nmr-processing 3.4.1 → 4.0.0

package/src/peaks/util/jAnalyzer.ts

@@ -219,13 +219,13 @@ function updateSignal(signal: SignalInternMandatory, jCouplings: number[]) {
   // Update the limits of the signal
   let peaks = signal.peaksComp; // Always in Hz
   let nbPeaks = peaks.length;
-  signal.startX = peaks[0].x / signal.observe - peaks[0].shape.width;
+  signal.startX = peaks[0].x / signal.observe - peaks[0].width;
   signal.stopX =
-    peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].shape.width;
+    peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].width;
   signal.integralData.from =
-    peaks[0].x / signal.observe - peaks[0].shape.width * 3;
+    peaks[0].x / signal.observe - peaks[0].width * 3;
   signal.integralData.to =
-    peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].shape.width * 3;
+    peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].width * 3;
   // Compile the pattern and format the constant couplings
   signal.maskPattern = signal.mask2;
   signal.multiplicity = abstractPattern(signal, jCouplings);
@@ -466,9 +466,7 @@ function symmetrize(
     peaks[i] = {
       x: peak[jAxis] * newSignal.observe,
       intensity: peak[intensity],
-      shape: {
-        width: peak.shape.width,
-      },
+      width: peak.width,
     };
   }
   // Join the peaks that are closer than 0.25 Hz
@@ -480,7 +478,7 @@ function symmetrize(
       peaks[i].intensity = peaks[i].intensity + peaks[i + 1].intensity;
       peaks[i].x /= peaks[i].intensity;
       peaks[i].intensity /= 2;
-      peaks[i].shape.width += peaks[i + 1].shape.width;
+      peaks[i].width += peaks[i + 1].width;
       peaks.splice(i + 1, 1);
     }
   }
@@ -528,11 +526,11 @@ function symmetrize(
         if (Math.abs(diffL - diffR) < maxError) {
           avg = Math.min(peaks[left].intensity, peaks[right].intensity);
           avgWidth = Math.min(
-            peaks[left].shape.width,
-            peaks[right].shape.width,
+            peaks[left].width,
+            peaks[right].width,
           );
           peaks[left].intensity = peaks[right].intensity = avg;
-          peaks[left].shape.width = peaks[right].shape.width = avgWidth;
+          peaks[left].width = peaks[right].width = avgWidth;
           middle = [
             middle[0] + (peaks[right].x + peaks[left].x) / 2,
             middle[1] + 1,
@@ -712,5 +710,5 @@ function chemicalShift(peaks: Peak1DIntern[], mask: boolean[] = []) {
  * @private
  */
 function getArea(peak: Peak1DIntern) {
-  return Math.abs(peak.intensity * peak.shape.width * 1.57); // 1.772453851);
+  return Math.abs(peak.intensity * peak.width * 1.57); // 1.772453851);
 }

package/src/ranges/rangesToXY.ts

@@ -1,7 +1,7 @@
 import { DoubleArray } from 'cheminfo-types';
 import arraySequentialFill from 'ml-array-sequential-fill';
+import type { Shape1D } from 'ml-peak-shape-generator';
 import { SpectrumGenerator } from 'spectrum-generator';
-import type { Shape1DOptions } from 'spectrum-generator';
 
 import { hackSignalsToXY } from '../signals/hackSignalsToXY';
 import type { MakeMandatory } from '../types/MakeMandatory';
@@ -40,7 +40,7 @@ export interface RangeToXYOptions {
    * options of signals.
    * @default { kind: 'gaussian' }
    */
-  shape: Shape1DOptions;
+  shape: Shape1D;
 }
 function checkForSignals(
   ranges: NMRRange[],

package/src/signals/signalsToXY.ts

@@ -1,6 +1,6 @@
 import rescale from 'ml-array-rescale';
 import arraySequentialFill from 'ml-array-sequential-fill';
-import type { Shape1DOptions } from 'spectrum-generator';
+import type { Shape1D } from 'ml-peak-shape-generator';
 
 import type { MakeMandatory } from '../types/MakeMandatory';
 import type { NMRSignal1D } from '../types/NMRSignal1D';
@@ -25,7 +25,7 @@ export interface OptionsSignalsToXY {
   /**
    * Shape options for ml-spectrum-generator
    */
-  shape?: Shape1DOptions;
+  shape?: Shape1D;
   /**
    * The linewidth of the output spectrum, expresed in Hz.
    * @default 1

package/src/signals/simulation/simulate1D.ts

@@ -1,9 +1,10 @@
 import binarySearch from 'binary-search';
+import { DataXY } from 'cheminfo-types';
 import { Matrix, EVD } from 'ml-matrix';
 import type { Matrix as MatrixClassType } from 'ml-matrix';
+import type { Shape1D } from 'ml-peak-shape-generator';
 import { SparseMatrix } from 'ml-sparse-matrix';
 import { SpectrumGenerator } from 'spectrum-generator';
-import type { Shape1DOptions } from 'spectrum-generator';
 
 import type { SpinSystem } from '../../types/spinSystem';
 
@@ -46,7 +47,7 @@ interface Simulate1DOptions {
    * Shape options
    * @default {kind:'gaussian'}
    */
-  shape?: Shape1DOptions;
+  shape?: Shape1D;
 }
 
 /**
@@ -59,7 +60,7 @@ export default function simulate1D(
    */
   spinSystem: SpinSystem,
   options: Simulate1DOptions = {},
-) {
+): DataXY {
   let {
     lineWidth = 1,
     maxClusterSize = 8,

package/src/types/NMRPeak1D.ts

@@ -1,11 +1,5 @@
-export interface NMRPeak1D {
+import type { Peak1D } from 'ml-gsd';
+
+export interface NMRPeak1D extends Peak1D {
   kind?: string;
-  x: number;
-  y: number;
-  shape: {
-    width: number;
-    noiseLevel?: number;
-    soft?: boolean;
-    kind?: string;
-  };
 }

package/src/xy/xyAutoPeaksPicking.ts

@@ -1,12 +1,17 @@
 import { DataXY } from 'cheminfo-types';
 import { gsd, joinBroadPeaks, optimizePeaks } from 'ml-gsd';
+import type {
+  Peak1D,
+  IGSDOptions,
+  IOptimizePeaksOptions,
+  IJoinBroadPeaksOptions,
+} from 'ml-gsd';
 import {
   xyExtract,
   xNoiseSanPlot,
   xAbsoluteMedian,
 } from 'ml-spectra-processing';
 
-import type { NMRPeak1D } from '../types/NMRPeak1D';
 /**
  * Implementation of the peak picking method described by Cobas in:
  * A new approach to improving automated analysis of proton NMR spectra
@@ -20,63 +25,19 @@ interface OptionsGetCutOff {
   thresholdFactor: number;
 }
 
-interface OptionsGetPeakList {
-  /**
-   * Noise threshold in spectrum y units. Default is three/thresholdFactor times the absolute median of data.y.
-   * @default `median(data.y) * (options.thresholdFactor || 3)`
-   */
-  noiseLevel?: number;
-  /**
-   * Threshold to determine if a given peak should be considered as a noise, bases on its relative height compared to the highest peak.
-   * @default 0.01
-   */
-  minMaxRatio: number;
-  /**
-   * If broadRatio is higher than 0, then all the peaks which second derivative smaller than broadRatio * maxAbsSecondDerivative will be marked with the soft mask equal to true.
-   * @default 0.00025
-   */
-  broadRatio: number;
-  /**
-   * Select the peak intensities from a smoothed version of the independent variables.
-   * @default true
-   */
-  smoothY: boolean;
+export interface IGetPeakListOptions
+  extends IGSDOptions,
+    IOptimizePeaksOptions,
+    IJoinBroadPeaksOptions {
   /**
    * If it is true, the peaks parameters will be optimized.
    * @default false
    */
   optimize: boolean;
-  /**
-   * factor to determine the width at the moment to group the peaks in signals in 'GSD.optimizePeaks' function.
-   * @default 4
-   */
-  factorWidth: number;
-  /**
-   * if it is true, it optimizes the x and intensity by extrapolation.
-   */
-  realTopDetection: boolean;
-  /**
-   * options to shape used to adapt the FWHM
-   * @default {kind:'gaussian'}
-   */
-  shape: { kind: string };
-  /**
-   * options for optimization step, kind represent the algorithm
-   * @default {kind:'lm'}
-   */
-  optimization: { kind: string };
-  /**
-   * Threshold to determine if some peak is candidate to clustering into range.
-   * @default 0.25
-   */
-  broadWidth: number;
-  /**
-   * Options for savitz Golay
-   */
-  sgOptions: { windowSize: number; polynomial: number };
 }
 
-export interface OptionsXYAutoPeaksPicking extends Partial<OptionsGetPeakList> {
+export interface OptionsXYAutoPeaksPicking
+  extends Partial<IGetPeakListOptions> {
   /**
    * Low limit value in the x axis to extract a sub set of points from the input data.
    */
@@ -105,7 +66,7 @@ export interface OptionsXYAutoPeaksPicking extends Partial<OptionsGetPeakList> {
 export function xyAutoPeaksPicking(
   data: DataXY,
   options: OptionsXYAutoPeaksPicking = {},
-): NMRPeak1D[] {
+): Peak1D[] {
   const {
     from,
     to,
@@ -131,7 +92,7 @@ export function xyAutoPeaksPicking(
 
   const cutOff = getCutOff(data.y, { noiseLevel, useSanPlot, thresholdFactor });
 
-  let getPeakOptions = {
+  let getPeakOptions: IGetPeakListOptions = {
     shape,
     broadWidth,
     optimize,
@@ -154,7 +115,7 @@ export function xyAutoPeaksPicking(
   return peaks;
 }
 
-function getPeakList(data: DataXY, options: OptionsGetPeakList) {
+function getPeakList(data: DataXY, options: IGetPeakListOptions) {
   const {
     shape,
     broadWidth,
@@ -173,15 +134,15 @@ function getPeakList(data: DataXY, options: OptionsGetPeakList) {
     shape,
     sgOptions,
     minMaxRatio,
-    broadRatio,
     noiseLevel,
     smoothY,
     realTopDetection,
   });
 
   if (broadWidth) {
-    peakList = joinBroadPeaks(peakList, {
-      width: broadWidth,
+    peakList = joinBroadPeaks(data, peakList, {
+      broadRatio,
+      broadWidth,
       shape,
       optimization,
     });
@@ -198,7 +159,7 @@ function getPeakList(data: DataXY, options: OptionsGetPeakList) {
   return peakList;
 }
 
-function getNegativePeaks(data: DataXY, options: OptionsGetPeakList) {
+function getNegativePeaks(data: DataXY, options: IGetPeakListOptions) {
   let { x, y } = data;
   let negativeDataY = new Float64Array(data.y.length);
   for (let i = 0; i < negativeDataY.length; i++) {

package/src/types/ml-gsd/index.d.ts

@@ -1,164 +0,0 @@
-declare module 'ml-gsd' {
-  export interface XYNumberArray {
-    x: Array<number> | Float64Array;
-    y: Array<number> | Float64Array;
-  }
-
-  export interface GSDOptions {
-    /**
-     * Noise threshold in spectrum y units. Default is three/thresholdFactor times the absolute median of data.y.
-     * @default `median(data.y) * (options.thresholdFactor || 3)`
-     */
-    noiseLevel?: number;
-    /**
-     * Threshold to determine if a given peak should be considered as a noise, bases on its relative height compared to the highest peak.
-     * @default 0.01
-     */
-    minMaxRatio?: number;
-    /**
-     * If broadRatio is higher than 0, then all the peaks which second derivative smaller than broadRatio * maxAbsSecondDerivative will be marked with the soft mask equal to true.
-     * @default 0.00025
-     */
-    broadRatio?: number;
-    /**
-     * Select the peak intensities from a smoothed version of the independent variables.
-     * @default true
-     */
-    smoothY?: boolean;
-    /**
-     * if it is true, it optimizes the x and intensity by extrapolation.
-     * @default false
-     */
-    realTopDetection?: boolean;
-    /**
-     * options to shape used to adapt the FWHM
-     * @default {kind:'gaussian'}
-     */
-    shape?: { kind: string };
-    /**
-     * Options for savitz Golay
-     */
-    sgOptions?: { windowSize: number; polynomial: number };
-    /**
-     * filter based on intensity of the first derive.
-     * @default -1
-     */
-    /**
-     * Peaks are local maximum(true) or minimum(false)
-     * @default true
-     */
-    maxCriteria?: boolean;
-    /**
-     * Filters based on the amplitude of the first derivative
-     * @default -1
-     */
-    derivativeThreshold?: number;
-    /**
-     * Factor to multiply the calculated height (usually 2)
-     * @default 0
-     */
-    heightFactor?: number;
-  }
-
-  export interface GSDPeak {
-    x: number;
-    y: number;
-    shape: {
-      width: number;
-      noiseLevel?: number;
-      soft?: boolean;
-      kind?: string;
-    };
-  }
-
-  export interface OptimizePeaksOptions {
-    /**
-     * factor to determine the width at the moment to group the peaks in signals in 'GSD.optimizePeaks' function.
-     * @default 1
-     */
-    factorWidth?: number;
-    /**
-     * times of width to use to optimize peaks
-     * @default 2
-     */
-    factorLimits?: number;
-    /**
-     * options to shape used to adapt the FWHM
-     * @default {kind:'gaussian'}
-     */
-    shape?: { kind: string };
-    /**
-     * options for optimization step
-     */
-    optimization?: OptimizationOptions;
-  }
-
-  export interface OptimizationOptions {
-    /**
-     * represent the algorithm to optimize.
-     * @default {kind:'lm'}
-     */
-    kind?: string;
-    /**
-     * Time limit to stop the optimization in seconds.
-     * @default 10
-     */
-    timeout?: number;
-  }
-
-  export interface OptimizedPeak {
-    x: number;
-    y: number;
-    shape: {
-      width: number;
-      noiseLevel?: number;
-      soft?: boolean;
-      kind?: string;
-      mu?: number;
-    };
-  }
-
-  export function gsd(data: XYNumberArray, options?: GSDOptions): GSDPeak[];
-
-  export function optimizePeaks(
-    data: XYNumberArray,
-    peakList: GSDPeak[],
-    options?: OptimizePeaksOptions,
-  ): OptimizedPeak[];
-
-  export function joinBroadPeaks(
-    peakList: GSDPeak[],
-    options?: JoinBroadPeaksOptions,
-  ): GSDPeak[];
-
-  export interface JoinBroadPeaksOptions {
-    /**
-     * @default 0.25
-     */
-    width: number;
-    /**
-     * @default { kind: 'gaussian' }
-     */
-    shape: { kind: string };
-    /**
-     * @default { kind: 'lm', timeout: 10 }
-     */
-    optimization: OptimizationOptions;
-  }
-
-  export function groupPeaks(peakList: GSDPeak[], factor?: number): GSDPeak[][];
-
-  export function broadenPeaks(
-    peakList: GSDPeak[],
-    options?: {
-      /**
-       * @default 2
-       */
-      factor: number;
-      /**
-       * @default false
-       */
-      overlap: boolean;
-    },
-  ): GSDPeak[];
-}