npm - nmr-processing - Versions diffs - 8.1.0 → 8.2.0 - Mend

nmr-processing 8.1.0 → 8.2.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (52) hide show

package/lib/assignment/utils/getAssignment/checkIDs.d.ts +1 -1
package/lib/assignment/utils/getAssignment/checkIDs.js.map +1 -1
package/lib/index.d.ts +2 -0
package/lib/index.js +2 -0
package/lib/index.js.map +1 -1
package/lib/peaks/peaksToRanges.d.ts +16 -0
package/lib/peaks/peaksToRanges.js +2 -1
package/lib/peaks/peaksToRanges.js.map +1 -1
package/lib/peaks/solventSuppression.d.ts +1 -1
package/lib/peaks/solventSuppression.js +34 -26
package/lib/peaks/solventSuppression.js.map +1 -1
package/lib/peaks/util/jAnalyzer.js +3 -2
package/lib/peaks/util/jAnalyzer.js.map +1 -1
package/lib/ranges/markSolventSignal.d.ts +3 -0
package/lib/ranges/markSolventSignal.js +107 -0
package/lib/ranges/markSolventSignal.js.map +1 -0
package/lib/xyz/util/formatZone.d.ts +3 -0
package/lib/xyz/util/formatZone.js +38 -0
package/lib/xyz/util/formatZone.js.map +1 -0
package/lib/xyz/xyzAutoZonesPicking.d.ts +1 -2
package/lib/xyz/xyzAutoZonesPicking.js +2 -34
package/lib/xyz/xyzAutoZonesPicking.js.map +1 -1
package/lib/xyz/xyzJResAnalyzer.d.ts +6 -1
package/lib/xyz/xyzJResAnalyzer.js +9 -8
package/lib/xyz/xyzJResAnalyzer.js.map +1 -1
package/lib-esm/assignment/utils/getAssignment/checkIDs.js.map +1 -1
package/lib-esm/index.js +2 -0
package/lib-esm/index.js.map +1 -1
package/lib-esm/peaks/peaksToRanges.js +1 -1
package/lib-esm/peaks/peaksToRanges.js.map +1 -1
package/lib-esm/peaks/solventSuppression.js +32 -21
package/lib-esm/peaks/solventSuppression.js.map +1 -1
package/lib-esm/peaks/util/jAnalyzer.js +3 -2
package/lib-esm/peaks/util/jAnalyzer.js.map +1 -1
package/lib-esm/ranges/markSolventSignal.js +100 -0
package/lib-esm/ranges/markSolventSignal.js.map +1 -0
package/lib-esm/xyz/util/formatZone.js +34 -0
package/lib-esm/xyz/util/formatZone.js.map +1 -0
package/lib-esm/xyz/xyzAutoZonesPicking.js +1 -33
package/lib-esm/xyz/xyzAutoZonesPicking.js.map +1 -1
package/lib-esm/xyz/xyzJResAnalyzer.js +9 -8
package/lib-esm/xyz/xyzJResAnalyzer.js.map +1 -1
package/package.json +2 -2
package/src/assignment/utils/getAssignment/checkIDs.ts +1 -1
package/src/index.ts +3 -0
package/src/peaks/peaksToRanges.ts +1 -1
package/src/peaks/solventSuppression.ts +57 -34
package/src/peaks/util/jAnalyzer.ts +4 -2
package/src/ranges/markSolventSignal.ts +121 -0
package/src/xyz/util/formatZone.ts +36 -0
package/src/xyz/xyzAutoZonesPicking.ts +1 -35
package/src/xyz/xyzJResAnalyzer.ts +14 -7

package/lib/xyz/xyzAutoZonesPicking.js CHANGED Viewed

@@ -34,6 +34,7 @@ const ml_simple_clustering_1 = __importDefault(require("ml-simple-clustering"));
 const determineRealTop_1 = require("../peaks/util/determineRealTop");
 const getKernel_1 = require("../peaks/util/getKernel");
 const PeakOptimizer = __importStar(require("../peaks/util/peakOptimizer"));
+const formatZone_1 = require("./util/formatZone");
 const smallFilter = [
     [0, 0, 1, 2, 2, 2, 1, 0, 0],
     [0, 1, 4, 7, 7, 7, 4, 1, 0],
@@ -107,42 +108,9 @@ function xyzAutoZonesPicking(spectraData, options) {
     if (enhanceSymmetry) {
         signals = PeakOptimizer.enhanceSymmetry(signals);
     }
-    return formatZones(signals);
+    return (0, formatZone_1.formatZones)(signals);
 }
 exports.xyzAutoZonesPicking = xyzAutoZonesPicking;
-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/xyz/xyzAutoZonesPicking.js.map CHANGED Viewed

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package/lib/xyz/xyzJResAnalyzer.d.ts CHANGED Viewed

@@ -19,6 +19,11 @@ interface XYZJResAnalyzerOptions extends CompilePatternOptions {
      * @default 0
      */
     reference?: number;
+    /**
+     * if it is true returns zones instead of signals 2D
+     * @default false
+     */
+    getZones?: boolean;
 }
-export declare function xyzJResAnalyzer(signals: NMRSignal2D[], options?: XYZJResAnalyzerOptions): NMRSignal2D[];
+export declare function xyzJResAnalyzer(signals: NMRSignal2D[], options?: XYZJResAnalyzerOptions): NMRSignal2D[] | import("./NMRZone").NMRZone[];
 export {};

package/lib/xyz/xyzJResAnalyzer.js CHANGED Viewed

@@ -6,25 +6,26 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.xyzJResAnalyzer = void 0;
 const ml_simple_clustering_1 = __importDefault(require("ml-simple-clustering"));
 const jAnalyzer_1 = __importDefault(require("../peaks/util/jAnalyzer"));
+const formatZone_1 = require("./util/formatZone");
 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 ? (0, formatZone_1.formatZones)(signals2D) : signals2D;
 }
 exports.xyzJResAnalyzer = xyzJResAnalyzer;
 function compilePattern(signals, options) {
@@ -74,9 +75,9 @@ 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/xyz/xyzJResAnalyzer.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib-esm/assignment/utils/getAssignment/checkIDs.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib-esm/index.js CHANGED Viewed

@@ -27,4 +27,6 @@ export * from './xyz/xyzJResAnalyzer';
 export * from './databases/getDatabase';
 export * from './databases/carbonImpurities';
 export * from './databases/protonImpurities';
+export * from './peaks/solventSuppression';
+export * from './ranges/markSolventSignal';
 //# sourceMappingURL=index.js.map

package/lib-esm/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib-esm/peaks/peaksToRanges.js CHANGED Viewed

@@ -176,7 +176,7 @@ export function peaksToRanges(data, peakList, options = {}) {
  * @return {array} nmr signals
  * @private
  */
-function detectSignals(data, peakList, options = {}) {
+export function detectSignals(data, peakList, options = {}) {
     let { integrationSum = 100, integralType = 'sum', frequencyCluster = 16, frequency = 400, nucleus = '1H', } = options;
     let signal1D = assignSignal(peakList[0], frequency, nucleus);
     let peaks;

package/lib-esm/peaks/peaksToRanges.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/lib-esm/peaks/solventSuppression.js CHANGED Viewed

@@ -1,4 +1,4 @@
-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';
@@ -7,19 +7,16 @@ import { signalsToSpinSystem } from '../signals/simulation/signalsToSpinSystem';
 import { simulateXYPeaks } from '../signals/simulation/simulateXYPeaks';
 import { splitSpinSystem } from '../signals/simulation/splitSpinSystem';
 export function solventSuppression(peakList, solvent, options = {}) {
-    const peaks = [...peakList];
-    sortAscending(peaks);
+    const peaks = [...peakList].sort((a, b) => a.x - b.x);
     const xValues = peaks.map((peak) => peak.x);
-    const { markSolventPeaks = false } = options;
-    let solventSignals = solvent; //addDummySignals(solvent);
-    // solventSignals = solventSignals.slice(0, solventSignals.findIndex((signal) => signal.delta > 400));
-    for (const solventSignal of solventSignals) {
-        const solventXYPeaks = solventSignal.peaks
+    const { markSolventPeaks = false, solventZoneExtension = 1.2 } = options;
+    for (const solventSignal of solvent) {
+        let solventXYPeaks = solventSignal.peaks
             ? solventSignal.peaks
             : getSolventPeaks(solventSignal);
-        sortAscending(solventXYPeaks);
-        let upIndex = xFindClosestIndex(xValues, solventXYPeaks[solventXYPeaks.length - 1].x + 1);
-        let lowIndex = xFindClosestIndex(xValues, solventXYPeaks[0].x - 1);
+        solventXYPeaks.sort((a, b) => a.x - b.x);
+        let upIndex = xFindClosestIndex(xValues, solventXYPeaks[solventXYPeaks.length - 1].x + solventZoneExtension);
+        let lowIndex = xFindClosestIndex(xValues, solventXYPeaks[0].x - solventZoneExtension);
         if (upIndex === lowIndex)
             continue;
         const nearPeaks = peaks.slice(lowIndex, upIndex + 1);
@@ -27,7 +24,7 @@ export function solventSuppression(peakList, solvent, options = {}) {
         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;
@@ -42,7 +39,7 @@ export function solventSuppression(peakList, solvent, options = {}) {
                 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);
@@ -53,23 +50,32 @@ export function solventSuppression(peakList, solvent, options = {}) {
         const maxPosition = xMaxValue(positionResiduals);
         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(nearPeaks[minIndex], solventSignal, solventXYPeaks);
+        if (minScore < 0) {
+            new Error('There is not a correct match with the pattern');
+            return peaks;
+        }
+        const { peaks: shiftedSolventPeaks } = getShiftedSolventPeaks(nearPeaks[minIndex], solventSignal, solventXYPeaks);
         const diff = getDiffMatrix(shiftedSolventPeaks, nearPeaks);
         const { rowAssignments, gain } = linearSumAssignment(diff, {
             maximaze: false,
         });
-        if (gain === -1)
+        if (gain < 0) {
+            new Error('The gain is below to zero');
             return peaks;
+        }
         if (markSolventPeaks) {
             for (let index of rowAssignments) {
                 peaks[index + lowIndex].kind = 'solvent';
@@ -98,13 +104,21 @@ function getSolventPeaks(signal, options = {}) {
 function getShiftedSolventPeaks(peak, solventSignal, solventXYPeaks) {
     const shiftedSolventPeaks = 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, nearPeaks) {
     const diff = getDiffMatrix(shiftedSolventPeaks, nearPeaks);
@@ -123,9 +137,6 @@ function getClosestPeaks(shiftedSolventPeaks, nearPeaks) {
     assignmentPeaks.forEach((peak, i, arr) => (arr[i].y /= maxValue));
     return assignmentPeaks;
 }
-function sortAscending(peaks) {
-    return peaks[0].x > peaks[1].x ? peaks.sort((a, b) => a.x - b.x) : peaks;
-}
 function getDiffMatrix(rows, columns) {
     const nbColumns = columns.length;
     const nbRows = rows.length;

package/lib-esm/peaks/solventSuppression.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ 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package/lib-esm/peaks/util/jAnalyzer.js CHANGED Viewed

@@ -8,11 +8,12 @@ let maxErrorIter1 = 2.5; // Hz
 let maxErrorIter2 = 1; // Hz
 let jAxisKeys = { jAxis: 'x', intensity: 'intensity' };
 function checkSignalForCompilePattern(signal) {
-    if (!signal.symRank) {
+    if (!('symRank' in signal)) {
         throw new Error('Internal error, symRank was not calculated');
     }
-    if (!signal.mask)
+    if (!('mask' in signal)) {
         throw new Error('Internal Error, mask was not added');
+    }
 }
 export default {
     /**

package/lib-esm/peaks/util/jAnalyzer.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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