nmr-processing 8.1.0 → 8.2.0

package/lib-esm/ranges/markSolventSignal.js

@@ -0,0 +1,100 @@
+import generateID from '../assignment/utils/generateID';
+import { addIDs } from '../assignment/utils/getAssignment/checkIDs';
+import { detectSignals } from '../peaks/peaksToRanges';
+import { solventSuppression } from '../peaks/solventSuppression';
+export function markSolventPeaks(input, solventSignals, options = {}) {
+    const { frequency = 400 } = options;
+    const ranges = addIDs([...input]);
+    let peakList = [];
+    for (const range of ranges) {
+        const rangeID = range.id;
+        for (const signal of range.signals || []) {
+            const signalID = signal.id;
+            for (let peak of signal.peaks || []) {
+                peakList.push({
+                    ...peak,
+                    rangeID,
+                    signalID,
+                });
+            }
+        }
+    }
+    const peaks = solventSuppression(peakList, solventSignals, {
+        markSolventPeaks: true,
+    });
+    const signalsWithSolvent = getSignalIDsWithSolvent(peaks);
+    for (let range of ranges) {
+        if (!range.signals)
+            continue;
+        for (let signal of range.signals) {
+            if (!signalsWithSolvent.includes(signal.id))
+                continue;
+            const signalPeaks = [];
+            const solventSignalPeaks = [];
+            for (let peak of peaks) {
+                if (peak.signalID === signal.id) {
+                    const { signalID, rangeID, ...newPeak } = peak;
+                    if (peak.kind === 'solvent') {
+                        solventSignalPeaks.push(newPeak);
+                    }
+                    else {
+                        signalPeaks.push(newPeak);
+                    }
+                }
+            }
+            const newSignals = signalPeaks.length > 0
+                ? detectSignals({ x: [], y: [] }, signalPeaks, {
+                    integralType: 'peak',
+                    frequency,
+                })
+                : [];
+            solventSignalPeaks.sort((a, b) => a.x - b.x);
+            const lowPPMValue = solventSignalPeaks[0].x;
+            const highPPMValue = solventSignalPeaks[solventSignalPeaks.length - 1].x;
+            const newSolventSignals = detectSignals({ x: [], y: [] }, solventSignalPeaks, {
+                integralType: 'peak',
+                frequencyCluster: (highPPMValue - lowPPMValue) * frequency,
+                frequency,
+            });
+            range.signals = [
+                ...adaptSignals(newSignals),
+                ...adaptSignals(newSolventSignals),
+                ...range.signals.filter((currSignal) => currSignal.id !== signal.id),
+            ];
+        }
+    }
+    return ranges;
+}
+function getSignalIDsWithSolvent(solventPeaks) {
+    const uniqueSignalID = new Set();
+    for (let peak of solventPeaks) {
+        if (peak.kind !== 'solvent')
+            continue;
+        uniqueSignalID.add(peak.signalID);
+    }
+    return Array.from(uniqueSignalID);
+}
+function adaptSignals(signals) {
+    const newSignals = [];
+    for (let signal of signals) {
+        const signalResult = {
+            id: generateID(),
+            delta: signal.delta,
+            kind: signal.kind || 'signal',
+            multiplicity: signal.multiplicity,
+            integration: signal.integralData.value,
+        };
+        signalResult.peaks = signal.peaks.map((peak) => {
+            const newResult = {
+                y: peak.intensity,
+                ...peak,
+            };
+            delete newResult.intensity;
+            return newResult;
+        });
+        signalResult.js = signal.nmrJs || [];
+        newSignals.push(signalResult);
+    }
+    return newSignals;
+}
+//# sourceMappingURL=markSolventSignal.js.map

package/lib-esm/ranges/markSolventSignal.js.map

@@ -0,0 +1 @@
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package/lib-esm/xyz/util/formatZone.js

@@ -0,0 +1,34 @@
+export function formatZones(signals) {
+    let zones = [];
+    for (const signal of signals) {
+        let minMax1 = [Number.MAX_VALUE, 0];
+        let minMax2 = [Number.MAX_VALUE, 0];
+        for (const peak of signal.peaks || []) {
+            if (peak.minX < minMax1[0]) {
+                minMax1[0] = peak.minX;
+            }
+            if (peak.maxX > minMax1[1]) {
+                minMax1[1] = peak.maxX;
+            }
+            if (peak.minY < minMax2[0]) {
+                minMax2[0] = peak.minY;
+            }
+            if (peak.maxY > minMax2[1]) {
+                minMax2[1] = peak.maxY;
+            }
+        }
+        zones.push({
+            x: {
+                from: minMax1[0],
+                to: minMax1[1],
+            },
+            y: {
+                from: minMax2[0],
+                to: minMax2[1],
+            },
+            signals: [signal],
+        });
+    }
+    return zones;
+}
+//# sourceMappingURL=formatZone.js.map

package/lib-esm/xyz/util/formatZone.js.map

@@ -0,0 +1 @@
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package/lib-esm/xyz/xyzAutoZonesPicking.js

@@ -5,6 +5,7 @@ import simpleClustering from 'ml-simple-clustering';
 import { determineRealTop } from '../peaks/util/determineRealTop';
 import { getKernel } from '../peaks/util/getKernel';
 import * as PeakOptimizer from '../peaks/util/peakOptimizer';
+import { formatZones } from './util/formatZone';
 const smallFilter = [
     [0, 0, 1, 2, 2, 2, 1, 0, 0],
     [0, 1, 4, 7, 7, 7, 4, 1, 0],
@@ -80,39 +81,6 @@ export function xyzAutoZonesPicking(spectraData, options) {
     }
     return formatZones(signals);
 }
-function formatZones(signals) {
-    let zones = [];
-    for (const signal of signals) {
-        let minMax1 = [Number.MAX_VALUE, 0];
-        let minMax2 = [Number.MAX_VALUE, 0];
-        for (const peak of signal.peaks || []) {
-            if (peak.minX < minMax1[0]) {
-                minMax1[0] = peak.minX;
-            }
-            if (peak.maxX > minMax1[1]) {
-                minMax1[1] = peak.maxX;
-            }
-            if (peak.minY < minMax2[0]) {
-                minMax2[0] = peak.minY;
-            }
-            if (peak.maxY > minMax2[1]) {
-                minMax2[1] = peak.maxY;
-            }
-        }
-        zones.push({
-            x: {
-                from: minMax1[0],
-                to: minMax1[1],
-            },
-            y: {
-                from: minMax2[0],
-                to: minMax2[1],
-            },
-            signals: [signal],
-        });
-    }
-    return zones;
-}
 const createSignals2D = (peaks, options) => {
     let { nCols, nRows, absoluteData, originalData, observedFrequencies, tolerances, nuclei, realTopDetection, minY, maxY, minX, maxX, } = options;
     let [nucleusX, nucleusY] = nuclei;

package/lib-esm/xyz/xyzAutoZonesPicking.js.map

@@ -1 +1 @@
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package/lib-esm/xyz/xyzJResAnalyzer.js

@@ -1,24 +1,25 @@
 import simpleClustering from 'ml-simple-clustering';
 import jAnalyzer from '../peaks/util/jAnalyzer';
+import { formatZones } from './util/formatZone';
 export function xyzJResAnalyzer(signals, options = {}) {
-    let { reference = 0, referenceMaxShiftError = 0.08, tolerances = [10, 100], nuclei = ['1H', '1H'], observedFrequencies = [400, 400], jAnalyzer = {
+    let { reference = 0, getZones = false, referenceMaxShiftError = 0.08, tolerances = [10, 100], nuclei = ['1H', '1H'], observedFrequencies = [400, 400], jAnalyzer = {
         jAxisKey: { jAxis: 'y', intensity: 'z' },
     }, } = options;
-    let temporalSignals = compilePattern(signals, {
+    let temporalSignals = compilePattern([...signals], {
         observedFrequencies,
         tolerances,
         nuclei,
         jAnalyzer,
     });
     //check if the signal are symmetric around the reference
-    let result = [];
+    let signals2D = [];
     for (const tempSignal of temporalSignals) {
         let delta = tempSignal.y.delta;
         if (Math.abs(delta - reference) > referenceMaxShiftError)
             continue;
-        result.push(tempSignal);
+        signals2D.push(tempSignal);
     }
-    return result;
+    return getZones ? formatZones(signals2D) : signals2D;
 }
 function compilePattern(signals, options) {
     let { observedFrequencies, tolerances, nuclei, jAnalyzer: jAnalyzerOptions, } = options;
@@ -67,9 +68,9 @@ function compilePattern(signals, options) {
             }
             if (peaksO.length > 0) {
                 peaksO.reverse();
-                let ranges = createSignals2D(peaksO, signalOptions);
-                for (const range of ranges) {
-                    newSignals.push(range);
+                let signals2D = createSignals2D(peaksO, signalOptions);
+                for (const signal of signals2D) {
+                    newSignals.push(signal);
                 }
             }
         }

package/lib-esm/xyz/xyzJResAnalyzer.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nmr-processing",
-  "version": "8.1.0",
+  "version": "8.2.0",
   "description": "Pure functions allowing to process NMR spectra.",
   "main": "./lib/index.js",
   "module": "./lib-esm/index.js",
@@ -60,7 +60,7 @@
     "form-data": "^4.0.0",
     "gyromagnetic-ratio": "^1.0.0",
     "is-any-array": "^2.0.0",
-    "linear-sum-assignment": "^1.0.3",
+    "linear-sum-assignment": "^1.0.4",
     "ml-array-mean": "^1.1.6",
     "ml-array-rescale": "^1.3.7",
     "ml-array-sequential-fill": "^1.1.8",

package/src/assignment/utils/getAssignment/checkIDs.ts

@@ -42,7 +42,7 @@ export function hasIDs(
   }
 }
 
-export function addIDs(data: NMRRange[] | NMRZone[]) {
+export function addIDs<T extends NMRRange[] | NMRZone[]>(data: T) {
   for (const element of data) {
     if (!element.id) element.id = generateID();
     for (let signal of element.signals || []) {

package/src/index.ts

@@ -37,6 +37,9 @@ export * from './databases/getDatabase';
 export * from './databases/carbonImpurities';
 export * from './databases/protonImpurities';
 
+export * from './peaks/solventSuppression';
+export * from './ranges/markSolventSignal';
+
 export type { NMRSignal1D } from './signals/NMRSignal1D';
 export type { NMRSignal2D, Signal2DProjection } from './xyz/NMRSignal2D';
 export type { NMRRange } from './xy/NMRRange';

package/src/peaks/peaksToRanges.ts

@@ -281,7 +281,7 @@ export function peaksToRanges(
  * @private
  */
 
-function detectSignals(
+export function detectSignals(
   data: DataXY,
   peakList: NMRPeak1DIntern[],
   options: OptionsDetectSignals = {},

package/src/peaks/solventSuppression.ts

@@ -1,5 +1,5 @@
 import { PointXY } from 'cheminfo-types';
-import linearSumAssignment from 'linear-sum-assignment';
+import { linearSumAssignment } from 'linear-sum-assignment';
 import { Matrix } from 'ml-matrix';
 import { gaussianFct } from 'ml-peak-shape-generator';
 import { xFindClosestIndex, xMaxValue } from 'ml-spectra-processing';
@@ -12,45 +12,47 @@ import { splitSpinSystem } from '../signals/simulation/splitSpinSystem';
 
 import { NMRPeak1D } from './NMRPeak1D';
 
-export function solventSuppression(
-  peakList: NMRPeak1D[],
+export function solventSuppression<T extends NMRPeak1D>(
+  peakList: T[],
   solvent: NMRSignal1D[],
   options: any = {},
 ) {
-  const peaks = [...peakList];
-  sortAscending(peaks);
-  const xValues = peaks.map((peak) => peak.x);
+  const peaks = [...peakList].sort((a, b) => a.x - b.x);
 
-  const { markSolventPeaks = false } = options;
+  const xValues = peaks.map((peak) => peak.x);
 
-  let solventSignals = solvent; //addDummySignals(solvent);
-  // solventSignals = solventSignals.slice(0, solventSignals.findIndex((signal) => signal.delta > 400));
+  const { markSolventPeaks = false, solventZoneExtension = 1.2 } = options;
 
-  for (const solventSignal of solventSignals) {
-    const solventXYPeaks = solventSignal.peaks
+  for (const solventSignal of solvent) {
+    let solventXYPeaks = solventSignal.peaks
       ? solventSignal.peaks
       : getSolventPeaks(solventSignal);
-    sortAscending(solventXYPeaks);
+    solventXYPeaks.sort((a, b) => a.x - b.x);
+
     let upIndex = xFindClosestIndex(
       xValues,
-      solventXYPeaks[solventXYPeaks.length - 1].x + 1,
+      solventXYPeaks[solventXYPeaks.length - 1].x + solventZoneExtension,
     );
-    let lowIndex = xFindClosestIndex(xValues, solventXYPeaks[0].x - 1);
+    let lowIndex = xFindClosestIndex(
+      xValues,
+      solventXYPeaks[0].x - solventZoneExtension,
+    );
+
     if (upIndex === lowIndex) continue;
     const nearPeaks = peaks.slice(lowIndex, upIndex + 1);
+
     const amplitudeResiduals = [];
     const deltaResiduals = [];
     const positionResiduals = [];
     for (let peak of nearPeaks) {
-      const shiftedSolventPeaks = getShiftedSolventPeaks(
-        peak,
-        solventSignal,
-        solventXYPeaks,
-      );
+      const { peaks: shiftedSolventPeaks, delta: currentDelta } =
+        getShiftedSolventPeaks(peak, solventSignal, solventXYPeaks);
+
       const closestPeaks = getClosestPeaks(shiftedSolventPeaks, nearPeaks);
       let deltaResidual = 0;
       let amplitudeResidual = 0;
       let positionResidual = 0;
+
       for (let i = 0; i < closestPeaks.length; i++) {
         amplitudeResidual += Math.abs(
           shiftedSolventPeaks[i].y - closestPeaks[i].y,
@@ -63,8 +65,12 @@ export function solventSuppression(
         amplitudeResidual = Number.MAX_SAFE_INTEGER;
         positionResidual = Number.MAX_SAFE_INTEGER;
       } else {
-        positionResidual = gaussianFct(solventSignal.delta - peak.x, 0.5);
+        positionResidual = gaussianFct(
+          Math.abs(solventSignal.delta - currentDelta),
+          0.5,
+        );
       }
+
       amplitudeResiduals.push(amplitudeResidual);
       deltaResiduals.push(deltaResidual);
       positionResiduals.push(positionResidual);
@@ -76,18 +82,28 @@ export function solventSuppression(
 
     let minIndex = -1;
     let minScore = Number.MAX_SAFE_INTEGER;
+    let score = [];
     for (let i = 0; i < deltaResiduals.length; i++) {
       const value =
         (amplitudeResiduals[i] / maxAmplitude +
           deltaResiduals[i] / maxDelta +
-          (1 - positionResiduals[i]) / maxPosition) /
+          1 -
+          positionResiduals[i] / maxPosition) /
         3;
+
+      score.push(value);
       if (minScore > value) {
         minIndex = i;
         minScore = value;
       }
     }
-    const shiftedSolventPeaks = getShiftedSolventPeaks(
+
+    if (minScore < 0) {
+      new Error('There is not a correct match with the pattern');
+      return peaks;
+    }
+
+    const { peaks: shiftedSolventPeaks } = getShiftedSolventPeaks(
       nearPeaks[minIndex],
       solventSignal,
       solventXYPeaks,
@@ -96,7 +112,11 @@ export function solventSuppression(
     const { rowAssignments, gain } = linearSumAssignment(diff, {
       maximaze: false,
     });
-    if (gain === -1) return peaks;
+
+    if (gain < 0) {
+      new Error('The gain is below to zero');
+      return peaks;
+    }
 
     if (markSolventPeaks) {
       for (let index of rowAssignments) {
@@ -131,27 +151,34 @@ function getSolventPeaks(
   return peaks.filter((peak) => peak.x < 1000);
 }
 
-function getShiftedSolventPeaks(
-  peak: PointXY,
+function getShiftedSolventPeaks<T extends PointXY>(
+  peak: T,
   solventSignal: any,
-  solventXYPeaks: PointXY[],
+  solventXYPeaks: T[],
 ) {
   const shiftedSolventPeaks: PointXY[] = JSON.parse(
     JSON.stringify(solventXYPeaks),
   );
   // shift x values of solventPeaks to center it to the current peak.
-  const deltaPPM = peak.x - solventSignal.delta;
+  let deltaPPM = peak.x - solventSignal.delta;
+  if (solventXYPeaks.length > 1 && solventXYPeaks.length % 2 === 0) {
+    deltaPPM += solventXYPeaks[0].x;
+  }
   const maxIntensity = shiftedSolventPeaks.reduce(
     (max, current) => (current.y > max ? current.y : max),
     shiftedSolventPeaks[0].y,
   );
+  let currentDelta = 0;
   for (let shiftedSolventPeak of shiftedSolventPeaks) {
     shiftedSolventPeak.x += deltaPPM;
     shiftedSolventPeak.y /= maxIntensity;
+    currentDelta += shiftedSolventPeak.x;
   }
-  return shiftedSolventPeaks;
+  return {
+    peaks: shiftedSolventPeaks,
+    delta: currentDelta / shiftedSolventPeaks.length,
+  };
 }
-
 function getClosestPeaks(shiftedSolventPeaks: PointXY[], nearPeaks: PointXY[]) {
   const diff = getDiffMatrix(shiftedSolventPeaks, nearPeaks);
   const { rowAssignments, gain } = linearSumAssignment(diff, {
@@ -169,11 +196,7 @@ function getClosestPeaks(shiftedSolventPeaks: PointXY[], nearPeaks: PointXY[]) {
   return assignmentPeaks;
 }
 
-function sortAscending(peaks: PointXY[]) {
-  return peaks[0].x > peaks[1].x ? peaks.sort((a, b) => a.x - b.x) : peaks;
-}
-
-function getDiffMatrix(rows: PointXY[], columns: PointXY[]) {
+function getDiffMatrix<T extends PointXY>(rows: T[], columns: T[]) {
   const nbColumns = columns.length;
   const nbRows = rows.length;
   const diff = new Matrix(nbRows, nbColumns);

package/src/peaks/util/jAnalyzer.ts

@@ -62,10 +62,12 @@ type SignalInternMandatory = MakeMandatory<
 function checkSignalForCompilePattern(
   signal: SignalIntern,
 ): asserts signal is SignalInternMandatory {
-  if (!signal.symRank) {
+  if (!('symRank' in signal)) {
     throw new Error('Internal error, symRank was not calculated');
   }
-  if (!signal.mask) throw new Error('Internal Error, mask was not added');
+  if (!('mask' in signal)) {
+    throw new Error('Internal Error, mask was not added');
+  }
 }
 
 export interface OpitonsCompilePatter {