@zakodium/nmrium-core-plugins 0.6.18 → 0.6.20

package/dist/nmrium-core-plugins.js

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-`)[1].split(" ")[1];P(e,"relaxationTime",a)}if(P(e,"numberOfScans",t[`${n}NS`]||t[`${n}QM_NSCANS`]),D(e,"groupDelay",t[`${n}GRPDLY`]),D(e,"dspfvs",t[`${n}DSPFVS`]),D(e,"decim",t[`${n}DECIM`]),e.isFid&&("groupDelay"in e||C(["dspfvs","decim"],e))){let{groupDelay:a,dspfvs:c,decim:l}=e,m=rr(a?.[0]??0,c?.[0],l?.[0]);D(e,"digitalFilter",m)}if(C(["numberOfPoints","spectralWidth"],e)){let{spectralWidth:a,numberOfPoints:c}=e,l=c.map((m,u)=>e.isFid?e.acquisitionTime[0]/(m-1):a[u]/(m-1));D(e,"increment",l)}}function $(e,t=","){if(e&&typeof e=="string")return e.split(t)}function or(e,t,r){let{prefix:n=""}=r,i=e.dimension<2,o=e.dataClass?.[0].toUpperCase()==="NTUPLES",s=C(["LAST","FIRST","VARDIM","SYMBOL"],t,n);if(i&&(o||s)&&(D(e,"last",$(t[`${n}LAST`])),D(e,"first",$(t[`${n}FIRST`])),D(e,"varDim",$(t[`${n}VARDIM`])),D(e,"symbols",$(t[`${n}SYMBOL`])),e.symbols&&Array.isArray(e.symbols))){e.symbols.includes("R")&&e.symbols.includes("I")&&(e.isComplex=!0);let a=e.symbols.findIndex(c=>c.toLowerCase()==="x");if(P(e,"firstX",e.first[a]),P(e,"lastX",e.last[a]),P(e,"numberOfPoints",e.varDim[a]),!("spectralWidth"in e)){let{lastX:c,numberOfPoints:l,firstX:m,originFrequency:u}=e;D(e,"spectralWidth",e.isFid?ne([l,c],f=>f[0]/(2*f[1])):ne([c,m,u],f=>Math.abs(f[0]-f[1])/f[2]))}}}import{normalizeNucleus as uo}from"nmr-processing";function Fe(e,t,r){let n=[];if(e[`${r}AXNUC`]&&(n=e[`${r}AXNUC`],Array.isArray(n)||(n=[n]),n=v(n)),n.length===0&&e[`${r}NUC1`]&&(n=e[`${r}NUC1`],Array.isArray(n)||(n=[n]),n=v(n)),n.length===0&&e[".NUCLEUS"]){let i=$(e[".NUCLEUS"]);if(e[`${r}SYMBOL`]){let o=e[`${r}SYMBOL`].split(","),s=o.findIndex(c=>c.includes("2")),a=o.findIndex(c=>c.includes("1"));s!==-1&&a!==-1&&i?n=v([i[s],i[a]]):n=v(i).toReversed()}else n=v(i)}return n.length===0&&e[".OBSERVENUCLEUS"]&&(n=v([e[".OBSERVENUCLEUS"]])),n.length===0&&t.experiment&&(n=v(sr(t.experiment[0]))),po(e)&&(n=[e["2D_X_NUCLEUS"].replaceAll(/[^A-Za-z0-9]/g,""),e["2D_Y_NUCLEUS"].replaceAll(/[^A-Za-z0-9]/g,"")]),t.experiment&&(t.experiment[0].match("jres")||t.experiment[0].match("dosy"))&&(n=sr(t.experiment[0])),n.map(uo)}function po(e){return e["2D_X_NUCLEUS"]&&!e["2D_X_NUCLEUS"].includes("off")&&e["2D_Y_NUCLEUS"]&&!e["2D_Y_NUCLEUS"].includes("off")}function sr(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 v(e){if(!e)return[];let t=e.map(n=>String(n).replaceAll(/[^A-Za-z0-9]/g,"").replace("NA","").replace("off","")),r=0;for(let n of t)n||r++;return r===0?t:[]}function ar(e,t,r){let{logger:n,prefix:i=""}=r;if(e.nucleus=Fe(t,e,i),e.nucleus.length===0)if(n)n.warn("No nucleus detected, assuming 1H"),e.nucleus=["1H"];else throw new Error("No nucleus detected");e.dimension=e.nucleus.length}function cr(e,t,r={}){let{prefix:n="",separator:i=`
+`)[1].split(" ")[1];P(e,"relaxationTime",a)}if(P(e,"numberOfScans",t[`${n}NS`]||t[`${n}QM_NSCANS`]),D(e,"groupDelay",t[`${n}GRPDLY`]),D(e,"dspfvs",t[`${n}DSPFVS`]),D(e,"decim",t[`${n}DECIM`]),e.isFid&&("groupDelay"in e||C(["dspfvs","decim"],e))){let{groupDelay:a,dspfvs:c,decim:l}=e,m=rr(a?.[0]??0,c?.[0],l?.[0]);D(e,"digitalFilter",m)}if(C(["numberOfPoints","spectralWidth"],e)){let{spectralWidth:a,numberOfPoints:c}=e,l=c.map((m,u)=>e.isFid?e.acquisitionTime[0]/(m-1):a[u]/(m-1));D(e,"increment",l)}}function $(e,t=","){if(e&&typeof e=="string")return e.split(t)}function or(e,t,r){let{prefix:n=""}=r,i=e.dimension<2,o=e.dataClass?.[0].toUpperCase()==="NTUPLES",s=C(["LAST","FIRST","VARDIM","SYMBOL"],t,n);if(i&&(o||s)&&(D(e,"last",$(t[`${n}LAST`])),D(e,"first",$(t[`${n}FIRST`])),D(e,"varDim",$(t[`${n}VARDIM`])),D(e,"symbols",$(t[`${n}SYMBOL`])),e.symbols&&Array.isArray(e.symbols))){e.symbols.includes("R")&&e.symbols.includes("I")&&(e.isComplex=!0);let a=e.symbols.findIndex(c=>c.toLowerCase()==="x");if(P(e,"firstX",e.first[a]),P(e,"lastX",e.last[a]),P(e,"numberOfPoints",e.varDim[a]),!("spectralWidth"in e)){let{lastX:c,numberOfPoints:l,firstX:m,originFrequency:u}=e;D(e,"spectralWidth",e.isFid?ne([l,c],f=>f[0]/(2*f[1])):ne([c,m,u],f=>Math.abs(f[0]-f[1])/f[2]))}}}import{normalizeNucleus as uo}from"nmr-processing";function Fe(e,t,r){let n=[];if(e[`${r}AXNUC`]&&(n=e[`${r}AXNUC`],Array.isArray(n)||(n=[n]),n=v(n)),n.length===0&&e[`${r}NUC1`]&&(n=e[`${r}NUC1`],Array.isArray(n)||(n=[n]),n=v(n)),n.length===0&&e[".NUCLEUS"]){let s=$(e[".NUCLEUS"]);if(e[`${r}SYMBOL`]){let a=e[`${r}SYMBOL`].split(","),c=a.findIndex(m=>m.includes("2")),l=a.findIndex(m=>m.includes("1"));c!==-1&&l!==-1&&s?n=v([s[c],s[l]]):n=v(s).toReversed()}else n=v(s)}n.length===0&&e[".OBSERVENUCLEUS"]&&(n=v([e[".OBSERVENUCLEUS"]])),n.length===0&&t.experiment&&(n=v(sr(t.experiment[0]))),po(e)&&(n=[e["2D_X_NUCLEUS"].replaceAll(/[^A-Za-z0-9]/g,""),e["2D_Y_NUCLEUS"].replaceAll(/[^A-Za-z0-9]/g,"")]);let{pulseSequence:i=[""],experiment:o}=t;return!i[0].toLowerCase().match("1d")&&o&&(o[0].match("jres")||o[0].match("dosy"))&&(n=sr(t.experiment[0])),n.map(uo)}function po(e){return e["2D_X_NUCLEUS"]&&!e["2D_X_NUCLEUS"].includes("off")&&e["2D_Y_NUCLEUS"]&&!e["2D_Y_NUCLEUS"].includes("off")}function sr(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 v(e){if(!e)return[];let t=e.map(n=>String(n).replaceAll(/[^A-Za-z0-9]/g,"").replace("NA","").replace("off","")),r=0;for(let n of t)n||r++;return r===0?t:[]}function ar(e,t,r){let{logger:n,prefix:i=""}=r;if(e.nucleus=Fe(t,e,i),e.nucleus.length===0)if(n)n.warn("No nucleus detected, assuming 1H"),e.nucleus=["1H"];else throw new Error("No nucleus detected");e.dimension=e.nucleus.length}function cr(e,t,r={}){let{prefix:n="",separator:i=`
 `}=r;D(e,"spectralWidth",t[`${n}SweepWidth`]/e.originFrequency[0]);let o=t[`${n}.PULSESEQUENCE`].split(i),s=[];t[".OBSERVENUCLEUS"]&&s.push(t[".OBSERVENUCLEUS"]),t.INDIRECTNUCLEUS&&s.push(t.INDIRECTNUCLEUS),e.nucleus=v(s),e.pulseSequence=o[0];let a=o.slice(2,-1);if(s.length>1)if(s[0]===s[1])e.spectralWidth.push(e.spectralWidth[0]);else{let c=JSON.stringify(a).match(/\$\$SW1=\s*(?<sw>[+-]?(?:[0-9]*[.])?[0-9]+)/);if(c?.groups){let{originFrequency:l}=e,m=Number.parseFloat(c.groups.sw);e.spectralWidth.push(m/l[1])}}}function xe(e,t={}){let{prefix:r="",logger:n}=t,i={creator:Kt(e),dimension:0,nucleus:[],isFid:!1,isFt:!1},o=JSON.stringify(e),s=/\r\n/.exec(o)?`\r
 `:`
 `,a=[Yt,ar,Wt,Zt],{creator:c=""}=i;c.includes("nanalysis")?a.push(er):c.toLocaleLowerCase().includes("oxford instruments")&&a.push(cr),c!=="mnova"&&c!=="mestre"&&a.push(ir),a.push(or,Qt);for(let l of a)l(i,e,{prefix:r,logger:n,separator:s});return go(i)}function go(e){return e.dimension===1&&(e.nucleus=[e.nucleus]),Object.fromEntries(Object.entries(e).map(([t,r])=>[t,fo(r)&&r.length===1?r[0]:r]))}var ho={keepRecordsRegExp:/.*/,keepFiles:!0};async function De(e,t={}){let r={spectra:[],molecules:[]},{converter:n={},selector:i={},logger:o}=t,s=ze(e,{logger:o,...Fo(i)}),a=[];for(let l of s)a.push(He(l,{...ho,...n,keepFiles:!0}).then(m=>bo(m,t)));let c=await Promise.allSettled(a);for(let l=0;l<c.length;l++){let m=c[l];if(m.status==="fulfilled"){let u=be(m.value.info);r.spectra.push({...m.value,info:{...m.value.info,...u}})}else if(m.reason){let u=s[l].name;o?.warn(`Bruker data: ${u}, fails with: ${m.reason}`);continue}}return o&&o[r.spectra.length>0?"info":"debug"](`Loaded ${r.spectra.length} spectra from Bruker files`),yo(r)}function bo(e,t={}){let{logger:r}=t,n={...e.info,...e.meta},i=xe(n,{logger:r}),o={},{isFid:s}=i;if(xo(e)){let f=e.minMax;for(let g in f){let y=f[g];y&&(y.z=U(y.z))}o.components=e.minMax}else i.dimension===1&&(o.components=e.spectra);let{source:a}=e,{expno:c,name:l,files:m}=a;n.vdlist&&(n.vdlistValues=ye(n.vdlist));let u={dependentVariables:[o],meta:n,info:{...i,experimentNumber:c,name:l}};return m&&(u.selector={files:m.map(f=>f.relativePath)}),Do(u,e),u}function Fo(e){let{general:t={},bruker:r={}}=e,{processingNumbers:n,experimentNumbers:i,...o}=r;return{...t,...o,processingNumbers:lr(n),experimentNumbers:lr(i)}}function lr(e){if(e)return e.split(/[^\d]+/).filter(Boolean).map(t=>Number.parseInt(t,10))}function xo(e){let{info:t}=e;return t.twoD}function Do(e,t){if(!("integrals"in t))return;let{integrals:r=[]}=t;e.integrals={values:r.map(n=>{let{from:i,to:o,integration:s}=n;return{from:i,to:o,integral:s,kind:"signal"}})}}function Ao(e,t){let{selector:r,converter:n,logger:i}=t??{};return De(e,{converter:n?.bruker,selector:r,logger:i})}function Ge(){return So({id:"@zakodium/nmrium-core-plugins#BrukerLoaderPlugin",version:1,shouldSerialize:!0,migrations:[],onReadProcess:{onFiles:Ao}})}import{defineNMRiumPlugin as ss}from"@zakodium/nmrium-core";import{formatSpectra as rs}from"@zakodium/nmrium-core";import{createTree as ns}from"jcampconverter";function mr(e,t,r={}){let{selector:n={}}=r;for(let i=0;i<e.spectra.length;i++){let o=e.spectra[i];o.selector={files:[t.relativePath],jcamp:{index:i,...n}}}return e}import{convert as Io}from"jcampconverter";function Ye(e,t,r){let{dataType:n,children:i}=e,o=n==="LINK"&&i?i:[e];for(let s of o){if(s.dataType==="LINK"){Ye(s,t,r);continue}let a=Io(s.jcamp,r);t.push(...a.flatten)}}function fr(e,t={}){let r=[],n=dr(e,t);for(let s of n?e:[])s.dataType==="LINK"?s.children=Ke(s.children,t):s=Ke([s],t)[0],r.push(s);let{name:i,logger:o}=t;return e.length===0&&o?.warn(`There is no data ${i?`in ${i}`:"in the JCAMP-DX"}`),r}function Ke(e=[],t={}){let{name:r,logger:n,tree:i=[],dataSelection:o="both"}=t,s=[];for(let m of e){let{dataType:u,dataClass:f}=m;if(u==="LINK")m.children=Ke(m.children,t);else if(i.some(g=>{let{dataClass:y=f,dataType:p=u}=g;return f===y&&u===p})){n?.warn(`Skipping ${f} and ${u} ${r?`in ${r}`:"in the JCAMP-DX"}, 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@zakodium/nmrium-core-plugins",
-  "version": "0.6.18",
+  "version": "0.6.20",
   "description": "Recommended plugins for NMRium, loaders of common formats like bruker or jcamp, and some post-processing plugins",
   "author": "Zakodium Sàrl",
   "license": "CC-BY-NC-SA-4.0",
@@ -36,7 +36,7 @@
     "bruker-data-test": "^1.0.0",
     "esbuild": "^0.27.0",
     "fifo-logger": "^2.0.1",
-    "jcamp-data-test": "^2.4.0",
+    "jcamp-data-test": "^2.5.0",
     "jeol-data-test": "^1.0.0",
     "jest-matcher-deep-close-to": "^3.0.2",
     "msw": "^2.12.3",
@@ -47,18 +47,18 @@
   },
   "dependencies": {
     "@date-fns/utc": "^2.1.1",
-    "@zakodium/nmrium-core": "^0.5.0",
+    "@zakodium/nmrium-core": "^0.5.1",
     "cheminfo-types": "^1.8.1",
     "convert-to-jcamp": "^6.0.0",
     "date-fns": "^4.1.0",
-    "file-collection": "^6.3.0",
+    "file-collection": "^6.5.0",
     "gyromagnetic-ratio": "^2.0.0",
     "is-any-array": "^2.0.1",
-    "jcampconverter": "^12.0.3",
+    "jcampconverter": "^12.0.4",
     "linear-sum-assignment": "^1.0.9",
     "lodash.merge": "^4.6.2",
-    "ml-spectra-processing": "^14.18.1",
-    "nmr-processing": "^22.0.0",
+    "ml-spectra-processing": "^14.18.2",
+    "nmr-processing": "^22.0.1",
     "openchemlib": "^9.18.2",
     "openchemlib-utils": "^8.8.1",
     "sdf-parser": "^7.0.4"
@@ -66,5 +66,5 @@
   "volta": {
     "extends": "../../../package.json"
   },
-  "gitHead": "0ff1a936a58bd6558cb50d8ec618e2dbf2f1f70b"
+  "gitHead": "30e7019e4d2d497e5b1bd1822eee7a7319073725"
 }