@zakodium/nmrium-core-plugins 0.1.10 → 0.3.0

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

@@ -1,37 +1,15 @@
 import type { DataSelectionOption } from '@zakodium/nmrium-core';
-import type { FileCollection } from 'file-collection';
 import type { Logger } from 'cheminfo-types';
 import { NMRiumCore } from '@zakodium/nmrium-core';
 import type { NmriumData } from '@zakodium/nmrium-core';
 import type { NMRiumPlugin } from '@zakodium/nmrium-core';
-import type { NMRiumPluginMigration } from '@zakodium/nmrium-core';
-import type { NMRiumPluginOnReadProcess } from '@zakodium/nmrium-core';
-import type { ParsingOptions } from '@zakodium/nmrium-core';
 import type { Spectrum1D } from '@zakodium/nmrium-core';
 import type { StateMolecule } from '@zakodium/nmrium-core';
 
 export declare function autoPostProcessing(): NMRiumPlugin;
 
-export declare class AutoPostProcessingPlugin implements NMRiumPlugin {
-    id: string;
-    version: number;
-    migrations: NMRiumPluginMigration[];
-    onReadProcess: NMRiumPluginOnReadProcess;
-    constructor();
-    private onPostProcessing;
-}
-
 export declare function brukerLoader(): NMRiumPlugin;
 
-export declare class BrukerLoaderPlugin implements NMRiumPlugin {
-    id: string;
-    version: number;
-    migrations: NMRiumPluginMigration[];
-    onReadProcess: NMRiumPluginOnReadProcess;
-    constructor();
-    onReadProcessFiles: (files: FileCollection, options?: ParsingOptions) => Promise<NmriumData>;
-}
-
 declare interface FilterTreeByDataTypeDataClass {
     /**
      * dataClass to be filter out of the tree, default value is
@@ -59,16 +37,6 @@ declare interface JCAMPDXConverterOptions {
 
 export declare function jcampDXLoader(): NMRiumPlugin;
 
-export declare class JCAMPDXLoaderPlugin implements NMRiumPlugin {
-    id: string;
-    version: number;
-    migrations: NMRiumPluginMigration[];
-    onReadProcess: NMRiumPluginOnReadProcess;
-    constructor();
-    private onReadProcessFile;
-    private getJCAMPDXSelector;
-}
-
 declare interface JCAMPDXParsingOptions {
     name?: string;
     converter?: JCAMPDXConverterOptions;
@@ -85,44 +53,22 @@ declare interface JCAMPDXSelectorOptions {
 
 export declare function jeolLoader(): NMRiumPlugin;
 
-export declare class JEOLLoaderPlugin implements NMRiumPlugin {
-    id: string;
-    version: number;
-    migrations: NMRiumPluginMigration[];
-    onReadProcess: NMRiumPluginOnReadProcess;
-    constructor();
-    private onReadProcessFile;
-}
-
 export declare function molfileLoader(): NMRiumPlugin;
 
-export declare class MolfileLoaderPlugin implements NMRiumPlugin {
-    id: string;
-    version: number;
-    migrations: NMRiumPluginMigration[];
-    onReadProcess: NMRiumPluginOnReadProcess;
-    constructor();
-    private onReadProcessFile;
-}
-
 export declare function nmreDATALoader(core: NMRiumCore): NMRiumPlugin;
 
-export declare class NMReDATALoaderPlugin implements NMRiumPlugin {
-    #private;
-    id: string;
-    version: number;
-    migrations: NMRiumPluginMigration[];
-    onReadProcess: NMRiumPluginOnReadProcess;
-    constructor(core: NMRiumCore);
-    onReadProcessFiles: (files: FileCollection, options?: ParsingOptions) => Promise<NmriumData>;
-}
-
 declare interface ParseSDFOptions {
     mixedEOL?: boolean;
 }
 
 export declare function processJCAMPDX(text: string, options?: JCAMPDXParsingOptions): NmriumData;
 
+/**
+ * Load the molecules from a SDF text (could be a molfile as well but a molfile is a SDF without $$$$ at the end)
+ * @param text
+ * @param options
+ * @returns
+ */
 export declare function readSDF(text: string, options?: ParseSDFOptions): StateMolecule[];
 
 export declare function readSMILES(text: string): StateMolecule[];
@@ -138,39 +84,12 @@ export declare function recommended(core: NMRiumCore, plugins?: NMRiumPlugin[]):
 
 export declare function sdfLoader(): NMRiumPlugin;
 
-export declare class SDFLoaderPlugin implements NMRiumPlugin {
-    id: string;
-    version: number;
-    migrations: NMRiumPluginMigration[];
-    onReadProcess: NMRiumPluginOnReadProcess;
-    constructor();
-    private onReadProcessFile;
-}
-
 export declare function smilesLoader(): NMRiumPlugin;
 
-export declare class SMILESLoaderPlugin implements NMRiumPlugin {
-    id: string;
-    version: number;
-    migrations: NMRiumPluginMigration[];
-    onReadProcess: NMRiumPluginOnReadProcess;
-    constructor();
-    private onReadProcessFile;
-}
-
 export declare function spectrum1DToJCAMPDX(spectrum: Spectrum1D, options?: {
     onlyReal?: boolean;
 }): string;
 
 export declare function varianLoader(): NMRiumPlugin;
 
-export declare class VarianLoaderPlugin implements NMRiumPlugin {
-    id: string;
-    version: number;
-    migrations: NMRiumPluginMigration[];
-    onReadProcess: NMRiumPluginOnReadProcess;
-    constructor();
-    onReadProcessFiles: (files: FileCollection, options?: ParsingOptions) => Promise<NmriumData>;
-}
-
 export { }

package/dist/nmrium-core-plugins.js

@@ -1,20 +1,20 @@
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o.length>0&&o!=="undefined"?o:e.dimension?`${e.dimension}d`:""}import{getOneIfArray as Et}from"@zakodium/nmrium-core";var di=["no","exponential","modifiedGaussian","sine","qsine","trap","user","sinc","qsinc","traf","trafs"];function gi(e){return e in Tt}function Ve(e,t){let{prefix:r="",index:n=0}=t,i=Et(e[`${r}WDW`],n),o=di[i?Number(i):0],s={};if(!gi(o))return s;let a=Tt[o];if(a){let{kind:c,parameters:l}=a,m={};for(let p in l){let f=l[p],{source:g,processor:y}=f;if(g){let u=Et(e[`${r}${g}`],n);if(!u)continue;let h=Number(u);m[p]=y?y(h):h}else f.value!==void 0&&(m[p]=f.value)}s[c]={apply:!0,options:m}}return s}var 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t=e.dimensions[0],r=e.dependentVariables,n=t.quantityName,i=t.count,o=t.increment.magnitude,s=t.originOffset.magnitude,a=t.coordinatesOffset.magnitude,c=r[0].components[0],l=new Float64Array(i),m=new Float64Array(i);for(let u=c.length-1,h=0;u>0;u-=2)l[h]=c[u-1],m[h++]=c[u];let p={},[f,g]=[0,0];switch(n){case"frequency":g=0+a/s*1e6,f=o/s*1e6,p.re=l,p.im=m;break;case"time":g=s,f=o,p.re=l.reverse(),p.im=m.reverse().map(u=>-u);break;default:break}let y=[];for(let u=0;u<i;u++)y.push(g+u*f);return p.x=y,p}function As(e){let t=e.dimensions,r=e.dependentVariables,n=t[0].quantityName,i=[],o=[],s=Number.MIN_SAFE_INTEGER,a=Number.MAX_SAFE_INTEGER,c=Number.MAX_SAFE_INTEGER,l=Number.MIN_SAFE_INTEGER;for(let f of r[0].components){let g=new Float64Array(f.length/2),y=new Float64Array(f.length/2);for(let u=f.length-1,h=0;u>0;u-=2){let d=f[u-1],b=f[u];d>s&&(s=d),d<a&&(a=d),b>l&&(l=b),b<c&&(c=b),g[h]=d,y[h++]=b}if(n==="frequency")i.push(g),o.push(y);else{let u=g.length,h=new 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+`,index:i=0}=r;this.eol=n,this.index=i,this.lines=t.split(this.eol),this.length=this.lines.length}readLine(){if(this.index>=this.length)throw new Error(`Last index is ${this.length-1}. Current index ${this.index}.`);return this.lines[this.index++]}readLines(t){let r=this.lines.slice(this.index,this.index+t);return this.index+=t,r}},Ce=class{softwareVersion;typeOfFile;vendorIdStatus;constructor(t){this.softwareVersion=t&2**6-1,this.typeOfFile={fidFile:(t&64)!==0,dataFile:(t&128)!==0,data3DFile:(t&256)!==0},this.vendorIdStatus={isVar:(t&0)!==0,isQOne:(t&2048)!==0,isMakeFid:(t&4096)!==0,isJeol:(t&8192)!==0,isBru:(t&16384)!==0,isMag:(t&6144)!==0,isOx:(t&10240)!==0,ipVers:(t&63)!==0,ipFileId:(t&1984)!==0,ipVendorId:(t&30720)!==0}}},Re=class{npPhMode;npAvMode;npPwrMode;nfPhMode;nfAvMode;nfPwrMode;niPhMode;niAvMode;niPwrMode;ni2PhMode;ni2AvMode;ni2PwrMode;niPaMode;ni2PaMode;constructor(t){this.npPhMode=(t&1)!==0,this.npAvMode=(t&2)!==0,this.npPwrMode=(t&4)!==0,this.nfPhMode=(t&16)!==0,this.nfAvMode=(t&32)!==0,this.nfPwrMode=(t&64)!==0,this.niPhMode=(t&256)!==0,this.niAvMode=(t&512)!==0,this.niPwrMode=(t&1024)!==0,this.ni2PhMode=(t&8)!==0,this.ni2AvMode=(t&256)!==0,this.ni2PwrMode=(t&8192)!==0,this.niPaMode=(t&16384)!==0,this.ni2PaMode=(t&32768)!==0}};var we=class{scale;status;index;mode;ctCount;lpVal;rpVal;lvl;tlt;data;constructor(t,r,n){n&&(t.offset=n),this.scale=t.readInt16(),this.status=new Ee(t.readInt16()),this.index=t.readInt16(),this.mode=new Re(t.readInt16()),this.ctCount=t.readInt32(),this.lpVal=t.readFloat32(),this.rpVal=t.readFloat32(),this.lvl=t.readFloat32(),this.tlt=t.readFloat32(),this.data=aa(t,r)}};function aa(e,t){let{np:r,nTraces:n,status:{isFloat32:i,isInt32:o}}=t;return i?dt(e,n,r,"readFloat32"):o?dt(e,n,r,"readInt32"):dt(e,n,r,"readInt16")}function dt(e,t,r,n){let i=[],o;n==="readFloat32"?o={re:new Float32Array(r/2),im:new Float32Array(r/2)}:n==="readInt32"?o={re:new Int32Array(r/2),im:new Int32Array(r/2)}:o={re:new Int16Array(r/2),im:new Int16Array(r/2)};for(let s=0;s<t;s++){for(let a=0;a<r;a+=2)o.re[a>>>1]=e[n](),o.im[a>>>1]=e[n]();i[s]=o}return i}var ve=class{nBlocks;nTraces;np;eBytes;tBytes;bBytes;version;status;nBlockHeaders;constructor(t){t.offset=0,this.nBlocks=t.readInt32(),this.nTraces=t.readInt32(),this.np=t.readInt32(),this.eBytes=t.readInt32(),this.tBytes=t.readInt32(),this.bBytes=t.readInt32(),this.version=new Ce(t.readInt16()),this.status=new Te(t.readInt16()),this.nBlockHeaders=t.readInt32()}};var gt=class{name;subType;basicType;maxValue;minValue;stepSize;gGroup;dGroup;protection;active;intptr;constructor(t){let r=t.split(" ");this.name=r[0],this.subType=Number.parseInt(r[1],10),this.basicType=Number.parseInt(r[2],10),this.maxValue=Number.parseFloat(r[3]),this.minValue=Number.parseFloat(r[4]),this.stepSize=Number.parseFloat(r[5]),this.gGroup=Number.parseInt(r[6],10),this.dGroup=Number.parseInt(r[7],10),this.protection=Number.parseInt(r[8],10),this.active=Number.parseInt(r[9],10),this.intptr=Number.parseInt(r[10],10)}};function Rn(e){let t=[],r=new Oe(e.readChars(e.length));for(;r.index<r.length-1;){let n=[],i=[],o=new gt(r.readLine()),s=r.readLine();if(o.basicType!==0){if(o.basicType===1)n=s.split(" ").slice(1).map(m=>Number.parseFloat(m));else if(o.basicType===2){n=s.split('"').slice(1,2);let l=Number.parseInt(s.split(" ")[0],10);for(;l>1;)n.push(r.readLine().split('"')[1]),l--}}let a=r.readLine(),c=Number.parseInt(a.split(" ")[0],10);c!==0&&(o.basicType===1?i=a.split(" ").slice(1):o.basicType===2&&(i=a.split('"').filter((l,m)=>m%2===1))),t.push({...o,values:n,enumerable:c,enumerables:i})}return t}async function wn(e){let t={};function r(c,l){return c.then(m=>{t[l]=m})}let n=[];for(let c of e)switch(c.name.toLowerCase()){case"fid":{n.push(r(c.arrayBuffer(),"fidB"));break}case"procpar":{n.push(r(c.arrayBuffer(),"procparB"));break}default:break}if(await Promise.all(n),!t.fidB||!t.procparB)throw new RangeError("fid and procpar must exist.");let i=new R(t.fidB);Cn(i);let o=new ve(i);if(o.nBlocks!==1)throw new Error("We currently do not support 2D varian spectra ");let s=Rn(new R(t.procparB)),a;for(let c of s)if(c.name==="at"){a=c.values[0];break}if(typeof a!="number")throw new Error("acquisition time parameter must exist and be a number.");{let c=ca({from:0,to:a,length:o.np/2,distribution:"uniform"}),l=new we(i,o);return{meta:o,fid:l,procpar:s,x:c}}}import{isAnyArray as pa}from"is-any-array";import{xMultiply as fa}from"ml-spectra-processing";import{normalizeNucleus as la}from"nmr-processing";function vn(e,t){let{meta:r,procpar:n}=e,i={};for(let b of n)i[b.name]=b.values;let o={},s={},{np:a,solvent:c,sfrq:l,reffrq:m,temp:p,rp:f,sw:g,rfl:y,rfp:u}=i;D(o,"numberOfPoints",a&&Number(q(a))/2),D(o,"solvent",q(c)),D(o,"originFrequency",q(l)),D(o,"baseFrequency",q(m)),(Number.isNaN(o.originFrequency)||o.originFrequency===0)&&(o.originFrequency=400,t?.warn("The frequency could not be determined and was set to 400MHz")),D(o,"temperature",q(p)),D(o,"phc0",f&&Number(f[0])),D(s,"rfl",y&&Number(q(y))),D(s,"rfp",u&&Number(q(u))),D(s,"sw",g&&Number(q(g)));for(let b in s){let F=s[b];Array.isArray(F)&&F.length===1&&(s[b]=F[0])}if(!("baseFrequency"in o)&&"originFrequency"in o){let b=Number.parseFloat(o.originFrequency);if(["sw","rfl","rfp"].every(F=>F in s)){let{sw:F=1,rfl:S=1,rfp:I=1}=ma(s,["sw","rfl","rfp"]);D(o,"baseFrequency",b-(F/2-S+I)/1e6)}else D(o,"baseFrequency",b)}let{baseFrequency:h,originFrequency:d}=o;D(o,"frequencyOffset",(d-h)*1e6),D(o,"spectralWidth",g&&Number(g[0])/o.baseFrequency);for(let b in o)o[b].length===1&&(o[b]=o[b][0]);return i.tn&&(o.nucleus=i.tn.map(la)),o.dimension=1,o.isFid=!r.status.isSpectrum,{info:o,meta:{...s,...Ln(r),...i}}}function q(e){return e&&(Array.isArray(e)?e[0]:e)}function ma(e,t){let r={};for(let n of t){let i=e[n];i&&typeof i=="number"&&(r[n]=i)}return r}function Ln(e){let t={};for(let r of Object.keys(e)){let n=e[r];typeof n=="object"&&n!==null&&n.constructor&&n.constructor!==Object?t[r]=Ln(n):t[r]=n}return t}function kn(e){let t={},r=new Set(e.files.map(n=>n.relativePath));for(let n of e){let i=n.name.toLowerCase();if(i.match(/^(?:fid|procpar|text|log)$/)){if(i.match(/^(?:fid|text|log)$/)){let a=n.relativePath.replace(/(?:fid|text|log)$/,"procpar");if(!r.has(a))continue}let o=n.relativePath.split("/"),s=o.slice(0,-1).join("/");t[s]||(t[s]={name:o.at(-2),files:[]}),t[s].files.push(n)}}return Object.values(t)}async function _n(e,t={}){let{keepSource:r,logger:n}=t,i=kn(e);n&&n.debug(`Found ${Object.keys(i).length} varian experiments`);let o=[],s={spectra:[],molecules:[]};for(let c of i){let{name:l,files:m}=c,p=wn(m).then(f=>{let{info:g,meta:y}=vn(f),u=f.fid.data[0],h=pa(u.im),d={data:{...u,x:f.x},meta:y,info:{isComplex:h,name:l,...g},display:{name:l}};if(g.isFid&&h){let{im:b}=d.data;fa(b,-1,{output:b})}m&&r&&(d.sourceSelector={files:m.map(b=>b.relativePath)}),s.spectra.push(d)});o.push(p)}let a=await Promise.allSettled(o);for(let c=0;c<a.length;c++){let l=a[c];if(l.status==="rejected"&&l.reason){let m=i[c].name;n?.warn(`Varian data: ${m}, fails with: ${l.reason}`)}}return s.spectra.length>0&&n?.info(`Loaded ${s.spectra.length}  spectra from Varian files`),ua(s)}function ga(e,t){let{keepSource:r,logger:n}=t??{};return _n(e,{keepSource:r,logger:n})}function yt(){return da({id:"@zakodium/nmrium-core-plugins#VarianLoaderPlugin",version:1,migrations:[],onReadProcess:{onFiles:ga}})}function ha(e,t=[]){return[ut(e),yt(),Ge(),Qe(),at(),pt(),ft(),st(),$e()].concat(t)}function ba(e=[]){let t=new ya;return t.registerPlugins(ha(t,e)),t}import{getOneIfArray as jn}from"@zakodium/nmrium-core";import{from1DNMRVariables as Fa}from"convert-to-jcamp";function qn(e,t){return e.filters.find(r=>r.name===t)}function xa(e,t={}){let{onlyReal:r=!1}=t,{info:n,meta:i,data:o}=e,{owner:s,title:a,isFid:c,spectralWidth:l,baseFrequency:m,originFrequency:p,nucleus:f,solvent:g,scaleFactor:y,frequencyOffset:u,decim:h,dspfvs:d,digitalFilter:b}=n,F=jn(m||p),{x:S,re:I,im:x}=o,A=new Float64Array(I),M=!r&&x?new Float64Array(x):void 0,T=qn(e,"fft")?.enabled,j={owner:s,isFid:c,title:a,nucleus:f,solvent:g,scaleFactor:y,spectralWidth:l,frequencyOffset:u,originFrequency:p,baseFrequency:F,dataType:!c||T?"NMR SPECTRUM":"NMR FID",dataClass:!r&&x?"NTUPLES":"XYDATA"};if(c){let se=e.filters.find(J=>J.name==="digitalFilter");if(se&&!T){let{value:{digitalFilterValue:J},enabled:ke}=se;if(ke){let k=Math.floor(J);A.set(I.slice(I.length-k)),A.set(I.slice(0,I.length-k),k),x&&M&&(M.set(x.slice(x.length-k)),M.set(x.slice(0,x.length-k),k))}}ht(j,"decim",h),ht(j,"dspfvs",d),ht(j,"digitalFilter",b)}let re=Da(i,Bn),Le={xyEncoding:"DIFDUP",nmrInfo:j,meta:re},oe={x:{data:S,label:n.isFid?"TIME":"FREQUENCY",units:n.isFid?"second":"HZ",symbol:"X"},r:{data:A,label:`${n.isFid?"FID":"SPECTRUM"}/REAL`,units:"ARBITRARY UNITS",symbol:"R"}};return M&&(oe.i={data:M,label:`${n.isFid?"FID":"SPECTRUM"}/IMAG`,units:"ARBITRARY UNITS",symbol:"I"}),Fa(oe,Le)}function ht(e,t,r){r!==void 0&&(e[t]=jn(r))}var Bn=["title","decim","dspfvs","grpdly","bf1","sw","offset",".solvent","owner","firsty","page","vardim","symbol","symbols","varform","vartype","datatype","dataclass",".observefrequency",".observenucleus","ncproc"];function Da(e,t=Bn){let r=new Set(t);return Object.fromEntries(Object.entries(e).filter(([n])=>!r.has(n.toLocaleLowerCase().replaceAll(/[\s|_]*/g,""))))}export{$e as autoPostProcessing,Ge as brukerLoader,ba as default,ba as init,Qe as jcampDXLoader,st as jeolLoader,at as molfileLoader,ut as nmreDATALoader,vr as processJCAMPDX,Pn as readSDF,Tn as readSMILES,ha as recommended,pt as sdfLoader,ft as smilesLoader,xa as spectrum1DToJCAMPDX,yt as varianLoader};

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@zakodium/nmrium-core-plugins",
-  "version": "0.1.10",
+  "version": "0.3.0",
   "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",
@@ -18,51 +18,52 @@
     "#assets": "./src/assets.js"
   },
   "scripts": {
-    "bundle": "node scripts/esbuild.js && npm run bundle-types",
-    "bundle-types": "npm run tsc && yarn g:api-extractor",
+    "bundle": "node scripts/esbuild.js && yarn bundle-types",
+    "bundle-types": "yarn tsc && yarn g:api-extractor",
     "clean": "rimraf types dist coverage",
-    "prepack": "npm run clean && npm run bundle",
+    "prepack": "yarn clean && yarn bundle",
     "test": "yarn g:test-only && yarn g:check-types && yarn g:eslint && yarn g:prettier",
     "tsc": "tsc --project tsconfig.types.json"
   },
   "devDependencies": {
     "@types/lodash.merge": "^4.6.9",
-    "@types/node": "^24.3.0",
+    "@types/node": "^24.5.2",
     "@zakodium/bruker-parser": "^0.0.0",
     "@zakodium/jeol-parser": "^0.0.0",
-    "@zakodium/nmr-types": "^0.1.1",
+    "@zakodium/nmr-types": "^0.2.0",
     "@zakodium/nmredata": "^0.0.0",
     "@zakodium/varian-parser": "^0.0.0",
     "bruker-data-test": "^1.0.0",
-    "esbuild": "^0.25.9",
+    "esbuild": "^0.25.10",
     "fifo-logger": "^2.0.1",
-    "jcamp-data-test": "^2.1.1",
+    "jcamp-data-test": "^2.4.0",
     "jeol-data-test": "^1.0.0",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "msw": "^2.10.5",
+    "msw": "^2.11.2",
     "nmredata-data-test": "^1.0.0",
     "rimraf": "^6.0.1",
     "vitest": "^3.2.4"
   },
   "dependencies": {
     "@date-fns/utc": "^2.1.1",
-    "@zakodium/nmrium-core": "^0.1.7",
+    "@zakodium/nmrium-core": "^0.2.0",
     "cheminfo-types": "^1.8.1",
     "convert-to-jcamp": "^6.0.0",
     "date-fns": "^4.1.0",
     "file-collection": "^5.1.1",
     "gyromagnetic-ratio": "^2.0.0",
     "is-any-array": "^2.0.1",
-    "jcampconverter": "^11.0.5",
+    "jcampconverter": "^11.1.0",
     "linear-sum-assignment": "^1.0.7",
     "lodash.merge": "^4.6.2",
     "ml-spectra-processing": "^14.17.1",
-    "nmr-processing": "^19.1.0",
-    "openchemlib": "^9.7.0",
-    "openchemlib-utils": "^8.3.1",
+    "nmr-processing": "^19.3.0",
+    "openchemlib": "^9.8.0",
+    "openchemlib-utils": "^8.5.0",
     "sdf-parser": "^7.0.4"
   },
   "volta": {
     "extends": "../../../package.json"
-  }
-}
+  },
+  "gitHead": "00d3759d3c814dd1d18a2a72a095b7dc02796dc7"
+}