atomicNumber:t=1,atomMap:s,molfile:i}=n,o=[],a=em.fromMolfile(i),m=new tm(a).diaIDsAndInfo,l=Qn(e.couplings,m,s),c=es(e.shifts,m,s);for(let d of c){let{atoms:g,value:u}=d;if(!g.some(C=>C.nucleusType.atomicNumber===t))continue;let p={delta:u,nbAtoms:g.length,...ss(g,s,m),js:ns(l,g)};o.push(p)}return os(o)}function rs(e){return{molarFraction:{value:e.v,low:e.vl,high:e.vh},fieldStrength:e.f,baseItensity:e.bi,intensityLimit:e.il,spinSystemFlags:e.sf,spinSystemType:gm(e.sst),analysisType:e.at,inchiKey:e.ik,populations:nm(e.p),lineShapes:cm(e.l),shiftGroups:lm(e.sg),shifts:sm(e.s),couplingGroups:mm(e.cg),couplings:im(e.c),atoms:om(e.a),bonds:am(e.b)}}function nm(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,population:{value:t.v,low:t.vl,high:t.vh},spinSystemFlags:t.sf});return n}function sm(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,shiftGroup:t.sg});return n}function im(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,couplingGroup:t.cg,shifts:{from:t.s[0],to:t.s[1]}});return n}function om(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,nucleusType:dm(t.nc),cipRank:{canonical:t.crcan,rd:t.crrd,nmr:t.crnmr},ordinal:t.o,stereochemistryFlags:t.rs,spinSystemFlags:t.sf,formalcharge:t.fc,partialCharge:t.c,coordinates2D:t.c2d,coordinates3D:t.c3d,parent2D:t.p2d,shift:t.s});return n}function am(e){let n=[];for(let t of e)n.push({id:t.id,bondType:rm(t.b),stereochemistryFlags:t.rs,spinSystemFlags:t.sf,atoms:t.a});return n}function rm(e){switch(e){case 0:return"NONE";case 1:return"SINGLE";case 2:return"DOUBLE";case 3:return"TRIPLE";case 4:return"CONJUGATED";case 5:return"SINGLE_UP";case 6:return"SINGLE_DOWN";default:throw new Error(`Unknown bond type: ${e}`)}}function lm(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,shift:{value:t.v,low:t.vl,high:t.vh},spin2:t.s,spinCount:t.c,exchangeable:t.ex,spinSystemFlags:t.sf,gamma:t.g,iterationWeight:t.iw,response:{value:t.rs.v,low:t.rs.vl,high:t.rs.vh,sf:t.rs.sf},population:t.p,lineShape:t.l});return n}function mm(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.parentID,name:t.name,remarks:t.remarks,coupling:{value:t.v,low:t.vl,high:t.vh},spinSystemFlags:t.sf,couplingType:t.t});return n}function cm(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,spinSystemFlags:t.sf,lineWidth:{value:t.l.v,low:t.l.low,high:t.l.high},gaussian:{value:t.g.v,low:t.g.low,high:t.g.high}});return n}function gm(e){switch(e){case 0:return"NONE";case 1:return"SOLUTE";case 2:return"SOLVENT";case 4:return"IMPURITY";case 8:return"REFERENCE";case 16:return"CALIBRANT";case 32:return"ERROR_MESSAGE";default:throw new Error(`Unexpected spinSystemType: ${e}`)}}function dm(e){return{atomicNumber:(e&65024)>>9,isotope:e&511}}function ls(e,n){let{logger:t}=n;t.debug("Parsing CT json results");let s=rs(e),i=um(s),o=fm(s);return{...s,shifts:i,couplings:o}}function um(e){let n=e.shifts,t=pm(e),s=ms(e),i=[];for(let o of n){let a=t[o.shiftGroup];if(!a)throw new Error(`Shift group ${o.shiftGroup} not found`);let r=s[o.id];if(!r)throw new Error(`Atom not found: ${o.id}`);i.push({atoms:r,value:a.shift.value})}return i}function fm(e){let n=e.couplings,t=Cm(e.couplingGroups),s=ms(e),i=[];for(let o of n){let a=t[o.couplingGroup];if(!a)throw new Error(`Coupling group ${o.couplingGroup} not found`);let r=s[o.shifts.from];if(!r)throw new Error(`Atom not found: ${o.shifts.from}`);let m=s[o.shifts.to];if(!m)throw new Error(`Atom not found: ${o.shifts.to}`);i.push({from:r,to:m,value:a.coupling.value})}return i}function ms(e){let n={};for(let t of e.atoms){if(!t.shift)continue;let s=t.shift;n[s]||(n[s]=[]),n[s].push(t)}return n}function pm(e){let n={};for(let t of e.shiftGroups)n[t.id]=t;return n}function Cm(e){let n={};for(let t of e)n[t.id]=t;return n}function cs(e){let n={};for(let t of e)n[t.name]=t.ordinal;return n}function n5(e,n,t){let s=ls(e,{logger:console}),i=cs(s.atoms),o=as(s,{atomMap:i,molfile:n,...t});return{...s,signals:o}}var i5=[{names:["acetic 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wt(e,n){let{x:t,re:s,im:i}=e,o=ne({shapes:n,windowOptions:{dw:t[1]-t[0],length:s.length}}),a=z(s,{windowData:o}),r=z(i,{windowData:o});return{x:t,re:a,im:r}}var xm={updateXDomain:!0,updateYDomain:!1},Om={exponential:{apply:!0,options:{lineBroadening:.3}},sineBell:{apply:!1,options:{offset:0}},sineSquare:{apply:!1,options:{offset:0}},traf:{apply:!1,options:{lineBroadening:.3}},gaussian:{apply:!1,options:{lineBroadening:.3,lineBroadeningCenter:0}}};function Sm(e,n){if(!us(e))throw new Error("apodization not applicable on this data");let{x:t,re:s,im:i}=e.data,o=wt({x:t,re:s,im:i},n);e.data={...e.data,...o}}function us(e){return!!(e.info.isComplex&&e.info.isFid)}function vm(e,n){return{once:!0,reduce:n}}var fs={name:"apodization",label:"Apodization / Window functions",domainUpdateRules:xm,apply:Sm,reduce:vm,isApplicable:us};import{xSequentialFillFromStep as wm}from"ml-spectra-processing";import{xEnsureFloat64 as Os,xMaxValue as Mm}from"ml-spectra-processing";import{matrixCreateEmpty as 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b=0;b<p.re.length;b++){let x=p.re[b]*c[b+r-f],v=p.im[b]*d[b+r-f],S=p.re[b]*d[b+r-f],H=p.im[b]*c[b+r-f];h+=x-v,D+=S+H}c[r-f-1]=h,d[r-f-1]=D}let C=new Float64Array(t.length),y=new Float64Array(s.length);return C.set(c.subarray(0,r),0),y.set(d.subarray(0,r),0),o<0?(C.set(t.slice(0,t.length-r),r),y.set(s.slice(0,t.length-r),r)):(C.set(t.slice(o),r),y.set(s.slice(o),r)),{re:C,im:y}}function Rm(e,n){let{U:t,V:s,svals:i}=hs(e),o=e.re.length,a=e.re[0].length,r=i.length,m=Mm(i)*1e-7,l={re:new Float64Array(a),im:new Float64Array(a)};for(let c=0;c<a;c++){let d=0,g=0;for(let u=0;u<r;u++)if(i[u]>m){let p=0,C=0;for(let b=0;b<o;b++){let x=t.re[b][u]*n.re[b],v=-t.im[b][u]*n.im[b],S=t.re[b][u]*n.im[b],H=-t.im[b][u]*n.re[b];p+=x-v,C+=S+H}let y=p/i[u],f=C/i[u],h=s.re[c][u],D=s.im[c][u];d+=h*y-D*f,g+=h*f+D*y}l.re[c]=d,l.im[c]=g}return l}var Am={updateXDomain:!0,updateYDomain:!0};function Nm(e,n={}){if(!Ss(e))throw new Error("Digital Filter is not applicable on this data");let{info:t,filters:s,data:i,data:{re:o,im:a}}=e,{lpNumberOfCoefficients:r=0,tdOff:m=0}=t,{nbCoefficients:l=r,nbPoints:c=m/2,nbInputs:d=Math.floor(o.length/2-l-c)}=n,{re:g,im:u}=re({re:o,im:a},{nbCoefficients:l,nbInputs:d,nbPoints:c}),p=s.find(y=>y.name==="backwardLinearPrediction");p&&(p.value={nbCoefficients:l,nbPoints:c,nbInputs:d});let C=i.x;Object.assign(i,{re:g,im:u,x:c<0?wm({from:0,size:g.length,step:C[1]-C[0]}):C})}function Ss(e){return!!(e.info.isComplex&&e.info.isFid)}function km(e,n){return{once:!0,reduce:n}}var vs={name:"backwardLinearPrediction",label:"Backward Linear Prediction Filter",domainUpdateRules:Am,apply:Nm,reduce:km,isApplicable:Ss};import{xEnsureFloat64 as ac}from"ml-spectra-processing";import Im from"ml-airpls";import{xEnsureFloat64 as Tm,xFindClosestIndex as Em}from"ml-spectra-processing";function Ps(e,n){let{lambda:t=50,anchors:s=[],maxIterations:i,tolerance:o,autoDownsample:a=!0}=n,r=Array.from(new Float64Array(e.x.length));if(s.length>0)for(let l of s){let c=Em(e.x,l);r[c]=1}let{baseline:m}=Im(e.x,e.y,{maxIterations:i,lambda:t,tolerance:o,controlPoints:r,autoDownsample:a});return Tm(m)}import{CholeskyDecomposition as qm,Matrix as kt}from"ml-matrix";import{calculateAdaptiveWeights as Ym,xFindClosestIndex as Wm,xMultiply as Zm,xSequentialFillFromStep as Um}from"ml-spectra-processing";function Fs(e,n,t){if(n===0)return 1;if(e===0||n>e)return 0;if(n>e-n&&(n=e-n),!t)return zm(e,n);if(t[n]>0)return t[n];let s=1,i=e;for(let o=1;o<=n;o++){if(t[o]>0){i--,s=t[o];continue}s*=i--,s/=o,t[o]=s}return s}function zm(e,n){let t=1,s=e;for(let i=1;i<=n;i++)t*=s--,t/=i;return t}import{xyMedianYAtXs as Bm}from"ml-spectra-processing";function J(e,n,t={}){let{windowSize:s=Math.max(1,Math.floor(e.y.length/100))}=t;return Bm(e,n,{windowSize:s})}import{Matrix as Xm}from"ml-matrix";function js(e){let n=e.rows,t=e.columns,s=new Xm(n,n);for(let i=0;i<n;i++)for(let o=0;o<n;o++){let a=0;for(let r=0;r<t;r++)a+=e.get(o,r)*e.get(i,r);s.set(o,i,a)}return s}import{matrixCreateEmpty as Lm}from"ml-spectra-processing";function Ms(e,n){let t=e.rows,s=e.columns,i=n.columns;if(n.rows!==t)throw new Error("Matrix dimensions are incompatible for multiplication");let o=Lm({nbRows:i,nbColumns:s});for(let a=0;a<s;a++)for(let r=0;r<i;r++){let m=0;for(let l=0;l<t;l++)m+=e.get(l,a)*n.get(l,r);o[r][a]=m}return o}function Rs(e,n,t={}){let{maxIterations:s=100,tolerance:i=1e-6,factorStd:o=3,learningRate:a=.3,anchors:r,medianWindow:m}=t,{y:l}=e,{anchors:c,weights:d,controlPoints:g}=$m(e,r,m),u=l.slice(),p=new Float64Array(l.length),C=0,y=1/0,{logger:f}=t,h=Math.max(1,l.length-1);for(let x=0;x<c.x.length;x++)c.x[x]/=h;let{binomialCoefficients:D,bernsteinMatrix:b}=Vm(l,n);for(;C<s&&y>i;){let x=Gm(c,{binomialCoefficients:D,degree:n,weights:d,logger:f});if(!x)return u;let S=Ms(b,x)[0];Ym(l,S,d,{controlPoints:g,learningRate:a,factorStd:o}),y=Jm(S,p,l.length),p.set(S),u=S,C++}return u}function Vm(e,n){let t=e.length,s=n,i=Math.max(1,t-1),o=new 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t=e.length;if(t<2)throw new Error("Need at least 2 knots.");if(t!==n.length)throw new Error("xs and ys must be the same length.");let s=Array.from({length:t},(f,h)=>h).toSorted((f,h)=>e[f]-e[h]),i=s.map(f=>e[f]),o=s.map(f=>n[f]),a=t-1,r=new Float64Array(a);for(let f=0;f<a;f++)r[f]=i[f+1]-i[f];let m=new Float64Array(t);for(let f=1;f<a;f++)m[f]=3/r[f]*(o[f+1]-o[f])-3/r[f-1]*(o[f]-o[f-1]);let l=new Float64Array(t),c=new Float64Array(t),d=new Float64Array(t);l[0]=1;for(let f=1;f<a;f++)l[f]=2*(i[f+1]-i[f-1])-r[f-1]*c[f-1],c[f]=r[f]/l[f],d[f]=(m[f]-r[f-1]*d[f-1])/l[f];l[a]=1;let g=new Float64Array(t);for(let f=a-1;f>=0;f--)g[f]=d[f]-c[f]*g[f+1];let u=[],p=[],C=[],y=[];for(let f=0;f<a;f++)u.push(o[f]),p.push((o[f+1]-o[f])/r[f]-r[f]*(g[f+1]+2*g[f])/3),C.push(g[f]),y.push((g[f+1]-g[f])/(3*r[f]));return{xs:i,a:u,b:p,c:C,d:y}}function Qm(e,n){let{xs:t,a:s,b:i,c:o,d:a}=e,r=t.length-1,m=0,l=r-1;for(;m<l;){let g=m+l+1>>1;t[g]<=n?m=g:l=g-1}let c=Math.min(m,r-1),d=n-t[c];return s[c]+d*(i[c]+d*(o[c]+d*a[c]))}function ec(e,n){let{xs:t,a:s,b:i,c:o,d:a}=e,r=t.length-1,m=new Float64Array(n.length),l=0;for(let c=0;c<n.length;c++){let d=n[c];for(;l<r-1&&t[l+1]<=d;)l++;let g=d-t[l];m[c]=s[l]+g*(i[l]+g*(o[l]+g*a[l]))}return m}function tc(e,n){let t=e.length,s=new Float64Array(t-1);for(let o=0;o<t-1;o++)s[o]=Math.abs(e[o+1]-e[o]);s.toSorted();let i=Math.max(0,Math.floor((t-1)*n/100)-1);return Math.max(s[i],1e-12)}import{PolynomialRegression as nc}from"ml-regression-polynomial";import{xyEquallySpaced as sc}from"ml-spectra-processing";function As({x:e,y:n},t){let{degree:s,anchors:i=[]}=t,o={x:structuredClone(i),y:[]};if(o.x.length<2){let r=sc({x:e,y:n},{numberOfPoints:4096});o.x=r.x,o.y=r.y}else{let{y:r}=J({x:e,y:n},o.x);o.y=r}return new nc(o.x,o.y,s,{interceptAtZero:!1}).predict(e)}import{xFindClosestIndex as ic,xWhittakerSmoother as oc}from"ml-spectra-processing";function Ns(e,n={}){let{anchors:t=[],lambda:s=2e3,maxIterations:i=20,tolerance:o=.001,learningRate:a=.2}=n,r=new Float64Array(e.x.length);if(t.length>0)for(let l of t){let c=ic(e.x,l);r[c]=1}return oc(e.y,{lambda:s,maxIterations:i,learningRate:a,tolerance:o,controlPoints:r})}function ks({x:e,y:n},t){let{algorithm:s}=t;switch(s){case"airpls":return Ps({x:e,y:n},t);case"polynomial":return As({x:e,y:n},t);case"whittaker":return Ns({x:e,y:n},t);case"bernstein":{let{degree:i}=t,o=Rs({x:e,y:n},i,t);return ac(o)}case"cubic":return ws({x:e,y:n},t);default:throw new Error(`baselineCorrection: algorithm unknown: ${t.algorithm}`)}}var rc={updateXDomain:!1,updateYDomain:!1};function lc(e,n){if(!Is(e))throw new Error("Baseline correction not applicable on this data");let{x:t,re:s}=e.data,i=ks({x:t,y:s},n),o=new Float64Array(t.length);for(let a=0;a<s.length;a++)o[a]=s[a]-i[a];Object.assign(e.data,{re:o})}function Is(e){return!e.info.isFid}function mc(e,n){return{once:!0,reduce:n}}var Ts={name:"baselineCorrection",label:"Baseline correction",domainUpdateRules:rc,apply:lc,reduce:mc,isApplicable:Is};var cc={updateXDomain:!0,updateYDomain:!0};function gc(e,n){if(!Es(e))throw new Error("Digital filter is not applicable on this data");let{digitalFilterValue:t}=n,s=new Float64Array(e.data.re),i=new Float64Array(e.data.im),o=new Float64Array(s.length),a=new Float64Array(i.length),r=Math.floor(t);o.set(s.slice(r)),a.set(i.slice(r)),e.data.re=o,e.data.im=a}function Es(e){return!!(e.info.isComplex&&e.info.isFid)}function dc(e,n){return{once:!0,reduce:n}}var zs={name:"digitalFilter",label:"Digital Filter",domainUpdateRules:cc,apply:gc,reduce:dc,isApplicable:Es};import{xEnsureFloat64 as It,xyEquallySpaced as Bs}from"ml-spectra-processing";var uc={updateXDomain:!1,updateYDomain:!1};function fc(e,n={}){if(!Xs(e))throw new Error("Equally spaced is not applicable on this 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Pc={updateXDomain:!0,updateYDomain:!0};function Fc(e){if(!Vs(e))throw new Error("fft not applicable on this data");wc(e);let n=e.filters.some(o=>o.name==="digitalFilter"&&o.enabled),{info:{aqMod:t}}=e;t===1&&Rc(e),xc(e.data.x.length)||Zs(e);let{data:s,info:i}=e;if(Object.assign(s,Oc({re:s.re,im:i.reverse?vc(s.im,-1):s.im},{applyZeroShift:!0})),n){let{digitalFilter:o=0}=i,a=Math.floor(o),r=(o-a)*Math.PI*2,m=a%2?180*I:0;Object.assign(s,Sc(s,m,-r,{reverse:!0}))}s.x=Mc(e),e.info={...i,isFid:!1,isFt:!0}}function Vs(e){return!!(e.info.isComplex&&e.info.isFid)}function jc(e,n){return{once:!0,reduce:n}}function Mc(e){let n=e.info,t=Number(n.baseFrequency),s=Number(n.frequencyOffset),i=Number(n.spectralWidth),o=s/t,a=.5*i,r=e.data.x.length,m=o-a,l=i/(r-1),c=new Float64Array(r);for(let d=0;d<r;d++)c[d]=m,m+=l;return c}function Rc(e){let n=e.data,t=n.re.length,s=new Float64Array(n.re),i=new Float64Array(n.im),o=Us(n.re.slice(t*.75>>0,t)),a=Us(n.im.slice(t*.75>>0,t));for(let r=0;r<t;r++)s[r]-=o,i[r]-=a;return Object.assign(e.data,{re:s,im:i}),e}function wc(e){let{data:n}=e;if(n.x.length!==n.re.length||n.x.length!==n.im.length)throw new Error("The length of data should be equal")}var Gs={name:"fft",label:"FFT",domainUpdateRules:Pc,apply:Fc,reduce:jc,isApplicable:Vs};import{xSequentialFillFromStep as kc}from"ml-spectra-processing";import{Matrix as Ac,SVD as Nc}from"ml-matrix";function Js(e,n){let{nbCoefficients:t,nbInputs:s,nbPoints:i}=n;if(e.length<s+t+i)throw new RangeError("data length should be bigger than nbInputs + nbCoefficients + nbPoints");let o=e.length-i-2,a=[];for(let d=0;d<s;d++){let g=new Float64Array(t);for(let u=0;u<t;u++)g[u]=e[o-d-u];a.push(g)}let r=new Nc(a),m=new Float64Array(s);for(let d=0;d<s;d++)m[d]=e[o-d+1];let l=r.solve(Ac.from1DArray(m.length,1,m)).to1DArray(),{output:c=Float64Array.from(e)}=n;for(let d=0;d<i;d++){let g=0;for(let u=0;u<l.length;u++)g+=l[u]*c[o+1+d-u];c[o+d+2]=g}return{output:c,predicted:c.slice(o+2)}}function le(e,n){let{re:t,im:s}=e,{nbCoefficients:i,nbPoints:o,nbInputs:a=t.length}=n,r=Math.abs(o),m=o<0?r:0,l=2*Math.ceil((a+r+i)/2);if(t.length<l-m)throw new RangeError(`The sum of nbPoints, nbInputs and nbCoefficients should be less than data length (${t.length})`);let c=new Float64Array(2*l),d=t.length-l+m;for(let p=0;p<l-m;p++)c.set([t[d+p],s[d+p]],2*p);Js(c,{nbInputs:a*2,nbCoefficients:i,nbPoints:r*2,output:c});let g=new Float64Array(t.length+m),u=new Float64Array(m+s.length);o<0?(g.set(t),u.set(s)):(g.set(t.slice(0,t.length-o)),u.set(s.slice(0,s.length-o)));for(let p=0;p<2*r;p+=2)g[g.length-1-(p>>1)]=c[c.length-2-p],u[g.length-1-(p>>1)]=c[c.length-1-p];return{re:g,im:u}}function me(e,n,t){let s=2*e,i=2*n;if(t===0){if(s<n)return 0;if(n<s&&s<i)return n;if(i<s)return t-n}return n<t?t-n:0}var Ic={updateXDomain:!0,updateYDomain:!0};function Tc(e,n={}){if(!$s(e))throw new Error("Digital filter is not applicable on this data");let{info:t,filters:s,data:i,data:{x:o,re:a,im:r}}=e,{lpNumberOfCoefficients:m=0,linearPredictionBin:l=0,spectrumSize:c=a.length,numberOfPoints:d=a.length}=t,{nbPoints:g=me(c,d,l)/-2,nbCoefficients:u=m,nbInputs:p=Math.floor(a.length-g-u)}=n,C=s.find(h=>h.name==="forwardLinearPrediction");C&&(C.value={nbCoefficients:u,nbPoints:g,nbInputs:p});let{re:y,im:f}=le({re:a,im:r},{nbCoefficients:u,nbInputs:p,nbPoints:g});Object.assign(i,{re:y,im:f,x:g<0?kc({from:0,size:y.length,step:o[1]-o[0]}):o})}function $s(e){return!!(e.info.isComplex&&e.info.isFid)}function Ec(e,n){return{once:!0,reduce:n}}var _s={name:"forwardLinearPrediction",label:"Forward Linear Prediction Filter",domainUpdateRules:Ic,apply:Tc,reduce:Ec,isApplicable:$s};import{reimAbsolute as zc,reimAutoPhaseCorrection as Bc,reimPhaseCorrection as Xc,xEnsureFloat64 as Ks}from"ml-spectra-processing";var Lc={updateXDomain:!1,updateYDomain:!1};function qc(e,n={}){if(!ti(e))throw new Error("Phase correction not applicable on this 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qi={name:"baselineCorrectionTwoDimensions",label:"Baseline correction",domainUpdateRules:E0,apply:z0,reduce:B0,isApplicable:Li};import{matrixMinMaxZ as Yi}from"ml-spectra-processing";var X0={updateXDomain:!0,updateYDomain:!0};function L0(e,n={}){if(!Wi(e))throw new Error("Backward linear prediction on dimension 1 is not applicable on this data");let{data:t,data:{re:s,im:i},info:o,filters:a}=e,r=s.z,m=i.z,l=r.length,c=r[0].length,d=[],g=[],{lpNumberOfCoefficients:u=[15,15],tdOff:p=[0,0]}=o,{nbCoefficients:C=u[0],nbPoints:y=p[0]/2,nbInputs:f=Math.floor(c-Math.max(y,0)-C)}=n;if(y===0||C===0)return;let h=a.find(v=>v.name==="blpDimension1");h&&(h.value={nbCoefficients:C,nbPoints:y,nbInputs:f});for(let v=0;v<l;v++){let{re:S,im:H}=re({re:r[v],im:m[v]},{nbInputs:f,nbPoints:y,nbCoefficients:C});d.push(S),g.push(H)}let D=Yi(d),b=Yi(g),x={re:{...s,z:d,minZ:D.min,maxZ:D.max},im:{...i,z:g,minZ:b.min,maxZ:b.max}};if(y<0){let 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S=0;S<c;S++){let{re:H,im:O}=re({re:T(r,S),im:T(m,S)},{nbInputs:C,nbPoints:p,nbCoefficients:u});E(h,H,S),E(D,O,S)}let b=Vi(h),x=Vi(D),v={re:{...o,z:h,minZ:b.min,maxZ:b.max},im:{...a,z:D,minZ:x.min,maxZ:x.max}};if(p<0){let{minY:S,maxY:H}=o,O=(H-S)/(l-1),P=H+O*f;v.re.maxY=P,v.im.maxY=P}Object.assign(i,v)}function Gi(e){let{isComplex:n,isFt:t,isFtDimensionOne:s}=e.info;return!!(n&&s&&!t)}function Z0(e,n){return{once:!0,reduce:n}}var Ji={name:"blpDimension2",label:"Backward-LP Dimension 2",domainUpdateRules:Y0,apply:W0,reduce:Z0,isApplicable:Gi};function $i(e,n){let{digitalFilterValue:t=0}=n,s=new Float64Array(e.re),i=new Float64Array(e.im),o=Math.floor(t),a=0;o+=0;let r=new Float64Array(s.length),m=new Float64Array(i.length);return r.set(s.slice(o)),r.set(s.slice(a,o),s.length-o),m.set(i.slice(o)),m.set(i.slice(a,o),i.length-o),{re:r,im:m}}var U0={updateXDomain:!1,updateYDomain:!1};function V0(e,n){if(!_i(e))throw new Error("Digital filter on dimension 1 is not applicable on this data");let{data:t,data:{re:s,im:i}}=e,o=s.z,a=i.z,r=o.length,m=[],l=[],{digitalFilterValue:c}=n;if(!(!c||c===0)){for(let d=0;d<r;d++){let{re:g,im:u}=$i({re:o[d],im:a[d]},{digitalFilterValue:c});m.push(g),l.push(u)}Object.assign(t.re,{z:m}),Object.assign(t.im,{z:l})}}function _i(e){return!!(e.info.isComplex&&e.info.isFid)}function G0(e,n){return{once:!0,reduce:n}}var Ki={name:"digitalFilter2D",label:"Digital filter on Dimension 1",domainUpdateRules:U0,apply:V0,reduce:G0,isApplicable:_i};import{xEnsureFloat64 as ao}from"ml-spectra-processing";import{matrixCreateEmpty as to,nextPowerOfTwo as J0,reimMatrixFFT as $0,reimMatrixPhaseCorrection as _0}from"ml-spectra-processing";function Pe(e){for(let n of e)for(let t=0;t<n.length;t++)n[t]=-n[t];return e}import{xMean as Qi}from"ml-spectra-processing";function eo(e,n){let{digitalFilterValue:t=0}=n,s=Math.round(t);for(let i=0;i<e.re.length;i++){let o=e.re[i],a=e.im[i],r=o.length,m=Qi(o.slice(r*.75>>0,r-s)),l=Qi(a.slice(r*.75>>0,r-s));for(let c=s;c<r-s;c++)o[c]-=m,a[c]-=l}}function no(e,n={}){let{reverse:t,digitalFilterValue:s=0}=n;eo(e,{digitalFilterValue:s}),t&&(e.im=Pe(e.im));let i=K0(e);$0(i,{inPlace:!0,applyZeroShift:!0});let{phaseCorrection:o={}}=n,a=Math.floor(s),r=s*Math.PI*2,l=a%2?180*I:0,c=-r,{ph0:d,ph1:g,mode:u="no"}=o;return u==="pk"&&d!==void 0&&g!==void 0&&(l+=d*Math.PI/180,c+=g*Math.PI/180),_0(i,l,c,{reverse:!0,inPlace:!0}),i}function K0(e){let n=e.re.length,t=J0(e.re[0].length);if(t>e.re[0].length){let s={re:to({nbRows:n,nbColumns:t}),im:to({nbRows:n,nbColumns:t})},{re:i,im:o}=e;for(let a=0;a<n;a++)s.re[a].set(i[a]),s.im[a].set(o[a]);return s}return e}import{xAdd as Q0,xMultiply as eg,xSubtract as Lt}from"ml-spectra-processing";function so(e){let{re:{z:n},im:{z:t}}=e,s=[],i=[],o=n.length,a=o-o%2;for(let r=0;r<a;r+=2){let m=n[r],l=t[r],c=n[r+1],d=t[r+1];s.push(Lt(eg(d,-1),l),Lt(c,m)),i.push(Q0(c,m),Lt(d,l))}return{re:s,im:i}}import{matrixCreateEmpty as io,nextPowerOfTwo as tg}from"ml-spectra-processing";function oo(e){let{data:n,info:t,meta:s={}}=e,{nuslist:i,NusTD:o}=s,a=t.acquisitionScheme?.toLowerCase(),r=n.re.z[0].length,m=tg(o[1]),l={re:[],im:[]};if(a==="echo-antiecho"){let c=i.map(g=>g*2),d=["re","im"];for(let g of d){let u=n[g].z,p=io({nbRows:m,nbColumns:r,ArrayConstructor:Float64Array}),C=n.re.z.length/2;for(let y=0;y<C;y++){let f=c[y];p[f].set(u[2*y]),p[f+1].set(u[2*y+1])}l[g]=p}}else{let c=["re","im"];for(let d of c){let g=n[d].z,u=io({nbRows:m,nbColumns:r,ArrayConstructor:Float64Array}),p=n.re.z.length;for(let C=0;C<p;C++){let y=i[C];u[y].set(g[C])}l[d]=u}}e.data={re:{...n.re,z:l.re},im:{...n.im,z:l.im}}}var ng={updateXDomain:!0,updateYDomain:!0};function sg(e,n){if(!ro(e))throw new Error("fft dimension 1 not applicable on this data");let{data:t,info:s,meta:{nuslist:i=[]}={}}=e,{digitalFilter:o=0,reverse:a=[!1,!1]}=s,r=s.acquisitionScheme?.toLowerCase();if(t.re.z.length!==t.im.z.length||t.re.z[0].length!==t.im.z[0].length)throw new RangeError("real and imaginary data must have the same dimensionality");let m=r==="echo-antiecho"?so(t):{re:t.re.z,im:t.im.z},{re:l,im:c}=no(m,{acquisitionScheme:r,...n,reverse:a[0],digitalFilterValue:o});t.re.z=l.map(ao),t.im.z=c.map(ao);let{isFid:d,...g}=s;e.info={...g,isFid:!1,isFtDimensionOne:!0},i.length>0&&oo(e)}function ro(e){return!!(e.info.isComplex&&e.info.isFid)}function ig(e,n){return{once:!0,reduce:n}}var lo={name:"fftDimension1",label:"FFT Dimension 1",domainUpdateRules:ng,apply:sg,reduce:ig,isApplicable:ro};import{matrixMinMaxZ as cg}from"ml-spectra-processing";import{nextPowerOfTwo as og,reimMatrixFFTByColumns as ag,reimMatrixPhaseCorrection as rg}from"ml-spectra-processing";function co(e,n={}){let t=e.re.length&-2;t>e.re.length&&(e.re.splice(t,1),e.im.splice(t,1));let s=e.re[0].length,{acquisitionScheme:i="",reverse:o}=n,a={...n},r={};if(i==="notPhaseSensitive"){Pe(e.im);let m=mo(e,a);r.rr=m.re,r.ir=m.im}else for(let m in e){let l=i==="SEQ"?t:t/2,c=new Array(l),d=new Array(l),g=e[m];if(i==="SEQ")for(let u=0;u<l;u++)c[u]=g[u],d[u]=new Float64Array(s);else{for(let u=0;u<l;u++)c[u]=g[2*u],d[u]=g[2*u+1];if(o&&Pe(d),["states-tppi","tppi"].includes(i))for(let u=0;u<l;u+=2)for(let p=0;p<s;p++)c[u][p]=-c[u][p],d[u][p]=-d[u][p]}mo({re:c,im:d},a),m==="re"?(r.rr=c,r.ri=d):(r.ir=c,r.ii=d)}return r}function mo(e,n){let{acquisitionScheme:t,phaseCorrection:s={}}=n;for(let m=0;m<e.re.length;m++)e.re[m][0]*=.5,e.im[m][0]*=.5;lg(e);let i=ag(e,{applyZeroShift:t!=="SEQ",inPlace:!0}),{mode:o,ph0:a,ph1:r}=s;if(o&&o==="mc"||t==="notPhaseSensitive"){let{re:m,im:l}=i,c=m.length,d=m[0].length;for(let g=0;g<c;g++){let u=m[g],p=l[g];for(let C=0;C<d;C++)m[g][C]=mg(u[C],p[C])}}return o==="pk"&&a!==void 0&&r!==void 0&&rg(i,a*Math.PI/180,r*Math.PI/180,{direction:"columns",inPlace:!0}),i}function lg(e){let n=e.re[0].length,t=og(e.re.length);if(t>e.re.length){let s=e.re.length;for(let i=s;i<t;i++)e.re.push(new Float64Array(n)),e.im.push(new Float64Array(n))}}function mg(e,n){let t=Math.abs(e),s=Math.abs(n);return s>t?s+.4*t:t+.4*s}function go(e){let n=[],t=[];for(let s=0;s<e.baseFrequency.length;s++){let i=e.baseFrequency[s],o=e.frequencyOffset[s],a=e.spectralWidth[s],r=o/i;n.push(r-a*.5),t.push(r+a*.5)}return{minX:n[0],maxX:t[0],minY:n[1],maxY:t[1]}}var gg={updateXDomain:!0,updateYDomain:!0};function dg(e,n){if(!uo(e))throw new Error("fft dimension 2 not applicable on this data");let t=e.data;if(t.re.z.length!==t.im.z.length||t.re.z[0].length!==t.im.z[0].length)throw new RangeError("real and imaginary data must have the same dimensionality");let s={re:t.re.z,im:t.im.z},{reverse:i=[!1,!1],acquisitionScheme:o}=e.info,a=co({re:s.re,im:s.im},{reverse:i[1],acquisitionScheme:o,...n});e.data={...ug(a,e.info)},e.info={...e.info,isFt:!0}}function ug(e,n){let t={},{acquisitionScheme:s}=n,i=go(n),o=a=>{for(let r of a){let m=e[r],{min:l,max:c}=cg(m);t[r]={z:m,maxZ:c,minZ:l,...i}}return t};return o(s==="notPhaseSensitive"?["rr","ir"]:["rr","ir","ri","ii"])}function uo(e){let{isComplex:n,isFtDimensionOne:t,isFt:s}=e.info;return!!(n&&t&&!s)}function fg(e,n){return{once:!0,reduce:n}}var fo={name:"fftDimension2",label:"FFT Dimension 2",domainUpdateRules:gg,apply:dg,reduce:fg,isApplicable:uo};import{matrixMinMaxZ as po}from"ml-spectra-processing";var pg={updateXDomain:!0,updateYDomain:!0};function Cg(e,n={}){if(!Co(e))throw new Error("Forward Linear Prediction on dimension 1 is not applicable on this data");let{info:t,data:s,data:{re:i,im:o},filters:a}=e,r=i.z,m=o.z,l=r.length,c=r[0].length,d=[],g=[],{lpNumberOfCoefficients:u=[0,0],linearPredictionBin:p=[0,0],spectrumSize:C=[c,l],numberOfPoints:y=[c,l]}=t,{nbPoints:f=me(C[0],y[0],p[0])/-2,nbCoefficients:h=u[0],nbInputs:D=Math.floor(c-h-Math.max(f,0))}=n,b=a.find(H=>H.name==="flpDimension1");if(b&&(b.value={nbCoefficients:h,nbPoints:f,nbInputs:D}),Math.abs(f)===0||h===0)return;for(let H=0;H<l;H++){let{re:O,im:P}=le({re:r[H].slice(),im:m[H].slice()},{nbCoefficients:h,nbInputs:D,nbPoints:f});d.push(O),g.push(P)}let x=po(d),v=po(g),S={re:{...i,z:d,minZ:x.min,maxZ:x.max},im:{...o,z:g,minZ:v.min,maxZ:v.max}};if(f<0){let{minX:H,maxX:O}=i,P=(O-H)/(c-1);S.re.maxX=O+P*Math.abs(f)}Object.assign(s,S)}function Co(e){return!!(e.info.isComplex&&e.info.isFid)}function yg(e,n){return{once:!0,reduce:n}}var yo={name:"flpDimension1",label:"Fordward-LP Dimension 1",domainUpdateRules:pg,apply:Cg,reduce:yg,isApplicable:Co};import{matrixCreateEmpty as bo,matrixMinMaxZ as ho}from"ml-spectra-processing";var bg={updateXDomain:!0,updateYDomain:!0};function hg(e,n={}){if(!Do(e))throw new Error("Forward linear prediction on dimension 2 is not applicable on this data");let{info:t,data:s,data:{re:i,im:o},filters:a}=e,r=i.z,m=o.z,l=r.length,c=r[0].length,{lpNumberOfCoefficients:d=[0,0],linearPredictionBin:g=[0,0],spectrumSize:u=[c,l],numberOfPoints:p=[c,l]}=t,{nbPoints:C=me(u[1],p[1],g[1])/-2,nbCoefficients:y=d[1],nbInputs:f=Math.floor(l-y-Math.max(C,0))}=n,h=a.find(O=>O.name==="flpDimension2");if(h&&(h.value={nbCoefficients:y,nbPoints:C,nbInputs:f}),Math.abs(C)===0||y===0)return;let D=C<0?-1*C:0,b=bo({nbRows:l+D,nbColumns:c}),x=bo({nbRows:l+D,nbColumns:c});for(let O=0;O<c;O++){let{re:P,im:j}=le({re:T(r,O),im:T(m,O)},{nbPoints:C,nbCoefficients:y,nbInputs:f});E(b,P,O),E(x,j,O)}let v=ho(b),S=ho(x),H={re:{...i,z:b,minZ:v.min,maxZ:v.max},im:{...o,z:x,minZ:S.min,maxZ:S.max}};Object.assign(s,H)}function Do(e){let{isComplex:n,isFt:t,isFtDimensionOne:s}=e.info;return!!(n&&s&&!t)}function Dg(e,n){return{once:!0,reduce:n}}var Ho={name:"flpDimension2",label:"Fordward-LP Dimension 2",domainUpdateRules:bg,apply:hg,reduce:Dg,isApplicable:Do};import{matrixMinMaxZ as vo,nextPowerOfTwo as Fg,xHilbertTransform as Po}from"ml-spectra-processing";import{matrixCreateEmpty as _e,matrixHilbertTransform as Hg,nextPowerOfTwo as xg,reimMatrixFFT as So}from"ml-spectra-processing";function Yt(e,n){let{nusLength:t,nusIndices:s}=n,i=xg(t),o=e.re.z[0].length,a=Math.max(i,Math.min(i*4,1024)),r={re:_e({nbRows:o,nbColumns:a}),im:_e({nbRows:o,nbColumns:a})},m={re:_e({nbRows:o,nbColumns:a}),im:_e({nbRows:o,nbColumns:a})};for(let x=0;x<o;x++){let v=r.re[x],S=r.im[x];for(let H of s)v[H]=e.re.z[H][x],S[H]=-e.im.z[H][x];v[0]*=.5,S[0]*=.5}So(r,{inPlace:!0});let l=Oo(r.re),{maxThreshold:c=.75,increaseFactor:d=7,percentToReachMax:g=1,threshold:u=.5,iterations:p=100,istMaxResolution:C=1}=n;xo(r,m,l,u);let y=c-u,f=Math.round(g*p),h=d/f,D=y/Math.tanh(d);for(let x=0;x<=p;x++){Object.assign(r,Og(r,s));let v=Oo(r.re);if(v<=C*l/100)break;xo(r,m,v,x>f?c:Math.tanh(x*h)*D+u)}let b=qt(m,{inverse:!0});for(let x=0;x<b.re.length;x++)b.re[x][0]/=.5,b.im[x][0]/=.5;return{re:{...e.re,z:vg(b.re,i)},im:{...e.im,z:Pg(b.im,i)}}}function xo(e,n,t,s){let i=t*s,o=e.re,a=n.re;for(let r=0;r<o.length;r++){let m=o[r],l=a[r];for(let c=0;c<m.length;c++){let d=m[c];if(d>i){let g=d-i;l[c]+=g,m[c]=i}else if(d<-i){let g=d+i;l[c]+=g,m[c]=-i}}}}function Og(e,n){let t=qt(e,{inverse:!0}),s=t.re.length,i=new Float64Array(n.length),o=new Float64Array(n.length);for(let a=0;a<s;a++){let r=t.re[a],m=t.im[a];for(let l=0;l<n.length;l++){let c=n[l];i[l]=r[c],o[l]=m[c]}r.fill(0),m.fill(0);for(let l=0;l<n.length;l++){let c=n[l];r[c]=i[l],m[c]=o[l]}}return qt(t)}function qt(e,n={}){let{inverse:t=!1}=n,{re:s,im:i}=e;return t&&(Hg(s,{output:i}),Sg(i)),So({re:s,im:i},{inverse:t})}function Sg(e){for(let n of e)for(let t=0;t<n.length;t++)n[t]=-n[t];return e}function vg(e,n){let t=e.length,s=[];for(let i=0;i<n;i++){let o=new Float64Array(t);for(let a=0;a<t;a++)o[a]=e[a][i];s.push(o)}return s}function Pg(e,n){let t=e.length,s=[];for(let i=0;i<n;i++){let o=new Float64Array(t);for(let a=0;a<t;a++)o[a]=-e[a][i];s.push(o)}return s}function Oo(e){let n=0,t=0,s=e[0].length;for(let i of e)for(let o=0;o<s;o++){let a=i[o];a>t?t=a:a<n&&(n=a)}return Math.max(t,-n)}var jg={updateXDomain:!0,updateYDomain:!0};function Mg(e){if(!Fo(e))throw new Error("NUS reconstruction requires data with the direct dimension (rows) already FFT-processed (F2 domain).");let{data:n,meta:t={},info:s}=e;if(n.re.z.length!==n.im.z.length||n.re.z[0].length!==n.im.z[0].length)throw new RangeError("real and imaginary data must have the same dimensionality");let i=s.acquisitionScheme?.toLowerCase(),{nuslist:o,NusTD:a}=t,r={re:n.re,im:n.im},m=Fg(a[1]),l={re:[],im:[]};if(i==="echo-antiecho"){m/=2;let g=r.re.z,u=g.length/2,p=[],C=[];for(let b=0;b<u;b++)p.push(g[2*b]),C.push(g[2*b+1]);let y={re:{...r.re,z:p},im:{...r.im,z:C}},f=Yt(y,{nusIndices:o,nusLength:m}),h=[],D=f.re.z.length;for(let b=0;b<D;b++)h.push(f.re.z[b],f.im.z[b]);l.re=h;for(let b=0;b<D;b++)l.im.push(Po(f.re.z[b]),Po(f.im.z[b]))}else{let g=Yt(r,{nusIndices:o,nusLength:m});l.re=g.re.z,l.im=g.im.z}let c=vo(l.re),d=vo(l.im);e.data={re:{...r.re,z:l.re,minZ:c.min,maxZ:c.max},im:{...r.im,z:l.im,minZ:d.min,maxZ:d.max}}}function Fo(e){let{nuslist:n}=e.meta??{},{isComplex:t,isFtDimensionOne:s,isFt:i}=e.info;return!!(n.length>0&&t&&s&&!i)}function Rg(e,n){return{once:!0,reduce:n}}var jo={name:"nusDimension2",label:"NUS Reconstruction",domainUpdateRules:jg,apply:Mg,reduce:Rg,isApplicable:Fo};import{Matrix as et,MatrixTransposeView as Ro,WrapperMatrix2D as Ng}from"ml-matrix";import{SparseMatrix as tt}from"ml-sparse-matrix";import{matrixCreateEmpty as kg,xMaxIndex as Ig}from"ml-spectra-processing";function ue(e){if(["rr","ir","ri","ii"].some(n=>!(n in e)))throw new Error("four quadrants should has ir, ri and ii quadrants")}function Ke(e){if(["rr","ri"].some(n=>!(n in e)))throw new Error("Two quadrants should has ri 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wo(e,n={}){let{absolute:t,phases:s,threshold:i,nonZeros:o}=zg(e,n),a=No(t,s,i),{columns:r,rows:m,values:l}=o,c=Ig(l),d={x:r[c],y:m[c]};return Tg(a,{pivot:d,absolute:t,phases:s,threshold:i})}function Tg(e,n){let t=-30,s=30,i=8,o=Number.MAX_SAFE_INTEGER,a=Number.MAX_SAFE_INTEGER,{pivot:r,absolute:m}=n,{x:l}=r,{columns:c}=m,d=0,g=30,u=Eg(n);for(;i>0&&d!==o;){o=d;for(let C=t;C<=s+1;C+=g){let y=e([u-C*l/c,C]);y<a&&([a,d]=[y,C])}t=u+Math.sign(u)*g,s=t,i--}t=d-g,s=d+g;let p=5;for(i=5,o=Number.MAX_SAFE_INTEGER;i>0;){o=d;let C=(s-t)/(p-1);for(let y=t;y<=s+1;y+=C){let f=e([u-y*l/c,y]);f<a&&([a,d]=[f,y])}t=d-C,s=d+C,i--}return{ph0:u-d*l/c,ph1:d}}function Eg(e){let{pivot:t,absolute:s,phases:i,threshold:o}=e,{rows:a,columns:r}=s,m=new tt(a,r,{threshold:0}),l=new tt(a,r,{threshold:0}),{x:c,y:d}=t;for(let H=d-40;H<d+40;H++)for(let O=c-40;O<c+40;O++)m.set(H,O,s.get(H,O)),l.set(H,O,i.get(H,O));let g=No(m,l,o),u=-15,p=15,C=12,y=0,f=Number.MAX_SAFE_INTEGER,h=Number.MAX_SAFE_INTEGER,D=15;for(;C>0&&y!==f;){f=y;for(let H=u;H<p+1;H+=D){let O=g([H,0]);O<=h&&([h,y]=[O,H])}u=y+Math.sign(y)*D,p=u,C--}u=y-15,p=y+15;let b=5;for(C=5;C>0;){let H=(p-u)/(b-1);for(let O=u;O<=p;O+=H){let P=g([O,0]);P<h&&([h,y]=[P,O])}u=y-H,p=y+H,C--}let x=s.get(d,c),v=i.get(d,c);return x*Math.cos(v+y*I)<0?y-Math.sign(y)*180:y}function zg(e,n={}){let{re:t,im:s}=e,{transpose:i=!1}=n,o=i?new Ro(new et(t)):new et(t),a=i?new Ro(new et(s)):new et(s),{rows:r,columns:m}=o,l=kg({nbRows:r,nbColumns:m});for(let y=0;y<r;y++)for(let f=0;f<m;f++)l[y][f]=Math.hypot(o.get(y,f),a.get(y,f));let{threshold:c=new Ng(l).mean()*2}=n,d=new tt(l,{threshold:c}),g=new tt(d.rows,d.columns,{threshold:-1}),u=d.getNonZeros(),{columns:p,rows:C}=u;for(let y=0;y<C.length;y++){let[f,h]=[C[y],p[y]];g.set(f,h,Math.atan2(a.get(f,h),o.get(f,h)))}return{absolute:d,phases:g,threshold:c,nonZeros:u}}function No(e,n,t){let s=e.columns;return i=>{let[o,a]=[...i],r=0;return e.forEachNonZero((m,l,c)=>{let d=o+l*a/s,g=c*Math.cos(n.get(m,l)+d*I);return Math.abs(g)>=t&&(r+=1),c}),r}}import{reimMatrixPhaseCorrection as Bg}from"ml-spectra-processing";function Zt(e,n){ue(e);let{quad:t}=n;return t==="imag"?fe(e,{...n,applyPhaseCorrection:ko,keys:{re:"ir",im:"ii"}}):fe(e,{...n,applyPhaseCorrection:ko,keys:{re:"rr",im:"ri"}})}function ko(e,n){let{ph0:t,ph1:s,reverse:i=!0,inPlace:o=!0}=n;return Bg(e,t*I,s*I,{reverse:i,inPlace:o,direction:"columns"})}function Ut(e,n){let t=e,{horizontal:s,vertical:i}=n;return Io(s)&&(t=Qe(t,s)),Io(i)&&(t=Zt(t,i),t=Zt(t,{...i,quad:"imag"})),t}function Io(e){return e?e?.ph0!==0||e?.ph1!==0:!1}var Xg={updateXDomain:!1,updateYDomain:!1};function Lg(e,n){if(!qg(e,n))throw new Error("Phase correction is not applicable to raw data");let{data:t,filters:s}=e;if("horizontal"in n||"vertical"in n)e.data={...t,...Ut(t,n)};else{let i=Ao(t,n.automatic);e.data={...t,...Ut(t,i)};let 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ee={zeroFillingDimension1:Zo,zeroFillingDimension2:Jo,apodizationDimension1:Ni,apodizationDimension2:Ei,phaseCorrectionTwoDimensions:Eo,baselineCorrectionTwoDimensions:qi,digitalFilter2D:Ki,nusDimension2:jo,symmetrizeCosyLike:qo,fftDimension1:lo,fftDimension2:fo,blpDimension1:Zi,blpDimension2:Ji,flpDimension1:yo,flpDimension2:Ho,shift2DX:zo,shift2DY:Bo};function $o(e){let{data:n,info:t}=e,{minX:s,maxX:i,minY:o,maxY:a}=t.isFt?n.rr:n.re,r=Math.abs(i-s)/1e4,m=Math.abs(a-o)/1e4;return{x:r,y:m}}function _o(e,n,t){let s=e.x||{from:0,to:0},i=e.y||{from:0,to:0};if(!n.zones?.values)return!1;for(let{x:o,y:a}of n.zones.values)if(Math.abs(s.from-o.from)<t.x&&Math.abs(s.to-o.to)<t.x&&Math.abs(i.from-a.from)<t.y&&Math.abs(i.to-a.to)<t.y)return!0;return!1}function Ko(e){let n={x:0,y:0};if(e?.filters)for(let t of e.filters)t.name===ee.shift2DX.name&&(n.x=t?.enabled?t.value.shift:0),t.name===ee.shift2DY.name&&(n.y=t?.enabled?t.value.shift:0);return n}function gd(e,n,t){let{x:s,y:i}=e;if(n==="origin")return{...e,x:{...s,originalDelta:s.delta-t.x},y:{...i,originalDelta:i.delta-t.y}};if(s.originalDelta===void 0||i.originalDelta===void 0)throw new TypeError('originalDelta must exist when shiftTarget is "current"');return{...e,x:{...s,originalDelta:s.originalDelta,delta:s.originalDelta+t.x},y:{...i,originalDelta:i.originalDelta,delta:i.originalDelta+t.y}}}function dd(e,n,t){let{x:s,y:i}=e;return n==="origin"?{x:{...s,originalFrom:s.from-t.x,originalTo:s.to-t.x},y:{...i,originalFrom:i.from-t.y,originalTo:i.to-t.y}}:{x:{...s,from:(s?.originalFrom||0)+t.x,to:(s?.originalTo||0)+t.x},y:{...i,from:(i?.originalFrom||0)+t.y,to:(i?.originalTo||0)+t.y}}}function ud(e,n,t){let{x:s,y:i,originalX:o=0,originalY:a=0}=e;return n==="origin"?{...e,originalX:s-t.x,originalY:i-t.y}:{...e,x:o+t.x,y:a+t.y}}function Qo(e,n,t={}){let{checkIsExisting:s=!0,shiftTarget:i="origin"}=t,o=Ko(n),a=$o(n);return s&&(e=e.filter(r=>!_o(r,n,a))),e.map(r=>{r.x=r.x||{from:0,to:0},r.y=r.y||{from:0,to:0};let m=r.signals.map(l=>{let{id:c,kind:d}=l,g;return l.peaks&&(g=l.peaks.map(u=>{let p=ud(u,i,o);return{...u,...p,id:u.id||crypto.randomUUID()}})),{...gd(l,i,o),peaks:g,id:c||crypto.randomUUID(),kind:Q(d)}});return{...r,id:r.id||crypto.randomUUID(),...dd(r,i,o),signals:m,kind:Q(r.kind??m[0]?.kind)}})}import{WrapperMatrix2D as yd}from"ml-matrix";import{xBoxPlot as ea}from"ml-spectra-processing";import{color as fd}from"d3-color";import{interpolateRgbBasis as pd}from"d3-interpolate";import{xMinMaxValues as Cd}from"ml-spectra-processing";function nt(e,n){let{minMax:t=Cd(e),colors:s=["blue","cyan","yellow","red"]}=n,{min:i,max:o}=t,a=1/(o-i),r=[],m=pd(s);for(let l of e)r.push(fd(m((l-i)*a))?.formatHex());return r}function f6(e,n={}){let t=new yd(e),s=bd(t),i=Object.keys(s);for(let o=1;o<t.columns;o++){let a=ea(t.getColumn(o));for(let r of 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n=ta(e);if(!n)throw new Error(`multiplet ${e} is not supported`);let{value:t,label:s}=n;return e===s?t:s}import{addMissingShape as Sd}from"ml-gsd";import{getShape1D as vd}from"ml-peak-shape-generator";import{generateSpectrum as xd}from"spectrum-generator";function na(e,n){return n in e}function st(e,n){let{frequency:t,convertTo:s,output:i=structuredClone(e)}=n,o=Hd(s,t);for(let a of i)if(a.width=o(a.width),na(a,"shape")){let r=a.shape;r.fwhm&&(r.fwhm=o(r.fwhm))}return i}function Hd(e,n){switch(e){case"ppm":return t=>t/n;case"hz":return t=>t*n;default:throw new Error(`Does not support convert to ${e}`)}}function pe(e,n){return st(e,{...n,convertTo:"ppm"})}function sa(e,n){let{frequency:t,nbPoints:s=1024,shape:i}=n;if(!t)throw new Error("frequency is mandatory");let o=pe(e,{frequency:t});return xd(o,{generator:{...Od(o,n),nbPoints:s,shape:i}})}function Od(e,n){if("to"in n&&"from"in n)return{from:n.from,to:n.to};e.sort((r,m)=>r.x-m.x);let t=e[0],s=e.at(-1),{frequency:i,from:o=t.x-t.width*2/i,to:a=s.x+s.width*2/i}=n;return{from:o,to:a}}function X6(e,n){let t=Sd([e])[0],s=vd(t.shape).getFactor(),{frequency:i,from:o=t.x-e.width*s/i,to:a=t.x+e.width*s/i}=n;return sa([e],{...n,from:o,to:a})}import{xSequentialFillFromTo as Pd}from"ml-spectra-processing";function ia(e,n){let{from:t=0,to:s=10,nbPoints:i=1024,frequency:o=400,t2Relaxation:a=new Float64Array(e.length).fill(100)}=n,r=new Float64Array(i),m=new Float64Array(i),l=(s+t)/2,c=Math.abs(s-t),d=i/(c*o),g=Pd({size:i,from:0,to:d}),u=Math.PI*2;for(let p=0;p<e.length;p++){let{x:C,y}=e[p],f=a[p]*.001,h=u*o*(C-l);for(let D=0;D<i;D++)r[D]+=y*Math.exp(-g[D]/f)*Math.cos(h*g[D]),m[D]+=y*Math.exp(-g[D]/f)*Math.sin(h*g[D])}return{re:r,im:m}}import{linearSumAssignment as ra}from"linear-sum-assignment";import{Matrix as Fd}from"ml-matrix";import{gaussianFct as jd}from"ml-peak-shape-generator";import{xFindClosestIndex as oa,xMaxValue as la}from"ml-spectra-processing";function ma(e,n,t={}){let s=structuredClone(e);s.sort((r,m)=>r.x-m.x);let i=s.map(r=>r.x),{markSolventPeaks:o=!1,solventZoneExtension:a=1.2}=t;for(let r of n){let m=r.peaks||Md(r);m.sort((O,P)=>O.x-P.x);let l=oa(i,m.at(-1).x+a),c=oa(i,m[0].x-a),d=s.filter((O,P)=>P>=c&&P<=l),g=[],u=[],p=[];for(let O of d){let{peaks:P,delta:j}=aa(O,r,m),F=Rd(P,d),R=0,w=0,M=0;for(let A=0;A<F.length;A++)w+=Math.abs(P[A].y-F[A].y),R+=Math.abs(P[A].x-F[A].x);F.length===0?(R=Number.MAX_SAFE_INTEGER,w=Number.MAX_SAFE_INTEGER,M=Number.MAX_SAFE_INTEGER):M=jd(Math.abs(r.delta-j),.5),g.push(w),u.push(R),p.push(M)}let[C,y,f]=[g,u,p].map(O=>{let P=la(O);return P===0?1:P}),h=-1,D=Number.MAX_SAFE_INTEGER,b=[];for(let O=0;O<u.length;O++){let P=(g[O]/C+u[O]/y+1-p[O]/f)/3;b.push(P),D>P&&(h=O,D=P)}if(D<0||h<0)return s;let{peaks:x}=aa(d[h],r,m),v=ca(x,d),{rowAssignments:S,gain:H}=ra(v,{maximaze:!1});if(H<0)return s;if(o)for(let O of S)s[O+c].kind="residualSolvent";else{S.sort((O,P)=>P-O);for(let O of S)s.splice(O+c,1)}}return 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qa=[{names:["CD2Cl2"],smiles:"[2H]C([2H])(Cl)Cl",ranges:[{signals:[{delta:53.5,assignment:"CD2",js:[{spin:1,nbCouplings:2,coupling:27.6}]}],from:53.73,to:54.73}],nucleus:"13C",solvent:"cd2cl2"},{names:["CDCl3"],smiles:"[2H]C(Cl)(Cl)Cl",ranges:[{signals:[{delta:77,assignment:"CD",js:[{spin:1,nbCouplings:1,coupling:32.2}]}],from:76.58,to:77.45}],nucleus:"13C",solvent:"cdcl3"},{names:["DMSO-d6"],smiles:"C([2H])([2H])([2H])S(=O)C([2H])([2H])[2H]",ranges:[{signals:[{delta:40,assignment:"CD3",js:[{spin:1,nbCouplings:3,coupling:21}]}],from:39.15,to:40.78}],nucleus:"13C",solvent:"dmso"},{names:["C6H6","Benzene"],smiles:"",ranges:[{signals:[{delta:127.7,assignment:"CD",js:[{spin:1,nbCouplings:1,coupling:24.26}]}],from:127.45,to:127.92}],nucleus:"13C",solvent:"c6h6"}];function lf(e,n){let{frequency:t,solventFeatures:s,tolerance:i=.1,minScore:o=.99}=n,{delta:a,js:r}=s.ranges[0].signals[0],m=ff(r[0],t),l=e.map(gf),c=cf(l,m,{delta:a,minScore:o,tolerance:i});if(c.length>0)for(let d of 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o){i[a]||(i[a]=[]);let r=i[a];for(let{signals:m=[]}of t)for(let l of m){let{delta:c,assignment:d="",js:g=[],multiplicity:u=""}=l;r.push({shift:c,proton:d,coupling:g.length>0?g[0].coupling:0,multiplicity:u})}}}var yf=["water"];function Ua(e,n={}){let{error:t=.025,solvent:s,frequency:i=400}=n,o=structuredClone(e),a=hf(s);if(!a)return o;for(let r=o.length-1;r>=0;r--){let m=o[r];bf({...m,width:m.width/i},a,t)&&(o[r].kind="impurity")}return o}function bf(e,n,t){let s=t+e.width;for(let i of yf){let o=n[i];for(let a of o)if(Math.abs(a.shift-e.x)<s)return!0}return!1}function hf(e=""){if(!e)return null;let n=e.toLocaleLowerCase();return n==="(cd3)2so"&&(n="dmso"),n==="meod"&&(n="cd3od"),he[n]?he[n]:null}function Va(e,n){let{impurities:t={},peakPicking:s,ranges:i={},identifyImpurities:o=!1}=n,{frequency:a}=s,{solvent:r}=t,m=$(e,s);return o&&(m=Ua(m,{...t,frequency:a})),be(e,m,{compile:!0,solvent:r,...i})}function Dh(e,n){let{from:t,to:s,sgOptions:i}=n.peakPicking,{fromIndex:o,toIndex:a}=Df(e.x,{from:t,to:s}),r=i?.windowSize??7;if(a-o<=r)return n.logger?.info("Too small window for accurate multiplicity determination"),[{from:e.x[o],to:e.x[a],signals:[{delta:Hf(e,{fromIndex:o,toIndex:a}).x,multiplicity:"",js:[]}]}];let{ranges:m={}}=n,{nucleus:l=""}=m;switch(l){case"1H":return Va(e,n);case"13C":return Wa(e,n);default:return Za(e,n)}}import{BaseRegression as xf}from"ml-regression-base";import{SimpleLinearRegression as Of}from"ml-regression-simple-linear";import{xyCheck as Sf}from"ml-spectra-processing";function vh(e,n){Sf(e,{minLength:2});let{x:t,y:s}=e,{gyromagneticRatio:i,gradientPulseDuration:o,timeCorrection:a}=n,r=new Float64Array(t.length),m=new Float64Array(t.length);for(let p=0;p<t.length;p++)r[p]=Math.log(s[p]),m[p]=t[p]**2;let l=new Of(m,r),{slope:c,intercept:d}=l.toJSON(),g=-c/a/(i*o)**2,u=Math.exp(d);return{regression:new Qt(g,u,n),coefficient:g,signalAbsenseDiffussion:u}}var Qt=class extends xf{coefficient;signalAbsenseDiffussion;gyromagneticRatio;gradientPulseDuration;timeCorrection;constructor(n,t,s){let{gyromagneticRatio:i,gradientPulseDuration:o,timeCorrection:a}=s;super(),this.coefficient=n,this.signalAbsenseDiffussion=t,this.gyromagneticRatio=i,this.gradientPulseDuration=o,this.timeCorrection=a}_predict(n){return this.signalAbsenseDiffussion*Math.exp(-this.timeCorrection*this.coefficient*(n*this.gyromagneticRatio*this.gradientPulseDuration)**2)}};import{levenbergMarquardt as vf}from"ml-levenberg-marquardt";import{BaseRegression as Pf}from"ml-regression-base";import{xyCheck as Ff}from"ml-spectra-processing";var jf={damping:1.5,maxIterations:100,errorTolerance:1e-8};function Rh(e,n={}){Ff(e,{minLength:2});let{optimization:t={}}=n,{options:s={},shapeFunc:i=Mf}=t,{x:o,y:a}=e,r=o.length-1,m=o[r],l=a[r],c=[a[0]-a[0]*.5,0],d=[l+l*.5,m],g=[l,(c[1]+d[1])*.5],u=vf(e,i,{initialValues:g,minValues:c,maxValues:d,...jf,...s}),[p,C]=u.parameterValues;return{relaxationT1:C,fullMagnetization:p,regression:new en(p,C)}}function Mf(e){let[n,t]=e;return s=>n*(1-2*Math.exp(-s/t))}var en=class extends Pf{fullMagnetization;relaxationT1;constructor(n,t){super(),this.relaxationT1=t,this.fullMagnetization=n}_predict(n){return this.fullMagnetization*(1-2*Math.exp(-n/this.relaxationT1))}};import{ExponentialRegression as Rf}from"ml-regression-exponential";import{xyCheck as wf}from"ml-spectra-processing";function kh(e){wf(e,{minLength:2});let{x:n,y:t}=e,s=new Rf(n,t),{A:i,B:o}=s.toJSON();return{regression:s,rateConstant:i,initialConcentration:o}}import{optimizePeaks as Af}from"ml-gsd";function Bh(e,n,t){let{frequency:s}=t,i=pe(n,{frequency:s}),o=Af(e,i,t);return ye(o,{frequency:s,output:o})}import{optimizePeaks as Nf}from"ml-gsd";var Ga=[{groupingFactor:10,optimization:{kind:"lm",options:{maxIterations:20,errorTolerance:.001}},parameters:{fwhm:{optimize:!0,min:e=>(e.shape?.fwhm??0)/2,max:e=>(e.shape?.fwhm??0)*2},mu:{optimize:!1},x:{optimize:!1},y:{optimize:!0,init:e=>e.y*.8}}},{groupingFactor:10,optimization:{kind:"lm",options:{maxIterations:20,errorTolerance:5e-4}},parameters:{fwhm:{optimize:!0,min:e=>(e.shape?.fwhm??0)/2,max:e=>(e.shape?.fwhm??0)*2},mu:{optimize:!1},x:{optimize:!1},y:{optimize:!0}}},{groupingFactor:10,optimization:{kind:"lm",options:{maxIterations:20,errorTolerance:1e-5}},parameters:{fwhm:{optimize:!0,min:e=>(e.shape?.fwhm??0)/2,max:e=>(e.shape?.fwhm??0)*2},mu:{optimize:!0},x:{optimize:!1},y:{optimize:!0}}},{groupingFactor:10,optimization:{kind:"lm",options:{maxIterations:20,errorTolerance:5e-4}},parameters:{fwhm:{optimize:!0,min:e=>(e.shape?.fwhm??0)/3,max:e=>(e.shape?.fwhm??0)*3},mu:{optimize:!0},x:{optimize:!0},y:{optimize:!0}}},{groupingFactor:10,optimization:{kind:"lm",options:{maxIterations:20,errorTolerance:1e-4}},parameters:{fwhm:{optimize:!0,min:e=>(e.shape?.fwhm??0)/2,max:e=>(e.shape?.fwhm??0)*2},mu:{optimize:!1},x:{optimize:!0},y:{optimize:!0}}},{groupingFactor:10,optimization:{kind:"lm",options:{maxIterations:20,errorTolerance:1e-8}},parameters:{fwhm:{optimize:!0,min:e=>(e.shape?.fwhm??0)/2,max:e=>(e.shape?.fwhm??0)*2},mu:{optimize:!0},x:{optimize:!0},y:{optimize:!0}}}];function 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o9(e,n){let{enabled:t,id:s,logger:i}=n;e.filters=e.filters.slice(0).map(o=>({...o,enabled:o.id===s?t??!o.enabled:o.enabled})),we(e,{logger:i})}function a9(e,n,t){let s=e.filters.find(i=>i.id===n);e.filters=e.filters.slice(0).filter(i=>i.id!==n),!(s&&!s.enabled)&&we(e,{logger:t})}function yr(e,n,t={}){let{filterIndex:s}=t,i=crypto.randomUUID(),o={...n,id:i,enabled:!0};typeof s=="number"&&s!==-1?e.filters=[...e.filters.slice(0,s+1),o,...e.filters.slice(s+1)]:e.filters.push(o)}function pt(e,n,t){let{name:s,value:i}=n,o=Date.now();ee[s].apply(e,i);let a=Date.now()-o;t?.debug(`Filter: ${s} takes ${a} ms`)}export{ce as Filters1D,ur as Filters1DManager,ee as Filters2D,hr as Filters2DManager,_ as MultiplicityPatterns,ji as RangeUtilities,$t as XYAutoPeaksPickingWindowSizeError,wt as apodizationXReIm,z as apodize,kn as calculateRelativeFrequency,i5 as carbonImpurities,Et as checkIntegralKind,x6 as checkMultiplicity,Xe as couplingACSPatterns,Mt as couplingPatterns,ne as 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signalJoinCouplings,Kl as signalKindLabelMapping,Be as signalKindsToInclude,Je as signalMultiplicityPattern,Nn as signals2DToZ,m7 as signalsJoin,p7 as signalsToFID,b7 as signalsToRanges,Te as signalsToXY,Mn as simulate1D,ma as solventSuppression,ae as splitPatterns,F6 as translateMultiplet,Fi as updateIntegralsRelativeValues,Ri as updateRanges,Mi as updateRangesRelativeValues,j7 as xBackwardLinearPrediction,Js as xForwardLinearPrediction,A7 as xreimMultipletAnalysis,li as xreimTrim,$ as xyAutoPeaksPicking,Dh as xyAutoRangesPicking,ks as xyBaselineCalculation,vh as xyCalculateDiffussionCoefficient,Rh as xyCalculateT1,$h as xyGetPivot,kh as xyKineticFirstOrder,Bh as xyPeaksOptimization,Uh as xyPeaksOptimizationByStages,Ao as xyzAutoPhaseCorrection,or as xyzAutoSignalsPicking,CD as xyzAutoZonesPicking,Ut as xyzPhaseCorrection,hD as xyzZoneIntegration,gt as xyzZonesIntegration};
+var Dr=Object.defineProperty;var yt=(e,n)=>{for(var t in n)Dr(e,t,{get:n[t],enumerable:!0})};export*from"gyromagnetic-ratio";import{xEnsureFloat64 as Hr}from"ml-spectra-processing";function z(e,n){let{windowData:t,output:s=new Float64Array(e)}=n,i=s.length;if(i!==t.length)throw new RangeError("window function and data should have the same length");for(let o=0;o<i;o++)s[o]*=t[o];return Hr(s)}import{xDivide as xr,xMaxValue as Or}from"ml-spectra-processing";function an(e,n){let t=new Float64Array(n);for(let s=0;s<n;s++)t[s]=e(s);return t}function rn(e,n){let{dw:t}=n,{lineBroadening:s}=e,i=-s*Math.PI*t;return o=>Math.exp(i*o)}function ln(e,n){let{dw:t,length:s}=n,{lineBroadening:i,lineBroadeningCenter:o}=e;if(o>1||o<0)throw new Error("The lineBroadeningCenter of gaussian shape should be inside of the window function: 0 - 1");let a=Math.PI*i*t,r=o*(s-1);return m=>Math.exp(-1*((r-m)*a)**2)}function mn(e,n){return bt({exponent:1,...e},n)}function 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b=D.pathInfo;if(b.paths.length===0||!C.x[b.oclID])continue;let x=b.paths;for(let v of x){if(!C.y[l[v.to].oclID])continue;let S={x:b,y:l[v.to]},H=`${S.x.oclID}-${S.y.oclID}`;if(H===`${b.oclID}-${b.oclID}`||y[H])continue;let O={id:crypto.randomUUID(),x:0,y:0,z:100},P={id:crypto.randomUUID(),x:{delta:0,diaIDs:[],atoms:[]},y:{delta:0,diaIDs:[],atoms:[]},peaks:[]};for(let j of["x","y"]){let F=S[j].oclID;O[j]=C[j][F].delta,P[j].delta=C[j][F].delta,P[j].diaIDs=[F];let{atoms:R}=C[j][F];R&&(P[j].atoms=R)}P.peaks=[O],y[H]=P}}r&&Rr(y,{paths:l,signalsByDiaID:C});let f=Object.values(y),h=wr(f,{joinDistance:m,from:t,to:s});return{nuclei:fn({from:t,to:s}),joinedSignals:f,signals:Mr(f),zones:h}}function jr(e,n){let{fromLabel:t,toLabel:s,minLength:i,maxLength:o=Number.MAX_SAFE_INTEGER}=n,a=e.diaIDs,r=e.moleculeWithH,m=e.distanceMatrix,l=pn.getAtomicNoFromLabel(t),c=pn.getAtomicNoFromLabel(s),d=[];for(let g=0;g<r.getAllAtoms();g++){let u={oclID:a[g],paths:[]};for(let 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c=Math.hypot(t[s]/(r-a),t[i]/(l-m)),d=vr(o.to2DArray(),{method:"centroid"}),g=Cn([d],c),u=[];for(let p of g){let C=[];p.isLeaf&&C.push(e[p.index]);for(let y of p.children)for(let f of y.indices())C.push(e[f]);u.push({id:crypto.randomUUID(),...Ar(C,{joinDistance:t,from:s,to:i}),signals:C})}return u}function Ar(e,n){let{joinDistance:t,from:s,to:i}=n,o=Number.MAX_SAFE_INTEGER,a=Number.MAX_SAFE_INTEGER,r=Number.MIN_SAFE_INTEGER,m=Number.MIN_SAFE_INTEGER;for(let l of e)l.x.delta<o&&(o=l.x.delta),l.x.delta>r&&(r=l.x.delta),l.y.delta<a&&(a=l.y.delta),l.y.delta>m&&(m=l.y.delta);return{x:{from:o-t[s],to:r+t[s]},y:{from:a-t[i],to:m+t[i]}}}function Cn(e,n){let t=e.length;for(let s=0;s<e.length;s++){let i=e[s];i.height>n&&(e.push(...i.children),e.splice(s--,1))}return e.length<t?Cn(e,n):e}async function yn(e,n){let{minLength:t,maxLength:s,predictions:{H:i},includeDiagonal:o=!0,minCoupling:a=1.5}=n;if(!i)throw new Error("prediction is not availaible");let r={...n,from:"H",to:"H",includeDiagonal:o};return(!t||!s)&&(r.correlationPaths=kr(e,i,a)),se(e,r)}function kr(e,n,t){let s=e.diaIDs,i=[],o={},a=n.signals;for(let l of a){let c=l.diaIDs[0];o[c]??={};for(let d of l.js){if(!d.diaIDs||d.diaIDs.length===0)throw new Error("should contains assigned coupling by atoms");let g=d.diaIDs[0];o[c][g]=Math.max(d.coupling,o[c][g]??Number.MIN_SAFE_INTEGER)}}let r=e.moleculeWithH,m=Nr.getAtomicNoFromLabel("H");for(let l=0;l<r.getAllAtoms();l++){let c={oclID:s[l],paths:[]};for(let d=0;d<r.getAllAtoms();d++)l!==d&&r.getAtomicNo(d)===m&&r.getAtomicNo(l)===m&&o[s[l]]?.[s[d]]>=t&&c.paths.push({from:l,to:d});i.push(c)}return i}function bn(e,n){async function t(s){let i=await fetch(n,{headers:{accept:"application/json","content-type":"application/json"},method:"POST",body:JSON.stringify({molfile:s.toMolfile({version:3})})});if(i.status!==200){let a=await i.text();throw new Error(`${i.statusText}: ${a}`)}let{data:o}=await i.json();return{nucleus:o.nucleus,joinedSignals:o.joinedSignals??[],signals:o.signals??[],ranges:o.ranges??[]}}return Object.defineProperty(t,"name",{value:`default${e[0].toUpperCase()}${e.slice(1)}Predictor`}),t}var hn=bn("proton","https://nmr-prediction.service.zakodium.com/v1/predict/proton"),Dn=bn("carbon","https://nmr-prediction.service.zakodium.com/v1/predict/carbon");async function Ae(e,n,t){let{cache:s,predictorOptions:i}=t;if(typeof s=="function"){let a=await s(e);if(a)return a}let o=await n(e,i);return typeof s=="function"&&await s(e,o),o}async function Hn(e,n={}){let{predictor:t=Dn,predictorOptions:s={},cache:i}=n;return e.molecule.getAllAtoms()===0?{nucleus:"13C",joinedSignals:[],signals:[],ranges:[]}:Ae(e,t,{cache:i,predictorOptions:s})}async function xn(e,n){let{minLength:t=2,maxLength:s=3,joinDistance:i}=n;return se(e,{...n,from:"H",to:"C",minLength:t,maxLength:s,joinDistance:i})}async function On(e,n){let{minLength:t=1,maxLength:s=1,joinDistance:i}=n;return se(e,{...n,from:"H",to:"C",minLength:t,maxLength:s,joinDistance:i})}async function Sn(e,n={}){let{predictor:t=hn,cache:s,predictorOptions:i={}}=n;return e.molecule.getAllAtoms()===0?{nucleus:"1H",joinedSignals:[],signals:[],ranges:[]}:Ae(e,t,{cache:s,predictorOptions:i})}function ht(e,n){if(e in n)return!0;let t="hsqc"in n||"hmbc"in n;return e==="C"?t:e==="H"?t||"cosy"in n:!1}var Tr={cosy:{predictor:yn,required:["H"],message:"Proton prediction is missing so COSY could not be generated."},hsqc:{predictor:On,required:["H","C"],message:"Carbon and / or proton prediction is missing so HSQC could not be generated."},hmbc:{predictor:xn,required:["H","C"],message:"Carbon and / or proton prediction is missing so HMBC could not be generated."}};async function Y(e,n={}){let{logger:t,joinDistance:s={H:.05,C:.5},predictOptions:i={H:{},C:{},hsqc:{},hmbc:{},cosy:{}}}=n,o=new Ir(e),a=ht("H",i)?await Sn(o,{...i?.H}):void 0,r=ht("C",i)?await Hn(o,i?.C):void 0,m={},l=o.diaIDs,c={};vn(a,l)&&(c.H=a,"H"in i&&(m.proton=a)),vn(r,l)&&(c.C=r,"C"in i&&(m.carbon=r));let g=["cosy","hsqc","hmbc"].filter(p=>p in i).map(async p=>{let{predictor:C,required:y,message:f}=Tr[p];if(y.every(h=>h in c)){let h=await C(o,{predictions:c,...i[p],joinDistance:s});return{key:p,result:h}}else t&&t.warn(f);return{key:p,result:void 0}}),u=await Promise.all(g);for(let{key:p,result:C}of u)C&&(m[p]=C);return{diaIDs:o.diaIDs,hoses:o.hoseCodes,distanceMatrix:o.distanceMatrix,moleculeWithHydrogens:o.moleculeWithH,groupedDiaIDs:o.getGroupedDiastereotopicAtomIDs()||[],molfile:o.toMolfile(),molfileWithH:o.toMolfileWithH(),spectra:m}}function vn(e,n=[]){if(!e||e.ranges.length===0)return!1;let{signals:t}=e;for(let s of t)if(!s.diaIDs?.every(o=>n.includes(o)))return!1;return!0}import{xIsMonotonic as ml,xRescale as cl,xSequentialFillFromTo as gl}from"ml-spectra-processing";var _=[{label:"singlet",value:"s",multiplicity:1,names:[]},{label:"doublet",value:"d",multiplicity:2,names:[]},{label:"triplet",value:"t",multiplicity:3,names:[]},{label:"quartet",value:"q",multiplicity:4,names:[]},{label:"quintet",value:"i",acs:"quint",multiplicity:5,names:["quint","qui","qnt","pentet","pnt","pent"]},{label:"sextet",value:"h",multiplicity:6,names:["x","sxt","sext","hexuplet","hex"]},{label:"septet",value:"p",acs:"sept",multiplicity:7,names:["sept","spt","heptet","hpt","hept"]},{label:"octet",value:"o",multiplicity:8,names:["oct"]},{label:"nonet",value:"n",multiplicity:9,names:["non"]},{label:"multiplet",value:"m",multiplicity:null,names:["massive"]}];var Dt={};for(let{value:e,multiplicity:n,names:t}of _){n&&(Dt[e]=n-1);for(let s of t)n&&(Dt[s]=n-1)}var X=Dt;function ie(e){let n=structuredClone(e),t=e.reduce((s,i)=>{let{atoms:o=[]}=i;return Math.max(...o,s)},0)+1;for(let[s,i]of 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t=0;t<e.rows;t++)for(let s=t;s<e.columns;s++)e.get(t,s)===0&&(n.set(t,s,0),n.set(s,t,0));return n}function qr(e){for(let n of e){if(!n.js)throw new Error("there is not js");if(!n.atoms)throw new Error("there is not atoms");for(let t of n.js)if(!t.atoms)throw new Error("there is not atoms")}}function W(e){qr(e);let n=e.length,t=[],s=Lr.zeros(n,n),i={};for(let o=0;o<n;o++){t.push(e[o].delta);let a=e[o].atoms[0];i[a]=o}for(let o=0;o<n;o++){let{atoms:a,js:r}=e[o],m=a[0];for(let l of r){let{coupling:c,atoms:d}=l,g=d[0];s.set(i[m],i[g],c),s.set(i[g],i[m],c)}}return L({couplingConstants:s,chemicalShifts:t})}import{generateSpectrum as il}from"spectrum-generator";import Vr from"binary-search";import{EVD as Gr,Matrix as Jr}from"ml-matrix";import{SparseMatrix as ke}from"ml-sparse-matrix";import{SparseMatrix as Yr}from"ml-sparse-matrix";function Pn(e,n){let t=2*e*n,s=new Yr(t,t,{initialCapacity:2*e*n});for(let i=0;i<e;i++){let o=2*i*n,a=2*i*n;for(let r=0;r<n;r++)s.set(o+n+r,a+r,1)}return s}import{SparseMatrix as Wr}from"ml-sparse-matrix";function xt(e,n){let t=2*e*n,s=new Wr(t,t,{initialCapacity:2*e*n});for(let i=0;i<e;i++){let o=2*i*n,a=2*i*n;for(let r=0;r<n;r++)s.set(o+r,a+n+r,.5),s.set(o+n+r,a+r,.5)}return s}import{SparseMatrix as Zr}from"ml-sparse-matrix";function Ot(e,n){let t=2*e*n,s=new Zr(t,t,{initialCapacity:2*e*n});for(let i=0;i<e;i++){let o=2*i*n,a=2*i*n;for(let r=0;r<n;r++)s.set(o+r,a+n+r,-.5),s.set(o+n+r,a+r,.5)}return s}import{SparseMatrix as Ur}from"ml-sparse-matrix";function Ne(e,n){let t=2*e*n,s=new Ur(t,t,{initialCapacity:2*e*n});for(let i=0;i<e;i++){let o=2*i*n,a=o+n;for(let r=0;r<n;r++)s.set(o+r,o+r,.5),s.set(a+r,a+r,-.5)}return s}var St=.01;function Fn(e,n={}){let{lineWidth:t=1,maxClusterSize:s=8,frequency:i=400}=n,o=L(e),a=o.chemicalShifts.slice();for(let l=0;l<a.length;l++)a[l]=a[l]*i;let r=o.levels,m=[];for(let l of o.clusters){let c=l.map(y=>y<0?-y-1:y),d=1,g=0,u=[],p=[];if(l.length>s){let y=0;for(;l[y++]<0;);y=l[y-1],u.push(-a[y]);for(let f=0;f<l.length;f++)if(l[f]<0){let h=o.couplingConstants.get(y,c[f])/2,D=u.length;for(let b=0;b<D;b++)u.push(u[b]+h),u[b]-=h}u.sort((f,h)=>f-h),g=u.length,d=1;for(let f=0;f<g;f++)p.push(1)}else{let y=_r(a,o.couplingConstants,r,o.connectivity,c),f=y.rows,h=new Gr(y),D=h.eigenvectorMatrix,b=h.realEigenvalues,x=new ke(f,f),v=l.length;d=0;for(let F=0;F<v;F++){let R={rows:2**F},w={rows:2**(v-F-1)},M=Pn(R.rows,w.rows);l[F]>=0?(x.add(M.mul(l[F]+1)),d++):x.add(M.mul(l[F]))}let S=Jr.zeros(f,f);x.forEachNonZero((F,R,w)=>{if(w>0)for(let M=0;M<D.columns;M++){let A=D.get(R,M);A!==0&&S.set(F,M,S.get(F,M)+A)}return w});let H=S.clone();x.forEachNonZero((F,R,w)=>{if(w<0)for(let M=0;M<D.columns;M++){let A=D.get(R,M);A!==0&&H.set(F,M,H.get(F,M)+A)}return w});let O=D.transpose();S=O.mmul(S);let P=new ke(S.to2DArray(),{threshold:St});H=O.mmul(H);let j=new ke(H.to2DArray(),{threshold:St});j.forEachNonZero((F,R,w)=>w),$r(j,St),j.forEachNonZero((F,R,w)=>{let M=P.get(F,R);M=Math.min(Math.abs(M),Math.abs(w)),M*=M,g+=M;let A=b[F]-b[R],N=Vr(u,A,(k,De)=>k-De);return N<0?(u.splice(-1-N,0,A),p.splice(-1-N,0,M)):p[N]+=M,w})}let C=u.length;if(C>0){d/=g;let y=t/64,f=u[0],h=p[0],D=1;for(let b=1;b<C;b++)Math.abs(u[b]-f/D)<y?(h+=p[b],f+=u[b],D++):(m.push({x:-f/D/i,y:h*d}),f=u[b],h=p[b],D=1);m.push({x:-f/D/i,y:h*d})}}return m.filter(l=>l.x<1e3)}function $r(e,n){e.forEachNonZero((t,s,i)=>Math.abs(i)<=n?0:i)}function _r(e,n,t,s,i){let o=1;for(let r of i)o*=t[r];let a=new ke(o,o);for(let r=0;r<i.length;r++){let m=i[r],l={rows:2**r},c={rows:2**(i.length-r-1)},d=e[m],g=Ne(l.rows,c.rows);a.add(g.mul(d));for(let u=0;u<i.length;u++){let p=i[u];if(s.get(m,p)===1){let C={rows:2**u},y={rows:2**(i.length-u-1)},f=xt(l.rows,c.rows).mmul(xt(C.rows,y.rows));f.add(Ot(l.rows,c.rows).mul(-1).mmul(Ot(C.rows,y.rows))),f.add(Ne(l.rows,c.rows).mmul(Ne(C.rows,y.rows))),a.add(f.mul(n.get(m,p)/2))}}}return a}import el from"binary-search";import{EVD as tl,Matrix as nl}from"ml-matrix";import{SparseMatrix as q}from"ml-sparse-matrix";import{SparseMatrix as Kr}from"ml-sparse-matrix";function jn(e){let n=(e-1)/2,t=[],s=[];for(let l=0;l<e;l++)t.push(e-1-l-n),s.push(Math.sqrt(n*(n+1)-t[l]*(t[l]+1)));let i=vt(s,1,e,e);for(let l=0;l<e;l++)s[l]=Math.sqrt(n*(n+1)-t[l]*(t[l]-1));let o=vt(s,-1,e,e),a=i.clone().add(o).mul(.5),r=o.clone().mul(-1).add(i).mul(-.5),m=vt(t,0,e,e);return{x:a,y:r,z:m,m:o,p:i}}function vt(e,n,t,s){let i=new Kr(t,s,{initialCapacity:20});for(let o=0;o<e.length;o++)o-n>=0&&o-n<t&&o<s&&i.set(o-n,o,e[o]);return i}var Qr=jn(2);function Oe(e){return e===2?Qr:jn(e)}var Ie=.01;function Z(e,n={}){let{lineWidth:t=1,maxClusterSize:s=8,frequency:i=400}=n,o=L(e),a=o.chemicalShifts.slice();for(let l=0;l<a.length;l++)a[l]=a[l]*i;let r=o.levels,m=[];for(let l of o.clusters){let c=l.map(y=>y<0?-y-1:y),d=1,g=0,u=[],p=[];if(l.length>s){let y=0;for(;l[y++]<0;);y=l[y-1],u.push(-a[y]);for(let f=0;f<l.length;f++)if(l[f]<0){let h=o.couplingConstants.get(y,c[f])/2,D=u.length;for(let b=0;b<D;b++)u.push(u[b]+h),u[b]-=h}u.sort((f,h)=>f-h),g=u.length,d=1;for(let f=0;f<g;f++)p.push(1)}else{let y=sl(a,o.couplingConstants,r,o.connectivity,c),f=y.rows,h=new tl(y),D=h.eigenvectorMatrix,b=h.realEigenvalues,x=new q(f,f),v=l.length;d=0;for(let F=0;F<v;F++){let R=Oe(r[c[F]]),w=1;for(let k=0;k<F;k++)w*=r[c[k]];let M=q.eye(w);w=1;for(let k=F+1;k<v;k++)w*=r[c[k]];let A=q.eye(w),N=M.kroneckerProduct(R.m).kroneckerProduct(A);l[F]>=0?(x.add(N.mul(l[F]+1)),d++):x.add(N.mul(l[F]))}let S=nl.zeros(f,f);x.forEachNonZero((F,R,w)=>{if(w>0)for(let M=0;M<D.columns;M++){let A=D.get(R,M);A!==0&&S.set(F,M,S.get(F,M)+A)}return w});let H=S.clone();x.forEachNonZero((F,R,w)=>{if(w<0)for(let M=0;M<D.columns;M++){let A=D.get(R,M);A!==0&&H.set(F,M,H.get(F,M)+A)}return w});let O=D.transpose();S=O.mmul(S);let P=new q(S.to2DArray(),{threshold:Ie});Mn(P,Ie),H=O.mmul(H);let j=new q(H.to2DArray(),{threshold:Ie});j.forEachNonZero((F,R,w)=>w),Mn(j,Ie),j.forEachNonZero((F,R,w)=>{let M=S.get(F,R);M=Math.min(Math.abs(M),Math.abs(w)),M*=M,g+=M;let A=b[F]-b[R],N=el(u,A,(k,De)=>k-De);return N<0?(u.splice(-1-N,0,A),p.splice(-1-N,0,M)):p[N]+=M,w})}let C=u.length;if(C>0){d/=g;let y=t/64,f=u[0],h=p[0],D=1;for(let b=1;b<C;b++)Math.abs(u[b]-f/D)<y?(h+=p[b],f+=u[b],D++):(m.push({x:-f/D/i,y:h*d}),f=u[b],h=p[b],D=1);m.push({x:-f/D/i,y:h*d})}}return m.filter(l=>l.x<1e3)}function Mn(e,n){e.forEachNonZero((t,s,i)=>Math.abs(i)<=n?0:i)}function sl(e,n,t,s,i){let o=1;for(let r of i)o*=t[r];let a=new q(o,o);for(let r=0;r<i.length;r++){let m=i[r],l=Oe(t[m]),c=1;for(let C=0;C<r;C++)c*=t[i[C]];let d=q.eye(c);c=1;for(let C=r+1;C<i.length;C++)c*=t[i[C]];let g=q.eye(c),u=e[m],p=d.kroneckerProduct(l.z).kroneckerProduct(g);a.add(p.mul(u));for(let C=0;C<i.length;C++){let y=i[C];if(s.get(m,y)===1){let f=Oe(t[y]),h=1;for(let v=0;v<C;v++)h*=t[i[v]];let D=q.eye(h);h=1;for(let v=C+1;v<i.length;v++)h*=t[i[v]];let b=q.eye(h),x=d.kroneckerProduct(l.x).kroneckerProduct(g).mmul(D.kroneckerProduct(f.x).kroneckerProduct(b));x.add(d.kroneckerProduct(l.y).kroneckerProduct(g).mul(-1).mmul(D.kroneckerProduct(f.y).kroneckerProduct(b))),x.add(d.kroneckerProduct(l.z).kroneckerProduct(g).mmul(D.kroneckerProduct(f.z).kroneckerProduct(b))),a.add(x.mul(n.get(m,y)/2))}}}return a}function Rn(e,n={}){let t=L(e),{lineWidth:s=1,frequency:i=400,from:o=0,to:a=10,nbPoints:r=16*1024,noise:m,baseline:l,shape:c={kind:"gaussian"},isProton:d=t.levels.every(u=>u===2)}=n,g=d?Fn(t,n):Z(t,n);return il(g,{generator:{from:o,to:a,nbPoints:r},peakOptions:{shape:c,width:s/i},noise:m,baseline:l})}import{agnes as ol}from"ml-hclust";import{Matrix as al}from"ml-matrix";function U(e,n={}){let t=L(e),{chemicalShifts:s,couplingConstants:i,connectivity:o}=t,{frequency:a=400,maxClusterSize:r=8}=n,m=rl(s,i,a),l=ol(m,{method:"single",isDistanceMatrix:!0}),c=[],d=s.length;Pt(l,c,{maxClusterSize:r,force:!1,nSpins:d,connectivity:o});let g=ll(c,r),u=g.length,p=[];for(let C=0;C<u;C++){let y=[];for(let f=0;f<d;f++){let h=g[C][f];h!==0&&y.push(h<0?-(f+1):f)}p.push(y)}return p}function Pt(e,n,t){let{maxClusterSize:s,force:i,nSpins:o,connectivity:a}=t;if(!i&&e.size<=s)n.push(wn(e.indices(),o));else for(let r of e.children)if(r.size<=s){let m=wn(r.indices(),o),l=0;for(let c=0;c<o;c++)if(m[c]===1){for(let d=0;d<o;d++)a.get(c,d)===1&&m[d]===0&&(m[d]=-1,l++);l++}l<=s?n.push(m):r.index<0?Pt(r,n,{maxClusterSize:s,force:!0,nSpins:o,connectivity:a}):(m[r.index]=2,n.push(m))}else Pt(r,n,{maxClusterSize:s,force:!1,nSpins:o,connectivity:a})}function rl(e,n,t){let s=n.rows,i=n.columns,o=al.zeros(s,s);for(let a=0;a<s;a++)for(let r=a;r<i;r++){let m=n.get(a,r);if(e[a]-e[r]!==0){let l=1-Math.abs(m/((e[a]-e[r])*t));o.set(a,r,l),o.set(r,a,l)}else a===r||m!==0||(o.set(a,r,1),o.set(r,a,1))}return o.to2DArray()}function ll(e,n){for(let t=e.length-1;t>=0;t--){let s=e[t],i=s.length,o=0;for(;o<i&&s[o++]!==-1;);if(!(o>=i))for(let a=e.length-1;a>=t+1;a--){let r=e[a],m=0,l=0;for(let c=0;c<i;c++)s[c]*r[c]===-1&&l++,(s[c]!==0||r[c]!==0)&&m++;if(l>0&&m<=n){for(let c=0;c<i;c++)r[c]===1?s[c]=1:r[c]===-1&&s[c]!==1&&(s[c]=-1);e.splice(a,1)}}}return e}function wn(e,n){let t=new Int16Array(n);for(let s of e)t[s]=1;return t}function dl(e){for(let n of e){if(!n.js)throw new Error("There is not js");if(!n.atoms)throw new Error("There is not atoms");for(let t of n.js)if(!t.atoms)throw new Error("There is not atoms")}}function Te(e,n={}){let t=ie(e);dl(t);let{frequency:s=400,shape:i={kind:"gaussian"},from:o=0,to:a=10,lineWidth:r=1,nbPoints:m=16*1024,maxValue:l=1e8,maxClusterSize:c=8,...d}=n;if(t.length===0)return{x:gl({from:o,to:a,size:m}),y:new Float64Array(m)};let g=W(t);g.clusters=U(g,{frequency:s,maxClusterSize:c});let u=Rn(g,{frequency:s,from:o,to:a,nbPoints:m,lineWidth:r,shape:i,maxClusterSize:c,...d});return l&&ml(u.y)===0&&(u.y=cl(u.y,{max:l})),u}import{getGyromagneticRatio as An}from"gyromagnetic-ratio";function Se(e,n){let{nucleus:t,frequency:s}=n,i=An(e),o=An(t);if(!o||!i)throw new Error(`${e} or ${t} is not supported`);return s*i/o}var s1=Se;function Nn(e,n){let{nbPoints:t,lineWidth:s,frequency:i}=n,o=[];for(let a in e)if(a==="proton"||a==="carbon"){let r=e[a];if(!r)continue;o.push(ul(r,{nbPoints:t,lineWidth:s,...n[a],experiment:a,frequency:i}))}return o}function ul(e,n){let{frequency:t=400,experiment:s}=n,i=Se(e.nucleus,{nucleus:"1H",frequency:t}),{x:o,y:a}=Te(e.signals,{...n,frequency:i});return{data:{x:o,re:a,im:null},info:{nucleus:e.nucleus,dimension:1,isComplex:!1,originFrequency:i,baseFrequency:i,pulseSequence:"prediction",experiment:s,isFt:!0},ranges:{values:e.ranges}}}import{xEnsureFloat64 as fl}from"ml-spectra-processing";import{generateSpectrum2D as pl}from"spectrum-generator";function K(e){return typeof e!="object"?{x:e,y:e}:{...e}}function kn(e,n={}){let{from:t=-1,to:s=12,nbPoints:i=512,factor:o=3}=n,{width:a=.02}=n,r={x:[],y:[],z:[]};for(let c of e)r.x.push(c.x.delta),r.y.push(c.y.delta),r.z.push(1e6);let{z:m,...l}=pl(Cl(r),{generator:{from:K(t),to:K(s),nbPoints:K(i)},peaks:{width:K(a),factor:o}});return{z:m.map(fl),...l}}function Cl(e){let n=structuredClone(e);for(let t=0;t<n.x.length;t++)for(let s=t+1;s<n.x.length;s++)n.x[t]===n.x[s]&&n.y[t]===n.y[s]&&(n.z[t]+=n.z[s],n.x.splice(s,1),n.y.splice(s,1),n.z.splice(s,1),s--);return n}function In(e,n){let t=Se(e[1],{nucleus:e[0],frequency:n});return[n,t]}function En(e,n){let t=[];for(let s in e){if(!bl(s)||!e[s])continue;let i=e[s];t.push(yl(i,{experiment:s,...n}))}return t}function yl(e,n){let{signals:t,zones:s,nuclei:i}=e,{experiment:o,frequency:a,width:r=hl(i),nbPoints:m,fromTo:l}=n,c=In(i,a),d=l[Tn(i[0])],g=l[Tn(i[1])],u=Dl(r,c),p=kn(t,{from:{x:d.from,y:g.from},to:{x:d.to,y:g.to},nbPoints:m,factor:3,width:u}),C=c.join(",");return{data:{rr:{...p,noise:.01}},info:{nucleus:i,originFrequency:C,baseFrequency:C,pulseSequence:o,experiment:"2d"},zones:{values:s}}}function bl(e){return["cosy","hsqc","hmbc"].includes(e)}function hl(e){return{x:8,y:e[0]===e[1]?8:24}}function Dl(e,n){let t=K(e);return{x:t.x/n[0],y:t.y/n[1]}}function Tn(e){return e.includes("H")?"proton":"carbon"}async function x1(e,n={}){let{logger:t,simulation:s={oneD:{},twoD:{}},prediction:i={}}=n,{spectra:o}=await Y(e,{logger:t,...i});!("frequency"in s)&&t&&t.warn("Frequency is settled to 400 MHz");let{frequency:a=400,oneD:r,twoD:m}=s,l={proton:{from:-1,to:12},carbon:{from:-10,to:220},nbPoints:65536,lineWidth:1,...r},c={frequency:a,fromTo:{proton:l.proton,carbon:l.carbon},nbPoints:{x:1024,y:1024},...m},d=Nn(o,{frequency:a,...l}),g=En(o,c);return{spectra:[...d,...g],molecules:[{molfile:e.toMolfile()}]}}import{TreeSet as Sl}from"ml-tree-set";function zn(e){let{restrictionByCS:n,predictions:t,targets:s,useIntegrationRestriction:i}=e,{tolerance:o,chemicalShiftRestriction:a}=n,r=Math.abs(o),m={};for(let l in t){let c=t[l];if(c.error&&(c.error=Math.abs(c.error)),m[l]=[],s)for(let d in s){let g=s[d];if(i&&g.integration>0?c.nbAtoms-g.integration<1:!0)if(!a||c.delta===void 0)m[l].push(d);else{let p=r;c.error&&(p=Math.max(p,c.error));let C=g.signals&&g.signals.length>0?g.signals[0].delta:(g.to+g.from)/2;Math.abs(c.delta-C-r)<4*r&&m[l].push(d)}}m[l].push("*")}return m}function Bn(e,n){let{useIntegrationRestriction:t,diaIDPeerPossibleAssignment:s,nbAllowedUnAssigned:i,restrictionByCS:o,predictions:a,targets:r}=n,{useChemicalShiftScore:m}=o,l=0,c=e.length,d={},g=[];for(let y=0;y<e.length;y++){let f=e[y];f&&f!=="*"&&(g.push(y),d[f]||(d[f]=[]),d[f].push(s[y])),f==="*"&&l++}if(l>i)return 0;let u=Object.keys(d);if(u.length===0)return 0;if(t)for(let y of u){let f=d[y],h=0;for(let b of f){let x=a[b];h+=x.allHydrogens}let{integration:D}=r[y];if(h-D>=.5)return 0}let p=m?Hl(e,n):1,C=l/c;return p-C}function Hl(e,n){let{tolerance:t}=n.restrictionByCS,{diaIDPeerPossibleAssignment:s,predictions:i,targets:o}=n,a=0,r=0;for(let m=0;m<e.length;m++){let l=e[m];if(l&&l!=="*"){r++;let c=s[m],d=i[c],g=o[l],u=t;if(d.error&&(u=Math.max(d.error,t)),d.delta===void 0)a+=1;else{let p=g.signals&&g.signals.length>0?g.signals[0].delta:(g.to+g.from)/2,C=Math.abs(d.delta-p);C<u?a+=1:(C=Math.abs(C-u),a+=-.25/u*C+1)}}}return r>0&&(a/=r),a}function Ft(e,n,t,s){let{nSources:i,restrictionByCS:o,timeout:a,timeStart:r,maxSolutions:m,targets:l,predictions:c,lowerBoundScore:d,nbAllowedUnAssigned:g,possibleAssignmentMap:u,useIntegrationRestriction:p,diaIDPeerPossibleAssignment:C}=e;if(Date.now()-r>a)return;let y=C[n],f=u[y];for(let h of f){t[n]=h;let D=Bn(t,{useIntegrationRestriction:p,diaIDPeerPossibleAssignment:C,nbAllowedUnAssigned:g,restrictionByCS:o,predictions:c,targets:l});if(D===0){h==="*"&&(t[n]=null);continue}n===i-1&&D>=d?xl(s,{predictions:c,partial:t,score:D,maxSolutions:m}):n<i-1&&Ft({nSources:i,restrictionByCS:o,timeout:a,timeStart:r,maxSolutions:m,targets:l,predictions:c,lowerBoundScore:d,nbAllowedUnAssigned:g,possibleAssignmentMap:u,useIntegrationRestriction:p,diaIDPeerPossibleAssignment:C},n+1,structuredClone(t),s)}}function xl(e,n){let{score:t,maxSolutions:s,partial:i,predictions:o}=n;e.nSolutions++;let a={assignment:structuredClone(i),score:t/Ol(i,o)};if(e.nSolutions>=s){let r=e.solutions.last();a.score>r.score&&(e.solutions.pollLast(),e.solutions.add(a))}else e.solutions.add(a),e.nSolutions++}function Ol(e,n){let t=Object.keys(n).length,s=new Set(e),i=t-s.size;return i>0?2*i:1}var vl=(e,n)=>n.score-e.score;async function Ee(e){let{restrictionByCS:n={},useIntegrationRestriction:t,timeout:s,minScore:i,nbAllowedUnAssigned:o,maxSolutions:a,targets:r,joinedSignals:m}=e,{tolerance:l=1,useChemicalShiftScore:c=!1,chemicalShiftRestriction:d=!0}=n,g=m.length,u={};for(let b of m){let x=b.diaIDs[0],v=b.atoms[0];u[x]={...b,diaIDIndex:v,allHydrogens:b.nbAtoms}}let p=zn({restrictionByCS:{tolerance:l,useChemicalShiftScore:c,chemicalShiftRestriction:d},useIntegrationRestriction:t,predictions:u,targets:r}),C=Object.keys(p),y=new Array(g).fill(null),f={solutions:new Sl(vl),nSolutions:0},h=Date.now();Ft({nSources:g,restrictionByCS:{tolerance:l,useChemicalShiftScore:c,chemicalShiftRestriction:d},timeout:s,timeStart:h,targets:r,predictions:u,maxSolutions:a,lowerBoundScore:i,nbAllowedUnAssigned:o,possibleAssignmentMap:p,diaIDPeerPossibleAssignment:C,useIntegrationRestriction:t},0,y,f);let D=[];for(let b of f.solutions.elements){let{assignment:x,score:v}=b,S=structuredClone(r);for(let H=0;H<x.length;H++){let O=x[H];if(typeof O!="string")continue;let P=S[O];(!P.signals||P.signals.length===0)&&(P.signals=[{delta:(P.to+P.from)/2}]);let j=P.signals[0];j.diaIDs||(j.diaIDs=[]),O&&j.diaIDs.push(C[H])}D.push({score:v,assignment:Object.values(S)})}return D}function Pl(e){for(let n of e){if(!n.atoms)throw new Error("signal has not atoms property");if(!n.diaIDs)throw new Error("signal has not diaIDs property");if(!n.nbAtoms)throw new Error("signal has not nbAtoms property")}}function Fl(e){for(let n of e)if(n.integration===void 0)throw new Error("ranges has not integration property")}async function B1(e,n,t={}){let{restrictionByCS:s,minScore:i=1,maxSolutions:o=10,nbAllowedUnAssigned:a=0,timeout:r=6e3,predictionOptions:m={}}=t;if(!n)throw new Error("It is needed a OCL molecule instance to assign");let{spectra:l}=await Y(n,{predictOptions:{H:m}}),c=l.proton?.joinedSignals||[];Fl(e),Pl(c);let d={};for(let g of e){let{id:u=crypto.randomUUID()}=g;d[u]=structuredClone(g)}return Ee({restrictionByCS:s,timeout:r,minScore:i,nbAllowedUnAssigned:a,maxSolutions:o,targets:d,joinedSignals:c,useIntegrationRestriction:!0})}function jl(e){for(let n of e){if(!n.atoms)throw new Error("signal has not atoms property");if(!n.diaIDs)throw new Error("signal has not diaIDs property");if(!n.nbAtoms)throw new Error("signal has not nbAtoms property")}}function Ml(e){let n=structuredClone(e);for(let t of n)t.integration===void 0&&(t.integration=0);return n}async function Y1(e,n,t={}){let{restrictionByCS:s={},minScore:i=1,maxSolutions:o=10,nbAllowedUnAssigned:a=0,timeout:r=6e3,predictionOptions:m={}}=t,{spectra:l}=await Y(n,{predictOptions:{C:m}}),c=l.carbon?.joinedSignals||[];jl(c);let d=Ml(e),g={};for(let u of d){let{id:p=crypto.randomUUID()}=u;g[p]=structuredClone(u)}return Ee({restrictionByCS:s,timeout:r,minScore:i,nbAllowedUnAssigned:a,maxSolutions:o,targets:g,joinedSignals:c,useIntegrationRestriction:!1})}import{ensureHeterotopicChiralBonds as $l}from"openchemlib-utils";import{TreeSet as Wn}from"ml-tree-set";import{getConnectivityMatrix as Bl}from"openchemlib-utils";import{getCorrelationDelta as Rl}from"nmr-correlation";function Xn(e,n){let{restrictionByCS:t,predictions:s,targets:i}=n,{tolerance:o,chemicalShiftRestriction:a}=t,r=Object.keys(s);for(let m of r){let l=o[m],c=s[m],d=i[m];e[m]||(e[m]={});for(let g in c){let u=c[g];if(e[m][g]=[],d)for(let p in d){let C=d[p],{integration:y,protonsCount:f}=C;if(y?m==="H"?u.nbAtoms-y<1:f.length>0?f.includes(u.protonsCount):!0:!0)if(!a||u.delta===void 0)e[m][g].push(p);else{let D=Rl(C);if(D===void 0)throw new Error("Correlation has not delta");Math.abs(u.delta-D-l)<4*l&&e[m][g].push(p)}}e[m][g].push("*")}}return e}import{getCorrelationDelta as Al}from"nmr-correlation";function wl(e,n,t){let s=e[0],{H:i=[]}=n[s].attachment,o=[{targetIDs:[s],attachments:new Set(i)}];for(let a=1;a<e.length;a++){let r=e[a],m=n[r],{H:l=[]}=m.attachment,c=!0;for(let d of o)if(l.some(u=>d.attachments.has(u))){c=!1,d.targetIDs.push(r);for(let u of l)d.attachments.add(u);break}c&&o.push({targetIDs:[r],attachments:new Set(l)})}return o.map(a=>({atomType:"C",targetIDs:a.targetIDs,integration:t?Array.from(a.attachments).reduce((r,m)=>t[m].integration+r,0):0}))}var Ln=wl;function qn(e,n){let{diaIDPeerPossibleAssignment:t,infoByAtomTypes:s,restrictionByCS:i,predictions:o,targets:a,correlations:r}=n,{tolerance:m,useChemicalShiftScore:l}=i,c=0,d=0,g={},u={},p=Object.keys(e);for(let S of p){let H=0,{nbAllowedUnAssigned:O}=s[S],P={},j=e[S]||[];g[S]=P,u[S]=[],d+=j.length;for(let F=0;F<j.length;F++){let R=j[F];R&&R!=="*"&&(u[S].push(F),P[R]||(P[R]=[]),P[R].push(t[S][F])),R==="*"&&H++}if(H>O)return 0;c+=H}let C={};for(let S in g)C[S]=Object.keys(g[S]);if(Object.values(C).every(S=>S.length===0))return 0;let f=kl.bind({},o),h=[];for(let S in e)if(S==="C"&&C[S].length>0)h.push(...Ln(C[S],a[S],r));else for(let H of C[S])h.push({atomType:S,targetIDs:[H],integration:a.H[H].integration});for(let S of h){let{integration:H,atomType:O,targetIDs:P}=S;if(H===void 0||Number.isNaN(H))continue;let j=0;for(let F of P){let R=g[O][F];for(let w of R){let{prediction:M,atomType:A}=f(w);O===A&&(j+=M.allHydrogens)}}if(j-H>=5)return 0}let D=1,b=1;if(l){b=0,D=0;for(let S of Object.keys(e)){let H=e[S],O=a[S];for(let P=0;P<H.length;P++){let j=H[P];if(j&&j!=="*"){D++;let F=t[S][P],R=o[S][F],w=O[j],M=m[S];if(R.delta===void 0)b+=1;else{let A=Al(w);if(A===void 0)throw new Error("correlation has not delta");let N=Math.abs(R.delta-A);N<M?b+=1:(N=Math.abs(N-M),b+=-.25/M*N+1)}}}}D>0&&(b/=D)}let x=0;if(Il(C)>1){let S={},H=[];for(let P of Object.keys(u))H=H.concat(u[P].map(j=>({index:j,atomType:P})));for(let P=0;P<H.length;P++){let{atomType:j,index:F}=H[P],R=o[j][t[j][F]];for(let w=P+1;w<H.length;w++){let{atomType:M,index:A}=H[w],N=o[M][t[M][A]],De=R.pathLength[N.diaIDIndex]<5,He=e[j][F],xe=e[M][A];if(!He||!xe)continue;let Ct=He>xe?`${xe} ${He}`:`${He} ${xe}`,sn=Nl({from:{targetID:He,atomType:j},to:{targetID:xe,atomType:M}},a),on=De?sn?1:0:sn?0:1;S[Ct]=S[Ct]?Math.max(S[Ct],on):on}}let O=0;for(let P in S)O+=S[P];x=O/(H.length*(H.length-1)/2)}let v=c/d;return b===0?x-v:x===0?b-v:(b+x)/2-v}function Nl(e,n){let{from:t,to:s}=e;if(t.targetID===s.targetID)return!0;let 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v=structuredClone(n);v[C].currentIndex+=1,jt({currentAtomTypes:i,restrictionByCS:o,timeout:a,timeStart:r,maxSolutions:m,targets:l,predictions:c,correlations:d,lowerBoundScore:g,possibleAssignmentMap:u,diaIDPeerPossibleAssignment:p},v,structuredClone(t),s)}}}}function Tl(e,n){let{score:t,maxSolutions:s,partial:i,predictions:o}=n,a={assignment:structuredClone(i),score:t/zl(i,o)};if(e.nSolutions>=s){let r=e.solutions.last();a.score>r.score&&(e.solutions.pollLast(),e.solutions.add(a))}else e.solutions.add(a),e.nSolutions++}function El(e,n){let t=!0;for(let s of e){let{currentIndex:i,nSources:o}=n[s];t=t&&i>=o-1}return t}function zl(e,n){let t=0;for(let s in n){let i=Object.keys(n[s]).length,o=new Set(e[s]);t+=i-o.size}return t>0?2*t:1}function V(e){return"ranges"in e}function Yn(e,n){for(let t=0;t<n.length;t++){let s=n[t],i=V(s)?s.ranges:s.zones;for(let o=0;o<i.length;o++){let a=i[o].signals||[];for(let 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D=C[h],b=s[p][f];for(let x of D.link){let{spectrumIndex:v,elementIndex:S,signalIndex:H}=a[x.signal.id],O=c[v];if(V(O)){let{ranges:P}=O,F=P[S].signals[H];if(F.diaIDs||(F.diaIDs=[]),F.diaIDs.includes(b))continue;F.diaIDs.push(b)}else{let P=x.axis,j=O.zones[S].signals[H];if(j[P].diaIDs||(j[P].diaIDs=[]),j[P].diaIDs?.includes(b))continue;j[P].diaIDs?.push(b)}}}}m.push({score:g,assignment:c})}return m}function Yl(e,n,t){return e.nSolutions>0?e.solutions.elements.map(s=>{let i=s.assignment;for(let o of t)i[o]=Vn(n[o].nSources);return i}):Wl(n,t)}function Wl(e,n){let t={},s=Object.keys(e);for(let i of s){let o=n.includes(i)?null:"*";t[i]=Vn(e[i].nSources,o)}return[t]}function Vn(e,n=null){let t=new Array(e);for(let s=0;s<e;s++)t[s]=n;return t}async function Zl(e){let{molecule:n,predictedSignals:t,options:s,atomType:i}=e;if(t)return t;let{spectra:o}=await Y(n,{predictOptions:s});return o[i==="C"?"carbon":"proton"]?.joinedSignals||[]}function Gn(e=[]){let n=structuredClone(e),t=[];for(let s of n){if(!("info"in s))throw new Error("each spectrum should contain info properties with nucleus information");if(V(s)){let{info:i,id:o}=s,a=ze(s.ranges);t.push({id:o,info:i,ranges:a})}else{let{info:i,id:o,zones:a}=s,r=ze(a);t.push({id:o,info:i,zones:r})}}return t}function Ul(e){for(let n of e){if(!n.id)throw new Error("A range/zone has not an ID");for(let t of n.signals||[])if(!t.id)throw new Error("A signal has not an ID")}}function ze(e){for(let n of e){n.id||(n.id=crypto.randomUUID());for(let t of n.signals||[])t.id||(t.id=crypto.randomUUID())}return Ul(e),e}import{buildCorrelationData as Gl}from"nmr-correlation";function Jn(e=[]){let n=structuredClone(e),t=[];for(let s of n)if(V(s)){let{id:i,info:o}=s,a=Vl({id:i,info:o,ranges:s.ranges});t.push({id:i,info:o,ranges:{values:a}})}else{let{id:i,info:o,zones:a}=s;t.push({id:i,info:o,zones:{values:a}})}return t}function Vl(e){if(e.info.nucleus!=="1H")return e.ranges;let n=e.ranges.reduce((t,s)=>t+(s.integration??0),0);for(let t of e.ranges)if(t.integration&&(t.integration*=100/n,t.signals)){let s=t.signals.reduce((i,o)=>i+(o.integration??0),0);for(let i of t.signals)i.integration?i.integration*=t.integration/s:i.integration=t.integration}return e.ranges}function $n(e,n){let{H:t=[]}=e,s=0;for(let i of t){let o=n[i];s+=Number(o.link[0].signal.integration)}return s}function _n(e,n={}){let{tolerance:t={C:.25,H:.05}}=n,s=Jn(e),o=Gl(s,{tolerance:t}).values.map(r=>({...r,integration:0})),a={H:{},C:{}};for(let r of o){if(r.pseudo)continue;let{id:m,atomType:l,link:c,attachment:d}=r;(l==="H"||l==="C")&&(a[l][m]=r,l==="H"?a[l][m].integration=c[0].signal.integration||0:a[l][m].integration=$n(d,o),a[l][m]=r)}return{targets:a,correlations:o}}function Mt(e,n=[]){let t=Jl(e),{hasHSQC:s,types:i}=t;if(n.length>0)return{assignmentOrder:n,experimentTypes:t};let o=[];return s?o.push(["C"],["H"]):o.push(i.filter(a=>a==="H"||a==="C")),{assignmentOrder:o,experimentTypes:t}}function Jl(e){let n=new Set;for(let t of e)for(let s of t.link){let i=s.experimentType;i==="1d"&&(i=s.atomType[0].toUpperCase()),n.add(i)}return{types:Array.from(n),hasProton:n.has("H"),hasCarbon:n.has("C"),hasHSQC:n.has("hsqc")}}async function vC(e,n={}){let{restrictionByCS:t={},justAssign:s,minScore:i=.01,maxSolutions:o=10,nbAllowedUnAssigned:a,timeout:r=6e3,predictionOptions:m={},predictions:l={},correlation:c={}}=n,{tolerance:d={H:.2,C:1},useChemicalShiftScore:g=!1,chemicalShiftRestriction:u=!0}=t,p=e.molecule;if(!p)throw new Error("It is needed a molecule to assign");p.addImplicitHydrogens(),$l(p);let C=Gn(e.spectra),{targets:y,correlations:f}=_n(C,c),{assignmentOrder:h}=Mt(f,s);return await Un({restrictionByCS:{tolerance:d,useChemicalShiftScore:g,chemicalShiftRestriction:u},spectra:C,molecule:p,timeout:r,minScore:i,maxSolutions:o,assignmentOrder:h,nbAllowedUnAssigned:a,correlations:f,targets:y,predictionOptions:m,predictions:l})}var _l={unspecified:"Unspecified",unknown:"Unknown",signal:"Signal",residualSolvent:"Residual solvent",reference:"Reference",nmrSolvent:"NMR Solvent",impurity:"Impurity",standard:"Standard",artifact:"Artifact",p1:"Product 1",p2:"Product 2",p3:"Product 3"};function Kl(e){return typeof e=="string"&&_l[e]!==void 0}function Q(e){return e===void 0?"signal":Kl(e)?e:"unspecified"}var Be=new Set(["signal"]);var Kn=_.toSorted((e,n)=>e.multiplicity===null&&n.multiplicity===null?0:e.multiplicity===null?1:n.multiplicity===null?-1:e.multiplicity-n.multiplicity),Rt=Kn.map(e=>e.value),Xe=Kn.map(e=>e.acs||e.value);import{Molecule as Ql}from"openchemlib";import{TopicMolecule as em}from"openchemlib-utils";function ve(e,n,t){let{name:s}=e,i=t[s],{idCode:o}=n[i];if(i===void 0)throw new Error("atom map does not exists");return{...e,idCode:o,atom:i}}function Qn(e,n,t){let s=[];for(let i of e){let{from:o,to:a}=i;s.push({...i,from:o.map(r=>ve(r,n,t)),to:a.map(r=>ve(r,n,t))})}return s}function es(e,n,t){let s=[];for(let i of e){let{atoms:o}=i;s.push({...i,atoms:o.map(a=>ve(a,n,t))})}return s}function ns(e,n){let t=[],s=wt(n),i=n[0].nucleusType.atomicNumber;for(let o of e){let a=wt(o.from),r=ts(s,a),l=o[r?"to":"from"],c=r?a:wt(o.to),{nucleusType:{atomicNumber:d},idCode:g}=l[0];!ts(s,c)||d!==i||t.push({coupling:o.value,atoms:l.map(u=>u.atom),diaIDs:[g]})}return t}function ts(e,n){for(let t of e)if(n.has(t))return!0;return!1}function wt(e){let n=e.filter(t=>t.shift!==null).map(t=>t.shift);return new Set(n)}function ss(e,n,t){let s=new Set,i=[];for(let o of e){let{name:a}=o,r=n[a],{idCode:m}=t[r];if(!r)throw new Error("atom mapping does not exists");s.add(m),i.push(r)}return{diaIDs:Array.from(s),atoms:i}}function is(e){let n=[];for(let t of e){let{atoms:s=[],...i}=t;if(s.length>1)for(let o of s)n.push({...i,atoms:[o]});else n.push(t)}return n}function os(e){let n=[];for(let t of e){let s=is(t.js);for(let i of t.atoms){let o={...t,atoms:[i],nbAtoms:1,js:s};n.push(o)}}return n}function as(e,n){let{atomicNumber:t=1,atomMap:s,molfile:i}=n,o=[],a=Ql.fromMolfile(i),m=new em(a).diaIDsAndInfo,l=Qn(e.couplings,m,s),c=es(e.shifts,m,s);for(let d of c){let{atoms:g,value:u}=d;if(!g.some(C=>C.nucleusType.atomicNumber===t))continue;let p={delta:u,nbAtoms:g.length,...ss(g,s,m),js:ns(l,g)};o.push(p)}return os(o)}function rs(e){return{molarFraction:{value:e.v,low:e.vl,high:e.vh},fieldStrength:e.f,baseItensity:e.bi,intensityLimit:e.il,spinSystemFlags:e.sf,spinSystemType:cm(e.sst),analysisType:e.at,inchiKey:e.ik,populations:tm(e.p),lineShapes:mm(e.l),shiftGroups:rm(e.sg),shifts:nm(e.s),couplingGroups:lm(e.cg),couplings:sm(e.c),atoms:im(e.a),bonds:om(e.b)}}function tm(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,population:{value:t.v,low:t.vl,high:t.vh},spinSystemFlags:t.sf});return n}function nm(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,shiftGroup:t.sg});return n}function sm(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,couplingGroup:t.cg,shifts:{from:t.s[0],to:t.s[1]}});return n}function im(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,nucleusType:gm(t.nc),cipRank:{canonical:t.crcan,rd:t.crrd,nmr:t.crnmr},ordinal:t.o,stereochemistryFlags:t.rs,spinSystemFlags:t.sf,formalcharge:t.fc,partialCharge:t.c,coordinates2D:t.c2d,coordinates3D:t.c3d,parent2D:t.p2d,shift:t.s});return n}function om(e){let n=[];for(let t of e)n.push({id:t.id,bondType:am(t.b),stereochemistryFlags:t.rs,spinSystemFlags:t.sf,atoms:t.a});return n}function am(e){switch(e){case 0:return"NONE";case 1:return"SINGLE";case 2:return"DOUBLE";case 3:return"TRIPLE";case 4:return"CONJUGATED";case 5:return"SINGLE_UP";case 6:return"SINGLE_DOWN";default:throw new Error(`Unknown bond type: ${e}`)}}function rm(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,shift:{value:t.v,low:t.vl,high:t.vh},spin2:t.s,spinCount:t.c,exchangeable:t.ex,spinSystemFlags:t.sf,gamma:t.g,iterationWeight:t.iw,response:{value:t.rs.v,low:t.rs.vl,high:t.rs.vh,sf:t.rs.sf},population:t.p,lineShape:t.l});return n}function lm(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.parentID,name:t.name,remarks:t.remarks,coupling:{value:t.v,low:t.vl,high:t.vh},spinSystemFlags:t.sf,couplingType:t.t});return n}function mm(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,spinSystemFlags:t.sf,lineWidth:{value:t.l.v,low:t.l.low,high:t.l.high},gaussian:{value:t.g.v,low:t.g.low,high:t.g.high}});return n}function cm(e){switch(e){case 0:return"NONE";case 1:return"SOLUTE";case 2:return"SOLVENT";case 4:return"IMPURITY";case 8:return"REFERENCE";case 16:return"CALIBRANT";case 32:return"ERROR_MESSAGE";default:throw new Error(`Unexpected spinSystemType: ${e}`)}}function gm(e){return{atomicNumber:(e&65024)>>9,isotope:e&511}}function ls(e,n){let{logger:t}=n;t.debug("Parsing CT json results");let s=rs(e),i=dm(s),o=um(s);return{...s,shifts:i,couplings:o}}function dm(e){let n=e.shifts,t=fm(e),s=ms(e),i=[];for(let o of n){let a=t[o.shiftGroup];if(!a)throw new Error(`Shift group ${o.shiftGroup} not found`);let r=s[o.id];if(!r)throw new Error(`Atom not found: ${o.id}`);i.push({atoms:r,value:a.shift.value})}return i}function um(e){let n=e.couplings,t=pm(e.couplingGroups),s=ms(e),i=[];for(let o of n){let a=t[o.couplingGroup];if(!a)throw new Error(`Coupling group ${o.couplingGroup} not found`);let r=s[o.shifts.from];if(!r)throw new Error(`Atom not found: ${o.shifts.from}`);let m=s[o.shifts.to];if(!m)throw new Error(`Atom not found: ${o.shifts.to}`);i.push({from:r,to:m,value:a.coupling.value})}return i}function ms(e){let n={};for(let t of e.atoms){if(!t.shift)continue;let s=t.shift;n[s]||(n[s]=[]),n[s].push(t)}return n}function fm(e){let n={};for(let t of e.shiftGroups)n[t.id]=t;return n}function pm(e){let n={};for(let t of e)n[t.id]=t;return n}function cs(e){let n={};for(let t of e)n[t.name]=t.ordinal;return n}function t5(e,n,t){let s=ls(e,{logger:console}),i=cs(s.atoms),o=as(s,{atomMap:i,molfile:n,...t});return{...s,signals:o}}var s5=[{names:["acetic 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data");let{info:t,filters:s,data:i,data:{re:o,im:a}}=e,{lpNumberOfCoefficients:r=0,tdOff:m=0}=t,{nbCoefficients:l=r,nbPoints:c=m/2,nbInputs:d=Math.floor(o.length/2-l-c)}=n,{re:g,im:u}=re({re:o,im:a},{nbCoefficients:l,nbInputs:d,nbPoints:c}),p=s.find(y=>y.name==="backwardLinearPrediction");p&&(p.value={nbCoefficients:l,nbPoints:c,nbInputs:d});let C=i.x;Object.assign(i,{re:g,im:u,x:c<0?Rm({from:0,size:g.length,step:C[1]-C[0]}):C})}function Ss(e){return!!(e.info.isComplex&&e.info.isFid)}function Nm(e,n){return{once:!0,reduce:n}}var vs={name:"backwardLinearPrediction",label:"Backward Linear Prediction Filter",domainUpdateRules:wm,apply:Am,reduce:Nm,isApplicable:Ss};import{xEnsureFloat64 as oc}from"ml-spectra-processing";import km from"ml-airpls";import{xEnsureFloat64 as Im,xFindClosestIndex as Tm}from"ml-spectra-processing";function Ps(e,n){let{lambda:t=50,anchors:s=[],maxIterations:i,tolerance:o,autoDownsample:a=!0}=n,r=Array.from(new Float64Array(e.x.length));if(s.length>0)for(let l of s){let c=Tm(e.x,l);r[c]=1}let{baseline:m}=km(e.x,e.y,{maxIterations:i,lambda:t,tolerance:o,controlPoints:r,autoDownsample:a});return Im(m)}import{CholeskyDecomposition as Lm,Matrix as It}from"ml-matrix";import{calculateAdaptiveWeights as qm,xFindClosestIndex as Ym,xMultiply as Wm,xSequentialFillFromStep as Zm}from"ml-spectra-processing";function Fs(e,n,t){if(n===0)return 1;if(e===0||n>e)return 0;if(n>e-n&&(n=e-n),!t)return Em(e,n);if(t[n]>0)return t[n];let s=1,i=e;for(let o=1;o<=n;o++){if(t[o]>0){i--,s=t[o];continue}s*=i--,s/=o,t[o]=s}return s}function Em(e,n){let t=1,s=e;for(let i=1;i<=n;i++)t*=s--,t/=i;return t}import{xyMedianYAtXs as zm}from"ml-spectra-processing";function J(e,n,t={}){let{windowSize:s=Math.max(1,Math.floor(e.y.length/100))}=t;return zm(e,n,{windowSize:s})}import{Matrix as Bm}from"ml-matrix";function js(e){let n=e.rows,t=e.columns,s=new Bm(n,n);for(let i=0;i<n;i++)for(let o=0;o<n;o++){let a=0;for(let r=0;r<t;r++)a+=e.get(o,r)*e.get(i,r);s.set(o,i,a)}return s}import{matrixCreateEmpty as Xm}from"ml-spectra-processing";function Ms(e,n){let t=e.rows,s=e.columns,i=n.columns;if(n.rows!==t)throw new Error("Matrix dimensions are incompatible for multiplication");let o=Xm({nbRows:i,nbColumns:s});for(let a=0;a<s;a++)for(let r=0;r<i;r++){let m=0;for(let l=0;l<t;l++)m+=e.get(l,a)*n.get(l,r);o[r][a]=m}return o}function Rs(e,n,t={}){let{maxIterations:s=100,tolerance:i=1e-6,factorStd:o=3,learningRate:a=.3,anchors:r,medianWindow:m}=t,{y:l}=e,{anchors:c,weights:d,controlPoints:g}=Jm(e,r,m),u=l.slice(),p=new Float64Array(l.length),C=0,y=1/0,{logger:f}=t,h=Math.max(1,l.length-1);for(let x=0;x<c.x.length;x++)c.x[x]/=h;let{binomialCoefficients:D,bernsteinMatrix:b}=Um(l,n);for(;C<s&&y>i;){let x=Vm(c,{binomialCoefficients:D,degree:n,weights:d,logger:f});if(!x)return u;let S=Ms(b,x)[0];qm(l,S,d,{controlPoints:g,learningRate:a,factorStd:o}),y=Gm(S,p,l.length),p.set(S),u=S,C++}return u}function Um(e,n){let t=e.length,s=n,i=Math.max(1,t-1),o=new 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Float64Array(a.y.length).fill(1),{x:l,y:c}=a;return{controlPoints:r,weights:m,anchors:{x:$m(l,e.x),y:c}}}let i=new Float64Array(s).fill(0),o=new Float64Array(s).fill(1);return{anchors:{...e,x:Zm({from:0,step:1,size:s})},weights:o,controlPoints:i}}function $m(e,n){let t=new Float64Array(e.length);for(let s=0;s<e.length;s++)t[s]=Ym(n,e[s]);return t}import{xEnsureFloat64 as We}from"ml-spectra-processing";function ws(e,n={}){let{anchors:t=[],noiseThreshold:s=1,maxIterations:i=10,tolerance:o=1e-6,noisePercentile:a=10,medianWindow:r=Math.max(1,Math.floor(e.y.length/100)),noiseLevel:m=ec(e.y,a)}=n,l=s*m,c,d;if(t.length>2){c=We(t);let C=J(e,c,{windowSize:r});d=We(C.y)}else c=We(e.x),d=We(e.y);let g=e.y.length,u=new Float64Array(g),p=c.length;for(let C=0;C<i;C++){let y=_m(c,d),f=Qm(y,e.x),h=0;for(let b=0;b<g;b++){let x=f[b]-u[b];h+=x*x}if(u=f,h=Math.sqrt(h/g),C>0&&h<o*m)break;let D=0;for(let b=0;b<p;b++){let x=Km(y,c[b]);d[b]>x+l&&(d[b]=x,D++)}if(D===0&&C>0)break}return u}function _m(e,n){let t=e.length;if(t<2)throw new Error("Need at least 2 knots.");if(t!==n.length)throw new Error("xs and ys must be the same length.");let s=Array.from({length:t},(f,h)=>h).toSorted((f,h)=>e[f]-e[h]),i=s.map(f=>e[f]),o=s.map(f=>n[f]),a=t-1,r=new Float64Array(a);for(let f=0;f<a;f++)r[f]=i[f+1]-i[f];let m=new Float64Array(t);for(let f=1;f<a;f++)m[f]=3/r[f]*(o[f+1]-o[f])-3/r[f-1]*(o[f]-o[f-1]);let l=new Float64Array(t),c=new Float64Array(t),d=new Float64Array(t);l[0]=1;for(let f=1;f<a;f++)l[f]=2*(i[f+1]-i[f-1])-r[f-1]*c[f-1],c[f]=r[f]/l[f],d[f]=(m[f]-r[f-1]*d[f-1])/l[f];l[a]=1;let g=new Float64Array(t);for(let f=a-1;f>=0;f--)g[f]=d[f]-c[f]*g[f+1];let u=[],p=[],C=[],y=[];for(let f=0;f<a;f++)u.push(o[f]),p.push((o[f+1]-o[f])/r[f]-r[f]*(g[f+1]+2*g[f])/3),C.push(g[f]),y.push((g[f+1]-g[f])/(3*r[f]));return{xs:i,a:u,b:p,c:C,d:y}}function Km(e,n){let{xs:t,a:s,b:i,c:o,d:a}=e,r=t.length-1,m=0,l=r-1;for(;m<l;){let g=m+l+1>>1;t[g]<=n?m=g:l=g-1}let c=Math.min(m,r-1),d=n-t[c];return s[c]+d*(i[c]+d*(o[c]+d*a[c]))}function Qm(e,n){let{xs:t,a:s,b:i,c:o,d:a}=e,r=t.length-1,m=new Float64Array(n.length),l=0;for(let c=0;c<n.length;c++){let d=n[c];for(;l<r-1&&t[l+1]<=d;)l++;let g=d-t[l];m[c]=s[l]+g*(i[l]+g*(o[l]+g*a[l]))}return m}function ec(e,n){let t=e.length,s=new Float64Array(t-1);for(let o=0;o<t-1;o++)s[o]=Math.abs(e[o+1]-e[o]);s.toSorted();let i=Math.max(0,Math.floor((t-1)*n/100)-1);return Math.max(s[i],1e-12)}import{PolynomialRegression as tc}from"ml-regression-polynomial";import{xyEquallySpaced as nc}from"ml-spectra-processing";function As({x:e,y:n},t){let{degree:s,anchors:i=[]}=t,o={x:structuredClone(i),y:[]};if(o.x.length<2){let r=nc({x:e,y:n},{numberOfPoints:4096});o.x=r.x,o.y=r.y}else{let{y:r}=J({x:e,y:n},o.x);o.y=r}return new tc(o.x,o.y,s,{interceptAtZero:!1}).predict(e)}import{xFindClosestIndex as sc,xWhittakerSmoother as ic}from"ml-spectra-processing";function Ns(e,n={}){let{anchors:t=[],lambda:s=2e3,maxIterations:i=20,tolerance:o=.001,learningRate:a=.2}=n,r=new Float64Array(e.x.length);if(t.length>0)for(let l of t){let c=sc(e.x,l);r[c]=1}return ic(e.y,{lambda:s,maxIterations:i,learningRate:a,tolerance:o,controlPoints:r})}function ks({x:e,y:n},t){let{algorithm:s}=t;switch(s){case"airpls":return Ps({x:e,y:n},t);case"polynomial":return As({x:e,y:n},t);case"whittaker":return Ns({x:e,y:n},t);case"bernstein":{let{degree:i}=t,o=Rs({x:e,y:n},i,t);return oc(o)}case"cubic":return ws({x:e,y:n},t);default:throw new Error(`baselineCorrection: algorithm unknown: ${t.algorithm}`)}}var ac={updateXDomain:!1,updateYDomain:!1};function rc(e,n){if(!Is(e))throw new Error("Baseline correction not applicable on this data");let{x:t,re:s}=e.data,i=ks({x:t,y:s},n),o=new Float64Array(t.length);for(let a=0;a<s.length;a++)o[a]=s[a]-i[a];Object.assign(e.data,{re:o})}function Is(e){return!e.info.isFid}function lc(e,n){return{once:!0,reduce:n}}var Ts={name:"baselineCorrection",label:"Baseline correction",domainUpdateRules:ac,apply:rc,reduce:lc,isApplicable:Is};var mc={updateXDomain:!0,updateYDomain:!0};function cc(e,n){if(!Es(e))throw new Error("Digital filter is not applicable on this data");let{digitalFilterValue:t}=n,s=new Float64Array(e.data.re),i=new Float64Array(e.data.im),o=new Float64Array(s.length),a=new Float64Array(i.length),r=Math.floor(t);o.set(s.slice(r)),a.set(i.slice(r)),e.data.re=o,e.data.im=a}function Es(e){return!!(e.info.isComplex&&e.info.isFid)}function gc(e,n){return{once:!0,reduce:n}}var zs={name:"digitalFilter",label:"Digital Filter",domainUpdateRules:mc,apply:cc,reduce:gc,isApplicable:Es};import{xEnsureFloat64 as Tt,xyEquallySpaced as Bs}from"ml-spectra-processing";var dc={updateXDomain:!1,updateYDomain:!1};function uc(e,n={}){if(!Xs(e))throw new Error("Equally spaced is not applicable on this data");let{from:t,to:s,numberOfPoints:i,exclusions:o}=n,{x:a,re:r,im:m}=e.data,l=Bs({x:a,y:r},{from:t,to:s,numberOfPoints:i,exclusions:o});if(e.data.x=Tt(l.x),e.data.re=Tt(l.y),m){let c=Bs({x:a,y:r},{from:t,to:s,numberOfPoints:i,exclusions:o});e.data.im=Tt(c.y)}}function Xs(e){return!!(e.info.isComplex&&!e.info.isFid)}function fc(e,n){return{once:!1,reduce:n}}var Ls={name:"equallySpaced",label:"Equally spaced",domainUpdateRules:dc,apply:uc,reduce:fc,isApplicable:Xs};import{xySetYValue as qs}from"ml-spectra-processing";var pc={updateXDomain:!1,updateYDomain:!1};function Cc(e,n){if(!Ys(e))throw new Error("Exclusion zones filter not applicable on this data");let{x:t,re:s,im:i}=e.data;e.data.re=Float64Array.from(qs({x:t,y:s},{zones:n}).y),e.data.im=i&&Float64Array.from(qs({x:t,y:s},{zones:n}).y)}function Ys(e){return!!e.info.isFt}function yc(e,n){return{once:!0,reduce:bc(e.concat(n))}}var Ws={name:"exclusionZones",label:"Exclusion zones",domainUpdateRules:pc,apply:Cc,reduce:yc,isApplicable:Ys};function bc(e=[],n={}){let{from:t=Number.NEGATIVE_INFINITY,to:s=Number.POSITIVE_INFINITY}=n;t>s&&([t,s]=[s,t]),e=e.map(a=>a.from>a.to?{...a,from:a.to,to:a.from}:{...a}),e.sort((a,r)=>a.from!==r.from?a.from-r.from:a.to-r.to);for(let a of e)t>a.from&&(a.from=t),s<a.to&&(a.to=s);if(e=e.filter(a=>a.from<=a.to),e.length===0)return[];let i=e[0],o=[i];for(let a=1;a<e.length;a++){let r=e[a];r.from<=i.to?i.to<r.to&&(i.to=r.to):(i=r,o.push(i))}return o}import{isPowerOfTwo as Hc,reimFFT as xc,reimPhaseCorrection as Oc,xMean as Us,xMultiply as Sc}from"ml-spectra-processing";var I=Math.PI/180;import{nextPowerOfTwo as hc,xSequentialFillFromStep as Dc}from"ml-spectra-processing";function Zs(e){let{x:n,re:t,im:s}=e.data,i=hc(n.length),o=new Float64Array(i),a=new Float64Array(i);o.set(t.slice(0,i)),a.set(s.slice(0,i));let r=Dc({from:n[0],size:i,step:n[1]-n[0]});e.data={...e.data,re:o,im:a,x:r}}var vc={updateXDomain:!0,updateYDomain:!0};function Pc(e){if(!Vs(e))throw new Error("fft not applicable on this data");Rc(e);let n=e.filters.some(o=>o.name==="digitalFilter"&&o.enabled),{info:{aqMod:t}}=e;t===1&&Mc(e),Hc(e.data.x.length)||Zs(e);let{data:s,info:i}=e;if(Object.assign(s,xc({re:s.re,im:i.reverse?Sc(s.im,-1):s.im},{applyZeroShift:!0})),n){let{digitalFilter:o=0}=i,a=Math.floor(o),r=(o-a)*Math.PI*2,m=a%2?180*I:0;Object.assign(s,Oc(s,m,-r,{reverse:!0}))}s.x=jc(e),e.info={...i,isFid:!1,isFt:!0}}function Vs(e){return!!(e.info.isComplex&&e.info.isFid)}function Fc(e,n){return{once:!0,reduce:n}}function jc(e){let n=e.info,t=Number(n.baseFrequency),s=Number(n.frequencyOffset),i=Number(n.spectralWidth),o=s/t,a=.5*i,r=e.data.x.length,m=o-a,l=i/(r-1),c=new Float64Array(r);for(let d=0;d<r;d++)c[d]=m,m+=l;return c}function Mc(e){let n=e.data,t=n.re.length,s=new Float64Array(n.re),i=new Float64Array(n.im),o=Us(n.re.slice(t*.75>>0,t)),a=Us(n.im.slice(t*.75>>0,t));for(let r=0;r<t;r++)s[r]-=o,i[r]-=a;return Object.assign(e.data,{re:s,im:i}),e}function Rc(e){let{data:n}=e;if(n.x.length!==n.re.length||n.x.length!==n.im.length)throw new Error("The length of data should be equal")}var Gs={name:"fft",label:"FFT",domainUpdateRules:vc,apply:Pc,reduce:Fc,isApplicable:Vs};import{xSequentialFillFromStep as Nc}from"ml-spectra-processing";import{Matrix as wc,SVD as Ac}from"ml-matrix";function Js(e,n){let{nbCoefficients:t,nbInputs:s,nbPoints:i}=n;if(e.length<s+t+i)throw new RangeError("data length should be bigger than nbInputs + nbCoefficients + nbPoints");let o=e.length-i-2,a=[];for(let d=0;d<s;d++){let g=new Float64Array(t);for(let u=0;u<t;u++)g[u]=e[o-d-u];a.push(g)}let r=new Ac(a),m=new Float64Array(s);for(let d=0;d<s;d++)m[d]=e[o-d+1];let l=r.solve(wc.from1DArray(m.length,1,m)).to1DArray(),{output:c=Float64Array.from(e)}=n;for(let d=0;d<i;d++){let g=0;for(let u=0;u<l.length;u++)g+=l[u]*c[o+1+d-u];c[o+d+2]=g}return{output:c,predicted:c.slice(o+2)}}function le(e,n){let{re:t,im:s}=e,{nbCoefficients:i,nbPoints:o,nbInputs:a=t.length}=n,r=Math.abs(o),m=o<0?r:0,l=2*Math.ceil((a+r+i)/2);if(t.length<l-m)throw new RangeError(`The sum of nbPoints, nbInputs and nbCoefficients should be less than data length (${t.length})`);let c=new Float64Array(2*l),d=t.length-l+m;for(let p=0;p<l-m;p++)c.set([t[d+p],s[d+p]],2*p);Js(c,{nbInputs:a*2,nbCoefficients:i,nbPoints:r*2,output:c});let g=new Float64Array(t.length+m),u=new Float64Array(m+s.length);o<0?(g.set(t),u.set(s)):(g.set(t.slice(0,t.length-o)),u.set(s.slice(0,s.length-o)));for(let p=0;p<2*r;p+=2)g[g.length-1-(p>>1)]=c[c.length-2-p],u[g.length-1-(p>>1)]=c[c.length-1-p];return{re:g,im:u}}function me(e,n,t){let s=2*e,i=2*n;if(t===0){if(s<n)return 0;if(n<s&&s<i)return n;if(i<s)return t-n}return n<t?t-n:0}var kc={updateXDomain:!0,updateYDomain:!0};function Ic(e,n={}){if(!$s(e))throw new Error("Digital filter is not applicable on this data");let{info:t,filters:s,data:i,data:{x:o,re:a,im:r}}=e,{lpNumberOfCoefficients:m=0,linearPredictionBin:l=0,spectrumSize:c=a.length,numberOfPoints:d=a.length}=t,{nbPoints:g=me(c,d,l)/-2,nbCoefficients:u=m,nbInputs:p=Math.floor(a.length-g-u)}=n,C=s.find(h=>h.name==="forwardLinearPrediction");C&&(C.value={nbCoefficients:u,nbPoints:g,nbInputs:p});let{re:y,im:f}=le({re:a,im:r},{nbCoefficients:u,nbInputs:p,nbPoints:g});Object.assign(i,{re:y,im:f,x:g<0?Nc({from:0,size:y.length,step:o[1]-o[0]}):o})}function $s(e){return!!(e.info.isComplex&&e.info.isFid)}function Tc(e,n){return{once:!0,reduce:n}}var _s={name:"forwardLinearPrediction",label:"Forward Linear Prediction Filter",domainUpdateRules:kc,apply:Ic,reduce:Tc,isApplicable:$s};import{reimAbsolute as Ec,reimAutoPhaseCorrection as zc,reimPhaseCorrection as Bc,xEnsureFloat64 as Ks}from"ml-spectra-processing";var Xc={updateXDomain:!1,updateYDomain:!1};function Lc(e,n={}){if(!ti(e))throw new Error("Phase correction not applicable on this 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S=0;S<c;S++){let{re:H,im:O}=re({re:T(r,S),im:T(m,S)},{nbInputs:C,nbPoints:p,nbCoefficients:u});E(h,H,S),E(D,O,S)}let b=Vi(h),x=Vi(D),v={re:{...o,z:h,minZ:b.min,maxZ:b.max},im:{...a,z:D,minZ:x.min,maxZ:x.max}};if(p<0){let{minY:S,maxY:H}=o,O=(H-S)/(l-1),P=H+O*f;v.re.maxY=P,v.im.maxY=P}Object.assign(i,v)}function Gi(e){let{isComplex:n,isFt:t,isFtDimensionOne:s}=e.info;return!!(n&&s&&!t)}function W0(e,n){return{once:!0,reduce:n}}var Ji={name:"blpDimension2",label:"Backward-LP Dimension 2",domainUpdateRules:q0,apply:Y0,reduce:W0,isApplicable:Gi};function $i(e,n){let{digitalFilterValue:t=0}=n,s=new Float64Array(e.re),i=new Float64Array(e.im),o=Math.floor(t),a=0;o+=0;let r=new Float64Array(s.length),m=new Float64Array(i.length);return r.set(s.slice(o)),r.set(s.slice(a,o),s.length-o),m.set(i.slice(o)),m.set(i.slice(a,o),i.length-o),{re:r,im:m}}var Z0={updateXDomain:!1,updateYDomain:!1};function U0(e,n){if(!_i(e))throw new Error("Digital filter on dimension 1 is not applicable on this data");let{data:t,data:{re:s,im:i}}=e,o=s.z,a=i.z,r=o.length,m=[],l=[],{digitalFilterValue:c}=n;if(!(!c||c===0)){for(let d=0;d<r;d++){let{re:g,im:u}=$i({re:o[d],im:a[d]},{digitalFilterValue:c});m.push(g),l.push(u)}Object.assign(t.re,{z:m}),Object.assign(t.im,{z:l})}}function _i(e){return!!(e.info.isComplex&&e.info.isFid)}function V0(e,n){return{once:!0,reduce:n}}var Ki={name:"digitalFilter2D",label:"Digital filter on Dimension 1",domainUpdateRules:Z0,apply:U0,reduce:V0,isApplicable:_i};import{xEnsureFloat64 as ao}from"ml-spectra-processing";import{matrixCreateEmpty as to,nextPowerOfTwo as G0,reimMatrixFFT as J0,reimMatrixPhaseCorrection as $0}from"ml-spectra-processing";function Pe(e){for(let n of e)for(let t=0;t<n.length;t++)n[t]=-n[t];return e}import{xMean as Qi}from"ml-spectra-processing";function eo(e,n){let{digitalFilterValue:t=0}=n,s=Math.round(t);for(let i=0;i<e.re.length;i++){let o=e.re[i],a=e.im[i],r=o.length,m=Qi(o.slice(r*.75>>0,r-s)),l=Qi(a.slice(r*.75>>0,r-s));for(let c=s;c<r-s;c++)o[c]-=m,a[c]-=l}}function no(e,n={}){let{reverse:t,digitalFilterValue:s=0}=n;eo(e,{digitalFilterValue:s}),t&&(e.im=Pe(e.im));let i=_0(e);J0(i,{inPlace:!0,applyZeroShift:!0});let{phaseCorrection:o={}}=n,a=Math.floor(s),r=s*Math.PI*2,l=a%2?180*I:0,c=-r,{ph0:d,ph1:g,mode:u="no"}=o;return u==="pk"&&d!==void 0&&g!==void 0&&(l+=d*Math.PI/180,c+=g*Math.PI/180),$0(i,l,c,{reverse:!0,inPlace:!0}),i}function _0(e){let n=e.re.length,t=G0(e.re[0].length);if(t>e.re[0].length){let s={re:to({nbRows:n,nbColumns:t}),im:to({nbRows:n,nbColumns:t})},{re:i,im:o}=e;for(let a=0;a<n;a++)s.re[a].set(i[a]),s.im[a].set(o[a]);return s}return e}import{xAdd as K0,xMultiply as Q0,xSubtract as qt}from"ml-spectra-processing";function so(e){let{re:{z:n},im:{z:t}}=e,s=[],i=[],o=n.length,a=o-o%2;for(let r=0;r<a;r+=2){let m=n[r],l=t[r],c=n[r+1],d=t[r+1];s.push(qt(Q0(d,-1),l),qt(c,m)),i.push(K0(c,m),qt(d,l))}return{re:s,im:i}}import{matrixCreateEmpty as io,nextPowerOfTwo as eg}from"ml-spectra-processing";function oo(e){let{data:n,info:t,meta:s={}}=e,{nuslist:i,NusTD:o}=s,a=t.acquisitionScheme?.toLowerCase(),r=n.re.z[0].length,m=eg(o[1]),l={re:[],im:[]};if(a==="echo-antiecho"){let c=i.map(g=>g*2),d=["re","im"];for(let g of d){let u=n[g].z,p=io({nbRows:m,nbColumns:r,ArrayConstructor:Float64Array}),C=n.re.z.length/2;for(let y=0;y<C;y++){let f=c[y];p[f].set(u[2*y]),p[f+1].set(u[2*y+1])}l[g]=p}}else{let c=["re","im"];for(let d of c){let g=n[d].z,u=io({nbRows:m,nbColumns:r,ArrayConstructor:Float64Array}),p=n.re.z.length;for(let C=0;C<p;C++){let y=i[C];u[y].set(g[C])}l[d]=u}}e.data={re:{...n.re,z:l.re},im:{...n.im,z:l.im}}}var tg={updateXDomain:!0,updateYDomain:!0};function ng(e,n){if(!ro(e))throw new Error("fft dimension 1 not applicable on this data");let{data:t,info:s,meta:{nuslist:i=[]}={}}=e,{digitalFilter:o=0,reverse:a=[!1,!1]}=s,r=s.acquisitionScheme?.toLowerCase();if(t.re.z.length!==t.im.z.length||t.re.z[0].length!==t.im.z[0].length)throw new RangeError("real and imaginary data must have the same dimensionality");let m=r==="echo-antiecho"?so(t):{re:t.re.z,im:t.im.z},{re:l,im:c}=no(m,{acquisitionScheme:r,...n,reverse:a[0],digitalFilterValue:o});t.re.z=l.map(ao),t.im.z=c.map(ao);let{isFid:d,...g}=s;e.info={...g,isFid:!1,isFtDimensionOne:!0},i.length>0&&oo(e)}function ro(e){return!!(e.info.isComplex&&e.info.isFid)}function sg(e,n){return{once:!0,reduce:n}}var lo={name:"fftDimension1",label:"FFT Dimension 1",domainUpdateRules:tg,apply:ng,reduce:sg,isApplicable:ro};import{matrixMinMaxZ as mg}from"ml-spectra-processing";import{nextPowerOfTwo as ig,reimMatrixFFTByColumns as og,reimMatrixPhaseCorrection as ag}from"ml-spectra-processing";function co(e,n={}){let t=e.re.length&-2;t>e.re.length&&(e.re.splice(t,1),e.im.splice(t,1));let s=e.re[0].length,{acquisitionScheme:i="",reverse:o}=n,a={...n},r={};if(i==="notPhaseSensitive"){Pe(e.im);let m=mo(e,a);r.rr=m.re,r.ir=m.im}else for(let m in e){let l=i==="SEQ"?t:t/2,c=new Array(l),d=new Array(l),g=e[m];if(i==="SEQ")for(let u=0;u<l;u++)c[u]=g[u],d[u]=new Float64Array(s);else{for(let u=0;u<l;u++)c[u]=g[2*u],d[u]=g[2*u+1];if(o&&Pe(d),["states-tppi","tppi"].includes(i))for(let u=0;u<l;u+=2)for(let p=0;p<s;p++)c[u][p]=-c[u][p],d[u][p]=-d[u][p]}mo({re:c,im:d},a),m==="re"?(r.rr=c,r.ri=d):(r.ir=c,r.ii=d)}return r}function mo(e,n){let{acquisitionScheme:t,phaseCorrection:s={}}=n;for(let m=0;m<e.re.length;m++)e.re[m][0]*=.5,e.im[m][0]*=.5;rg(e);let i=og(e,{applyZeroShift:t!=="SEQ",inPlace:!0}),{mode:o,ph0:a,ph1:r}=s;if(o&&o==="mc"||t==="notPhaseSensitive"){let{re:m,im:l}=i,c=m.length,d=m[0].length;for(let g=0;g<c;g++){let u=m[g],p=l[g];for(let C=0;C<d;C++)m[g][C]=lg(u[C],p[C])}}return o==="pk"&&a!==void 0&&r!==void 0&&ag(i,a*Math.PI/180,r*Math.PI/180,{direction:"columns",inPlace:!0}),i}function rg(e){let n=e.re[0].length,t=ig(e.re.length);if(t>e.re.length){let s=e.re.length;for(let i=s;i<t;i++)e.re.push(new Float64Array(n)),e.im.push(new Float64Array(n))}}function lg(e,n){let t=Math.abs(e),s=Math.abs(n);return s>t?s+.4*t:t+.4*s}function go(e){let n=[],t=[];for(let s=0;s<e.baseFrequency.length;s++){let i=e.baseFrequency[s],o=e.frequencyOffset[s],a=e.spectralWidth[s],r=o/i;n.push(r-a*.5),t.push(r+a*.5)}return{minX:n[0],maxX:t[0],minY:n[1],maxY:t[1]}}var cg={updateXDomain:!0,updateYDomain:!0};function gg(e,n){if(!uo(e))throw new Error("fft dimension 2 not applicable on this data");let t=e.data;if(t.re.z.length!==t.im.z.length||t.re.z[0].length!==t.im.z[0].length)throw new RangeError("real and imaginary data must have the same dimensionality");let s={re:t.re.z,im:t.im.z},{reverse:i=[!1,!1],acquisitionScheme:o}=e.info,a=co({re:s.re,im:s.im},{reverse:i[1],acquisitionScheme:o,...n});e.data={...dg(a,e.info)},e.info={...e.info,isFt:!0}}function dg(e,n){let t={},{acquisitionScheme:s}=n,i=go(n),o=a=>{for(let r of a){let m=e[r],{min:l,max:c}=mg(m);t[r]={z:m,maxZ:c,minZ:l,...i}}return t};return o(s==="notPhaseSensitive"?["rr","ir"]:["rr","ir","ri","ii"])}function uo(e){let{isComplex:n,isFtDimensionOne:t,isFt:s}=e.info;return!!(n&&t&&!s)}function ug(e,n){return{once:!0,reduce:n}}var fo={name:"fftDimension2",label:"FFT Dimension 2",domainUpdateRules:cg,apply:gg,reduce:ug,isApplicable:uo};import{matrixMinMaxZ as po}from"ml-spectra-processing";var fg={updateXDomain:!0,updateYDomain:!0};function pg(e,n={}){if(!Co(e))throw new Error("Forward Linear Prediction on dimension 1 is not applicable on this data");let{info:t,data:s,data:{re:i,im:o},filters:a}=e,r=i.z,m=o.z,l=r.length,c=r[0].length,d=[],g=[],{lpNumberOfCoefficients:u=[0,0],linearPredictionBin:p=[0,0],spectrumSize:C=[c,l],numberOfPoints:y=[c,l]}=t,{nbPoints:f=me(C[0],y[0],p[0])/-2,nbCoefficients:h=u[0],nbInputs:D=Math.floor(c-h-Math.max(f,0))}=n,b=a.find(H=>H.name==="flpDimension1");if(b&&(b.value={nbCoefficients:h,nbPoints:f,nbInputs:D}),Math.abs(f)===0||h===0)return;for(let H=0;H<l;H++){let{re:O,im:P}=le({re:r[H].slice(),im:m[H].slice()},{nbCoefficients:h,nbInputs:D,nbPoints:f});d.push(O),g.push(P)}let x=po(d),v=po(g),S={re:{...i,z:d,minZ:x.min,maxZ:x.max},im:{...o,z:g,minZ:v.min,maxZ:v.max}};if(f<0){let{minX:H,maxX:O}=i,P=(O-H)/(c-1);S.re.maxX=O+P*Math.abs(f)}Object.assign(s,S)}function Co(e){return!!(e.info.isComplex&&e.info.isFid)}function Cg(e,n){return{once:!0,reduce:n}}var yo={name:"flpDimension1",label:"Fordward-LP Dimension 1",domainUpdateRules:fg,apply:pg,reduce:Cg,isApplicable:Co};import{matrixCreateEmpty as bo,matrixMinMaxZ as ho}from"ml-spectra-processing";var yg={updateXDomain:!0,updateYDomain:!0};function bg(e,n={}){if(!Do(e))throw new Error("Forward linear prediction on dimension 2 is not applicable on this data");let{info:t,data:s,data:{re:i,im:o},filters:a}=e,r=i.z,m=o.z,l=r.length,c=r[0].length,{lpNumberOfCoefficients:d=[0,0],linearPredictionBin:g=[0,0],spectrumSize:u=[c,l],numberOfPoints:p=[c,l]}=t,{nbPoints:C=me(u[1],p[1],g[1])/-2,nbCoefficients:y=d[1],nbInputs:f=Math.floor(l-y-Math.max(C,0))}=n,h=a.find(O=>O.name==="flpDimension2");if(h&&(h.value={nbCoefficients:y,nbPoints:C,nbInputs:f}),Math.abs(C)===0||y===0)return;let D=C<0?-1*C:0,b=bo({nbRows:l+D,nbColumns:c}),x=bo({nbRows:l+D,nbColumns:c});for(let O=0;O<c;O++){let{re:P,im:j}=le({re:T(r,O),im:T(m,O)},{nbPoints:C,nbCoefficients:y,nbInputs:f});E(b,P,O),E(x,j,O)}let v=ho(b),S=ho(x),H={re:{...i,z:b,minZ:v.min,maxZ:v.max},im:{...o,z:x,minZ:S.min,maxZ:S.max}};Object.assign(s,H)}function Do(e){let{isComplex:n,isFt:t,isFtDimensionOne:s}=e.info;return!!(n&&s&&!t)}function hg(e,n){return{once:!0,reduce:n}}var Ho={name:"flpDimension2",label:"Fordward-LP Dimension 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b=Yt(m,{inverse:!0});for(let x=0;x<b.re.length;x++)b.re[x][0]/=.5,b.im[x][0]/=.5;return{re:{...e.re,z:Sg(b.re,i)},im:{...e.im,z:vg(b.im,i)}}}function xo(e,n,t,s){let i=t*s,o=e.re,a=n.re;for(let r=0;r<o.length;r++){let m=o[r],l=a[r];for(let c=0;c<m.length;c++){let d=m[c];if(d>i){let g=d-i;l[c]+=g,m[c]=i}else if(d<-i){let g=d+i;l[c]+=g,m[c]=-i}}}}function xg(e,n){let t=Yt(e,{inverse:!0}),s=t.re.length,i=new Float64Array(n.length),o=new Float64Array(n.length);for(let a=0;a<s;a++){let r=t.re[a],m=t.im[a];for(let l=0;l<n.length;l++){let c=n[l];i[l]=r[c],o[l]=m[c]}r.fill(0),m.fill(0);for(let l=0;l<n.length;l++){let c=n[l];r[c]=i[l],m[c]=o[l]}}return Yt(t)}function Yt(e,n={}){let{inverse:t=!1}=n,{re:s,im:i}=e;return t&&(Dg(s,{output:i}),Og(i)),So({re:s,im:i},{inverse:t})}function Og(e){for(let n of e)for(let t=0;t<n.length;t++)n[t]=-n[t];return e}function Sg(e,n){let t=e.length,s=[];for(let i=0;i<n;i++){let o=new Float64Array(t);for(let a=0;a<t;a++)o[a]=e[a][i];s.push(o)}return s}function vg(e,n){let t=e.length,s=[];for(let i=0;i<n;i++){let o=new Float64Array(t);for(let a=0;a<t;a++)o[a]=-e[a][i];s.push(o)}return s}function Oo(e){let n=0,t=0,s=e[0].length;for(let i of e)for(let o=0;o<s;o++){let a=i[o];a>t?t=a:a<n&&(n=a)}return Math.max(t,-n)}var Fg={updateXDomain:!0,updateYDomain:!0};function jg(e){if(!Fo(e))throw new Error("NUS reconstruction requires data with the direct dimension (rows) already FFT-processed (F2 domain).");let{data:n,meta:t={},info:s}=e;if(n.re.z.length!==n.im.z.length||n.re.z[0].length!==n.im.z[0].length)throw new RangeError("real and imaginary data must have the same dimensionality");let i=s.acquisitionScheme?.toLowerCase(),{nuslist:o,NusTD:a}=t,r={re:n.re,im:n.im},m=Pg(a[1]),l={re:[],im:[]};if(i==="echo-antiecho"){m/=2;let g=r.re.z,u=g.length/2,p=[],C=[];for(let b=0;b<u;b++)p.push(g[2*b]),C.push(g[2*b+1]);let y={re:{...r.re,z:p},im:{...r.im,z:C}},f=Wt(y,{nusIndices:o,nusLength:m}),h=[],D=f.re.z.length;for(let b=0;b<D;b++)h.push(f.re.z[b],f.im.z[b]);l.re=h;for(let b=0;b<D;b++)l.im.push(Po(f.re.z[b]),Po(f.im.z[b]))}else{let g=Wt(r,{nusIndices:o,nusLength:m});l.re=g.re.z,l.im=g.im.z}let c=vo(l.re),d=vo(l.im);e.data={re:{...r.re,z:l.re,minZ:c.min,maxZ:c.max},im:{...r.im,z:l.im,minZ:d.min,maxZ:d.max}}}function Fo(e){let{nuslist:n}=e.meta??{},{isComplex:t,isFtDimensionOne:s,isFt:i}=e.info;return!!(n.length>0&&t&&s&&!i)}function Mg(e,n){return{once:!0,reduce:n}}var jo={name:"nusDimension2",label:"NUS Reconstruction",domainUpdateRules:Fg,apply:jg,reduce:Mg,isApplicable:Fo};import{Matrix as et,MatrixTransposeView as Ro,WrapperMatrix2D as Ag}from"ml-matrix";import{SparseMatrix as tt}from"ml-sparse-matrix";import{matrixCreateEmpty as Ng,xMaxIndex as kg}from"ml-spectra-processing";function ue(e){if(["rr","ir","ri","ii"].some(n=>!(n in e)))throw new Error("four quadrants should has ir, ri and ii quadrants")}function Ke(e){if(["rr","ri"].some(n=>!(n in e)))throw new Error("Two quadrants should has ri 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wo(e,n={}){let{absolute:t,phases:s,threshold:i,nonZeros:o}=Eg(e,n),a=No(t,s,i),{columns:r,rows:m,values:l}=o,c=kg(l),d={x:r[c],y:m[c]};return Ig(a,{pivot:d,absolute:t,phases:s,threshold:i})}function Ig(e,n){let t=-30,s=30,i=8,o=Number.MAX_SAFE_INTEGER,a=Number.MAX_SAFE_INTEGER,{pivot:r,absolute:m}=n,{x:l}=r,{columns:c}=m,d=0,g=30,u=Tg(n);for(;i>0&&d!==o;){o=d;for(let C=t;C<=s+1;C+=g){let y=e([u-C*l/c,C]);y<a&&([a,d]=[y,C])}t=u+Math.sign(u)*g,s=t,i--}t=d-g,s=d+g;let p=5;for(i=5,o=Number.MAX_SAFE_INTEGER;i>0;){o=d;let C=(s-t)/(p-1);for(let y=t;y<=s+1;y+=C){let f=e([u-y*l/c,y]);f<a&&([a,d]=[f,y])}t=d-C,s=d+C,i--}return{ph0:u-d*l/c,ph1:d}}function Tg(e){let{pivot:t,absolute:s,phases:i,threshold:o}=e,{rows:a,columns:r}=s,m=new tt(a,r,{threshold:0}),l=new tt(a,r,{threshold:0}),{x:c,y:d}=t;for(let H=d-40;H<d+40;H++)for(let O=c-40;O<c+40;O++)m.set(H,O,s.get(H,O)),l.set(H,O,i.get(H,O));let g=No(m,l,o),u=-15,p=15,C=12,y=0,f=Number.MAX_SAFE_INTEGER,h=Number.MAX_SAFE_INTEGER,D=15;for(;C>0&&y!==f;){f=y;for(let H=u;H<p+1;H+=D){let O=g([H,0]);O<=h&&([h,y]=[O,H])}u=y+Math.sign(y)*D,p=u,C--}u=y-15,p=y+15;let b=5;for(C=5;C>0;){let H=(p-u)/(b-1);for(let O=u;O<=p;O+=H){let P=g([O,0]);P<h&&([h,y]=[P,O])}u=y-H,p=y+H,C--}let x=s.get(d,c),v=i.get(d,c);return x*Math.cos(v+y*I)<0?y-Math.sign(y)*180:y}function Eg(e,n={}){let{re:t,im:s}=e,{transpose:i=!1}=n,o=i?new Ro(new et(t)):new et(t),a=i?new Ro(new et(s)):new et(s),{rows:r,columns:m}=o,l=Ng({nbRows:r,nbColumns:m});for(let y=0;y<r;y++)for(let f=0;f<m;f++)l[y][f]=Math.hypot(o.get(y,f),a.get(y,f));let{threshold:c=new Ag(l).mean()*2}=n,d=new tt(l,{threshold:c}),g=new tt(d.rows,d.columns,{threshold:-1}),u=d.getNonZeros(),{columns:p,rows:C}=u;for(let y=0;y<C.length;y++){let[f,h]=[C[y],p[y]];g.set(f,h,Math.atan2(a.get(f,h),o.get(f,h)))}return{absolute:d,phases:g,threshold:c,nonZeros:u}}function No(e,n,t){let s=e.columns;return i=>{let[o,a]=[...i],r=0;return e.forEachNonZero((m,l,c)=>{let d=o+l*a/s,g=c*Math.cos(n.get(m,l)+d*I);return Math.abs(g)>=t&&(r+=1),c}),r}}import{reimMatrixPhaseCorrection as zg}from"ml-spectra-processing";function Ut(e,n){ue(e);let{quad:t}=n;return t==="imag"?fe(e,{...n,applyPhaseCorrection:ko,keys:{re:"ir",im:"ii"}}):fe(e,{...n,applyPhaseCorrection:ko,keys:{re:"rr",im:"ri"}})}function ko(e,n){let{ph0:t,ph1:s,reverse:i=!0,inPlace:o=!0}=n;return zg(e,t*I,s*I,{reverse:i,inPlace:o,direction:"columns"})}function Vt(e,n){let t=e,{horizontal:s,vertical:i}=n;return Io(s)&&(t=Qe(t,s)),Io(i)&&(t=Ut(t,i),t=Ut(t,{...i,quad:"imag"})),t}function Io(e){return e?e?.ph0!==0||e?.ph1!==0:!1}var Bg={updateXDomain:!1,updateYDomain:!1};function Xg(e,n){if(!Lg(e,n))throw new Error("Phase correction is not applicable to raw data");let{data:t,filters:s}=e;if("horizontal"in n||"vertical"in n)e.data={...t,...Vt(t,n)};else{let i=Ao(t,n.automatic);e.data={...t,...Vt(t,i)};let 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rd={updateXDomain:!0,updateYDomain:!0};function ld(e,n){if(!Go(e))throw new Error("Zero filling on dimension 2 is not applicable on this data");let{data:t,data:{re:s,im:i}}=e,o=s.z,a=i.z,r=o.length,m=o[0].length,{nbPoints:l}=n,c=Uo({nbRows:l,nbColumns:m}),d=Uo({nbRows:l,nbColumns:m});for(let D=0;D<m;D++){let{re:b,im:x}=ad({re:T(o,D),im:T(a,D)},l);E(c,b,D),E(d,x,D)}let g=Vo(c),u=Vo(d),p={re:{...s,z:c,minZ:g.min,maxZ:g.max},im:{...i,z:d,minZ:u.min,maxZ:u.max}},{minY:C,maxY:y}=s,f=(y-C)/(r-1),h=C+f*(l-1);p.re.maxY=h,p.im.maxY=h,Object.assign(t,p)}function Go(e){let{isComplex:n,isFt:t,isFtDimensionOne:s}=e.info;return!!(n&&s&&!t)}function md(e,n){return{once:!0,reduce:n}}var Jo={name:"zeroFillingDimension2",label:"Zero filling on Dimension 2",domainUpdateRules:rd,apply:ld,reduce:md,isApplicable:Go};var ee={zeroFillingDimension1:Zo,zeroFillingDimension2:Jo,apodizationDimension1:Ni,apodizationDimension2:Ei,phaseCorrectionTwoDimensions:Eo,baselineCorrectionTwoDimensions:qi,digitalFilter2D:Ki,nusDimension2:jo,symmetrizeCosyLike:qo,fftDimension1:lo,fftDimension2:fo,blpDimension1:Zi,blpDimension2:Ji,flpDimension1:yo,flpDimension2:Ho,shift2DX:zo,shift2DY:Bo};function $o(e){let{data:n,info:t}=e,{minX:s,maxX:i,minY:o,maxY:a}=t.isFt?n.rr:n.re,r=Math.abs(i-s)/1e4,m=Math.abs(a-o)/1e4;return{x:r,y:m}}function _o(e,n,t){let s=e.x||{from:0,to:0},i=e.y||{from:0,to:0};if(!n.zones?.values)return!1;for(let{x:o,y:a}of n.zones.values)if(Math.abs(s.from-o.from)<t.x&&Math.abs(s.to-o.to)<t.x&&Math.abs(i.from-a.from)<t.y&&Math.abs(i.to-a.to)<t.y)return!0;return!1}function Ko(e){let n={x:0,y:0};if(e?.filters)for(let t of e.filters)t.name===ee.shift2DX.name&&(n.x=t?.enabled?t.value.shift:0),t.name===ee.shift2DY.name&&(n.y=t?.enabled?t.value.shift:0);return n}function cd(e,n,t){let{x:s,y:i}=e;if(n==="origin")return{...e,x:{...s,originalDelta:s.delta-t.x},y:{...i,originalDelta:i.delta-t.y}};if(s.originalDelta===void 0||i.originalDelta===void 0)throw new TypeError('originalDelta must exist when shiftTarget is "current"');return{...e,x:{...s,originalDelta:s.originalDelta,delta:s.originalDelta+t.x},y:{...i,originalDelta:i.originalDelta,delta:i.originalDelta+t.y}}}function gd(e,n,t){let{x:s,y:i}=e;return n==="origin"?{x:{...s,originalFrom:s.from-t.x,originalTo:s.to-t.x},y:{...i,originalFrom:i.from-t.y,originalTo:i.to-t.y}}:{x:{...s,from:(s?.originalFrom||0)+t.x,to:(s?.originalTo||0)+t.x},y:{...i,from:(i?.originalFrom||0)+t.y,to:(i?.originalTo||0)+t.y}}}function dd(e,n,t){let{x:s,y:i,originalX:o=0,originalY:a=0}=e;return n==="origin"?{...e,originalX:s-t.x,originalY:i-t.y}:{...e,x:o+t.x,y:a+t.y}}function Qo(e,n,t={}){let{checkIsExisting:s=!0,shiftTarget:i="origin"}=t,o=Ko(n),a=$o(n);return s&&(e=e.filter(r=>!_o(r,n,a))),e.map(r=>{r.x=r.x||{from:0,to:0},r.y=r.y||{from:0,to:0};let m=r.signals.map(l=>{let{id:c,kind:d}=l,g;return l.peaks&&(g=l.peaks.map(u=>{let p=dd(u,i,o);return{...u,...p,id:u.id||crypto.randomUUID()}})),{...cd(l,i,o),peaks:g,id:c||crypto.randomUUID(),kind:Q(d)}});return{...r,id:r.id||crypto.randomUUID(),...gd(r,i,o),signals:m,kind:Q(r.kind??m[0]?.kind)}})}import{WrapperMatrix2D as Cd}from"ml-matrix";import{xBoxPlot as ea}from"ml-spectra-processing";import{color as ud}from"d3-color";import{interpolateRgbBasis as fd}from"d3-interpolate";import{xMinMaxValues as pd}from"ml-spectra-processing";function nt(e,n){let{minMax:t=pd(e),colors:s=["blue","cyan","yellow","red"]}=n,{min:i,max:o}=t,a=1/(o-i),r=[],m=fd(s);for(let l of e)r.push(ud(m((l-i)*a))?.formatHex());return r}function u6(e,n={}){let t=new Cd(e),s=yd(t),i=Object.keys(s);for(let o=1;o<t.columns;o++){let a=ea(t.getColumn(o));for(let r of 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n=ta(e);if(!n)throw new Error(`multiplet ${e} is not supported`);let{value:t,label:s}=n;return e===s?t:s}import{addMissingShape as Od}from"ml-gsd";import{getShape1D as Sd}from"ml-peak-shape-generator";import{generateSpectrum as Hd}from"spectrum-generator";function na(e,n){return n in e}function st(e,n){let{frequency:t,convertTo:s,output:i=structuredClone(e)}=n,o=Dd(s,t);for(let a of i)if(a.width=o(a.width),na(a,"shape")){let r=a.shape;r.fwhm&&(r.fwhm=o(r.fwhm))}return i}function Dd(e,n){switch(e){case"ppm":return t=>t/n;case"hz":return t=>t*n;default:throw new Error(`Does not support convert to ${e}`)}}function pe(e,n){return st(e,{...n,convertTo:"ppm"})}function sa(e,n){let{frequency:t,nbPoints:s=1024,shape:i}=n;if(!t)throw new Error("frequency is mandatory");let o=pe(e,{frequency:t});return Hd(o,{generator:{...xd(o,n),nbPoints:s,shape:i}})}function xd(e,n){if("to"in n&&"from"in n)return{from:n.from,to:n.to};e.sort((r,m)=>r.x-m.x);let t=e[0],s=e.at(-1),{frequency:i,from:o=t.x-t.width*2/i,to:a=s.x+s.width*2/i}=n;return{from:o,to:a}}function B6(e,n){let t=Od([e])[0],s=Sd(t.shape).getFactor(),{frequency:i,from:o=t.x-e.width*s/i,to:a=t.x+e.width*s/i}=n;return sa([e],{...n,from:o,to:a})}import{xSequentialFillFromTo as vd}from"ml-spectra-processing";function ia(e,n){let{from:t=0,to:s=10,nbPoints:i=1024,frequency:o=400,t2Relaxation:a=new Float64Array(e.length).fill(100)}=n,r=new Float64Array(i),m=new Float64Array(i),l=(s+t)/2,c=Math.abs(s-t),d=i/(c*o),g=vd({size:i,from:0,to:d}),u=Math.PI*2;for(let p=0;p<e.length;p++){let{x:C,y}=e[p],f=a[p]*.001,h=u*o*(C-l);for(let D=0;D<i;D++)r[D]+=y*Math.exp(-g[D]/f)*Math.cos(h*g[D]),m[D]+=y*Math.exp(-g[D]/f)*Math.sin(h*g[D])}return{re:r,im:m}}import{linearSumAssignment as ra}from"linear-sum-assignment";import{Matrix as Pd}from"ml-matrix";import{gaussianFct as Fd}from"ml-peak-shape-generator";import{xFindClosestIndex as oa,xMaxValue as la}from"ml-spectra-processing";function ma(e,n,t={}){let s=structuredClone(e);s.sort((r,m)=>r.x-m.x);let i=s.map(r=>r.x),{markSolventPeaks:o=!1,solventZoneExtension:a=1.2}=t;for(let r of n){let m=r.peaks||jd(r);m.sort((O,P)=>O.x-P.x);let l=oa(i,m.at(-1).x+a),c=oa(i,m[0].x-a),d=s.filter((O,P)=>P>=c&&P<=l),g=[],u=[],p=[];for(let O of d){let{peaks:P,delta:j}=aa(O,r,m),F=Md(P,d),R=0,w=0,M=0;for(let A=0;A<F.length;A++)w+=Math.abs(P[A].y-F[A].y),R+=Math.abs(P[A].x-F[A].x);F.length===0?(R=Number.MAX_SAFE_INTEGER,w=Number.MAX_SAFE_INTEGER,M=Number.MAX_SAFE_INTEGER):M=Fd(Math.abs(r.delta-j),.5),g.push(w),u.push(R),p.push(M)}let[C,y,f]=[g,u,p].map(O=>{let P=la(O);return P===0?1:P}),h=-1,D=Number.MAX_SAFE_INTEGER,b=[];for(let O=0;O<u.length;O++){let P=(g[O]/C+u[O]/y+1-p[O]/f)/3;b.push(P),D>P&&(h=O,D=P)}if(D<0||h<0)return s;let{peaks:x}=aa(d[h],r,m),v=ca(x,d),{rowAssignments:S,gain:H}=ra(v,{maximaze:!1});if(H<0)return s;if(o)for(let O of S)s[O+c].kind="residualSolvent";else{S.sort((O,P)=>P-O);for(let O of S)s.splice(O+c,1)}}return s}function jd(e,n={}){let t=ie([e]),s=W(t),{frequency:i=400,maxClusterSize:o=8}=n;return s.clusters=U(s,{frequency:i,maxClusterSize:o}),Z(s).filter(r=>r.x<1e3)}function aa(e,n,t){let s=structuredClone(t),i=e.x-n.delta;t.length>1&&t.length%2===0&&(i+=t[0].x);let o=la(s.map(r=>r.y)),a=0;for(let r of s)r.x+=i,r.y/=o,a+=r.x;return{peaks:s,delta:a/s.length}}function Md(e,n){let t=ca(e,n),{rowAssignments:s,gain:i}=ra(t,{maximaze:!1});if(i===-1)return[];let o=[],a=Number.NEGATIVE_INFINITY;for(let r of s)a<n[r].y&&(a=n[r].y),o.push({...n[r]});for(let r of o)r.y/=a;return o}function ca(e,n){let t=n.length,s=e.length,i=new Pd(s,t);for(let o=0;o<s;o++)for(let a=0;a<t;a++)i.set(o,a,Math.abs(e[o].x-n[a].x));return i}import{xyObjectCheck as Rd,xyObjectMinMaxValues as wd}from"ml-spectra-processing";function ga(e,n){Rd(e,{minLength:1});let{minX:t,maxX:s,thresholdFactor:i=.2}=n,{minY:o,maxY:a}=wd(e),r=Ad(o,a)*i,m=e[0],l=Number.MAX_SAFE_INTEGER;for(let c of e)if(Math.abs(c.y)>=r){let 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o){i[a]||(i[a]=[]);let r=i[a];for(let{signals:m=[]}of t)for(let l of m){let{delta:c,assignment:d="",js:g=[],multiplicity:u=""}=l;r.push({shift:c,proton:d,coupling:g.length>0?g[0].coupling:0,multiplicity:u})}}}var Cf=["water"];function Ua(e,n={}){let{error:t=.025,solvent:s,frequency:i=400}=n,o=structuredClone(e),a=bf(s);if(!a)return o;for(let r=o.length-1;r>=0;r--){let m=o[r];yf({...m,width:m.width/i},a,t)&&(o[r].kind="impurity")}return o}function yf(e,n,t){let s=t+e.width;for(let i of Cf){let o=n[i];for(let a of o)if(Math.abs(a.shift-e.x)<s)return!0}return!1}function bf(e=""){if(!e)return null;let n=e.toLocaleLowerCase();return n==="(cd3)2so"&&(n="dmso"),n==="meod"&&(n="cd3od"),he[n]?he[n]:null}function Va(e,n){let{impurities:t={},peakPicking:s,ranges:i={},identifyImpurities:o=!1}=n,{frequency:a}=s,{solvent:r}=t,m=$(e,s);return o&&(m=Ua(m,{...t,frequency:a})),be(e,m,{compile:!0,solvent:r,...i})}function hh(e,n){let{from:t,to:s,sgOptions:i}=n.peakPicking,{fromIndex:o,toIndex:a}=hf(e.x,{from:t,to:s}),r=i?.windowSize??7;if(a-o<=r)return n.logger?.info("Too small window for accurate multiplicity determination"),[{from:e.x[o],to:e.x[a],signals:[{delta:Df(e,{fromIndex:o,toIndex:a}).x,multiplicity:"",js:[]}]}];let{ranges:m={}}=n,{nucleus:l=""}=m;switch(l){case"1H":return Va(e,n);case"13C":return Wa(e,n);default:return Za(e,n)}}import{BaseRegression as Hf}from"ml-regression-base";import{SimpleLinearRegression as xf}from"ml-regression-simple-linear";import{xyCheck as Of}from"ml-spectra-processing";function Sh(e,n){Of(e,{minLength:2});let{x:t,y:s}=e,{gyromagneticRatio:i,gradientPulseDuration:o,timeCorrection:a}=n,r=new Float64Array(t.length),m=new Float64Array(t.length);for(let p=0;p<t.length;p++)r[p]=Math.log(s[p]),m[p]=t[p]**2;let l=new xf(m,r),{slope:c,intercept:d}=l.toJSON(),g=-c/a/(i*o)**2,u=Math.exp(d);return{regression:new en(g,u,n),coefficient:g,signalAbsenseDiffussion:u}}var en=class extends Hf{coefficient;signalAbsenseDiffussion;gyromagneticRatio;gradientPulseDuration;timeCorrection;constructor(n,t,s){let{gyromagneticRatio:i,gradientPulseDuration:o,timeCorrection:a}=s;super(),this.coefficient=n,this.signalAbsenseDiffussion=t,this.gyromagneticRatio=i,this.gradientPulseDuration=o,this.timeCorrection=a}_predict(n){return this.signalAbsenseDiffussion*Math.exp(-this.timeCorrection*this.coefficient*(n*this.gyromagneticRatio*this.gradientPulseDuration)**2)}};import{levenbergMarquardt as Sf}from"ml-levenberg-marquardt";import{BaseRegression as vf}from"ml-regression-base";import{xyCheck as Pf}from"ml-spectra-processing";var Ff={damping:1.5,maxIterations:100,errorTolerance:1e-8};function 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i9(e,n){let{enabled:t,id:s,logger:i}=n;e.filters=e.filters.slice(0).map(o=>({...o,enabled:o.id===s?t??!o.enabled:o.enabled})),we(e,{logger:i})}function o9(e,n,t){let s=e.filters.find(i=>i.id===n);e.filters=e.filters.slice(0).filter(i=>i.id!==n),!(s&&!s.enabled)&&we(e,{logger:t})}function yr(e,n,t={}){let{filterIndex:s}=t,i=crypto.randomUUID(),o={...n,id:i,enabled:!0};typeof s=="number"&&s!==-1?e.filters=[...e.filters.slice(0,s+1),o,...e.filters.slice(s+1)]:e.filters.push(o)}function pt(e,n,t){let{name:s,value:i}=n,o=Date.now();ee[s].apply(e,i);let a=Date.now()-o;t?.debug(`Filter: ${s} takes ${a} ms`)}export{ce as Filters1D,ur as Filters1DManager,ee as Filters2D,hr as Filters2DManager,_ as MultiplicityPatterns,ji as RangeUtilities,_t as XYAutoPeaksPickingWindowSizeError,At as apodizationXReIm,z as apodize,In as calculateRelativeFrequency,s5 as carbonImpurities,zt as checkIntegralKind,H6 as checkMultiplicity,Xe as couplingACSPatterns,Rt as couplingPatterns,ne as createApodizationWindowData,xm as default1DApodization,Q as ensureValidSignalKind,no as fftDirectDimension,co as fftIndirectDimension,ta as findMultiplet,ga as findPivot,Y1 as get13CAssignments,Ze as get1DErrorFactor,B1 as get1HAssignments,$o as get2DErrorFactor,vC as getAssignments,q4 as getBaselineAnchors,H4 as getBaselineZones,Di as getBaselineZonesByDietrich,p5 as getDatabase,s1 as getFrequency,Bt as getPeakDelta,Se as getRelativeFrequency,ge as getShiftX,da as isEmptyMolecule,s8 as isMolfileNotEmpty,xi as isRangeExists,_o as isZoneExists,Oi as mapIntegrals,Si as mapPeaks,Pi as mapRanges,Qo as mapZones,f8 as markSolventPeaks,u6 as matrixToBoxPlot,b6 as matrixToStocsy,D7 as normalizeNucleus,i7 as optimizeSignals,t5 as parseCT,B6 as peakToXY,ia as peaksToFID,sa as peaksToXY,Y as predict,x1 as predictSpectra,ds as protonImpurities,Le as rangeFromSignal,P8 as rangesToACS,j8 as rangesToTSV,N8 as rangesToXY,re as reimComplexBackwardLinearPrediction,S7 as resurrect,at as signalJoinCouplings,_l as signalKindLabelMapping,Be as signalKindsToInclude,Je as signalMultiplicityPattern,kn as signals2DToZ,l7 as signalsJoin,f7 as signalsToFID,y7 as signalsToRanges,Te as signalsToXY,Rn as simulate1D,ma as solventSuppression,ae as splitPatterns,P6 as translateMultiplet,Fi as updateIntegralsRelativeValues,Ri as updateRanges,Mi as updateRangesRelativeValues,F7 as xBackwardLinearPrediction,Js as xForwardLinearPrediction,w7 as xreimMultipletAnalysis,li as xreimTrim,$ as xyAutoPeaksPicking,hh as xyAutoRangesPicking,ks as xyBaselineCalculation,Sh as xyCalculateDiffussionCoefficient,Mh as xyCalculateT1,Jh as xyGetPivot,Nh as xyKineticFirstOrder,zh as xyPeaksOptimization,Zh as xyPeaksOptimizationByStages,Ao as xyzAutoPhaseCorrection,or as xyzAutoSignalsPicking,pD as xyzAutoZonesPicking,Vt as xyzPhaseCorrection,bD as xyzZoneIntegration,gt as xyzZonesIntegration};