nmr-processing 7.4.3 → 8.2.0

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/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 @@
-{"version":3,"file":"getFrequency.js","sourceRoot":"","sources":["../../src/utilities/getFrequency.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAU,MAAM,gCAAgC,CAAC;AAgB3E;;GAEG;AACH,MAAM,UAAU,YAAY;AAC1B;;GAEG;AACH,OAAgB,EAChB,mBAAwC;IAExC,MAAM,EAAE,OAAO,EAAE,UAAU,EAAE,SAAS,EAAE,GAAG,mBAAmB,CAAC;IAE/D,cAAc,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC;IAEpC,OAAO,CACL,CAAC,SAAS,GAAG,iBAAiB,CAAC,OAAiB,CAAC,CAAC;QAClD,iBAAiB,CAAC,UAAoB,CAAC,CACxC,CAAC;AACJ,CAAC;AAED,SAAS,cAAc,CAAC,GAAG,OAAkB;IAC3C,IAAI,MAAM,GAAa,EAAE,CAAC;IAC1B,KAAK,MAAM,CAAC,IAAI,OAAO,EAAE;QACvB,IAAI,CAAC,CAAC,CAAC,IAAI,iBAAiB,CAAC,EAAE;YAC7B,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;SAChB;KACF;IACD,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE;QACvB,MAAM,IAAI,KAAK,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,mBAAmB,CAAC,CAAC;KAC3D;AACH,CAAC"}
+{"version":3,"file":"getFrequency.js","sourceRoot":"","sources":["../../src/utilities/getFrequency.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAU,MAAM,oBAAoB,CAAC;AAgB/D;;GAEG;AACH,MAAM,UAAU,YAAY;AAC1B;;GAEG;AACH,OAAgB,EAChB,mBAAwC;IAExC,MAAM,EAAE,OAAO,EAAE,UAAU,EAAE,SAAS,EAAE,GAAG,mBAAmB,CAAC;IAE/D,cAAc,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC;IAEpC,OAAO,CACL,CAAC,SAAS,GAAG,iBAAiB,CAAC,OAAiB,CAAC,CAAC;QAClD,iBAAiB,CAAC,UAAoB,CAAC,CACxC,CAAC;AACJ,CAAC;AAED,SAAS,cAAc,CAAC,GAAG,OAAkB;IAC3C,IAAI,MAAM,GAAa,EAAE,CAAC;IAC1B,KAAK,MAAM,CAAC,IAAI,OAAO,EAAE;QACvB,IAAI,CAAC,CAAC,CAAC,IAAI,iBAAiB,CAAC,EAAE;YAC7B,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;SAChB;KACF;IACD,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE;QACvB,MAAM,IAAI,KAAK,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,mBAAmB,CAAC,CAAC;KAC3D;AACH,CAAC"}

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 @@
+{"version":3,"file":"formatZone.js","sourceRoot":"","sources":["../../../src/xyz/util/formatZone.ts"],"names":[],"mappings":"AAGA,MAAM,UAAU,WAAW,CAAC,OAAsB;IAChD,IAAI,KAAK,GAAc,EAAE,CAAC;IAC1B,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;QAC5B,IAAI,OAAO,GAAG,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC;QACpC,IAAI,OAAO,GAAG,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC;QACpC,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,KAAK,IAAI,EAAE,EAAE;YACrC,IAAI,IAAI,CAAC,IAAI,GAAG,OAAO,CAAC,CAAC,CAAC,EAAE;gBAC1B,OAAO,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC;aACxB;YACD,IAAI,IAAI,CAAC,IAAI,GAAG,OAAO,CAAC,CAAC,CAAC,EAAE;gBAC1B,OAAO,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC;aACxB;YACD,IAAI,IAAI,CAAC,IAAI,GAAG,OAAO,CAAC,CAAC,CAAC,EAAE;gBAC1B,OAAO,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC;aACxB;YACD,IAAI,IAAI,CAAC,IAAI,GAAG,OAAO,CAAC,CAAC,CAAC,EAAE;gBAC1B,OAAO,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC;aACxB;SACF;QACD,KAAK,CAAC,IAAI,CAAC;YACT,CAAC,EAAE;gBACD,IAAI,EAAE,OAAO,CAAC,CAAC,CAAC;gBAChB,EAAE,EAAE,OAAO,CAAC,CAAC,CAAC;aACf;YACD,CAAC,EAAE;gBACD,IAAI,EAAE,OAAO,CAAC,CAAC,CAAC;gBAChB,EAAE,EAAE,OAAO,CAAC,CAAC,CAAC;aACf;YACD,OAAO,EAAE,CAAC,MAAM,CAAC;SAClB,CAAC,CAAC;KACJ;IACD,OAAO,KAAK,CAAC;AACf,CAAC"}

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;