npm - @zakodium/nmrium-core-plugins - Versions diffs - 0.1.7 → 0.1.9 - Mend

@zakodium/nmrium-core-plugins 0.1.7 → 0.1.9

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.

Files changed (3) hide show

package/dist/nmrium-core-plugins.d.ts +2 -2
package/dist/nmrium-core-plugins.js +17 -15
package/package.json +16 -14

package/dist/nmrium-core-plugins.d.ts CHANGED Viewed

@@ -46,9 +46,9 @@ declare interface FilterTreeByDataTypeDataClass {
 }
 /**
- * Init NMRiumCore with recommended plugins.
+ * Init NMRiumCore with recommended plugins and plugins passed as argument.
  */
-declare function init(): NMRiumCore;
+declare function init(plugins?: NMRiumPlugin[]): NMRiumCore;
 export default init;
 export { init }

package/dist/nmrium-core-plugins.js CHANGED Viewed

@@ -1,18 +1,20 @@
-var Yr=Object.defineProperty;var Nt=(e,t)=>{for(var n in t)Yr(e,n,{get:t[n],enumerable:!0})};import{NMRiumCore as Ls}from"@zakodium/nmrium-core";import{Filters1D as ii,Filters2D as oi}from"nmr-processing";import{getOneIfArray as Kr}from"@zakodium/nmrium-core";function te(e={},t={},n={}){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?`${e.dimension}d`:"";if(i=i.toLowerCase(),i.includes("zg")||i.includes("single_pulse_dec")||i.includes("udeft"))return"1d";if(i.includes("hsqct")||i.includes("invi")&&(i.includes("ml")||i.includes("di")))return"hsqctocsy";if(i.includes("hsqc")||i.includes("invi"))return"hsqc";if(i.includes("hmbc")||i.includes("inv4")&&i.includes("lp"))return"hmbc";if(i.includes("hmqc"))return"hmqc";if(i.includes("cosy"))return"cosy";if(i.includes("jres"))return"jres";if(i.includes("dosy"))return"dosy";if(i.includes("tocsy")||i.includes("mlev")||i.includes("dipsi"))return"tocsy";if(i.includes("noesy"))return"noesy";if(i.includes("roesy"))return"roesy";if(i.includes("dept"))return"dept";if(i.includes("jmod")||i.includes("apt"))return"aptjmod";if(i.includes("inad"))return"inadequate";if(i.includes("adeq"))return"adequate";let{prefix:r=""}=n,o=(Kr(t[`${r}SPECTYP`])||"").replace(/^<(.*)>$/,"$1").toLowerCase();return o.length>0&&o!=="undefined"?o:e.dimension?`${e.dimension}d`:""}import{getOneIfArray as At}from"@zakodium/nmrium-core";var Zr=["no","exponential","modifiedGaussian","sine","qsine","trap","user","sinc","qsinc","traf","trafs"];function Qr(e){return e in Mt}function Be(e,t){let{prefix:n="",index:i=0}=t,r=At(e[`${n}WDW`],i),o=Zr[r?Number(r):0],s={};if(!Qr(o))return s;let a=Mt[o];if(a){let{kind:l,parameters:c}=a,u={};for(let f in c){let d=c[f],{source:g,processor:h}=d;if(g){let p=At(e[`${n}${g}`],i);if(!p)continue;let b=Number(p);u[f]=h?h(b):b}else d.value!==void 0&&(u[f]=d.value)}s[l]={apply:!0,options:u}}return s}var Mt={exponential:{kind:"exponential",parameters:{lineBroadening:{source:"LB"}}},modifiedGaussian:{kind:"gaussian",parameters:{lineBroadening:{source:"LB"},lineBroadeningCenter:{source:"GB"}}},sine:{kind:"sineBell",parameters:{offset:{source:"SSB",processor:e=>1/e},exponent:{value:1}}},qsine:{kind:"sineSquare",parameters:{offset:{source:"SSB",processor:e=>1/e}}},traf:{kind:"traf",parameters:{lineBroadening:{source:"LB"}}}};var It={sineBell:Et({offset:0})},Rt={cosy:{...It},hmbc:{...It},hsqc:{sineBell:Et({offset:.5})}},ei={...Rt};function Ue(e="",t=1){let n=ti(e),i={},r=t===1?Rt[n||""]:ei[n||""];return r&&(i=structuredClone(r)),i}function Et(e){return{apply:!0,options:e}}function ti(e){let n=e.toLowerCase().match(/cosy|hsqc|hmbc/);return n?n[0]:null}function Tt(e,t={}){let{prefix:n="",experiment:i=te(e)}=t;return e[`${n}WDW`]?{f2:Be(e,{...t,index:0}),f1:Be(e,{...t,index:1})}:{f2:Ue(i,1),f1:Ue(i,2)}}import{Filters1D as ni}from"nmr-processing";var $e=["digitalFilter","backwardLinearPrediction","forwardLinearPrediction","apodization","zeroFilling","fft",["shiftX","phaseCorrection","baselineCorrection"]],U={};for(let e=0;e<$e.length;e++){let t=$e[e];for(let n of Array.isArray(t)?t:[t])U[n]=e}for(let e of Object.values(ni))e.name in U||(U[e.name]=$e.length);import{Filters2D as ri}from"nmr-processing";var ze=["digitalFilter2D","blpDimension1","flpDimension1","apodizationDimension1","zeroFillingDimension1","fftDimension1","blpDimension2","flpDimension2","nusDimension2","apodizationDimension2","zeroFillingDimension2","fftDimension2","phaseCorrectionTwoDimensions",["shift2DX","shift2DY","symmetrizeCosyLike"]],$={};for(let e=0;e<ze.length;e++){let t=ze[e];for(let n of Array.isArray(t)?t:[t])$[n]=e}for(let e of Object.values(ri))e.name in $||($[e.name]=ze.length);var si=new Set(["backwardLinearPrediction","forwardLinearPrediction","digitalFilter2D","phaseCorrectionTwoDimensions","blpDimension1","flpDimension1","apodizationDimension1","apodizationDimension2","zeroFillingDimension1","fftDimension1","blpDimension2","flpDimension2","zeroFillingDimension2","fftDimension2","nusDimension2","symmetrizeCosyLike"]);function ai(e,t){let{filter:n,experimentalFeatures:i=!1}=t,{name:r}=n;({...ii,...oi})[r]&&(e.some(s=>s.name===r)||(i||!si.has(r))&&e.push({...n,enabled:!0}))}function Ot(e,t={}){let{data:n}=e;if(!n)return;let{autoProcessing:i,experimentalFeatures:r}=t,o=(a,l)=>ai(a,{...l,experimentalFeatures:r}),{spectra:s}=n;for(let a of s){let{data:l,info:c,meta:u,filters:f}=a,{dimension:d,isFid:g}=c;if(g){if(d===1){let h=l.re.length,{tdOff:p,digitalFilter:b}=c;if(b&&b>0&&o(f,{filter:{name:"digitalFilter",value:{digitalFilterValue:b}}}),!i)continue;p&&Math.abs(p)>0&&o(f,{filter:{name:"backwardLinearPrediction",value:{nbInputs:h/2}}}),o(f,{filter:{name:"apodization",value:{exponential:{apply:!0,options:{lineBroadening:1}}}}}),o(f,{filter:{name:"zeroFilling",value:{nbPoints:2*h}}}),o(f,{filter:{name:"fft",value:{}}}),o(f,{filter:{name:"phaseCorrection",value:ci(c)}}),f.sort((m,y)=>U[m.name]-U[y.name])}else if(d===2){if(!i||!r)continue;let h=l.re.z.length,p=l.re.z[0].length,{tdOff:b,experiment:m=""}=c,y=c.spectrumSize;Array.isArray(y)&&y.length>1?(y[0]<=p&&(y[0]=p*2),y[0]<=h&&(y[0]=h*2)):y=[p*2,2*h];let F=m.toLowerCase().includes("cosy");b&&Math.abs(b[0])>0&&o(f,{filter:{name:"blpDimension1",value:{nbInputs:p/2}}});let x=Tt(u,{experiment:m});o(f,{filter:{name:"apodizationDimension1",value:x.f2}}),o(f,{filter:{name:"zeroFillingDimension1",value:{nbPoints:y[0]}}}),o(f,{filter:{name:"fftDimension1",value:{}}}),u&&"nuslist"in u&&o(f,{filter:{name:"nusDimension2",value:{}}}),o(f,{filter:{name:"apodizationDimension2",value:x.f1}}),o(f,{filter:{name:"zeroFillingDimension2",value:{nbPoints:y[F?0:1]}}}),F?o(f,{filter:{name:"symmetrizeCosyLike",value:{}}}):o(f,{filter:{name:"phaseCorrectionTwoDimensions",value:{}}}),o(f,{filter:{name:"fftDimension2",value:{}}}),f.sort((N,D)=>$[N.name]-$[D.name])}}}}function ci(e){let{phc0:t=0,phc1:n=0}=e;return Ct([t,n])?{}:{ph0:t,ph1:n}}function Ct(e){return Array.isArray(e)?e.every(t=>!t&&t===0):Ct([e])}var ne=class{id="@zakodium/nmrium-core-plugins#AutoPostProcessingPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={onProcessing:this.onPostProcessing.bind(this)}}onPostProcessing(t,n){Ot(t,n)}};function Je(){return new ne}import{FileCollection as nc}from"file-collection";var wt=["acqus","acqu2s"],re=["procs","proc2s"];function vt(e){return e.is1D?li(e):e.is2D?mi(e):{checked:!1,message:"Multi-dimensional n > 2 is not supported"}}function li(e){let t=e.isFID?["acqus"]:["acqus","procs"],n=t.every(i=>e[i]);return{checked:n,message:n?"":`File: ${e[e.isFID?"fid":"1r"]?.relativePath} is ignored, files: ${t.join(",")} are required.`}}function mi(e){let t=e.isFID?wt:wt.concat(re),n=t.every(i=>e[i]);return n&&e.isFID&&re.some(i=>e[i])&&!re.every(i=>e[i])&&(n=!1,t.push(...re)),{checked:n,message:n?"":`File: ${e.name} is ignored, files: ${t.join(",")} are required.`}}function We(e,t={}){let{logger:n,processingNumbers:i,experimentNumbers:r,dataSelection:o="both",keep1D:s=!0,keep2D:a=!0,onlyFirstProcessedData:l=!0}=t,c={},u=e.files.map(g=>g.relativePath);for(let g of e){let h,p,b,m=g.relativePath.split("/"),y=m.indexOf("pdata");if(y!==-1)h=Number(m[y+1]),p=Number(m[y-1]),b=m.slice(0,-3).join("/");else if(pi(g,u)){let 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b){if(F.js.every(x=>x===F.js[0])){y.push(F);continue}if(F.multiplicity!==F.js.length+1){y.push(F);continue}for(let x=0;x<F.multiplicity-1;x++)y.push({value:"d",multiplicity:2,js:[F.js[x]]})}y.sort((F,x)=>x.js[0]-F.js[0]),g.js=y.map(F=>({coupling:F.js[0],multiplicity:F.value}))}typeof o.assignment=="string"&&(g.assignment=So(o.assignment)),typeof o.multiplicity=="string"&&(g.multiplicity=o.multiplicity),r.multiplets.push(g)}return r}function Do(e){let t={};for(let n in e){let i=e[n],r=typeof i=="number"?i:Number.parseFloat(i);Number.isNaN(r)||(t[n]=r)}return t}var xo={quot:'"',apos:"'",comma:",",amp:"&",lpar:"(",rpar:")",lt:"<",gt:">",colon:":",semi:";"};function So(e){return e.replaceAll(/&(\w+);/gi,(t,n)=>xo[n.toLowerCase()]||t)}function un(e){let t=e.split(/\r?\n/).filter(i=>i.trim()!==""),n=[];for(let i of t)if(i.startsWith("(")){let[r,o,s]=Z(i).map(Number.parseFloat);n.push({id:r,x:o,y:s})}return n}function pn(e,t={}){let n={};if(!e["OBSERVED MULTIPLETS"])return[];let i=mn(e["OBSERVED MULTIPLETS"],t);if(!i)return[];let{multiplets:r}=i;for(let o of r){let{id:s,from:a,to:l,integration:c=0,...u}=o;n[s]={from:a,to:l,integration:c,signals:[{id:s,...u}]}}if(e["OBSERVED MULTIPLETS PEAKS"]){let o=un(e["OBSERVED MULTIPLETS PEAKS"]),s={};for(let a of o){let{id:l,x:c,y:u}=a;s[l]||(s[l]=[]),s[l].push({x:c,y:u,width:.05})}for(let a in n)s[a]&&(n[a].signals[0].peaks=s[a])}return H(Object.values(n))}function fn(e,t){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})),r=[...t.nucleus[0].matchAll(/[0-9]*(?<element>[A-Z][a-z]?)/g,"$element")][0].groups.element;return i.find(o=>o.element===r)?.count||100}function dn(e){let t={};return".PHASE0"in e&&(t.ph0=Number.parseFloat(e[".PHASE0"]),t.ph1=Number.parseFloat(e[".PHASE1"])),t}function tt(e){let{ph0:t,ph1:n}=e;return Number.isFinite(t)&&Number.isFinite(n)}import{generateID as 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Se(e.fileCollection,{converter:r?.bruker,selector:n});default:throw new Error("There is not a supported source")}}var Ce=class{id="@zakodium/nmrium-core-plugins#NMReDATALoaderPlugin";version=1;migrations=[];onReadProcess;#e;constructor(t){this.#e=t,this.onReadProcess={onFiles:this.onReadProcessFiles}}onReadProcessFiles=(t,r)=>Ln(t,this.#e,r)};function xt(e){return new Ce(e)}import{parse as Qs}from"sdf-parser";function kn(e,t={}){let{mixedEOL:r}=t,{molecules:n}=Qs(e,{mixedEOL:r}),i=[];for(let{molfile:o}of n){let s=K(o);i.push(...s)}return i}async function _n(e,t={}){let{logger:r,mixedEOL:n}=t,i=await e.text(),o=kn(i,{mixedEOL:n}),s={molecules:o,spectra:[]};return r&&r[o.length>0?"info":"debug"](`Loaded ${s.molecules.length} molecules from the ${e.name} file`),s}var we=class{id="@zakodium/nmrium-core-plugins#SDFLoaderPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={supportedExtensions:["sdf"],onFile:this.onReadProcessFile.bind(this)}}onReadProcessFile(t,r={}){let{logger:n}=r;return n?.debug(`Reading sdf file: ${t.name}`),_n(t,{logger:n})}};function Dt(){return new we}import{Molecule as ea}from"openchemlib";function qn(e){let t=[],r=e.split(/\r?\n/).filter(Boolean);for(let n of r){let o=ea.fromSmiles(n).toMolfile();t.push({molfile:o})}return t}async function jn(e,t={}){let r=await e.text(),n=qn(r),i={molecules:n,spectra:[]};return t.logger?.info(`Found ${n.length} molecules from the ${e.name} file`),i}var ve=class{id="@zakodium/nmrium-core-plugins#SMILESLoaderPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={supportedExtensions:["smi","smiles"],onFile:this.onReadProcessFile.bind(this)}}onReadProcessFile(t,r={}){let{logger:n}=r;return jn(t,{logger:n})}};function St(){return new ve}import{formatSpectra as oa}from"@zakodium/nmrium-core";import{createFromToArray as ra}from"ml-spectra-processing/utils";function Bn(e){e.setLittleEndian();let t=e.offset,r=96;e.offset=r/8;let n=e.readInt32(),i=[2,4],o=[2**25,2**26];if(!i.includes(n))if(o.includes(n))e.setBigEndian();else throw new Error(`Unexpected value of eBytes (${n}). Expect one of
+                    ${i.concat(o).join(",")}`);return e.offset=t,e.isBigEndian()?"BE":"LE"}var Le=class{storesData;isSpectrum;isInt32;isFloat32;isComplex;isHypercomplex;isBaselineCorrected;constructor(t){if(this.storesData=(t&1)!==0,!this.storesData)throw new Error("No data stored in file. Exiting...");if(this.isSpectrum=(t&2)!==0,this.isSpectrum)throw new Error("Script only analyzes FIDs. Found spectrum.");if(this.isInt32=(t&4)!==0,this.isFloat32=(t&8)!==0,this.isComplex=(t&16)!==0,this.isHypercomplex=(t&32)!==0,this.isHypercomplex)throw new Error("Script does not analyze hypercomplex data (yet).");this.isBaselineCorrected=(t&64)!==0}},ke=class extends Le{moreBlocks;npComplex;nfComplex;niComplex;ni2Complex;constructor(t){super(t),this.moreBlocks=(t&128)!==0,this.npComplex=(t&256)!==0,this.nfComplex=(t&512)!==0,this.niComplex=(t&1024)!==0,this.ni2Complex=(t&2048)!==0}},_e=class extends Le{isAcqPar;isSecondFT;isTransformed;is3D;isNp;isNf;isNi;isNi2;constructor(t){super(t),this.isAcqPar=(t&128)!==0,this.isSecondFT=(t&256)!==0,this.isTransformed=(t&512)!==0,this.is3D=(t&1024)!==0,this.isNp=(t&2048)!==0,this.isNf=(t&4096)!==0,this.isNi=(t&8192)!==0,this.isNi2=(t&16384)!==0}},qe=class{lines;length;index;eol;constructor(t,r={}){let{eol:n=`
+`,index:i=0}=r;this.eol=n,this.index=i,this.lines=t.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(t){let r=this.lines.slice(this.index,this.index+t);return this.index+=t,r}},je=class{softwareVersion;typeOfFile;vendorIdStatus;constructor(t){this.softwareVersion=t&2**6-1,this.typeOfFile={fidFile:(t&64)!==0,dataFile:(t&128)!==0,data3DFile:(t&256)!==0},this.vendorIdStatus={isVar:(t&0)!==0,isQOne:(t&2048)!==0,isMakeFid:(t&4096)!==0,isJeol:(t&8192)!==0,isBru:(t&16384)!==0,isMag:(t&6144)!==0,isOx:(t&10240)!==0,ipVers:(t&63)!==0,ipFileId:(t&1984)!==0,ipVendorId:(t&30720)!==0}}},Be=class{npPhMode;npAvMode;npPwrMode;nfPhMode;nfAvMode;nfPwrMode;niPhMode;niAvMode;niPwrMode;ni2PhMode;ni2AvMode;ni2PwrMode;niPaMode;ni2PaMode;constructor(t){this.npPhMode=(t&1)!==0,this.npAvMode=(t&2)!==0,this.npPwrMode=(t&4)!==0,this.nfPhMode=(t&16)!==0,this.nfAvMode=(t&32)!==0,this.nfPwrMode=(t&64)!==0,this.niPhMode=(t&256)!==0,this.niAvMode=(t&512)!==0,this.niPwrMode=(t&1024)!==0,this.ni2PhMode=(t&8)!==0,this.ni2AvMode=(t&256)!==0,this.ni2PwrMode=(t&8192)!==0,this.niPaMode=(t&16384)!==0,this.ni2PaMode=(t&32768)!==0}};var Ue=class{scale;status;index;mode;ctCount;lpVal;rpVal;lvl;tlt;data;constructor(t,r,n){n&&(t.offset=n),this.scale=t.readInt16(),this.status=new ke(t.readInt16()),this.index=t.readInt16(),this.mode=new Be(t.readInt16()),this.ctCount=t.readInt32(),this.lpVal=t.readFloat32(),this.rpVal=t.readFloat32(),this.lvl=t.readFloat32(),this.tlt=t.readFloat32(),this.data=ta(t,r)}};function ta(e,t){let{np:r,nTraces:n,status:{isFloat32:i,isInt32:o}}=t;return i?Mt(e,n,r,"readFloat32"):o?Mt(e,n,r,"readInt32"):Mt(e,n,r,"readInt16")}function Mt(e,t,r,n){let i=[],o;n==="readFloat32"?o={re:new Float32Array(r/2),im:new Float32Array(r/2)}:n==="readInt32"?o={re:new Int32Array(r/2),im:new Int32Array(r/2)}:o={re:new Int16Array(r/2),im:new Int16Array(r/2)};for(let s=0;s<t;s++){for(let a=0;a<r;a+=2)o.re[a>>>1]=e[n](),o.im[a>>>1]=e[n]();i[s]=o}return i}var $e=class{nBlocks;nTraces;np;eBytes;tBytes;bBytes;version;status;nBlockHeaders;constructor(t){t.offset=0,this.nBlocks=t.readInt32(),this.nTraces=t.readInt32(),this.np=t.readInt32(),this.eBytes=t.readInt32(),this.tBytes=t.readInt32(),this.bBytes=t.readInt32(),this.version=new je(t.readInt16()),this.status=new _e(t.readInt16()),this.nBlockHeaders=t.readInt32()}};var Pt=class{name;subType;basicType;maxValue;minValue;stepSize;gGroup;dGroup;protection;active;intptr;constructor(t){let r=t.split(" ");this.name=r[0],this.subType=Number.parseInt(r[1],10),this.basicType=Number.parseInt(r[2],10),this.maxValue=Number.parseFloat(r[3]),this.minValue=Number.parseFloat(r[4]),this.stepSize=Number.parseFloat(r[5]),this.gGroup=Number.parseInt(r[6],10),this.dGroup=Number.parseInt(r[7],10),this.protection=Number.parseInt(r[8],10),this.active=Number.parseInt(r[9],10),this.intptr=Number.parseInt(r[10],10)}};function Un(e){let t=[],r=new qe(e.readChars(e.length));for(;r.index<r.length-1;){let n=[],i=[],o=new Pt(r.readLine()),s=r.readLine();if(o.basicType!==0){if(o.basicType===1)n=s.split(" ").slice(1).map(m=>Number.parseFloat(m));else if(o.basicType===2){n=s.split('"').slice(1,2);let l=Number.parseInt(s.split(" ")[0],10);for(;l>1;)n.push(r.readLine().split('"')[1]),l--}}let a=r.readLine(),c=Number.parseInt(a.split(" ")[0],10);c!==0&&(o.basicType===1?i=a.split(" ").slice(1):o.basicType===2&&(i=a.split('"').filter((l,m)=>m%2===1))),t.push({...o,values:n,enumerable:c,enumerables:i})}return t}async function $n(e){let t={};function r(c,l){return c.then(m=>{t[l]=m})}let n=[];for(let c of e)switch(c.name.toLowerCase()){case"fid":{n.push(r(c.arrayBuffer(),"fidB"));break}case"procpar":{n.push(r(c.arrayBuffer(),"procparB"));break}default:break}if(await Promise.all(n),!t.fidB||!t.procparB)throw new RangeError("fid and procpar must exist.");let i=new C(t.fidB);Bn(i);let o=new $e(i);if(o.nBlocks!==1)throw new Error("We currently do not support 2D varian spectra ");let s=Un(new C(t.procparB)),a;for(let c of s)if(c.name==="at"){a=c.values[0];break}if(typeof a!="number")throw new Error("acquisition time parameter must exist and be a number.");{let c=ra({from:0,to:a,length:o.np/2,distribution:"uniform"}),l=new Ue(i,o);return{meta:o,fid:l,procpar:s,x:c}}}import{isAnyArray as sa}from"is-any-array";import{xMultiply as aa}from"ml-spectra-processing";import{normalizeNucleus as na}from"nmr-processing";function zn(e,t){let{meta:r,procpar:n}=e,i={};for(let b of n)i[b.name]=b.values;let o={},s={},{np:a,solvent:c,sfrq:l,reffrq:m,temp:p,rp:f,sw:g,rfl:y,rfp:u}=i;D(o,"numberOfPoints",a&&Number(q(a))/2),D(o,"solvent",q(c)),D(o,"originFrequency",q(l)),D(o,"baseFrequency",q(m)),(Number.isNaN(o.originFrequency)||o.originFrequency===0)&&(o.originFrequency=400,t?.warn("The frequency could not be determined and was set to 400MHz")),D(o,"temperature",q(p)),D(o,"phc0",f&&Number(f[0])),D(s,"rfl",y&&Number(q(y))),D(s,"rfp",u&&Number(q(u))),D(s,"sw",g&&Number(q(g)));for(let b in s){let F=s[b];Array.isArray(F)&&F.length===1&&(s[b]=F[0])}if(!("baseFrequency"in o)&&"originFrequency"in o){let b=Number.parseFloat(o.originFrequency);if(["sw","rfl","rfp"].every(F=>F in s)){let{sw:F=1,rfl:S=1,rfp:P=1}=ia(s,["sw","rfl","rfp"]);D(o,"baseFrequency",b-(F/2-S+P)/1e6)}else D(o,"baseFrequency",b)}let{baseFrequency:h,originFrequency:d}=o;D(o,"frequencyOffset",(d-h)*1e6),D(o,"spectralWidth",g&&Number(g[0])/o.baseFrequency);for(let b in o)o[b].length===1&&(o[b]=o[b][0]);return i.tn&&(o.nucleus=i.tn.map(na)),o.dimension=1,o.isFid=!r.status.isSpectrum,{info:o,meta:{...s,...Jn(r),...i}}}function q(e){return e&&(Array.isArray(e)?e[0]:e)}function ia(e,t){let r={};for(let n of t){let i=e[n];i&&typeof i=="number"&&(r[n]=i)}return r}function Jn(e){let t={};for(let r of Object.keys(e)){let n=e[r];typeof n=="object"&&n!==null&&n.constructor&&n.constructor!==Object?t[r]=Jn(n):t[r]=n}return t}function Wn(e){let t={},r=new Set(e.files.map(n=>n.relativePath));for(let n of e){let i=n.name.toLowerCase();if(i.match(/^(?:fid|procpar|text|log)$/)){if(i.match(/^(?:fid|text|log)$/)){let a=n.relativePath.replace(/(?:fid|text|log)$/,"procpar");if(!r.has(a))continue}let o=n.relativePath.split("/"),s=o.slice(0,-1).join("/");t[s]||(t[s]={name:o.at(-2),files:[]}),t[s].files.push(n)}}return Object.values(t)}async function Xn(e,t={}){let{keepSource:r,logger:n}=t,i=Wn(e);n&&n.debug(`Found ${Object.keys(i).length} varian experiments`);let o=[],s={spectra:[],molecules:[]};for(let c of i){let{name:l,files:m}=c,p=$n(m).then(f=>{let{info:g,meta:y}=zn(f),u=f.fid.data[0],h=sa(u.im),d={data:{...u,x:f.x},meta:y,info:{isComplex:h,name:l,...g},display:{name:l}};if(g.isFid&&h){let{im:b}=d.data;aa(b,-1,{output:b})}m&&r&&(d.sourceSelector={files:m.map(b=>b.relativePath)}),s.spectra.push(d)});o.push(p)}let a=await Promise.allSettled(o);for(let c=0;c<a.length;c++){let l=a[c];if(l.status==="rejected"&&l.reason){let m=i[c].name;n?.warn(`Varian data: ${m}, fails with: ${l.reason}`)}}return s.spectra.length>0&&n?.info(`Loaded ${s.spectra.length}  spectra from Varian files`),oa(s)}var ze=class{id="@zakodium/nmrium-core-plugins#VarianLoaderPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={onFiles:this.onReadProcessFiles}}onReadProcessFiles=(t,r)=>{let{keepSource:n,logger:i}=r??{};return Xn(t,{keepSource:n,logger:i})}};function At(){return new ze}function la(e,t=[]){return[xt(e),At(),it(),ct(),yt(),Dt(),St(),gt(),Ke()].concat(t)}function ma(e=[]){let t=new ca;return t.registerPlugins(la(t,e)),t}import{getOneIfArray as Hn}from"@zakodium/nmrium-core";import{from1DNMRVariables as ua}from"convert-to-jcamp";function Vn(e,t){return e.filters.find(r=>r.name===t)}function pa(e,t={}){let{onlyReal:r=!1}=t,{info:n,meta:i,data:o}=e,{owner:s,title:a,isFid:c,spectralWidth:l,baseFrequency:m,originFrequency:p,nucleus:f,solvent:g,scaleFactor:y,frequencyOffset:u,decim:h,dspfvs:d,digitalFilter:b}=n,F=Hn(m||p),{x:S,re:P,im:x}=o,M=new Float64Array(P),A=!r&&x?new Float64Array(x):void 0,O=Vn(e,"fft")?.enabled,j={owner:s,isFid:c,title:a,nucleus:f,solvent:g,scaleFactor:y,spectralWidth:l,frequencyOffset:u,originFrequency:p,baseFrequency:F,dataType:!c||O?"NMR SPECTRUM":"NMR FID",dataClass:!r&&x?"NTUPLES":"XYDATA"};if(c){let se=e.filters.find(J=>J.name==="digitalFilter");if(se&&!O){let{value:{digitalFilterValue:J},enabled:We}=se;if(We){let k=Math.floor(J);M.set(P.slice(P.length-k)),M.set(P.slice(0,P.length-k),k),x&&A&&(A.set(x.slice(x.length-k)),A.set(x.slice(0,x.length-k),k))}}Nt(j,"decim",h),Nt(j,"dspfvs",d),Nt(j,"digitalFilter",b)}let re=fa(i,Gn),Je={xyEncoding:"DIFDUP",nmrInfo:j,meta:re},oe={x:{data:S,label:n.isFid?"TIME":"FREQUENCY",units:n.isFid?"second":"HZ",symbol:"X"},r:{data:M,label:`${n.isFid?"FID":"SPECTRUM"}/REAL`,units:"ARBITRARY UNITS",symbol:"R"}};return A&&(oe.i={data:A,label:`${n.isFid?"FID":"SPECTRUM"}/IMAG`,units:"ARBITRARY UNITS",symbol:"I"}),ua(oe,Je)}function Nt(e,t,r){r!==void 0&&(e[t]=Hn(r))}var Gn=["title","decim","dspfvs","grpdly","bf1","sw","offset",".solvent","owner","firsty","page","vardim","symbol","symbols","varform","vartype","datatype","dataclass",".observefrequency",".observenucleus","ncproc"];function fa(e,t=Gn){let r=new Set(t);return Object.fromEntries(Object.entries(e).filter(([n])=>!r.has(n.toLocaleLowerCase().replaceAll(/[\s|_]*/g,""))))}export{le as AutoPostProcessingPlugin,Me as BrukerLoaderPlugin,Ne as JCAMPDXLoaderPlugin,Re as JEOLLoaderPlugin,Oe as MolfileLoaderPlugin,Ce as NMReDATALoaderPlugin,we as SDFLoaderPlugin,ve as SMILESLoaderPlugin,ze as VarianLoaderPlugin,Ke as autoPostProcessing,it as brukerLoader,ma as default,ma as init,ct as jcampDXLoader,gt as jeolLoader,yt as molfileLoader,xt as nmreDATALoader,zr as processJCAMPDX,kn as readSDF,qn as readSMILES,la as recommended,Dt as sdfLoader,St as smilesLoader,pa as spectrum1DToJCAMPDX,At as varianLoader};

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@zakodium/nmrium-core-plugins",
-  "version": "0.1.7",
+  "version": "0.1.9",
   "description": "Recommended plugins for NMRium, loaders of common formats like bruker or jcamp, and some post-processing plugins",
   "author": "Zakodium Sàrl",
   "license": "CC-BY-NC-SA-4.0",
@@ -27,37 +27,39 @@
   },
   "devDependencies": {
     "@types/lodash.merge": "^4.6.9",
-    "@types/node": "^24.0.14",
+    "@types/node": "^24.2.0",
     "@zakodium/bruker-parser": "^0.0.0",
     "@zakodium/jeol-parser": "^0.0.0",
-    "@zakodium/nmr-types": "^0.1.0",
+    "@zakodium/nmr-types": "^0.1.1",
     "@zakodium/nmredata": "^0.0.0",
     "@zakodium/varian-parser": "^0.0.0",
     "bruker-data-test": "^1.0.0",
-    "esbuild": "^0.25.5",
+    "esbuild": "^0.25.8",
     "fifo-logger": "^2.0.0",
-    "jcamp-data-test": "^2.0.0",
+    "jcamp-data-test": "^2.1.0",
     "jeol-data-test": "^1.0.0",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "msw": "^2.10.2",
+    "msw": "^2.10.4",
     "nmredata-data-test": "^1.0.0",
     "rimraf": "^6.0.1",
     "vitest": "^3.2.4"
   },
   "dependencies": {
-    "@zakodium/nmrium-core": "^0.1.4",
+    "@date-fns/utc": "^2.1.1",
+    "@zakodium/nmrium-core": "^0.1.6",
     "cheminfo-types": "^1.8.1",
-    "convert-to-jcamp": "^5.4.11",
-    "file-collection": "^5.0.0",
+    "convert-to-jcamp": "^6.0.0",
+    "date-fns": "^4.1.0",
+    "file-collection": "^5.1.0",
     "gyromagnetic-ratio": "^2.0.0",
     "is-any-array": "^2.0.1",
-    "jcampconverter": "^11.0.4",
+    "jcampconverter": "^11.0.5",
     "linear-sum-assignment": "^1.0.7",
     "lodash.merge": "^4.6.2",
-    "ml-spectra-processing": "^14.12.0",
-    "nmr-processing": "^19.0.3",
-    "openchemlib": "^9.5.1",
-    "openchemlib-utils": "^8.1.5",
+    "ml-spectra-processing": "^14.14.1",
+    "nmr-processing": "^19.1.0",
+    "openchemlib": "^9.6.0",
+    "openchemlib-utils": "^8.2.0",
     "sdf-parser": "^7.0.4"
   },
   "volta": {