fix: negative peak picking

refactor: rename function maxValue to maxAbsoluteValue

src/component/1d/tool/PeakPointer.tsx

@@ -1,14 +1,13 @@
-import max from 'ml-array-max';
 import { Spectrum1D } from 'nmr-load-save';
 
-import { get1DDataXY } from '../../../data/data1d/Spectrum1D/get1DDataXY';
 import { useBrushTracker } from '../../EventsTrackers/BrushTracker';
 import { useMouseTracker } from '../../EventsTrackers/MouseTracker';
 import { useChartData } from '../../context/ChartContext';
 import { useScaleChecked } from '../../context/ScaleContext';
 import { useActiveSpectrum } from '../../hooks/useActiveSpectrum';
 import useSpectraByActiveNucleus from '../../hooks/useSpectraPerNucleus';
 import { options } from '../../toolbar/ToolTypes';
+import { getClosePeak } from '../../utility/getClosePeak';
 
 const styles = {
   radius: 10,
@@ -18,31 +17,8 @@ const styles = {
   SVGPadding: 1,
 };
 
-interface PeakPosition {
-  x: number;
-  y: number;
-}
-
 const LookWidth = 10;
 
-function getClosePeak(
-  spectrum: Spectrum1D,
-  range: number[],
-): PeakPosition | null {
-  const datum = get1DDataXY(spectrum);
-  const maxIndex = datum.x.findIndex((number) => number >= range[1]) - 1;
-  const minIndex = datum.x.findIndex((number) => number >= range[0]);
-
-  const yDataRange = datum.y.slice(minIndex, maxIndex);
-  if (!yDataRange || yDataRange.length === 0) return null;
-
-  const y = max(yDataRange);
-  const xIndex = minIndex + yDataRange.indexOf(y);
-  const x = datum.x[xIndex];
-
-  return { x, y };
-}
-
 function PeakPointer() {
   const {
     height,
@@ -74,14 +50,17 @@ function PeakPointer() {
 
   if (spectrumIndex === -1) return null;
 
-  const range = [
+  const [from, to] = [
     scaleX().invert(position.x - LookWidth),
     scaleX().invert(position.x + LookWidth),
   ].sort((a, b) => {
     return a - b;
   });
 
-  const closePeak = getClosePeak(spectra[spectrumIndex] as Spectrum1D, range);
+  const closePeak = getClosePeak(spectra[spectrumIndex] as Spectrum1D, {
+    from,
+    to,
+  });
   if (!closePeak) return null;
 
   const x = scaleX()(closePeak.x);

src/component/reducer/actions/PeaksActions.ts

@@ -1,5 +1,4 @@
 import { v4 } from '@lukeed/uuid';
-import { NmrData1D } from 'cheminfo-types';
 import { Draft, original } from 'immer';
 import { xFindClosestIndex } from 'ml-spectra-processing';
 import {
@@ -12,7 +11,6 @@ import { Peak1D, OptionsXYAutoPeaksPicking } from 'nmr-processing';
 
 import {
   getShiftX,
-  lookupPeak,
   autoPeakPicking,
   optimizePeaks,
 } from '../../../data/data1d/Spectrum1D';
@@ -23,6 +21,7 @@ import { State } from '../Reducer';
 import { getActiveSpectrum } from '../helper/getActiveSpectrum';
 import getRange from '../helper/getRange';
 import { ActionType } from '../types/ActionType';
+import { getClosePeak } from '../../utility/getClosePeak';
 
 type AddPeakAction = ActionType<'ADD_PEAK', { x: number }>;
 type AddPeaksAction = ActionType<'ADD_PEAKS', { startX: number; endX: number }>;
@@ -74,7 +73,7 @@ function handleAddPeak(draft: Draft<State>, action: AddPeakAction) {
     const startX = mouseXPosition - xShift;
     const endX = mouseXPosition + xShift;
     const [from, to] = getRange(draft, { startX, endX });
-    const candidatePeak = lookupPeak(state.data[index].data as NmrData1D, {
+    const candidatePeak = getClosePeak(state.data[index] as Spectrum1D, {
       from,
       to,
     });
@@ -108,7 +107,7 @@ function handleAddPeaks(draft: Draft<State>, action: AddPeaksAction) {
     const [from, to] = getRange(draft, { startX, endX });
 
     if (from !== to) {
-      const peak = lookupPeak(datumOriginal.data, { from, to });
+      const peak = getClosePeak(datumOriginal, { from, to });
 
       const shiftX = getShiftX(draft.data[index] as Spectrum1D);
 

src/component/utility/getClosePeak.ts

@@ -0,0 +1,32 @@
+import { Spectrum1D } from 'nmr-load-save';
+
+import { get1DDataXY } from '../../data/data1d/Spectrum1D';
+
+import { maxAbsoluteValue } from './maxAbsoluteValue';
+
+interface PeakPosition {
+  x: number;
+  y: number;
+}
+
+export function getClosePeak(
+  spectrum: Spectrum1D,
+  lookRange: {
+    from: number;
+    to: number;
+  },
+): PeakPosition | null {
+  const { from, to } = lookRange;
+  const datum = get1DDataXY(spectrum);
+  const maxIndex = datum.x.findIndex((number) => number >= to) - 1;
+  const minIndex = datum.x.findIndex((number) => number >= from);
+
+  const yDataRange = datum.y.slice(minIndex, maxIndex);
+  if (!yDataRange || yDataRange.length === 0) return null;
+
+  const y = maxAbsoluteValue(yDataRange);
+  const xIndex = minIndex + yDataRange.indexOf(y);
+  const x = datum.x[xIndex];
+
+  return { x, y };
+}

src/component/utility/maxAbsoluteValue.ts

@@ -0,0 +1,31 @@
+import { NumberArray } from 'cheminfo-types';
+import {
+  XGetFromToIndexOptions,
+  xCheck,
+  xGetFromToIndex,
+} from 'ml-spectra-processing';
+
+//This function is an adapted version of the xMaxAbsoluteValue function from ml-spectra-processing. It identifies the maximum absolute value and returns the corresponding maximum value along with its sign
+export function maxAbsoluteValue(
+  array: NumberArray,
+  options: XGetFromToIndexOptions = {},
+): number {
+  xCheck(array);
+
+  const { fromIndex, toIndex } = xGetFromToIndex(array, options);
+  let maxValue = array[fromIndex];
+  let sign = 1;
+
+  for (let i = fromIndex + 1; i <= toIndex; i++) {
+    if (array[i] >= 0) {
+      if (array[i] > maxValue) {
+        maxValue = array[i];
+        sign = 1;
+      }
+    } else if (-array[i] > maxValue) {
+      maxValue = -array[i];
+      sign = Math.sign(array[i]);
+    }
+  }
+  return maxValue * sign;
+}

src/data/data1d/Spectrum1D/index.ts

@@ -5,7 +5,6 @@ export { initiateDatum1D } from './initiateDatum1D';
 export { changeIntegralsRelative } from './integrals/changeIntegralsRelative';
 export { isSpectrum1D } from './isSpectrum1D';
 export { autoPeakPicking } from './peaks/autoPeakPicking';
-export { lookupPeak } from './peaks/lookupPeak';
 export { optimizePeaks } from './peaks/optimizePeaks';
 export { addRange } from './ranges/addRange';
 export { changeRange } from './ranges/changeRange';