add negative peaks to 2D spectra

package.json

@@ -49,19 +49,19 @@
     "@types/d3-random": "^3.0.3",
     "@types/jest": "^29.5.12",
     "cheminfo-build": "^1.2.0",
-    "cheminfo-types": "^1.7.2",
+    "cheminfo-types": "^1.7.3",
     "eslint": "^8.57.0",
-    "eslint-config-cheminfo-typescript": "^12.2.0",
+    "eslint-config-cheminfo-typescript": "^12.4.0",
     "jest": "^29.7.0",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "ml-savitzky-golay-generalized": "^4.0.1",
-    "prettier": "^3.2.5",
-    "rimraf": "^5.0.5",
-    "ts-jest": "^29.1.2",
-    "typescript": "^5.4.2"
+    "ml-savitzky-golay-generalized": "^4.2.0",
+    "prettier": "^3.3.2",
+    "rimraf": "^5.0.7",
+    "ts-jest": "^29.1.4",
+    "typescript": "^5.4.5"
   },
   "dependencies": {
     "ml-peak-shape-generator": "^4.1.2",
-    "ml-spectra-processing": "^14.2.0"
+    "ml-spectra-processing": "^14.5.0"
   }
 }

src/Spectrum2DGenerator.ts

@@ -1,10 +1,11 @@
+import { NumberArray } from 'cheminfo-types';
 import { getShape2D, Shape2DClass } from 'ml-peak-shape-generator';
 import type {
   Shape2D,
   Shape2DInstance,
   XYNumber,
 } from 'ml-peak-shape-generator';
-import { matrixMinMaxZ } from 'ml-spectra-processing';
+import { matrixCreateEmpty, matrixMinMaxZ } from 'ml-spectra-processing';
 
 import type { Data2D } from './types/Data2D';
 import type { Peak2D, Peak2DSeries } from './types/Peaks2D';
@@ -27,12 +28,12 @@ const convertWidthToFWHM = (shape: Shape2DClass, width: number | XYNumber) => {
 
 export interface OptionsSG2D {
   /**
-   * First x value (inclusive).
+   * First xy value (inclusive).
    * @default `0`
    */
   from?: number | XYNumber;
   /**
-   * Last x value (inclusive).
+   * Last xy value (inclusive).
    * @default `100`
    */
   to?: number | XYNumber;
@@ -99,7 +100,7 @@ export interface Spectrum2D {
   maxY: number;
   minZ: number;
   maxZ: number;
-  z: Float64Array[] | number[][];
+  z: NumberArray[];
 }
 
 export class Spectrum2DGenerator {
@@ -145,7 +146,10 @@ export class Spectrum2DGenerator {
     this.data = {
       x: new Float64Array(nbPoints.x),
       y: new Float64Array(nbPoints.y),
-      z: createMatrix(this.nbPoints),
+      z: matrixCreateEmpty({
+        nbRows: this.nbPoints.y,
+        nbColumns: this.nbPoints.x,
+      }),
     };
 
     for (const axis of axis2D) {
@@ -289,7 +293,7 @@ export class Spectrum2DGenerator {
             this.data.x[xIndex] - position.x,
             this.data.y[yIndex] - position.y,
           );
-        if (value > 1e-6) {
+        if (Math.abs(value) > 1e-6) {
           this.data.z[yIndex][xIndex] += value;
         }
       }
@@ -367,11 +371,3 @@ function assertNumber(value: number, name: string) {
     throw new TypeError(`${name} option must be a number`);
   }
 }
-
-function createMatrix(nbPoints: XYNumber) {
-  const zMatrix = new Array(nbPoints.y);
-  for (let i = 0; i < nbPoints.y; i++) {
-    zMatrix[i] = new Float64Array(nbPoints.x);
-  }
-  return zMatrix;
-}

src/__tests__/generateSpectrum2D.test.ts

@@ -1,4 +1,4 @@
-import { xMaxValue } from 'ml-spectra-processing';
+import { xMaxValue, xMinMaxValues } from 'ml-spectra-processing';
 
 import type { Spectrum2D } from '../Spectrum2DGenerator';
 import { generateSpectrum2D } from '../Spectrum2DGenerator';
@@ -66,6 +66,31 @@ describe('generateSpectrum with one peak and small window', () => {
     checkMax(spectrum, 10);
   });
 
+  it('should have negative min value', () => {
+    const spectrum = generateSpectrum2D(
+      [
+        { x: 1, y: 1, z: 0.3, width: 0.01 },
+        { x: 1.3, y: 0.8, z: -0.3, width: 0.01 },
+      ],
+      {
+        generator: {
+          nbPoints: 101,
+          from: { x: 0.6, y: 0.6 },
+          to: { x: 2, y: 1.5 },
+        },
+      },
+    );
+
+    let max = Number.MIN_SAFE_INTEGER;
+    let min = Number.MAX_SAFE_INTEGER;
+    for (const row of spectrum.z) {
+      const rowMinMax = xMinMaxValues(row);
+      if (max < rowMinMax.max) max = rowMinMax.max;
+      if (min > rowMinMax.min) min = rowMinMax.min;
+    }
+    expect(max).toBeCloseTo(0.3, 0);
+    expect(min).toBeCloseTo(-0.3, 0);
+  });
   it('should work with shape 17/4, peak width 0.2', () => {
     const spectrum = generateSpectrum2D([[10, 10, 1]], {
       generator: {