@zakodium/nmrium-core-plugins 0.1.2 → 0.1.4
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/nmrium-core-plugins.js +8 -8
- package/package.json +19 -15
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import{NMRiumCore as ms}from"@zakodium/nmrium-core";import{Filters1D as Or,Filters2D as wr}from"nmr-processing";import{getOneIfArray as xr}from"@zakodium/nmrium-core";function re(e={},r={},t={}){e===null&&(e={}),typeof e=="string"&&(e={pulseSequence:e});let i=Array.isArray(e.pulseSequence)?e.pulseSequence[0]:e.pulseSequence||"";if(typeof i!="string")return e.dimension?`${e.dimension}d`:"";if(i=i.toLowerCase(),i.includes("zg")||i.includes("single_pulse_dec")||i.includes("udeft"))return"1d";if(i.includes("hsqct")||i.includes("invi")&&(i.includes("ml")||i.includes("di")))return"hsqctocsy";if(i.includes("hsqc")||i.includes("invi"))return"hsqc";if(i.includes("hmbc")||i.includes("inv4")&&i.includes("lp"))return"hmbc";if(i.includes("hmqc"))return"hmqc";if(i.includes("cosy"))return"cosy";if(i.includes("jres"))return"jres";if(i.includes("dosy"))return"dosy";if(i.includes("tocsy")||i.includes("mlev")||i.includes("dipsi"))return"tocsy";if(i.includes("noesy"))return"noesy";if(i.includes("roesy"))return"roesy";if(i.includes("dept"))return"dept";if(i.includes("jmod")||i.includes("apt"))return"aptjmod";if(i.includes("inad"))return"inadequate";if(i.includes("adeq"))return"adequate";let{prefix:n=""}=t,s=(xr(r[`${n}SPECTYP`])||"").replace(/^<(.*)>$/,"$1").toLowerCase();return s.length>0&&s!=="undefined"?s:e.dimension?`${e.dimension}d`:""}import{getOneIfArray as He}from"@zakodium/nmrium-core";var Mr=["no","exponential","modifiedGaussian","sine","qsine","trap","user","sinc","qsinc","traf","trafs"];function Rr(e){return e in Ze}function Me(e,r){let{prefix:t="",index:i=0}=r,n=He(e[`${t}WDW`],i),s=Mr[n?Number(n):0],o={};if(!Rr(s))return o;let l=Ze[s];if(l){let{kind:a,parameters:m}=l,f={};for(let c in m){let b=m[c],{source:u,processor:y}=b;if(u){let g=He(e[`${t}${u}`],i);if(!g)continue;let p=Number(g);f[c]=y?y(p):p}else b.value!==void 0&&(f[c]=b.value)}o[a]={apply:!0,options:f}}return o}var Ze={exponential:{kind:"exponential",parameters:{lineBroadening:{source:"LB"}}},modifiedGaussian:{kind:"gaussian",parameters:{lineBroadening:{source:"LB"},lineBroadeningCenter:{source:"GB"}}},sine:{kind:"sineBell",parameters:{offset:{source:"SSB",processor:e=>1/e},exponent:{value:1}}},qsine:{kind:"sineSquare",parameters:{offset:{source:"SSB",processor:e=>1/e}}},traf:{kind:"traf",parameters:{lineBroadening:{source:"LB"}}}};var Ke={sineBell:et({offset:0})},Qe={cosy:{...Ke},hmbc:{...Ke},hsqc:{sineBell:et({offset:.5})}},Ir={...Qe};function Re(e="",r=1){let t=Er(e),i={},n=r===1?Qe[t||""]:Ir[t||""];return n&&(i=structuredClone(n)),i}function et(e){return{apply:!0,options:e}}function Er(e){let t=e.toLowerCase().match(/cosy|hsqc|hmbc/);return t?t[0]:null}function tt(e,r={}){let{prefix:t="",experiment:i=re(e)}=r;return e[`${t}WDW`]?{f2:Me(e,{...r,index:0}),f1:Me(e,{...r,index:1})}:{f2:Re(i,1),f1:Re(i,2)}}import{Filters1D as Cr}from"nmr-processing";var Ie=["digitalFilter","backwardLinearPrediction","forwardLinearPrediction","apodization","zeroFilling","fft",["shiftX","phaseCorrection","baselineCorrection"]],z={};for(let e=0;e<Ie.length;e++){let r=Ie[e];for(let t of Array.isArray(r)?r:[r])z[t]=e}for(let e of Object.values(Cr))e.name in z||(z[e.name]=Ie.length);import{Filters2D as Tr}from"nmr-processing";var Ee=["digitalFilter2D","blpDimension1","flpDimension1","apodizationDimension1","zeroFillingDimension1","fftDimension1","blpDimension2","flpDimension2","nusDimension2","apodizationDimension2","zeroFillingDimension2","fftDimension2","phaseCorrectionTwoDimensions",["shift2DX","shift2DY","symmetrizeCosyLike"]],W={};for(let e=0;e<Ee.length;e++){let r=Ee[e];for(let t of Array.isArray(r)?r:[r])W[t]=e}for(let e of Object.values(Tr))e.name in W||(W[e.name]=Ee.length);var vr=new Set(["backwardLinearPrediction","forwardLinearPrediction","digitalFilter2D","phaseCorrectionTwoDimensions","blpDimension1","flpDimension1","apodizationDimension1","apodizationDimension2","zeroFillingDimension1","fftDimension1","blpDimension2","flpDimension2","zeroFillingDimension2","fftDimension2","nusDimension2","symmetrizeCosyLike"]);function Lr(e,r){let{filter:t,experimentalFeatures:i=!1}=r,{name:n}=t;({...Or,...wr})[n]&&(e.some(o=>o.name===n)||(i||!vr.has(n))&&e.push({...t,enabled:!0}))}function rt(e,r={}){let{data:t}=e;if(!t)return e;let{autoProcessing:i,experimentalFeatures:n}=r,s=(l,a)=>Lr(l,{...a,experimentalFeatures:n}),{spectra:o}=t;for(let l of o){let{data:a,info:m,meta:f,filters:c}=l,{dimension:b,isFid:u}=m;if(u){if(b===1){let y=a.re.length,{tdOff:g,digitalFilter:p}=m;if(p&&p>0&&s(c,{filter:{name:"digitalFilter",value:{digitalFilterValue:p}}}),!i)continue;g&&Math.abs(g)>0&&s(c,{filter:{name:"backwardLinearPrediction",value:{nbInputs:y/2}}}),s(c,{filter:{name:"apodization",value:{exponential:{apply:!0,options:{lineBroadening:1}}}}}),s(c,{filter:{name:"zeroFilling",value:{nbPoints:2*y}}}),s(c,{filter:{name:"fft",value:{}}}),s(c,{filter:{name:"phaseCorrection",value:kr(m)}}),c.sort((d,h)=>z[d.name]-z[h.name])}else if(b===2){if(!i||!n)continue;let y=a.re.z.length,g=a.re.z[0].length,{tdOff:p,experiment:d=""}=m,h=m.spectrumSize;Array.isArray(h)&&h.length>1?(h[0]<=g&&(h[0]=g*2),h[0]<=y&&(h[0]=y*2)):h=[g*2,2*y];let F=d.toLowerCase().includes("cosy");p&&Math.abs(p[0])>0&&s(c,{filter:{name:"blpDimension1",value:{nbInputs:g/2}}});let N=tt(f,{experiment:d});s(c,{filter:{name:"apodizationDimension1",value:N.f2}}),s(c,{filter:{name:"zeroFillingDimension1",value:{nbPoints:h[0]}}}),s(c,{filter:{name:"fftDimension1",value:{}}}),f&&"nuslist"in f&&s(c,{filter:{name:"nusDimension2",value:{}}}),s(c,{filter:{name:"apodizationDimension2",value:N.f1}}),s(c,{filter:{name:"zeroFillingDimension2",value:{nbPoints:h[F?0:1]}}}),F?s(c,{filter:{name:"symmetrizeCosyLike",value:{}}}):s(c,{filter:{name:"phaseCorrectionTwoDimensions",value:{}}}),s(c,{filter:{name:"fftDimension2",value:{}}}),c.sort((x,S)=>W[x.name]-W[S.name])}}}}function kr(e){let{phc0:r=0,phc1:t=0}=e;return nt([r,t])?{}:{ph0:r,ph1:t}}function nt(e){return Array.isArray(e)?e.every(r=>!r&&r===0):nt([e])}var ne=class{id="@zakodium/nmrium-core-plugins#AutoPostProcessingPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={onProcessing:this.onPostProcessing.bind(this)}}onPostProcessing(r,t){rt(r,t)}};function Ce(){return new 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this.lastWrittenByte-this.byteOffset}_updateLastWrittenByte(){this.offset>this.lastWrittenByte&&(this.lastWrittenByte=this.offset)}};import{createStepArray as Yr,xMinMaxValues as Gr}from"ml-spectra-processing";import{isAnyArray as Zr}from"is-any-array";import{matrixCreateEmpty as Kr,xSequentialFillFromStep as Qr}from"ml-spectra-processing";var st=["acqus","acqu2s"],ie=["procs","proc2s"];function Ur(e){return e.is1D?$r(e):e.is2D?jr(e):{checked:!1,message:"Multi-dimensional n > 2 is not supported"}}function $r(e){let r=e.isFID?["acqus"]:["acqus","procs"],t=r.every(i=>e[i]);return{checked:t,message:t?"":`File: ${e[e.isFID?"fid":"1r"]?.relativePath} is ignored, files: ${r.join(",")} are required.`}}function jr(e){let r=e.isFID?st:st.concat(ie),t=r.every(i=>e[i]);return t&&e.isFID&&ie.some(i=>e[i])&&!ie.every(i=>e[i])&&(t=!1,r.push(...ie)),{checked:t,message:t?"":`File: ${e.name} is ignored, files: ${r.join(",")} are required.`}}function ct(e,r={}){let{logger:t,processingNumbers:i,experimentNumbers:n,dataSelection:s="both",keep1D:o=!0,keep2D:l=!0,onlyFirstProcessedData:a=!0}=r,m={},f=e.files.map(u=>u.relativePath);for(let u of e){let y,g,p,d,h=u.relativePath.split("/"),F=h.indexOf("pdata");if(F!==-1)y=Number(h[F+1]),g=Number(h[F-1]),d=h.slice(0,-3).join("/");else if(Wr(u,f)){let N=h.indexOf(u.name);g=Number(h[N-1]),d=h.slice(0,-1).join("/")}else continue;if(Number.isNaN(g)&&(g=void 0),Number.isNaN(y)&&(y=void 0),!(n&&!n.includes(g))){if(m[d]||(m[d]={name:d,expno:g,processedData:{},fileCollectionItems:[]}),p=m[d],u.name==="vdlist"&&(p.vdlist=u),u.name==="difflist"&&(p.difflist=u),y){p.processedData[y]||(p.processedData[y]={fileCollectionItems:[],name:d,expno:g,procno:y});let N=p.processedData[y];N.fileCollectionItems.push(u),u.name.match(/^(1r|1i|2rr|2ir|2ii|2ri|procs|proc2s|title|integrals.txt)$/)&&(N[u.name]=u),u.name==="2rr"&&(N.is2D=!0,N.isFT=!0),u.name==="1r"&&(N.is1D=!0,N.isFT=!0)}else p.fileCollectionItems.push(u),u.name.match(/^(ser|fid|acqus|acqu2s|nuslist)$/)&&(p[u.name]=u),u.name==="ser"&&(p.is2D=!0,p.isFID=!0),u.name==="fid"&&(p.is1D=!0,p.isFID=!0);u.name==="QuantFactorSample.xml"&&(p.quantFactorSample=u)}}if(i)for(let u in m){let y=m[u].processedData,g={};for(let p in y)i.includes(Number.parseInt(p,10))&&(g[p]=y[p]);m[u].processedData=g}else if(a)for(let u in m){let y=m[u].processedData,g=Object.keys(y).sort((p,d)=>Number(p)-Number(d))[0];g!==void 0&&(m[u].processedData={firstProcessedNumber:y[g]})}let c=Xr(t),b=[];for(let u in m){let y=m[u],{processedData:g,...p}=y;if(c(y,s)){let h=Object.keys(g);if(h.length>0){let F=g[h[0]];F.procs&&(p.fileCollectionItems.push(F.procs),p.procs=F.procs),F.proc2s&&(p.fileCollectionItems.push(F.proc2s),p.proc2s=F.proc2s),F["integrals.txt"]&&(p.integrals=F["integrals.txt"])}b.push(p)}let d="ser"in p||"fid"in p;if(s==="fid"||s==="preferFID"&&d){t?.warn("Skipping FT data because it does not match the import filters");continue}for(let h in g){let F=g[h];(F["1r"]||F["2rr"])&&(p.acqus&&F.fileCollectionItems.push(p.acqus),p.acqu2s&&F.fileCollectionItems.push(p.acqu2s),p.vdlist&&(F.vdlist=p.vdlist),b.push({integrals:F["integrals.txt"],acqus:p.acqus,acqu2s:p.acqu2s,...F}))}}return o||(t?.warn("Skipping 1D data because it does not match the import filters"),b=b.filter(u=>!u.is1D)),l||(t?.warn("Skipping 2D data because it does not match the import filters"),b=b.filter(u=>!u.is2D)),zr(b,r.logger)}function zr(e,r){return e.filter(t=>{let{checked:i,message:n}=Ur(t);return i||r?.warn(n),i})}function Wr(e,r){return e.name.match(/^(ser|acqus|acqu2s|nuslist|vdlist|difflist|QuantFactorSample.xml)$/)||e.name.match(/^(fid)$/)&&r.includes(e.relativePath.replace(/fid$/,"acqus"))}function Xr(e){return(r,t)=>{let{processedData:i}=r,n=Object.keys(i),s=n.length>0&&["1r","1i","2rr"].some(a=>a in i[n[0]]),o="ser"in r||"fid"in r,l=o&&(t!=="ft"&&t!=="preferFT"||t==="preferFT"&&!s);return o&&!l&&e?.warn("Skipping RAW data because it does not match import filters"),l}}function mt(e){if(e===void 0||Array.isArray(e)&&e.length===0)return{epoch:null,date:""};let r=e[0]*1e3;return{epoch:r,date:new Date(r).toUTCString()}}function ut(e,r){for(let t in r.meta)e.meta[t]===void 0&&(e.meta[t]=r.meta[t]);for(let t in r.info)e.info[t]===void 0&&(e.info[t]=r.info[t]);for(let t in e.meta)Array.isArray(e.meta[t])||(e.meta[t]=[e.meta[t]])}async function X(e,r){if(!e)return{info:{},meta:{}};let t=await e.text(),{keepRecordsRegExp:i=/.*/}=r,n=Vr(t,{keepRecordsRegExp:i});return n.flatten.length===0?{}:n.flatten[0]}async function Jr(e){let r=(await e.integrals.text()).split(/\r?\n/).slice(3).filter(Boolean),t=[];for(let i=1;i<r.length;i++){let n=r[i].replace(/^\s*/,"").replaceAll(/[\s\t]+/g,";").match(/\d+;(?<from>[0-9.]+);(?<to>[0-9.]+);(?<integration>[0-9.]+)/);if(n){let{from:s,to:o,integration:l}=n.groups;t.push({from:Number.parseFloat(s),to:Number.parseFloat(o),integration:Number.parseFloat(l)})}}return t}function 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import{NMRiumCore as As}from"@zakodium/nmrium-core";import{Filters1D as Lr,Filters2D as kr}from"nmr-processing";import{getOneIfArray as Ir}from"@zakodium/nmrium-core";function ne(e={},r={},t={}){e===null&&(e={}),typeof e=="string"&&(e={pulseSequence:e});let i=Array.isArray(e.pulseSequence)?e.pulseSequence[0]:e.pulseSequence||"";if(typeof i!="string")return 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3
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V={};ut(V,{ECHO_ANTIECHO:()=>Nn,QF:()=>hn,QSEC:()=>yn,STATES:()=>Fn,STATES_TPPI:()=>Sn,TTPI:()=>bn});var hn=1,yn=2,bn=3,Fn=4,Sn=5,Nn=6;import{formatSpectra as wn}from"@zakodium/nmrium-core";function le(e){let r=[];for(let t of e){if(!t)continue;let{groups:{value:i,unit:n}={}}=t.trim().match(/[$$]*\s*(?<value>[\d.]+)\s*(?<unit>[a-zA-Z]+)/)||{};r.push(Dn(i,n))}return r}function Dn(e,r){switch(r.toLowerCase()){case"s":return Number.parseFloat(e);case"ms":return Number.parseFloat(e)/1e3;case"m":case"min":return Number.parseFloat(e)*60;default:return Number.NaN}}import{isAnyArray as St}from"is-any-array";function $(e){if(Pn(e))return An(e)?e.map(Ft):Ft(e);if(typeof e=="object"&&e!==null){let r={};for(let t in e)r[t]=$(e[t]);return r}return e}function Pn(e){return St(e)}function Ft(e){return Float64Array.from(e)}function An(e){return St(e[0])}import{getOneIfArray as ee}from"@zakodium/nmrium-core";import{getGyromagneticRatio as Rn}from"gyromagnetic-ratio";import{isAnyArray as qe}from"is-any-array";import{getFrequency as In}from"nmr-processing";import{isAnyArray as J}from"is-any-array";function me(e){return typeof e=="number"}function ce(e){let{phc0:r,phc1:t}=e;return!J(r)&&!me(r)||!J(t)&&!me(t)||J(r)&&!me(r[0])||J(t)&&!me(t[0])?{}:(J(t)?t[0]*=-1:t*=-1,J(r)?r[0]*=-1:r*=-1,{phc0:r,phc1:t})}function Dt(e,r,t){if(e>0)return Number(e);if(r>14||r===0)return 0;if(Nt[r]){let i=Nt[r];if(!i[t])throw new Error(`decim ${t} not in lookup table for dspfvs ${r}`);return i[t]}else throw new Error(`dspfvs ${r} not in lookup table`)}var Nt={10:{2:44.75,3:33.5,4:66.625,6:59.08333333333333,8:68.5625,12:60.375,16:69.53125,24:61.02083333333333,32:70.015625,48:61.34375,64:70.2578125,96:61.50520833333333,128:70.37890625,192:61.5859375,256:70.439453125,384:61.62630208333333,512:70.4697265625,768:61.646484375,1024:70.48486328125,1536:61.65657552083333,2048:70.492431640625},11:{2:46,3:36.5,4:48,6:50.16666666666667,8:53.25,12:69.5,16:72.25,24:70.16666666666667,32:72.75,48:70.5,64:73,96:70.66666666666667,128:72.5,192:71.33333333333333,256:72.25,384:71.66666666666667,512:72.125,768:71.83333333333333,1024:72.0625,1536:71.91666666666667,2048:72.03125},12:{2:46,3:36.5,4:48,6:50.16666666666667,8:53.25,12:69.5,16:71.625,24:70.16666666666667,32:72.125,48:70.5,64:72.375,96:70.66666666666666,128:72.5,192:71.333333333,256:72.25,384:71.66666666666667,512:72.125,768:71.83333333333333,1024:72.0625,1536:71.91666666666667,2048:72.03125},13:{2:2.75,3:2.833333333333333,4:2.875,6:2.916666666666667,8:2.9375,12:2.958333333333333,16:2.96875,24:2.979166666666667,32:2.984375,48:2.989583333333333,64:2.9921875,96:2.994791666666667}};import{normalizeNucleus as Mn}from"nmr-processing";function z(e,r=","){if(e&&typeof e=="string")return e.split(r)}function ue(e,r,t){let i=[];if(e[`${t}AXNUC`]&&(i=e[`${t}AXNUC`],Array.isArray(i)||(i=[i]),i=k(i)),i.length===0&&e[`${t}NUC1`]&&(i=e[`${t}NUC1`],Array.isArray(i)||(i=[i]),i=k(i)),i.length===0&&e[".NUCLEUS"]){let n=z(e[".NUCLEUS"]);if(e[`${t}SYMBOL`]){let s=e[`${t}SYMBOL`].split(","),o=s.findIndex(a=>a.includes("2")),l=s.findIndex(a=>a.includes("1"));o!==-1&&l!==-1&&n?i=k([n[o],n[l]]):i=k(n).reverse()}else i=k(n)}return i.length===0&&e[".OBSERVENUCLEUS"]&&(i=k([e[".OBSERVENUCLEUS"]])),i.length===0&&r.experiment&&(i=k(Pt(r.experiment[0]))),xn(e)&&(i=[e["2D_X_NUCLEUS"].replaceAll(/[^A-Za-z0-9]/g,""),e["2D_Y_NUCLEUS"].replaceAll(/[^A-Za-z0-9]/g,"")]),r.experiment&&(r.experiment[0].match("jres")||r.experiment[0].match("dosy"))&&(i=Pt(r.experiment[0])),i.map(Mn)}function xn(e){return e["2D_X_NUCLEUS"]&&!e["2D_X_NUCLEUS"].includes("off")&&e["2D_Y_NUCLEUS"]&&!e["2D_Y_NUCLEUS"].includes("off")}function Pt(e){return typeof e!="string"?[]:(e=e.toLowerCase(),e.includes("jres")?["1H","Hz"]:e.includes("dosy")?["1H","D"]:e.includes("hmbc")||e.includes("hsqc")?["1H","13C"]:e.includes("cosy")||e.includes("tocsy")?["1H","1H"]:[])}function k(e){if(!e)return[];let r=e.map(i=>String(i).replaceAll(/[^A-Za-z0-9]/g,"").replace("NA","").replace("off","")),t=0;for(let i of r)i||t++;return t===0?r:[]}function D(e,r,t,i=!1){t===void 0||r in e&&!i||(Array.isArray(t)?e[r]=t.map(At):e[r]=[At(t)])}function At(e){return typeof e=="string"&&(e.startsWith("<")&&e.endsWith(">")&&(e=e.slice(1,-1)),e=e.replace(/\$.*/,"").trim()),e}function fe(e,r={}){let{prefix:t="",logger:i}=r,n={dimension:0,nucleus:[],isFid:!1,isFt:!1},s=JSON.stringify(e),o=/\r\n/.exec(s)?`\r
|
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4
4
|
`:`
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5
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-
`,{JCAMPDX:l="",ORIGIN:a=""}=e,
|
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6
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-
`}=t;D(e,"spectralWidth",r[`${i}SweepWidth`]/e.originFrequency[0]);let s=r[`${i}.PULSESEQUENCE`].split(n),o=[];r[".OBSERVENUCLEUS"]&&o.push(r[".OBSERVENUCLEUS"]),r.INDIRECTNUCLEUS&&o.push(r.INDIRECTNUCLEUS),e.nucleus=k(o),e.pulseSequence=s[0];let l=s.slice(2,-1);if(o.length>1)if(o[0]===o[1])e.spectralWidth.push(e.spectralWidth[0]);else{let a=JSON.stringify(l).match(/\$\$SW1=\s*(?<sw>[+-]?(?:[0-9]*[.])?[0-9]+)/);if(a?.groups){let{originFrequency:
|
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7
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-
because it didn't match the import filters`);continue}o.push(f)}let l=[],a=o.some(xt),m=o.some(At);for(let f of o){if(s!=="both"&&f.dataType!=="LINK"){if(xt(f)&&(s==="ft"||s==="preferFT"&&m)){i?.warn(`Skipping raw data ${t?`in ${t}`:"in the JCAMP-DX"} because it didn't match the import filters`);continue}if(At(f)&&(s==="fid"||s==="preferFID"&&a)){i?.warn(`Skipping FFT data ${t?`in ${t}`:"in the JCAMP-DX"} because it didn't match the import filters`);continue}}l.push(f)}return l}function At(e){return e.dataType?.toUpperCase().includes("SPECTRUM")&&e.dataClass&&!e.dataClass.toUpperCase().includes("PEAK")}function xt(e){return e.dataType?.toUpperCase().includes("FID")}function Rt(e,r={}){let{logger:t,name:i=""}=r;for(let n of e){if(n.dataType==="LINK"&&Rt(n.children,r))return!0;let{dataType:s=""}=n,o=s.toLowerCase();if(o.length>0){if(o.includes("spectrum")&&!o.includes("nmr"))return t?.warn(`File ${i} was ignored because it is a ${s}`),!1;if(o.includes("nmr"))return!0}}return!1}import{generateID as Ct}from"@zakodium/nmrium-core";import{parseJcampCS as On}from"jcampconverter";import*as wn from"openchemlib";import{isMolfileNotEmpty as Mn}from"nmr-processing";import{Molecule as Rn}from"openchemlib";async function It(e,r={}){let t=await e.text(),i=J(t),n={molecules:i,spectra:[]};return i.length===0&&r.logger?.debug(`${e.name} is an empty molfile`),n}function J(e){let r=[];if(!Mn(e))return[];let i=Rn.fromMolfile(e).toMolfile();return r.push({molfile:i}),r}import{isMolfileNotEmpty as En}from"nmr-processing";import*as Cn from"openchemlib";import{getDiastereotopicAtomIDsFromMolfile as Tn}from"openchemlib-utils";var In=new Set(["ndnmrspectrum","ndnmrfid","nmrspectrum","nmrfid"]);function de(e){let{dataType:r="",dataClass:t=""}=e,i=r.replaceAll(/\s/g,"").toLowerCase(),n=t.replaceAll(/\s/g,"").toLowerCase();return In.has(i)&&n!=="peaktable"}function Et(e,r,t={}){let{spectra:i,info:n,meta:s}=e,o=i[0].data,l=[],a={x:"delta",y:"intensity",w:"width",m:"multiplicity",a:"atom"},{logger:m,name:f,spectraData:c}=t,{CROSSREFERENCE:b}=n,u=typeof b!="string"?b:b.split(/\r?\n/).map(S=>S.trim()).filter(Boolean),y=u.find(S=>S?.toLowerCase().includes("structure"));if(y===void 0)return m&&m.warn(`There is not a structure reference for ${f} file, assignment object could not be completed`),null;let g=Number.parseInt(y?.toLowerCase().replace(/_/,"").replace(/structure:\s*blockid\s*=\s*(?<blockId>.*)/,"$<blockId>"),10);if(Number.isNaN(g)||g<1)return m&&m.warn(`Structure block_id not found for ${f} file, assignment object could not be completed`),null;let d=c?.molecules?.find(S=>S.blockId===g)?.molfile??"";if(d===""){let S=r.find(M=>M.info.BLOCKID===g),{MOLFILE:A=""}=S?.meta||{};d=A}if(!En(d))return m&&m.warn(`Empty molfile for ${f} file with structure block_id = ${g}, assignment object could not be completed`),null;let h=Tn(Cn,d),F=ce({...n,...s},{},"");for(let S=0;S<o.x.length;S++){let A={};for(let M in o){let I=o[M][S];typeof I=="string"&&I.startsWith("<")&&I.endsWith(">")&&(I=I.slice(1,-1)),A[a[M]]=I}if("atom"in A){let M=h.map[A.atom-1];F.includes("1H")?M.nbHydrogens>0?(A.diaIDs=M.hydrogenOCLIDs,A.nbHydrogens=M.nbHydrogens):(A.diaIDs=[M.oclID],A.nbHydrogens=M.nbHydrogens):(A.diaIDs=[M.oclID],A.nbHydrogens=1)}l.push(A)}let N={};for(let S of l){let{delta:A,diaIDs:M}=S,I=`${A}_${M.join("_")}`;if(N[I])N[I].atoms.push(S.atom);else{let{atom:Pe,...P}=S;N[I]={...P,atoms:[S.atom]}}}let x=[];for(let S of u)S.toLowerCase().includes("spectrum")&&x.push(Number(S.toLowerCase().replace(/_/,"").replace(/.*:\s*blockid=(?<blockId>.*)/,"$<blockId>")));if(x.length===0){for(let S of r)if(de(S)){let{BLOCKID:A}=S.info;x.push(Number(A))}x.length>1&&(x=[],m&&m.warn(`There is not a spectral cross-reference for the peak assignment in the ${f} file`))}return{moleculeBlockID:g,spectraBlockIDs:x,assignments:Object.values(N),molecule:h.molecule}}function Tt(e,r,t,i){for(let n of e){let{meta:s,dataClass:o="",dataType:l="",info:a}=n,m=Number.parseInt(String(a.BLOCKID),10);s.MOLFILE?qn(String(s.MOLFILE),r,m):n.jcampCS&&kn(n,r,m),vn(o,l)&&Ln(r,n,e,i),de(n)&&t.push(n)}}function vn(e,r){return e?.toLowerCase().includes("assignments")&&r?.toLowerCase().includes("assignments")}function Ln(e,r,t,i){let n=Et(r,t,{spectraData:e,logger:i.logger,name:i.name});if(e.assignmentsByBlocks||(e.assignmentsByBlocks={}),n){let{spectraBlockIDs:s}=n;for(let o of s)e.assignmentsByBlocks[o]=n}}function kn(e,r,t){r.molecules||(r.molecules=[]);let i=On(e,{OCL:wn}),n=J(i?.molfile||"");n.length>0&&r.molecules.push({id:Ct(),blockId:t,...n[0]})}function qn(e,r,t){r.molecules||(r.molecules=[]);let i=J(String(e));r.molecules.push({id:Ct(),blockId:t,...i[0]})}import{generateID as Wt}from"@zakodium/nmrium-core";import{matrixMinMaxZ as zt,reimPhaseCorrection as Yn}from"ml-spectra-processing";import{xyAutoRangesPicking as Gn}from"nmr-processing";function Y(e){return e.slice(0,Math.max(0,e.lastIndexOf(".")))}function G(e){e.sort((r,t)=>r.from-t.from);for(let r=0;r<e.length-1;r++)e[r].to>e[r+1].from&&(e[r].to=Math.max(e[r+1].to,e[r].to),e[r].signals=e[r].signals.concat(e[r+1].signals),e[r].integration+=e[r+1].integration,e.splice(r+1,1),r--);return e}import{splitPatterns as jn}from"nmr-processing";import{xMaxValue as Bn}from"ml-spectra-processing";function ee(e){return e.trim().slice(1,-1).split(/,\s*/).map(r=>r.trim())}var _n={I:"id",X:"from",Y:"to",Hs:"delta",An:"integration",H:"nbAtoms",C:"multiplicity",N:"assignment","(J)":"js"},Ot=["I","X","Y","Hs","An","H","C","N","(J)"];function wt(e){let r={headersFromParenthesis:[],headersFromComments:[],comments:[],data:[],multiplets:[]},t=e.split(/\r?\n/).filter(i=>i.trim()!=="");if(t.length===0)return r;if(t[0].startsWith("(")&&!t[0].match(/\d/)){let i=t.shift();r.headersFromParenthesis=ee(i)}return r.comments=t.filter(i=>i.startsWith("$$")).map(i=>i.replace(/^\$\$\s*/,"")),r.headersFromComments=$n(r.comments),r.data=t.filter(i=>!i.startsWith("$$")).map(ee),r.multiplets=Un(r),r}function Un(e,r={}){let{logger:t}=r,i=e.data[0].map((a,m)=>m).filter(a=>e.data.every(m=>Number.isNaN(m[a])||Number.isNaN(Number(m[a]))));if(t?.trace(`Parsing JCAMP-DX assignment: stringColumnIndexes: ${i.join(",")}`),i.length===0)return t?.warn("Parsing JCAMP-DX assignment: No string columns found. Skipping parsing of assignment."),[];let n=i[0],s;if(e.headersFromParenthesis.length>0&&e.headersFromParenthesis[n]==="C")s=e.headersFromParenthesis;else if(e.headersFromComments.length>0&&e.headersFromComments[n]==="C")s=e.headersFromComments;else if(Ot[n]==="C")s=Ot;else return t?.warn("No header found for multiplicity. Skipping parsing of assignment."),[];return Bn(e.data.map(a=>a.length))>s.length&&t?.warn("Some assignments are containing more values than headers"),e.data.map(a=>{let m={};for(let f=0;f<s.length;f++){let c=s[f];m[_n[c]||c]=a[f]}return m})}function $n(e){return e.map(r=>r.split(":")[0].trim()).filter(r=>r.length>0)}function vt(e,r={}){let{logger:t}=r,i=wt(e),n={multiplets:[],comments:i.comments};for(let s of i.multiplets){let{id:o,from:l,to:a,delta:m,integration:f,nbAtoms:c,multiplicity:b}=s,u={id:o,js:[],multiplicity:"",...zn({from:l,to:a,delta:m,integration:f,nbAtoms:c})};if(typeof s.js=="string"){let y=s.js.split(/\s+/).map(Number.parseFloat),g=0,p=jn(b).map(F=>{let N=(F?.multiplicity||1)-1;return g+=N,{value:F.value,multiplicity:F?.multiplicity,js:y.slice(g-N,g)}}),d=p.reduce((F,N)=>F+(N.multiplicity?N.multiplicity-1:0),0);y.length!==d&&t?.warn(`The number of j values (${y.length}) is not equal to the sum of the multiplicities - 1 (${d})`);let h=[];for(let F of p){if(F.js.every(N=>N===F.js[0])){h.push(F);continue}if(F.multiplicity!==F.js.length+1){h.push(F);continue}for(let N=0;N<F.multiplicity-1;N++)h.push({value:"d",multiplicity:2,js:[F.js[N]]})}h.sort((F,N)=>N.js[0]-F.js[0]),u.js=h.map(F=>({coupling:F.js[0],multiplicity:F.value}))}typeof s.assignment=="string"&&(u.assignment=Xn(s.assignment)),typeof s.multiplicity=="string"&&(u.multiplicity=s.multiplicity),n.multiplets.push(u)}return n}function zn(e){let r={};for(let t in e){let i=e[t],n=typeof i=="number"?i:Number.parseFloat(i);Number.isNaN(n)||(r[t]=n)}return r}var Wn={quot:'"',apos:"'",comma:",",amp:"&",lpar:"(",rpar:")",lt:"<",gt:">",colon:":",semi:";"};function Xn(e){return e.replaceAll(/&(\w+);/gi,(r,t)=>Wn[t.toLowerCase()]||r)}function Lt(e){let r=e.split(/\r?\n/).filter(i=>i.trim()!==""),t=[];for(let i of r)if(i.startsWith("(")){let[n,s,o]=ee(i).map(Number.parseFloat);t.push({id:n,x:s,y:o})}return t}function kt(e,r={}){let t={};if(!e["OBSERVED MULTIPLETS"])return[];let i=vt(e["OBSERVED MULTIPLETS"],r);if(!i)return[];let{multiplets:n}=i;for(let s of n){let{id:o,from:l,to:a,integration:m=0,...f}=s;t[o]={from:l,to:a,integration:m,signals:[{id:o,...f}]}}if(e["OBSERVED MULTIPLETS PEAKS"]){let s=Lt(e["OBSERVED MULTIPLETS PEAKS"]),o={};for(let l of s){let{id:a,x:m,y:f}=l;o[a]||(o[a]=[]),o[a].push({x:m,y:f,width:.05})}for(let l in t)o[l]&&(t[l].signals[0].peaks=o[l])}return G(Object.values(t))}function qt(e,r){let i=[...e.getMolecularFormula().formula.matchAll(/(?<element>[A-Z][a-z]?)(?<count>\d*)/g)].map(s=>({element:s?.groups?.element,count:s?.groups?.count?Number(s.groups.count):1})),n=[...r.nucleus[0].matchAll(/[0-9]*(?<element>[A-Z][a-z]?)/g,"$element")][0].groups.element;return i.find(s=>s.element===n)?.count||100}function Bt(e){let r={};return".PHASE0"in e&&(r.ph0=Number.parseFloat(e[".PHASE0"]),r.ph1=Number.parseFloat(e[".PHASE1"])),r}function _e(e){let{ph0:r,ph1:t}=e;return Number.isFinite(r)&&Number.isFinite(t)}import{generateID as _t}from"@zakodium/nmrium-core";function Ut(e,r,t){for(let i=0;i<e.length;i++){if(r.includes(i))continue;let{delta:n,multiplicity:s="",diaIDs:o}=e[i],l=Number(n)-.01,a=Number(n)+.01;t.push({from:l,to:a,integration:1,id:_t(),signals:[{id:_t(),delta:n,multiplicity:s,diaIDs:o}]})}}import{linearSumAssignment as Vn}from"linear-sum-assignment";import{xCostMatrix as Jn}from"ml-spectra-processing";function $t(e,r){let t=e.map(o=>o.delta),i=r.map(o=>o.delta),n=Jn(i,t,{fct:(o,l)=>Math.abs(o-l)}),{rowAssignments:s}=Vn(n,{maximaze:!1});return Array.from(s)}function jt(e,r){let{assignments:t,ranges:i}=r;t?.sort((o,l)=>l.delta-o.delta);let n=[],s=[];for(let o of i){let l=0,{from:a,to:m}=o,f=[];for(let c=l;c<t.length;c++){let{delta:b}=t[c];b<=m&&b>=a?(f.push(t[c]),s.push(c)):b>m&&(l=c)}if(f.length>0){let c=o.signals,b=[],u=f.length>1&&c.length>1?$t(c,f):[0];for(let y=0;y<f.length;y++){let 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`}=t;D(e,"spectralWidth",r[`${i}SweepWidth`]/e.originFrequency[0]);let s=r[`${i}.PULSESEQUENCE`].split(n),o=[];r[".OBSERVENUCLEUS"]&&o.push(r[".OBSERVENUCLEUS"]),r.INDIRECTNUCLEUS&&o.push(r.INDIRECTNUCLEUS),e.nucleus=k(o),e.pulseSequence=s[0];let l=s.slice(2,-1);if(o.length>1)if(o[0]===o[1])e.spectralWidth.push(e.spectralWidth[0]);else{let a=JSON.stringify(l).match(/\$\$SW1=\s*(?<sw>[+-]?(?:[0-9]*[.])?[0-9]+)/);if(a?.groups){let{originFrequency:c}=e,f=Number.parseFloat(a.groups.sw);e.spectralWidth.push(f/c[1])}}return e}function On(e,r){let{T1NUCLEUS:t,T2NUCLEUS:i,PAGE:n}=r;e.pulseSequence=r.EXPERIMENT||r[".PULSESEQUENCE"];let s=[],{dimension:o,isComplex:l}=e;if(o===2&&e.pulseSequence==="T1"){let f=l?2:1;for(let m=0;m<n.length;m+=f){let b=n[m].replace(/T1=/,"");s.push(Number(b))}r.vdlistValues=s}e.nucleus=o>1?[i,t]:i;let{phc0:a,phc1:c}=e;if(a&&c){let f=ce({phc0:a,phc1:c});e={...e,...f}}}var vn={keepRecordsRegExp:/.*/,keepFiles:!0};async function de(e,r={}){let t={spectra:[],molecules:[]},{converter:i={},selector:n={},logger:s}=r,o=pt(e,{logger:s,...kn(n)}),l=[];for(let c of o)l.push(bt(c,{...vn,...i}).then(f=>Ln(f,r)));let a=await Promise.allSettled(l);for(let c=0;c<a.length;c++){let f=a[c];if(f.status==="fulfilled"){let m=ce(f.value.info);t.spectra.push({...f.value,info:{...f.value.info,...m}})}else if(f.reason){let m=o[c].name;s?.warn(`Bruker data: ${m}, fails with: ${f.reason}`);continue}}return s&&s[t.spectra.length>0?"info":"debug"](`Loaded ${t.spectra.length} spectra from Bruker files`),wn(t)}function Ln(e,r={}){let{keepSource:t=!1,logger:i}=r,n={...e.info,...e.meta},s=fe(n,{logger:i}),o={},{isFid:l}=s;if(qn(e)){let u=e.minMax;for(let y in u){let g=u[y];g&&(g.z=$(g.z))}o.components=e.minMax}else s.dimension===1&&(o.components=e.spectra);let{source:a}=e,{expno:c,name:f,files:m}=a;n.vdlist&&(n.vdlistValues=le(n.vdlist));let b={dependentVariables:[o],meta:n,info:{...s,experimentNumber:c,name:f}};return m&&t&&(b.sourceSelector={files:m.map(u=>u.relativePath)}),Bn(b,e),b}function kn(e){let{general:r={},bruker:t={}}=e,{processingNumbers:i,experimentNumbers:n,...s}=t;return{...r,...s,processingNumbers:Mt(i),experimentNumbers:Mt(n)}}function Mt(e){if(e)return e.split(/[^\d]+/).filter(Boolean).map(r=>Number.parseInt(r,10))}function qn(e){let{info:r}=e;return r.twoD}function Bn(e,r){if(!("integrals"in r))return;let{integrals:t=[]}=r;e.integrals={values:t.map(i=>{let{from:n,to:s,integration:o}=i;return{from:n,to:s,integral:o,kind:"signal"}})}}var ge=class{id="@zakodium/nmrium-core-plugins#BrukerLoaderPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={onFiles:this.onReadProcessFiles}}onReadProcessFiles=(r,t)=>{let{sourceSelector:i,converter:n,keepSource:s,logger:o}=t??{};return de(r,{converter:n?.bruker,selector:i,keepSource:s,logger:o})}};function Be(){return new ge}import{formatSpectra as bi}from"@zakodium/nmrium-core";import{createTree as Fi}from"jcampconverter";function xt(e,r,t={}){let{selector:i={},keepSource:n=!1}=t;if(!n)return e;for(let s=0;s<e.spectra.length;s++){let o=e.spectra[s];o.sourceSelector={files:[r.relativePath],jcamp:{index:s,...i}}}return e}import{convert as _n}from"jcampconverter";function _e(e,r,t){let{dataType:i,children:n}=e,s=i==="LINK"&&n?n:[e];for(let o of s){if(o.dataType==="LINK"){_e(o,r,t);continue}let l=_n(o.jcamp,t);r.push(...l.flatten)}}function Et(e,r={}){let t=[],i=Tt(e,r);for(let o of i?e:[])o.dataType==="LINK"?o.children=Ue(o.children,r):o=Ue([o],r)[0],t.push(o);let{name:n,logger:s}=r;return e.length===0&&s?.warn(`There is no data ${n?`in ${n}`:"in the JCAMP-DX"}`),t}function Ue(e=[],r={}){let{name:t,logger:i,tree:n=[],dataSelection:s="both"}=r,o=[];for(let f of e){let{dataType:m,dataClass:b}=f;if(m==="LINK")f.children=Ue(f.children,r);else if(n.some(u=>{let{dataClass:y=b,dataType:g=m}=u;return b===y&&m===g})){i?.warn(`Skipping ${b} and ${m} ${t?`in ${t}`:"in the JCAMP-DX"},
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7
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because it didn't match the import filters`);continue}o.push(f)}let l=[],a=o.some(It),c=o.some(Rt);for(let f of o){if(s!=="both"&&f.dataType!=="LINK"){if(It(f)&&(s==="ft"||s==="preferFT"&&c)){i?.warn(`Skipping raw data ${t?`in ${t}`:"in the JCAMP-DX"} because it didn't match the import filters`);continue}if(Rt(f)&&(s==="fid"||s==="preferFID"&&a)){i?.warn(`Skipping FFT data ${t?`in ${t}`:"in the JCAMP-DX"} because it didn't match the import filters`);continue}}l.push(f)}return l}function Rt(e){return e.dataType?.toUpperCase().includes("SPECTRUM")&&e.dataClass&&!e.dataClass.toUpperCase().includes("PEAK")}function It(e){return e.dataType?.toUpperCase().includes("FID")}function Tt(e,r={}){let{logger:t,name:i=""}=r;for(let n of e){if(n.dataType==="LINK"&&Tt(n.children,r))return!0;let{dataType:s=""}=n,o=s.toLowerCase();if(o.length>0){if(o.includes("spectrum")&&!o.includes("nmr"))return t?.warn(`File ${i} was ignored because it is a ${s}`),!1;if(o.includes("nmr"))return!0}}return!1}import{generateID as wt}from"@zakodium/nmrium-core";import{parseJcampCS as Vn}from"jcampconverter";import*as Jn from"openchemlib";import{isMolfileNotEmpty as Un}from"nmr-processing";import{Molecule as $n}from"openchemlib";async function Ct(e,r={}){let t=await e.text(),i=Y(t),n={molecules:i,spectra:[]};return i.length===0&&r.logger?.debug(`${e.name} is an empty molfile`),n}function Y(e){let r=[];if(!Un(e))return[];let i=$n.fromMolfile(e).toMolfile();return r.push({molfile:i}),r}import{isMolfileNotEmpty as jn}from"nmr-processing";import*as Wn from"openchemlib";import{getDiastereotopicAtomIDsFromMolfile as Xn}from"openchemlib-utils";var zn=new Set(["ndnmrspectrum","ndnmrfid","nmrspectrum","nmrfid"]);function he(e){let{dataType:r="",dataClass:t=""}=e,i=r.replaceAll(/\s/g,"").toLowerCase(),n=t.replaceAll(/\s/g,"").toLowerCase();return zn.has(i)&&n!=="peaktable"}function Ot(e,r,t={}){let{spectra:i,info:n,meta:s}=e,o=i[0].data,l=[],a={x:"delta",y:"intensity",w:"width",m:"multiplicity",a:"atom"},{logger:c,name:f,spectraData:m}=t,{CROSSREFERENCE:b}=n,u=typeof b!="string"?b:b.split(/\r?\n/).map(S=>S.trim()).filter(Boolean),y=u.find(S=>S?.toLowerCase().includes("structure"));if(y===void 0)return c&&c.warn(`There is not a structure reference for ${f} file, assignment object could not be completed`),null;let g=Number.parseInt(y?.toLowerCase().replace(/_/,"").replace(/structure:\s*blockid\s*=\s*(?<blockId>.*)/,"$<blockId>"),10);if(Number.isNaN(g)||g<1)return c&&c.warn(`Structure block_id not found for ${f} file, assignment object could not be completed`),null;let d=m?.molecules?.find(S=>S.blockId===g)?.molfile??"";if(d===""){let S=r.find(x=>x.info.BLOCKID===g),{MOLFILE:A=""}=S?.meta||{};d=A}if(!jn(d))return c&&c.warn(`Empty molfile for ${f} file with structure block_id = ${g}, assignment object could not be completed`),null;let h=Xn(Wn,d),F=ue({...n,...s},{},"");for(let S=0;S<o.x.length;S++){let A={};for(let x in o){let I=o[x][S];typeof I=="string"&&I.startsWith("<")&&I.endsWith(">")&&(I=I.slice(1,-1)),A[a[x]]=I}if("atom"in A){let x=h.map[A.atom-1];F.includes("1H")?x.nbHydrogens>0?(A.diaIDs=x.hydrogenOCLIDs,A.nbHydrogens=x.nbHydrogens):(A.diaIDs=[x.oclID],A.nbHydrogens=x.nbHydrogens):(A.diaIDs=[x.oclID],A.nbHydrogens=1)}l.push(A)}let N={};for(let S of l){let{delta:A,diaIDs:x}=S,I=`${A}_${x.join("_")}`;if(N[I])N[I].atoms.push(S.atom);else{let{atom:Me,...P}=S;N[I]={...P,atoms:[S.atom]}}}let M=[];for(let S of u)S.toLowerCase().includes("spectrum")&&M.push(Number(S.toLowerCase().replace(/_/,"").replace(/.*:\s*blockid=(?<blockId>.*)/,"$<blockId>")));if(M.length===0){for(let S of r)if(he(S)){let{BLOCKID:A}=S.info;M.push(Number(A))}M.length>1&&(M=[],c&&c.warn(`There is not a spectral cross-reference for the peak assignment in the ${f} file`))}return{moleculeBlockID:g,spectraBlockIDs:M,assignments:Object.values(N),molecule:h.molecule}}function vt(e,r,t,i){for(let n of e){let{meta:s,dataClass:o="",dataType:l="",info:a}=n,c=Number.parseInt(String(a.BLOCKID),10);s.MOLFILE?Zn(String(s.MOLFILE),r,c):n.jcampCS&&Gn(n,r,c),Yn(o,l)&&Hn(r,n,e,i),he(n)&&t.push(n)}}function Yn(e,r){return e?.toLowerCase().includes("assignments")&&r?.toLowerCase().includes("assignments")}function Hn(e,r,t,i){let n=Ot(r,t,{spectraData:e,logger:i.logger,name:i.name});if(e.assignmentsByBlocks||(e.assignmentsByBlocks={}),n){let{spectraBlockIDs:s}=n;for(let o of s)e.assignmentsByBlocks[o]=n}}function Gn(e,r,t){r.molecules||(r.molecules=[]);let i=Vn(e,{OCL:Jn}),n=Y(i?.molfile||"");n.length>0&&r.molecules.push({id:wt(),blockId:t,...n[0]})}function Zn(e,r,t){r.molecules||(r.molecules=[]);let i=Y(String(e));r.molecules.push({id:wt(),blockId:t,...i[0]})}import{generateID as Jt}from"@zakodium/nmrium-core";import{matrixMinMaxZ as Vt,reimPhaseCorrection as li}from"ml-spectra-processing";import{xyAutoRangesPicking as mi}from"nmr-processing";function H(e){return e.slice(0,Math.max(0,e.lastIndexOf(".")))}function G(e){e.sort((r,t)=>r.from-t.from);for(let r=0;r<e.length-1;r++)e[r].to>e[r+1].from&&(e[r].to=Math.max(e[r+1].to,e[r].to),e[r].signals=e[r].signals.concat(e[r+1].signals),e[r].integration+=e[r+1].integration,e.splice(r+1,1),r--);return e}import{splitPatterns as ri}from"nmr-processing";import{xMaxValue as Kn}from"ml-spectra-processing";function te(e){return e.trim().slice(1,-1).split(/,\s*/).map(r=>r.trim())}var Qn={I:"id",X:"from",Y:"to",Hs:"delta",An:"integration",H:"nbAtoms",C:"multiplicity",N:"assignment","(J)":"js"},Lt=["I","X","Y","Hs","An","H","C","N","(J)"];function kt(e){let r={headersFromParenthesis:[],headersFromComments:[],comments:[],data:[],multiplets:[]},t=e.split(/\r?\n/).filter(i=>i.trim()!=="");if(t.length===0)return r;if(t[0].startsWith("(")&&!t[0].match(/\d/)){let i=t.shift();r.headersFromParenthesis=te(i)}return r.comments=t.filter(i=>i.startsWith("$$")).map(i=>i.replace(/^\$\$\s*/,"")),r.headersFromComments=ti(r.comments),r.data=t.filter(i=>!i.startsWith("$$")).map(te),r.multiplets=ei(r),r}function ei(e,r={}){let{logger:t}=r,i=e.data[0].map((a,c)=>c).filter(a=>e.data.every(c=>Number.isNaN(c[a])||Number.isNaN(Number(c[a]))));if(t?.trace(`Parsing JCAMP-DX assignment: stringColumnIndexes: ${i.join(",")}`),i.length===0)return t?.warn("Parsing JCAMP-DX assignment: No string columns found. 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Skipping parsing of assignment."),[];return Kn(e.data.map(a=>a.length))>s.length&&t?.warn("Some assignments are containing more values than headers"),e.data.map(a=>{let c={};for(let f=0;f<s.length;f++){let m=s[f];c[Qn[m]||m]=a[f]}return c})}function ti(e){return e.map(r=>r.split(":")[0].trim()).filter(r=>r.length>0)}function qt(e,r={}){let{logger:t}=r,i=kt(e),n={multiplets:[],comments:i.comments};for(let s of i.multiplets){let{id:o,from:l,to:a,delta:c,integration:f,nbAtoms:m,multiplicity:b}=s,u={id:o,js:[],multiplicity:"",...ni({from:l,to:a,delta:c,integration:f,nbAtoms:m})};if(typeof s.js=="string"){let y=s.js.split(/\s+/).map(Number.parseFloat),g=0,p=ri(b).map(F=>{let N=(F?.multiplicity||1)-1;return g+=N,{value:F.value,multiplicity:F?.multiplicity,js:y.slice(g-N,g)}}),d=p.reduce((F,N)=>F+(N.multiplicity?N.multiplicity-1:0),0);y.length!==d&&t?.warn(`The number of j values (${y.length}) is not equal to the sum of the multiplicities - 1 (${d})`);let h=[];for(let F of p){if(F.js.every(N=>N===F.js[0])){h.push(F);continue}if(F.multiplicity!==F.js.length+1){h.push(F);continue}for(let N=0;N<F.multiplicity-1;N++)h.push({value:"d",multiplicity:2,js:[F.js[N]]})}h.sort((F,N)=>N.js[0]-F.js[0]),u.js=h.map(F=>({coupling:F.js[0],multiplicity:F.value}))}typeof s.assignment=="string"&&(u.assignment=si(s.assignment)),typeof s.multiplicity=="string"&&(u.multiplicity=s.multiplicity),n.multiplets.push(u)}return n}function ni(e){let r={};for(let t in e){let i=e[t],n=typeof i=="number"?i:Number.parseFloat(i);Number.isNaN(n)||(r[t]=n)}return r}var ii={quot:'"',apos:"'",comma:",",amp:"&",lpar:"(",rpar:")",lt:"<",gt:">",colon:":",semi:";"};function si(e){return e.replaceAll(/&(\w+);/gi,(r,t)=>ii[t.toLowerCase()]||r)}function Bt(e){let r=e.split(/\r?\n/).filter(i=>i.trim()!==""),t=[];for(let i of r)if(i.startsWith("(")){let[n,s,o]=te(i).map(Number.parseFloat);t.push({id:n,x:s,y:o})}return t}function _t(e,r={}){let t={};if(!e["OBSERVED MULTIPLETS"])return[];let i=qt(e["OBSERVED MULTIPLETS"],r);if(!i)return[];let{multiplets:n}=i;for(let s of n){let{id:o,from:l,to:a,integration:c=0,...f}=s;t[o]={from:l,to:a,integration:c,signals:[{id:o,...f}]}}if(e["OBSERVED MULTIPLETS PEAKS"]){let s=Bt(e["OBSERVED MULTIPLETS PEAKS"]),o={};for(let l of s){let{id:a,x:c,y:f}=l;o[a]||(o[a]=[]),o[a].push({x:c,y:f,width:.05})}for(let l in t)o[l]&&(t[l].signals[0].peaks=o[l])}return G(Object.values(t))}function Ut(e,r){let i=[...e.getMolecularFormula().formula.matchAll(/(?<element>[A-Z][a-z]?)(?<count>\d*)/g)].map(s=>({element:s?.groups?.element,count:s?.groups?.count?Number(s.groups.count):1})),n=[...r.nucleus[0].matchAll(/[0-9]*(?<element>[A-Z][a-z]?)/g,"$element")][0].groups.element;return i.find(s=>s.element===n)?.count||100}function $t(e){let r={};return".PHASE0"in e&&(r.ph0=Number.parseFloat(e[".PHASE0"]),r.ph1=Number.parseFloat(e[".PHASE1"])),r}function $e(e){let{ph0:r,ph1:t}=e;return Number.isFinite(r)&&Number.isFinite(t)}import{generateID as zt}from"@zakodium/nmrium-core";function jt(e,r,t){for(let i=0;i<e.length;i++){if(r.includes(i))continue;let{delta:n,multiplicity:s="",diaIDs:o}=e[i],l=Number(n)-.01,a=Number(n)+.01;t.push({from:l,to:a,integration:1,id:zt(),signals:[{id:zt(),delta:n,multiplicity:s,diaIDs:o}]})}}import{linearSumAssignment as oi}from"linear-sum-assignment";import{xCostMatrix as ai}from"ml-spectra-processing";function Wt(e,r){let t=e.map(o=>o.delta),i=r.map(o=>o.delta),n=ai(i,t,{fct:(o,l)=>Math.abs(o-l)}),{rowAssignments:s}=oi(n,{maximaze:!1});return Array.from(s)}function Xt(e,r){let{assignments:t,ranges:i}=r;t?.sort((o,l)=>l.delta-o.delta);let n=[],s=[];for(let o of i){let l=0,{from:a,to:c}=o,f=[];for(let m=l;m<t.length;m++){let{delta:b}=t[m];b<=c&&b>=a?(f.push(t[m]),s.push(m)):b>c&&(l=m)}if(f.length>0){let m=o.signals,b=[],u=f.length>1&&m.length>1?Wt(m,f):[0];for(let y=0;y<f.length;y++){let g=u[y],{delta:p,multiplicity:d,diaIDs:h}=f[y];g>-1?b.push({...m[g],diaIDs:h}):b.push({delta:p,multiplicity:d,diaIDs:h})}o.signals=b,n.push(o)}}jt(t,s,n),n.sort((o,l)=>o.from-l.from),e.ranges={values:G(n).map(o=>{let{integration:l,...a}=o;return a}),options:{sum:r.integrationSum,isSumConstant:!0,sumAuto:!0}},e.ranges.options.moleculeId=String(r.moleculeId)}function Yt(e,r,t,i,n){let{logger:s}=n,o={components:Ht(e)?pi(e,t.isFid):ui(e)},{name:l=t.title||`jcamp_${Jt()}`}=n,a={dependentVariables:[o],meta:r,info:{...t,name:H(l)}};return ci(e)&&fi(a,i,r,e,t,{logger:s}),a}function Ht(e){return"minMax"in e}function ci(e){return!Ht(e)}function ui(e){return e.spectra.map(r=>{let t=$(r.data);return{...r,data:t}})}function pi(e,r){let t={...e.minMax,z:$(e.minMax?.z)};return r?di(t):{rr:t}}function fi(e,r,t,i,n,s){let{assignmentsByBlocks:o}=r,l=$t(t);$e(l)&&gi(e,l);let a=String(i.info.BLOCKID);if(o?.[a]){let{molecule:c,assignments:f,moleculeBlockID:m}=o[a],b=Ut(c,n),u=$(i.spectra[0].data);if(u.x[0]>u.x[1])for(let d of i.spectra)d.data.x.reverse(),d.data.y.reverse();if($e(l)&&i.spectra.length>1){let{re:d}=hi(i,l);u.y=d}let{x:y,y:g}=u,p=_t(t,s)??mi({x:y,y:g},{peakPicking:{frequency:n.originFrequency},ranges:{frequency:n.originFrequency,integrationSum:b}});Xt(e,{moleculeId:m,ranges:p,assignments:f,integrationSum:b})}}function di(e){let{z:r,...t}=e,i=[],n=[];for(let l=0;l<r.length;l+=2)i.push(r[l].slice()),n.push(r[l+1].slice());let s=Vt(i),o=Vt(n);return{re:{...t,z:i,minZ:s.min,maxZ:s.max},im:{...t,z:n,minZ:o.min,maxZ:o.max}}}function gi(e,r){let{ph0:t,ph1:i}=r;e.filters||(e.filters=[]),e.filters.push({id:Jt(),name:"phaseCorrection",value:{ph0:t,ph1:i,absolute:!1},enabled:!0})}function hi(e,r){let{ph0:t,ph1:i}=r,{re:n,im:s}=li({re:e.spectra[0].data.y,im:e.spectra[1].data.y},t*Math.PI/180,i*Math.PI/180);return{re:n,im:s}}function Gt(e,r,t){let{logger:i}=t,n=[];for(let s of e)if(s.spectra&&s.spectra.length>0||s.minMax){yi(s);let o={...s.info,...s.meta},l=fe(o,{logger:i});if(l.experiment==="wobble_curve")continue;n.push(Yt(s,o,l,r,t))}return n}function yi(e){let r=e.meta["BRUKER FILE EXP"];if(!r)return;let i=(Array.isArray(r)?r:[r]).find(s=>s.slice(0,10).includes("vdlist"));if(!i)return;let n=i.split(`
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`).slice(1);e.info.vdlistValues=le(n)}async function ye(e,r={}){let t=await e.text(),i=Zt(t,{name:e.name,...r});return xt(i,e,r)}function Zt(e,r={}){let t={spectra:[],molecules:[]},{name:i,converter:n={},selector:s={},logger:o}=r,{keepRecordsRegExp:l=/.*/}=n,a={keepSpectra:!0,noContour:!0,noTrimRegExp:/\$MOLFILE/,keepRecordsRegExp:l,logger:o},c=Et(Fi(e),{name:i,...s,logger:o});for(let f of c)Si(f,t,a,i);if(Ni(t,s),t.spectra.length===0&&c.length>0){let f=t.molecules.length===0?" nor molecule":"";o?.warn(`No spectra${f} data was loaded from file ${i}`)}return bi(t)}function Si(e,r,t,i){let n=[],s=[],o={molecules:[]},{logger:l}=t,a={name:i,logger:l};_e(e,s,t),vt(s,o,n,a),r.spectra.push(...Gt(n,o,a)),r.molecules.push(...o.molecules)}function Ni(e,r){r.index!==void 0&&(e.spectra=e.spectra.slice(r.index,r.index+1))}var 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i,n={},s=[];n.fileIdentifier=t.readChars(8),n.endian=Di[t.readInt8()],n.majorVersion=t.readUint8(),n.minorVersion=t.readUint16(),n.dataDimensionNumber=t.readUint8(),n.dataDimensionExist=t.readByte().toString(2).split("").map(P=>!!Number(P)),i=t.readByte(),n.dataType=Ai[i>>6],n.dataFormat=Mi[i&63],n.dataInstrument=Pi[t.readInt8()],n.translate=R(t,8,"readUint8"),n.dataAxisType=R(t,8,"readUint8").map(P=>xi[P]),n.dataUnits=Qt(t,8),n.title=Z(t,124);for(i in R(t,4,"readUint8"))s.push(Kt[i>>4],Kt[i&15]);n.dataAxisRanged=s,n.dataPoints=R(t,8,"readUint32"),n.dataOffsetStart=R(t,8,"readUint32"),n.dataOffsetStop=R(t,8,"readUint32"),n.dataAxisStart=R(t,8,"readFloat64"),n.dataAxisStop=R(t,8,"readFloat64"),s=new Uint8Array(4);for(let P=0;P<4;P++)s[P]=t.readByte();let o=1990+(s[0]>>1),l=(s[0]<<3&8)+(s[1]>>5),a=s[2]&31;n.creationTime={year:o,month:l,day:a};for(let 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Me={info:{sampleName:L(m,"sample_id").value,creationTime:n.creationTime,revisionTime:n.revisionTime,author:n.author,comment:n.comment,solvent:L(m,"solvent").value,temperature:C(m,"temp_get"),probeName:L(m,"probe_id").value,fieldStrength:C(m,"field_strength"),experiment:L(m,"experiment").value,dimension:n.dataDimensionNumber,nucleus:p,date:d,epoch:h,pulseStrength90:C(m,"x90"),numberOfScans:L(m,"scans").value,relaxationTime:C(m,"relaxation_delay"),dataPoints:n.dataPoints.slice(0,n.dataDimensionNumber),dataOffsetStart:n.dataOffsetStart,dataOffsetStop:n.dataOffsetStop,dataUnits:I,dataSections:Object.keys(u),originFrequency:A,frequencyOffset:x,acquisitionTime:F,spectralWidth:N,spectralWidthClipped:M,dataAxisStart:n.dataAxisStart,dataAxisStop:n.dataAxisStop,resolution:S,decimationRate:L(m,"decimation_rate").value,paramList:JSON.stringify(m.paramArray.map(P=>P.name))},headers:n,parameters:m,data:u};return Me.info.digitalFilter=Oi(m,r),Me}import{formatSpectra as ki,getOneIfArray as 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m=We(e,c,f),{componentLabels:b=m.componentLabels}=t;return{type:"internal",quantityType:nr[i],numericType:rr[r],encoding:n,name:s,unit:o,quantityName:l,componentLabels:b,sparseSampling:a,description:t.description||"",application:t.application||"",components:m.components,dataLength:m.dataLength}}function wi(e){return K(e.re)&&K(e.im)}function vi(e){return!K(e.re[0])}function We(e,r,t){let i=[],n=[],s=[];if(wi(e))if(vi(e)){i[0]=je(r[0],t[0],e.re.length);let o=new Float64Array(i[0]);for(let l=0;l<i[0];l+=2){let a=l+r[0]*2;o[l]=e.re[a/2],o[l+1]=e.im[a/2]}s.push(o),n.push("complex")}else if(K(e.re[0])){i[0]=Li(r[1],t[1],e.re.length),i[1]=je(r[0],t[0],e.re[0].length);for(let o=0;o<i[0];o++){let l=new Float64Array(i[1]);for(let a=0;a<i[1];a+=2){let c=a+r[0]*2;l[a]=e.re[o][c/2],l[a+1]=e.im[o][c/2]}s.push(l)}}else throw new Error("check your object");else if(K(e.re.re)){i[0]=je(r[1],t[1],e.re.re.length);let o=We(e.re,r,t).components,l=We(e.im,r,t).components;for(let a=0;a<i[0]/2;a++)s.push(o[a],l[a])}else throw new Error("check the dimension or the type of data in your array");return{dataLength:i,componentLabels:n,components:s}}function Li(e,r,t){return r-e+1<t?r-e+1:t}function je(e,r,t){return r-e+1<t?(r-e+1)*2:t*2}async function or(e,r={}){let t=await e.arrayBuffer(),{name:i=H(e.name),keepSource:n=!1}=r,s={spectra:[],molecules:[]},l=Wi(t)[0],{metadata:a,...c}=l.description,f=0,m=c.dimension===1?"1d":"2d",b="NMR SPECTRUM",u=c.dimension===1?c.nucleus[0]:c.nucleus,y=c.spectralWidthClipped[0],g;l.dependentVariables&&(c.dimension===1?g=zi(l):c.dimension===2&&(g=ji(l)));for(let d in c)Array.isArray(c[d])&&c[d].length===1&&(c[d]=c[d][0]);let p={data:g,info:{...c,acquisitionMode:f,experiment:m,type:b,nucleus:u,spectralWidthClipped:y,name:i},meta:a};return n&&(p.sourceSelector={files:[e.relativePath]}),s.spectra=[p],ki(s)}function zi(e){let 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hr(e,r={}){let{mixedEOL:t}=r,{molecules:i}=is(e,{mixedEOL:t}),n=[];for(let{molfile:s}of i){let o=Y(s);n.push(...o)}return n}async function yr(e,r={}){let{logger:t,mixedEOL:i}=r,n=await e.text(),s=hr(n,{mixedEOL:i}),o={molecules:s,spectra:[]};return t&&t[s.length>0?"info":"debug"](`Loaded ${o.molecules.length} molecules from the ${e.name} file`),o}var De=class{id="@zakodium/nmrium-core-plugins#SDFLoaderPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={supportedExtensions:["sdf"],onFile:this.onReadProcessFile.bind(this)}}onReadProcessFile(r,t={}){let{logger:i}=t;return i?.debug(`Reading sdf file: ${r.name}`),yr(r,{logger:i})}};function Ye(){return new De}import{Molecule as ss}from"openchemlib";function br(e){let r=[],t=e.split(/\r?\n/).filter(Boolean);for(let i of t){let s=ss.fromSmiles(i).toMolfile();r.push({molfile:s})}return r}async function Fr(e,r={}){let t=await e.text(),i=br(t),n={molecules:i,spectra:[]};return r.logger?.info(`Found ${i.length} molecules from the ${e.name} file`),n}var Pe=class{id="@zakodium/nmrium-core-plugins#SMILESLoaderPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={supportedExtensions:["smi","smiles"],onFile:this.onReadProcessFile.bind(this)}}onReadProcessFile(r,t={}){let{logger:i}=t;return Fr(r,{logger:i})}};function He(){return new Pe}import{formatSpectra as Ss}from"@zakodium/nmrium-core";import{createFromToArray as os}from"ml-spectra-processing/utils";function as(e){e.setLittleEndian();let r=e.offset,t=32*3;e.offset=t/8;let i=e.readInt32(),n=[2,4],s=[2**25,2**26];if(!n.includes(i))if(s.includes(i))e.setBigEndian();else throw new Error(`Unexpected value of eBytes (${i}). 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9
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+
${n.concat(s).join(",")}`);return e.offset=r,e.isBigEndian()?"BE":"LE"}var Sr=class{storesData;isSpectrum;isInt32;isFloat32;isComplex;isHypercomplex;isBaselineCorrected;constructor(e){if(this.storesData=(e&1)!==0,!this.storesData)throw new Error("No data stored in file. Exiting...");if(this.isSpectrum=(e&2)!==0,this.isSpectrum)throw new Error("Script only analyzes FIDs. Found spectrum.");if(this.isInt32=(e&4)!==0,this.isFloat32=(e&8)!==0,this.isComplex=(e&16)!==0,this.isHypercomplex=(e&32)!==0,this.isHypercomplex)throw new Error("Script does not analyze hypercomplex data (yet).");this.isBaselineCorrected=(e&64)!==0}},ls=class extends Sr{moreBlocks;npComplex;nfComplex;niComplex;ni2Complex;constructor(e){super(e),this.moreBlocks=(e&128)!==0,this.npComplex=(e&256)!==0,this.nfComplex=(e&512)!==0,this.niComplex=(e&1024)!==0,this.ni2Complex=(e&2048)!==0}},ms=class extends Sr{isAcqPar;isSecondFT;isTransformed;is3D;isNp;isNf;isNi;isNi2;constructor(e){super(e),this.isAcqPar=(e&128)!==0,this.isSecondFT=(e&256)!==0,this.isTransformed=(e&512)!==0,this.is3D=(e&1024)!==0,this.isNp=(e&2048)!==0,this.isNf=(e&4096)!==0,this.isNi=(e&8192)!==0,this.isNi2=(e&16384)!==0}},cs=class{lines;length;index;eol;constructor(e,r={}){let{eol:t=`
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10
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+
`,index:i=0}=r;this.eol=t,this.index=i,this.lines=e.split(this.eol),this.length=this.lines.length}readLine(){if(this.index>=this.length)throw new Error(`Last index is ${this.length-1}. Current index ${this.index}.`);return this.lines[this.index++]}readLines(e){let r=this.lines.slice(this.index,this.index+e);return 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Ae=class{id="@zakodium/nmrium-core-plugins#VarianLoaderPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={onFiles:this.onReadProcessFiles}}onReadProcessFiles=(r,t)=>{let{keepSource:i,logger:n}=t??{};return Mr(r,{keepSource:i,logger:n})}};function Ze(){return new Ae}function Ms(e,r=[]){return[Je(e),Ze(),Be(),ze(),Ve(),Ye(),He(),Xe(),Oe()].concat(r)}function xs(){let e=new As;return e.registerPlugins(Ms(e)),e}import{getOneIfArray as Rr}from"@zakodium/nmrium-core";import{from1DNMRVariables as Rs}from"convert-to-jcamp";function xr(e,r){return e.filters.find(t=>t.name===r)}function Is(e,r={}){let{info:t,meta:i,data:n}=e,{onlyReal:s=!1}=r,{isFid:o,spectralWidth:l}=t,a=Rr(t.baseFrequency||t.originFrequency),{x:c,re:f,im:m}=n,b=new Float64Array(f),u=!s&&m?new Float64Array(m):void 0,y={};re(y,"SW",l),re(y,"BF1",a);let g=xr(e,"fft")?.enabled,p={originFrequency:t.originFrequency,dataType:!t.isFid||g?"NMR SPECTRUM":"NMR FID",dataClass:!s&&m?"NTUPLES":"XYDATA"};if(o){let F=e.filters.find(N=>N.name==="digitalFilter");if(F&&!g){let{value:{digitalFilterValue:N},enabled:M}=F;if(M){let S=Math.floor(N);b.set(f.slice(f.length-S)),b.set(f.slice(0,f.length-S),S),m&&u&&(u.set(m.slice(m.length-S)),u.set(m.slice(0,m.length-S),S))}}re(p,"decim",t.decim),re(p,"dspfvs",t.dspfvs),re(p,"digitalFilter",t.digitalFilter)}let d={xyEncoding:"DIFDUP",info:{...t,...p},meta:{...i,...y}},h={x:{data:c,label:t.isFid?"TIME":"FREQUENCY",units:t.isFid?"second":"HZ",symbol:"X"},r:{data:b,label:`${t.isFid?"FID":"SPECTRUM"}/REAL`,units:"ARBITRARY UNITS",symbol:"R"}};return u&&(h.i={data:u,label:`${t.isFid?"FID":"SPECTRUM"}/IMAG`,units:"ARBITRARY UNITS",symbol:"I"}),Rs(h,d)}function re(e,r,t){t!==void 0&&(e[r]=Rr(t))}export{ie as AutoPostProcessingPlugin,ge as BrukerLoaderPlugin,be as JCAMPDXLoaderPlugin,Fe as JEOLLoaderPlugin,Se as MolfileLoaderPlugin,Ne as NMReDATALoaderPlugin,De as SDFLoaderPlugin,Pe as SMILESLoaderPlugin,Ae as VarianLoaderPlugin,Oe as autoPostProcessing,Be as brukerLoader,xs as default,xs as init,ze as jcampDXLoader,Xe as jeolLoader,Ve as molfileLoader,Je as nmreDATALoader,Zt as processJCAMPDX,hr as readSDF,br as readSMILES,Ms as recommended,Ye as sdfLoader,He as smilesLoader,Is as spectrum1DToJCAMPDX,Ze as varianLoader};
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package/package.json
CHANGED
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@@ -1,11 +1,16 @@
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1
1
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{
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2
2
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"name": "@zakodium/nmrium-core-plugins",
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3
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-
"version": "0.1.
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3
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+
"version": "0.1.4",
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4
4
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"description": "Recommended plugins for NMRium, loaders of common formats like bruker or jcamp, and some post-processing plugins",
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5
5
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"author": "Zakodium Sàrl",
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6
6
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"license": "CC-BY-NC-SA-4.0",
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7
7
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"type": "module",
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8
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-
"exports":
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8
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+
"exports": {
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9
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+
".": {
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10
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+
"nmrium-internal": "./src/index.ts",
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11
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+
"default": "./dist/nmrium-core-plugins.js"
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12
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+
}
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13
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},
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9
14
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"files": [
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10
15
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"dist"
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11
16
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],
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@@ -13,9 +18,8 @@
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13
18
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"#assets": "./src/assets.js"
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14
19
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},
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20
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"scripts": {
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16
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-
"api-extractor": "api-extractor run --local",
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17
21
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"bundle": "node scripts/esbuild.js && npm run bundle-types",
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18
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-
"bundle-types": "npm run tsc &&
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22
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+
"bundle-types": "npm run tsc && yarn g:api-extractor",
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19
23
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"clean": "rimraf types dist coverage",
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20
24
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"dev:eslint-fix": "eslint --cache --fix $(git diff --name-only --relative) --quiet",
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21
25
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"prepack": "npm run clean && npm run bundle",
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@@ -24,37 +28,37 @@
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24
28
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"tsc": "tsc --project tsconfig.types.json"
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25
29
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},
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30
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"devDependencies": {
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27
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-
"@microsoft/api-extractor": "^7.52.7",
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28
31
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"@types/lodash.merge": "^4.6.9",
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29
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-
"@types/node": "^22.15.
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32
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+
"@types/node": "^22.15.31",
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30
33
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"@zakodium/bruker-parser": "^0.0.0",
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31
34
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"@zakodium/jeol-parser": "^0.0.0",
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35
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+
"@zakodium/nmr-types": "^0.0.1",
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32
36
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"@zakodium/varian-parser": "^0.0.0",
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33
37
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"bruker-data-test": "^0.5.4",
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34
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-
"esbuild": "^0.25.
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38
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+
"esbuild": "^0.25.5",
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35
39
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"fifo-logger": "^1.0.0",
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36
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-
"jcamp-data-test": "^0.
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40
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+
"jcamp-data-test": "^1.0.0",
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37
41
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"jeol-data-test": "^0.5.2",
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38
42
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"jest-matcher-deep-close-to": "^3.0.2",
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39
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-
"msw": "^2.
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43
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+
"msw": "^2.10.2",
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40
44
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"nmredata-data-test": "^0.4.0",
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41
45
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"rimraf": "^6.0.1",
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42
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-
"vitest": "^3.
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46
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+
"vitest": "^3.2.3"
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43
47
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},
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44
48
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"dependencies": {
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|
45
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-
"@zakodium/nmrium-core": "^0.1.
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|
49
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+
"@zakodium/nmrium-core": "^0.1.3",
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46
50
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"cheminfo-types": "^1.8.1",
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47
51
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"convert-to-jcamp": "^5.4.11",
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48
52
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"filelist-utils": "^1.11.3",
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49
53
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"gyromagnetic-ratio": "^2.0.0",
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50
54
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"is-any-array": "^2.0.1",
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51
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-
"jcampconverter": "^11.0.
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55
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+
"jcampconverter": "^11.0.3",
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52
56
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"linear-sum-assignment": "^1.0.7",
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53
57
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"lodash.merge": "^4.6.2",
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54
58
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"ml-spectra-processing": "^14.12.0",
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55
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-
"nmr-processing": "^
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56
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-
"nmredata": "^1.0.
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57
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-
"openchemlib": "^9.
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59
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+
"nmr-processing": "^19.0.0",
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60
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+
"nmredata": "^1.0.1",
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61
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+
"openchemlib": "^9.2.0",
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58
62
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"openchemlib-utils": "^8.1.1",
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59
63
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"sdf-parser": "^7.0.4"
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|
60
64
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},
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