nmr-processing 9.5.0 → 9.5.1-pre.1685396168

package/src/types/Ranges/Ranges.ts

@@ -0,0 +1,19 @@
+import { NMRRange } from '../..';
+import { SumOptions as Options } from '../Options/SumOptions';
+import { Signal1D } from '../Signals/Signal1D';
+
+export interface Ranges {
+  values: Array<Range>;
+  options: Options;
+}
+
+export interface Range
+  extends Omit<NMRRange, 'signals' | 'id' | 'integration'> {
+  id: string;
+  originFrom?: number;
+  originTo?: number;
+  absolute: number;
+  signals: Signal1D[];
+  integration: number;
+  nbAtoms?: number;
+}

package/src/types/Signals/Signal.ts

@@ -0,0 +1,4 @@
+export interface Signal {
+  id: string;
+  kind?: string;
+}

package/src/types/Signals/Signal1D.ts

@@ -0,0 +1,8 @@
+import { NMRSignal1D } from '../../signals/NMRSignal1D';
+
+type ObjectKeys = 'id' | 'multiplicity' | 'js';
+export interface Signal1D
+  extends Required<Pick<NMRSignal1D, ObjectKeys>>,
+    Omit<NMRSignal1D, ObjectKeys> {
+  originDelta?: number;
+}

package/src/types/Signals/Signal2D.ts

@@ -0,0 +1,21 @@
+import { FromTo } from 'cheminfo-types';
+
+import type { Peak2D } from '../Peaks/Peak2D';
+
+import type { Signal } from './Signal';
+
+interface SignalAxis {
+  delta: number;
+  diaIDs?: string[];
+  originDelta: number;
+}
+
+export interface Signal2D extends Signal {
+  sign?: number;
+  x: SignalAxis;
+  y: SignalAxis;
+  peaks?: Peak2D[];
+  j?: {
+    pathLength?: number | FromTo;
+  };
+}

package/src/types/Spectrum/BaseSpectrum.ts

@@ -0,0 +1,8 @@
+import { NmrLoaderSelectors } from '../Options/ParsingOptions';
+
+export interface BaseSpectrum {
+  id: string;
+  sourceSelector?: NmrLoaderSelectors;
+  meta: any;
+  customInfo: any;
+}

package/src/types/Spectrum/Spectrum.ts

@@ -0,0 +1,4 @@
+import { Spectrum1D } from './Spectrum1D';
+import { Spectrum2D } from './Spectrum2D';
+
+export type Spectrum = Spectrum1D | Spectrum2D;

package/src/types/Spectrum/Spectrum1D.ts

@@ -0,0 +1,23 @@
+import { Data1D } from '../Data1D';
+import { Display1D } from '../Display1D';
+import { Filter } from '../Filter';
+import { Info1D } from '../Info/Info1D';
+import { Integrals } from '../Integrals';
+import { Peaks } from '../Peaks/Peaks';
+import { Ranges } from '../Ranges/Ranges';
+
+import { BaseSpectrum } from './BaseSpectrum';
+
+export interface Spectrum1D extends BaseSpectrum {
+  data: Data1D;
+  originalData?: Data1D;
+  peaks: Peaks;
+  display: Display1D;
+  integrals: Integrals;
+  ranges: Ranges;
+  info: Info1D;
+  originalInfo?: Info1D;
+  filters: Array<Filter>;
+}
+
+export type Spectrum1DSource = Partial<Spectrum1D>;

package/src/types/Spectrum/Spectrum2D.ts

@@ -0,0 +1,19 @@
+import { Data2D } from '../Data2D';
+import { Display2D } from '../Display2D';
+import { Filter } from '../Filter';
+import { Info2D } from '../Info/Info2D';
+import { Zones } from '../Zones/Zones';
+
+import { BaseSpectrum } from './BaseSpectrum';
+
+export interface Spectrum2D extends BaseSpectrum {
+  zones: Zones;
+  data: Data2D;
+  info: Info2D;
+  originalInfo?: Info2D;
+  display: Display2D;
+  originalData?: Data2D;
+  filters: Array<Filter>;
+}
+
+export type Spectrum2DSource = Partial<Spectrum2D>;

package/src/types/Zones/Zone.ts

@@ -0,0 +1,15 @@
+import { FromTo } from 'cheminfo-types';
+
+import { Signal2D } from '../Signals/Signal2D';
+
+interface ZoneAxis extends FromTo {
+  diaIDs?: string[];
+}
+
+export interface Zone {
+  id: string;
+  x: ZoneAxis;
+  y: ZoneAxis;
+  signals: Array<Signal2D>;
+  kind?: string;
+}

package/src/types/Zones/Zones.ts

@@ -0,0 +1,6 @@
+import { Zone } from './Zone';
+
+export interface Zones {
+  values: Array<Zone>;
+  options?: any;
+}

package/src/types/common/MapOptions.ts

@@ -0,0 +1,6 @@
+export type ShiftTarget = 'origin' | 'current';
+
+export interface MapOptions {
+  checkIsExisting?: boolean;
+  shiftTarget?: ShiftTarget;
+}

package/src/utilities/checkData2DFid.ts

@@ -0,0 +1,10 @@
+import { Data2D, Data2DFid } from 'cheminfo-types';
+
+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/utilities/cloneData1D.ts

@@ -0,0 +1,6 @@
+import { Data1D } from '../types/Data1D';
+
+export function cloneData1D(datum: Data1D) {
+  const { x, re, im } = datum || { x: [], re: [], im: [] };
+  return { x: x.slice(), re: re.slice(), im: im?.slice() || null };
+}

package/src/utilities/cloneData2D.ts

@@ -0,0 +1,27 @@
+import { Data2D, Data2DFid, Data2DFt, MinMaxContent } from 'cheminfo-types';
+
+export function cloneData2D(data: Data2D) {
+  const newData: any = {};
+
+  if (isData2DFt(data)) {
+    for (const key in data) {
+      addCloneData(newData, key, data[key as keyof Data2DFt]);
+    }
+  } else {
+    for (const key in data) {
+      addCloneData(newData, key, data[key as keyof Data2DFid]);
+    }
+  }
+  return newData;
+}
+
+function isData2DFt(data: Data2D): data is Data2DFt {
+  return 're' in data;
+}
+
+function addCloneData(newData: any, key: string, data?: MinMaxContent) {
+  if (data) {
+    const { z, ...other } = data;
+    newData[key] = { z: z.slice(), ...other };
+  }
+}

package/src/utilities/getSum.ts

@@ -0,0 +1,24 @@
+/**
+ * Sum values for specific key in the object
+ * @param values array of object
+ * @param key key
+ * @param check custom check function to to indicate if certain object included or not in the summation
+ * @returns number
+ */
+
+export function getSum<Type>(
+  values: Type[],
+  key: keyof Extract<Type, string>,
+  check: ((value: Type) => boolean) | null = null,
+) {
+  let sum = 0;
+  for (const current of values) {
+    if (check?.(current)) {
+      //@ts-expect-error number check is done after
+      const value = current[key];
+      if (!value || isNaN(value)) continue;
+      sum += Math.abs(value);
+    }
+  }
+  return sum;
+}

package/src/xyz/Entry2D.ts

@@ -0,0 +1,12 @@
+import { Data2D } from 'cheminfo-types';
+
+import { Filter } from '../types/Filter';
+
+export interface Entry2D {
+  id?: string;
+  info: Record<string, any>;
+  originalInfo?: Record<string, any>;
+  data: Data2D;
+  originalData?: Data2D;
+  filters: Array<Filter>;
+}

package/src/xyz/quadrature.ts

@@ -0,0 +1,68 @@
+import { Data2D, DoubleArray } from 'cheminfo-types';
+import { xAdd, xMultiply, xSubtract } from 'ml-spectra-processing';
+
+import { checkData2DFid, Data2DFidComplete } from '../utilities/checkData2DFid';
+
+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,
+  ApodizationFilterOptions,
+} 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?: ApodizationFilterOptions;
+  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,
+  ApodizationFilterOptions,
+} from '../../../apodization/apodization';
+
+import { zeroFilling, ZeroFillingOptions } from './zeroFilling';
+
+interface PhaseCorrection {
+  mode?: string;
+  ph0?: number;
+  ph1?: number;
+}
+
+export interface IndirectDimensionOptions {
+  fnMode?: string;
+  zeroFilling?: ZeroFillingOptions;
+  apodization?: ApodizationFilterOptions;
+  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 };
+}

package/src/xyz/util/padData.ts

@@ -1,8 +1,9 @@
-import Matrix from 'ml-matrix';
+import { MinMaxContent } from 'cheminfo-types';
 
-import { Data2D } from '../Data2D';
-
-export function padData(spectraData: Data2D, options: { width: number }) {
+export function padData(
+  spectraData: MinMaxContent,
+  options: { width: number },
+) {
   let { minX, maxX, minY, maxY } = spectraData;
 
   const width = options.width;
@@ -20,15 +21,20 @@ export function padData(spectraData: Data2D, options: { width: number }) {
 
   let xOffset = xDiff / 2;
   let yOffset = yDiff / 2;
-  let newMatrix = Matrix.zeros(nbSubSpectra + yDiff, nbPoints + xDiff);
+
+  const newMatrix: Float64Array[] = [];
+  for (let i = 0; i < nbSubSpectra + yDiff; i++) {
+    newMatrix.push(new Float64Array(nbPoints + xDiff));
+  }
   for (let i = 0; i < nbSubSpectra; i++) {
     for (let j = 0; j < nbPoints; j++) {
-      newMatrix.set(i + yOffset, j + xOffset, spectraData.z[i][j]);
+      newMatrix[i + yOffset].set(spectraData.z[i], xOffset);
     }
   }
 
   return {
-    z: newMatrix.to2DArray(),
+    ...spectraData,
+    z: newMatrix,
     minX: minX - xOffset * xInterval,
     maxX: maxX + xOffset * xInterval,
     minY: minY - yOffset * yInterval,

package/src/xyz/xyzAutoSignalsPicking.ts

@@ -1,4 +1,5 @@
 import { v4 as generateID } from '@lukeed/uuid';
+import { MinMaxContent } from 'cheminfo-types';
 import * as convolution from 'ml-matrix-convolution';
 import * as matrixPeakFinders from 'ml-matrix-peaks-finder';
 import type { Peak2D } from 'ml-matrix-peaks-finder';
@@ -11,7 +12,6 @@ import type { GetKernelOptions } from '../peaks/util/getKernel';
 import * as PeakOptimizer from '../peaks/util/peakOptimizer';
 import { MakeMandatory } from '../utilities/MakeMandatory';
 
-import { Data2D } from './Data2D';
 import type { NMRSignal2D } from './NMRSignal2D';
 import { padData } from './util/padData';
 
@@ -89,7 +89,7 @@ export type NMRSignal2DWithID<T extends Peak2D = Peak2D> = MakeMandatory<
 >;
 
 export function xyzAutoSignalsPicking(
-  spectraData: Data2D,
+  spectraData: MinMaxContent,
   options: XYZAutoSignalsPickingOptions,
 ) {
   let {