@zakodium/nmrium-core-plugins 0.1.1 → 0.1.3

package/LICENSE

@@ -0,0 +1,438 @@
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package/README.md

@@ -9,11 +9,7 @@
 
 # nmrium-core-plugins
 
-[![NPM version][npm-image]][npm-url]
-[![npm download][download-image]][download-url]
-[![DOI][doi-image]][doi-url]
-
-Package containing core plugins to work with nmrium.
+Package containing core plugins to work with NMRium.
 It provides essential loaders:
 
 - bruker
@@ -77,7 +73,7 @@ console.log(result);
 //   molecules: [],
 // }
 
-// readSource function accept a partial FileCollectionItems and a baseURL to generate a 
+// readSource function accept a partial FileCollectionItems and a baseURL to generate a
 // data structure with a source object inside with { files, filter, baseURL }
 
 const nmriumObject = await core.readFromWebSource(
@@ -105,11 +101,3 @@ It returns an array of plugins, you have to register them in the core.
 © 2025 Zakodium Sàrl. This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. [CC BY-NC-SA 4.0](./LICENSE)
 
 This package is based on MIT-licensed code that can be found here: https://doi.org/10.5281/zenodo.7100132
-
-[npm-image]: https://img.shields.io/npm/v/@zakodium/nmrium-core-plugins.svg
-[npm-url]: https://www.npmjs.com/package/@zakodium/nmrium-core-plugins
-[download-image]: https://img.shields.io/npm/dm/@zakodium/nmrium-core-plugins.svg
-[download-url]: https://www.npmjs.com/package/@zakodium/nmrium-core-plugins
-[doi-image]: https://zenodo.org/badge/DOI/10.5281/zenodo.7101438.svg
-<!-- TODO: fix doi-url for nmrium-core-plugins package -->
-[doi-url]: https://doi.org/10.5281/zenodo.7101438

package/dist/nmrium-core-plugins.js

@@ -0,0 +1,10 @@
+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 e.dimension?`${e.dimension}d`:"";if(i=i.toLowerCase(),i.includes("zg")||i.includes("single_pulse_dec")||i.includes("udeft"))return"1d";if(i.includes("hsqct")||i.includes("invi")&&(i.includes("ml")||i.includes("di")))return"hsqctocsy";if(i.includes("hsqc")||i.includes("invi"))return"hsqc";if(i.includes("hmbc")||i.includes("inv4")&&i.includes("lp"))return"hmbc";if(i.includes("hmqc"))return"hmqc";if(i.includes("cosy"))return"cosy";if(i.includes("jres"))return"jres";if(i.includes("dosy"))return"dosy";if(i.includes("tocsy")||i.includes("mlev")||i.includes("dipsi"))return"tocsy";if(i.includes("noesy"))return"noesy";if(i.includes("roesy"))return"roesy";if(i.includes("dept"))return"dept";if(i.includes("jmod")||i.includes("apt"))return"aptjmod";if(i.includes("inad"))return"inadequate";if(i.includes("adeq"))return"adequate";let{prefix:n=""}=t,s=(Ir(r[`${n}SPECTYP`])||"").replace(/^<(.*)>$/,"$1").toLowerCase();return s.length>0&&s!=="undefined"?s:e.dimension?`${e.dimension}d`:""}import{getOneIfArray as Ke}from"@zakodium/nmrium-core";var Er=["no","exponential","modifiedGaussian","sine","qsine","trap","user","sinc","qsinc","traf","trafs"];function Tr(e){return e in Qe}function Ie(e,r){let{prefix:t="",index:i=0}=r,n=Ke(e[`${t}WDW`],i),s=Er[n?Number(n):0],o={};if(!Tr(s))return o;let l=Qe[s];if(l){let{kind:a,parameters:m}=l,f={};for(let c in m){let b=m[c],{source:u,processor:y}=b;if(u){let g=Ke(e[`${t}${u}`],i);if(!g)continue;let p=Number(g);f[c]=y?y(p):p}else b.value!==void 0&&(f[c]=b.value)}o[a]={apply:!0,options:f}}return o}var Qe={exponential:{kind:"exponential",parameters:{lineBroadening:{source:"LB"}}},modifiedGaussian:{kind:"gaussian",parameters:{lineBroadening:{source:"LB"},lineBroadeningCenter:{source:"GB"}}},sine:{kind:"sineBell",parameters:{offset:{source:"SSB",processor:e=>1/e},exponent:{value:1}}},qsine:{kind:"sineSquare",parameters:{offset:{source:"SSB",processor:e=>1/e}}},traf:{kind:"traf",parameters:{lineBroadening:{source:"LB"}}}};var et={sineBell:rt({offset:0})},tt={cosy:{...et},hmbc:{...et},hsqc:{sineBell:rt({offset:.5})}},Cr={...tt};function Ee(e="",r=1){let t=Or(e),i={},n=r===1?tt[t||""]:Cr[t||""];return n&&(i=structuredClone(n)),i}function rt(e){return{apply:!0,options:e}}function Or(e){let t=e.toLowerCase().match(/cosy|hsqc|hmbc/);return t?t[0]:null}function nt(e,r={}){let{prefix:t="",experiment:i=ne(e)}=r;return e[`${t}WDW`]?{f2:Ie(e,{...r,index:0}),f1:Ie(e,{...r,index:1})}:{f2:Ee(i,1),f1:Ee(i,2)}}import{Filters1D as wr}from"nmr-processing";var Te=["digitalFilter","backwardLinearPrediction","forwardLinearPrediction","apodization","zeroFilling","fft",["shiftX","phaseCorrection","baselineCorrection"]],z={};for(let e=0;e<Te.length;e++){let r=Te[e];for(let t of Array.isArray(r)?r:[r])z[t]=e}for(let e of Object.values(wr))e.name in z||(z[e.name]=Te.length);import{Filters2D as vr}from"nmr-processing";var Ce=["digitalFilter2D","blpDimension1","flpDimension1","apodizationDimension1","zeroFillingDimension1","fftDimension1","blpDimension2","flpDimension2","nusDimension2","apodizationDimension2","zeroFillingDimension2","fftDimension2","phaseCorrectionTwoDimensions",["shift2DX","shift2DY","symmetrizeCosyLike"]],W={};for(let e=0;e<Ce.length;e++){let r=Ce[e];for(let t of Array.isArray(r)?r:[r])W[t]=e}for(let e of Object.values(vr))e.name in W||(W[e.name]=Ce.length);var qr=new Set(["backwardLinearPrediction","forwardLinearPrediction","digitalFilter2D","phaseCorrectionTwoDimensions","blpDimension1","flpDimension1","apodizationDimension1","apodizationDimension2","zeroFillingDimension1","fftDimension1","blpDimension2","flpDimension2","zeroFillingDimension2","fftDimension2","nusDimension2","symmetrizeCosyLike"]);function Br(e,r){let{filter:t,experimentalFeatures:i=!1}=r,{name:n}=t;({...Lr,...kr})[n]&&(e.some(o=>o.name===n)||(i||!qr.has(n))&&e.push({...t,enabled:!0}))}function it(e,r={}){let{data:t}=e;if(!t)return e;let{autoProcessing:i,experimentalFeatures:n}=r,s=(l,a)=>Br(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:_r(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 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+`}=t;P(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:m}=e,f=Number.parseFloat(a.groups.sw);e.spectralWidth.push(f/m[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 c=0;c<n.length;c+=f){let b=n[c].replace(/T1=/,"");s.push(Number(b))}r.vdlistValues=s}e.nucleus=o>1?[i,t]:i;let{phc0:a,phc1:m}=e;if(a&&m){let f=me({phc0:a,phc1:m});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 m of o)l.push(bt(m,{...vn,...i}).then(f=>Ln(f,r)));let a=await Promise.allSettled(l);for(let m=0;m<a.length;m++){let f=a[m];if(f.status==="fulfilled"){let c=me(f.value.info);t.spectra.push({...f.value,info:{...f.value.info,...c}})}else if(f.reason){let c=o[m].name;s?.warn(`Bruker data: ${c}, 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:m,name:f,files:c}=a;n.vdlist&&(n.vdlistValues=le(n.vdlist));let b={dependentVariables:[o],meta:n,info:{...s,experimentNumber:m,name:f}};return c&&t&&(b.sourceSelector={files:c.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:c,dataClass:b}=f;if(c==="LINK")f.children=Ue(f.children,r);else if(n.some(u=>{let{dataClass:y=b,dataType:g=c}=u;return b===y&&c===g})){i?.warn(`Skipping ${b} and ${c} ${t?`in ${t}`:"in the JCAMP-DX"}, 
+        because it didn't match the import filters`);continue}o.push(f)}let l=[],a=o.some(It),m=o.some(Rt);for(let f of o){if(s!=="both"&&f.dataType!=="LINK"){if(It(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(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 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li}from"ml-spectra-processing";import{xyAutoRangesPicking as ci}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 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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 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Me={info:{sampleName:L(c,"sample_id").value,creationTime:n.creationTime,revisionTime:n.revisionTime,author:n.author,comment:n.comment,solvent:L(c,"solvent").value,temperature:C(c,"temp_get"),probeName:L(c,"probe_id").value,fieldStrength:C(c,"field_strength"),experiment:L(c,"experiment").value,dimension:n.dataDimensionNumber,nucleus:p,date:d,epoch:h,pulseStrength90:C(c,"x90"),numberOfScans:L(c,"scans").value,relaxationTime:C(c,"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(c,"decimation_rate").value,paramList:JSON.stringify(c.paramArray.map(D=>D.name))},headers:n,parameters:c,data:u};return Me.info.digitalFilter=Oi(c,r),Me}import{formatSpectra as ki,getOneIfArray as qi}from"@zakodium/nmrium-core";import{getGyromagneticRatio as Bi}from"gyromagnetic-ratio";import{isAnyArray as _i}from"is-any-array";import Ui from"lodash.merge";import{normalizeNucleus as $i}from"nmr-processing";import{isAnyArray as K}from"is-any-array";var rr={0:"uint8",1:"uint16",2:"uint32",3:"uint64",4:"int8",5:"int16",6:"int32",7:"int64",8:"float32",9:"float64",10:"complex64",11:"complex128"},nr={0:"scalar",1:"vector",2:"matrix",3:"symetricMatrix",4:"pixel"};function ir(e,r,t={}){let{quantityType:i=0,encoding:n="none",name:s="",unit:o="",quantityName:l="",sparseSampling:a={},from:m=[0],to:f=[-1]}=t;if(K(e))throw new Error("JEOL with an array of data is not yet supported");if(!("re"in e&&"im"in e))throw new Error("Only re/im data is supported");let c=We(e,m,f),{componentLabels:b=c.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:c.components,dataLength:c.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]=ze(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]=ze(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 m=a+r[0]*2;l[a]=e.re[o][m/2],l[a+1]=e.im[o][m/2]}s.push(l)}}else throw new Error("check your object");else if(K(e.re.re)){i[0]=ze(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 ze(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,...m}=l.description,f=0,c=m.dimension===1?"1d":"2d",b="NMR SPECTRUM",u=m.dimension===1?m.nucleus[0]:m.nucleus,y=m.spectralWidthClipped[0],g;l.dependentVariables&&(m.dimension===1?g=ji(l):m.dimension===2&&(g=zi(l)));for(let d in m)Array.isArray(m[d])&&m[d].length===1&&(m[d]=m[d][0]);let p={data:g,info:{...m,acquisitionMode:f,experiment:c,type:b,nucleus:u,spectralWidthClipped:y,name:i},meta:a};return n&&(p.sourceSelector={files:[e.relativePath]}),s.spectra=[p],ki(s)}function ji(e){let r=e.dimensions[0],t=e.dependentVariables,i=r.quantityName,n=r.count,s=r.increment.magnitude,o=r.originOffset.magnitude,l=r.coordinatesOffset.magnitude,a=t[0].components[0],m=new Float64Array(n),f=new Float64Array(n);for(let g=a.length-1,p=0;g>0;g-=2)m[p]=a[g-1],f[p++]=a[g];let c={},[b,u]=[0,0];switch(i){case"frequency":u=0+l/o*1e6,b=s/o*1e6,c.re=m,c.im=f;break;case"time":u=o,b=s,c.re=m.reverse(),c.im=f.reverse().map(g=>-g);break;default:break}let y=[];for(let g=0;g<n;g++)y.push(u+g*b);return c.x=y,c}function zi(e){let r=e.dimensions,t=e.dependentVariables,i=r[0].quantityName,n=[],s=[],o=Number.MIN_SAFE_INTEGER,l=Number.MAX_SAFE_INTEGER,a=Number.MAX_SAFE_INTEGER,m=Number.MIN_SAFE_INTEGER;for(let b of t[0].components){let u=new Float64Array(b.length/2),y=new Float64Array(b.length/2);for(let g=b.length-1,p=0;g>0;g-=2){let d=b[g-1],h=b[g];d>o&&(o=d),d<l&&(l=d),h>m&&(m=h),h<a&&(a=h),u[p]=d,y[p++]=h}if(i==="frequency")n.push(u),s.push(y);else{let g=u.length,p=new Float64Array(y.length);for(let d=0,h=g-1;d<g;d++)p[d]=-y[h--];n.push(u.reverse()),s.push(p)}}let f={re:{z:n,minZ:l,maxZ:o},im:{z:s,minZ:a,maxZ:m}},c=["X","Y"];for(let b=0;b<c.length;b++){let u=r[b].count,y=r[b].increment.magnitude,g=r[b].originOffset.magnitude,p=r[b].coordinatesOffset.magnitude,d=c[b];for(let h of["re","im"])i==="frequency"?(f[h][`min${d}`]=0+p/g*1e6,f[h][`max${d}`]=u*(y/g)*1e6):(f[h][`min${d}`]=g,f[h][`max${d}`]=u*y)}return f}function Wi(e){let r=tr(e),t=r.info,i=r.headers,n=r.parameters,{dimension:s}=t,o={};for(let p of n.paramArray){let{name:d,value:h}=p;o[d]=ar(h,s)}delete n.paramArray;let l=r.data,a={};a.title=`title: ${i.title} / comment: ${i.comment} / author:${i.author} / site: ${i.site}`,a.nucleus=t.nucleus.map($i),a.sampleName=t.sampleName,a.date=t.date,a.epoch=t.epoch,a.localeDate=new 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FID",dataClass:!s&&c?"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),c&&u&&(u.set(c.slice(c.length-S)),u.set(c.slice(0,c.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:m,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,Pe as SDFLoaderPlugin,De as SMILESLoaderPlugin,Ae as VarianLoaderPlugin,Oe as autoPostProcessing,Be as brukerLoader,xs as default,xs as init,je 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};

package/package.json

@@ -1,83 +1,65 @@
 {
   "name": "@zakodium/nmrium-core-plugins",
-  "version": "0.1.1",
+  "version": "0.1.3",
   "description": "Recommended plugins for NMRium, loaders of common formats like bruker or jcamp, and some post-processing plugins",
-  "author": "",
+  "author": "Zakodium Sàrl",
   "license": "CC-BY-NC-SA-4.0",
   "type": "module",
   "exports": {
     ".": {
-      "types": "./dist/nmrium-core-plugins.d.ts",
-      "require": "./dist/nmrium-core-plugins.cjs",
-      "default": "./dist/nmrium-core-plugins.mjs"
+      "nmrium-internal": "./src/index.ts",
+      "default": "./dist/nmrium-core-plugins.js"
     }
   },
   "files": [
-    "dist/nmrium-core-plugins.d.ts",
-    "dist/nmrium-core-plugins.cjs",
-    "dist/nmrium-core-plugins.mjs"
+    "dist"
   ],
   "imports": {
     "#assets": "./src/assets.js"
   },
   "scripts": {
-    "api-extractor": "api-extractor run --local",
-    "bundle": "npm run bundle-cjs && npm run bundle-esm && npm run bundle-types",
-    "bundle-common": "esbuild src/index.ts --bundle --packages=external --minify",
-    "bundle-cjs": "npm run bundle-common -- --format=cjs --outfile=./dist/nmrium-core-plugins.cjs",
-    "bundle-esm": "npm run bundle-common -- --format=esm --outfile=./dist/nmrium-core-plugins.mjs",
-    "bundle-types": "npm run tsc && npm run api-extractor",
-    "check-types": "tsc --noEmit",
+    "bundle": "node scripts/esbuild.js && npm run bundle-types",
+    "bundle-types": "npm run tsc && yarn g:api-extractor",
     "clean": "rimraf types dist coverage",
-    "eslint": "eslint src --cache",
-    "eslint-fix": "npm run eslint -- --fix",
     "dev:eslint-fix": "eslint --cache --fix $(git diff --name-only --relative) --quiet",
-    "prepack": "npm run bundle",
-    "prettier": "prettier --check src",
-    "prettier-write": "prettier --write src",
+    "prepack": "npm run clean && npm run bundle",
     "dev:prettier-write": "prettier --write $(git diff --name-only --relative)",
-    "test": "npm run test-only && npm run eslint && npm run prettier && npm run check-types",
-    "test-only": "vitest run --coverage",
+    "test": "yarn g:test-only && yarn g:check-types && yarn g:eslint && yarn g:prettier",
     "tsc": "tsc --project tsconfig.types.json"
   },
   "devDependencies": {
-    "@microsoft/api-extractor": "^7.52.1",
     "@types/lodash.merge": "^4.6.9",
-    "@types/node": "^22.13.11",
-    "@vitest/coverage-istanbul": "^3.0.9",
+    "@types/node": "^22.15.29",
+    "@zakodium/bruker-parser": "^0.0.0",
+    "@zakodium/jeol-parser": "^0.0.0",
+    "@zakodium/varian-parser": "^0.0.0",
     "bruker-data-test": "^0.5.4",
-    "esbuild": "^0.25.1",
-    "eslint": "^9.22.0",
-    "eslint-config-cheminfo-typescript": "^18.0.0",
+    "esbuild": "^0.25.5",
     "fifo-logger": "^1.0.0",
-    "jcamp-data-test": "^0.8.3",
+    "jcamp-data-test": "^1.0.0",
     "jeol-data-test": "^0.5.2",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "msw": "^2.7.5",
+    "msw": "^2.8.6",
     "nmredata-data-test": "^0.4.0",
-    "prettier": "^3.5.3",
     "rimraf": "^6.0.1",
-    "typescript": "^5.8.2",
-    "vitest": "^3.0.9"
+    "vitest": "^3.1.4"
   },
   "dependencies": {
-    "@zakodium/nmrium-core": "^0.1.0",
-    "brukerconverter": "^8.0.3",
+    "@zakodium/nmrium-core": "^0.1.2",
+    "cheminfo-types": "^1.8.1",
     "convert-to-jcamp": "^5.4.11",
     "filelist-utils": "^1.11.3",
-    "gyromagnetic-ratio": "^1.2.1",
+    "gyromagnetic-ratio": "^2.0.0",
     "is-any-array": "^2.0.1",
-    "jcampconverter": "^11.0.1",
-    "jeolconverter": "^1.0.4",
+    "jcampconverter": "^11.0.3",
     "linear-sum-assignment": "^1.0.7",
     "lodash.merge": "^4.6.2",
-    "ml-spectra-processing": "^14.11.0",
-    "nmr-processing": "^18.0.1",
-    "nmredata": "^1.0.0",
-    "openchemlib": "^9.0.1",
-    "openchemlib-utils": "^8.1.0",
-    "sdf-parser": "^7.0.4",
-    "varian-converter": "^2.0.1"
+    "ml-spectra-processing": "^14.12.0",
+    "nmr-processing": "^18.1.0",
+    "nmredata": "^1.0.1",
+    "openchemlib": "^9.2.0",
+    "openchemlib-utils": "^8.1.1",
+    "sdf-parser": "^7.0.4"
   },
   "volta": {
     "extends": "../../../package.json"

package/dist/nmrium-core-plugins.cjs

@@ -1,6 +0,0 @@
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package/dist/nmrium-core-plugins.mjs

@@ -1,6 +0,0 @@
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f){if(b.js.every(N=>N===b.js[0])){h.push(b);continue}if(b.multiplicity!==b.js.length+1){h.push(b);continue}for(let N=0;N<b.multiplicity-1;N++)h.push({value:"d",multiplicity:2,js:[b.js[N]]})}h.sort((b,N)=>N.js[0]-b.js[0]),y.js=h.map(b=>({coupling:b.js[0],multiplicity:b.value}))}typeof o.assignment=="string"&&(y.assignment=vr(o.assignment)),typeof o.multiplicity=="string"&&(y.multiplicity=o.multiplicity),n.multiplets.push(y)}return n}function kr(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 wr={quot:'"',apos:"'",comma:",",amp:"&",lpar:"(",rpar:")",lt:"<",gt:">",colon:":",semi:";"};function vr(e){return e.replaceAll(/&(\w+);/gi,(r,t)=>wr[t.toLowerCase()]||r)}function et(e){let r=e.split(/\r?\n/).filter(i=>i.trim()!==""),t=[];for(let i of r)if(i.startsWith("(")){let[n,o,s]=z(i).map(Number.parseFloat);t.push({id:n,x:o,y:s})}return t}function tt(e,r={}){let t={};if(!e["OBSERVED MULTIPLETS"])return[];let i=Qe(e["OBSERVED MULTIPLETS"],r);if(!i)return[];let{multiplets:n}=i;for(let o of n){let{id:s,from:l,to:a,integration:m=0,...u}=o;t[s]={from:l,to:a,integration:m,signals:[{id:s,...u}]}}if(e["OBSERVED MULTIPLETS PEAKS"]){let o=et(e["OBSERVED MULTIPLETS PEAKS"]),s={};for(let l of o){let{id:a,x:m,y:u}=l;s[a]||(s[a]=[]),s[a].push({x:m,y:u,width:.05})}for(let l in t)s[l]&&(t[l].signals[0].peaks=s[l])}return q(Object.values(t))}function rt(e,r){let i=[...e.getMolecularFormula().formula.matchAll(/(?<element>[A-Z][a-z]?)(?<count>\d*)/g)].map(o=>({element:o?.groups?.element,count:o?.groups?.count?Number(o.groups.count):1})),n=[...r.nucleus[0].matchAll(/[0-9]*(?<element>[A-Z][a-z]?)/g,"$element")][0].groups.element;return i.find(o=>o.element===n)?.count||100}function nt(e){let r={};return".PHASE0"in e&&(r.ph0=Number.parseFloat(e[".PHASE0"]),r.ph1=Number.parseFloat(e[".PHASE1"])),r}function he(e){let{ph0:r,ph1:t}=e;return Number.isFinite(r)&&Number.isFinite(t)}import{generateID as it}from"@zakodium/nmrium-core";function ot(e,r,t){for(let i=0;i<e.length;i++){if(r.includes(i))continue;let{delta:n,multiplicity:o="",diaIDs:s}=e[i],l=Number(n)-.01,a=Number(n)+.01;t.push({from:l,to:a,integration:1,id:it(),signals:[{id:it(),delta:n,multiplicity:o,diaIDs:s}]})}}import{linearSumAssignment as qr}from"linear-sum-assignment";import{xCostMatrix as $r}from"ml-spectra-processing";function st(e,r){let t=e.map(s=>s.delta),i=r.map(s=>s.delta),n=$r(i,t,{fct:(s,l)=>Math.abs(s-l)}),{rowAssignments:o}=qr(n,{maximaze:!1});return Array.from(o)}function at(e,r){let{assignments:t,ranges:i}=r;t?.sort((s,l)=>l.delta-s.delta);let n=[],o=[];for(let s of i){let l=0,{from:a,to:m}=s,u=[];for(let c=l;c<t.length;c++){let{delta:g}=t[c];g<=m&&g>=a?(u.push(t[c]),o.push(c)):g>m&&(l=c)}if(u.length>0){let c=s.signals,g=[],y=u.length>1&&c.length>1?st(c,u):[0];for(let d=0;d<u.length;d++){let 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n){let{name:m,files:u}=a,c=new Tn(u),g=kn(c).then(y=>{let{info:d,meta:p}=Et(y),f=y.fid.data[0],F=En(f.im),h={data:{...f,x:y.x},meta:p,info:{isComplex:F,name:m,...d},display:{name:m}};if(d.isFid&&F){let{im:b}=h.data;Ln(b,-1,{output:b})}u&&t&&(h.sourceSelector={files:u.map(b=>b.relativePath)}),s.spectra.push(h)});o.push(g)}let l=await Promise.allSettled(o);for(let a=0;a<l.length;a++){let m=l[a];if(m.status==="rejected"&&m.reason){let u=n[a].name;i?.warn(`Varian data: ${u}, fails with: ${m.reason}`)}}return s.spectra.length>0&&i?.info(`Loaded ${s.spectra.length}  spectra from Varian files`),In(s)}var se=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 wt(r,{keepSource:i,logger:n})}};function Ae(){return new se}function vn(e,r=[]){return[Se(e),Ae(),de(),be(),De(),Re(),Me(),Ne(),ue()].concat(r)}function qn(){let e=new wn;return e.registerPlugins(vn(e)),e}import{getOneIfArray as qt}from"@zakodium/nmrium-core";import{from1DNMRVariables as $n}from"convert-to-jcamp";function vt(e,r){return e.filters.find(t=>t.name===r)}function jn(e,r={}){let{info:t,meta:i,data:n}=e,{onlyReal:o=!1}=r,{isFid:s,spectralWidth:l}=t,a=qt(t.baseFrequency||t.originFrequency),{x:m,re:u,im:c}=n,g=new Float64Array(u),y=!o&&c?new Float64Array(c):void 0,d={};B(d,"SW",l),B(d,"BF1",a);let p=vt(e,"fft")?.enabled,f={originFrequency:t.originFrequency,dataType:!t.isFid||p?"NMR SPECTRUM":"NMR FID",dataClass:!o&&c?"NTUPLES":"XYDATA"};if(s){let b=e.filters.find(N=>N.name==="digitalFilter");if(b&&!p){let{value:{digitalFilterValue:N},enabled:S}=b;if(S){let D=Math.floor(N);g.set(u.slice(u.length-D)),g.set(u.slice(0,u.length-D),D),c&&y&&(y.set(c.slice(c.length-D)),y.set(c.slice(0,c.length-D),D))}}B(f,"decim",t.decim),B(f,"dspfvs",t.dspfvs),B(f,"digitalFilter",t.digitalFilter)}let F={xyEncoding:"DIFDUP",info:{...t,...f},meta:{...i,...d}},h={x:{data:m,label:t.isFid?"TIME":"FREQUENCY",units:t.isFid?"second":"HZ",symbol:"X"},r:{data:g,label:`${t.isFid?"FID":"SPECTRUM"}/REAL`,units:"ARBITRARY UNITS",symbol:"R"}};return y&&(h.i={data:y,label:`${t.isFid?"FID":"SPECTRUM"}/IMAG`,units:"ARBITRARY UNITS",symbol:"I"}),$n(h,F)}function B(e,r,t){t!==void 0&&(e[r]=qt(t))}export{W as AutoPostProcessingPlugin,K as BrukerLoaderPlugin,ee as JCAMPDXLoaderPlugin,te as JEOLLoaderPlugin,re as MolfileLoaderPlugin,ne as NMReDATALoaderPlugin,ie as SDFLoaderPlugin,oe as SMILESLoaderPlugin,se as VarianLoaderPlugin,ue as autoPostProcessing,de as brukerLoader,qn as default,qn as init,be as jcampDXLoader,Ne as jeolLoader,De as molfileLoader,Se as nmreDATALoader,ft as processJCAMPDX,Ct as readSDF,It as readSMILES,vn as recommended,Re as sdfLoader,Me as smilesLoader,jn as spectrum1DToJCAMPDX,Ae as varianLoader};