npm - nmr-processing - Versions diffs - 3.4.0 → 6.0.0 - Mend

nmr-processing 3.4.0 → 6.0.0

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 (148) hide show

package/lib/assignment/get13CAssignments.js.map +1 -1
package/lib/assignment/utils/buildAssignments.js +0 -1
package/lib/assignment/utils/buildAssignments.js.map +1 -1
package/lib/assignment/utils/createMapPossibleAssignments.js +0 -1
package/lib/assignment/utils/createMapPossibleAssignments.js.map +1 -1
package/lib/constants/couplingValues.js.map +1 -1
package/lib/index.d.ts +1 -1
package/lib/index.js +1 -1
package/lib/peaks/peaksFilterImpurities.js +1 -1
package/lib/peaks/peaksFilterImpurities.js.map +1 -1
package/lib/peaks/peaksToRanges.js +11 -17
package/lib/peaks/peaksToRanges.js.map +1 -1
package/lib/peaks/util/determineRealTop.d.ts +2 -2
package/lib/peaks/util/determineRealTop.js +3 -2
package/lib/peaks/util/determineRealTop.js.map +1 -1
package/lib/peaks/util/jAnalyzer.js +12 -13
package/lib/peaks/util/jAnalyzer.js.map +1 -1
package/lib/peaks/util/peakOptimizer.d.ts +2 -2
package/lib/peaks/util/peakOptimizer.js.map +1 -1
package/lib/prediction/predictAll.js +1 -1
package/lib/prediction/predictAll.js.map +1 -1
package/lib/prediction/predictHSQC.js.map +1 -1
package/lib/prediction/predictProton.js +1 -1
package/lib/prediction/predictProton.js.map +1 -1
package/lib/prediction/utils/getFilteredIDiaIDs.js.map +1 -1
package/lib/prediction/utils/getNuclei.js +1 -1
package/lib/prediction/utils/getNuclei.js.map +1 -1
package/lib/prediction/utils/getPredictions.d.ts +2 -2
package/lib/prediction/utils/queryByHOSE.js.map +1 -1
package/lib/ranges/rangesToXY.d.ts +2 -2
package/lib/ranges/rangesToXY.js +10 -2
package/lib/ranges/rangesToXY.js.map +1 -1
package/lib/signal/signalJoinCouplings.d.ts +1 -1
package/lib/signal/signalJoinCouplings.js +3 -3
package/lib/signal/signalJoinCouplings.js.map +1 -1
package/lib/signals/signalsJoin.d.ts +1 -1
package/lib/signals/signalsJoin.js +7 -7
package/lib/signals/signalsJoin.js.map +1 -1
package/lib/signals/signalsToXY.d.ts +2 -2
package/lib/signals/simulation/simulate1D.d.ts +4 -3
package/lib/signals/simulation/simulate1D.js.map +1 -1
package/lib/signals/simulation/splitSpinSystem.js.map +1 -1
package/lib/types/NMRPeak1D.d.ts +2 -9
package/lib/types/NMRSignal2D.d.ts +6 -6
package/lib/types/NMRZone.d.ts +3 -7
package/lib/types/jcoupling.d.ts +1 -1
package/lib/types/modules/nmr-parser.d.ts +11 -0
package/lib/types/modules/nmr-parser.js +2 -0
package/lib/types/modules/nmr-parser.js.map +1 -0
package/lib/types/prediction1D.d.ts +2 -2
package/lib/utilities/joinPatterns.js.map +1 -1
package/lib/xy/xyAutoPeaksPicking.d.ts +4 -60
package/lib/xy/xyAutoPeaksPicking.js +3 -3
package/lib/xy/xyAutoPeaksPicking.js.map +1 -1
package/lib/xyz/{xyzAutoPeaksPicking.d.ts → xyzAutoZonesPicking.d.ts} +2 -2
package/lib/xyz/{xyzAutoPeaksPicking.js → xyzAutoZonesPicking.js} +38 -24
package/lib/xyz/xyzAutoZonesPicking.js.map +1 -0
package/lib/xyz/xyzJResAnalyzer.js.map +1 -1
package/lib-esm/assignment/get13CAssignments.js.map +1 -1
package/lib-esm/assignment/utils/buildAssignments.js +0 -1
package/lib-esm/assignment/utils/buildAssignments.js.map +1 -1
package/lib-esm/assignment/utils/createMapPossibleAssignments.js +0 -1
package/lib-esm/assignment/utils/createMapPossibleAssignments.js.map +1 -1
package/lib-esm/constants/couplingValues.js.map +1 -1
package/lib-esm/index.js +1 -1
package/lib-esm/peaks/peaksFilterImpurities.js +1 -1
package/lib-esm/peaks/peaksFilterImpurities.js.map +1 -1
package/lib-esm/peaks/peaksToRanges.js +11 -17
package/lib-esm/peaks/peaksToRanges.js.map +1 -1
package/lib-esm/peaks/util/determineRealTop.js +4 -3
package/lib-esm/peaks/util/determineRealTop.js.map +1 -1
package/lib-esm/peaks/util/jAnalyzer.js +12 -13
package/lib-esm/peaks/util/jAnalyzer.js.map +1 -1
package/lib-esm/peaks/util/peakOptimizer.js.map +1 -1
package/lib-esm/prediction/predictAll.js +1 -1
package/lib-esm/prediction/predictAll.js.map +1 -1
package/lib-esm/prediction/predictHSQC.js.map +1 -1
package/lib-esm/prediction/predictProton.js +1 -1
package/lib-esm/prediction/predictProton.js.map +1 -1
package/lib-esm/prediction/utils/getFilteredIDiaIDs.js.map +1 -1
package/lib-esm/prediction/utils/getNuclei.js +1 -1
package/lib-esm/prediction/utils/getNuclei.js.map +1 -1
package/lib-esm/prediction/utils/queryByHOSE.js.map +1 -1
package/lib-esm/ranges/rangesToXY.js +10 -2
package/lib-esm/ranges/rangesToXY.js.map +1 -1
package/lib-esm/signal/signalJoinCouplings.js +3 -3
package/lib-esm/signal/signalJoinCouplings.js.map +1 -1
package/lib-esm/signals/signalsJoin.js +7 -7
package/lib-esm/signals/signalsJoin.js.map +1 -1
package/lib-esm/signals/simulation/simulate1D.js.map +1 -1
package/lib-esm/signals/simulation/splitSpinSystem.js.map +1 -1
package/lib-esm/types/modules/nmr-parser.js +2 -0
package/lib-esm/types/modules/nmr-parser.js.map +1 -0
package/lib-esm/utilities/joinPatterns.js.map +1 -1
package/lib-esm/xy/xyAutoPeaksPicking.js +3 -3
package/lib-esm/xy/xyAutoPeaksPicking.js.map +1 -1
package/lib-esm/xyz/{xyzAutoPeaksPicking.js → xyzAutoZonesPicking.js} +36 -22
package/lib-esm/xyz/xyzAutoZonesPicking.js.map +1 -0
package/lib-esm/xyz/xyzJResAnalyzer.js.map +1 -1
package/package.json +19 -16
package/src/assignment/get13CAssignments.ts +4 -1
package/src/assignment/utils/buildAssignments.ts +2 -5
package/src/assignment/utils/createMapPossibleAssignments.ts +4 -2
package/src/constants/couplingValues.ts +1 -1
package/src/index.ts +1 -1
package/src/peaks/peaksFilterImpurities.ts +1 -1
package/src/peaks/peaksToRanges.ts +11 -17
package/src/peaks/util/determineRealTop.ts +6 -9
package/src/peaks/util/jAnalyzer.ts +14 -16
package/src/peaks/util/peakOptimizer.ts +4 -3
package/src/prediction/predictAll.ts +5 -5
package/src/prediction/predictHSQC.ts +4 -1
package/src/prediction/predictProton.ts +1 -1
package/src/prediction/utils/getFilteredIDiaIDs.ts +1 -2
package/src/prediction/utils/getNuclei.ts +3 -3
package/src/prediction/utils/getPredictions.ts +3 -3
package/src/prediction/utils/queryByHOSE.ts +1 -1
package/src/ranges/rangesToXY.ts +12 -5
package/src/signal/signalJoinCouplings.ts +3 -3
package/src/signals/signalsJoin.ts +7 -7
package/src/signals/signalsToXY.ts +3 -3
package/src/signals/simulation/simulate1D.ts +4 -3
package/src/signals/simulation/splitSpinSystem.ts +10 -2
package/src/types/NMRPeak1D.ts +3 -9
package/src/types/NMRSignal2D.ts +7 -7
package/src/types/NMRZone.ts +6 -6
package/src/types/dataStructure.ts +1 -1
package/src/types/jcoupling.ts +1 -1
package/src/types/ml-matrix-peaks-finder/index.d.ts +2 -2
package/src/types/ml-simple-clustering/index.d.ts +1 -1
package/src/types/ml-spectra-processing/index.d.ts +8 -2
package/src/types/modules/nmr-parser.ts +17 -0
package/src/types/openchemlib-utils/index..d.ts +17 -6
package/src/types/prediction1D.ts +2 -2
package/src/utilities/joinPatterns.ts +0 -1
package/src/xy/xyAutoPeaksPicking.ts +19 -58
package/src/xyz/{xyzAutoPeaksPicking.ts → xyzAutoZonesPicking.ts} +40 -24
package/src/xyz/xyzJResAnalyzer.ts +4 -4
package/CHANGELOG.md +0 -543
package/lib/types/MPFPeak.d.ts +0 -9
package/lib/types/MPFPeak.js +0 -3
package/lib/types/MPFPeak.js.map +0 -1
package/lib/xyz/xyzAutoPeaksPicking.js.map +0 -1
package/lib-esm/types/MPFPeak.js +0 -2
package/lib-esm/types/MPFPeak.js.map +0 -1
package/lib-esm/xyz/xyzAutoPeaksPicking.js.map +0 -1
package/src/types/MPFPeak.ts +0 -9
package/src/types/ml-gsd/index.d.ts +0 -164

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

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package/lib-esm/prediction/predictAll.js CHANGED Viewed

@@ -17,7 +17,7 @@ export async function predictAll(molecule, options = {}) {
     }
     predictions = {
         H: xPrediction,
-        C: yPrediction
+        C: yPrediction,
     };
     const { molfile, diaIDs } = xPrediction;
     const spectra = {

package/lib-esm/prediction/predictAll.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib-esm/prediction/predictHSQC.js.map CHANGED Viewed

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

@@ -69,7 +69,7 @@ function protonParser(result, molecule, diaIDs) {
                 atoms: [linked],
                 diaIDs: [diaIDs[linked]],
                 multiplicity: 'd',
-                distance: distanceMatrix[atom][linked],
+                pathLength: distanceMatrix[atom][linked],
             });
             signal.js.sort((a, b) => b.coupling - a.coupling);
         }

package/lib-esm/prediction/predictProton.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib-esm/prediction/utils/getFilteredIDiaIDs.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib-esm/prediction/utils/getNuclei.js CHANGED Viewed

@@ -3,6 +3,6 @@ const nucleusMap = {
     c: '13C',
 };
 export function getNuclei(input) {
-    return Object.values(input).map((e) => (nucleusMap[e.toLowerCase()]));
+    return Object.values(input).map((e) => nucleusMap[e.toLowerCase()]);
 }
 //# sourceMappingURL=getNuclei.js.map

package/lib-esm/prediction/utils/getNuclei.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib-esm/prediction/utils/queryByHOSE.js.map CHANGED Viewed

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

@@ -25,7 +25,15 @@ export function rangesToXY(ranges, options = {}) {
     };
     let spectrum = new Float64Array(nbPoints);
     for (const range of ranges) {
-        const { integration, signals } = range;
+        const { integration, signals = [] } = range;
+        const { multiplicity: rangeMulplicity = '' } = range;
+        if (rangeMulplicity === 'm' && signals.length < 1) {
+            const { from, to } = range;
+            signals.push({
+                delta: (from + to) / 2,
+                multiplicity: 'm',
+            });
+        }
         let rangeSpectrum = new Float64Array(nbPoints);
         for (const signal of signals) {
             const { multiplicity } = signal;
@@ -89,8 +97,8 @@ function normalizeSpectrum(spectrum, signals, options = {}) {
         return acc + integration;
     }, 0), } = options;
     const sum = spectrum.reduce((acc, element) => acc + element, 0);
-    const norma = (integration / sum) * 1e6;
     if (sum !== 0) {
+        const norma = (integration / sum) * 1e6;
         for (let i = 0; i < spectrum.length; i++) {
             spectrum[i] *= norma;
         }

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

@@ -11,7 +11,7 @@ const takeCareDiaIDs = (a, b, tolerance) => localeCompareJcouplingKeys(a, b) ===
 /**
  * Join couplings smaller than a define tolerance.
  * The resulting coupling should be an average of the existing one.
- * If distance is specified and is not always the same this property will be removed.
+ * If pathLength is specified and is not always the same this property will be removed.
  */
 export function signalJoinCouplings(signal, options = {}) {
     const { tolerance = 0.05, ignoreDiaIDs = false } = options;
@@ -55,7 +55,7 @@ function groupJCouplings(signal, comparator, tolerance) {
             .filter((group) => group.diaIDs)
             .map((group) => group.diaIDs)
             .flat());
-        let distances = distinctValues(group.map((group) => group.distance));
+        let distances = distinctValues(group.map((group) => group.pathLength));
         let multiplicity = joinPatterns(group
             .filter((group) => group.multiplicity)
             .map((group) => group.multiplicity));
@@ -66,7 +66,7 @@ function groupJCouplings(signal, comparator, tolerance) {
         if (diaIDs.length === 1)
             newJ.diaIDs = diaIDs;
         if (distances.length === 1 && distances[0])
-            newJ.distance = distances[0];
+            newJ.pathLength = distances[0];
         if (assignment.length > 0)
             newJ.assignment = assignment;
         if (atoms.length > 0)

package/lib-esm/signal/signalJoinCouplings.js.map CHANGED Viewed

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

@@ -3,8 +3,8 @@ import sum from 'ml-array-sum';
 import { signalJoinCouplings } from '../signal/signalJoinCouplings';
 const localeCompare = (a, b) => a.localeCompare(b);
 const localeCompareJcouplingKeys = (a, b) => {
-    const aa = `${a.diaIDs.join(' ')}${a.distance}`;
-    const bb = `${b.diaIDs.join(' ')}${b.distance}`;
+    const aa = `${a.diaIDs.join(' ')}${a.pathLength}`;
+    const bb = `${b.diaIDs.join(' ')}${b.pathLength}`;
     return localeCompare(aa, bb);
 };
 function checkForMandatory(signals) {
@@ -16,8 +16,8 @@ function checkForMandatory(signals) {
         for (const jcoupling of signal.js) {
             if (!jcoupling.diaIDs)
                 throw new Error('there is not diaIDs');
-            if (!jcoupling.distance)
-                throw new Error('there is not distance');
+            if (!jcoupling.pathLength)
+                throw new Error('there is not pathLength');
         }
     }
 }
@@ -35,7 +35,7 @@ export function signalsJoin(signals, options = {}) {
         signal.js = signal.js.sort(localeCompareJcouplingKeys);
         const keyDiaIDs = signal.diaIDs.join(' ');
         let id = `${keyDiaIDs} ${signal.js
-            .map((j) => `${j.diaIDs.join(' ')} ${j.distance}`)
+            .map((j) => `${j.diaIDs.join(' ')} ${j.pathLength}`)
             .sort(localeCompare)
             .join(' ')}`;
         if (!groupedSignals[id]) {
@@ -46,13 +46,13 @@ export function signalsJoin(signals, options = {}) {
     // for each group we need to combine assignments and average couplings
     let newSignals = [];
     Object.values(groupedSignals).forEach((group) => {
-        // joining couplings only if diaID and distance are equal
+        // joining couplings only if diaID and pathLength are equal
         let js = [];
         for (let i = 0; i < group[0].js.length; i++) {
             const coupling = group[0].js[i];
             js.push({
                 diaIDs: coupling.diaIDs,
-                distance: coupling.distance,
+                pathLength: coupling.pathLength,
                 multiplicity: coupling.multiplicity,
                 coupling: mean(group.map((item) => item.js[i].coupling)),
             });

package/lib-esm/signals/signalsJoin.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib-esm/types/modules/nmr-parser.js ADDED Viewed

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1	+ "use strict";
2	+ //# sourceMappingURL=nmr-parser.js.map

package/lib-esm/types/modules/nmr-parser.js.map ADDED Viewed

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1	+ {"version":3,"file":"nmr-parser.js","sourceRoot":"","sources":["../../../src/types/modules/nmr-parser.ts"],"names":[],"mappings":""}

package/lib-esm/utilities/joinPatterns.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"joinPatterns.js","sourceRoot":"","sources":["../../src/utilities/joinPatterns.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAC;AAE7D,MAAM,UAAU,YAAY,CAAC,QAAkB;IAC7C,MAAM,GAAG,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,GAAG,EAAE,OAAO,EAAE,EAAE;QAC3C,IAAI,KAAK,CAAC,cAAc,CAAC,OAAO,CAAC,CAAC,EAAE;YAClC,MAAM,IAAI,KAAK,CACb,WAAW,OAAO,cAAc,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CACxE,CAAC;SACH;QACD,OAAO,GAAG,GAAG,cAAc,CAAC,OAAO,CAAC,CAAC;IACvC,CAAC,EAAE,CAAC,CAAC,CAAC;IAEN,IAAI,CAAC,gBAAgB,CAAC,GAAG,CAAC,EAAE;QAC1B,MAAM,IAAI,KAAK,CAAC,kCAAkC,CAAC,CAAC;KACrD;IAED,OAAO,gBAAgB,CAAC,GAAG,CAAC,CAAC;AAC/B,CAAC"}

package/lib-esm/xy/xyAutoPeaksPicking.js CHANGED Viewed

@@ -32,14 +32,14 @@ function getPeakList(data, options) {
         shape,
         sgOptions,
         minMaxRatio,
-        broadRatio,
         noiseLevel,
         smoothY,
         realTopDetection,
     });
     if (broadWidth) {
-        peakList = joinBroadPeaks(peakList, {
-            width: broadWidth,
+        peakList = joinBroadPeaks(data, peakList, {
+            broadRatio,
+            broadWidth,
             shape,
             optimization,
         });

package/lib-esm/xy/xyAutoPeaksPicking.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib-esm/xyz/{xyzAutoPeaksPicking.js → xyzAutoZonesPicking.js} RENAMED Viewed

@@ -16,7 +16,7 @@ const smallFilter = [
     [0, 1, 3, 7, 7, 7, 3, 1, 0],
     [0, 0, 1, 2, 2, 2, 1, 0, 0],
 ];
-export function xyzAutoPeaksPicking(spectraData, options) {
+export function xyzAutoZonesPicking(spectraData, options) {
     let { sizeToPad = 14, realTopDetection = true, thresholdFactor = 0.5, nuclei = ['1H', '1H'], observedFrequencies, enhanceSymmetry = false, clean = true, maxPercentCutOff = 0.03, tolerances = [24, 24], convolutionByFFT = true, kernel: kernelOptions, } = options;
     if (!Array.isArray(observedFrequencies) &&
         !ArrayBuffer.isView(observedFrequencies)) {
@@ -78,7 +78,40 @@ export function xyzAutoPeaksPicking(spectraData, options) {
     if (enhanceSymmetry) {
         signals = PeakOptimizer.enhanceSymmetry(signals);
     }
-    return signals;
+    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;
@@ -107,9 +140,6 @@ const createSignals2D = (peaks, options) => {
         peaks[i].maxX = minX + dx * peaks[i].maxX;
         peaks[i].maxY = minY + dy * peaks[i].maxY;
         // Still having problems to correctly detect peaks on those areas. So I'm removing everything there.
-        if (peaks[i].y < -1 || peaks[i].y >= 210) {
-            peaks.splice(i, 1);
-        }
     }
     // The connectivity matrix is an square and symmetric matrix, so we'll only store the upper diagonal in an
     // array like form
@@ -143,8 +173,6 @@ const createSignals2D = (peaks, options) => {
                 },
             };
             let peaks2D = [];
-            let minMax1 = [Number.MAX_VALUE, 0];
-            let minMax2 = [Number.MAX_VALUE, 0];
             let sumZ = 0;
             for (let jPeak = 0; jPeak < cluster.length; jPeak++) {
                 if (cluster[jPeak] === 1) {
@@ -152,22 +180,8 @@ const createSignals2D = (peaks, options) => {
                     signal.x.delta += peaks[jPeak].x * peaks[jPeak].z;
                     signal.y.delta += peaks[jPeak].y * peaks[jPeak].z;
                     sumZ += peaks[jPeak].z;
-                    if (peaks[jPeak].minX < minMax1[0]) {
-                        minMax1[0] = peaks[jPeak].minX;
-                    }
-                    if (peaks[jPeak].maxX > minMax1[1]) {
-                        minMax1[1] = peaks[jPeak].maxX;
-                    }
-                    if (peaks[jPeak].minY < minMax2[0]) {
-                        minMax2[0] = peaks[jPeak].minY;
-                    }
-                    if (peaks[jPeak].maxY > minMax2[1]) {
-                        minMax2[1] = peaks[jPeak].maxY;
-                    }
                 }
             }
-            signal.x.fromTo = { from: minMax1[0], to: minMax1[1] };
-            signal.y.fromTo = { from: minMax2[0], to: minMax2[1] };
             signal.x.delta /= sumZ;
             signal.y.delta /= sumZ;
             signal.peaks = peaks2D;
@@ -205,4 +219,4 @@ const padData = (spectraData, options) => {
         maxY: maxY + yOffset * yInterval,
     };
 };
-//# sourceMappingURL=xyzAutoPeaksPicking.js.map
+//# sourceMappingURL=xyzAutoZonesPicking.js.map

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

@@ -0,0 +1 @@

+ 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