nmr-processing 9.3.7 → 9.3.8-pre.1681135907

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nmr-processing",
-  "version": "9.3.7",
+  "version": "9.3.8-pre.1681135907",
   "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": "^29.2.3",
-    "cheminfo-build": "^1.1.11",
+    "@types/jest": "^29.5.0",
+    "cheminfo-build": "^1.2.0",
     "cheminfo-types": "^1.4.0",
-    "eslint": "^8.34.0",
-    "eslint-config-cheminfo-typescript": "^11.2.2",
-    "jest": "^29.3.1",
+    "eslint": "^8.36.0",
+    "eslint-config-cheminfo-typescript": "^11.3.1",
+    "jest": "^29.5.0",
     "jest-matcher-deep-close-to": "^3.0.2",
     "md5": "^2.3.0",
     "nmr-xy-testdata": "^0.5.1",
-    "openchemlib": "^8.0.1",
-    "prettier": "^2.8.4",
-    "rimraf": "^4.1.2",
-    "ts-jest": "^29.0.3",
-    "typescript": "^4.9.3"
+    "openchemlib": "^8.2.0",
+    "prettier": "^2.8.7",
+    "rimraf": "^4.4.1",
+    "ts-jest": "^29.0.5",
+    "typescript": "^5.0.2"
   },
   "dependencies": {
     "@lukeed/uuid": "^2.0.0",
@@ -60,12 +60,12 @@
     "form-data": "^4.0.0",
     "gyromagnetic-ratio": "^1.0.0",
     "is-any-array": "^2.0.0",
-    "linear-sum-assignment": "^1.0.4",
+    "linear-sum-assignment": "^1.0.5",
     "ml-array-mean": "^1.1.6",
     "ml-array-rescale": "^1.3.7",
     "ml-array-sum": "^1.1.6",
-    "ml-direct": "^0.1.1",
-    "ml-gsd": "^12.1.2",
+    "ml-direct": "^0.1.3",
+    "ml-gsd": "^12.1.3",
     "ml-hclust": "^3.1.0",
     "ml-levenberg-marquardt": "^4.1.0",
     "ml-matrix": "^6.10.4",
@@ -74,11 +74,11 @@
     "ml-peak-shape-generator": "^4.1.2",
     "ml-simple-clustering": "^0.1.0",
     "ml-sparse-matrix": "^2.1.0",
-    "ml-spectra-processing": "^11.17.0",
+    "ml-spectra-processing": "^12.0.0",
     "ml-tree-set": "^0.1.1",
     "nmr-correlation": "^2.3.3",
     "nmredata": "^0.9.2",
-    "openchemlib-utils": "^2.1.2",
-    "spectrum-generator": "^8.0.6"
+    "openchemlib-utils": "^2.4.0",
+    "spectrum-generator": "^8.0.7"
   }
 }

package/src/apodization/apodization.ts

@@ -10,23 +10,25 @@ export interface DataReIm {
   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 function apodization(data: DataReIm, options: ApodizationOptions) {
+export function apodization(data: DataReIm, options: ApodizationOptions = {}) {
   const { compose: composeOptions, pointsToShift } = options;
+
+  if (!composeOptions) return { ...data, windowData: [] };
+
   const windowData = compose(composeOptions);
 
   const applyWindowOptions = {
     windowData,
     pointsToShift,
   };
-
   const re = applyWindow(data.re, applyWindowOptions);
   const im = applyWindow(data.im, applyWindowOptions);
 

package/src/apodization/applyWindow.ts

@@ -42,7 +42,6 @@ export function applyWindow(data: DoubleArray, options: ApplyWindowOptions) {
   for (let i = start, j = 0; i < firstEndPoint; i++) {
     output[i] *= windowData[j++];
   }
-
   for (let i = dataLength - 1, j = 0; i > dataLength - pointsToShift - 1; i--) {
     output[i] *= windowData[j++];
   }

package/src/apodization/compose.ts

@@ -36,6 +36,7 @@ export function compose(shapeOptions: ShapeOptions) {
       'length' in shapeOptions ? shapeOptions.length : dataLength - start;
 
     const windowData = getData(getFunction(shape), length);
+
     applyWindow(data, {
       windowData,
       length,

package/src/apodization/getFunction.ts

@@ -1,6 +1,7 @@
 import type { WindowFunctions } from './shapes/WindowFunctions';
 import { exponential } from './shapes/exponential';
 import { lorentzToGauss } from './shapes/lorentzToGauss';
+import { sineBell } from './shapes/sineBell';
 
 export function getFunction(shape: WindowFunctions) {
   const { kind, options } = shape;
@@ -9,6 +10,8 @@ export function getFunction(shape: WindowFunctions) {
       return exponential(options);
     case 'lorentzToGauss':
       return lorentzToGauss(options);
+    case 'sineBell':
+      return sineBell(options);
     default:
       throw Error(`Unknown distribution ${kind as string}`);
   }

package/src/apodization/shapes/WindowFunctions.ts

@@ -1,5 +1,6 @@
 import type { ExponentialOptions } from './exponential';
 import type { LorentzToGaussOptions } from './lorentzToGauss';
+import { SineBellOptions } from './sineBell';
 
 interface Exponential {
   kind: 'exponential';
@@ -11,4 +12,9 @@ interface LorentToGauss {
   options: LorentzToGaussOptions;
 }
 
-export type WindowFunctions = Exponential | LorentToGauss;
+interface SineBell {
+  kind: 'sineBell';
+  options: SineBellOptions;
+}
+
+export type WindowFunctions = Exponential | LorentToGauss | SineBell;

package/src/apodization/shapes/sineBell.ts

@@ -0,0 +1,41 @@
+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 function sineBell(options: SineBellOptions) {
+  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: number) => Math.pow(Math.sin(c1 + c2 * i), exponent);
+}

package/src/apodization/utils/getData.ts

@@ -9,7 +9,6 @@ export function getData(func: (i: number) => number, length: number) {
     data[i] = value;
     if (value > max) max = value;
   }
-
   for (let i = 0; i < length; i++) data[i] /= max;
   return data;
 }

package/src/utilities/checkData2DFid.ts

@@ -0,0 +1,10 @@
+import { Data2D, Data2DFid } from '../xyz/Data2D';
+
+export type Data2DFidComplete = Required<Data2DFid>;
+export function checkData2DFid(
+  data: Data2D,
+): asserts data is Data2DFidComplete {
+  if (!('re' in data && 'im' in data)) {
+    throw new Error('imaginary (im) data should exists');
+  }
+}

package/src/xyz/Data2D.ts

@@ -0,0 +1,25 @@
+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/src/xyz/quadrature.ts

@@ -0,0 +1,69 @@
+import { DoubleArray } from 'cheminfo-types';
+import { xAdd, xMultiply, xSubtract } from 'ml-spectra-processing';
+
+import { checkData2DFid, Data2DFidComplete } from '../utilities/checkData2DFid';
+import { Data2D } from './Data2D';
+
+export function quadrature(data: Data2D, options: { fnMode: string }) {
+  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,
+      };
+  }
+}
+
+function echoQuadrature(data: Data2DFidComplete) {
+  const {
+    re: { z: reMatrix },
+    im: { z: imMatrix },
+  } = data;
+
+  const newRe: DoubleArray[] = [];
+  const newIm: DoubleArray[] = [];
+  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(xSubtract(xMultiply(imSine, -1), imCosine));
+    newRe.push(xSubtract(reSine, reCosine));
+    newIm.push(xAdd(reSine, reCosine));
+    newIm.push(xSubtract(imSine, imCosine));
+  }
+
+  return { re: newRe, im: newIm };
+}
+
+function shrQuadrature(data: Data2DFidComplete) {
+  const { re, im } = data;
+  return { re: re.z, im: im.z };
+}
+
+function ttpiQuadrature(data: Data2DFidComplete) {
+  const newRe: DoubleArray[] = [];
+  const newIm: DoubleArray[] = [];
+
+  const {
+    re: { z: reMatrix },
+    im: { z: imMatrix },
+  } = data;
+  for (let i = 0; i < reMatrix.length; i++) {
+    newRe.push(i % 2 ? reMatrix[i].slice() : xMultiply(reMatrix[i], -1));
+    newIm.push(i % 2 ? imMatrix[i].slice() : xMultiply(imMatrix[i], -1));
+  }
+
+  return { re: newRe, im: newIm };
+}

package/src/xyz/util/fft2d/digitalFilter.ts

@@ -0,0 +1,24 @@
+import { DataReIm } from 'ml-spectra-processing';
+
+export function digitalFilter(
+  data: DataReIm,
+  options: { digitalFilterValue: number },
+) {
+  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 };
+}

package/src/xyz/util/fft2d/fftDirectDimension.ts

@@ -0,0 +1,111 @@
+import { DoubleArray } from 'cheminfo-types';
+import Matrix from 'ml-matrix';
+import {
+  reimAutoPhaseCorrection,
+  reimFFT,
+  reimPhaseCorrection,
+} from 'ml-spectra-processing';
+
+import {
+  apodization,
+  ApodizationOptions,
+} from '../../../apodization/apodization';
+
+import { digitalFilter } from './digitalFilter';
+import { removeDCOffset } from './removeDCOffset';
+import { zeroFilling, 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 function fftDirectDimension(
+  data: { re: DoubleArray[]; im: DoubleArray[] },
+  options: DirectDimensionOptions,
+) {
+  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?.nbPoints || 2 ** Math.round(Math.log2(nbColumns * f2Factor));
+
+  const reFFT = new Matrix(nbRows, nbPointsF2);
+  const imFFT = new Matrix(nbRows, nbPointsF2);
+
+  const { apodization: apodizationF2 } = options;
+  let {
+    ph0: ph0F2,
+    ph1: ph1F2,
+    mode: pcModeF2 = 'no',
+  } = options?.phaseCorrection || {};
+
+  for (let i = 0; i < nbRows; i++) {
+    const newData = digitalFilter(
+      { re: reData[i], im: imData[i] },
+      { digitalFilterValue },
+    );
+
+    Object.assign(newData, removeDCOffset(newData, { digitalFilterValue }));
+
+    if (apodizationF2) {
+      const { re: aRe, im: aIm } = apodization(newData, apodizationF2);
+      Object.assign(newData, { re: aRe, im: aIm });
+    }
+
+    Object.assign(
+      newData,
+      zeroFilling(newData, { digitalFilterValue, nbPoints: nbPointsF2 }),
+    );
+
+    Object.assign(newData, reimFFT(newData, { applyZeroShift: true }));
+
+    const dfResidual =
+      (digitalFilterValue - Math.round(digitalFilterValue)) * Math.PI * 2;
+    if (dfResidual > 0) {
+      Object.assign(newData, reimPhaseCorrection(newData, 0, -dfResidual));
+    }
+
+    if (
+      i === 0 &&
+      pcModeF2 === 'pk' &&
+      ph0F2 === undefined &&
+      ph1F2 === undefined
+    ) {
+      const phased = reimAutoPhaseCorrection(newData, { magnitudeMode: false });
+      ph0F2 = phased.ph0;
+      ph1F2 = phased.ph1;
+    }
+    if (pcModeF2 === 'pk' && ph0F2 !== undefined && ph1F2 !== undefined) {
+      Object.assign(
+        newData,
+        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,
+  };
+}

package/src/xyz/util/fft2d/fftIndirectDimension.ts

@@ -0,0 +1,123 @@
+import { DoubleArray } from 'cheminfo-types';
+import Matrix from 'ml-matrix';
+import {
+  reimAbsolute,
+  reimAutoPhaseCorrection,
+  reimFFT,
+  reimPhaseCorrection,
+} from 'ml-spectra-processing';
+
+import {
+  apodization,
+  ApodizationOptions,
+} from '../../../apodization/apodization';
+
+import { zeroFilling, ZeroFillingOptions } from './zeroFilling';
+
+interface PhaseCorrection {
+  mode?: string;
+  ph0?: number;
+  ph1?: number;
+}
+
+export interface IndirectDimensionOptions {
+  fnMode?: string;
+  zeroFilling?: ZeroFillingOptions;
+  apodization?: ApodizationOptions;
+  phaseCorrection?: PhaseCorrection;
+}
+
+export function fftIndirectDimension(
+  data: { re: DoubleArray[] | Matrix; im: DoubleArray[] | Matrix },
+  options: IndirectDimensionOptions,
+) {
+  const reData = Matrix.checkMatrix(data.re);
+  const imData = Matrix.checkMatrix(data.im);
+
+  const nbRows = reData.rows;
+  const nbColumns = reData.columns;
+
+  const { zeroFilling: zeroFillingF1 } = options;
+  const { factor: f1Factor = 2 } = zeroFillingF1 || {};
+  const nbPointsF1 =
+    zeroFillingF1?.nbPoints || 2 ** Math.round(Math.log2(nbRows * f1Factor));
+  const { apodization: apodizationF1 } = options;
+  let {
+    ph0: ph0F1,
+    ph1: ph1F1,
+    mode: pcModeF1,
+  } = options.phaseCorrection || {};
+
+  const reResult = new Matrix(nbPointsF1, nbColumns);
+  const imResult = new Matrix(nbPointsF1, nbColumns);
+  for (let i = 0; i < nbColumns; i++) {
+    const { re: aRe, im: aIm } = apodization(
+      {
+        re: reData.getColumn(i),
+        im: imData.getColumn(i),
+      },
+      apodizationF1,
+    );
+
+    const newRe = [];
+    const newIm = [];
+    if (options.fnMode === 'echo') {
+      for (let j = 0; j < aRe.length; j += 2) {
+        newRe.push(aRe[j]);
+        newIm.push(aRe[j + 1]);
+      }
+    } else {
+      for (let j = 0; j < aRe.length; j++) {
+        newRe.push(aRe[j]);
+        newIm.push(-aIm[j]);
+      }
+    }
+
+    let transformed = reimFFT(
+      zeroFilling(
+        {
+          re: newRe,
+          im: newIm,
+        },
+        { digitalFilterValue: 0, nbPoints: nbPointsF1 },
+      ),
+      { applyZeroShift: true },
+    );
+    let { re, im } = transformed;
+
+    if (options.phaseCorrection?.mode === 'mc') {
+      re = reimAbsolute({ re, im });
+      im = new Float64Array(im.length);
+    }
+
+    if (pcModeF1 === 'pk') {
+      if (i === 0 && ph0F1 === undefined && ph1F1 === undefined) {
+        //here we can improve it by checking if the experiment is phase sensitive.
+        const phased = reimAutoPhaseCorrection(
+          { re, im },
+          { magnitudeMode: false },
+        );
+        ph0F1 = phased.ph0;
+        ph1F1 = phased.ph1;
+      }
+      if (ph0F1 !== undefined && ph1F1 !== undefined) {
+        Object.assign(
+          transformed,
+          reimPhaseCorrection(
+            transformed,
+            (ph0F1 * Math.PI) / 180,
+            (ph1F1 * Math.PI) / 180,
+          ),
+        );
+      }
+    }
+
+    reResult.setColumn(i, re);
+    imResult.setColumn(i, im);
+  }
+
+  return {
+    re: reResult,
+    im: imResult,
+  };
+}

package/src/xyz/util/fft2d/removeDCOffset.ts

@@ -0,0 +1,19 @@
+import { DataReIm, xMean } from 'ml-spectra-processing';
+
+export function removeDCOffset(data: DataReIm, options: any) {
+  let { digitalFilterValue = 0 } = options;
+  const nbPoints = data.re.length;
+  const newRe = new Float64Array(data.re);
+  const newIm = new Float64Array(data.im);
+  const averageRe = xMean(
+    data.re.slice((nbPoints * 0.75) >> 0, nbPoints - digitalFilterValue),
+  );
+  const averageIm = xMean(
+    data.im.slice((nbPoints * 0.75) >> 0, nbPoints - digitalFilterValue),
+  );
+  for (let i = digitalFilterValue; i < nbPoints - digitalFilterValue; i++) {
+    newRe[i] -= averageRe;
+    newIm[i] -= averageIm;
+  }
+  return { re: newRe, im: newIm };
+}

package/src/xyz/util/fft2d/zeroFilling.ts

@@ -0,0 +1,39 @@
+import { DataReIm } from 'ml-spectra-processing';
+
+export interface ZeroFillingOptions {
+  nbPoints?: number;
+  factor?: number;
+  digitalFilterValue?: number;
+}
+
+export function zeroFilling(data: DataReIm, options: ZeroFillingOptions) {
+  let { nbPoints, factor = 2, digitalFilterValue: grpdly = 0 } = options;
+
+  if (!nbPoints) {
+    nbPoints = 2 ** Math.round(Math.log2(data.re.length * factor));
+  }
+
+  let pointsToShift;
+  if (grpdly > 0) {
+    pointsToShift = Math.floor(grpdly);
+  } else {
+    pointsToShift = 0;
+  }
+
+  const { re, im } = data;
+
+  let newRE = new Float64Array(nbPoints);
+  let newIM = new Float64Array(nbPoints);
+
+  const length = Math.min(nbPoints, re.length);
+
+  newRE.set(re.slice(0, length - pointsToShift));
+  newIM.set(im.slice(0, length - pointsToShift));
+
+  if (pointsToShift > 0 && pointsToShift < nbPoints) {
+    newRE.set(re.slice(re.length - pointsToShift), nbPoints - pointsToShift);
+    newIM.set(im.slice(re.length - pointsToShift), nbPoints - pointsToShift);
+  }
+
+  return { re: newRE, im: newIM };
+}