nmr-processing 8.0.0 → 8.3.0

package/lib-esm/signals/simulation/simulate1D.js

@@ -1,9 +1,5 @@
-import binarySearch from 'binary-search';
-import { Matrix, EVD } from 'ml-matrix';
-import { SparseMatrix } from 'ml-sparse-matrix';
-import { SpectrumGenerator } from 'spectrum-generator';
-import getPauliMatrix from './getPauliMatrix';
-const smallValue = 1e-2;
+import { generateSpectrum } from 'spectrum-generator';
+import { simulateXYPeaks } from './simulateXYPeaks';
 /**
  * This function simulates a one dimensional nmr spectrum. This function returns an array containing the relative intensities of the spectrum in the specified simulation window (from-to).
  */
@@ -12,241 +8,21 @@ export default function simulate1D(
  * The SpinSystem object to be simulated
  */
 spinSystem, options = {}) {
-    let { lineWidth = 1, maxClusterSize = 8, frequency: frequencyMHz = 400, from = 0, to = 10, nbPoints = 1024, shape = {
+    let { lineWidth = 1, frequency: frequencyMHz = 400, from = 0, to = 10, nbPoints = 1024, shape = {
         kind: 'gaussian',
     }, } = options;
     let peakWidth = lineWidth / frequencyMHz;
-    let spectrumGenerator = new SpectrumGenerator({
-        from,
-        to,
-        nbPoints,
-        shape,
-        peakWidthFct: () => peakWidth,
+    const xyPeaks = simulateXYPeaks(spinSystem, options);
+    return generateSpectrum(xyPeaks, {
+        generator: {
+            from,
+            to,
+            nbPoints,
+        },
+        peakOptions: {
+            shape,
+            width: peakWidth,
+        },
     });
-    const chemicalShifts = spinSystem.chemicalShifts.slice();
-    for (let i = 0; i < chemicalShifts.length; i++) {
-        chemicalShifts[i] = chemicalShifts[i] * frequencyMHz;
-    }
-    const multiplicity = spinSystem.multiplicity;
-    for (const cluster of spinSystem.clusters) {
-        let clusterFake = cluster.map((cluster) => cluster < 0 ? -cluster - 1 : cluster);
-        let weight = 1;
-        let sumI = 0;
-        let frequencies = [];
-        let intensities = [];
-        if (cluster.length > maxClusterSize) {
-            // This is a single spin, but the cluster exceeds the maxClusterSize criteria
-            // we use the simple multiplicity algorithm
-            // Add the central peak. It will be split with every single J coupling.
-            let index = 0;
-            while (cluster[index++] < 0)
-                ;
-            index = cluster[index - 1];
-            frequencies.push(-chemicalShifts[index]);
-            for (let i = 0; i < cluster.length; i++) {
-                if (cluster[i] < 0) {
-                    let jc = spinSystem.couplingConstants.get(index, clusterFake[i]) / 2;
-                    let currentSize = frequencies.length;
-                    for (let j = 0; j < currentSize; j++) {
-                        frequencies.push(frequencies[j] + jc);
-                        frequencies[j] -= jc;
-                    }
-                }
-            }
-            frequencies.sort((a, b) => a - b);
-            sumI = frequencies.length;
-            weight = 1;
-            for (let i = 0; i < sumI; i++) {
-                intensities.push(1);
-            }
-        }
-        else {
-            const hamiltonian = getHamiltonian(chemicalShifts, spinSystem.couplingConstants, multiplicity, spinSystem.connectivity, clusterFake);
-            const hamSize = hamiltonian.rows;
-            // TODO: add support for sparse matrix in matrix types.
-            // @ts-expect-error sparse matrix not supported
-            const evd = new EVD(hamiltonian);
-            const V = evd.eigenvectorMatrix;
-            const diagB = evd.realEigenvalues;
-            const assignmentMatrix = new SparseMatrix(hamSize, hamSize);
-            const multLen = cluster.length;
-            weight = 0;
-            for (let n = 0; n < multLen; n++) {
-                const L = getPauliMatrix(multiplicity[clusterFake[n]]);
-                let temp = 1;
-                for (let j = 0; j < n; j++) {
-                    temp *= multiplicity[clusterFake[j]];
-                }
-                const A = SparseMatrix.eye(temp);
-                temp = 1;
-                for (let j = n + 1; j < multLen; j++) {
-                    temp *= multiplicity[clusterFake[j]];
-                }
-                const B = SparseMatrix.eye(temp);
-                const tempMat = A.kroneckerProduct(L.m).kroneckerProduct(B);
-                if (cluster[n] >= 0) {
-                    assignmentMatrix.add(tempMat.mul(cluster[n] + 1));
-                    weight++;
-                }
-                else {
-                    assignmentMatrix.add(tempMat.mul(cluster[n]));
-                }
-            }
-            let rhoip = Matrix.zeros(hamSize, hamSize);
-            assignmentMatrix.forEachNonZero((i, j, v) => {
-                if (v > 0) {
-                    for (let k = 0; k < V.columns; k++) {
-                        let element = V.get(j, k);
-                        if (element !== 0) {
-                            rhoip.set(i, k, rhoip.get(i, k) + element);
-                        }
-                    }
-                }
-                return v;
-            });
-            let rhoip2 = rhoip.clone();
-            assignmentMatrix.forEachNonZero((i, j, v) => {
-                if (v < 0) {
-                    for (let k = 0; k < V.columns; k++) {
-                        let element = V.get(j, k);
-                        if (element !== 0) {
-                            rhoip2.set(i, k, rhoip2.get(i, k) + element);
-                        }
-                    }
-                }
-                return v;
-            });
-            const tV = V.transpose();
-            rhoip = tV.mmul(rhoip);
-            const sparseRhoip = new SparseMatrix(rhoip.to2DArray(), {
-                threshold: smallValue,
-            });
-            triuTimesAbs(sparseRhoip, smallValue);
-            rhoip2 = tV.mmul(rhoip2);
-            const sparseRhoip2 = new SparseMatrix(rhoip2.to2DArray(), {
-                threshold: smallValue,
-            });
-            sparseRhoip2.forEachNonZero((i, j, v) => {
-                return v;
-            });
-            triuTimesAbs(sparseRhoip2, smallValue);
-            sparseRhoip2.forEachNonZero((i, j, v) => {
-                let val = rhoip.get(i, j);
-                val = Math.min(Math.abs(val), Math.abs(v));
-                val *= val;
-                sumI += val;
-                let valFreq = diagB[i] - diagB[j];
-                let insertIn = binarySearch(frequencies, valFreq, (a, b) => a - b);
-                if (insertIn < 0) {
-                    frequencies.splice(-1 - insertIn, 0, valFreq);
-                    intensities.splice(-1 - insertIn, 0, val);
-                }
-                else {
-                    intensities[insertIn] += val;
-                }
-            });
-        }
-        const numFreq = frequencies.length;
-        if (numFreq > 0) {
-            weight /= sumI;
-            const diff = lineWidth / 64;
-            let valFreq = frequencies[0];
-            let inte = intensities[0];
-            let count = 1;
-            for (let i = 1; i < numFreq; i++) {
-                if (Math.abs(frequencies[i] - valFreq / count) < diff) {
-                    inte += intensities[i];
-                    valFreq += frequencies[i];
-                    count++;
-                }
-                else {
-                    spectrumGenerator.addPeak({
-                        x: -valFreq / count / frequencyMHz,
-                        y: inte * weight,
-                    });
-                    valFreq = frequencies[i];
-                    inte = intensities[i];
-                    count = 1;
-                }
-            }
-            spectrumGenerator.addPeak({
-                x: -valFreq / count / frequencyMHz,
-                y: inte * weight,
-            });
-        }
-    }
-    return spectrumGenerator.getSpectrum();
-}
-function triuTimesAbs(A, val) {
-    A.forEachNonZero((i, j, v) => {
-        if (i > j)
-            return 0;
-        if (Math.abs(v) <= val)
-            return 0;
-        return v;
-    });
-}
-/**
- * Create a hamiltonian matrix for the given spinsystem
- * @param {Array} chemicalShifts - An array containing the chemical shift in Hz
- * @param {Array} couplingConstants - An array containing the coupling constants in Hz
- * @param {Array} multiplicity - An array specifiying the multiplicities of each scalar coupling
- * @param {Array} conMatrix - A one step connectivity matrix for the given spin system
- * @param {Array} cluster - An binary array specifiying the spins to be considered for this hamiltonial
- * @return {object}
- */
-function getHamiltonian(chemicalShifts, couplingConstants, multiplicity, conMatrix, cluster) {
-    let hamSize = 1;
-    for (const element of cluster) {
-        hamSize *= multiplicity[element];
-    }
-    const clusterHam = new SparseMatrix(hamSize, hamSize);
-    for (let pos = 0; pos < cluster.length; pos++) {
-        let n = cluster[pos];
-        const L = getPauliMatrix(multiplicity[n]);
-        let A1, B1;
-        let temp = 1;
-        for (let i = 0; i < pos; i++) {
-            temp *= multiplicity[cluster[i]];
-        }
-        A1 = SparseMatrix.eye(temp);
-        temp = 1;
-        for (let i = pos + 1; i < cluster.length; i++) {
-            temp *= multiplicity[cluster[i]];
-        }
-        B1 = SparseMatrix.eye(temp);
-        const alpha = chemicalShifts[n];
-        const kronProd = A1.kroneckerProduct(L.z).kroneckerProduct(B1);
-        clusterHam.add(kronProd.mul(alpha));
-        for (let pos2 = 0; pos2 < cluster.length; pos2++) {
-            const k = cluster[pos2];
-            if (conMatrix.get(n, k) === 1) {
-                const S = getPauliMatrix(multiplicity[k]);
-                let A2, B2;
-                let temp = 1;
-                for (let i = 0; i < pos2; i++) {
-                    temp *= multiplicity[cluster[i]];
-                }
-                A2 = SparseMatrix.eye(temp);
-                temp = 1;
-                for (let i = pos2 + 1; i < cluster.length; i++) {
-                    temp *= multiplicity[cluster[i]];
-                }
-                B2 = SparseMatrix.eye(temp);
-                const kron1 = A1.kroneckerProduct(L.x)
-                    .kroneckerProduct(B1)
-                    .mmul(A2.kroneckerProduct(S.x).kroneckerProduct(B2));
-                kron1.add(A1.kroneckerProduct(L.y)
-                    .kroneckerProduct(B1)
-                    .mul(-1)
-                    .mmul(A2.kroneckerProduct(S.y).kroneckerProduct(B2)));
-                kron1.add(A1.kroneckerProduct(L.z)
-                    .kroneckerProduct(B1)
-                    .mmul(A2.kroneckerProduct(S.z).kroneckerProduct(B2)));
-                clusterHam.add(kron1.mul(couplingConstants.get(n, k) / 2));
-            }
-        }
-    }
-    return clusterHam;
 }
 //# sourceMappingURL=simulate1D.js.map

package/lib-esm/signals/simulation/simulate1D.js.map

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+{"version":3,"file":"simulate1D.js","sourceRoot":"","sources":["../../../src/signals/simulation/simulate1D.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AAKtD,OAAO,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AAEpD;;GAEG;AAEH,MAAM,CAAC,OAAO,UAAU,UAAU;AAChC;;GAEG;AACH,UAAsB,EACtB,UAA6B,EAAE;IAE/B,IAAI,EACF,SAAS,GAAG,CAAC,EACb,SAAS,EAAE,YAAY,GAAG,GAAG,EAC7B,IAAI,GAAG,CAAC,EACR,EAAE,GAAG,EAAE,EACP,QAAQ,GAAG,IAAI,EACf,KAAK,GAAG;QACN,IAAI,EAAE,UAAU;KACjB,GACF,GAAG,OAAO,CAAC;IAEZ,IAAI,SAAS,GAAG,SAAS,GAAG,YAAY,CAAC;IAEzC,MAAM,OAAO,GAAG,eAAe,CAAC,UAAU,EAAE,OAAO,CAAC,CAAC;IAErD,OAAO,gBAAgB,CAAC,OAAO,EAAE;QAC/B,SAAS,EAAE;YACT,IAAI;YACJ,EAAE;YACF,QAAQ;SACT;QACD,WAAW,EAAE;YACX,KAAK;YACL,KAAK,EAAE,SAAS;SACjB;KACF,CAAC,CAAC;AACL,CAAC"}

package/lib-esm/signals/simulation/simulateXYPeaks.js

@@ -0,0 +1,239 @@
+import binarySearch from 'binary-search';
+import { Matrix, EVD } from 'ml-matrix';
+import { SparseMatrix } from 'ml-sparse-matrix';
+import getPauliMatrix from './getPauliMatrix';
+const smallValue = 1e-2;
+export function simulateXYPeaks(
+/**
+ * The SpinSystem object to be simulated
+ */
+spinSystem, options = {}) {
+    let { lineWidth = 1, maxClusterSize = 8, frequency: frequencyMHz = 400, } = options;
+    const chemicalShifts = spinSystem.chemicalShifts.slice();
+    for (let i = 0; i < chemicalShifts.length; i++) {
+        chemicalShifts[i] = chemicalShifts[i] * frequencyMHz;
+    }
+    const multiplicity = spinSystem.multiplicity;
+    const xyPeaks = [];
+    for (const cluster of spinSystem.clusters) {
+        let clusterFake = cluster.map((cluster) => cluster < 0 ? -cluster - 1 : cluster);
+        let weight = 1;
+        let sumI = 0;
+        let frequencies = [];
+        let intensities = [];
+        if (cluster.length > maxClusterSize) {
+            // This is a single spin, but the cluster exceeds the maxClusterSize criteria
+            // we use the simple multiplicity algorithm
+            // Add the central peak. It will be split with every single J coupling.
+            let index = 0;
+            while (cluster[index++] < 0)
+                ;
+            index = cluster[index - 1];
+            frequencies.push(-chemicalShifts[index]);
+            for (let i = 0; i < cluster.length; i++) {
+                if (cluster[i] < 0) {
+                    let jc = spinSystem.couplingConstants.get(index, clusterFake[i]) / 2;
+                    let currentSize = frequencies.length;
+                    for (let j = 0; j < currentSize; j++) {
+                        frequencies.push(frequencies[j] + jc);
+                        frequencies[j] -= jc;
+                    }
+                }
+            }
+            frequencies.sort((a, b) => a - b);
+            sumI = frequencies.length;
+            weight = 1;
+            for (let i = 0; i < sumI; i++) {
+                intensities.push(1);
+            }
+        }
+        else {
+            const hamiltonian = getHamiltonian(chemicalShifts, spinSystem.couplingConstants, multiplicity, spinSystem.connectivity, clusterFake);
+            const hamSize = hamiltonian.rows;
+            // TODO: add support for sparse matrix in matrix types.
+            // @ts-expect-error sparse matrix not supported
+            const evd = new EVD(hamiltonian);
+            const V = evd.eigenvectorMatrix;
+            const diagB = evd.realEigenvalues;
+            const assignmentMatrix = new SparseMatrix(hamSize, hamSize);
+            const multLen = cluster.length;
+            weight = 0;
+            for (let n = 0; n < multLen; n++) {
+                const L = getPauliMatrix(multiplicity[clusterFake[n]]);
+                let temp = 1;
+                for (let j = 0; j < n; j++) {
+                    temp *= multiplicity[clusterFake[j]];
+                }
+                const A = SparseMatrix.eye(temp);
+                temp = 1;
+                for (let j = n + 1; j < multLen; j++) {
+                    temp *= multiplicity[clusterFake[j]];
+                }
+                const B = SparseMatrix.eye(temp);
+                const tempMat = A.kroneckerProduct(L.m).kroneckerProduct(B);
+                if (cluster[n] >= 0) {
+                    assignmentMatrix.add(tempMat.mul(cluster[n] + 1));
+                    weight++;
+                }
+                else {
+                    assignmentMatrix.add(tempMat.mul(cluster[n]));
+                }
+            }
+            let rhoip = Matrix.zeros(hamSize, hamSize);
+            assignmentMatrix.forEachNonZero((i, j, v) => {
+                if (v > 0) {
+                    for (let k = 0; k < V.columns; k++) {
+                        let element = V.get(j, k);
+                        if (element !== 0) {
+                            rhoip.set(i, k, rhoip.get(i, k) + element);
+                        }
+                    }
+                }
+                return v;
+            });
+            let rhoip2 = rhoip.clone();
+            assignmentMatrix.forEachNonZero((i, j, v) => {
+                if (v < 0) {
+                    for (let k = 0; k < V.columns; k++) {
+                        let element = V.get(j, k);
+                        if (element !== 0) {
+                            rhoip2.set(i, k, rhoip2.get(i, k) + element);
+                        }
+                    }
+                }
+                return v;
+            });
+            const tV = V.transpose();
+            rhoip = tV.mmul(rhoip);
+            const sparseRhoip = new SparseMatrix(rhoip.to2DArray(), {
+                threshold: smallValue,
+            });
+            triuTimesAbs(sparseRhoip, smallValue);
+            rhoip2 = tV.mmul(rhoip2);
+            const sparseRhoip2 = new SparseMatrix(rhoip2.to2DArray(), {
+                threshold: smallValue,
+            });
+            sparseRhoip2.forEachNonZero((i, j, v) => {
+                return v;
+            });
+            triuTimesAbs(sparseRhoip2, smallValue);
+            sparseRhoip2.forEachNonZero((i, j, v) => {
+                let val = rhoip.get(i, j);
+                val = Math.min(Math.abs(val), Math.abs(v));
+                val *= val;
+                sumI += val;
+                let valFreq = diagB[i] - diagB[j];
+                let insertIn = binarySearch(frequencies, valFreq, (a, b) => a - b);
+                if (insertIn < 0) {
+                    frequencies.splice(-1 - insertIn, 0, valFreq);
+                    intensities.splice(-1 - insertIn, 0, val);
+                }
+                else {
+                    intensities[insertIn] += val;
+                }
+            });
+        }
+        const numFreq = frequencies.length;
+        if (numFreq > 0) {
+            weight /= sumI;
+            const diff = lineWidth / 64;
+            let valFreq = frequencies[0];
+            let inte = intensities[0];
+            let count = 1;
+            for (let i = 1; i < numFreq; i++) {
+                if (Math.abs(frequencies[i] - valFreq / count) < diff) {
+                    inte += intensities[i];
+                    valFreq += frequencies[i];
+                    count++;
+                }
+                else {
+                    xyPeaks.push({
+                        x: -valFreq / count / frequencyMHz,
+                        y: inte * weight,
+                    });
+                    valFreq = frequencies[i];
+                    inte = intensities[i];
+                    count = 1;
+                }
+            }
+            xyPeaks.push({
+                x: -valFreq / count / frequencyMHz,
+                y: inte * weight,
+            });
+        }
+    }
+    return xyPeaks;
+}
+function triuTimesAbs(A, val) {
+    A.forEachNonZero((i, j, v) => {
+        if (i > j)
+            return 0;
+        if (Math.abs(v) <= val)
+            return 0;
+        return v;
+    });
+}
+/**
+ * Create a hamiltonian matrix for the given spinsystem
+ * @param {Array} chemicalShifts - An array containing the chemical shift in Hz
+ * @param {Array} couplingConstants - An array containing the coupling constants in Hz
+ * @param {Array} multiplicity - An array specifiying the multiplicities of each scalar coupling
+ * @param {Array} conMatrix - A one step connectivity matrix for the given spin system
+ * @param {Array} cluster - An binary array specifiying the spins to be considered for this hamiltonial
+ * @return {object}
+ */
+function getHamiltonian(chemicalShifts, couplingConstants, multiplicity, conMatrix, cluster) {
+    let hamSize = 1;
+    for (const element of cluster) {
+        hamSize *= multiplicity[element];
+    }
+    const clusterHam = new SparseMatrix(hamSize, hamSize);
+    for (let pos = 0; pos < cluster.length; pos++) {
+        let n = cluster[pos];
+        const L = getPauliMatrix(multiplicity[n]);
+        let A1, B1;
+        let temp = 1;
+        for (let i = 0; i < pos; i++) {
+            temp *= multiplicity[cluster[i]];
+        }
+        A1 = SparseMatrix.eye(temp);
+        temp = 1;
+        for (let i = pos + 1; i < cluster.length; i++) {
+            temp *= multiplicity[cluster[i]];
+        }
+        B1 = SparseMatrix.eye(temp);
+        const alpha = chemicalShifts[n];
+        const kronProd = A1.kroneckerProduct(L.z).kroneckerProduct(B1);
+        clusterHam.add(kronProd.mul(alpha));
+        for (let pos2 = 0; pos2 < cluster.length; pos2++) {
+            const k = cluster[pos2];
+            if (conMatrix.get(n, k) === 1) {
+                const S = getPauliMatrix(multiplicity[k]);
+                let A2, B2;
+                let temp = 1;
+                for (let i = 0; i < pos2; i++) {
+                    temp *= multiplicity[cluster[i]];
+                }
+                A2 = SparseMatrix.eye(temp);
+                temp = 1;
+                for (let i = pos2 + 1; i < cluster.length; i++) {
+                    temp *= multiplicity[cluster[i]];
+                }
+                B2 = SparseMatrix.eye(temp);
+                const kron1 = A1.kroneckerProduct(L.x)
+                    .kroneckerProduct(B1)
+                    .mmul(A2.kroneckerProduct(S.x).kroneckerProduct(B2));
+                kron1.add(A1.kroneckerProduct(L.y)
+                    .kroneckerProduct(B1)
+                    .mul(-1)
+                    .mmul(A2.kroneckerProduct(S.y).kroneckerProduct(B2)));
+                kron1.add(A1.kroneckerProduct(L.z)
+                    .kroneckerProduct(B1)
+                    .mmul(A2.kroneckerProduct(S.z).kroneckerProduct(B2)));
+                clusterHam.add(kron1.mul(couplingConstants.get(n, k) / 2));
+            }
+        }
+    }
+    return clusterHam;
+}
+//# sourceMappingURL=simulateXYPeaks.js.map

package/lib-esm/signals/simulation/simulateXYPeaks.js.map

@@ -0,0 +1 @@
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package/lib-esm/signals/simulation/splitSpinSystem.js

@@ -52,20 +52,18 @@ function splitCluster(cluster, clusterList, options) {
                 if (count <= maxClusterSize) {
                     clusterList.push(members);
                 }
+                else if (child.index < 0) {
+                    splitCluster(child, clusterList, {
+                        maxClusterSize,
+                        force: true,
+                        nSpins,
+                        connectivity,
+                    });
+                }
                 else {
-                    if (child.index < 0) {
-                        splitCluster(child, clusterList, {
-                            maxClusterSize,
-                            force: true,
-                            nSpins,
-                            connectivity,
-                        });
-                    }
-                    else {
-                        // We have to threat this spin alone and use the resurrection algorithm instead of the simulation
-                        members[child.index] = 2;
-                        clusterList.push(members);
-                    }
+                    // We have to threat this spin alone and use the resurrection algorithm instead of the simulation
+                    members[child.index] = 2;
+                    clusterList.push(members);
                 }
             }
             else {

package/lib-esm/signals/simulation/splitSpinSystem.js.map

@@ -1 +1 @@
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package/lib-esm/utilities/getFrequency.js

@@ -1,4 +1,4 @@
-import { gyromagneticRatio } from '../constants/gyromagneticRatio';
+import { gyromagneticRatio } from 'gyromagnetic-ratio';
 /**
  * calculate the frequency of a nucleus with respect to a reference nucleus
  */

package/lib-esm/utilities/getFrequency.js.map

@@ -1 +1 @@
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package/lib-esm/utilities/rangeFromSignal.js

@@ -1,13 +1,13 @@
 import { couplingValues } from '../constants/couplingValues';
-export function rangeFromSignal(signal, options = {}) {
+export function rangeFromSignal(signal, options) {
     const { nucleus = '1h', frequency = 400 } = options;
     const { tolerance = getTolerance(nucleus) / frequency } = options;
-    let halfWidth = (signal.js || []).reduce((total, j) => {
-        const { coupling, multiplicity = 'd' } = j;
-        return total + (couplingValues[multiplicity] * coupling) / frequency;
-    }, 0) /
-        2 +
-        tolerance;
+    let halfWidth = 0;
+    for (const js of signal.js || []) {
+        const { coupling, multiplicity = 'd' } = js;
+        halfWidth += (couplingValues[multiplicity] * coupling) / frequency;
+    }
+    halfWidth = tolerance + halfWidth / 2;
     return {
         from: signal.delta - halfWidth,
         to: signal.delta + halfWidth,

package/lib-esm/utilities/rangeFromSignal.js.map

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