feat: carbon solvent labelling (#3693)

* feat: example of auto ranges options to works with carbon spectrum and solvent labelling

* chore: compile only if nucleus is a proton

* chore: fix peaksFilterImpurities by updating nmr-processing

* chore: handle sensitivity from the options of autoPeakPicking function

* chore: set default sensitivity to 100

* chore: default sensitivity to 100

* chore: move the rangePicking option and use the info.nucleus instead of view information

* chore: update nmr-processing to 19.3.2

* chore: adapt ranges panel test case to new result

Author: jobo322

src/component/reducer/actions/RangesActions.ts

@@ -231,12 +231,15 @@ function handleAutoRangesDetection(
     const detectionOptions: any = {
       rangePicking: {
         integrationSum: 100,
-        compile: true,
-        frequencyCluster: 16,
+        compile: nucleus === '1H',
+        frequencyCluster: nucleus === '1H' ? 16 : 0,
         clean: 0.3,
         keepPeaks: true,
+        joinOverlapRanges: nucleus === '1H',
       },
       peakPicking: {
+        smoothY: false,
+        sensitivity: 100,
         broadWidth: 0.05,
         thresholdFactor: 8,
         minMaxRatio,
@@ -257,25 +260,23 @@ function handleAutoRangesDetection(
 //action
 function handleAutoSpectraRangesDetection(draft: Draft<State>) {
   const peakPicking = {
+    sensitivity: 100,
     thresholdFactor: 8,
     minMaxRatio: 0.05,
   };
-  const rangePicking = {
-    integrationSum: 100,
-    compile: true,
-    frequencyCluster: 16,
-    clean: 0.3,
-    keepPeaks: true,
-  };
-  const {
-    data,
-    view: {
-      spectra: { activeTab: nucleus },
-    },
-    molecules,
-  } = draft;
+  const { data, molecules } = draft;
+
   for (const datum of data) {
     if (datum.info.dimension === 1) {
+      const nucleus = datum.info.nucleus as string;
+      const rangePicking = {
+        integrationSum: 100,
+        compile: nucleus === '1H',
+        frequencyCluster: nucleus === '1H' ? 16 : 0,
+        clean: 0.3,
+        keepPeaks: true,
+        joinOverlapRanges: nucleus === '1H',
+      };
       detectRanges(datum as Spectrum1D, {
         peakPicking,
         rangePicking,

src/data/data1d/Spectrum1D/peaks/autoPeakPicking.ts

@@ -9,6 +9,7 @@ export function autoPeakPicking(spectrum: Spectrum1D, options: any) {
     maxNumberOfPeaks,
     noiseFactor,
     direction,
+    sensitivity = 100,
     windowFromIndex,
     windowToIndex,
   } = options;
@@ -28,6 +29,7 @@ export function autoPeakPicking(spectrum: Spectrum1D, options: any) {
     {
       frequency,
       direction,
+      sensitivity,
       shape: { kind: 'lorentzian' },
       noiseLevel: noise * noiseFactor,
       minMaxRatio, // Threshold to determine if a given peak should be considered as a noise

src/data/data1d/Spectrum1D/ranges/autoRangesDetection.ts

@@ -8,6 +8,7 @@ const defaultPeakPickingOptions = {
   realTopDetection: true,
   maxCriteria: true,
   smoothY: true,
+  sensitivity: 100,
   broadWidth: 0.25,
   broadRatio: 0.0025,
   integrationSum: 100,
@@ -23,7 +24,7 @@ export default function autoRangesDetection(
 
   let { re, x } = spectrum.data;
 
-  const { originFrequency, nucleus } = spectrum.info;
+  const { originFrequency, nucleus, solvent } = spectrum.info;
 
   const { windowFromIndex, windowToIndex, peakPicking, rangePicking } = options;
 
@@ -34,12 +35,13 @@ export default function autoRangesDetection(
   };
 
   const rangesOptions = {
-    frequency: originFrequency,
     nucleus,
-    compile: true,
-    frequencyCluster: 13,
-    keepPeaks: true,
     clean: 0.3,
+    keepPeaks: true,
+    compile: nucleus === '1H',
+    frequency: originFrequency,
+    joinOverlapRanges: nucleus === '1H',
+    frequencyCluster: nucleus === '1H' ? 13 : 0,
     ...rangePicking,
   };
 
@@ -54,6 +56,7 @@ export default function autoRangesDetection(
   const ranges = xyAutoRangesPicking(
     { x, y: re },
     {
+      impurities: { solvent },
       peakPicking: peakPickingOptions,
       ranges: rangesOptions,
     },

src/data/data1d/__tests__/autoPeakPicking.test.ts

@@ -12,6 +12,7 @@ describe('test peakPicking', () => {
   it('check baseline', () => {
     const datum = initiateDatum1D({ data, info: { originFrequency: 150 } });
     const peaks = autoPeakPicking(datum, {
+      sensitivity: 100,
       maxNumberOfPeaks: 20,
       minMaxRatio: 0.1,
     });

test-e2e/panels/ranges.test.ts

@@ -367,10 +367,10 @@ test('Auto peak picking on all spectra', async ({ page }) => {
   await test.step("Check 13C spectrum's ranges", async () => {
     // switch to 13C tab.
     await nmrium.page.click('_react=SpectraTabs >> _react=Tab[tabid="13C"]');
-    await expect(nmrium.page.getByTestId('range')).toHaveCount(15);
+    await expect(nmrium.page.getByTestId('range')).toHaveCount(17);
     await expect(
       nmrium.page.locator('_react=RangesPanel >> _react=PanelHeader'),
-    ).toContainText('[ 15 ]');
+    ).toContainText('[ 17 ]');
   });
 
   await test.step("Check 1H,1H spectrum's ranges", async () => {