nmr-processing 9.5.1 → 9.5.2-pre.1685982544

package/src/datum/MatrixFilter.ts

@@ -0,0 +1,58 @@
+import type { FilterXYType } from 'ml-signal-processing';
+
+interface BaseField {
+  key: string;
+  level: number;
+  name: string;
+  description: string;
+}
+
+interface Field<T> extends BaseField {
+  default: T;
+}
+
+interface LabelField extends BaseField {
+  type: 'label';
+}
+
+interface SelectField extends Field<any> {
+  type: 'select';
+  choices: any[];
+}
+interface StringField extends Field<string> {
+  type: 'string';
+}
+interface NumberField extends Field<number> {
+  type: 'number';
+}
+interface BooleanField extends Field<boolean> {
+  type: 'boolean';
+}
+
+type CommonField =
+  | SelectField
+  | StringField
+  | NumberField
+  | BooleanField
+  | LabelField;
+
+interface ListField extends Field<string[]> {
+  type: 'list';
+  properties: Record<string, CommonField>;
+}
+
+type Properties =
+  | ListField
+  | SelectField
+  | StringField
+  | NumberField
+  | BooleanField
+  | LabelField;
+
+export type MatrixProperties = Record<string /*filed name*/, Properties>;
+
+export interface MatrixFilter {
+  name: FilterXYType['name'] /*filter name*/;
+  properties: MatrixProperties;
+  options: any;
+}

package/src/datum/MatrixOptions.ts

@@ -0,0 +1,25 @@
+import { ExclusionZone } from './ExclusionZone';
+import { MatrixFilter } from './MatrixFilter';
+
+export interface MatrixOptions {
+  /**
+   * Matrix generation filters
+   * @default []
+   *
+   */
+  filters: (MatrixFilter & { options: object })[];
+  /**
+   * Exclusion zones
+   * @default []
+   */
+  exclusionsZones: ExclusionZone[];
+  /**
+   * range
+   */
+  range: { from: number; to: number };
+
+  /**
+   * number of points
+   */
+  numberOfPoints: number;
+}

package/src/datum/data1d/Entry1D.ts

@@ -0,0 +1,18 @@
+import { Data1D } from '../../types/Data1D';
+import { Filter } from '../../types/Filter';
+import { Info1D } from '../../types/Info/Info1D';
+import { Integrals } from '../../types/Integrals';
+import { Peaks } from '../../types/Peaks/Peaks';
+import { Ranges } from '../../types/Ranges/Ranges';
+
+export interface Entry1D {
+  id?: string;
+  data: Data1D;
+  originalData?: Data1D;
+  peaks: Peaks;
+  integrals: Integrals;
+  ranges: Ranges;
+  info: Info1D;
+  originalInfo?: Info1D;
+  filters: Array<Filter>;
+}

package/src/datum/data1d/filter1d/apodization/apodization.ts

@@ -0,0 +1,53 @@
+import { Data1D } from '../../../../types/Data1D';
+import { Info1D } from '../../../../types/Info/Info1D';
+import { FilterDomainUpdateRules } from '../../../FiltersManager';
+import { Entry1D } from '../../Entry1D';
+
+import { apodizationFilter } from './apodizationFilter';
+
+export const id = 'apodization';
+export const name = 'Apodization';
+export const DOMAIN_UPDATE_RULES: Readonly<FilterDomainUpdateRules> = {
+  updateXDomain: true,
+  updateYDomain: false,
+};
+
+export interface ApodizationOptions {
+  lineBroadening: number;
+  gaussBroadening: number;
+  lineBroadeningCenter: number;
+}
+
+type Entry1DApodizationFilter = Partial<Omit<Entry1D, 'info'>> & {
+  info: Partial<Info1D>;
+  data: Data1D;
+};
+
+export function apply(
+  datum1D: Entry1DApodizationFilter,
+  options: ApodizationOptions,
+) {
+  if (!isApplicable(datum1D)) {
+    throw new Error('apodization not applicable on this data');
+  }
+  const newData = apodizationFilter(datum1D, options);
+
+  datum1D.data = {
+    ...datum1D.data,
+    re: newData.re as Float64Array,
+    im: newData.im as Float64Array,
+  };
+}
+export function isApplicable(
+  datum1D: Entry1DApodizationFilter,
+): datum1D is Entry1DApodizationFilter & { data: Required<Data1D> } {
+  if (datum1D.info.isComplex && datum1D.info.isFid) return true;
+  return false;
+}
+
+export function reduce(previousValue: any, newValue: any) {
+  return {
+    once: true,
+    reduce: newValue,
+  };
+}

package/src/datum/data1d/filter1d/apodization/apodizationFilter.ts

@@ -0,0 +1,54 @@
+import { apodization } from '../../../../apodization/apodization';
+import { Data1D } from '../../../../types/Data1D';
+import { Info1D } from '../../../../types/Info/Info1D';
+import { Entry1D } from '../../Entry1D';
+
+import { ApodizationOptions } from './apodization';
+
+type Entry1DApodizationFilter = Partial<Omit<Entry1D, 'info'>> & {
+  info: Partial<Info1D>;
+  data: Required<Data1D>;
+};
+
+export function apodizationFilter(
+  datum1D: Entry1DApodizationFilter,
+  options: ApodizationOptions,
+) {
+  const { lineBroadening, gaussBroadening, lineBroadeningCenter } = options;
+
+  const grpdly = datum1D.info?.digitalFilter || 0;
+  const pointsToShift = grpdly > 0 ? Math.floor(grpdly) : 0;
+
+  const re = datum1D.data.re;
+  const im = datum1D.data.im;
+  const t = datum1D.data.x;
+
+  const length = re.length;
+  const dw = (t[length - 1] - t[0]) / (length - 1); //REPLACE CONSTANT with calculated value... : for this we need AQ or DW to set it right...
+
+  return apodization(
+    { re, im },
+    {
+      pointsToShift,
+      compose: {
+        length,
+        shapes: [
+          {
+            start: 0,
+            shape: {
+              kind: 'lorentzToGauss',
+              options: {
+                length,
+                dw,
+                exponentialHz:
+                  gaussBroadening > 0 ? lineBroadening : -lineBroadening,
+                gaussianHz: gaussBroadening,
+                center: lineBroadeningCenter,
+              },
+            },
+          },
+        ],
+      },
+    },
+  );
+}

package/src/datum/data1d/filter1d/baselineCorrection.ts

@@ -0,0 +1,83 @@
+import airPLS from 'ml-airpls';
+import baselineRegression from 'ml-baseline-correction-regression';
+import { xyEquallySpaced } from 'ml-spectra-processing';
+
+import { FilterDomainUpdateRules } from '../../FiltersManager';
+import { Entry1D } from '../Entry1D';
+
+export const id = 'baselineCorrection';
+export const name = 'Baseline correction';
+export const DOMAIN_UPDATE_RULES: Readonly<FilterDomainUpdateRules> = {
+  updateXDomain: false,
+  updateYDomain: true,
+};
+
+export type BaselineAlgorithms = 'airpls' | 'polynomial';
+
+export interface PolynomialOptions {
+  zones: Array<{ from: number; to: number; id: string }>;
+  algorithm: 'polynomial';
+  degree: number;
+}
+
+export interface AirplsOptions {
+  zones: Array<{ from: number; to: number; id: string }>;
+  algorithm: 'airpls';
+  maxIterations: number;
+  tolerance: number;
+}
+
+export type BaselineCorrectionOptions = PolynomialOptions | AirplsOptions;
+
+export function apply(datum1D: Entry1D, options: BaselineCorrectionOptions) {
+  if (!isApplicable(datum1D)) {
+    throw new Error('baselineCorrection not applicable on this data');
+  }
+  const { algorithm } = options;
+  let { x, re } = datum1D.data;
+
+  let corrected;
+  switch (algorithm) {
+    case 'airpls':
+      corrected = airPLS(x, re, options).corrected;
+      break;
+    case 'polynomial':
+      {
+        const { degree, zones } = options;
+        let reduced = xyEquallySpaced(
+          { x, y: re },
+          { numberOfPoints: 4096, zones },
+        );
+        let result = baselineRegression(reduced.x, reduced.y, {
+          regressionOptions: degree,
+        });
+        let { regression } = result;
+        corrected = new Float64Array(x.length);
+        for (let i = 0; i < re.length; i++) {
+          corrected[i] = re[i] - regression.predict(x[i]);
+        }
+      }
+
+      break;
+    default:
+      // eslint-disable-next-line @typescript-eslint/restrict-template-expressions
+      throw new Error(`baselineCorrection: algorithm unknown: ${algorithm}`);
+  }
+
+  Object.assign(datum1D.data, { re: corrected });
+}
+
+export function isApplicable(datum1D: Entry1D) {
+  if (!datum1D.info.isFid) return true;
+  return false;
+}
+
+export function reduce(
+  previousValue: BaselineCorrectionOptions,
+  newValue: BaselineCorrectionOptions,
+) {
+  return {
+    once: true,
+    reduce: newValue,
+  };
+}

package/src/datum/data1d/filter1d/digitalFilter.ts

@@ -0,0 +1,66 @@
+import { Data1D } from '../../../types/Data1D';
+import { Info1D } from '../../../types/Info/Info1D';
+import { FilterDomainUpdateRules } from '../../FiltersManager';
+import { Entry1D } from '../Entry1D';
+
+export const id = 'digitalFilter';
+export const name = 'Digital Filter';
+export const DOMAIN_UPDATE_RULES: Readonly<FilterDomainUpdateRules> = {
+  updateXDomain: true,
+  updateYDomain: true,
+};
+
+type Entry1DDigitalFilter = Partial<Omit<Entry1D, 'info'>> &
+  Required<Pick<Entry1D, 'data' | 'filters'>> & { info: Partial<Info1D> };
+
+/**
+ * Move points from the beginning to the end of FID and performs a first order phase correction
+ * @param {Datum1d} datum1d
+ */
+
+export function apply(spectrum: Entry1DDigitalFilter, options: any = {}) {
+  if (!isApplicable(spectrum)) {
+    throw new Error('Digital Filter is not applicable on this data');
+  }
+  let { digitalFilterValue } = options;
+
+  if (!digitalFilterValue) {
+    digitalFilterValue = spectrum.info.digitalFilter || 0;
+    const filter = spectrum.filters.find((filter) => filter.name === id);
+    if (filter) {
+      filter.value = { digitalFilterValue };
+    }
+  }
+
+  let re = new Float64Array(spectrum.data.re);
+  let im = new Float64Array(spectrum.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);
+
+  spectrum.data.re = newRe;
+  spectrum.data.im = newIm;
+}
+
+export function isApplicable(
+  datum1D: Entry1DDigitalFilter,
+): datum1D is Entry1DDigitalFilter & { data: Required<Data1D> } {
+  if (datum1D.info.isComplex && datum1D.info.isFid) return true;
+  return false;
+}
+
+export function reduce() {
+  return {
+    once: true,
+    reduce: undefined,
+  };
+}

package/src/datum/data1d/filter1d/equallySpaced.ts

@@ -0,0 +1,66 @@
+import { xEnsureFloat64, xyEquallySpaced } from 'ml-spectra-processing';
+
+import { FilterDomainUpdateRules } from '../../FiltersManager';
+import { Entry1D } from '../Entry1D';
+
+export const id = 'equallySpaced';
+export const name = 'Equally spaced';
+export const DOMAIN_UPDATE_RULES: Readonly<FilterDomainUpdateRules> = {
+  updateXDomain: false,
+  updateYDomain: false,
+};
+
+/**
+ * Equally Spaced
+ * **
+ * Function that returns a Number array of equally spaced numberOfPoints
+ * containing a representation of intensities of the spectra arguments x
+ * and y.
+ *
+ * The options parameter contains an object in the following form:
+ * from: starting point
+ * to: last point
+ * numberOfPoints: number of points between from and to
+ * variant: "slot" or "smooth" - smooth is the default option
+ *
+ * The slot variant consist that each point in the new array is calculated
+ * averaging the existing points between the slot that belongs to the current
+ * value. The smooth variant is the same but takes the integral of the range
+ * of the slot and divide by the step size between two points in the new array.
+ *
+ * @param {Array<{from:number;to:number}>} options.exclusions
+ */
+
+export function apply(spectrum: Entry1D, options: any = {}) {
+  if (!isApplicable(spectrum)) {
+    throw new Error('Equally Spaced is not applicable on this data');
+  }
+  const { from, to, numberOfPoints, exclusions } = options;
+  const { x, re, im } = spectrum.data;
+  const XREdata = xyEquallySpaced(
+    { x, y: re },
+    { from, to, numberOfPoints, exclusions },
+  );
+
+  spectrum.data.x = xEnsureFloat64(XREdata.x);
+  spectrum.data.re = xEnsureFloat64(XREdata.y);
+  if (im) {
+    const XIMdata = xyEquallySpaced(
+      { x, y: re },
+      { from, to, numberOfPoints, exclusions },
+    );
+    spectrum.data.im = xEnsureFloat64(XIMdata.y);
+  }
+}
+
+export function isApplicable(spectrum: Entry1D) {
+  if (spectrum.info.isComplex && !spectrum.info.isFid) return true;
+  return false;
+}
+
+export function reduce() {
+  return {
+    once: false,
+    reduce: null,
+  };
+}

package/src/datum/data1d/filter1d/exclusionZones.ts

@@ -0,0 +1,34 @@
+import { xySetYValue, zonesNormalize } from 'ml-spectra-processing';
+
+import { FilterDomainUpdateRules } from '../../FiltersManager';
+import { Entry1D } from '../Entry1D';
+
+export const id = 'exclusionZones';
+export const name = 'Exclusion zones';
+export const DOMAIN_UPDATE_RULES: Readonly<FilterDomainUpdateRules> = {
+  updateXDomain: false,
+  updateYDomain: false,
+};
+
+export function apply(spectrum: Entry1D, zones = []) {
+  if (!isApplicable(spectrum)) {
+    throw new Error('Exclusion Zones filter not applicable on this data');
+  }
+  const { x, re, im } = spectrum.data;
+  spectrum.data.re = Float64Array.from(xySetYValue({ x, y: re }, { zones }).y);
+  spectrum.data.im = im
+    ? Float64Array.from(xySetYValue({ x, y: re }, { zones }).y)
+    : im;
+}
+
+export function isApplicable(spectrum: Entry1D) {
+  if (spectrum.info.isFt) return true;
+  return false;
+}
+
+export function reduce(previousValue: any, newValue: any) {
+  return {
+    once: true,
+    reduce: zonesNormalize(previousValue.concat(newValue)),
+  };
+}

package/src/datum/data1d/filter1d/fft.ts

@@ -0,0 +1,143 @@
+import {
+  DataReIm,
+  reimFFT,
+  reimPhaseCorrection,
+  xMean,
+} from 'ml-spectra-processing';
+
+import { Data1D } from '../../../types/Data1D';
+import { Info1D } from '../../../types/Info/Info1D';
+import { FilterDomainUpdateRules } from '../../FiltersManager';
+import { Entry1D } from '../Entry1D';
+
+import { padDataToNextPowerOfTwo } from './utils/padDataToNextPowerOfTwo';
+
+export const id = 'fft';
+export const name = 'FFT';
+export const DOMAIN_UPDATE_RULES: Readonly<FilterDomainUpdateRules> = {
+  updateXDomain: true,
+  updateYDomain: true,
+};
+
+type Entry1DFt = Partial<Omit<Entry1D, 'info'>> &
+  Required<Pick<Entry1D, 'data' | 'filters'>> & { info: Partial<Info1D> };
+
+export function apply(datum1D: Entry1DFt) {
+  if (!isApplicable(datum1D)) {
+    throw new Error('fft not applicable on this data');
+  }
+
+  checkSameLength(datum1D);
+
+  let digitalFilterApplied = datum1D.filters.some(
+    (e) => e.name === 'digitalFilter' && e.flag,
+  );
+
+  const {
+    info: { aqMod },
+  } = datum1D;
+
+  if (aqMod === 1) {
+    removeDCOffset(datum1D, digitalFilterApplied);
+  }
+
+  if (!isPowerOfTwo(datum1D.data.x.length)) {
+    padDataToNextPowerOfTwo(datum1D, digitalFilterApplied);
+  }
+
+  const { data, info } = datum1D;
+  Object.assign(
+    data,
+    reimFFT(
+      {
+        re: data.re,
+        im: data.im,
+      },
+      { applyZeroShift: true },
+    ),
+  );
+
+  if (digitalFilterApplied) {
+    let { digitalFilter = 0 } = info;
+    let ph1 = (digitalFilter - Math.floor(digitalFilter)) * Math.PI * 2;
+    Object.assign(
+      data,
+      reimPhaseCorrection(data as DataReIm, 0, -ph1, { reverse: true }),
+    );
+  }
+
+  datum1D.data.x = generateXAxis(datum1D);
+  datum1D.info = { ...datum1D.info, isFid: false, isFt: true };
+}
+
+export function isApplicable(
+  datum1D: Entry1DFt,
+): datum1D is Entry1DFt & { data: Required<Data1D> } {
+  if (datum1D.info.isComplex && datum1D.info.isFid) return true;
+  return false;
+}
+
+export function reduce() {
+  return {
+    once: true,
+    reduce: undefined,
+  };
+}
+
+function generateXAxis(datum1D: Entry1DFt) {
+  const info = datum1D.info;
+  const baseFrequency = Number(info.baseFrequency);
+  const frequencyOffset = Number(info.frequencyOffset);
+  const spectralWidth = Number(info.spectralWidth);
+  const offset = frequencyOffset / baseFrequency;
+  let spectralHalfWidth = 0.5 * spectralWidth;
+  let nbPoints = datum1D.data.x.length;
+  let firstPoint = offset - spectralHalfWidth;
+  let dx = spectralWidth / (nbPoints - 1);
+  const xAxis = new Float64Array(nbPoints);
+  for (let i = 0; i < nbPoints; i++) {
+    xAxis[i] = firstPoint;
+    firstPoint += dx;
+  }
+  return xAxis;
+}
+
+function isPowerOfTwo(n: number) {
+  return n !== 0 && (n & (n - 1)) === 0;
+}
+
+function removeDCOffset(
+  spectrum: Partial<Entry1DFt> & { data: Required<Data1D> },
+  digitalFilterApplied: boolean,
+) {
+  let { digitalFilter = 0 } =
+    digitalFilterApplied && spectrum.info ? spectrum.info : {};
+  const data = spectrum.data;
+  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 - digitalFilter),
+  );
+  const averageIm = xMean(
+    data.im.slice((nbPoints * 0.75) >> 0, nbPoints - digitalFilter),
+  );
+  for (
+    let i = digitalFilterApplied ? 0 : digitalFilter;
+    i < nbPoints - digitalFilter;
+    i++
+  ) {
+    newRe[i] -= averageRe;
+    newIm[i] -= averageIm;
+  }
+
+  Object.assign(spectrum.data, { re: newRe, im: newIm });
+  return spectrum;
+}
+
+function checkSameLength(spectrum: { data: Required<Data1D> }) {
+  const { data } = spectrum;
+  if (data.x.length !== data.re.length || data.x.length !== data.im.length) {
+    throw new Error('The length of data should be equal');
+  }
+}