@zakodium/nmrium-core-plugins 0.0.1 → 0.1.1

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 (4) hide show
  1. package/dist/nmrium-core-plugins.cjs +5 -5
  2. package/dist/nmrium-core-plugins.d.ts +26 -15
  3. package/dist/nmrium-core-plugins.mjs +5 -5
  4. package/package.json +8 -8
package/dist/nmrium-core-plugins.cjs CHANGED
@@ -1,6 +1,6 @@
1
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m=a.nucleus.map(Kt.getGyromagneticRatio);a.baseFrequency=m.map(f=>t.fieldStrength.magnitude*f/(2*Math.PI*1e6)),a.pulseSequence=t.experiment,a.temperature=t.temperature?.unit?.toLowerCase()==="celsius"?273.15+t.temperature.magnitude:t.temperature.magnitude,a.digitalFilter=t.digitalFilter,a.pulseStrength90=1/(4*t.pulseStrength90.magnitude),a.numberOfScans=t.numberOfScans,a.relaxationTime=t.relaxationTime.magnitude,a.isComplex=t.dataSections.includes("im"),a.isFid=t.dataUnits[0]==="Second",a.isFt=t.dataUnits[0]==="Ppm",a.dimension=t.dimension,a.originFrequency=t.originFrequency.map(f=>f.magnitude/1e6).slice(0,o),a.numberOfPoints=t.dataPoints.slice(0,1),a.frequencyOffset=t.frequencyOffset.map((f,F)=>f.magnitude*a.baseFrequency[F]).slice(0,o),a.acquisitionTime=t.acquisitionTime.map(f=>f.magnitude).slice(0,o),a.spectralWidth=t.spectralWidth.map((f,F)=>f.magnitude/t.originFrequency[F].magnitude*1e6).slice(0,o),a.spectralWidthClipped=t.spectralWidthClipped.map((f,F)=>f.magnitude/a.baseFrequency[F]*1e6).slice(0,o);let u=[],c={},g;for(let f=0;f<t.dimension;f++){if(g={magnitude:t.acquisitionTime[f].magnitude/(t.dataPoints[f]-1),unit:"s"},t.dataUnits[f]==="Second")c.quantityName="time",c.originOffset={magnitude:0,unit:"s"},f===0?c.coordinatesOffset={magnitude:t.digitalFilter*g.magnitude,unit:"s"}:c.coordinatesOffset={magnitude:0,unit:"s"},c.reciprocal={originOffset:{magnitude:t.originFrequency[f].magnitude,unit:"Hz"},quantityName:"frequency",coordinatesOffset:{magnitude:t.frequencyOffset[f].magnitude*t.originFrequency[f].magnitude/1e6,unit:"Hz"}};else if(t.dataUnits[f]==="Ppm"){c.quantityName="frequency";let F=t.originFrequency[f].magnitude;c.originOffset={magnitude:F,unit:"Hz"};let h=t.dataOffsetStart[f],N=t.dataOffsetStop[f]-h+1;g={magnitude:kn(t,f)/(N-1),unit:"Hz"};let R=t.dataAxisStop[f]*F/1e6;c.coordinatesOffset={magnitude:R,unit:"Hz"},N!==t.dataPoints[f]&&(t.dataPoints[f]=N)}f===0?c.description="direct dimension":c.description="indirect dimension",u.push({label:String(i.dataAxisTitles[f]),count:Number(t.dataPoints[f]),increment:g,type:"linear",description:String(c.description)||"",application:c.application||{},coordinatesOffset:c.coordinatesOffset||0,originOffset:c.originOffset||0,quantityName:String(c.quantityName)||"",reciprocal:c.reciprocal||{},period:c.period||0,complexFFT:c.complexFFT||!1})}let y=[];y.push(Yt(l,11,{unit:"none",quantityName:"relative intensity",from:t.dataOffsetStart,to:t.dataOffsetStop}));let d={...a};return delete d.paramList,d.metadata={...Gt(i,o),...Gt(n,o),...(0,er.default)({},s)},[{timeStamp:Date.now(),description:d,dimensions:u,dependentVariables:y}]}function kn(e,r){let{spectralWidth:t,spectralWidthClipped:i}=e;return i[r].magnitude!=="NA"?i[r].magnitude:t[r].magnitude}function Gt(e,r){let t={};for(let i in e)t[i]=nr(e[i],r);return t}function nr(e,r){return(0,Zt.isAnyArray)(e)?r>1?e.slice(0,r):e[0]:e}var J=class{id="@zakodium/nmrium-core-plugins#JEOLLoaderPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={supportedExtensions:["jdf"],onFile:this.onReadProcessFile.bind(this)}}onReadProcessFile(r,t={}){let{logger:i,keepSource:n}=t;return i?.debug(`Reading JEOL file: ${r.name}`),rr(r,{name:r.name,keepSource:n,logger:i})}};function ye(){return new J}var _=class{id="@zakodium/nmrium-core-plugins#MolfileLoaderPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={supportedExtensions:["mol"],onFile:this.onReadProcessFile.bind(this)}}onReadProcessFile(r,t={}){let{logger:i}=t;return i?.debug(`Reading molfile file: ${r.name}`),Nt(r,{logger:i})}};function he(){return new _}var be=require("nmredata");var Be=require("@zakodium/nmrium-core");var ze=require("@zakodium/nmrium-core"),ir=require("ml-spectra-processing");function or(e,r){let{x:t,re:i}=r.data;return e.map(n=>{let o=(0,ir.xyIntegration)({x:t,y:i},{from:n.from,to:n.to}),s=[];for(let l of n.signals||[]){let{kind:a=null,id:m,js:u=[],diaIDs:c=[],...g}=l;s.push({...g,kind:a||"signal",js:u,id:m||(0,ze.generateID)(),diaIDs:c})}return{...n,id:n.id||(0,ze.generateID)(),kind:s?.[0].kind||"signal",absolute:o,signals:s}})}function sr(e,r){let t=[],{baseFrequency:i=500}=r.info;for(let n of e){let{delta:o,diaIDs:s=[],multiplicity:l="",integration:a=0}=n,m=n.jCoupling||[],u=wn({delta:o,js:m,frequency:i});if(m&&l&&m.length===l.length){m.sort((c,g)=>g.coupling-c.coupling);for(let c=0;c<m.length;c++)m[c].multiplicity=l[c]}t.push({id:(0,Be.generateID)(),...u,integration:a,signals:[{id:(0,Be.generateID)(),js:m,delta:o,diaIDs:s,multiplicity:l}]})}r.ranges.values=or(j(t),r)}function wn(e){let{delta:r,js:t=[],frequency:i}=e,n=.5;for(let o of t)n+=o.coupling;return n/=i,{from:r-n,to:r+n}}var Ue=require("@zakodium/nmrium-core"),vn=["x","y"],qn={x:0,y:0};function ar(e,r,t={}){let i=[],{shift:n=qn}=t,{originFrequency:o=[400,400]}=r.info,s={x:o[0],y:o[1]};for(let l of e){let a={x:{},y:{},id:(0,Ue.generateID)(),kind:"signal"},m={id:(0,Ue.generateID)(),kind:"signal",peaks:[]},u={x:10,y:10};for(let c of vn){let{coupling:g=[],delta:y,diaIDs:d=[]}=l[c];for(let p of g)u[c]+=p.coupling;if(l.activeCoupling){let{activeCoupling:p=[]}=l;for(let f of p)u[c]+=f.coupling}u[c]/=s[c],a[c]={from:y-u[c],to:y+u[c]},m[c]={delta:y,diaIDs:d,originalDelta:y-n[c]}}i.push({...a,signals:[m]})}r.zones.values=i}function cr(e){return $n(e.data)}function $n(e){return"rr"in e||!("x"in e)&&"re"in e}async function mr(e,r,t={}){let i={spectra:[],molecules:[]},n=await jn(e,r,t);if(n.spectra.length>0){let{spectra:o,molecules:s,usedFiles:l}=n;i.spectra.push(...o),i.molecules.push(...s);let a=e.files.length;for(let m=a-1;m>=0;m--){let u=e.files[m].relativePath;!u.match(/acqu.*/s)&&l.includes(u)&&e.files.splice(m,1)}}return i}async function jn(e,r,t){let i=[],n=await(0,be.getSDF)(e),o={spectra:[],molecules:[]};if(n.length===0)return{...o,usedFiles:i};let s=[];for(let a of n){let m=(0,be.nmrRecordToJSON)({sdf:a,fileCollection:e}).then(u=>{let{spectra:c,molecules:g=[]}=u;return i.push(a.root+a.filename),o.molecules.push(...g),zn(c,r,t)});s.push(m)}let l=await Promise.allSettled(s);for(let a of l)a.status==="fulfilled"?(o.spectra.push(...a.value.spectra),i.push(...a.value.usedFiles)):a.reason&&t?.logger?.error(a.reason);return{...o,usedFiles:i}}async function zn(e,r,t){let i=[],n=[],o={spectra:[],molecules:[]};for(let s of e){let l=Bn(s.source,r,t).then(a=>{let{spectra:m,files:u}=a;i.push(...u);for(let c of m)cr(c)?ar(s.signals,c):sr(s.signals,c);o.spectra.push(...m)});n.push(l)}return await Promise.allSettled(n),{...o,usedFiles:i}}async function Bn(e,r,t={}){let{file:i,jcampURL:n}=e,{converter:o}=t;if(n){let a=await Un(n,r,o?.jcamp);if(a)return{...a,files:[]}}let s=[];for(let a of i||[])s.push(Wn(a,t).then(m=>({...m,files:a.fileCollection.files.map(u=>u.relativePath)})));let l=await Promise.allSettled(s);for(let a of l){if(a.status==="fulfilled")return a.value;a.reason&&t?.logger?.error(a.reason)}return{spectra:[],molecules:[],files:[]}}async function Un(e,r,t={}){let i={entries:[{relativePath:e}]},n={name:$(e||""),xy:!0,noContours:!0,...t},{data:o}=await r.readFromWebSource(i,n);return o}async function Wn(e,r={}){let{converter:t,sourceSelector:i}=r;switch(e.type){case"jcamp":return fe(e.fileCollection.files[0],{name:e?.fileCollection.files[0].name||"",converter:t?.jcamp,selector:i?.jcamp,logger:r.logger,keepSource:r.keepSource});case"brukerFiles":return le(e.fileCollection,{converter:t?.bruker,selector:i});default:throw new Error("There is not a supported source")}}var V=class{constructor(r){this.core=r;this.onReadProcess={onFiles:this.onReadProcessFiles}}id="@zakodium/nmrium-core-plugins#NMReDATALoaderPlugin";version=1;migrations=[];onReadProcess;onReadProcessFiles=(r,t)=>mr(r,this.core,t)};function Fe(e){return new V(e)}var lr=require("sdf-parser");function We(e,r={}){let{mixedEOL:t}=r,{molecules:i}=(0,lr.parse)(e,{mixedEOL:t}),n=[];for(let{molfile:o}of i){let s=q(o);n.push(...s)}return n}async function ur(e,r={}){let{logger:t,mixedEOL:i}=r,n=await e.text(),o=We(n,{mixedEOL:i}),s={molecules:o,spectra:[]};return t&&t[o.length>0?"info":"debug"](`Loaded ${s.molecules.length} molecules from the ${e.name} file`),s}var H=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}`),ur(r,{logger:i})}};function Pe(){return new H}var pr=require("openchemlib");function Xe(e){let r=[],t=e.split(/\r?\n/).filter(Boolean);for(let i of t){let o=pr.Molecule.fromSmiles(i).toMolfile();r.push({molfile:o})}return r}async function fr(e,r={}){let t=await e.text(),i=Xe(t),n={molecules:i,spectra:[]};return r.logger?.info(`Found ${i.length} molecules from the ${e.name} file`),n}var Y=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 Ne(){return new Y}var br=require("@zakodium/nmrium-core"),Fr=require("filelist-utils"),Pr=require("is-any-array"),Nr=require("ml-spectra-processing"),Dr=require("varian-converter");var dr=require("nmr-processing");function gr(e,r){let{meta:t,procpar:i}=e,n={};for(let h of i)n[h.name]=h.values;let o={},s={},{np:l,solvent:a,sfrq:m,reffrq:u,temp:c,rp:g,sw:y,rfl:d,rfp:p}=n;P(o,"numberOfPoints",l&&Number(O(l))/2),P(o,"solvent",O(a)),P(o,"originFrequency",O(m)),P(o,"baseFrequency",O(u)),(Number.isNaN(o.originFrequency)||o.originFrequency===0)&&(o.originFrequency=400,r?.warn("The frequency could not be determined and was set to 400MHz")),P(o,"temperature",O(c)),P(o,"phc0",g&&Number(g[0])),P(s,"rfl",d&&Number(O(d))),P(s,"rfp",p&&Number(O(p))),P(s,"sw",y&&Number(O(y)));for(let h in s){let b=s[h];Array.isArray(b)&&b.length===1&&(s[h]=b[0])}if(!("baseFrequency"in o)&&"originFrequency"in o){let h=Number.parseFloat(o.originFrequency);if(["sw","rfl","rfp"].every(b=>b in s)){let{sw:b=1,rfl:N=1,rfp:S=1}=Xn(s,["sw","rfl","rfp"]);P(o,"baseFrequency",h-(b/2-N+S)/1e6)}else P(o,"baseFrequency",h)}let{baseFrequency:f,originFrequency:F}=o;P(o,"frequencyOffset",(F-f)*1e6),P(o,"spectralWidth",y&&Number(y[0])/o.baseFrequency);for(let h in o)o[h].length===1&&(o[h]=o[h][0]);return n.tn&&(o.nucleus=n.tn.map(dr.normalizeNucleus)),o.dimension=1,o.isFid=!t.status.isSpectrum,{info:o,meta:{...s,...yr(t),...n}}}function O(e){return e&&(Array.isArray(e)?e[0]:e)}function Xn(e,r){let t={};for(let i of r){let n=e[i];n&&typeof n=="number"&&(t[i]=n)}return t}function yr(e){let r={};for(let t of Object.keys(e)){let i=e[t];typeof i=="object"&&i!==null&&i.constructor&&i.constructor!==Object?r[t]=yr(i):r[t]=i}return r}function hr(e){let r={},t=new Set(e.files.map(i=>i.relativePath));for(let i of e){let n=i.name.toLowerCase();if(n.match(/^(?:fid|procpar|text|log)$/)){if(n.match(/^(?:fid|text|log)$/)){let l=i.relativePath.replace(/(?:fid|text|log)$/,"procpar");if(!t.has(l))continue}let o=i.relativePath.split("/"),s=o.slice(0,-1).join("/");r[s]||(r[s]={name:o.at(-2),files:[]}),r[s].files.push(i)}}return Object.values(r)}async function Sr(e,r={}){let{keepSource:t,logger:i}=r,n=hr(e);i&&i.debug(`Found ${Object.keys(n).length} varian experiments`);let o=[],s={spectra:[],molecules:[]};for(let a of n){let{name:m,files:u}=a,c=new Fr.FileCollection(u),g=(0,Dr.convert1D)(c).then(y=>{let{info:d,meta:p}=gr(y),f=y.fid.data[0],F=(0,Pr.isAnyArray)(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;(0,Nr.xMultiply)(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 ${s.spectra.length} spectra from Varian files`),(0,br.formatSpectra)(s)}var G=class{id="@zakodium/nmrium-core-plugins#VarianLoaderPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={onFiles:this.onReadProcessFiles}}onReadProcessFiles=(r,t)=>{let{keepSource:i,logger:n}=t??{};return Sr(r,{keepSource:i,logger:n})}};function De(){return new G}function Mr(e,r=[]){return[Fe(e),De(),ue(),de(),he(),Pe(),Ne(),ye(),te()].concat(r)}function Ar(){let e=new Rr.NMRiumCore;return e.registerPlugins(Mr(e)),e}var Je=require("@zakodium/nmrium-core"),Cr=require("convert-to-jcamp");function xr(e,r){return e.filters.find(t=>t.name===r)}function Or(e,r={}){let{info:t,meta:i,data:n}=e,{onlyReal:o=!1}=r,{isFid:s,spectralWidth:l}=t,a=(0,Je.getOneIfArray)(t.baseFrequency||t.originFrequency),{x:m,re:u,im:c}=n,g=new Float64Array(u),y=!o&&c?new Float64Array(c):void 0,d={};K(d,"SW",l),K(d,"BF1",a);let p=xr(e,"fft")?.enabled,f={originFrequency:t.originFrequency,dataType:!t.isFid||p?"NMR SPECTRUM":"NMR FID",dataClass:!o&&c?"NTUPLES":"XYDATA"};if(s){let b=e.filters.find(N=>N.name==="digitalFilter");if(b&&!p){let{value:{digitalFilterValue:N},enabled:S}=b;if(S){let D=Math.floor(N);g.set(u.slice(u.length-D)),g.set(u.slice(0,u.length-D),D),c&&y&&(y.set(c.slice(c.length-D)),y.set(c.slice(0,c.length-D),D))}}K(f,"decim",t.decim),K(f,"dspfvs",t.dspfvs),K(f,"digitalFilter",t.digitalFilter)}let F={xyEncoding:"DIFDUP",info:{...t,...f},meta:{...i,...d}},h={x:{data:m,label:t.isFid?"TIME":"FREQUENCY",units:t.isFid?"second":"HZ",symbol:"X"},r:{data:g,label:`${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"}),(0,Cr.from1DNMRVariables)(h,F)}function K(e,r,t){t!==void 0&&(e[r]=(0,Je.getOneIfArray)(t))}
package/dist/nmrium-core-plugins.d.ts CHANGED
@@ -10,6 +10,17 @@ import type { ParsingOptions } from '@zakodium/nmrium-core';
10
10
  import type { Spectrum1D } from '@zakodium/nmrium-core';
11
11
  import type { StateMolecule } from '@zakodium/nmrium-core';
12
12
 
13
+ export declare function autoPostProcessing(): NMRiumPlugin;
14
+
15
+ export declare class AutoPostProcessingPlugin implements NMRiumPlugin {
16
+ id: string;
17
+ version: number;
18
+ migrations: NMRiumPluginMigration[];
19
+ onReadProcess: NMRiumPluginOnReadProcess;
20
+ constructor();
21
+ private onPostProcessing;
22
+ }
23
+
13
24
  export declare function brukerLoader(): NMRiumPlugin;
14
25
 
15
26
  export declare class BrukerLoaderPlugin implements NMRiumPlugin {
@@ -41,40 +52,40 @@ declare function init(): NMRiumCore;
41
52
  export default init;
42
53
  export { init }
43
54
 
44
- declare interface JcampConverterOptions {
55
+ declare interface JCAMPDXConverterOptions {
45
56
  keepRecordsRegExp?: RegExp;
46
57
  profiling?: boolean;
47
58
  }
48
59
 
49
- export declare function jcampLoader(): NMRiumPlugin;
60
+ export declare function jcampDXLoader(): NMRiumPlugin;
50
61
 
51
- export declare class JcampLoaderPlugin implements NMRiumPlugin {
62
+ export declare class JCAMPDXLoaderPlugin implements NMRiumPlugin {
52
63
  id: string;
53
64
  version: number;
54
65
  migrations: NMRiumPluginMigration[];
55
66
  onReadProcess: NMRiumPluginOnReadProcess;
56
67
  constructor();
57
68
  private onReadProcessFile;
58
- private getJcampSelector;
69
+ private getJCAMPDXSelector;
59
70
  }
60
71
 
61
- declare interface JcampParsingOptions {
72
+ declare interface JCAMPDXParsingOptions {
62
73
  name?: string;
63
- converter?: JcampConverterOptions;
64
- selector?: JcampSelectorOptions;
74
+ converter?: JCAMPDXConverterOptions;
75
+ selector?: JCAMPDXSelectorOptions;
65
76
  keepSource?: boolean;
66
77
  logger?: Logger;
67
78
  }
68
79
 
69
- declare interface JcampSelectorOptions {
80
+ declare interface JCAMPDXSelectorOptions {
70
81
  index?: number;
71
82
  tree?: FilterTreeByDataTypeDataClass[];
72
83
  dataSelection?: DataSelectionOption;
73
84
  }
74
85
 
75
- export declare function jdfLoader(): NMRiumPlugin;
86
+ export declare function jeolLoader(): NMRiumPlugin;
76
87
 
77
- export declare class JDFLoaderPlugin implements NMRiumPlugin {
88
+ export declare class JEOLLoaderPlugin implements NMRiumPlugin {
78
89
  id: string;
79
90
  version: number;
80
91
  migrations: NMRiumPluginMigration[];
@@ -94,9 +105,9 @@ export declare class MolfileLoaderPlugin implements NMRiumPlugin {
94
105
  private onReadProcessFile;
95
106
  }
96
107
 
97
- export declare function nmreLoader(core: NMRiumCore): NMRiumPlugin;
108
+ export declare function nmreDATALoader(core: NMRiumCore): NMRiumPlugin;
98
109
 
99
- export declare class NMReLoaderPlugin implements NMRiumPlugin {
110
+ export declare class NMReDATALoaderPlugin implements NMRiumPlugin {
100
111
  private core;
101
112
  id: string;
102
113
  version: number;
@@ -110,7 +121,7 @@ declare interface ParseSDFOptions {
110
121
  mixedEOL?: boolean;
111
122
  }
112
123
 
113
- export declare function processJcamp(text: string, options?: JcampParsingOptions): NmriumData;
124
+ export declare function processJCAMPDX(text: string, options?: JCAMPDXParsingOptions): NmriumData;
114
125
 
115
126
  export declare function readSDF(text: string, options?: ParseSDFOptions): StateMolecule[];
116
127
 
@@ -138,7 +149,7 @@ export declare class SDFLoaderPlugin implements NMRiumPlugin {
138
149
 
139
150
  export declare function smilesLoader(): NMRiumPlugin;
140
151
 
141
- export declare class SmilesLoaderPlugin implements NMRiumPlugin {
152
+ export declare class SMILESLoaderPlugin implements NMRiumPlugin {
142
153
  id: string;
143
154
  version: number;
144
155
  migrations: NMRiumPluginMigration[];
@@ -147,7 +158,7 @@ export declare class SmilesLoaderPlugin implements NMRiumPlugin {
147
158
  private onReadProcessFile;
148
159
  }
149
160
 
150
- export declare function spectrum1DToJcamp(spectrum: Spectrum1D, options?: {
161
+ export declare function spectrum1DToJCAMPDX(spectrum: Spectrum1D, options?: {
151
162
  onlyReal?: boolean;
152
163
  }): string;
153
164
 
package/dist/nmrium-core-plugins.mjs CHANGED
@@ -1,6 +1,6 @@
1
- import{NMRiumCore as wn}from"@zakodium/nmrium-core";import{formatSpectra as Kt}from"@zakodium/nmrium-core";import{convertOneExperiment as Zt,groupByExperiments as Qt}from"brukerconverter";function U(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(jt(i,n))}return r}function jt(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 Oe}from"is-any-array";function I(e){if(Bt(e))return zt(e)?e.map(Ae):Ae(e);if(typeof e=="object"&&e!==null){let r={};for(let t in e)r[t]=I(e[t]);return r}return e}function Bt(e){return Oe(e)}function Ae(e){return Float64Array.from(e)}function zt(e){return Oe(e[0])}import{getOneIfArray as j}from"@zakodium/nmrium-core";import{getGyromagneticRatio as Vt}from"gyromagnetic-ratio";import{isAnyArray as ce}from"is-any-array";import{getFrequency as _t}from"nmr-processing";import{isAnyArray as T}from"is-any-array";function W(e){return typeof e=="number"}function J(e){let{phc0:r,phc1:t}=e;return!T(r)&&!W(r)||!T(t)&&!W(t)||T(r)&&!W(r[0])||T(t)&&!W(t[0])?{}:(T(t)?t[0]*=-1:t*=-1,T(r)?r[0]*=-1:r*=-1,{phc0:r,phc1:t})}function Ie(e,r,t){if(e>0)return Number(e);if(r>14||r===0)return 0;if(Ce[r]){let i=Ce[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 Ce={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 Ut}from"nmr-processing";function E(e,r=","){if(e&&typeof e=="string")return e.split(r)}function V(e,r,t){let i=[];if(e[`${t}AXNUC`]&&(i=e[`${t}AXNUC`],Array.isArray(i)||(i=[i]),i=O(i)),i.length===0&&e[`${t}NUC1`]&&(i=e[`${t}NUC1`],Array.isArray(i)||(i=[i]),i=O(i)),i.length===0&&e[".NUCLEUS"]){let n=E(e[".NUCLEUS"]);if(e[`${t}SYMBOL`]){let o=e[`${t}SYMBOL`].split(","),s=o.findIndex(a=>a.includes("2")),l=o.findIndex(a=>a.includes("1"));s!==-1&&l!==-1&&n?i=O([n[s],n[l]]):i=O(n).reverse()}else i=O(n)}return i.length===0&&e[".OBSERVENUCLEUS"]&&(i=O([e[".OBSERVENUCLEUS"]])),i.length===0&&r.experiment&&(i=O(Ee(r.experiment[0]))),Wt(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=Ee(r.experiment[0])),i.map(Ut)}function Wt(e){return e["2D_X_NUCLEUS"]&&!e["2D_X_NUCLEUS"].includes("off")&&e["2D_Y_NUCLEUS"]&&!e["2D_Y_NUCLEUS"].includes("off")}function Ee(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 O(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:[]}import{getOneIfArray as Jt}from"@zakodium/nmrium-core";function _(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,o=(Jt(r[`${n}SPECTYP`])||"").replace(/^<(.*)>$/,"$1").toLowerCase();return o.length>0&&o!=="undefined"?o:e.dimension?`${e.dimension}d`:""}function N(e,r,t,i=!1){t===void 0||r in e&&!i||(Array.isArray(t)?e[r]=t.map(Te):e[r]=[Te(t)])}function Te(e){return typeof e=="string"&&(e.startsWith("<")&&e.endsWith(">")&&(e=e.slice(1,-1)),e=e.replace(/\$.*/,"").trim()),e}function X(e,r={}){let{prefix:t="",logger:i}=r,n={dimension:0,nucleus:[],isFid:!1,isFt:!1},o=JSON.stringify(e),s=/\r\n/.exec(o)?`\r
1
+ import{NMRiumCore as wn}from"@zakodium/nmrium-core";import{Filters1D as _t,Filters2D as Vt}from"nmr-processing";import{getOneIfArray as jt}from"@zakodium/nmrium-core";function U(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,o=(jt(r[`${n}SPECTYP`])||"").replace(/^<(.*)>$/,"$1").toLowerCase();return o.length>0&&o!=="undefined"?o:e.dimension?`${e.dimension}d`:""}import{getOneIfArray as xe}from"@zakodium/nmrium-core";var zt=["no","exponential","modifiedGaussian","sine","qsine","trap","user","sinc","qsinc","traf","trafs"];function Bt(e){return e in Ce}function ae(e,r){let{prefix:t="",index:i=0}=r,n=xe(e[`${t}WDW`],i),o=zt[n?Number(n):0],s={};if(!Bt(o))return s;let l=Ce[o];if(l){let{kind:a,parameters:m}=l,u={};for(let c in m){let g=m[c],{source:y,processor:d}=g;if(y){let p=xe(e[`${t}${y}`],i);if(!p)continue;let f=Number(p);u[c]=d?d(f):f}else g.value!==void 0&&(u[c]=g.value)}s[a]={apply:!0,options:u}}return s}var Ce={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 Oe={sineBell:Te({offset:0})},Ie={cosy:{...Oe},hmbc:{...Oe},hsqc:{sineBell:Te({offset:.5})}},Ut={...Ie};function ce(e="",r=1){let t=Wt(e),i={},n=r===1?Ie[t||""]:Ut[t||""];return n&&(i=structuredClone(n)),i}function Te(e){return{apply:!0,options:e}}function Wt(e){let t=e.toLowerCase().match(/cosy|hsqc|hmbc/);return t?t[0]:null}function Ee(e,r={}){let{prefix:t="",experiment:i=U(e)}=r;return e[`${t}WDW`]?{f2:ae(e,{...r,index:0}),f1:ae(e,{...r,index:1})}:{f2:ce(i,1),f1:ce(i,2)}}import{Filters1D as Xt}from"nmr-processing";var me=["digitalFilter","backwardLinearPrediction","forwardLinearPrediction","apodization","zeroFilling","fft",["shiftX","phaseCorrection","baselineCorrection"]],E={};for(let e=0;e<me.length;e++){let r=me[e];for(let t of Array.isArray(r)?r:[r])E[t]=e}for(let e of Object.values(Xt))e.name in E||(E[e.name]=me.length);import{Filters2D as Jt}from"nmr-processing";var le=["digitalFilter2D","blpDimension1","flpDimension1","apodizationDimension1","zeroFillingDimension1","fftDimension1","blpDimension2","flpDimension2","nusDimension2","apodizationDimension2","zeroFillingDimension2","fftDimension2","phaseCorrectionTwoDimensions",["shift2DX","shift2DY","symmetrizeCosyLike"]],L={};for(let e=0;e<le.length;e++){let r=le[e];for(let t of Array.isArray(r)?r:[r])L[t]=e}for(let e of Object.values(Jt))e.name in L||(L[e.name]=le.length);var Ht=new Set(["backwardLinearPrediction","forwardLinearPrediction","digitalFilter2D","phaseCorrectionTwoDimensions","blpDimension1","flpDimension1","apodizationDimension1","apodizationDimension2","zeroFillingDimension1","fftDimension1","blpDimension2","flpDimension2","zeroFillingDimension2","fftDimension2","nusDimension2","symmetrizeCosyLike"]);function Yt(e,r){let{filter:t,experimentalFeatures:i=!1}=r,{name:n}=t;({..._t,...Vt})[n]&&(e.some(s=>s.name===n)||(i||!Ht.has(n))&&e.push({...t,enabled:!0}))}function Le(e,r={}){let{data:t}=e;if(!t)return e;let{autoProcessing:i,experimentalFeatures:n}=r,o=(l,a)=>Yt(l,{...a,experimentalFeatures:n}),{spectra:s}=t;for(let l of s){let{data:a,info:m,meta:u,filters:c}=l,{dimension:g,isFid:y}=m;if(y){if(g===1){let d=a.re.length,{tdOff:p,digitalFilter:f}=m;if(f&&f>0&&o(c,{filter:{name:"digitalFilter",value:{digitalFilterValue:f}}}),!i)continue;p&&Math.abs(p)>0&&o(c,{filter:{name:"backwardLinearPrediction",value:{nbInputs:d/2}}}),o(c,{filter:{name:"apodization",value:{exponential:{apply:!0,options:{lineBroadening:1}}}}}),o(c,{filter:{name:"zeroFilling",value:{nbPoints:2*d}}}),o(c,{filter:{name:"fft",value:{}}}),o(c,{filter:{name:"phaseCorrection",value:Gt(m)}}),c.sort((F,h)=>E[F.name]-E[h.name])}else if(g===2){if(!i||!n)continue;let d=a.re.z.length,p=a.re.z[0].length,{tdOff:f,experiment:F=""}=m,h=m.spectrumSize;Array.isArray(h)&&h.length>1?(h[0]<=p&&(h[0]=p*2),h[0]<=d&&(h[0]=d*2)):h=[p*2,2*d];let b=F.toLowerCase().includes("cosy");f&&Math.abs(f[0])>0&&o(c,{filter:{name:"blpDimension1",value:{nbInputs:p/2}}});let N=Ee(u,{experiment:F});o(c,{filter:{name:"apodizationDimension1",value:N.f2}}),o(c,{filter:{name:"zeroFillingDimension1",value:{nbPoints:h[0]}}}),o(c,{filter:{name:"fftDimension1",value:{}}}),u&&"nuslist"in u&&o(c,{filter:{name:"nusDimension2",value:{}}}),o(c,{filter:{name:"apodizationDimension2",value:N.f1}}),o(c,{filter:{name:"zeroFillingDimension2",value:{nbPoints:h[b?0:1]}}}),b?o(c,{filter:{name:"symmetrizeCosyLike",value:{}}}):o(c,{filter:{name:"phaseCorrectionTwoDimensions",value:{}}}),o(c,{filter:{name:"fftDimension2",value:{}}}),c.sort((S,D)=>L[S.name]-L[D.name])}}}}function Gt(e){let{phc0:r=0,phc1:t=0}=e;return ke([r,t])?{}:{ph0:r,ph1:t}}function ke(e){return Array.isArray(e)?e.every(r=>!r&&r===0):ke([e])}var W=class{id="@zakodium/nmrium-core-plugins#AutoPostProcessingPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={onProcessing:this.onPostProcessing.bind(this)}}onPostProcessing(r,t){Le(r,t)}};function ue(){return new W}import{formatSpectra as cr}from"@zakodium/nmrium-core";import{convertOneExperiment as mr,groupByExperiments as lr}from"brukerconverter";function X(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(Kt(i,n))}return r}function Kt(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 ve}from"is-any-array";function I(e){if(Zt(e))return Qt(e)?e.map(we):we(e);if(typeof e=="object"&&e!==null){let r={};for(let t in e)r[t]=I(e[t]);return r}return e}function Zt(e){return ve(e)}function we(e){return Float64Array.from(e)}function Qt(e){return ve(e[0])}import{getOneIfArray as j}from"@zakodium/nmrium-core";import{getGyromagneticRatio as rr}from"gyromagnetic-ratio";import{isAnyArray as fe}from"is-any-array";import{getFrequency as nr}from"nmr-processing";import{isAnyArray as k}from"is-any-array";function J(e){return typeof e=="number"}function _(e){let{phc0:r,phc1:t}=e;return!k(r)&&!J(r)||!k(t)&&!J(t)||k(r)&&!J(r[0])||k(t)&&!J(t[0])?{}:(k(t)?t[0]*=-1:t*=-1,k(r)?r[0]*=-1:r*=-1,{phc0:r,phc1:t})}function $e(e,r,t){if(e>0)return Number(e);if(r>14||r===0)return 0;if(qe[r]){let i=qe[r];if(!i[t])throw new Error(`decim ${t} not in lookup table for dspfvs ${r}`);return i[t]}else throw new Error(`dspfvs ${r} not in lookup table`)}var qe={10:{2:44.75,3:33.5,4:66.625,6:59.08333333333333,8:68.5625,12:60.375,16:69.53125,24:61.02083333333333,32:70.015625,48:61.34375,64:70.2578125,96:61.50520833333333,128:70.37890625,192:61.5859375,256:70.439453125,384:61.62630208333333,512:70.4697265625,768:61.646484375,1024:70.48486328125,1536:61.65657552083333,2048:70.492431640625},11:{2:46,3:36.5,4:48,6:50.16666666666667,8:53.25,12:69.5,16:72.25,24:70.16666666666667,32:72.75,48:70.5,64:73,96:70.66666666666667,128:72.5,192:71.33333333333333,256:72.25,384:71.66666666666667,512:72.125,768:71.83333333333333,1024:72.0625,1536:71.91666666666667,2048:72.03125},12:{2:46,3:36.5,4:48,6:50.16666666666667,8:53.25,12:69.5,16:71.625,24:70.16666666666667,32:72.125,48:70.5,64:72.375,96:70.66666666666666,128:72.5,192:71.333333333,256:72.25,384:71.66666666666667,512:72.125,768:71.83333333333333,1024:72.0625,1536:71.91666666666667,2048:72.03125},13:{2:2.75,3:2.833333333333333,4:2.875,6:2.916666666666667,8:2.9375,12:2.958333333333333,16:2.96875,24:2.979166666666667,32:2.984375,48:2.989583333333333,64:2.9921875,96:2.994791666666667}};import{normalizeNucleus as er}from"nmr-processing";function T(e,r=","){if(e&&typeof e=="string")return e.split(r)}function V(e,r,t){let i=[];if(e[`${t}AXNUC`]&&(i=e[`${t}AXNUC`],Array.isArray(i)||(i=[i]),i=C(i)),i.length===0&&e[`${t}NUC1`]&&(i=e[`${t}NUC1`],Array.isArray(i)||(i=[i]),i=C(i)),i.length===0&&e[".NUCLEUS"]){let n=T(e[".NUCLEUS"]);if(e[`${t}SYMBOL`]){let o=e[`${t}SYMBOL`].split(","),s=o.findIndex(a=>a.includes("2")),l=o.findIndex(a=>a.includes("1"));s!==-1&&l!==-1&&n?i=C([n[s],n[l]]):i=C(n).reverse()}else i=C(n)}return i.length===0&&e[".OBSERVENUCLEUS"]&&(i=C([e[".OBSERVENUCLEUS"]])),i.length===0&&r.experiment&&(i=C(je(r.experiment[0]))),tr(e)&&(i=[e["2D_X_NUCLEUS"].replaceAll(/[^A-Za-z0-9]/g,""),e["2D_Y_NUCLEUS"].replaceAll(/[^A-Za-z0-9]/g,"")]),r.experiment&&(r.experiment[0].match("jres")||r.experiment[0].match("dosy"))&&(i=je(r.experiment[0])),i.map(er)}function tr(e){return e["2D_X_NUCLEUS"]&&!e["2D_X_NUCLEUS"].includes("off")&&e["2D_Y_NUCLEUS"]&&!e["2D_Y_NUCLEUS"].includes("off")}function je(e){return typeof e!="string"?[]:(e=e.toLowerCase(),e.includes("jres")?["1H","Hz"]:e.includes("dosy")?["1H","D"]:e.includes("hmbc")||e.includes("hsqc")?["1H","13C"]:e.includes("cosy")||e.includes("tocsy")?["1H","1H"]:[])}function C(e){if(!e)return[];let r=e.map(i=>String(i).replaceAll(/[^A-Za-z0-9]/g,"").replace("NA","").replace("off","")),t=0;for(let i of r)i||t++;return t===0?r:[]}function P(e,r,t,i=!1){t===void 0||r in e&&!i||(Array.isArray(t)?e[r]=t.map(ze):e[r]=[ze(t)])}function ze(e){return typeof e=="string"&&(e.startsWith("<")&&e.endsWith(">")&&(e=e.slice(1,-1)),e=e.replace(/\$.*/,"").trim()),e}function Y(e,r={}){let{prefix:t="",logger:i}=r,n={dimension:0,nucleus:[],isFid:!1,isFt:!1},o=JSON.stringify(e),s=/\r\n/.exec(o)?`\r
2
2
  `:`
3
- `,{JCAMPDX:l="",ORIGIN:a=""}=e,m=String(l).toLowerCase()+String(a).toLowerCase();"SPECTROMETER/DATASYSTEM"in e&&(m=e["SPECTROMETER/DATASYSTEM"]);let u=(d=[])=>{for(let p of d)if(!(p in n))return!1;return!0};(m.includes("mestre")||m.includes("nova"))&&(m="mnova"),n.creator=m,e.LONGDATE&&ae(n,Date.parse(e.LONGDATE)),N(n,"pulseSequence",e[".PULSESEQUENCE"]||e[".PULPROG"]||e[`${t}PULPROG`]);let c=e[`${t}OWNER`];if(c&&N(n,"owner",c.replaceAll(/\$\$.*/gm,"")),N(n,"aqMod",e[`${t}AQ_mod`]),N(n,"experiment",_(n,e,{prefix:t})),n.nucleus=V(e,n,t),n.nucleus.length===0)if(i)i?.warn("There is not a nucleus detected, assuming 1H"),n.nucleus=["1H"];else throw new Error("There is not a nucleus detected");n.dimension=n.nucleus.length;let g=e[`${t}.ACQUISITIONSCHEME`]||e[`${t}FnMODE`];if(g&&N(n,"acquisitionScheme",Xt(j(g,1))),N(n,"acquisitionMode",e[`${t}.ACQUISITIONMODE`]),M(n,"lpNumberOfCoefficients",e[`${t}NCOEF`]),M(n,"linearPredictionBin",e[`${t}LPBIN`]),M(n,"tdOff",e[`${t}TDoff`]),N(n,"windowMultiplicationMode",e[`${t}WDW`]),N(n,"title",e.TITLE),N(n,"solvent",e[".SOLVENTNAME"]),N(n,"temperature",e[`${t}TE`]||e[".TE"]),N(n,"type",e.DATATYPE),N(n,"dataClass",e[`${t}DATACLASS`]),N(n,"phc1",e[`${t}PHC1`]),N(n,"phc0",e[`${t}PHC0`]),n.type){let d=n.type[0].toUpperCase();d.includes("FID")?(n.isFid=!0,n.isComplex=!0):d.includes("SPECTRUM")&&(n.isFt=!0)}if(N(n,"firstX",e[`${t}FIRSTX`]),N(n,"lastX",e[`${t}LASTX`]),N(n,"numberOfPoints",e[`${t}NPOINTS`]),N(n,"originFrequency",e[`${t}SFO1`]),n.dimension===1&&M(n,"originFrequency",e[".OBSERVEFREQUENCY"]),"originFrequency"in n&&(n.originFrequency=H(n.originFrequency)),!n.originFrequency&&n.dimension===2&&".OBSERVEFREQUENCY"in e){let{nucleus:d}=n,p=H(e[".OBSERVEFREQUENCY"]);if(ce(p)&&p.length>1){let f=e[`${t}SYMBOL`].split(","),F=f.findIndex(b=>b.includes("2")),h=f.findIndex(b=>b.includes("1"));F!==-1&&h!==-1?n.originFrequency=[p[F],p[h]]:n.originFrequency=p.slice()}else if(typeof p=="number"){let f=_t(d[1],{frequency:p,nucleus:d[0]});n.originFrequency=[p,f]}}if((!n.originFrequency||n.originFrequency.some(d=>Number.isNaN(d)||d===0))&&(n.originFrequency||(n.originFrequency=n.dimension>1?[400,400]:[400]),n.originFrequency=n.originFrequency.map(d=>Number.isNaN(d)||d===0?400:d),i?.warn("The frequency could not be determined and was set to 400 MHz")),m.toLocaleLowerCase().includes("oxford instruments")?Yt(n,e,{...r,separator:s}):m.includes("nanalysis")&&Gt(n,e),m!=="mnova"&&m!=="mestre"){let d=n.nucleus[0],p=Vt(d);if(N(n,"probeName",e[`${t}PROBHD`]),N(n,"baseFrequency",e[`${t}BF1`]),N(n,"baseFrequency",e[`${t}SF`]),M(n,"scaleFactor",e[`${t}NC_proc`]),"scaleFactor"in n)for(let b=0;b<n.scaleFactor.length;)n.scaleFactor[b]=2**n.scaleFactor[b++];if(!("baseFrequency"in n)&&"originFrequency"in n?N(n,"baseFrequency",n.originFrequency):n.baseFrequency=H(n.baseFrequency),!["baseFrequency","originFrequency"].some(b=>!n[b])&&p){let{baseFrequency:b}=n,P=2*Math.PI*(b[0]/p)*1e6;N(n,"fieldStrength",P)}M(n,"spectralWidth",e[`${t}SW`]),M(n,"spectralWidth",e[`${t}QM_SPECTRAL_WIDTH`]),n.dimension===1&&e[`${t}SweepWidth`]&&n.originFrequency&&M(n,"spectralWidth",e[`${t}SweepWidth`]/n.originFrequency[0]),N(n,"numberOfPoints",e[`${t}TD`],!0);let f=n.numberOfPoints;if(N(n,"spectrumSize",e[`${t}SI`]??f),N(n,"sampleName",e[`${t}NAME`]),e[`${t}FNTYPE`]!==void 0&&N(n,"acquisitionMode",Number.parseInt(e[`${t}FNTYPE`],10)),(e[`${t}VARNAME`]?e[`${t}VARNAME`].split(",")[0]:"")==="TIME"){let b=typeof e.LAST=="string"?e.LAST.replace(" 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b=j(e[`${t}DATE`]),P=Number.parseInt(b,10)*1e3;Number.isNaN(P)?ae(n,Date.parse(b)):ae(n,P)}n.solvent||N(n,"solvent",j(e[`${t}SOLVENT`]))}if(n.dimension<2&&"dataClass"in n&&n.dataClass[0].toUpperCase()==="NTUPLES"&&(N(n,"last",E(e[`${t}LAST`])),N(n,"first",E(e[`${t}FIRST`])),N(n,"varDim",E(e[`${t}VARDIM`])),N(n,"symbols",E(e[`${t}SYMBOL`])),n.symbols&&Array.isArray(n.symbols))){n.symbols.includes("R")&&n.symbols.includes("I")&&(n.isComplex=!0);let d=n.symbols.findIndex(p=>p.toLowerCase()==="x");if(M(n,"firstX",n.first[d]),M(n,"lastX",n.last[d]),M(n,"numberOfPoints",n.varDim[d]),!("spectralWidth"in n)){let{lastX:p,numberOfPoints:f,firstX:F}=n;N(n,"spectralWidth",n.isFid?f/(2*p):Math.abs(p-F)/n.originFrequency)}}if(`${t}REVERSE`in e){let d=e[`${t}REVERSE`];n.reverse=(Array.isArray(d)?d:[d]).map(p=>typeof p=="string"?p.includes("yes"):p)}let y=e[`${t}REFERENCE_POINT`];if(!("frequencyOffset"in n)&&y&&u(["spectralWidth","baseFrequency"])){let d=typeof y=="number"?y:e[`${t}REFERENCE_POINT`].match(/(?<reference>[+-]?\d+(?:\.\d+)?)\s*.*/),p;if(typeof y=="number"?p=y:(y.match(/(?<reference>[+-]?\d+(?:\.\d+)?)\s*.*/),p=Number(d?.groups?.reference)),!Number.isNaN(p)){let{spectralWidth:f,baseFrequency:F}=n;N(n,"frequencyOffset",.5*f*F-p)}}if(!("frequencyOffset"in n)&&u(["baseFrequency","originFrequency"])){let{baseFrequency:d,originFrequency:p}=n,f=d.map((F,h)=>(p[h]-F)*1e6);N(n,"frequencyOffset",f)}for(let d in n)n[d]&&n[d].length===1&&(n[d]=n[d][0]);return!n.frequencyOffset&&".SHIFTREFERENCE"in e&&Ht(e,n),Array.isArray(n.nucleus)||(n.nucleus=[n.nucleus]),n}function M(e,r,t){t!==void 0&&N(e,r,H(t))}function ae(e,r){if(!Number.isNaN(r)){e.epoch=r;let t=new Date(r);e.date=t.toUTCString(),e.localeDate=t.toLocaleString()}}function Ht(e,r){let t=e[".SHIFTREFERENCE"],i=t.trim().startsWith("(")?/\((?<data>[^)]+)\)/:/(?<data>[^)]+)/,n=t.match(i);if(n.groups.data){let o=n.groups.data.split(",");if(o.length<4)return;let s=Number.parseInt(r.numberOfPoints,10),{spectralWidth:l,baseFrequency:a}=r,m=Number.parseInt(o[2],10),u=Number.parseFloat(o[3]),c;if(r.isFid){if(["baseFrequency","numberOfPoints","spectralWidth"].some(g=>!(g in r)))return;c=u+(s*.5-m)*l/s}else{let g=Number.parseFloat(r.firstX),y=Number.parseFloat(r.lastX),d=(y+g)/2,p=(y-g)/(s+1),f=p<0?g:y+(m-1)*p;c=(d-f)/a+u}c!==void 0&&!Number.isNaN(c)&&(r.frequencyOffset=c*a)}}function H(e){if(ce(e)){let r=[];for(let t of e)r.push(typeof t=="string"?Number.parseFloat(t):t);return r}return typeof e=="string"?Number.parseFloat(e):e}function Xt(e){switch(String(ce(e)?e[1]:e).toLowerCase().replaceAll(/\s/g,"")){case"1":case"notphasesensitive":return"notPhaseSensitive";case"2":return"QSEQ";case"3":case"tppi":return"TPPI";case"4":case"states":return"States";case"5":case"tppi-states":return"States-TPPI";case"6":case"echo-antiecho":return"Echo-antiecho";default:return"undefined"}}function Yt(e,r,t={}){let{prefix:i="",separator:n=`
4
- `}=t;N(e,"spectralWidth",r[`${i}SweepWidth`]/e.originFrequency[0]);let o=r[`${i}.PULSESEQUENCE`].split(n),s=[];r[".OBSERVENUCLEUS"]&&s.push(r[".OBSERVENUCLEUS"]),r.INDIRECTNUCLEUS&&s.push(r.INDIRECTNUCLEUS),e.nucleus=O(s),e.pulseSequence=o[0];let l=o.slice(2,-1);if(s.length>1)if(s[0]===s[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,u=Number.parseFloat(a.groups.sw);e.spectralWidth.push(u/m[1])}}return e}function Gt(e,r){let{T1NUCLEUS:t,T2NUCLEUS:i,PAGE:n}=r;e.pulseSequence=r.EXPERIMENT||r[".PULSESEQUENCE"];let o=[],{dimension:s,isComplex:l}=e;if(s===2&&e.pulseSequence==="T1"){let u=l?2:1;for(let c=0;c<n.length;c+=u){let g=n[c].replace(/T1=/,"");o.push(Number(g))}r.vdlistValues=o}e.nucleus=s>1?[i,t]:i;let{phc0:a,phc1:m}=e;if(a&&m){let u=J({phc0:a,phc1:m});e={...e,...u}}}var er={keepRecordsRegExp:/.*/,keepFiles:!0};async function Y(e,r={}){let t={spectra:[],molecules:[]},{converter:i={},selector:n={},logger:o}=r,s=Qt(e,{logger:o,...rr(n)}),l=[];for(let m of s)l.push(Zt(m,{...er,...i}).then(u=>tr(u,r)));let a=await Promise.allSettled(l);for(let m=0;m<a.length;m++){let u=a[m];if(u.status==="fulfilled"){let c=J(u.value.info);t.spectra.push({...u.value,info:{...u.value.info,...c}})}else if(u.reason){let c=s[m].name;o?.warn(`Bruker data: ${c}, fails with: ${u.reason}`);continue}}return o&&o[t.spectra.length>0?"info":"debug"](`Loaded ${t.spectra.length} spectra from Bruker files`),Kt(t)}function tr(e,r={}){let{keepSource:t=!1,logger:i}=r,n={...e.info,...e.meta},o=X(n,{logger:i}),s={},{isFid:l}=o;if(nr(e)){let y=e.minMax;for(let d in y){let p=y[d];p&&(p.z=I(p.z))}s.components=e.minMax}else o.dimension===1&&(s.components=e.spectra);let{source:a}=e,{expno:m,name:u,files:c}=a;n.vdlist&&(n.vdlistValues=U(n.vdlist));let g={dependentVariables:[s],meta:n,info:{...o,experimentNumber:m,name:u}};return c&&t&&(g.sourceSelector={files:c.map(y=>y.relativePath)}),ir(g,e),g}function rr(e){let{general:r={},bruker:t={}}=e,{processingNumbers:i,experimentNumbers:n,...o}=t;return{...r,...o,processingNumbers:Le(i),experimentNumbers:Le(n)}}function Le(e){if(e)return e.split(/[^\d]+/).filter(Boolean).map(r=>Number.parseInt(r,10))}function nr(e){let{info:r}=e;return r.twoD}function ir(e,r){if(!("integrals"in r))return;let{integrals:t=[]}=r;e.integrals={values:t.map(i=>{let{from:n,to:o,integration:s}=i;return{from:n,to:o,integral:s,kind:"signal"}})}}var G=class{id="nmrium-core-plugins#BrukerLoaderPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={onFiles:this.onReadProcessFiles}}onReadProcessFiles=(r,t)=>{let{sourceSelector:i,converter:n,keepSource:o,logger:s}=t??{};return Y(r,{converter:n?.bruker,selector:i,keepSource:o,logger:s})}};function me(){return new G}import{formatSpectra as $r}from"@zakodium/nmrium-core";import{createTree as jr}from"jcampconverter";function ke(e,r,t={}){let{selector:i={},keepSource:n=!1}=t;if(!n)return e;for(let o=0;o<e.spectra.length;o++){let s=e.spectra[o];s.sourceSelector={files:[r.relativePath],jcamp:{index:o,...i}}}return e}import{convert as or}from"jcampconverter";function le(e,r,t){let{dataType:i,children:n}=e,o=i==="LINK"&&n?n:[e];for(let s of o){if(s.dataType==="LINK"){le(s,r,t);continue}let l=or(s.jcamp,t);r.push(...l.flatten)}}function qe(e,r={}){let t=[],i=$e(e,r);for(let s of i?e:[])s.dataType==="LINK"?s.children=ue(s.children,r):s=ue([s],r)[0],t.push(s);let{name:n,logger:o}=r;return e.length===0&&o?.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:o="both"}=r,s=[];for(let u of e){let{dataType:c,dataClass:g}=u;if(c==="LINK")u.children=ue(u.children,r);else if(n.some(y=>{let{dataClass:d=g,dataType:p=c}=y;return g===d&&c===p})){i?.warn(`Skipping ${g} and ${c} ${t?`in ${t}`:"in the JCAMP-DX"},
5
- because it didn't match the import filters`);continue}s.push(u)}let l=[],a=s.some(ve),m=s.some(we);for(let u of s){if(o!=="both"&&u.dataType!=="LINK"){if(ve(u)&&(o==="ft"||o==="preferFT"&&m)){i?.warn(`Skipping raw data ${t?`in ${t}`:"in the JCAMP-DX"} because it didn't match the import filters`);continue}if(we(u)&&(o==="fid"||o==="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(u)}return l}function we(e){return e.dataType?.toUpperCase().includes("SPECTRUM")&&e.dataClass&&!e.dataClass.toUpperCase().includes("PEAK")}function ve(e){return e.dataType?.toUpperCase().includes("FID")}function $e(e,r={}){let{logger:t,name:i=""}=r;for(let n of e){if(n.dataType==="LINK"&&$e(n.children,r))return!0;let{dataType:o=""}=n,s=o.toLowerCase();if(s.length>0){if(s.includes("spectrum")&&!s.includes("nmr"))return t?.warn(`File ${i} was ignored because it is a ${o}`),!1;if(s.includes("nmr"))return!0}}return!1}import{generateID as ze}from"@zakodium/nmrium-core";import{parseJcampCS as pr}from"jcampconverter";import*as fr from"openchemlib/full";import{isMolfileNotEmpty as sr}from"nmr-processing";import{Molecule as ar}from"openchemlib/full";async function je(e,r={}){let t=await e.text(),i=L(t),n={molecules:i,spectra:[]};return i.length===0&&r.logger?.debug(`${e.name} is an empty molfile`),n}function L(e){let r=[];if(!sr(e))return[];let i=ar.fromMolfile(e).toMolfile();return r.push({molfile:i}),r}import{isMolfileNotEmpty as mr}from"nmr-processing";import*as lr from"openchemlib/full";import{getDiastereotopicAtomIDsFromMolfile as ur}from"openchemlib-utils";var cr=new Set(["ndnmrspectrum","ndnmrfid","nmrspectrum","nmrfid"]);function K(e){let{dataType:r="",dataClass:t=""}=e,i=r.replaceAll(/\s/g,"").toLowerCase(),n=t.replaceAll(/\s/g,"").toLowerCase();return cr.has(i)&&n!=="peaktable"}function Be(e,r,t={}){let{spectra:i,info:n,meta:o}=e,s=i[0].data,l=[],a={x:"delta",y:"intensity",w:"width",m:"multiplicity",a:"atom"},{logger:m,name:u,spectraData:c}=t,{CROSSREFERENCE:g}=n,y=typeof g!="string"?g:g.split(/\r?\n/).map(S=>S.trim()).filter(Boolean),d=y.find(S=>S?.toLowerCase().includes("structure"));if(d===void 0)return m&&m.warn(`There is not a structure reference for ${u} file, assignment object could not be completed`),null;let p=Number.parseInt(d?.toLowerCase().replace(/_/,"").replace(/structure:\s*blockid\s*=\s*(?<blockId>.*)/,"$<blockId>"),10);if(Number.isNaN(p)||p<1)return m&&m.warn(`Structure block_id not found for ${u} file, assignment object could not be completed`),null;let F=c?.molecules?.find(S=>S.blockId===p)?.molfile??"";if(F===""){let S=r.find(x=>x.info.BLOCKID===p),{MOLFILE:D=""}=S?.meta||{};F=D}if(!mr(F))return m&&m.warn(`Empty molfile for ${u} file with structure block_id = ${p}, assignment object could not be completed`),null;let h=ur(lr,F),b=V({...n,...o},{},"");for(let S=0;S<s.x.length;S++){let D={};for(let x in s){let A=s[x][S];typeof A=="string"&&A.startsWith("<")&&A.endsWith(">")&&(A=A.slice(1,-1)),D[a[x]]=A}if("atom"in D){let x=h.map[D.atom-1];b.includes("1H")?x.nbHydrogens>0?(D.diaIDs=x.hydrogenOCLIDs,D.nbHydrogens=x.nbHydrogens):(D.diaIDs=[x.oclID],D.nbHydrogens=x.nbHydrogens):(D.diaIDs=[x.oclID],D.nbHydrogens=1)}l.push(D)}let P={};for(let S of l){let{delta:D,diaIDs:x}=S,A=`${D}_${x.join("_")}`;if(P[A])P[A].atoms.push(S.atom);else{let{atom:Bn,...$t}=S;P[A]={...$t,atoms:[S.atom]}}}let R=[];for(let S of y)S.toLowerCase().includes("spectrum")&&R.push(Number(S.toLowerCase().replace(/_/,"").replace(/.*:\s*blockid=(?<blockId>.*)/,"$<blockId>")));if(R.length===0){for(let S of r)if(K(S)){let{BLOCKID:D}=S.info;R.push(Number(D))}R.length>1&&(R=[],m&&m.warn(`There is not a spectral cross-reference for the peak assignment in the ${u} file`))}return{moleculeBlockID:p,spectraBlockIDs:R,assignments:Object.values(P),molecule:h.molecule}}function Ue(e,r,t,i){for(let n of e){let{meta:o,dataClass:s="",dataType:l="",info:a}=n,m=Number.parseInt(String(a.BLOCKID),10);o.MOLFILE?hr(String(o.MOLFILE),r,m):n.jcampCS&&yr(n,r,m),dr(s,l)&&gr(r,n,e,i),K(n)&&t.push(n)}}function dr(e,r){return e?.toLowerCase().includes("assignments")&&r?.toLowerCase().includes("assignments")}function gr(e,r,t,i){let n=Be(r,t,{spectraData:e,logger:i.logger,name:i.name});if(e.assignmentsByBlocks||(e.assignmentsByBlocks={}),n){let{spectraBlockIDs:o}=n;for(let s of o)e.assignmentsByBlocks[s]=n}}function yr(e,r,t){r.molecules||(r.molecules=[]);let i=pr(e,{OCL:fr}),n=L(i?.molfile||"");n.length>0&&r.molecules.push({id:ze(),blockId:t,...n[0]})}function hr(e,r,t){r.molecules||(r.molecules=[]);let i=L(String(e));r.molecules.push({id:ze(),blockId:t,...i[0]})}import{generateID as tt}from"@zakodium/nmrium-core";import{matrixMinMaxZ as et,reimPhaseCorrection as Or}from"ml-spectra-processing";import{xyAutoRangesPicking as Cr}from"nmr-processing";function k(e){return e.slice(0,Math.max(0,e.lastIndexOf(".")))}function w(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 Sr}from"nmr-processing";import{xMaxValue as br}from"ml-spectra-processing";function B(e){return e.trim().slice(1,-1).split(/,\s*/).map(r=>r.trim())}var Fr={I:"id",X:"from",Y:"to",Hs:"delta",An:"integration",H:"nbAtoms",C:"multiplicity",N:"assignment","(J)":"js"},We=["I","X","Y","Hs","An","H","C","N","(J)"];function Je(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=B(i)}return 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b=0;b<n.scaleFactor.length;)n.scaleFactor[b]=2**n.scaleFactor[b++];if(!("baseFrequency"in n)&&"originFrequency"in n?P(n,"baseFrequency",n.originFrequency):n.baseFrequency=H(n.baseFrequency),!["baseFrequency","originFrequency"].some(b=>!n[b])&&p){let{baseFrequency:b}=n,N=2*Math.PI*(b[0]/p)*1e6;P(n,"fieldStrength",N)}M(n,"spectralWidth",e[`${t}SW`]),M(n,"spectralWidth",e[`${t}QM_SPECTRAL_WIDTH`]),n.dimension===1&&e[`${t}SweepWidth`]&&n.originFrequency&&M(n,"spectralWidth",e[`${t}SweepWidth`]/n.originFrequency[0]),P(n,"numberOfPoints",e[`${t}TD`],!0);let f=n.numberOfPoints;if(P(n,"spectrumSize",e[`${t}SI`]??f),P(n,"sampleName",e[`${t}NAME`]),e[`${t}FNTYPE`]!==void 0&&P(n,"acquisitionMode",Number.parseInt(e[`${t}FNTYPE`],10)),(e[`${t}VARNAME`]?e[`${t}VARNAME`].split(",")[0]:"")==="TIME"){let b=typeof e.LAST=="string"?e.LAST.replace(" ","").split(",")[0]:e.LAST;M(n,"acquisitionTime",b)}if(!n.acquisitionTime&&u(["numberOfPoints","spectralWidth"])){let{spectralWidth:b,originFrequency:N}=n;P(n,"acquisitionTime",Number((f[0]-1)/(2*b[0]*N[0])))}if(e[`${t}P`]){let b=1e6/(j(e[`${t}P`]).split(s)[1].split(" ")[1]*4);P(n,"pulseStrength90",b)}if(e[`${t}D`]){let b=j(e[`${t}D`]).split(s)[1].split(" ")[1];M(n,"relaxationTime",b)}if(M(n,"numberOfScans",e[`${t}NS`]),M(n,"numberOfScans",e[`${t}QM_NSCANS`]),P(n,"groupDelay",e[`${t}GRPDLY`]),P(n,"dspfvs",e[`${t}DSPFVS`]),P(n,"decim",e[`${t}DECIM`]),n.isFid&&("groupDelay"in n||u(["dspfvs","decim"]))){let{groupDelay:b,dspfvs:N,decim:S}=n,D=$e(b?.[0]??0,N?.[0],S?.[0]);P(n,"digitalFilter",D)}let h;if(u(["numberOfPoints","spectralWidth"])){let{spectralWidth:b,numberOfPoints:N}=n;n.isFid?h=N.map(S=>n.acquisitionTime[0]/(S-1)):h=N.map((S,D)=>b[D]/(S-1))}if(P(n,"increment",h),e[`${t}DATE`]){let b=j(e[`${t}DATE`]),N=Number.parseInt(b,10)*1e3;Number.isNaN(N)?pe(n,Date.parse(b)):pe(n,N)}n.solvent||P(n,"solvent",j(e[`${t}SOLVENT`]))}if(n.dimension<2&&"dataClass"in n&&n.dataClass[0].toUpperCase()==="NTUPLES"&&(P(n,"last",T(e[`${t}LAST`])),P(n,"first",T(e[`${t}FIRST`])),P(n,"varDim",T(e[`${t}VARDIM`])),P(n,"symbols",T(e[`${t}SYMBOL`])),n.symbols&&Array.isArray(n.symbols))){n.symbols.includes("R")&&n.symbols.includes("I")&&(n.isComplex=!0);let d=n.symbols.findIndex(p=>p.toLowerCase()==="x");if(M(n,"firstX",n.first[d]),M(n,"lastX",n.last[d]),M(n,"numberOfPoints",n.varDim[d]),!("spectralWidth"in n)){let{lastX:p,numberOfPoints:f,firstX:F}=n;P(n,"spectralWidth",n.isFid?f/(2*p):Math.abs(p-F)/n.originFrequency)}}if(`${t}REVERSE`in e){let d=e[`${t}REVERSE`];n.reverse=(Array.isArray(d)?d:[d]).map(p=>typeof p=="string"?p.includes("yes"):p)}let y=e[`${t}REFERENCE_POINT`];if(!("frequencyOffset"in n)&&y&&u(["spectralWidth","baseFrequency"])){let d=typeof y=="number"?y:e[`${t}REFERENCE_POINT`].match(/(?<reference>[+-]?\d+(?:\.\d+)?)\s*.*/),p;if(typeof y=="number"?p=y:(y.match(/(?<reference>[+-]?\d+(?:\.\d+)?)\s*.*/),p=Number(d?.groups?.reference)),!Number.isNaN(p)){let{spectralWidth:f,baseFrequency:F}=n;P(n,"frequencyOffset",.5*f*F-p)}}if(!("frequencyOffset"in n)&&u(["baseFrequency","originFrequency"])){let{baseFrequency:d,originFrequency:p}=n,f=d.map((F,h)=>(p[h]-F)*1e6);P(n,"frequencyOffset",f)}for(let d in n)n[d]&&n[d].length===1&&(n[d]=n[d][0]);return!n.frequencyOffset&&".SHIFTREFERENCE"in e&&ir(e,n),Array.isArray(n.nucleus)||(n.nucleus=[n.nucleus]),n}function M(e,r,t){t!==void 0&&P(e,r,H(t))}function pe(e,r){if(!Number.isNaN(r)){e.epoch=r;let t=new Date(r);e.date=t.toUTCString(),e.localeDate=t.toLocaleString()}}function ir(e,r){let t=e[".SHIFTREFERENCE"],i=t.trim().startsWith("(")?/\((?<data>[^)]+)\)/:/(?<data>[^)]+)/,n=t.match(i);if(n.groups.data){let o=n.groups.data.split(",");if(o.length<4)return;let s=Number.parseInt(r.numberOfPoints,10),{spectralWidth:l,baseFrequency:a}=r,m=Number.parseInt(o[2],10),u=Number.parseFloat(o[3]),c;if(r.isFid){if(["baseFrequency","numberOfPoints","spectralWidth"].some(g=>!(g in r)))return;c=u+(s*.5-m)*l/s}else{let g=Number.parseFloat(r.firstX),y=Number.parseFloat(r.lastX),d=(y+g)/2,p=(y-g)/(s+1),f=p<0?g:y+(m-1)*p;c=(d-f)/a+u}c!==void 0&&!Number.isNaN(c)&&(r.frequencyOffset=c*a)}}function H(e){if(fe(e)){let r=[];for(let t of e)r.push(typeof t=="string"?Number.parseFloat(t):t);return r}return typeof e=="string"?Number.parseFloat(e):e}function or(e){switch(String(fe(e)?e[1]:e).toLowerCase().replaceAll(/\s/g,"")){case"1":case"notphasesensitive":return"notPhaseSensitive";case"2":return"QSEQ";case"3":case"tppi":return"TPPI";case"4":case"states":return"States";case"5":case"tppi-states":return"States-TPPI";case"6":case"echo-antiecho":return"Echo-antiecho";default:return"undefined"}}function sr(e,r,t={}){let{prefix:i="",separator:n=`
4
+ `}=t;P(e,"spectralWidth",r[`${i}SweepWidth`]/e.originFrequency[0]);let o=r[`${i}.PULSESEQUENCE`].split(n),s=[];r[".OBSERVENUCLEUS"]&&s.push(r[".OBSERVENUCLEUS"]),r.INDIRECTNUCLEUS&&s.push(r.INDIRECTNUCLEUS),e.nucleus=C(s),e.pulseSequence=o[0];let l=o.slice(2,-1);if(s.length>1)if(s[0]===s[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,u=Number.parseFloat(a.groups.sw);e.spectralWidth.push(u/m[1])}}return e}function ar(e,r){let{T1NUCLEUS:t,T2NUCLEUS:i,PAGE:n}=r;e.pulseSequence=r.EXPERIMENT||r[".PULSESEQUENCE"];let o=[],{dimension:s,isComplex:l}=e;if(s===2&&e.pulseSequence==="T1"){let u=l?2:1;for(let c=0;c<n.length;c+=u){let g=n[c].replace(/T1=/,"");o.push(Number(g))}r.vdlistValues=o}e.nucleus=s>1?[i,t]:i;let{phc0:a,phc1:m}=e;if(a&&m){let u=_({phc0:a,phc1:m});e={...e,...u}}}var ur={keepRecordsRegExp:/.*/,keepFiles:!0};async function G(e,r={}){let t={spectra:[],molecules:[]},{converter:i={},selector:n={},logger:o}=r,s=lr(e,{logger:o,...fr(n)}),l=[];for(let m of s)l.push(mr(m,{...ur,...i}).then(u=>pr(u,r)));let a=await Promise.allSettled(l);for(let m=0;m<a.length;m++){let u=a[m];if(u.status==="fulfilled"){let c=_(u.value.info);t.spectra.push({...u.value,info:{...u.value.info,...c}})}else if(u.reason){let c=s[m].name;o?.warn(`Bruker data: ${c}, fails with: ${u.reason}`);continue}}return o&&o[t.spectra.length>0?"info":"debug"](`Loaded ${t.spectra.length} spectra from Bruker files`),cr(t)}function pr(e,r={}){let{keepSource:t=!1,logger:i}=r,n={...e.info,...e.meta},o=Y(n,{logger:i}),s={},{isFid:l}=o;if(dr(e)){let y=e.minMax;for(let d in y){let p=y[d];p&&(p.z=I(p.z))}s.components=e.minMax}else o.dimension===1&&(s.components=e.spectra);let{source:a}=e,{expno:m,name:u,files:c}=a;n.vdlist&&(n.vdlistValues=X(n.vdlist));let g={dependentVariables:[s],meta:n,info:{...o,experimentNumber:m,name:u}};return c&&t&&(g.sourceSelector={files:c.map(y=>y.relativePath)}),gr(g,e),g}function fr(e){let{general:r={},bruker:t={}}=e,{processingNumbers:i,experimentNumbers:n,...o}=t;return{...r,...o,processingNumbers:Be(i),experimentNumbers:Be(n)}}function Be(e){if(e)return e.split(/[^\d]+/).filter(Boolean).map(r=>Number.parseInt(r,10))}function dr(e){let{info:r}=e;return r.twoD}function gr(e,r){if(!("integrals"in r))return;let{integrals:t=[]}=r;e.integrals={values:t.map(i=>{let{from:n,to:o,integration:s}=i;return{from:n,to:o,integral:s,kind:"signal"}})}}var K=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:o,logger:s}=t??{};return G(r,{converter:n?.bruker,selector:i,keepSource:o,logger:s})}};function de(){return new K}import{formatSpectra as Yr}from"@zakodium/nmrium-core";import{createTree as Gr}from"jcampconverter";function Ue(e,r,t={}){let{selector:i={},keepSource:n=!1}=t;if(!n)return e;for(let o=0;o<e.spectra.length;o++){let s=e.spectra[o];s.sourceSelector={files:[r.relativePath],jcamp:{index:o,...i}}}return e}import{convert as yr}from"jcampconverter";function ge(e,r,t){let{dataType:i,children:n}=e,o=i==="LINK"&&n?n:[e];for(let s of o){if(s.dataType==="LINK"){ge(s,r,t);continue}let l=yr(s.jcamp,t);r.push(...l.flatten)}}function Je(e,r={}){let t=[],i=_e(e,r);for(let s of i?e:[])s.dataType==="LINK"?s.children=ye(s.children,r):s=ye([s],r)[0],t.push(s);let{name:n,logger:o}=r;return e.length===0&&o?.warn(`There is no data ${n?`in ${n}`:"in the JCAMP-DX"}`),t}function ye(e=[],r={}){let{name:t,logger:i,tree:n=[],dataSelection:o="both"}=r,s=[];for(let u of e){let{dataType:c,dataClass:g}=u;if(c==="LINK")u.children=ye(u.children,r);else if(n.some(y=>{let{dataClass:d=g,dataType:p=c}=y;return g===d&&c===p})){i?.warn(`Skipping ${g} and ${c} ${t?`in ${t}`:"in the JCAMP-DX"},
5
+ because it didn't match the import filters`);continue}s.push(u)}let l=[],a=s.some(Xe),m=s.some(We);for(let u of s){if(o!=="both"&&u.dataType!=="LINK"){if(Xe(u)&&(o==="ft"||o==="preferFT"&&m)){i?.warn(`Skipping raw data ${t?`in ${t}`:"in the JCAMP-DX"} because it didn't match the import filters`);continue}if(We(u)&&(o==="fid"||o==="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(u)}return l}function We(e){return e.dataType?.toUpperCase().includes("SPECTRUM")&&e.dataClass&&!e.dataClass.toUpperCase().includes("PEAK")}function Xe(e){return e.dataType?.toUpperCase().includes("FID")}function _e(e,r={}){let{logger:t,name:i=""}=r;for(let n of e){if(n.dataType==="LINK"&&_e(n.children,r))return!0;let{dataType:o=""}=n,s=o.toLowerCase();if(s.length>0){if(s.includes("spectrum")&&!s.includes("nmr"))return t?.warn(`File ${i} was ignored because it is a ${o}`),!1;if(s.includes("nmr"))return!0}}return!1}import{generateID as Ye}from"@zakodium/nmrium-core";import{parseJcampCS as Sr}from"jcampconverter";import*as Rr from"openchemlib";import{isMolfileNotEmpty as hr}from"nmr-processing";import{Molecule as br}from"openchemlib";async function Ve(e,r={}){let t=await e.text(),i=w(t),n={molecules:i,spectra:[]};return i.length===0&&r.logger?.debug(`${e.name} is an empty molfile`),n}function w(e){let r=[];if(!hr(e))return[];let i=br.fromMolfile(e).toMolfile();return r.push({molfile:i}),r}import{isMolfileNotEmpty as Pr}from"nmr-processing";import*as Nr from"openchemlib";import{getDiastereotopicAtomIDsFromMolfile as Dr}from"openchemlib-utils";var Fr=new Set(["ndnmrspectrum","ndnmrfid","nmrspectrum","nmrfid"]);function Z(e){let{dataType:r="",dataClass:t=""}=e,i=r.replaceAll(/\s/g,"").toLowerCase(),n=t.replaceAll(/\s/g,"").toLowerCase();return Fr.has(i)&&n!=="peaktable"}function He(e,r,t={}){let{spectra:i,info:n,meta:o}=e,s=i[0].data,l=[],a={x:"delta",y:"intensity",w:"width",m:"multiplicity",a:"atom"},{logger:m,name:u,spectraData:c}=t,{CROSSREFERENCE:g}=n,y=typeof g!="string"?g:g.split(/\r?\n/).map(D=>D.trim()).filter(Boolean),d=y.find(D=>D?.toLowerCase().includes("structure"));if(d===void 0)return m&&m.warn(`There is not a structure reference for ${u} file, assignment object could not be completed`),null;let p=Number.parseInt(d?.toLowerCase().replace(/_/,"").replace(/structure:\s*blockid\s*=\s*(?<blockId>.*)/,"$<blockId>"),10);if(Number.isNaN(p)||p<1)return m&&m.warn(`Structure block_id not found for ${u} file, assignment object could not be completed`),null;let F=c?.molecules?.find(D=>D.blockId===p)?.molfile??"";if(F===""){let D=r.find(A=>A.info.BLOCKID===p),{MOLFILE:R=""}=D?.meta||{};F=R}if(!Pr(F))return m&&m.warn(`Empty molfile for ${u} file with structure block_id = ${p}, assignment object could not be completed`),null;let h=Dr(Nr,F),b=V({...n,...o},{},"");for(let D=0;D<s.x.length;D++){let R={};for(let A in s){let x=s[A][D];typeof x=="string"&&x.startsWith("<")&&x.endsWith(">")&&(x=x.slice(1,-1)),R[a[A]]=x}if("atom"in R){let A=h.map[R.atom-1];b.includes("1H")?A.nbHydrogens>0?(R.diaIDs=A.hydrogenOCLIDs,R.nbHydrogens=A.nbHydrogens):(R.diaIDs=[A.oclID],R.nbHydrogens=A.nbHydrogens):(R.diaIDs=[A.oclID],R.nbHydrogens=1)}l.push(R)}let N={};for(let D of l){let{delta:R,diaIDs:A}=D,x=`${R}_${A.join("_")}`;if(N[x])N[x].atoms.push(D.atom);else{let{atom:zn,...$t}=D;N[x]={...$t,atoms:[D.atom]}}}let S=[];for(let D of y)D.toLowerCase().includes("spectrum")&&S.push(Number(D.toLowerCase().replace(/_/,"").replace(/.*:\s*blockid=(?<blockId>.*)/,"$<blockId>")));if(S.length===0){for(let D of r)if(Z(D)){let{BLOCKID:R}=D.info;S.push(Number(R))}S.length>1&&(S=[],m&&m.warn(`There is not a spectral cross-reference for the peak assignment in the ${u} 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jr}from"ml-spectra-processing";import{xyAutoRangesPicking as zr}from"nmr-processing";function v(e){return e.slice(0,Math.max(0,e.lastIndexOf(".")))}function q(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 Lr}from"nmr-processing";import{xMaxValue as Or}from"ml-spectra-processing";function z(e){return e.trim().slice(1,-1).split(/,\s*/).map(r=>r.trim())}var Ir={I:"id",X:"from",Y:"to",Hs:"delta",An:"integration",H:"nbAtoms",C:"multiplicity",N:"assignment","(J)":"js"},Ke=["I","X","Y","Hs","An","H","C","N","(J)"];function Ze(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=z(i)}return 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e){let a={x:{},y:{},id:Rt(),kind:"signal"},m={id:Rt(),kind:"signal",peaks:[]},u={x:10,y:10};for(let c of yn){let{coupling:g=[],delta:y,diaIDs:d=[]}=l[c];for(let p of g)u[c]+=p.coupling;if(l.activeCoupling){let{activeCoupling:p=[]}=l;for(let f of p)u[c]+=f.coupling}u[c]/=s[c],a[c]={from:y-u[c],to:y+u[c]},m[c]={delta:y,diaIDs:d,originalDelta:y-n[c]}}i.push({...a,signals:[m]})}r.zones.values=i}function At(e){return bn(e.data)}function bn(e){return"rr"in e||!("x"in e)&&"re"in e}async function xt(e,r,t={}){let i={spectra:[],molecules:[]},n=await Nn(e,r,t);if(n.spectra.length>0){let{spectra:o,molecules:s,usedFiles:l}=n;i.spectra.push(...o),i.molecules.push(...s);let a=e.files.length;for(let m=a-1;m>=0;m--){let u=e.files[m].relativePath;!u.match(/acqu.*/s)&&l.includes(u)&&e.files.splice(m,1)}}return i}async function Nn(e,r,t){let i=[],n=await Fn(e),o={spectra:[],molecules:[]};if(n.length===0)return{...o,usedFiles:i};let s=[];for(let a of n){let m=Pn({sdf:a,fileCollection:e}).then(u=>{let{spectra:c,molecules:g=[]}=u;return i.push(a.root+a.filename),o.molecules.push(...g),Dn(c,r,t)});s.push(m)}let l=await Promise.allSettled(s);for(let a of l)a.status==="fulfilled"?(o.spectra.push(...a.value.spectra),i.push(...a.value.usedFiles)):a.reason&&t?.logger?.error(a.reason);return{...o,usedFiles:i}}async function Dn(e,r,t){let i=[],n=[],o={spectra:[],molecules:[]};for(let s of e){let l=Sn(s.source,r,t).then(a=>{let{spectra:m,files:u}=a;i.push(...u);for(let c of m)At(c)?Mt(s.signals,c):St(s.signals,c);o.spectra.push(...m)});n.push(l)}return await Promise.allSettled(n),{...o,usedFiles:i}}async function Sn(e,r,t={}){let{file:i,jcampURL:n}=e,{converter:o}=t;if(n){let a=await Rn(n,r,o?.jcamp);if(a)return{...a,files:[]}}let s=[];for(let a of i||[])s.push(Mn(a,t).then(m=>({...m,files:a.fileCollection.files.map(u=>u.relativePath)})));let l=await Promise.allSettled(s);for(let a of l){if(a.status==="fulfilled")return a.value;a.reason&&t?.logger?.error(a.reason)}return{spectra:[],molecules:[],files:[]}}async function Rn(e,r,t={}){let i={entries:[{relativePath:e}]},n={name:v(e||""),xy:!0,noContours:!0,...t},{data:o}=await r.readFromWebSource(i,n);return o}async function Mn(e,r={}){let{converter:t,sourceSelector:i}=r;switch(e.type){case"jcamp":return Q(e.fileCollection.files[0],{name:e?.fileCollection.files[0].name||"",converter:t?.jcamp,selector:i?.jcamp,logger:r.logger,keepSource:r.keepSource});case"brukerFiles":return G(e.fileCollection,{converter:t?.bruker,selector:i});default:throw new Error("There is not a supported source")}}var ne=class{constructor(r){this.core=r;this.onReadProcess={onFiles:this.onReadProcessFiles}}id="@zakodium/nmrium-core-plugins#NMReDATALoaderPlugin";version=1;migrations=[];onReadProcess;onReadProcessFiles=(r,t)=>xt(r,this.core,t)};function Se(e){return new ne(e)}import{parse as An}from"sdf-parser";function Ct(e,r={}){let{mixedEOL:t}=r,{molecules:i}=An(e,{mixedEOL:t}),n=[];for(let{molfile:o}of i){let s=w(o);n.push(...s)}return n}async function Ot(e,r={}){let{logger:t,mixedEOL:i}=r,n=await e.text(),o=Ct(n,{mixedEOL:i}),s={molecules:o,spectra:[]};return t&&t[o.length>0?"info":"debug"](`Loaded ${s.molecules.length} molecules from the ${e.name} file`),s}var ie=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}`),Ot(r,{logger:i})}};function Re(){return new ie}import{Molecule as xn}from"openchemlib";function It(e){let r=[],t=e.split(/\r?\n/).filter(Boolean);for(let i of t){let o=xn.fromSmiles(i).toMolfile();r.push({molfile:o})}return r}async function Tt(e,r={}){let t=await e.text(),i=It(t),n={molecules:i,spectra:[]};return r.logger?.info(`Found ${i.length} molecules from the ${e.name} file`),n}var oe=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 Tt(r,{logger:i})}};function Me(){return new oe}import{formatSpectra as In}from"@zakodium/nmrium-core";import{FileCollection as Tn}from"filelist-utils";import{isAnyArray as En}from"is-any-array";import{xMultiply as Ln}from"ml-spectra-processing";import{convert1D as kn}from"varian-converter";import{normalizeNucleus as Cn}from"nmr-processing";function Et(e,r){let{meta:t,procpar:i}=e,n={};for(let h of i)n[h.name]=h.values;let o={},s={},{np:l,solvent:a,sfrq:m,reffrq:u,temp:c,rp:g,sw:y,rfl:d,rfp:p}=n;P(o,"numberOfPoints",l&&Number(O(l))/2),P(o,"solvent",O(a)),P(o,"originFrequency",O(m)),P(o,"baseFrequency",O(u)),(Number.isNaN(o.originFrequency)||o.originFrequency===0)&&(o.originFrequency=400,r?.warn("The frequency could not be determined and was set to 400MHz")),P(o,"temperature",O(c)),P(o,"phc0",g&&Number(g[0])),P(s,"rfl",d&&Number(O(d))),P(s,"rfp",p&&Number(O(p))),P(s,"sw",y&&Number(O(y)));for(let h in s){let b=s[h];Array.isArray(b)&&b.length===1&&(s[h]=b[0])}if(!("baseFrequency"in o)&&"originFrequency"in o){let h=Number.parseFloat(o.originFrequency);if(["sw","rfl","rfp"].every(b=>b in s)){let{sw:b=1,rfl:N=1,rfp:S=1}=On(s,["sw","rfl","rfp"]);P(o,"baseFrequency",h-(b/2-N+S)/1e6)}else P(o,"baseFrequency",h)}let{baseFrequency:f,originFrequency:F}=o;P(o,"frequencyOffset",(F-f)*1e6),P(o,"spectralWidth",y&&Number(y[0])/o.baseFrequency);for(let h in o)o[h].length===1&&(o[h]=o[h][0]);return n.tn&&(o.nucleus=n.tn.map(Cn)),o.dimension=1,o.isFid=!t.status.isSpectrum,{info:o,meta:{...s,...Lt(t),...n}}}function O(e){return e&&(Array.isArray(e)?e[0]:e)}function On(e,r){let t={};for(let i of r){let n=e[i];n&&typeof n=="number"&&(t[i]=n)}return t}function Lt(e){let r={};for(let t of Object.keys(e)){let i=e[t];typeof i=="object"&&i!==null&&i.constructor&&i.constructor!==Object?r[t]=Lt(i):r[t]=i}return r}function kt(e){let r={},t=new Set(e.files.map(i=>i.relativePath));for(let i of e){let n=i.name.toLowerCase();if(n.match(/^(?:fid|procpar|text|log)$/)){if(n.match(/^(?:fid|text|log)$/)){let l=i.relativePath.replace(/(?:fid|text|log)$/,"procpar");if(!t.has(l))continue}let o=i.relativePath.split("/"),s=o.slice(0,-1).join("/");r[s]||(r[s]={name:o.at(-2),files:[]}),r[s].files.push(i)}}return Object.values(r)}async function wt(e,r={}){let{keepSource:t,logger:i}=r,n=kt(e);i&&i.debug(`Found ${Object.keys(n).length} varian experiments`);let o=[],s={spectra:[],molecules:[]};for(let a of 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};
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@zakodium/nmrium-core-plugins",
3
- "version": "0.0.1",
3
+ "version": "0.1.1",
4
4
  "description": "Recommended plugins for NMRium, loaders of common formats like bruker or jcamp, and some post-processing plugins",
5
5
  "author": "",
6
6
  "license": "CC-BY-NC-SA-4.0",
@@ -28,11 +28,11 @@
28
28
  "bundle-esm": "npm run bundle-common -- --format=esm --outfile=./dist/nmrium-core-plugins.mjs",
29
29
  "bundle-types": "npm run tsc && npm run api-extractor",
30
30
  "check-types": "tsc --noEmit",
31
- "clean": "rimraf types",
31
+ "clean": "rimraf types dist coverage",
32
32
  "eslint": "eslint src --cache",
33
33
  "eslint-fix": "npm run eslint -- --fix",
34
34
  "dev:eslint-fix": "eslint --cache --fix $(git diff --name-only --relative) --quiet",
35
- "prepack": "npm run bundle && npm run bundle-types",
35
+ "prepack": "npm run bundle",
36
36
  "prettier": "prettier --check src",
37
37
  "prettier-write": "prettier --write src",
38
38
  "dev:prettier-write": "prettier --write $(git diff --name-only --relative)",
@@ -51,6 +51,7 @@
51
51
  "eslint-config-cheminfo-typescript": "^18.0.0",
52
52
  "fifo-logger": "^1.0.0",
53
53
  "jcamp-data-test": "^0.8.3",
54
+ "jeol-data-test": "^0.5.2",
54
55
  "jest-matcher-deep-close-to": "^3.0.2",
55
56
  "msw": "^2.7.5",
56
57
  "nmredata-data-test": "^0.4.0",
@@ -60,22 +61,21 @@
60
61
  "vitest": "^3.0.9"
61
62
  },
62
63
  "dependencies": {
63
- "@zakodium/nmrium-core": "^0.0.1",
64
+ "@zakodium/nmrium-core": "^0.1.0",
64
65
  "brukerconverter": "^8.0.3",
65
66
  "convert-to-jcamp": "^5.4.11",
66
67
  "filelist-utils": "^1.11.3",
67
68
  "gyromagnetic-ratio": "^1.2.1",
68
69
  "is-any-array": "^2.0.1",
69
70
  "jcampconverter": "^11.0.1",
70
- "jeol-data-test": "^0.5.2",
71
71
  "jeolconverter": "^1.0.4",
72
72
  "linear-sum-assignment": "^1.0.7",
73
73
  "lodash.merge": "^4.6.2",
74
74
  "ml-spectra-processing": "^14.11.0",
75
- "nmr-processing": "^18.0.0",
75
+ "nmr-processing": "^18.0.1",
76
76
  "nmredata": "^1.0.0",
77
- "openchemlib": "^8.19.0",
78
- "openchemlib-utils": "^6.6.0",
77
+ "openchemlib": "^9.0.1",
78
+ "openchemlib-utils": "^8.1.0",
79
79
  "sdf-parser": "^7.0.4",
80
80
  "varian-converter": "^2.0.1"
81
81
  },