nmr-processing 9.3.6 → 9.3.8-pre.1681135907

package/lib/apodization/apodization.d.ts

@@ -6,17 +6,22 @@ export interface DataReIm {
     /** Array of im values */
     im: DoubleArray;
 }
-interface ApodizationOptions {
+export interface ApodizationOptions {
     /**
      * number of points at the end of the shape to apply the window function inverted
      * @default 0
      */
     pointsToShift?: number;
-    compose: ShapeOptions;
+    compose?: ShapeOptions;
 }
-export declare function apodization(data: DataReIm, options: ApodizationOptions): {
+export declare function apodization(data: DataReIm, options?: ApodizationOptions): {
+    windowData: never[];
+    /** Array of re values */
+    re: DoubleArray;
+    /** Array of im values */
+    im: DoubleArray;
+} | {
     re: DoubleArray;
     im: DoubleArray;
     windowData: Float64Array;
 };
-export {};

package/lib/apodization/apodization.js

@@ -3,8 +3,10 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.apodization = void 0;
 const applyWindow_1 = require("./applyWindow");
 const compose_1 = require("./compose");
-function apodization(data, options) {
+function apodization(data, options = {}) {
     const { compose: composeOptions, pointsToShift } = options;
+    if (!composeOptions)
+        return { ...data, windowData: [] };
     const windowData = (0, compose_1.compose)(composeOptions);
     const applyWindowOptions = {
         windowData,

package/lib/apodization/apodization.js.map

@@ -1 +1 @@
-{"version":3,"file":"apodization.js","sourceRoot":"","sources":["../../src/apodization/apodization.ts"],"names":[],"mappings":";;;AAEA,+CAA4C;AAC5C,uCAAkD;AAiBlD,SAAgB,WAAW,CAAC,IAAc,EAAE,OAA2B;IACrE,MAAM,EAAE,OAAO,EAAE,cAAc,EAAE,aAAa,EAAE,GAAG,OAAO,CAAC;IAC3D,MAAM,UAAU,GAAG,IAAA,iBAAO,EAAC,cAAc,CAAC,CAAC;IAE3C,MAAM,kBAAkB,GAAG;QACzB,UAAU;QACV,aAAa;KACd,CAAC;IAEF,MAAM,EAAE,GAAG,IAAA,yBAAW,EAAC,IAAI,CAAC,EAAE,EAAE,kBAAkB,CAAC,CAAC;IACpD,MAAM,EAAE,GAAG,IAAA,yBAAW,EAAC,IAAI,CAAC,EAAE,EAAE,kBAAkB,CAAC,CAAC;IAEpD,OAAO,EAAE,EAAE,EAAE,EAAE,EAAE,UAAU,EAAE,CAAC;AAChC,CAAC;AAbD,kCAaC"}
+{"version":3,"file":"apodization.js","sourceRoot":"","sources":["../../src/apodization/apodization.ts"],"names":[],"mappings":";;;AAEA,+CAA4C;AAC5C,uCAAkD;AAiBlD,SAAgB,WAAW,CAAC,IAAc,EAAE,UAA8B,EAAE;IAC1E,MAAM,EAAE,OAAO,EAAE,cAAc,EAAE,aAAa,EAAE,GAAG,OAAO,CAAC;IAE3D,IAAI,CAAC,cAAc;QAAE,OAAO,EAAE,GAAG,IAAI,EAAE,UAAU,EAAE,EAAE,EAAE,CAAC;IAExD,MAAM,UAAU,GAAG,IAAA,iBAAO,EAAC,cAAc,CAAC,CAAC;IAE3C,MAAM,kBAAkB,GAAG;QACzB,UAAU;QACV,aAAa;KACd,CAAC;IACF,MAAM,EAAE,GAAG,IAAA,yBAAW,EAAC,IAAI,CAAC,EAAE,EAAE,kBAAkB,CAAC,CAAC;IACpD,MAAM,EAAE,GAAG,IAAA,yBAAW,EAAC,IAAI,CAAC,EAAE,EAAE,kBAAkB,CAAC,CAAC;IAEpD,OAAO,EAAE,EAAE,EAAE,EAAE,EAAE,UAAU,EAAE,CAAC;AAChC,CAAC;AAfD,kCAeC"}

package/lib/apodization/applyWindow.js.map

@@ -1 +1 @@
-{"version":3,"file":"applyWindow.js","sourceRoot":"","sources":["../../src/apodization/applyWindow.ts"],"names":[],"mappings":";;;AA0BA;;GAEG;AACH,SAAgB,WAAW,CAAC,IAAiB,EAAE,OAA2B;IACxE,MAAM,UAAU,GAAG,IAAI,CAAC,MAAM,CAAC;IAE/B,MAAM,EACJ,UAAU,EACV,KAAK,GAAG,CAAC,EACT,MAAM,GAAG,UAAU,EACnB,aAAa,GAAG,CAAC,EACjB,MAAM,GAAG,IAAI,YAAY,CAAC,IAAI,CAAC,GAChC,GAAG,OAAO,CAAC;IAEZ,MAAM,aAAa,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,MAAM,EAAE,UAAU,GAAG,aAAa,CAAC,CAAC;IAC3E,KAAK,IAAI,CAAC,GAAG,KAAK,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,aAAa,EAAE,CAAC,EAAE,EAAE;QACjD,MAAM,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC,CAAC,EAAE,CAAC,CAAC;KAC9B;IAED,KAAK,IAAI,CAAC,GAAG,UAAU,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,GAAG,aAAa,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;QAC3E,MAAM,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC,CAAC,EAAE,CAAC,CAAC;KAC9B;IAED,OAAO,MAAM,CAAC;AAChB,CAAC;AArBD,kCAqBC"}
+{"version":3,"file":"applyWindow.js","sourceRoot":"","sources":["../../src/apodization/applyWindow.ts"],"names":[],"mappings":";;;AA0BA;;GAEG;AACH,SAAgB,WAAW,CAAC,IAAiB,EAAE,OAA2B;IACxE,MAAM,UAAU,GAAG,IAAI,CAAC,MAAM,CAAC;IAE/B,MAAM,EACJ,UAAU,EACV,KAAK,GAAG,CAAC,EACT,MAAM,GAAG,UAAU,EACnB,aAAa,GAAG,CAAC,EACjB,MAAM,GAAG,IAAI,YAAY,CAAC,IAAI,CAAC,GAChC,GAAG,OAAO,CAAC;IAEZ,MAAM,aAAa,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,MAAM,EAAE,UAAU,GAAG,aAAa,CAAC,CAAC;IAC3E,KAAK,IAAI,CAAC,GAAG,KAAK,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,aAAa,EAAE,CAAC,EAAE,EAAE;QACjD,MAAM,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC,CAAC,EAAE,CAAC,CAAC;KAC9B;IACD,KAAK,IAAI,CAAC,GAAG,UAAU,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,GAAG,aAAa,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;QAC3E,MAAM,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC,CAAC,EAAE,CAAC,CAAC;KAC9B;IAED,OAAO,MAAM,CAAC;AAChB,CAAC;AApBD,kCAoBC"}

package/lib/apodization/compose.js.map

@@ -1 +1 @@
-{"version":3,"file":"compose.js","sourceRoot":"","sources":["../../src/apodization/compose.ts"],"names":[],"mappings":";;;AAAA,+CAA4C;AAC5C,+CAA4C;AAE5C,6CAA0C;AAyB1C,SAAgB,OAAO,CAAC,YAA0B;IAChD,MAAM,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,GAAG,EAAE,EAAE,GAAG,YAAY,CAAC;IACzD,IAAI,IAAI,GAAG,IAAI,YAAY,CAAC,UAAU,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAChD,MAAM,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,EAAE;QACzB,MAAM,EAAE,KAAK,EAAE,KAAK,GAAG,CAAC,EAAE,GAAG,OAAO,CAAC;QACrC,MAAM,EAAE,OAAO,EAAE,YAAY,EAAE,GAAG,KAAK,CAAC;QACxC,MAAM,MAAM,GACV,QAAQ,IAAI,YAAY,CAAC,CAAC,CAAC,YAAY,CAAC,MAAM,CAAC,CAAC,CAAC,UAAU,GAAG,KAAK,CAAC;QAEtE,MAAM,UAAU,GAAG,IAAA,iBAAO,EAAC,IAAA,yBAAW,EAAC,KAAK,CAAC,EAAE,MAAM,CAAC,CAAC;QACvD,IAAA,yBAAW,EAAC,IAAI,EAAE;YAChB,UAAU;YACV,MAAM;YACN,KAAK;YACL,MAAM,EAAE,IAAI;SACb,CAAC,CAAC;IACL,CAAC,CAAC,CAAC;IACH,OAAO,IAAI,CAAC;AACd,CAAC;AAlBD,0BAkBC"}
+{"version":3,"file":"compose.js","sourceRoot":"","sources":["../../src/apodization/compose.ts"],"names":[],"mappings":";;;AAAA,+CAA4C;AAC5C,+CAA4C;AAE5C,6CAA0C;AAyB1C,SAAgB,OAAO,CAAC,YAA0B;IAChD,MAAM,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,GAAG,EAAE,EAAE,GAAG,YAAY,CAAC;IACzD,IAAI,IAAI,GAAG,IAAI,YAAY,CAAC,UAAU,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAChD,MAAM,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,EAAE;QACzB,MAAM,EAAE,KAAK,EAAE,KAAK,GAAG,CAAC,EAAE,GAAG,OAAO,CAAC;QACrC,MAAM,EAAE,OAAO,EAAE,YAAY,EAAE,GAAG,KAAK,CAAC;QACxC,MAAM,MAAM,GACV,QAAQ,IAAI,YAAY,CAAC,CAAC,CAAC,YAAY,CAAC,MAAM,CAAC,CAAC,CAAC,UAAU,GAAG,KAAK,CAAC;QAEtE,MAAM,UAAU,GAAG,IAAA,iBAAO,EAAC,IAAA,yBAAW,EAAC,KAAK,CAAC,EAAE,MAAM,CAAC,CAAC;QAEvD,IAAA,yBAAW,EAAC,IAAI,EAAE;YAChB,UAAU;YACV,MAAM;YACN,KAAK;YACL,MAAM,EAAE,IAAI;SACb,CAAC,CAAC;IACL,CAAC,CAAC,CAAC;IACH,OAAO,IAAI,CAAC;AACd,CAAC;AAnBD,0BAmBC"}

package/lib/apodization/getFunction.js

@@ -3,6 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.getFunction = void 0;
 const exponential_1 = require("./shapes/exponential");
 const lorentzToGauss_1 = require("./shapes/lorentzToGauss");
+const sineBell_1 = require("./shapes/sineBell");
 function getFunction(shape) {
     const { kind, options } = shape;
     switch (kind) {
@@ -10,6 +11,8 @@ function getFunction(shape) {
             return (0, exponential_1.exponential)(options);
         case 'lorentzToGauss':
             return (0, lorentzToGauss_1.lorentzToGauss)(options);
+        case 'sineBell':
+            return (0, sineBell_1.sineBell)(options);
         default:
             throw Error(`Unknown distribution ${kind}`);
     }

package/lib/apodization/getFunction.js.map

@@ -1 +1 @@
-{"version":3,"file":"getFunction.js","sourceRoot":"","sources":["../../src/apodization/getFunction.ts"],"names":[],"mappings":";;;AACA,sDAAmD;AACnD,4DAAyD;AAEzD,SAAgB,WAAW,CAAC,KAAsB;IAChD,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,KAAK,CAAC;IAChC,QAAQ,IAAI,EAAE;QACZ,KAAK,aAAa;YAChB,OAAO,IAAA,yBAAW,EAAC,OAAO,CAAC,CAAC;QAC9B,KAAK,gBAAgB;YACnB,OAAO,IAAA,+BAAc,EAAC,OAAO,CAAC,CAAC;QACjC;YACE,MAAM,KAAK,CAAC,wBAAwB,IAAc,EAAE,CAAC,CAAC;KACzD;AACH,CAAC;AAVD,kCAUC"}
+{"version":3,"file":"getFunction.js","sourceRoot":"","sources":["../../src/apodization/getFunction.ts"],"names":[],"mappings":";;;AACA,sDAAmD;AACnD,4DAAyD;AACzD,gDAA6C;AAE7C,SAAgB,WAAW,CAAC,KAAsB;IAChD,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,KAAK,CAAC;IAChC,QAAQ,IAAI,EAAE;QACZ,KAAK,aAAa;YAChB,OAAO,IAAA,yBAAW,EAAC,OAAO,CAAC,CAAC;QAC9B,KAAK,gBAAgB;YACnB,OAAO,IAAA,+BAAc,EAAC,OAAO,CAAC,CAAC;QACjC,KAAK,UAAU;YACb,OAAO,IAAA,mBAAQ,EAAC,OAAO,CAAC,CAAC;QAC3B;YACE,MAAM,KAAK,CAAC,wBAAwB,IAAc,EAAE,CAAC,CAAC;KACzD;AACH,CAAC;AAZD,kCAYC"}

package/lib/apodization/shapes/WindowFunctions.d.ts

@@ -1,5 +1,6 @@
 import type { ExponentialOptions } from './exponential';
 import type { LorentzToGaussOptions } from './lorentzToGauss';
+import { SineBellOptions } from './sineBell';
 interface Exponential {
     kind: 'exponential';
     options: ExponentialOptions;
@@ -8,5 +9,9 @@ interface LorentToGauss {
     kind: 'lorentzToGauss';
     options: LorentzToGaussOptions;
 }
-export type WindowFunctions = Exponential | LorentToGauss;
+interface SineBell {
+    kind: 'sineBell';
+    options: SineBellOptions;
+}
+export type WindowFunctions = Exponential | LorentToGauss | SineBell;
 export {};

package/lib/apodization/shapes/sineBell.d.ts

@@ -0,0 +1,27 @@
+export interface SineBellOptions {
+    /**
+     * Specifies the exponent of the sine-bell; Non-integer values are allowed.
+     * Common values are 1.0 (for ordinary sine-bell) and 2.0 (for squared-bell functions).
+     * @default 1
+     */
+    exponent?: number;
+    /**
+     * Specifies the starting point of the sine-bell in units of pi radians.
+     * Common values are 0.0 (for a sine window which starts height at 0.0) and
+     * 0.5 (for a cosine window, which starts at height 1.0).
+     * @default 0
+     */
+    offset?: number;
+    /**
+     * Specifies the ending point of the sine-bell in units of pi radians.
+     * Common values are 1.0 (for a window which goes to 0.0 height at the last point) and
+     * 0.95 (for a window which doesn't go all the way to 0.0).
+     * @default 1
+     */
+    end?: number;
+    /**
+     * Specifies the number of points in the window function.
+     */
+    length: number;
+}
+export declare function sineBell(options: SineBellOptions): (i: number) => number;

package/lib/apodization/shapes/sineBell.js

@@ -0,0 +1,17 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.sineBell = void 0;
+function sineBell(options) {
+    const { exponent = 1, offset = 0, end = 1, length } = options;
+    if (length === undefined) {
+        throw new Error('length options should exists for sineBell shape');
+    }
+    if (end < 0 || end > 1) {
+        throw new Error(`the end parameter should be [0-1]`);
+    }
+    const c1 = Math.PI * offset;
+    const c2 = (Math.PI * (end - offset)) / (length - 1);
+    return (i) => Math.pow(Math.sin(c1 + c2 * i), exponent);
+}
+exports.sineBell = sineBell;
+//# sourceMappingURL=sineBell.js.map

package/lib/apodization/shapes/sineBell.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"sineBell.js","sourceRoot":"","sources":["../../../src/apodization/shapes/sineBell.ts"],"names":[],"mappings":";;;AA2BA,SAAgB,QAAQ,CAAC,OAAwB;IAC/C,MAAM,EAAE,QAAQ,GAAG,CAAC,EAAE,MAAM,GAAG,CAAC,EAAE,GAAG,GAAG,CAAC,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC;IAE9D,IAAI,MAAM,KAAK,SAAS,EAAE;QACxB,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAC;KACpE;IAED,IAAI,GAAG,GAAG,CAAC,IAAI,GAAG,GAAG,CAAC,EAAE;QACtB,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAC;KACtD;IACD,MAAM,EAAE,GAAG,IAAI,CAAC,EAAE,GAAG,MAAM,CAAC;IAC5B,MAAM,EAAE,GAAG,CAAC,IAAI,CAAC,EAAE,GAAG,CAAC,GAAG,GAAG,MAAM,CAAC,CAAC,GAAG,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;IACrD,OAAO,CAAC,CAAS,EAAE,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAC;AAClE,CAAC;AAbD,4BAaC"}

package/lib/apodization/utils/getData.js.map

@@ -1 +1 @@
-{"version":3,"file":"getData.js","sourceRoot":"","sources":["../../../src/apodization/utils/getData.ts"],"names":[],"mappings":";;;AAAA;;GAEG;AACH,SAAgB,OAAO,CAAC,IAA2B,EAAE,MAAc;IACjE,MAAM,IAAI,GAAG,IAAI,YAAY,CAAC,MAAM,CAAC,CAAC;IACtC,IAAI,GAAG,GAAG,MAAM,CAAC,gBAAgB,CAAC;IAClC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE;QAC/B,MAAM,KAAK,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;QACtB,IAAI,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC;QAChB,IAAI,KAAK,GAAG,GAAG;YAAE,GAAG,GAAG,KAAK,CAAC;KAC9B;IAED,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE;QAAE,IAAI,CAAC,CAAC,CAAC,IAAI,GAAG,CAAC;IAChD,OAAO,IAAI,CAAC;AACd,CAAC;AAXD,0BAWC"}
+{"version":3,"file":"getData.js","sourceRoot":"","sources":["../../../src/apodization/utils/getData.ts"],"names":[],"mappings":";;;AAAA;;GAEG;AACH,SAAgB,OAAO,CAAC,IAA2B,EAAE,MAAc;IACjE,MAAM,IAAI,GAAG,IAAI,YAAY,CAAC,MAAM,CAAC,CAAC;IACtC,IAAI,GAAG,GAAG,MAAM,CAAC,gBAAgB,CAAC;IAClC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE;QAC/B,MAAM,KAAK,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;QACtB,IAAI,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC;QAChB,IAAI,KAAK,GAAG,GAAG;YAAE,GAAG,GAAG,KAAK,CAAC;KAC9B;IACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE;QAAE,IAAI,CAAC,CAAC,CAAC,IAAI,GAAG,CAAC;IAChD,OAAO,IAAI,CAAC;AACd,CAAC;AAVD,0BAUC"}

package/lib/assignment/utils/buildAssignments.js

@@ -13,8 +13,6 @@ const comparator = (a, b) => {
 async function buildAssignments(props) {
     const { restrictionByCS = {}, useIntegrationRestriction, timeout, minScore, nbAllowedUnAssigned, maxSolutions, targets, joinedSignals, } = props;
     const { tolerance = 1, useChemicalShiftScore = false, chemicalShiftRestriction = true, } = restrictionByCS;
-    let date = new Date();
-    let timeStart = date.getTime();
     let store = {
         solutions: new ml_tree_set_1.default(comparator),
         nSolutions: 0,
@@ -46,6 +44,7 @@ async function buildAssignments(props) {
         solutions: new ml_tree_set_1.default(comparator),
         nSolutions: 0,
     };
+    const timeStart = Date.now();
     (0, exploreTreeRec_1.exploreTreeRec)({
         nSources,
         restrictionByCS: {

package/lib/assignment/utils/buildAssignments.js.map

@@ -1 +1 @@
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package/lib/assignment/utils/exploreTreeRec.js

@@ -4,8 +4,7 @@ exports.exploreTreeRec = void 0;
 const partialScore_1 = require("./partialScore");
 function exploreTreeRec(props, currentIndex, partial, store) {
     const { nSources, restrictionByCS, timeout, timeStart, maxSolutions, targets, predictions, lowerBoundScore, nbAllowedUnAssigned, possibleAssignmentMap, useIntegrationRestriction, diaIDPeerPossibleAssignment, } = props;
-    const currentDate = new Date();
-    if (currentDate.getTime() - timeStart > timeout) {
+    if (Date.now() - timeStart > timeout) {
         new Error('timeout expired');
         return store;
     }

package/lib/assignment/utils/exploreTreeRec.js.map

@@ -1 +1 @@
-{"version":3,"file":"exploreTreeRec.js","sourceRoot":"","sources":["../../../src/assignment/utils/exploreTreeRec.ts"],"names":[],"mappings":";;;AAQA,iDAA8C;AAgB9C,SAAgB,cAAc,CAC5B,KAA0B,EAC1B,YAAoB,EACpB,OAA6B,EAC7B,KAAuB;IAEvB,MAAM,EACJ,QAAQ,EACR,eAAe,EACf,OAAO,EACP,SAAS,EACT,YAAY,EACZ,OAAO,EACP,WAAW,EACX,eAAe,EACf,mBAAmB,EACnB,qBAAqB,EACrB,yBAAyB,EACzB,2BAA2B,GAC5B,GAAG,KAAK,CAAC;IAEV,MAAM,WAAW,GAAG,IAAI,IAAI,EAAE,CAAC;IAC/B,IAAI,WAAW,CAAC,OAAO,EAAE,GAAG,SAAS,GAAG,OAAO,EAAE;QAC/C,IAAI,KAAK,CAAC,iBAAiB,CAAC,CAAC;QAC7B,OAAO,KAAK,CAAC;KACd;IAED,MAAM,KAAK,GAAG,2BAA2B,CAAC,YAAY,CAAC,CAAC;IACxD,MAAM,mBAAmB,GAAG,qBAAqB,CAAC,KAAK,CAAC,CAAC;IACzD,KAAK,IAAI,QAAQ,IAAI,mBAAmB,EAAE;QACxC,OAAO,CAAC,YAAY,CAAC,GAAG,QAAQ,CAAC;QACjC,IAAI,KAAK,GAAG,IAAA,2BAAY,EAAC,OAAO,EAAE;YAChC,yBAAyB;YACzB,2BAA2B;YAC3B,mBAAmB;YACnB,eAAe;YACf,WAAW;YACX,OAAO;SACR,CAAC,CAAC;QAEH,IAAI,KAAK,KAAK,CAAC,EAAE;YACf,IAAI,QAAQ,KAAK,GAAG,EAAE;gBACpB,OAAO,CAAC,YAAY,CAAC,GAAG,IAAI,CAAC;aAC9B;YACD,SAAS;SACV;QAED,IAAI,YAAY,KAAK,QAAQ,GAAG,CAAC,IAAI,KAAK,IAAI,eAAe,EAAE;YAC7D,WAAW,CAAC,KAAK,EAAE,EAAE,WAAW,EAAE,OAAO,EAAE,KAAK,EAAE,YAAY,EAAE,CAAC,CAAC;SACnE;aAAM,IAAI,YAAY,GAAG,QAAQ,GAAG,CAAC,EAAE;YACtC,cAAc,CACZ;gBACE,QAAQ;gBACR,eAAe;gBACf,OAAO;gBACP,SAAS;gBACT,YAAY;gBACZ,OAAO;gBACP,WAAW;gBACX,eAAe;gBACf,mBAAmB;gBACnB,qBAAqB;gBACrB,yBAAyB;gBACzB,2BAA2B;aAC5B,EACD,YAAY,GAAG,CAAC,EAChB,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,CAAC,EACnC,KAAK,CACN,CAAC;SACH;KACF;AACH,CAAC;AAvED,wCAuEC;AAcD,SAAS,WAAW,CAAC,KAAuB,EAAE,KAAuB;IACnE,IAAI,EAAE,KAAK,EAAE,YAAY,EAAE,OAAO,EAAE,WAAW,EAAE,GAAG,KAAK,CAAC;IAC1D,KAAK,IAAI,uBAAuB,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC;IACvD,KAAK,CAAC,UAAU,EAAE,CAAC;IACnB,IAAI,QAAQ,GAAuB;QACjC,UAAU,EAAE,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,CAAC;QAC/C,KAAK;KACN,CAAC;IAEF,IAAI,KAAK,CAAC,UAAU,IAAI,YAAY,EAAE;QACpC,IAAI,QAAQ,CAAC,KAAK,GAAG,KAAK,CAAC,SAAS,CAAC,IAAI,EAAE,CAAC,KAAK,EAAE;YACjD,KAAK,CAAC,SAAS,CAAC,QAAQ,EAAE,CAAC;YAC3B,KAAK,CAAC,SAAS,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC;SAC/B;KACF;SAAM;QACL,KAAK,CAAC,SAAS,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC;QAC9B,KAAK,CAAC,UAAU,EAAE,CAAC;KACpB;AACH,CAAC;AAED,SAAS,uBAAuB,CAC9B,OAA6B,EAC7B,WAAqC;IAErC,MAAM,SAAS,GAAG,MAAM,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,MAAM,CAAC;IAClD,IAAI,WAAW,GAAG,IAAI,GAAG,CAAC,OAAO,CAAC,CAAC;IACnC,IAAI,kBAAkB,GAAG,SAAS,GAAG,WAAW,CAAC,IAAI,CAAC;IACtD,OAAO,kBAAkB,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,kBAAkB,CAAC,CAAC,CAAC,CAAC,CAAC;AAC7D,CAAC"}
+{"version":3,"file":"exploreTreeRec.js","sourceRoot":"","sources":["../../../src/assignment/utils/exploreTreeRec.ts"],"names":[],"mappings":";;;AAQA,iDAA8C;AAgB9C,SAAgB,cAAc,CAC5B,KAA0B,EAC1B,YAAoB,EACpB,OAA6B,EAC7B,KAAuB;IAEvB,MAAM,EACJ,QAAQ,EACR,eAAe,EACf,OAAO,EACP,SAAS,EACT,YAAY,EACZ,OAAO,EACP,WAAW,EACX,eAAe,EACf,mBAAmB,EACnB,qBAAqB,EACrB,yBAAyB,EACzB,2BAA2B,GAC5B,GAAG,KAAK,CAAC;IAEV,IAAI,IAAI,CAAC,GAAG,EAAE,GAAG,SAAS,GAAG,OAAO,EAAE;QACpC,IAAI,KAAK,CAAC,iBAAiB,CAAC,CAAC;QAC7B,OAAO,KAAK,CAAC;KACd;IAED,MAAM,KAAK,GAAG,2BAA2B,CAAC,YAAY,CAAC,CAAC;IACxD,MAAM,mBAAmB,GAAG,qBAAqB,CAAC,KAAK,CAAC,CAAC;IACzD,KAAK,IAAI,QAAQ,IAAI,mBAAmB,EAAE;QACxC,OAAO,CAAC,YAAY,CAAC,GAAG,QAAQ,CAAC;QACjC,IAAI,KAAK,GAAG,IAAA,2BAAY,EAAC,OAAO,EAAE;YAChC,yBAAyB;YACzB,2BAA2B;YAC3B,mBAAmB;YACnB,eAAe;YACf,WAAW;YACX,OAAO;SACR,CAAC,CAAC;QAEH,IAAI,KAAK,KAAK,CAAC,EAAE;YACf,IAAI,QAAQ,KAAK,GAAG,EAAE;gBACpB,OAAO,CAAC,YAAY,CAAC,GAAG,IAAI,CAAC;aAC9B;YACD,SAAS;SACV;QAED,IAAI,YAAY,KAAK,QAAQ,GAAG,CAAC,IAAI,KAAK,IAAI,eAAe,EAAE;YAC7D,WAAW,CAAC,KAAK,EAAE,EAAE,WAAW,EAAE,OAAO,EAAE,KAAK,EAAE,YAAY,EAAE,CAAC,CAAC;SACnE;aAAM,IAAI,YAAY,GAAG,QAAQ,GAAG,CAAC,EAAE;YACtC,cAAc,CACZ;gBACE,QAAQ;gBACR,eAAe;gBACf,OAAO;gBACP,SAAS;gBACT,YAAY;gBACZ,OAAO;gBACP,WAAW;gBACX,eAAe;gBACf,mBAAmB;gBACnB,qBAAqB;gBACrB,yBAAyB;gBACzB,2BAA2B;aAC5B,EACD,YAAY,GAAG,CAAC,EAChB,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,CAAC,EACnC,KAAK,CACN,CAAC;SACH;KACF;AACH,CAAC;AAtED,wCAsEC;AAcD,SAAS,WAAW,CAAC,KAAuB,EAAE,KAAuB;IACnE,IAAI,EAAE,KAAK,EAAE,YAAY,EAAE,OAAO,EAAE,WAAW,EAAE,GAAG,KAAK,CAAC;IAC1D,KAAK,IAAI,uBAAuB,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC;IACvD,KAAK,CAAC,UAAU,EAAE,CAAC;IACnB,IAAI,QAAQ,GAAuB;QACjC,UAAU,EAAE,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,CAAC;QAC/C,KAAK;KACN,CAAC;IAEF,IAAI,KAAK,CAAC,UAAU,IAAI,YAAY,EAAE;QACpC,IAAI,QAAQ,CAAC,KAAK,GAAG,KAAK,CAAC,SAAS,CAAC,IAAI,EAAE,CAAC,KAAK,EAAE;YACjD,KAAK,CAAC,SAAS,CAAC,QAAQ,EAAE,CAAC;YAC3B,KAAK,CAAC,SAAS,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC;SAC/B;KACF;SAAM;QACL,KAAK,CAAC,SAAS,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC;QAC9B,KAAK,CAAC,UAAU,EAAE,CAAC;KACpB;AACH,CAAC;AAED,SAAS,uBAAuB,CAC9B,OAA6B,EAC7B,WAAqC;IAErC,MAAM,SAAS,GAAG,MAAM,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,MAAM,CAAC;IAClD,IAAI,WAAW,GAAG,IAAI,GAAG,CAAC,OAAO,CAAC,CAAC;IACnC,IAAI,kBAAkB,GAAG,SAAS,GAAG,WAAW,CAAC,IAAI,CAAC;IACtD,OAAO,kBAAkB,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,kBAAkB,CAAC,CAAC,CAAC,CAAC,CAAC;AAC7D,CAAC"}

package/lib/assignment/utils/getAssignment/buildAssignments.js

@@ -35,8 +35,6 @@ exports.getAllHydrogens = {
 };
 async function buildAssignments(props) {
     const { spectra, molecule, restrictionByCS, timeout, minScore, nbAllowedUnAssigned = {}, maxSolutions, correlations, assignmentOrder, predictionOptions, predictions: inputPrediction = {}, targets, } = props;
-    let date = new Date();
-    let timeStart = date.getTime();
     let lowerBoundScore = minScore;
     let store = {
         solutions: new ml_tree_set_1.default(comparator),
@@ -96,6 +94,7 @@ async function buildAssignments(props) {
             solutions: new ml_tree_set_1.default(comparator),
             nSolutions: 0,
         };
+        const timeStart = Date.now();
         for (let partial of sourceOfPartials) {
             (0, exploreTree_1.exploreTree)({
                 currentAtomTypes: atomTypesToPredict,

package/lib/assignment/utils/getAssignment/buildAssignments.js.map

@@ -1 +1 @@
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package/lib/assignment/utils/getAssignment/exploreTree.js

@@ -4,8 +4,7 @@ exports.exploreTree = void 0;
 const partialScore_1 = require("./partialScore");
 function exploreTree(props, infoByAtomTypes, partial, store) {
     const { currentAtomTypes, restrictionByCS, timeout, timeStart, maxSolutions, targets, predictions, correlations, lowerBoundScore, possibleAssignmentMap, diaIDPeerPossibleAssignment, } = props;
-    const currentDate = new Date();
-    if (currentDate.getTime() - timeStart > timeout) {
+    if (Date.now() - timeStart > timeout) {
         new Error('timeout expired');
         return store;
     }

package/lib/assignment/utils/getAssignment/exploreTree.js.map

@@ -1 +1 @@
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package/lib/signals/signalsToFID.d.ts

@@ -39,4 +39,7 @@ export interface SignalsToFIDOptions {
 export declare function signalsToFID(signals: NMRSignal1D[], options: SignalsToFIDOptions): {
     re: import("cheminfo-types").DoubleArray;
     im: import("cheminfo-types").DoubleArray;
+} | {
+    re: import("cheminfo-types").DoubleArray;
+    im: import("cheminfo-types").DoubleArray;
 };

package/lib/utilities/checkData2DFid.d.ts

@@ -0,0 +1,3 @@
+import { Data2D, Data2DFid } from '../xyz/Data2D';
+export type Data2DFidComplete = Required<Data2DFid>;
+export declare function checkData2DFid(data: Data2D): asserts data is Data2DFidComplete;

package/lib/utilities/checkData2DFid.js

@@ -0,0 +1,10 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.checkData2DFid = void 0;
+function checkData2DFid(data) {
+    if (!('re' in data && 'im' in data)) {
+        throw new Error('imaginary (im) data should exists');
+    }
+}
+exports.checkData2DFid = checkData2DFid;
+//# sourceMappingURL=checkData2DFid.js.map

package/lib/utilities/checkData2DFid.js.map

@@ -0,0 +1 @@
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package/lib/xyz/Data2D.d.ts

@@ -0,0 +1,21 @@
+import { DoubleArray } from 'cheminfo-types';
+export interface MinMaxContent {
+    z: DoubleArray[];
+    minX: number;
+    minY: number;
+    minZ: number;
+    maxX: number;
+    maxY: number;
+    maxZ: number;
+}
+export type Data2D = Data2DFid | Data2DFt;
+export interface Data2DFid {
+    re: MinMaxContent;
+    im?: MinMaxContent;
+}
+export interface Data2DFt {
+    rr: MinMaxContent;
+    ri?: MinMaxContent;
+    ir?: MinMaxContent;
+    ii?: MinMaxContent;
+}

package/lib/xyz/Data2D.js

@@ -0,0 +1,3 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+//# sourceMappingURL=Data2D.js.map

package/lib/xyz/Data2D.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"Data2D.js","sourceRoot":"","sources":["../../src/xyz/Data2D.ts"],"names":[],"mappings":""}

package/lib/xyz/quadrature.d.ts

@@ -0,0 +1,8 @@
+import { DoubleArray } from 'cheminfo-types';
+import { Data2D } from './Data2D';
+export declare function quadrature(data: Data2D, options: {
+    fnMode: string;
+}): {
+    re: DoubleArray[];
+    im: DoubleArray[];
+};

package/lib/xyz/quadrature.js

@@ -0,0 +1,54 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.quadrature = void 0;
+const ml_spectra_processing_1 = require("ml-spectra-processing");
+const checkData2DFid_1 = require("../utilities/checkData2DFid");
+function quadrature(data, options) {
+    (0, checkData2DFid_1.checkData2DFid)(data);
+    const { fnMode } = options;
+    switch (fnMode) {
+        case 'ttpi':
+            return ttpiQuadrature(data);
+        case 'states':
+            return shrQuadrature(data);
+        case 'echo':
+            return echoQuadrature(data);
+        default:
+            return {
+                re: data.re.z,
+                im: data.im.z,
+            };
+    }
+}
+exports.quadrature = quadrature;
+function echoQuadrature(data) {
+    const { re: { z: reMatrix }, im: { z: imMatrix }, } = data;
+    const newRe = [];
+    const newIm = [];
+    for (let i = 0; i < reMatrix.length; i += 2) {
+        let reCosine = reMatrix[i];
+        let imCosine = imMatrix[i];
+        let reSine = reMatrix[i + 1];
+        let imSine = imMatrix[i + 1];
+        newRe.push((0, ml_spectra_processing_1.xSubtract)((0, ml_spectra_processing_1.xMultiply)(imSine, -1), imCosine));
+        newRe.push((0, ml_spectra_processing_1.xSubtract)(reSine, reCosine));
+        newIm.push((0, ml_spectra_processing_1.xAdd)(reSine, reCosine));
+        newIm.push((0, ml_spectra_processing_1.xSubtract)(imSine, imCosine));
+    }
+    return { re: newRe, im: newIm };
+}
+function shrQuadrature(data) {
+    const { re, im } = data;
+    return { re: re.z, im: im.z };
+}
+function ttpiQuadrature(data) {
+    const newRe = [];
+    const newIm = [];
+    const { re: { z: reMatrix }, im: { z: imMatrix }, } = data;
+    for (let i = 0; i < reMatrix.length; i++) {
+        newRe.push(i % 2 ? reMatrix[i].slice() : (0, ml_spectra_processing_1.xMultiply)(reMatrix[i], -1));
+        newIm.push(i % 2 ? imMatrix[i].slice() : (0, ml_spectra_processing_1.xMultiply)(imMatrix[i], -1));
+    }
+    return { re: newRe, im: newIm };
+}
+//# sourceMappingURL=quadrature.js.map

package/lib/xyz/quadrature.js.map

@@ -0,0 +1 @@
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package/lib/xyz/util/fft2d/digitalFilter.d.ts

@@ -0,0 +1,7 @@
+import { DataReIm } from 'ml-spectra-processing';
+export declare function digitalFilter(data: DataReIm, options: {
+    digitalFilterValue: number;
+}): {
+    re: Float64Array;
+    im: Float64Array;
+};

package/lib/xyz/util/fft2d/digitalFilter.js

@@ -0,0 +1,20 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.digitalFilter = void 0;
+function digitalFilter(data, options) {
+    let { digitalFilterValue = 0 } = options;
+    let re = new Float64Array(data.re);
+    let im = new Float64Array(data.im);
+    let pointsToShift = Math.floor(digitalFilterValue);
+    const skip = 0;
+    pointsToShift += 0;
+    const newRe = new Float64Array(re.length);
+    const newIm = new Float64Array(im.length);
+    newRe.set(re.slice(pointsToShift));
+    newRe.set(re.slice(skip, pointsToShift), re.length - pointsToShift);
+    newIm.set(im.slice(pointsToShift));
+    newIm.set(im.slice(skip, pointsToShift), im.length - pointsToShift);
+    return { re: newRe, im: newIm };
+}
+exports.digitalFilter = digitalFilter;
+//# sourceMappingURL=digitalFilter.js.map

package/lib/xyz/util/fft2d/digitalFilter.js.map

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package/lib/xyz/util/fft2d/fftDirectDimension.d.ts

@@ -0,0 +1,24 @@
+import { DoubleArray } from 'cheminfo-types';
+import Matrix from 'ml-matrix';
+import { ApodizationOptions } from '../../../apodization/apodization';
+import { ZeroFillingOptions } from './zeroFilling';
+interface PhaseCorrection {
+    mode?: string;
+    ph0?: number;
+    ph1?: number;
+}
+export interface DirectDimensionOptions {
+    fnMode?: string;
+    digitalFilterValue?: number;
+    zeroFilling?: ZeroFillingOptions;
+    apodization?: ApodizationOptions;
+    phaseCorrection?: PhaseCorrection;
+}
+export declare function fftDirectDimension(data: {
+    re: DoubleArray[];
+    im: DoubleArray[];
+}, options: DirectDimensionOptions): {
+    re: Matrix;
+    im: Matrix;
+};
+export {};

package/lib/xyz/util/fft2d/fftDirectDimension.js

@@ -0,0 +1,57 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.fftDirectDimension = void 0;
+const ml_matrix_1 = __importDefault(require("ml-matrix"));
+const ml_spectra_processing_1 = require("ml-spectra-processing");
+const apodization_1 = require("../../../apodization/apodization");
+const digitalFilter_1 = require("./digitalFilter");
+const removeDCOffset_1 = require("./removeDCOffset");
+const zeroFilling_1 = require("./zeroFilling");
+function fftDirectDimension(data, options) {
+    const { re: reData, im: imData } = data;
+    const nbRows = reData.length;
+    const nbColumns = reData[0].length;
+    const { zeroFilling: zeroFillingF2, digitalFilterValue = 0 } = options;
+    const { factor: f2Factor = 2 } = zeroFillingF2 || {};
+    const nbPointsF2 = (zeroFillingF2 === null || zeroFillingF2 === void 0 ? void 0 : zeroFillingF2.nbPoints) || 2 ** Math.round(Math.log2(nbColumns * f2Factor));
+    const reFFT = new ml_matrix_1.default(nbRows, nbPointsF2);
+    const imFFT = new ml_matrix_1.default(nbRows, nbPointsF2);
+    const { apodization: apodizationF2 } = options;
+    let { ph0: ph0F2, ph1: ph1F2, mode: pcModeF2 = 'no', } = (options === null || options === void 0 ? void 0 : options.phaseCorrection) || {};
+    for (let i = 0; i < nbRows; i++) {
+        const newData = (0, digitalFilter_1.digitalFilter)({ re: reData[i], im: imData[i] }, { digitalFilterValue });
+        Object.assign(newData, (0, removeDCOffset_1.removeDCOffset)(newData, { digitalFilterValue }));
+        if (apodizationF2) {
+            const { re: aRe, im: aIm } = (0, apodization_1.apodization)(newData, apodizationF2);
+            Object.assign(newData, { re: aRe, im: aIm });
+        }
+        Object.assign(newData, (0, zeroFilling_1.zeroFilling)(newData, { digitalFilterValue, nbPoints: nbPointsF2 }));
+        Object.assign(newData, (0, ml_spectra_processing_1.reimFFT)(newData, { applyZeroShift: true }));
+        const dfResidual = (digitalFilterValue - Math.round(digitalFilterValue)) * Math.PI * 2;
+        if (dfResidual > 0) {
+            Object.assign(newData, (0, ml_spectra_processing_1.reimPhaseCorrection)(newData, 0, -dfResidual));
+        }
+        if (i === 0 &&
+            pcModeF2 === 'pk' &&
+            ph0F2 === undefined &&
+            ph1F2 === undefined) {
+            const phased = (0, ml_spectra_processing_1.reimAutoPhaseCorrection)(newData, { magnitudeMode: false });
+            ph0F2 = phased.ph0;
+            ph1F2 = phased.ph1;
+        }
+        if (pcModeF2 === 'pk' && ph0F2 !== undefined && ph1F2 !== undefined) {
+            Object.assign(newData, (0, ml_spectra_processing_1.reimPhaseCorrection)(newData, (ph0F2 * Math.PI) / 180, (ph1F2 * Math.PI) / 180));
+        }
+        reFFT.setRow(i, newData.re);
+        imFFT.setRow(i, newData.im);
+    }
+    return {
+        re: reFFT,
+        im: imFFT,
+    };
+}
+exports.fftDirectDimension = fftDirectDimension;
+//# sourceMappingURL=fftDirectDimension.js.map

package/lib/xyz/util/fft2d/fftDirectDimension.js.map

@@ -0,0 +1 @@
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package/lib/xyz/util/fft2d/fftIndirectDimension.d.ts

@@ -0,0 +1,23 @@
+import { DoubleArray } from 'cheminfo-types';
+import Matrix from 'ml-matrix';
+import { ApodizationOptions } from '../../../apodization/apodization';
+import { ZeroFillingOptions } from './zeroFilling';
+interface PhaseCorrection {
+    mode?: string;
+    ph0?: number;
+    ph1?: number;
+}
+export interface IndirectDimensionOptions {
+    fnMode?: string;
+    zeroFilling?: ZeroFillingOptions;
+    apodization?: ApodizationOptions;
+    phaseCorrection?: PhaseCorrection;
+}
+export declare function fftIndirectDimension(data: {
+    re: DoubleArray[] | Matrix;
+    im: DoubleArray[] | Matrix;
+}, options: IndirectDimensionOptions): {
+    re: Matrix;
+    im: Matrix;
+};
+export {};