@zakodium/nmrium-core 0.5.6 → 0.5.8

package/dist/nmrium-core.d.ts

@@ -1180,6 +1180,7 @@ export declare interface SerializeNmriumStateOptions {
     includeData?: IncludeData;
     includeSettings?: boolean;
     includeView?: boolean;
+    forceRawSpectra?: Array<Spectrum['id']>;
 }
 
 declare interface SourceNmriumData extends Source {

package/dist/nmrium-core.js

@@ -1,6 +1,6 @@
-var Me={NORMAL:"NORMAL",FORMULA:"FORMULA"};var De={RELATIVE:"relative",ABSOLUTE:"absolute",MIN:"min",MAX:"max"};var Ce=[{name:"pixels",unit:"px"},{name:"inches",unit:"in"},{name:"feet",unit:"ft"},{name:"yards",unit:"yd"},{name:"centimeters",unit:"cm"},{name:"millimeters",unit:"mm"},{name:"meters",unit:"m"},{name:"points",unit:"pt"},{name:"picas",unit:"pc"}];var N=13;var Ae=[{key:"CT",description:"CT from NMR Solutions"}];import{isAnyArray as Fe}from"is-any-array";import{xMultiply as B}from"ml-spectra-processing";var we=crypto.randomUUID.bind(crypto),b=we;function R(e){let{id:t=b(),meta:o,peaks:r={},filters:i=[],info:n={},ranges:c={},integrals:s={},selector:l,sourceId:a,dependentVariables:p=[],...m}=e,u={id:t,meta:o,filters:i},{data:f=Te(p[0].components)}=e;if(Array.isArray(n.nucleus)&&(n.nucleus=n.nucleus[0]),u.data={x:[],re:[],im:[],...f},"scaleFactor"in n){let{scaleFactor:d}=n,{re:S,im:y}=u.data;B(S,d,{output:S}),y&&B(y,d,{output:y})}l&&(u.selector=l),a&&(u.sourceId=a,u.fileCollectionId=a);let g=Fe(f.im);if(u.info={phc0:0,phc1:0,nucleus:"1H",isFid:!1,isComplex:g,dimension:1,name:n?.name||t,...n},n.isFid&&n.reverse&&g){let{im:d}=u.data;B(d,-1,{output:d}),u.info.reverse=!1}return u.display={isVisible:!0,isPeaksMarkersVisible:!0,isRealSpectrumVisible:!0,isVisibleInDomain:!0,...e.display},u.peaks={values:[],options:{},...r},u.ranges={values:[],options:{sum:null,isSumConstant:!0,sumAuto:!0},...c},u.integrals={values:[],options:{},...s},{...m,...u}}function Te(e){let t=e[0]?.data?.x||[],o=e[0]?.data?.re||e[0]?.data?.y||[],r=e[0]?.data?.im||e[1]?.data?.y||null;return t.length>0&&t[0]>t[1]&&(t.reverse(),o.reverse(),r&&r.reverse()),{x:t,re:o,im:r}}import{matrixToArray as Ee,xMinMaxValues as Le,xNoiseSanPlot as Ue}from"ml-spectra-processing";var K={z:[[]],minX:0,minY:0,maxX:0,maxY:0},ze={re:K,im:K},ke={rr:K};function C(e){let{id:t=b(),meta:o={},dependentVariables:r=[],info:i={},filters:n=[],zones:c=[],sourceId:s,...l}=e,a={id:t,meta:o,filters:n};s&&(a.sourceId=s,a.fileCollectionId=s),a.info={nucleus:["1H","1H"],isFid:!1,isComplex:!1,name:i?.name||b(),...i},a.originalInfo=structuredClone(a.info),a.display={isPositiveVisible:!0,isNegativeVisible:!0,isVisible:!0,dimension:2,...e.display,...e.display};let{data:p=r[0].components}=e;if(a.data={...a.info.isFid?ze:ke,...p},a.originalData=structuredClone(a.data),!("spectrumSize"in i)){let m=i.isFid?"re":"rr",u=a.data[m].z.length,f=u>0?a.data[m].z[0].length:0;a.info.spectrumSize=[f,u]}if(!i.isFid){let m=a.data.rr,u=Ee(m.z),{positive:f,negative:g}=Ue(u),{min:d,max:S}=Le(u);a.data.rr={...m,minZ:d,maxZ:S},a.info.noise={positive:f,negative:g}}return a.zones={values:[],options:{},...c},{...l,...a}}import{xSequentialFillFromTo as Ve}from"ml-spectra-processing";import{isAnyArray as je}from"is-any-array";function W(e,t=0){if(je(e)){let o=e.at(t);if(o!==void 0)return o;throw new RangeError("An array with a index out of boundaries")}return e}var _e=new Set(["t1ir","T1"]);function ae(e){let t=[];for(let o of e){let{info:{pulseSequence:r,isFid:i}}=o,{data:n,info:c,meta:{vdlistValues:s=[]}}=o;if(!(r&&_e.has(r))||s.length===0){t.push(o);continue}let a=i?"re":"rr",p={};for(let y in c)p[y]=W(c[y]);let{z:m,maxX:u,minX:f}=n[a],g=Ve({from:f,to:u,size:m[0].length}),[d,S]=Ke(o);for(let y=0;y<s.length;y++){let P={re:g,x:g};for(let x in n)P[Be(x)]=n[x].z.at(d*(y+S));t.push(R({data:P,info:{...p,name:`${p.name}_${s[y]}`,dimension:1,vd:s[y]}}))}}return t}function Be(e){return["rr","re"].includes(e)?"re":["im","ri","ir","ii"].includes(e)?"im":"x"}function Ke(e){let{meta:{PAGE:t}}=e,o=!0;if(t){let r=i=>Number.parseFloat(i.replace(/[F|T]1=/,""));o=r(t[0])>r(t[2])}return o?[-1,1]:[1,0]}var We=2,Xe=1;function Ye(e){let{spectra:t=[],molecules:o}=e,r=[];for(let i of t){let{info:n}=i;switch(n.dimension){case Xe:r.push(R(i));break;case We:r.push(C(i));break;default:throw new Error("dimension does not supported")}}return{molecules:o,spectra:ae(r)}}function Ze(e){return e}function h(e,t){return JSON.parse(JSON.stringify(e),function(r,i){if(r in t){this[t[r]]=i;return}return i})}function X(e){if(e?.version===1)return e;let t={...e,version:1},o={j:"js",signal:"signals",integral:"integration",peak:"peaks",diaID:"diaIDs"};for(let r of t.spectra){if(r.ranges){let i=h(r.ranges,o);r.ranges=Array.isArray(i)?{values:i}:i}else if(r.zones){let i=h(r.zones,o);r.zones=Array.isArray(i)?{values:i}:i}r.peaks&&(r.peaks=Array.isArray(r.peaks)?{values:r.peaks}:r.peaks),r.integrals&&(r.integrals=Array.isArray(r.integrals)?{values:r.integrals}:r.integrals)}return t}function Y(e){if(e?.version===2)return e;let t={...e,version:2},o={peaks:{delta:"x",originDelta:"originalX",intensity:"y"},ranges:{atomIDs:"atoms",intensity:"y"}};for(let r of t.spectra)r.peaks?r.peaks=h(r.peaks,o.peaks):r.ranges?r.ranges=h(r.ranges,o.ranges):r.zones&&(r.zones.values=$e(r.zones.values));return t}function $e(e){return e.map(t=>(t.signals&&(t.signals=t.signals.map(o=>{if(o.x&&o.y){let{x:{fromTo:r,...i},y:{fromTo:n,...c}}=o;o={...o,x:{...i,...r},y:{...c,...n}}}else{let{fromTo:r,deltaX:i,resolutionX:n,nucleusX:c,deltaY:s,resolutionY:l,nucleusY:a,shiftX:p,shiftY:m,...u}=o;o={...u,x:{from:r[0].from,to:r[0].to,delta:i,resolution:n,nucleus:c},y:{from:r[1].from,to:r[1].to,delta:s,resolution:l,nucleus:a}}}return o},[])),t),[])}var Ge={name:"apodization",label:"Apodization",value:{lineBroadening:1,gaussBroadening:0,lineBroadeningCenter:0}};function Z(e){if(e?.version===3)return e;let t={...e,version:3};for(let o of t.spectra)if(Array.isArray(o?.filters)&&o?.filters.length>0){let r=o.filters.findIndex(i=>i.name==="lineBroadening");if(r!==-1){let i={...o.filters[r],...Ge};o.filters[r]=o.filters[r-1],o.filters[r-1]=i}}return t}function $(e){if(e?.version===4)return e;let{version:t,...o}=e,r=[],i={};for(let{source:s,...l}of o.spectra){let a={},{info:p={},display:m={}}=l;if(p?.dimension===2&&!s?.jcampURL)if(p.isFt)a.data={rr:l.data};else continue;if(s?.jcampURL){let{jcampURL:g,jcampSpectrumIndex:d}=s,S=g.match(/(?<baseURL>^\w+:\/{2}\w+\/)(?<relativePath>.*)/);i[g]||(i[g]={baseURL:S?.groups.baseURL||"",relativePath:S?.groups.relativePath||g.replace(/^\.\//,"")}),a.sourceSelector={files:[i[g].relativePath]},d!==void 0&&(a.sourceSelector.jcamp={index:d})}a.filters=Je(l.filters);let{name:u,...f}=m;u&&(a.info={...p,name:u}),a.display=f,r.push({...l,...a})}let n={data:{...o,spectra:r},version:4},c={entries:Object.values(i)};return c.entries.length>0&&(n.data.source=c),n}function Je(e=[]){let t=[];for(let o of e){let{name:r,value:i}=o;switch(r){case"zeroFilling":t.push({...o,value:{nbPoints:i}});break;case"shiftX":case"shift2DX":case"shift2DY":t.push({...o,value:{shift:i}});break;default:t.push({...o})}}return t}function G(e){if(e?.version===5)return e;let t={...e,version:5},o={originFrom:"originalFrom",originTo:"originalTo",originDelta:"originalDelta",originX:"originalX",originY:"originalY",originZ:"originalZ"};for(let r of t?.data?.spectra||[])for(let i of["peaks","ranges","zones"])r?.[i]&&(r[i]=h(r[i],o));return t}function J(e){if(e?.version===6)return e;let t={...e,version:6};for(let o of t?.data?.spectra||[]){let{digitalFilter:r,fft:i,phaseCorrection:n}=qe(o);i?.flag&&r?.flag&&n&&Math.floor(r.value.digitalFilterValue)%2>0&&(n.value.ph0-=180)}return t}function qe(e,t=["phaseCorrection","fft","digitalFilter"]){let{filters:o=[]}=e,r={};for(let i of t)r[i]=o.find(n=>n.name===i);return r}function A(e,t="localStorage"){if(e?.version===7)return e;if(t==="nmrium")return le(e);let o={...e,version:7};for(let r in e.workspaces)o.workspaces[r]=le(o.workspaces[r]);return o}function le(e){let{formatting:{nuclei:t,panels:o}={nuclei:null,panels:null},version:r,...i}=e,n={...i};return t&&(n.nuclei=He(t)),o&&(n.panels=o),n}function He(e){let t=[],o={name:"nucleus",ppm:"ppmFormat",hz:"hzFormat"};for(let r in e)t.push(h(e[r],o));return t}function q(e){if(e?.version===7)return e;let t={...e,version:7};return t?.settings&&(t.settings=A(t.settings,"nmrium")),t}function w(e,t="localStorage"){if(e?.version===8)return e;if(t==="nmrium")return ce(e);let o={...e,version:8};for(let r in e.workspaces)o.workspaces[r]=ce(o.workspaces[r]);return o}function ce(e){let{version:t,...o}=e,r={...o};return r.display.panels=Qe(e),r}function Qe(e){let t={},o=e.display.panels;for(let r of Object.keys(o)){let{display:i,open:n}=o[r];t[r]={display:i,visible:i,open:n}}return t}function H(e){if(e?.version===8)return e;let t={...e,version:8};t?.settings&&(t.settings=w(t.settings,"nmrium"));for(let o of t?.data?.spectra||[]){let{filters:r=[]}=o;for(let s=0;s<r.length;s++){let{flag:l,isDeleteAllow:a,label:p,...m}=r[s];r[s]={...m,enabled:l}}let i=r.findIndex(s=>s.name==="apodization");if(i!==-1){let s=r[i],{lineBroadening:l,gaussBroadening:a,lineBroadeningCenter:p}=s.value;s.value={exponential:{apply:!0,options:{lineBroadening:a>0?-l:l}}},a>0&&(s.value.gaussian={apply:!0,options:{lineBroadening:.6*a,lineBroadeningCenter:p}}),r[i]=s}let n=r.findIndex(s=>s.name==="apodizationDimension1"),c=r.findIndex(s=>s.name==="apodizationDimension2");if(n!==-1){let s=r[n],{shapes:l}=s.value.compose;s.value=ue(l)}if(c!==-1){let s=r[c],{shapes:l}=s.value.compose;s.value=ue(l)}}return t}function ue(e){let t={};for(let{shape:o}of e){let{kind:r,options:i}=o;if(r==="sineBell"){let{exponent:n,offset:c}=i,s=n===2?"sineSquare":"sineBell";t[s]={apply:!0,options:{offset:c}}}}return t}function Q(e){let{version:t,plugins:o,...r}=e;return t===9?e:{version:9,plugins:{},...r}}function ee(e){if(e?.version>=10)return e;let t={...e,version:10};if(e.data){let{source:o,spectra:r,...i}=e.data,n=o?crypto.randomUUID():void 0,c=o?[{...o,id:n}]:[];t.data={...i,sources:c,spectra:o?r?.map(s=>({...s,sourceId:n})):r}}return t}function te(e){let{version:t}=e;if(t>=11)return e;let o={...e,version:11};return e?.view?.molecules&&(o.view=et(e.view)),o}function et(e){let{molecules:t,...o}=e,r={};for(let[i,n]of Object.entries(t)){let{showAtomNumber:c,...s}=n;r[i]={...s,atomAnnotation:"none",showLabel:!1}}return{molecules:r,...o}}function re(e){if(e?.version>=12)return e;let t={...e,version:12};if(t.data){let o=e.data.spectra??[],r=e.data.molecules??[];for(let i of o){let{sourceId:n,fileCollectionId:c,sourceSelector:s}=i;delete i.sourceId,delete i.fileCollectionId,delete i.sourceSelector,s&&(i.selector={...s,root:c??n})}for(let i of r){let{sourceId:n,fileCollectionId:c,sourceSelector:s}=i;delete i.sourceId,delete i.fileCollectionId,delete i.sourceSelector,s&&(i.selector={...s,root:c??n})}}return t}function oe(e){if(e?.version>=13)return e;let t={...e,version:13};if(t.data){let o=e.data.spectra??[];for(let r of o){let i=r.ranges?.values??[];for(let n of i){let{diaIDs:c,assignment:s,nbAtoms:l,signals:a=[]}=n,p=a.some(m=>m.diaIDs&&m.diaIDs.length>0);for(let m of a)!p&&c&&l&&(m.diaIDs=c,m.nbAtoms=l),!m.assignment&&s&&(m.assignment=s);delete n.diaIDs,delete n.assignment,delete n.nbAtoms}}}return t}function O(e,t){e.plugins||(e.plugins={});let o=e.plugins;for(let r of t.values()){if(!r.shouldSerialize){delete o[r.id];continue}o[r.id]||(o[r.id]={id:r.id,version:r.version}),o[r.id].id=r.id,o[r.id].version=r.version}}var tt=[X,Y,Z,$,G,J,q,H,Q,ee,te,re,oe];function pe(e,t,o){let r=structuredClone(e),i=Object.entries(e?.plugins??{});for(let[s,{version:l}]of i){let a=o.get(s);if(!(a&&a.version>=l)){if(a){console.warn(`Plugin "${a.id}" is loaded with a version older (${a.version}) than the one used to save the state (${l}).
+var Me={NORMAL:"NORMAL",FORMULA:"FORMULA"};var De={RELATIVE:"relative",ABSOLUTE:"absolute",MIN:"min",MAX:"max"};var Ce=[{name:"pixels",unit:"px"},{name:"inches",unit:"in"},{name:"feet",unit:"ft"},{name:"yards",unit:"yd"},{name:"centimeters",unit:"cm"},{name:"millimeters",unit:"mm"},{name:"meters",unit:"m"},{name:"points",unit:"pt"},{name:"picas",unit:"pc"}];var N=13;var Ae=[{key:"CT",description:"CT from NMR Solutions"}];import{isAnyArray as Fe}from"is-any-array";import{xMultiply as B}from"ml-spectra-processing";var we=crypto.randomUUID.bind(crypto),b=we;function R(e){let{id:t=b(),meta:o,peaks:r={},filters:i=[],info:n={},ranges:c={},integrals:s={},selector:l,sourceId:a,dependentVariables:m=[],...p}=e,u={id:t,meta:o,filters:i},{data:f=Te(m[0].components)}=e;if(Array.isArray(n.nucleus)&&(n.nucleus=n.nucleus[0]),u.data={x:[],re:[],im:[],...f},"scaleFactor"in n){let{scaleFactor:g}=n,{re:S,im:y}=u.data;B(S,g,{output:S}),y&&B(y,g,{output:y})}l&&(u.selector=l),a&&(u.sourceId=a,u.fileCollectionId=a);let d=Fe(f.im);if(u.info={phc0:0,phc1:0,nucleus:"1H",isFid:!1,isComplex:d,dimension:1,name:n?.name||t,...n},n.isFid&&n.reverse&&d){let{im:g}=u.data;B(g,-1,{output:g}),u.info.reverse=!1}return u.display={isVisible:!0,isPeaksMarkersVisible:!0,isRealSpectrumVisible:!0,isVisibleInDomain:!0,...e.display},u.peaks={values:[],options:{},...r},u.ranges={values:[],options:{sum:null,isSumConstant:!0,sumAuto:!0},...c},u.integrals={values:[],options:{},...s},{...p,...u}}function Te(e){let t=e[0]?.data?.x||[],o=e[0]?.data?.re||e[0]?.data?.y||[],r=e[0]?.data?.im||e[1]?.data?.y||null;return t.length>0&&t[0]>t[1]&&(t.reverse(),o.reverse(),r&&r.reverse()),{x:t,re:o,im:r}}import{matrixToArray as Ee,xMinMaxValues as Le,xNoiseSanPlot as Ue}from"ml-spectra-processing";var K={z:[[]],minX:0,minY:0,maxX:0,maxY:0},ze={re:K,im:K},ke={rr:K};function C(e){let{id:t=b(),meta:o={},dependentVariables:r=[],info:i={},filters:n=[],zones:c=[],sourceId:s,...l}=e,a={id:t,meta:o,filters:n};s&&(a.sourceId=s,a.fileCollectionId=s),a.info={nucleus:["1H","1H"],isFid:!1,isComplex:!1,name:i?.name||b(),...i},a.originalInfo=structuredClone(a.info),a.display={isPositiveVisible:!0,isNegativeVisible:!0,isVisible:!0,dimension:2,...e.display,...e.display};let{data:m=r[0].components}=e;if(a.data={...a.info.isFid?ze:ke,...m},a.originalData=structuredClone(a.data),!("spectrumSize"in i)){let p=i.isFid?"re":"rr",u=a.data[p].z.length,f=u>0?a.data[p].z[0].length:0;a.info.spectrumSize=[f,u]}if(!i.isFid){let p=a.data.rr,u=Ee(p.z),{positive:f,negative:d}=Ue(u),{min:g,max:S}=Le(u);a.data.rr={...p,minZ:g,maxZ:S},a.info.noise={positive:f,negative:d}}return a.zones={values:[],options:{},...c},{...l,...a}}import{xSequentialFillFromTo as Ve}from"ml-spectra-processing";import{isAnyArray as je}from"is-any-array";function W(e,t=0){if(je(e)){let o=e.at(t);if(o!==void 0)return o;throw new RangeError("An array with a index out of boundaries")}return e}var _e=new Set(["t1ir","T1"]);function ae(e){let t=[];for(let o of e){let{info:{pulseSequence:r,isFid:i}}=o,{data:n,info:c,meta:{vdlistValues:s=[]}}=o;if(!(r&&_e.has(r))||s.length===0){t.push(o);continue}let a=i?"re":"rr",m={};for(let y in c)m[y]=W(c[y]);let{z:p,maxX:u,minX:f}=n[a],d=Ve({from:f,to:u,size:p[0].length}),[g,S]=Ke(o);for(let y=0;y<s.length;y++){let P={re:d,x:d};for(let x in n)P[Be(x)]=n[x].z.at(g*(y+S));t.push(R({data:P,info:{...m,name:`${m.name}_${s[y]}`,dimension:1,vd:s[y]}}))}}return t}function Be(e){return["rr","re"].includes(e)?"re":["im","ri","ir","ii"].includes(e)?"im":"x"}function Ke(e){let{meta:{PAGE:t}}=e,o=!0;if(t){let r=i=>Number.parseFloat(i.replace(/[F|T]1=/,""));o=r(t[0])>r(t[2])}return o?[-1,1]:[1,0]}var We=2,Xe=1;function Ye(e){let{spectra:t=[],molecules:o}=e,r=[];for(let i of t){let{info:n}=i;switch(n.dimension){case Xe:r.push(R(i));break;case We:r.push(C(i));break;default:throw new Error("dimension does not supported")}}return{molecules:o,spectra:ae(r)}}function Ze(e){return e}function h(e,t){return JSON.parse(JSON.stringify(e),function(r,i){if(r in t){this[t[r]]=i;return}return i})}function X(e){if(e?.version===1)return e;let t={...e,version:1},o={j:"js",signal:"signals",integral:"integration",peak:"peaks",diaID:"diaIDs"};for(let r of t.spectra){if(r.ranges){let i=h(r.ranges,o);r.ranges=Array.isArray(i)?{values:i}:i}else if(r.zones){let i=h(r.zones,o);r.zones=Array.isArray(i)?{values:i}:i}r.peaks&&(r.peaks=Array.isArray(r.peaks)?{values:r.peaks}:r.peaks),r.integrals&&(r.integrals=Array.isArray(r.integrals)?{values:r.integrals}:r.integrals)}return t}function Y(e){if(e?.version===2)return e;let t={...e,version:2},o={peaks:{delta:"x",originDelta:"originalX",intensity:"y"},ranges:{atomIDs:"atoms",intensity:"y"}};for(let r of t.spectra)r.peaks?r.peaks=h(r.peaks,o.peaks):r.ranges?r.ranges=h(r.ranges,o.ranges):r.zones&&(r.zones.values=$e(r.zones.values));return t}function $e(e){return e.map(t=>(t.signals&&(t.signals=t.signals.map(o=>{if(o.x&&o.y){let{x:{fromTo:r,...i},y:{fromTo:n,...c}}=o;o={...o,x:{...i,...r},y:{...c,...n}}}else{let{fromTo:r,deltaX:i,resolutionX:n,nucleusX:c,deltaY:s,resolutionY:l,nucleusY:a,shiftX:m,shiftY:p,...u}=o;o={...u,x:{from:r[0].from,to:r[0].to,delta:i,resolution:n,nucleus:c},y:{from:r[1].from,to:r[1].to,delta:s,resolution:l,nucleus:a}}}return o},[])),t),[])}var Ge={name:"apodization",label:"Apodization",value:{lineBroadening:1,gaussBroadening:0,lineBroadeningCenter:0}};function Z(e){if(e?.version===3)return e;let t={...e,version:3};for(let o of t.spectra)if(Array.isArray(o?.filters)&&o?.filters.length>0){let r=o.filters.findIndex(i=>i.name==="lineBroadening");if(r!==-1){let i={...o.filters[r],...Ge};o.filters[r]=o.filters[r-1],o.filters[r-1]=i}}return t}function $(e){if(e?.version===4)return e;let{version:t,...o}=e,r=[],i={};for(let{source:s,...l}of o.spectra){let a={},{info:m={},display:p={}}=l;if(m?.dimension===2&&!s?.jcampURL)if(m.isFt)a.data={rr:l.data};else continue;if(s?.jcampURL){let{jcampURL:d,jcampSpectrumIndex:g}=s,S=d.match(/(?<baseURL>^\w+:\/{2}\w+\/)(?<relativePath>.*)/);i[d]||(i[d]={baseURL:S?.groups.baseURL||"",relativePath:S?.groups.relativePath||d.replace(/^\.\//,"")}),a.sourceSelector={files:[i[d].relativePath]},g!==void 0&&(a.sourceSelector.jcamp={index:g})}a.filters=Je(l.filters);let{name:u,...f}=p;u&&(a.info={...m,name:u}),a.display=f,r.push({...l,...a})}let n={data:{...o,spectra:r},version:4},c={entries:Object.values(i)};return c.entries.length>0&&(n.data.source=c),n}function Je(e=[]){let t=[];for(let o of e){let{name:r,value:i}=o;switch(r){case"zeroFilling":t.push({...o,value:{nbPoints:i}});break;case"shiftX":case"shift2DX":case"shift2DY":t.push({...o,value:{shift:i}});break;default:t.push({...o})}}return t}function G(e){if(e?.version===5)return e;let t={...e,version:5},o={originFrom:"originalFrom",originTo:"originalTo",originDelta:"originalDelta",originX:"originalX",originY:"originalY",originZ:"originalZ"};for(let r of t?.data?.spectra||[])for(let i of["peaks","ranges","zones"])r?.[i]&&(r[i]=h(r[i],o));return t}function J(e){if(e?.version===6)return e;let t={...e,version:6};for(let o of t?.data?.spectra||[]){let{digitalFilter:r,fft:i,phaseCorrection:n}=qe(o);i?.flag&&r?.flag&&n&&Math.floor(r.value.digitalFilterValue)%2>0&&(n.value.ph0-=180)}return t}function qe(e,t=["phaseCorrection","fft","digitalFilter"]){let{filters:o=[]}=e,r={};for(let i of t)r[i]=o.find(n=>n.name===i);return r}function A(e,t="localStorage"){if(e?.version===7)return e;if(t==="nmrium")return le(e);let o={...e,version:7};for(let r in e.workspaces)o.workspaces[r]=le(o.workspaces[r]);return o}function le(e){let{formatting:{nuclei:t,panels:o}={nuclei:null,panels:null},version:r,...i}=e,n={...i};return t&&(n.nuclei=He(t)),o&&(n.panels=o),n}function He(e){let t=[],o={name:"nucleus",ppm:"ppmFormat",hz:"hzFormat"};for(let r in e)t.push(h(e[r],o));return t}function q(e){if(e?.version===7)return e;let t={...e,version:7};return t?.settings&&(t.settings=A(t.settings,"nmrium")),t}function w(e,t="localStorage"){if(e?.version===8)return e;if(t==="nmrium")return ce(e);let o={...e,version:8};for(let r in e.workspaces)o.workspaces[r]=ce(o.workspaces[r]);return o}function ce(e){let{version:t,...o}=e,r={...o};return r.display.panels=Qe(e),r}function Qe(e){let t={},o=e.display.panels;for(let r of Object.keys(o)){let{display:i,open:n}=o[r];t[r]={display:i,visible:i,open:n}}return t}function H(e){if(e?.version===8)return e;let t={...e,version:8};t?.settings&&(t.settings=w(t.settings,"nmrium"));for(let o of t?.data?.spectra||[]){let{filters:r=[]}=o;for(let s=0;s<r.length;s++){let{flag:l,isDeleteAllow:a,label:m,...p}=r[s];r[s]={...p,enabled:l}}let i=r.findIndex(s=>s.name==="apodization");if(i!==-1){let s=r[i],{lineBroadening:l,gaussBroadening:a,lineBroadeningCenter:m}=s.value;s.value={exponential:{apply:!0,options:{lineBroadening:a>0?-l:l}}},a>0&&(s.value.gaussian={apply:!0,options:{lineBroadening:.6*a,lineBroadeningCenter:m}}),r[i]=s}let n=r.findIndex(s=>s.name==="apodizationDimension1"),c=r.findIndex(s=>s.name==="apodizationDimension2");if(n!==-1){let s=r[n],{shapes:l}=s.value.compose;s.value=ue(l)}if(c!==-1){let s=r[c],{shapes:l}=s.value.compose;s.value=ue(l)}}return t}function ue(e){let t={};for(let{shape:o}of e){let{kind:r,options:i}=o;if(r==="sineBell"){let{exponent:n,offset:c}=i,s=n===2?"sineSquare":"sineBell";t[s]={apply:!0,options:{offset:c}}}}return t}function Q(e){let{version:t,plugins:o,...r}=e;return t===9?e:{version:9,plugins:{},...r}}function ee(e){if(e?.version>=10)return e;let t={...e,version:10};if(e.data){let{source:o,spectra:r,...i}=e.data,n=o?crypto.randomUUID():void 0,c=o?[{...o,id:n}]:[];t.data={...i,sources:c,spectra:o?r?.map(s=>({...s,sourceId:n})):r}}return t}function te(e){let{version:t}=e;if(t>=11)return e;let o={...e,version:11};return e?.view?.molecules&&(o.view=et(e.view)),o}function et(e){let{molecules:t,...o}=e,r={};for(let[i,n]of Object.entries(t)){let{showAtomNumber:c,...s}=n;r[i]={...s,atomAnnotation:"none",showLabel:!1}}return{molecules:r,...o}}function re(e){if(e?.version>=12)return e;let t={...e,version:12};if(t.data){let o=e.data.spectra??[],r=e.data.molecules??[];for(let i of o){let{sourceId:n,fileCollectionId:c,sourceSelector:s}=i;delete i.sourceId,delete i.fileCollectionId,delete i.sourceSelector,s&&(i.selector={...s,root:c??n})}for(let i of r){let{sourceId:n,fileCollectionId:c,sourceSelector:s}=i;delete i.sourceId,delete i.fileCollectionId,delete i.sourceSelector,s&&(i.selector={...s,root:c??n})}}return t}function oe(e){if(e?.version>=13)return e;let t={...e,version:13};if(t.data){let o=e.data.spectra??[];for(let r of o){let i=r.ranges?.values??[];for(let n of i){let{diaIDs:c,assignment:s,nbAtoms:l,signals:a=[]}=n,m=a.some(p=>p.diaIDs&&p.diaIDs.length>0);for(let p of a)!m&&c&&l&&(p.diaIDs=c,p.nbAtoms=l),!p.assignment&&s&&(p.assignment=s);delete n.diaIDs,delete n.assignment,delete n.nbAtoms}}}return t}function O(e,t){e.plugins||(e.plugins={});let o=e.plugins;for(let r of t.values()){if(!r.shouldSerialize){delete o[r.id];continue}o[r.id]||(o[r.id]={id:r.id,version:r.version}),o[r.id].id=r.id,o[r.id].version=r.version}}var tt=[X,Y,Z,$,G,J,q,H,Q,ee,te,re,oe];function pe(e,t,o){let r=structuredClone(e),i=Object.entries(e?.plugins??{});for(let[s,{version:l}]of i){let a=o.get(s);if(!(a&&a.version>=l)){if(a){console.warn(`Plugin "${a.id}" is loaded with a version older (${a.version}) than the one used to save the state (${l}).
 NMRium may fail to load the state.
 Please update the plugin to the latest version.`);continue}console.warn(`Plugin "${s}@${l}" is not registered. NMRium may fail to load the state.
-Please consider open this file with the plugin installed.`)}}let n=new Set,c=()=>{let s=r.version;for(let l of o.values())for(let a of l.migrations){if(n.has(a)||s<a.minCore||a.maxCore&&s>a.maxCore)continue;if((r.plugins?.[l.id]?.version||0)===l.version)break;r=a.up(r),n.add(a)}};for(let s=e?.version||0;s<t;s++){let l=tt[s];r=l(r),c()}return c(),O(r,o),r}var rt=["topbar.right","topbar.about_us.modal"],ot=[],Qr=[...rt,...ot],it={},ie={};{let e=it,t=ie;for(let[o,r]of Object.entries(e))t[r]||(t[r]=[]),t[r]?.push(o)}function*me(e){let{slot:t,plugins:o,supportedToDeprecatedSlots:r=ie}=e,i=r[t];for(let[n,c]of o.entries()){let s=c.ui;if(!s)continue;let l=s[t];if(l){yield[n,l];continue}if(i)for(let a of i){let p=c.ui?.[a];if(p){yield[n,p],console.warn(`Plugin ${c.id} used deprecated slot "${a}". Please update this plugin to use "${t}" instead.`);break}}}}import{FileCollection as ct}from"file-collection";var ne={SDF:"sdf",MOL:"mol",NMRIUM:"nmrium",NMRIUM_ARCHIVE:"nmrium.zip",JSON:"json",JCAMP:"jcamp",DX:"dx",JDX:"jdx",JDF:"jdf",NMREDATA:"nmredata",SMILES:"smiles",SMI:"smi"};function v(e){return e.includes(".")?e.replace(/^.*\./,"").toLowerCase():""}function T(e,t={},o){let{data:r,...i}=e;if(!r)return e;let{spectra:n=[]}=r,{keep1D:c=!0,keep2D:s=!0,onlyReal:l}=t,a=l?"ft":t.dataSelection||"both",p=[];for(let m of n){if(!m.info){p.push(m);continue}let{isFid:u,dimension:f,name:g}=m.info;if(!F(f===1&&!c,g,o)&&!F(f===2&&!s,g,o)&&!F(u&&a==="ft",g,o)&&!F(!u&&a==="fid",g,o))if(l&&!u)if(m.info.isComplex=!1,nt(m)){let{rr:d}=m.data;p.push({...m,data:{rr:d}})}else{let{re:d,x:S}=m.data;p.push({...m,data:{re:d,x:S}})}else p.push(m)}return{data:{...r,spectra:p},...i}}function F(e,t,o){return e?(o?.warn(`Skipping ${t} because it didn't match the import filters.`),!0):!1}function nt(e){let{info:t}=e;return t?.dimension===2}function E(e){let{nmriumState:t,plugins:o,options:r}=e;for(let i of o.values()){let n=i.onReadProcess?.onProcessing;n&&n(t,r)}}async function L(e,t,o={}){let{selector:r,converter:i,logger:n}=o,c=[],s=[];for(let u of t.values()){let{onReadProcess:f}=u;f&&(f?.onFiles&&c.push(u),f?.supportedExtensions?.length&&f?.onFile&&s.push(u))}let l=await Promise.allSettled(c.map(u=>u.onReadProcess.onFiles(e,o))),a=[],p=await Promise.allSettled(e.files.flatMap(u=>{let f=v(u.name).toLowerCase();return s.flatMap(g=>{let{supportedExtensions:d,onFile:S}=g.onReadProcess;return d.includes(f)?(a.push({file:u,plugin:g}),S(u,{logger:n,selector:r,converter:i})):[]})})),m={spectra:[],molecules:[]};for(let u=0;u<l.length;u++){let f=l[u];switch(f.status){case"fulfilled":{let{spectra:g=[],molecules:d=[]}=f.value||{};m.spectra.push(...g),m.molecules.push(...d);break}case"rejected":{let g=f.reason,d=c[u];o.logger?.error(`Load file collection with plugin ${d.id}@${d.version} fails with: ${g}`);break}}}for(let u=0;u<p.length;u++){let f=p[u];switch(f.status){case"fulfilled":{let{spectra:g=[],molecules:d=[]}=f.value||{};m.spectra.push(...g),m.molecules.push(...d);break}case"rejected":{let g=f.reason,{file:d,plugin:S}=a[u];o.logger?.error(`Load file ${d.relativePath} with plugin ${S.id}@${S.version} fails with: ${g}`);break}}}return m}import{FileCollection as Se}from"file-collection";import{FileCollection as de}from"file-collection";import fe from"lodash.merge";import{xIsEquallySpaced as st}from"ml-spectra-processing";async function U(e){let{input:t,spectraResult:o,unserializedSpectrum:r,options:i,plugins:n,migrator:c}=e,l=(await M({input:t,migrator:c,plugins:n,options:{...i,selector:r.selector}}))?.nmriumState?.data?.spectra??[],a=l.pop();if(a){o.push(ge(r,a));for(let p of l)o.push(ge(r,at(p)))}}function ge(e,t){let{data:o,...r}=e;if(!t.selector?.root&&e.selector?.root&&(t.selector??=e.selector,t.selector.root=e.selector.root),"ranges"in t){let{data:i,...n}=t;return{...fe(n,r),data:i}}else if("zones"in t){let{data:i,...n}=t;return{...fe(n,r),data:i}}else return t}function at(e){return{...e,id:b()}}function z(e){let{spectrum:t,spectraResult:o,logger:r}=e,{dimension:i}=t.info;if(i===1){if(!st(t.data)){r?.error('The ".nmrium" file is corrupted; the X-axis values are not equally distant.');return}o.push(R(t))}else i===2&&o.push(C(t))}async function k(e){let{input:t,moleculesResult:o,unserializedMolecule:r,options:i,plugins:n,migrator:c}=e,{selector:s}=r,a=(await M({input:t,migrator:c,plugins:n,options:{...i,selector:s}}))?.nmriumState?.data?.molecules??[];for(let p of a)!p.selector?.root&&s?.root&&(p.selector??=s,p.selector.root=s.root),o.push({...r,...p})}function j(e){let{molecule:t,moleculesResult:o}=e;o.push(t)}async function V(e){let{nmriumObjectInput:t,options:o={},migrator:r,plugins:i,fromSourceOptions:n}=e,c=r(t),{data:s,...l}=c,a=new de;if(!s)return[{...l},a];let p={data:{...s,spectra:[],molecules:[]},...l},m=p.data,{sources:u=[],spectra:f,molecules:g}=m,d=await Promise.all(u.map(async P=>{let x=await de.fromSource(P,{unzip:{zipExtensions:["zip","nmredata"]}},n);if(!P.baseURL)for(let I of P.entries)I.baseURL||(I.baseURL=n?.baseURL);return[P.id,x]})),S=new Map(d),y=[];for(let P of s.spectra){let x=P.selector?.root??"",I=S.get(x);if(!I){z({spectrum:P,spectraResult:f,logger:o.logger});continue}y.push(U({input:I,spectraResult:f,unserializedSpectrum:P,migrator:r,plugins:i,options:o}))}for(let P of s.molecules??[]){let x=S.get(P.sourceId);if(!x){j({molecule:P,moleculesResult:g,logger:o.logger});continue}y.push(k({input:x,unserializedMolecule:P,moleculesResult:g,migrator:r,plugins:i,options:o}))}await Promise.allSettled(y);for(let[P,x]of S.entries())a.appendFileCollection(x,P);return[p,a]}async function _(e){let{file:t,options:o={},migrator:r,plugins:i,fromSourceOptions:n}=e,c=await t.arrayBuffer(),s=await(Se.isZip(c)?lt(c):t.text());return V({nmriumObjectInput:JSON.parse(s),plugins:i,migrator:r,options:o,fromSourceOptions:n})}async function lt(e){let t=await Se.fromZip(e);if(t.files.length===0)throw new Error("compressed nmrium file is corrupted");return t.files[0].text()}async function M(e){let{options:t={},input:o,migrator:r,plugins:i,fromSourceOptions:n}=e,{selectorRoot:c=crypto.randomUUID()}=t,s=mt(await ut(o),t.selector?.files),l=ft(s);if(l){let[g]=await _({file:l,migrator:r,plugins:i,options:t,fromSourceOptions:n});return{nmriumState:g,containsNmrium:!0,fileCollection:gt(s),selectorRoot:c}}let a=await L(s,i,t),p=T({version:13,data:a},t?.selector?.general,t.logger),{onLoadProcessing:m,experimentalFeatures:u}=t,f={...m,autoProcessing:m?.autoProcessing??!1,experimentalFeatures:u};return E({nmriumState:p,plugins:i,options:f}),dt(p,c),{nmriumState:p,containsNmrium:!1,fileCollection:s,selectorRoot:c}}function ut(e){return Array.isArray(e)?Promise.reject(new Error("For a set of fileCollectionItems pass a FileCollection instance")):pt(e)?Promise.resolve(e):new ct().appendExtendedSource({...e,uuid:crypto.randomUUID()})}function pt(e){return typeof e=="object"&&"files"in e}function mt(e,t){if(!t)return e;let o=new Set(t);return e.filter(r=>o.has(r.relativePath))}function ft(e){return e.files.find(t=>v(t.name).toLowerCase()===ne.NMRIUM)}function gt(e){return e.filter(t=>v(t.name).toLowerCase()!==ne.NMRIUM)}function dt(e,t){for(let o of e.data?.spectra??[])o.selector?.root||(o.selector??={root:t},o.selector.root||=t);for(let o of e.data?.molecules??[])o.selector?.root||(o.selector??={root:t},o.selector.root||=t)}import{FileCollection as yt}from"file-collection";async function ye(e){let t={},o=[];for(let r of e.sources)switch(r.relativePath){case"META-INF/NMRIUM_ARCHIVE":t.archive=r;break;case"META-INF/VERSION":o.push(r.text().then(i=>{t.version=Number.parseInt(i,10)}));break;case"state.json":o.push(r.text().then(i=>{t.state=JSON.parse(i)}));break;default:}return await Promise.all(o),t}function Pe(e){if(!e.archive)throw new Error("Not a valid NMRium archive");if(typeof e.version!="number"||Number.isNaN(e.version))throw new Error("Not a valid NMRium archive, no version specified");if(!e.state)throw new Error("NMRium Archive corrupted, state.json is missing")}function xe(e){return e.filter(t=>!St(t.relativePath))}function St(e){return e.startsWith("META-INF/")||e==="state.json"||e==="index.txt"}async function Ne(e){let{options:t,plugins:o,migrator:r}=e,i=await yt.fromIum(e.input),n=await ye(i);Pe(n);let c=xe(i),s=r(n.state),l={...s,data:{...s.data,spectra:[],molecules:[]}},a=l.data.spectra,p=l.data.molecules,m=Pt(i),u=[];for(let f of s.data.spectra)u.push(xt({subRoots:m,unserializedSpectrum:f,spectraResult:a,options:t,plugins:o,migrator:r}));for(let f of s.data.molecules??[])u.push(Nt({subRoots:m,unserializedMolecule:f,moleculesResult:p,options:t,plugins:o,migrator:r}));return await Promise.allSettled(u),[l,c]}function Pt(e){let t=new Map;return{get(o){let r=t.get(o);return r||(r=e.subroot(o),t.set(o,r)),r},[Symbol("debug")]:{ium:e,views:t}}}async function xt(e){let{subRoots:t}=e,{unserializedSpectrum:o,spectraResult:r}=e,{options:i,plugins:n,migrator:c}=e,{selector:s}=o,l=await he({subRoots:t,selector:s});if(!l)return z({spectrum:o,spectraResult:r,logger:i?.logger});await U({input:l,unserializedSpectrum:o,spectraResult:r,options:i,plugins:n,migrator:c})}async function Nt(e){let{subRoots:t}=e,{unserializedMolecule:o,moleculesResult:r}=e,{options:i,plugins:n,migrator:c}=e,{selector:s}=o,l=await he({subRoots:t,selector:s});if(!l)return j({molecule:o,moleculesResult:r,logger:i?.logger});await k({input:l,unserializedMolecule:o,moleculesResult:r,options:i,plugins:n,migrator:c})}async function he(e){let{subRoots:t,selector:o}=e;if(!o)return;let{root:r}=o;if(r)return t.get(r)}import{FileCollection as ht}from"file-collection";async function be(e){let{source:t,plugins:o,options:r={},sourceId:i=crypto.randomUUID()}=e,{converter:n,...c}=r,s={...t,id:i},l={spectra:[],molecules:[]},a=await ht.fromSource(s,{unzip:{zipExtensions:["zip","nmredata"]}}),{spectra:p=[],molecules:m=[]}=await L(a,o,{converter:{...n,bruker:{keepFiles:!0,...Reflect.get(n??{},"bruker")}},...c});l.spectra.push(...p),l.molecules.push(...m);for(let d of l.spectra)d.selector??={root:i},d.selector.root=i;for(let d of l.molecules)d.selector??={root:i},d.selector.root=i;l.sources??=[],l.sources.push(s);let u=T({version:13,data:l},r?.selector?.general),{onLoadProcessing:f}=c,g={filters:f?.filters,autoProcessing:f?.autoProcessing??!1,experimentalFeatures:r.experimentalFeatures};return E({nmriumState:u,plugins:o,options:g}),[u,a,i]}function D(e,t){let o={};for(let r in e)t.includes(r)||(o[r]=e[r]);return o}var bt=["data","originalData","info","originalInfo","meta","customInfo"],Rt=["data","originalData","info","originalInfo","meta","customInfo"],Ot=["selector","originalData","originalInfo"];function Re(e,t,o={}){let{version:r,data:i}=e;if(i.actionType)return e;let n={version:r,plugins:e.plugins},{includeData:c}=o;c!=="noData"&&(n.data=It({...i},c));let{includeSettings:s,includeView:l}=o;return s&&(n.settings=e.settings),l&&(n.view=e.view),O(n,t),n}function It(e,t="rawData"){let{spectra:o}=e;switch(t){case"dataSource":return vt(e);case"selfContained":case"selfContainedExternalDatasource":return Mt(e);case"rawData":return{...D(e,["sources"]),spectra:o.map(Oe)};default:return e}}function vt(e){let{spectra:t}=e;if(!e.sources)throw new Error("sources property should exists for dataSource serialization");return{...e,spectra:t.map(Dt)}}function Mt(e){let{spectra:t,sources:o,...r}=e;return{...r,spectra:t.map(Ct)}}function Dt(e){return D(e,bt)}function Ct(e){return"selector"in e?D(e,Rt):Oe(e)}function Oe(e){let{data:t,info:o,originalData:r,originalInfo:i}=e,n=D(e,Ot);return n.data=r||t,n.info=i||o,n}import{FileCollection as At}from"file-collection";async function Ie(e,t){let{state:o,aggregator:r,includeData:i=!0,includeSettings:n,includeView:c}=t,{spectra:s,molecules:l}=o.data;return At.fromCollection(r,{filter:{ignoreDotfiles:!1}}).toIum({includeData:i,mimetype:"chemical/x-nmrium+zip",*getExtraFiles(p){yield{relativePath:"META-INF/NMRIUM_ARCHIVE",data:""},yield{relativePath:"META-INF/VERSION",data:"0"},yield{relativePath:"state.json",data:wt(e,o,{includeData:i,includeView:c,includeSettings:n})},yield{relativePath:"index.txt",data:Ft({aggregator:r,spectra:s,molecules:l,index:p})}}})}function wt(e,t,o){let{includeData:r,includeView:i,includeSettings:n}=o,c=e(t,{includeData:r?"selfContained":"selfContainedExternalDatasource",includeView:i,includeSettings:n}),s=JSON.stringify(c,(l,a)=>ArrayBuffer.isView(a)?Array.from(a):a,2);return new Blob([s],{type:"application/json"})}function Ft(e){let{aggregator:t,spectra:o,molecules:r,index:i}=e,n=new Map,c=new Map(i.sources.map(l=>[l.uuid,l]));for(let l of o){let a=l.selector?.root;a&&(n.has(a)||n.set(a,t.subroot(a)))}for(let l of r){let a=l.selector?.root;a&&(n.has(a)||n.set(a,t.subroot(a)))}let s=[];for(let[l,a]of n.entries()){let p=new Map(a.sources.map(u=>[u.uuid,u])),m=`data/${l}/`;s.push(m);for(let u of a.files){let f=c.get(u.sourceUUID),g=p.get(u.sourceUUID),d=f?.baseURL?.startsWith("ium:/")?"embedded":"linked",y=i.paths[u.sourceUUID]?.replace(m,""),P=u.relativePath.replace(g?.relativePath??"",""),x=y?y+P:u.relativePath;s.push(`	${x}	(${d})`)}s.push(`
+Please consider open this file with the plugin installed.`)}}let n=new Set,c=()=>{let s=r.version;for(let l of o.values())for(let a of l.migrations){if(n.has(a)||s<a.minCore||a.maxCore&&s>a.maxCore)continue;if((r.plugins?.[l.id]?.version||0)===l.version)break;r=a.up(r),n.add(a)}};for(let s=e?.version||0;s<t;s++){let l=tt[s];r=l(r),c()}return c(),O(r,o),r}var rt=["topbar.right","topbar.about_us.modal"],ot=[],Qr=[...rt,...ot],it={},ie={};{let e=it,t=ie;for(let[o,r]of Object.entries(e))t[r]||(t[r]=[]),t[r]?.push(o)}function*me(e){let{slot:t,plugins:o,supportedToDeprecatedSlots:r=ie}=e,i=r[t];for(let[n,c]of o.entries()){let s=c.ui;if(!s)continue;let l=s[t];if(l){yield[n,l];continue}if(i)for(let a of i){let m=c.ui?.[a];if(m){yield[n,m],console.warn(`Plugin ${c.id} used deprecated slot "${a}". Please update this plugin to use "${t}" instead.`);break}}}}import{FileCollection as ct}from"file-collection";var ne={SDF:"sdf",MOL:"mol",NMRIUM:"nmrium",NMRIUM_ARCHIVE:"nmrium.zip",JSON:"json",JCAMP:"jcamp",DX:"dx",JDX:"jdx",JDF:"jdf",NMREDATA:"nmredata",SMILES:"smiles",SMI:"smi"};function v(e){return e.includes(".")?e.replace(/^.*\./,"").toLowerCase():""}function T(e,t={},o){let{data:r,...i}=e;if(!r)return e;let{spectra:n=[]}=r,{keep1D:c=!0,keep2D:s=!0,onlyReal:l}=t,a=l?"ft":t.dataSelection||"both",m=[];for(let p of n){if(!p.info){m.push(p);continue}let{isFid:u,dimension:f,name:d}=p.info;if(!F(f===1&&!c,d,o)&&!F(f===2&&!s,d,o)&&!F(u&&a==="ft",d,o)&&!F(!u&&a==="fid",d,o))if(l&&!u)if(p.info.isComplex=!1,nt(p)){let{rr:g}=p.data;m.push({...p,data:{rr:g}})}else{let{re:g,x:S}=p.data;m.push({...p,data:{re:g,x:S}})}else m.push(p)}return{data:{...r,spectra:m},...i}}function F(e,t,o){return e?(o?.warn(`Skipping ${t} because it didn't match the import filters.`),!0):!1}function nt(e){let{info:t}=e;return t?.dimension===2}function E(e){let{nmriumState:t,plugins:o,options:r}=e;for(let i of o.values()){let n=i.onReadProcess?.onProcessing;n&&n(t,r)}}async function L(e,t,o={}){let{selector:r,converter:i,logger:n}=o,c=[],s=[];for(let u of t.values()){let{onReadProcess:f}=u;f&&(f?.onFiles&&c.push(u),f?.supportedExtensions?.length&&f?.onFile&&s.push(u))}let l=await Promise.allSettled(c.map(u=>u.onReadProcess.onFiles(e,o))),a=[],m=await Promise.allSettled(e.files.flatMap(u=>{let f=v(u.name).toLowerCase();return s.flatMap(d=>{let{supportedExtensions:g,onFile:S}=d.onReadProcess;return g.includes(f)?(a.push({file:u,plugin:d}),S(u,{logger:n,selector:r,converter:i})):[]})})),p={spectra:[],molecules:[]};for(let u=0;u<l.length;u++){let f=l[u];switch(f.status){case"fulfilled":{let{spectra:d=[],molecules:g=[]}=f.value||{};p.spectra.push(...d),p.molecules.push(...g);break}case"rejected":{let d=f.reason,g=c[u];o.logger?.error(`Load file collection with plugin ${g.id}@${g.version} fails with: ${d}`);break}}}for(let u=0;u<m.length;u++){let f=m[u];switch(f.status){case"fulfilled":{let{spectra:d=[],molecules:g=[]}=f.value||{};p.spectra.push(...d),p.molecules.push(...g);break}case"rejected":{let d=f.reason,{file:g,plugin:S}=a[u];o.logger?.error(`Load file ${g.relativePath} with plugin ${S.id}@${S.version} fails with: ${d}`);break}}}return p}import{FileCollection as Se}from"file-collection";import{FileCollection as ge}from"file-collection";import fe from"lodash.merge";import{xIsEquallySpaced as st}from"ml-spectra-processing";async function U(e){let{input:t,spectraResult:o,unserializedSpectrum:r,options:i,plugins:n,migrator:c}=e,l=(await M({input:t,migrator:c,plugins:n,options:{...i,selector:r.selector}}))?.nmriumState?.data?.spectra??[],a=l.pop();if(a){o.push(de(r,a));for(let m of l)o.push(de(r,at(m)))}}function de(e,t){let{data:o,...r}=e;if(!t.selector?.root&&e.selector?.root&&(t.selector??=e.selector,t.selector.root=e.selector.root),"ranges"in t){let{data:i,...n}=t;return{...fe(n,r),data:i}}else if("zones"in t){let{data:i,...n}=t;return{...fe(n,r),data:i}}else return t}function at(e){return{...e,id:b()}}function z(e){let{spectrum:t,spectraResult:o,logger:r}=e,{dimension:i}=t.info;if(i===1){if(!st(t.data)){r?.error('The ".nmrium" file is corrupted; the X-axis values are not equally distant.');return}o.push(R(t))}else i===2&&o.push(C(t))}async function k(e){let{input:t,moleculesResult:o,unserializedMolecule:r,options:i,plugins:n,migrator:c}=e,{selector:s}=r,a=(await M({input:t,migrator:c,plugins:n,options:{...i,selector:s}}))?.nmriumState?.data?.molecules??[];for(let m of a)!m.selector?.root&&s?.root&&(m.selector??=s,m.selector.root=s.root),o.push({...r,...m})}function j(e){let{molecule:t,moleculesResult:o}=e;o.push(t)}async function V(e){let{nmriumObjectInput:t,options:o={},migrator:r,plugins:i,fromSourceOptions:n}=e,c=r(t),{data:s,...l}=c,a=new ge;if(!s)return[{...l},a];let m={data:{...s,spectra:[],molecules:[]},...l},p=m.data,{sources:u=[],spectra:f,molecules:d}=p,g=await Promise.all(u.map(async P=>{let x=await ge.fromSource(P,{unzip:{zipExtensions:["zip","nmredata"]}},n);if(!P.baseURL)for(let I of P.entries)I.baseURL||(I.baseURL=n?.baseURL);return[P.id,x]})),S=new Map(g),y=[];for(let P of s.spectra){let x=P.selector?.root??"",I=S.get(x);if(!I){z({spectrum:P,spectraResult:f,logger:o.logger});continue}y.push(U({input:I,spectraResult:f,unserializedSpectrum:P,migrator:r,plugins:i,options:o}))}for(let P of s.molecules??[]){let x=S.get(P.sourceId);if(!x){j({molecule:P,moleculesResult:d,logger:o.logger});continue}y.push(k({input:x,unserializedMolecule:P,moleculesResult:d,migrator:r,plugins:i,options:o}))}await Promise.allSettled(y);for(let[P,x]of S.entries())a.appendFileCollection(x,P);return[m,a]}async function _(e){let{file:t,options:o={},migrator:r,plugins:i,fromSourceOptions:n}=e,c="byteLength"in t?t:await t.arrayBuffer(),s=Se.isZip(c)?await lt(c):new TextDecoder("utf-8").decode(c);return V({nmriumObjectInput:JSON.parse(s),plugins:i,migrator:r,options:o,fromSourceOptions:n})}async function lt(e){let t=await Se.fromZip(e);if(t.files.length===0)throw new Error("compressed nmrium file is corrupted");return t.files[0].text()}async function M(e){let{options:t={},input:o,migrator:r,plugins:i,fromSourceOptions:n}=e,{selectorRoot:c=crypto.randomUUID()}=t,s=mt(await ut(o),t.selector?.files),l=ft(s);if(l){let[d]=await _({file:l,migrator:r,plugins:i,options:t,fromSourceOptions:n});return{nmriumState:d,containsNmrium:!0,fileCollection:dt(s),selectorRoot:c}}let a=await L(s,i,t),m=T({version:13,data:a},t?.selector?.general,t.logger),{onLoadProcessing:p,experimentalFeatures:u}=t,f={...p,autoProcessing:p?.autoProcessing??!1,experimentalFeatures:u};return E({nmriumState:m,plugins:i,options:f}),gt(m,c),{nmriumState:m,containsNmrium:!1,fileCollection:s,selectorRoot:c}}function ut(e){return Array.isArray(e)?Promise.reject(new Error("For a set of fileCollectionItems pass a FileCollection instance")):pt(e)?Promise.resolve(e):new ct().appendExtendedSource({...e,uuid:crypto.randomUUID()})}function pt(e){return typeof e=="object"&&"files"in e}function mt(e,t){if(!t)return e;let o=new Set(t);return e.filter(r=>o.has(r.relativePath))}function ft(e){return e.files.find(t=>v(t.name).toLowerCase()===ne.NMRIUM)}function dt(e){return e.filter(t=>v(t.name).toLowerCase()!==ne.NMRIUM)}function gt(e,t){for(let o of e.data?.spectra??[])o.selector?.root||(o.selector??={root:t},o.selector.root||=t);for(let o of e.data?.molecules??[])o.selector?.root||(o.selector??={root:t},o.selector.root||=t)}import{FileCollection as yt}from"file-collection";async function ye(e){let t={},o=[];for(let r of e.sources)switch(r.relativePath){case"META-INF/NMRIUM_ARCHIVE":t.archive=r;break;case"META-INF/VERSION":o.push(r.text().then(i=>{t.version=Number.parseInt(i,10)}));break;case"state.json":o.push(r.text().then(i=>{t.state=JSON.parse(i)}));break;default:}return await Promise.all(o),t}function Pe(e){if(!e.archive)throw new Error("Not a valid NMRium archive");if(typeof e.version!="number"||Number.isNaN(e.version))throw new Error("Not a valid NMRium archive, no version specified");if(!e.state)throw new Error("NMRium Archive corrupted, state.json is missing")}function xe(e){return e.filter(t=>!St(t.relativePath))}function St(e){return e.startsWith("META-INF/")||e==="state.json"||e==="index.txt"}async function Ne(e){let{options:t,plugins:o,migrator:r}=e,i=await yt.fromIum(e.input),n=await ye(i);Pe(n);let c=xe(i),s=r(n.state),l={...s,data:{...s.data,spectra:[],molecules:[]}},a=l.data.spectra,m=l.data.molecules,p=Pt(i),u=[];for(let f of s.data.spectra)u.push(xt({subRoots:p,unserializedSpectrum:f,spectraResult:a,options:t,plugins:o,migrator:r}));for(let f of s.data.molecules??[])u.push(Nt({subRoots:p,unserializedMolecule:f,moleculesResult:m,options:t,plugins:o,migrator:r}));return await Promise.allSettled(u),[l,c]}function Pt(e){let t=new Map;return{get(o){let r=t.get(o);return r||(r=e.subroot(o),t.set(o,r)),r},[Symbol("debug")]:{ium:e,views:t}}}async function xt(e){let{subRoots:t}=e,{unserializedSpectrum:o,spectraResult:r}=e,{options:i,plugins:n,migrator:c}=e,{selector:s}=o,l=await he({subRoots:t,selector:s});if(!l)return z({spectrum:o,spectraResult:r,logger:i?.logger});await U({input:l,unserializedSpectrum:o,spectraResult:r,options:i,plugins:n,migrator:c})}async function Nt(e){let{subRoots:t}=e,{unserializedMolecule:o,moleculesResult:r}=e,{options:i,plugins:n,migrator:c}=e,{selector:s}=o,l=await he({subRoots:t,selector:s});if(!l)return j({molecule:o,moleculesResult:r,logger:i?.logger});await k({input:l,unserializedMolecule:o,moleculesResult:r,options:i,plugins:n,migrator:c})}async function he(e){let{subRoots:t,selector:o}=e;if(!o)return;let{root:r}=o;if(r)return t.get(r)}import{FileCollection as ht}from"file-collection";async function be(e){let{source:t,plugins:o,options:r={},sourceId:i=crypto.randomUUID()}=e,{converter:n,...c}=r,s={...t,id:i},l={spectra:[],molecules:[]},a=await ht.fromSource(s,{unzip:{zipExtensions:["zip","nmredata"]}}),{spectra:m=[],molecules:p=[]}=await L(a,o,{converter:{...n,bruker:{keepFiles:!0,...Reflect.get(n??{},"bruker")}},...c});l.spectra.push(...m),l.molecules.push(...p);for(let g of l.spectra)g.selector??={root:i},g.selector.root=i;for(let g of l.molecules)g.selector??={root:i},g.selector.root=i;l.sources??=[],l.sources.push(s);let u=T({version:13,data:l},r?.selector?.general),{onLoadProcessing:f}=c,d={filters:f?.filters,autoProcessing:f?.autoProcessing??!1,experimentalFeatures:r.experimentalFeatures};return E({nmriumState:u,plugins:o,options:d}),[u,a,i]}function D(e,t){let o={};for(let r in e)t.includes(r)||(o[r]=e[r]);return o}var bt=["data","originalData","info","originalInfo","meta","customInfo"],Rt=["data","originalData","info","originalInfo","meta","customInfo"],Ot=["selector","originalData","originalInfo"];function Re(e,t,o={}){let{version:r,data:i}=e;if(i.actionType)return e;let n={version:r,plugins:e.plugins},{includeData:c,forceRawSpectra:s=[]}=o;c!=="noData"&&(n.data=It({...i},c,s));let{includeSettings:l,includeView:a}=o;return l&&(n.settings=e.settings),a&&(n.view=e.view),O(n,t),n}function It(e,t="rawData",o){let{spectra:r}=e;switch(t){case"dataSource":return vt(e);case"selfContained":case"selfContainedExternalDatasource":return Mt(e,o);case"rawData":return{...D(e,["sources"]),spectra:r.map(Oe)};default:return e}}function vt(e){let{spectra:t}=e;if(!e.sources)throw new Error("sources property should exists for dataSource serialization");return{...e,spectra:t.map(Dt)}}function Mt(e,t){let{spectra:o,sources:r,...i}=e;return{...i,spectra:o.map(n=>Ct(n,t))}}function Dt(e){return D(e,bt)}function Ct(e,t){return!("selector"in e)||t?.includes(e.id)?Oe(e):D(e,Rt)}function Oe(e){let{data:t,info:o,originalData:r,originalInfo:i}=e,n=D(e,Ot);return n.data=r||t,n.info=i||o,n}import{FileCollection as At}from"file-collection";async function Ie(e,t){let{state:o,aggregator:r,includeData:i=!0,includeSettings:n,includeView:c}=t,{spectra:s,molecules:l}=o.data;return At.fromCollection(r,{filter:{ignoreDotfiles:!1}}).toIum({includeData:i,mimetype:"chemical/x-nmrium+zip",*getExtraFiles(m){yield{relativePath:"META-INF/NMRIUM_ARCHIVE",data:""},yield{relativePath:"META-INF/VERSION",data:"0"},yield{relativePath:"state.json",data:wt(e,o,r,{includeData:i,includeView:c,includeSettings:n})},yield{relativePath:"index.txt",data:Ft({aggregator:r,spectra:s,molecules:l,index:m})}}})}function wt(e,t,o,r){let{includeData:i,includeView:n,includeSettings:c}=r,s=[];for(let m of t.data?.spectra??[]){let p=m.selector?.root;p&&o.subroot(p).files.length>0||s.push(m.id)}let l=e(t,{includeData:i?"selfContained":"selfContainedExternalDatasource",includeView:n,includeSettings:c,forceRawSpectra:s}),a=JSON.stringify(l,(m,p)=>ArrayBuffer.isView(p)?Array.from(p):p,2);return new Blob([a],{type:"application/json"})}function Ft(e){let{aggregator:t,spectra:o,molecules:r,index:i}=e,n=new Map,c=new Map(i.sources.map(l=>[l.uuid,l]));for(let l of o){let a=l.selector?.root;a&&(n.has(a)||n.set(a,t.subroot(a)))}for(let l of r){let a=l.selector?.root;a&&(n.has(a)||n.set(a,t.subroot(a)))}let s=[];for(let[l,a]of n.entries()){let m=new Map(a.sources.map(u=>[u.uuid,u])),p=`data/${l}/`;s.push(p);for(let u of a.files){let f=c.get(u.sourceUUID),d=m.get(u.sourceUUID),g=f?.baseURL?.startsWith("ium:/")?"embedded":"linked",y=i.paths[u.sourceUUID]?.replace(p,""),P=u.relativePath.replace(d?.relativePath??"",""),x=y?y+P:u.relativePath;s.push(`	${x}	(${g})`)}s.push(`
 `)}return s.join(`
 `)}var se=class{version=13;#e=new Map;registerPlugin(t){if(this.#e.has(t.id)){console.warn(`Plugin ${t.id} is already registered. skip.`),console.debug("Plugin already registered:",this.#e.get(t.id)),console.debug("Plugin to register:",t);return}this.#e.set(t.id,t)}registerPlugins(t){for(let o of t)this.registerPlugin(o)}migrate(t){return pe(t,this.version,this.#e)}read(t,o={},r){return M({input:t,options:o,fromSourceOptions:r,migrator:this.migrate.bind(this),plugins:this.#e})}readNMRiumArchive(t,o={}){return Ne({input:t,options:o,plugins:this.#e,migrator:this.migrate.bind(this)})}readNMRiumObject(t,o,r){return V({nmriumObjectInput:t,options:o,fromSourceOptions:r,plugins:this.#e,migrator:this.migrate.bind(this)})}readNMRiumFile(t,o={},r){return _({file:t,options:o,fromSourceOptions:r,plugins:this.#e,migrator:this.migrate.bind(this)})}readFromWebSource(t,o){return be({source:t,options:o,plugins:this.#e})}serializeNmriumState(t,o){return Re(t,this.#e,o)}serializeNmriumArchive(t){let o=this.serializeNmriumState.bind(this);return Ie(o,t)}serializePlugins(){let t={plugins:{}};return O(t,this.#e),t.plugins}slot(t){return me({slot:t,plugins:this.#e})}};function Tt(e,t){if(t>13)return 0;let o=-1;for(let r=0;r<e.length;r++)if(e[r].version>t){o=r;break}return o}var ve=[{version:6,fun:A},{version:7,fun:w}];function Et(e){let{version:t}=e||{},o=Tt(ve,t);if(o===-1)return{...e,version:13};let r=ve.slice(o);for(let i of r)e=i.fun(e);return e}export{Me as ANALYSIS_COLUMN_TYPES,De as ANALYSIS_COLUMN_VALUES_KEYS,N as CURRENT_EXPORT_VERSION,Ae as EXTERNAL_API_KEYS,se as NMRiumCore,Ze as defineNMRiumPlugin,Ye as formatSpectra,b as generateID,W as getOneIfArray,Et as migrateSettings,Ce as units};

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@zakodium/nmrium-core",
-  "version": "0.5.6",
+  "version": "0.5.8",
   "description": "The core of NMRium: types, state, state migration and plugin system.",
   "author": "Zakodium Sàrl",
   "license": "CC-BY-NC-SA-4.0",
@@ -31,12 +31,12 @@
     "jest-matcher-deep-close-to": "^3.0.2",
     "rimraf": "^6.1.2",
     "typescript": "~5.9.3",
-    "vitest": "^4.0.14"
+    "vitest": "^4.0.17"
   },
   "dependencies": {
     "cheminfo-types": "^1.8.1",
     "fifo-logger": "^2.0.1",
-    "file-collection": "^6.5.0",
+    "file-collection": "^6.6.0",
     "is-any-array": "^2.0.1",
     "lodash.merge": "^4.6.2",
     "ml-spectra-processing": "^14.18.2",
@@ -45,5 +45,5 @@
   "volta": {
     "extends": "../../../package.json"
   },
-  "gitHead": "72969d116c40fc5b22f159b6d75a91035594413f"
+  "gitHead": "e552115bcb0749324a1426ecf5382a7cc30e7f8a"
 }