nmr-processing 9.2.0 → 9.3.0

package/README.md

@@ -4,6 +4,7 @@
 [![build status][ci-image]][ci-url]
 [![Test coverage][codecov-image]][codecov-url]
 [![npm download][download-image]][download-url]
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5153274.svg)](https://doi.org/10.5281/zenodo.5153274)
 
 ## Introduction
 

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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package/lib/signals/signalsToFID.d.ts

@@ -0,0 +1,42 @@
+import { NMRSignal1D } from './NMRSignal1D';
+export interface SignalsToFIDOptions {
+    /**
+     * at the end of the superposition of all component, an exponential apodization will be applied
+     * in order to have FID like shape.
+     * @default 1
+     */
+    lb?: number;
+    /**
+     * lower limit of the spectrum
+     * @default 0
+     */
+    from?: number;
+    /**
+     * upper limit of the spectrum
+     * @default 10
+     */
+    to?: number;
+    /**
+     * number of points of the resulting FID
+     */
+    nbPoints?: number;
+    /**
+     * It is the frequency of the carrier (e.g. SFO1 for bruker spectrometers)
+     */
+    frequency?: number;
+    /**
+     * Maximum number of atoms on each cluster that can be considered to be simulated together.
+     * It affects the the quality and speed of the simulation.
+     */
+    maxClusterSize?: number;
+}
+/**
+ * it use the chemical shifts and the coupling between them in order to generate a FID.
+ * It does not propagate the hamiltonian of the spin system, instead it simulate all the
+ * frequencies in the spectrum (including second order) and add all the waves in a real and
+ * imaginary parts, that is why the couplings should be assigned in order to generate the spin system.
+ */
+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 +1,62 @@
+"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;
+/**
+ * it use the chemical shifts and the coupling between them in order to generate a FID.
+ * It does not propagate the hamiltonian of the spin system, instead it simulate all the
+ * frequencies in the spectrum (including second order) and add all the waves in a real and
+ * imaginary parts, that is why the couplings should be assigned in order to generate the spin system.
+ */
+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 / (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

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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

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package/lib-esm/signals/signalsToFID.js

@@ -0,0 +1,58 @@
+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;
+/**
+ * it use the chemical shifts and the coupling between them in order to generate a FID.
+ * It does not propagate the hamiltonian of the spin system, instead it simulate all the
+ * frequencies in the spectrum (including second order) and add all the waves in a real and
+ * imaginary parts, that is why the couplings should be assigned in order to generate the spin system.
+ */
+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 / (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": "9.2.0",
+  "version": "9.3.0",
   "description": "Pure functions allowing to process NMR spectra.",
   "main": "./lib/index.js",
   "module": "./lib-esm/index.js",
@@ -38,20 +38,20 @@
   },
   "homepage": "https://github.com/cheminfo/nmr-processing#readme",
   "devDependencies": {
-    "@types/jest": "^28.1.6",
+    "@types/jest": "^29.2.2",
     "cheminfo-build": "^1.1.11",
     "cheminfo-types": "^1.4.0",
-    "eslint": "^8.22.0",
-    "eslint-config-cheminfo-typescript": "^11.0.1",
-    "jest": "^28.1.3",
+    "eslint": "^8.27.0",
+    "eslint-config-cheminfo-typescript": "^11.2.2",
+    "jest": "^29.3.1",
     "jest-matcher-deep-close-to": "^3.0.2",
     "md5": "^2.3.0",
     "nmr-xy-testdata": "^0.5.1",
-    "openchemlib": "^8.0.0",
+    "openchemlib": "^8.0.1",
     "prettier": "^2.7.1",
     "rimraf": "^3.0.2",
-    "ts-jest": "^28.0.8",
-    "typescript": "^4.7.4"
+    "ts-jest": "^29.0.3",
+    "typescript": "^4.8.4"
   },
   "dependencies": {
     "@lukeed/uuid": "^2.0.0",
@@ -68,13 +68,13 @@
     "ml-gsd": "^12.1.2",
     "ml-hclust": "^3.1.0",
     "ml-levenberg-marquardt": "^4.1.0",
-    "ml-matrix": "^6.10.2",
+    "ml-matrix": "^6.10.4",
     "ml-matrix-convolution": "^1.0.0",
     "ml-matrix-peaks-finder": "^1.0.0",
     "ml-peak-shape-generator": "^4.1.2",
     "ml-simple-clustering": "^0.1.0",
     "ml-sparse-matrix": "^2.1.0",
-    "ml-spectra-processing": "^11.12.0",
+    "ml-spectra-processing": "^11.14.0",
     "ml-tree-set": "^0.1.1",
     "nmr-correlation": "^2.3.3",
     "openchemlib-utils": "^2.0.0",

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 +1,113 @@
+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 {
+  /**
+   * at the end of the superposition of all component, an exponential apodization will be applied
+   * in order to have FID like shape.
+   * @default 1
+   */
+  lb?: number;
+  /**
+   * lower limit of the spectrum
+   * @default 0
+   */
+  from?: number;
+  /**
+   * upper limit of the spectrum
+   * @default 10
+   */
+  to?: number;
+  /**
+   * number of points of the resulting FID
+   */
+  nbPoints?: number;
+  /**
+   * It is the frequency of the carrier (e.g. SFO1 for bruker spectrometers)
+   */
+  frequency?: number;
+  /**
+   * Maximum number of atoms on each cluster that can be considered to be simulated together.
+   * It affects the the quality and speed of the simulation.
+   */
+  maxClusterSize?: number;
+}
+
+const twoPi = Math.PI * 2;
+
+/**
+ * it use the chemical shifts and the coupling between them in order to generate a FID.
+ * It does not propagate the hamiltonian of the spin system, instead it simulate all the
+ * frequencies in the spectrum (including second order) and add all the waves in a real and
+ * imaginary parts, that is why the couplings should be assigned in order to generate the spin system.
+ */
+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 / (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;
+}