nmr-processing 9.1.0-pre.1663857509 → 9.2.0-pre.1668170175

package/lib/index.d.ts

@@ -20,6 +20,7 @@ export * from './signals/signalsToRanges';
 export * from './signals/signalsToXY';
 export * from './signals/signals2DToZ';
 export * from './signals/optimizeSignals';
+export * from './signals/signalsToFID';
 export * from './utilities/resurrect';
 export * from './utilities/rangeFromSignal';
 export * from './utilities/getFrequency';

package/lib/index.js

@@ -36,6 +36,7 @@ __exportStar(require("./signals/signalsToRanges"), exports);
 __exportStar(require("./signals/signalsToXY"), exports);
 __exportStar(require("./signals/signals2DToZ"), exports);
 __exportStar(require("./signals/optimizeSignals"), exports);
+__exportStar(require("./signals/signalsToFID"), exports);
 __exportStar(require("./utilities/resurrect"), exports);
 __exportStar(require("./utilities/rangeFromSignal"), exports);
 __exportStar(require("./utilities/getFrequency"), exports);

package/lib/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;AAAA,qDAAmC;AACnC,yDAAuC;AACvC,+DAA6C;AAE7C,gEAA8C;AAC9C,oDAAkC;AAClC,mDAAiC;AAEjC,6DAA2C;AAC3C,6DAA2C;AAC3C,2DAAyC;AACzC,2DAAyC;AACzC,2DAAyC;AACzC,0DAAwC;AACxC,iEAA+C;AAE/C,gEAA8C;AAC9C,iEAA+C;AAC/C,8DAA4C;AAE5C,uDAAqC;AACrC,sDAAoC;AAEpC,4DAA0C;AAC1C,wDAAsC;AACtC,yDAAuC;AACvC,4DAA0C;AAC1C,yDAAuC;AAEvC,wDAAsC;AACtC,8DAA4C;AAC5C,2DAAyC;AAEzC,0DAAwC;AACxC,2DAAyC;AACzC,2DAAyC;AAEzC,4DAA0C;AAC1C,wDAAsC;AAEtC,0DAAwC;AACxC,+DAA6C;AAC7C,+DAA6C;AAE7C,6DAA2C;AAC3C,6DAA2C;AAE3C,4DAA0C"}

package/lib/signals/signalsToFID.d.ts

@@ -0,0 +1,13 @@
+import { NMRSignal1D } from './NMRSignal1D';
+export interface SignalsToFIDOptions {
+    lb?: number;
+    from?: number;
+    to?: number;
+    nbPoints?: number;
+    frequency?: number;
+    maxClusterSize?: number;
+}
+export declare function signalsToFID(signals: NMRSignal1D[], options: SignalsToFIDOptions): {
+    re: import("cheminfo-types").DoubleArray;
+    im: import("cheminfo-types").DoubleArray;
+};

package/lib/signals/signalsToFID.js

@@ -0,0 +1,56 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.signalsToFID = void 0;
+const ml_spectra_processing_1 = require("ml-spectra-processing");
+const apodization_1 = require("../apodization/apodization");
+const signalsToSpinSystem_1 = require("./simulation/signalsToSpinSystem");
+const simulateXYPeaks_1 = require("./simulation/simulateXYPeaks");
+const splitSpinSystem_1 = require("./simulation/splitSpinSystem");
+const twoPi = Math.PI * 2;
+function signalsToFID(signals, options) {
+    const { lb = 1, from = 0, to = 10, nbPoints = 1024, frequency = 400, maxClusterSize = 8, } = options;
+    let spinSystem = (0, signalsToSpinSystem_1.signalsToSpinSystem)(signals);
+    spinSystem.clusters = (0, splitSpinSystem_1.splitSpinSystem)(spinSystem, {
+        frequency,
+        maxClusterSize,
+    });
+    const peaks = (0, simulateXYPeaks_1.simulateXYPeaks)(spinSystem, { frequency });
+    const re = new Float64Array(nbPoints);
+    const im = new Float64Array(nbPoints);
+    const sw = Math.abs(to - from);
+    const adquisitionTime = nbPoints / (2 * sw * frequency);
+    const time = (0, ml_spectra_processing_1.xSequentialFill)({
+        size: nbPoints,
+        from: 0,
+        to: adquisitionTime,
+    });
+    for (const peak of peaks) {
+        const { x, y } = peak;
+        const cs = x * frequency * twoPi;
+        for (let i = 0; i < nbPoints; i++) {
+            re[i] += y * Math.cos(cs * time[i]);
+            im[i] += y * Math.sin(cs * time[i]);
+        }
+    }
+    const { windowData, ...result } = (0, apodization_1.apodization)({ re, im }, {
+        pointsToShift: 0,
+        compose: {
+            length: nbPoints,
+            shapes: [
+                {
+                    start: 0,
+                    shape: {
+                        kind: 'exponential',
+                        options: {
+                            dw: adquisitionTime / (nbPoints - 1),
+                            lb,
+                        },
+                    },
+                },
+            ],
+        },
+    });
+    return result;
+}
+exports.signalsToFID = signalsToFID;
+//# sourceMappingURL=signalsToFID.js.map

package/lib/signals/signalsToFID.js.map

@@ -0,0 +1 @@
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package/lib-esm/index.js

@@ -20,6 +20,7 @@ export * from './signals/signalsToRanges';
 export * from './signals/signalsToXY';
 export * from './signals/signals2DToZ';
 export * from './signals/optimizeSignals';
+export * from './signals/signalsToFID';
 export * from './utilities/resurrect';
 export * from './utilities/rangeFromSignal';
 export * from './utilities/getFrequency';

package/lib-esm/index.js.map

@@ -1 +1 @@
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package/lib-esm/signals/signalsToFID.js

@@ -0,0 +1,52 @@
+import { xSequentialFill } from 'ml-spectra-processing';
+import { apodization } from '../apodization/apodization';
+import { signalsToSpinSystem } from './simulation/signalsToSpinSystem';
+import { simulateXYPeaks } from './simulation/simulateXYPeaks';
+import { splitSpinSystem } from './simulation/splitSpinSystem';
+const twoPi = Math.PI * 2;
+export function signalsToFID(signals, options) {
+    const { lb = 1, from = 0, to = 10, nbPoints = 1024, frequency = 400, maxClusterSize = 8, } = options;
+    let spinSystem = signalsToSpinSystem(signals);
+    spinSystem.clusters = splitSpinSystem(spinSystem, {
+        frequency,
+        maxClusterSize,
+    });
+    const peaks = simulateXYPeaks(spinSystem, { frequency });
+    const re = new Float64Array(nbPoints);
+    const im = new Float64Array(nbPoints);
+    const sw = Math.abs(to - from);
+    const adquisitionTime = nbPoints / (2 * sw * frequency);
+    const time = xSequentialFill({
+        size: nbPoints,
+        from: 0,
+        to: adquisitionTime,
+    });
+    for (const peak of peaks) {
+        const { x, y } = peak;
+        const cs = x * frequency * twoPi;
+        for (let i = 0; i < nbPoints; i++) {
+            re[i] += y * Math.cos(cs * time[i]);
+            im[i] += y * Math.sin(cs * time[i]);
+        }
+    }
+    const { windowData, ...result } = apodization({ re, im }, {
+        pointsToShift: 0,
+        compose: {
+            length: nbPoints,
+            shapes: [
+                {
+                    start: 0,
+                    shape: {
+                        kind: 'exponential',
+                        options: {
+                            dw: adquisitionTime / (nbPoints - 1),
+                            lb,
+                        },
+                    },
+                },
+            ],
+        },
+    });
+    return result;
+}
+//# sourceMappingURL=signalsToFID.js.map

package/lib-esm/signals/signalsToFID.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nmr-processing",
-  "version": "9.1.0-pre.1663857509",
+  "version": "9.2.0-pre.1668170175",
   "description": "Pure functions allowing to process NMR spectra.",
   "main": "./lib/index.js",
   "module": "./lib-esm/index.js",
@@ -64,7 +64,7 @@
     "ml-array-mean": "^1.1.6",
     "ml-array-rescale": "^1.3.7",
     "ml-array-sum": "^1.1.6",
-    "ml-direct": "^0.1.0",
+    "ml-direct": "^0.1.1",
     "ml-gsd": "^12.1.2",
     "ml-hclust": "^3.1.0",
     "ml-levenberg-marquardt": "^4.1.0",

package/src/index.ts

@@ -25,6 +25,7 @@ export * from './signals/signalsToRanges';
 export * from './signals/signalsToXY';
 export * from './signals/signals2DToZ';
 export * from './signals/optimizeSignals';
+export * from './signals/signalsToFID';
 
 export * from './utilities/resurrect';
 export * from './utilities/rangeFromSignal';

package/src/signals/signalsToFID.ts

@@ -0,0 +1,84 @@
+import { xSequentialFill } from 'ml-spectra-processing';
+
+import { apodization } from '../apodization/apodization';
+
+import { NMRSignal1D } from './NMRSignal1D';
+import { signalsToSpinSystem } from './simulation/signalsToSpinSystem';
+import { simulateXYPeaks } from './simulation/simulateXYPeaks';
+import { splitSpinSystem } from './simulation/splitSpinSystem';
+
+export interface SignalsToFIDOptions {
+  lb?: number;
+  from?: number;
+  to?: number;
+  nbPoints?: number;
+  frequency?: number;
+  maxClusterSize?: number;
+}
+
+const twoPi = Math.PI * 2;
+
+export function signalsToFID(
+  signals: NMRSignal1D[],
+  options: SignalsToFIDOptions,
+) {
+  const {
+    lb = 1,
+    from = 0,
+    to = 10,
+    nbPoints = 1024,
+    frequency = 400,
+    maxClusterSize = 8,
+  } = options;
+
+  let spinSystem = signalsToSpinSystem(signals);
+
+  spinSystem.clusters = splitSpinSystem(spinSystem, {
+    frequency,
+    maxClusterSize,
+  });
+
+  const peaks = simulateXYPeaks(spinSystem, { frequency });
+  const re = new Float64Array(nbPoints);
+  const im = new Float64Array(nbPoints);
+
+  const sw = Math.abs(to - from);
+  const adquisitionTime = nbPoints / (2 * sw * frequency);
+  const time = xSequentialFill({
+    size: nbPoints,
+    from: 0,
+    to: adquisitionTime,
+  });
+
+  for (const peak of peaks) {
+    const { x, y } = peak;
+    const cs = x * frequency * twoPi;
+    for (let i = 0; i < nbPoints; i++) {
+      re[i] += y * Math.cos(cs * time[i]);
+      im[i] += y * Math.sin(cs * time[i]);
+    }
+  }
+
+  const { windowData, ...result } = apodization(
+    { re, im },
+    {
+      pointsToShift: 0,
+      compose: {
+        length: nbPoints,
+        shapes: [
+          {
+            start: 0,
+            shape: {
+              kind: 'exponential',
+              options: {
+                dw: adquisitionTime / (nbPoints - 1),
+                lb,
+              },
+            },
+          },
+        ],
+      },
+    },
+  );
+  return result;
+}

package/src/signals/optimization/ml-direct.d.ts

@@ -1,21 +0,0 @@
-declare module 'ml-direct' {
-  export interface DirectOptions {
-    iterations?: number;
-    epsilon?: number;
-    tolerance?: number;
-    tolerance2?: number;
-    initialState?: any;
-  }
-
-  export default function direct(
-    objectiveFunction: (parameters: number[]) => number,
-    lowerBoundaries: number[],
-    upperBoundaries: number[],
-    options?: DirectOptions,
-  ): {
-    minFunctionValue: number;
-    iterations: number;
-    optima: number[][];
-    finalState: any;
-  };
-}