nmr-processing 9.7.8 → 9.8.0

package/src/xyz/xyzJResAnalyzer.ts

@@ -58,7 +58,7 @@ export function xyzJResAnalyzer(
   signals: NMRSignal2D[],
   options: XYZJResAnalyzerOptions = {},
 ) {
-  let {
+  const {
     reference = 0,
     getZones = false,
     referenceMaxShiftError = 0.08,
@@ -69,7 +69,7 @@ export function xyzJResAnalyzer(
       jAxisKey: { jAxis: 'y', intensity: 'z' },
     },
   } = options;
-  let temporalSignals = compilePattern(signals, {
+  const temporalSignals = compilePattern(signals, {
     observedFrequencies,
     tolerances,
     nuclei,
@@ -78,7 +78,7 @@ export function xyzJResAnalyzer(
   //check if the signal are symmetric around the reference
   let signals2D: any[] = [];
   for (const tempSignal of temporalSignals) {
-    let delta = tempSignal.y.delta;
+    const delta = tempSignal.y.delta;
     if (Math.abs(delta - reference) > referenceMaxShiftError) continue;
     signals2D.push(tempSignal);
   }
@@ -92,14 +92,14 @@ function compilePattern(
   signals: NMRSignal2D[],
   options: CompilePatternOptionsMandatory,
 ) {
-  let {
+  const {
     observedFrequencies,
     tolerances,
     nuclei,
     jAnalyzer: jAnalyzerOptions,
   } = options;
 
-  let signalOptions = {
+  const signalOptions = {
     observedFrequencies,
     tolerances,
     nuclei,
@@ -111,7 +111,7 @@ function compilePattern(
   const newSignals: SignalFlexiblePeaks[] = [];
   //adapt to 1D jAnalyzer
   for (const signal of signals) {
-    let peaks: Peak2DWidth[] = [];
+    const peaks: Peak2DWidth[] = [];
     for (const peak of signal.peaks || []) {
       peaks.push({
         ...peak,
@@ -145,10 +145,10 @@ function compilePattern(
       signal.multiplicity !== ''
     ) {
       // Create a new signal with the removed peaks
-      let peaksO: Peak1DIntern[] = [];
+      const peaksO: Peak1DIntern[] = [];
       for (let j = signal.maskPattern.length - 1; j >= 0; j--) {
         if (!signal.maskPattern[j]) {
-          let peakR = signal.peaks.splice(j, 1)[0];
+          const peakR = signal.peaks.splice(j, 1)[0];
           peaksO.push(peakR);
           signal.mask.splice(j, 1);
           signal.mask2?.splice(j, 1);
@@ -158,7 +158,7 @@ function compilePattern(
       }
       if (peaksO.length > 0) {
         peaksO.reverse();
-        let signals2D = createSignals2D(peaksO, signalOptions);
+        const signals2D = createSignals2D(peaksO, signalOptions);
 
         for (const signal of signals2D) {
           newSignals.push(signal);
@@ -175,17 +175,17 @@ function compilePattern(
 }
 
 function createSignals2D(peaksInput: Peak1DIntern[], options: any) {
-  let { observedFrequencies, tolerances, nuclei, dx, dy } = options;
+  const { observedFrequencies, tolerances, nuclei, dx, dy } = options;
 
   const peaks: Peak2DInternalCompiler[] = parse(stringify(peaksInput));
 
-  let [nucleusX, nucleusY] = nuclei;
-  let [toleranceX, toleranceY] = tolerances;
-  let [observeFrequencyX, observeFrequencyY] = observedFrequencies;
+  const [nucleusX, nucleusY] = nuclei;
+  const [toleranceX, toleranceY] = tolerances;
+  const [observeFrequencyX, observeFrequencyY] = observedFrequencies;
 
   // The connectivity matrix is an square and symmetric matrix, so we'll only store the upper diagonal in an
   // array like form
-  let connectivity: Array<0 | 1> = [];
+  const connectivity: Array<0 | 1> = [];
   for (let i = 0; i < peaks.length; i++) {
     for (let j = i; j < peaks.length; j++) {
       if (
@@ -199,12 +199,12 @@ function createSignals2D(peaksInput: Peak1DIntern[], options: any) {
       }
     }
   }
-  let clusters = simpleClustering(connectivity);
+  const clusters = simpleClustering(connectivity);
 
-  let signals: SignalIntern[] = [];
+  const signals: SignalIntern[] = [];
   if (clusters) {
-    for (let cluster of clusters) {
-      let signal: any = {
+    for (const cluster of clusters) {
+      const signal: any = {
         id: generateID(),
         nucleusX,
         nucleusY,
@@ -221,9 +221,9 @@ function createSignals2D(peaksInput: Peak1DIntern[], options: any) {
         shiftX: 0,
         shiftY: 0,
       };
-      let peaks2D: Peak2DInternalCompiler[] = [];
-      let minMax1 = [Number.MAX_VALUE, 0];
-      let minMax2 = [Number.MAX_VALUE, 0];
+      const peaks2D: Peak2DInternalCompiler[] = [];
+      const minMax1 = [Number.MAX_VALUE, 0];
+      const minMax2 = [Number.MAX_VALUE, 0];
       let sumZ = 0;
       for (let jPeak = cluster.length - 1; jPeak >= 0; jPeak--) {
         if (cluster[jPeak] === 1) {

package/src/xyz/xyzPhaseCorrectionDirectDimension.ts

@@ -0,0 +1,52 @@
+import { NmrData2DFt } from 'cheminfo-types';
+import { degreeToRadians } from '../constants/degreeToRadians';
+import Matrix from 'ml-matrix';
+import { reimPhaseCorrection } from 'ml-spectra-processing';
+import { applyOverImag } from './util/phaseCorrection/applyOverImag';
+import { applyOverReal } from './util/phaseCorrection/applyOverReal';
+
+interface ReimMatrix {
+  re: Matrix;
+  im: Matrix;
+}
+export interface PhaseCorrectionOptions {
+  ph0: number;
+  ph1: number;
+  applyPhaseCorrection: (
+    d: ReimMatrix,
+    o: { ph0: number; ph1: number },
+  ) => ReimMatrix;
+}
+
+export function xyzPhaseCorrectionDirectDimension(
+  data: NmrData2DFt,
+  options: PhaseCorrectionOptions,
+) {
+  applyOverReal(data, { ...options, applyPhaseCorrection });
+  if ('ri' in data && 'ii' in data) {
+    applyOverImag(data, { ...options, applyPhaseCorrection });
+  }
+  return data;
+}
+
+function applyPhaseCorrection(
+  data: { re: Matrix; im: Matrix },
+  options: { ph0: number; ph1: number },
+) {
+  const ph0 = options.ph0 * degreeToRadians;
+  const ph1 = options.ph1 * degreeToRadians;
+  const nbRows = data.re.rows;
+  for (let i = 0; i < nbRows; i++) {
+    const { re, im } = reimPhaseCorrection(
+      {
+        re: data.re.getRow(i),
+        im: data.im.getRow(i),
+      },
+      ph0,
+      ph1,
+    );
+    data.re.setRow(i, re);
+    data.im.setRow(i, im);
+  }
+  return data;
+}

package/src/xyz/xyzPhaseCorrectionIndirectDimension.ts

@@ -0,0 +1,45 @@
+import { NmrData2DFt } from 'cheminfo-types';
+import { degreeToRadians } from '../constants/degreeToRadians';
+import Matrix from 'ml-matrix';
+import { reimPhaseCorrection } from 'ml-spectra-processing';
+import { applyOverImag } from './util/phaseCorrection/applyOverImag';
+import { PhaseCorrectionOptions } from './xyzPhaseCorrectionDirectDimension';
+import { applyOverReal } from './util/phaseCorrection/applyOverReal';
+
+export type PhaseCorrectionIndirectDimensionOptions = PhaseCorrectionOptions & {
+  quad: 'imag' | 'real';
+};
+
+export function xyzPhaseCorrectionIndirectDimension(
+  data: NmrData2DFt,
+  options: PhaseCorrectionIndirectDimensionOptions,
+) {
+  const { quad } = options;
+  if (quad === 'real') {
+    return applyOverReal(data, { ...options, applyPhaseCorrection });
+  } else if (quad === 'imag') {
+    return applyOverImag(data, { ...options, applyPhaseCorrection });
+  }
+}
+
+function applyPhaseCorrection(
+  data: { re: Matrix; im: Matrix },
+  options: { ph0: number; ph1: number },
+) {
+  const ph0 = options.ph0 * degreeToRadians;
+  const ph1 = options.ph1 * degreeToRadians;
+  const nbColumns = data.re.columns;
+  for (let i = 0; i < nbColumns; i++) {
+    const { re, im } = reimPhaseCorrection(
+      {
+        re: data.re.getColumn(i),
+        im: data.im.getColumn(i),
+      },
+      ph0,
+      ph1,
+    );
+    data.re.setColumn(i, re);
+    data.im.setColumn(i, im);
+  }
+  return data;
+}

package/lib/assignment/utils/buildAssignments.js.map

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package/lib/assignment/utils/createMapPossibleAssignments.js.map

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package/lib/assignment/utils/exploreTreeRec.js.map

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package/lib/assignment/utils/getAssignment/buildAssignments.js.map

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package/lib/assignment/utils/getAssignment/checkIDs.js.map

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package/lib/assignment/utils/getAssignment/createMapPossibleAssignment.js.map

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package/lib/assignment/utils/getAssignment/exploreTree.js.map

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package/lib/assignment/utils/getAssignment/formatData.js.map

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package/lib/assignment/utils/getAssignment/getIntegrationOfAttachedProtons.js.map

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package/lib/assignment/utils/getAssignment/getTargetsAndCorrelations.js.map

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package/lib/assignment/utils/getAssignment/getWorkFlow.js.map

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package/lib/assignment/utils/getAssignment/groupCarbonTargetByIntegrationZone.js.map

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package/lib/assignment/utils/getAssignment/isSpectraData1D.js.map

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package/lib/assignment/utils/getAssignment/partialScore.js.map

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package/lib/assignment/utils/getAssignment/searchIndices.js.map

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package/lib/assignment/utils/partialScore.js.map

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package/lib-esm/assignment/utils/buildAssignments.js.map

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package/lib-esm/assignment/utils/createMapPossibleAssignments.js.map

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package/lib-esm/assignment/utils/exploreTreeRec.js.map

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package/lib-esm/assignment/utils/getAssignment/buildAssignments.js.map

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package/lib-esm/assignment/utils/getAssignment/checkIDs.js.map

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package/lib-esm/assignment/utils/getAssignment/createMapPossibleAssignment.js.map

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package/lib-esm/assignment/utils/getAssignment/exploreTree.js.map

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package/lib-esm/assignment/utils/getAssignment/formatData.js.map

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package/lib-esm/assignment/utils/getAssignment/getIntegrationOfAttachedProtons.js.map

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package/lib-esm/assignment/utils/getAssignment/getTargetsAndCorrelations.js.map

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package/lib-esm/assignment/utils/getAssignment/getWorkFlow.js.map

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package/lib-esm/assignment/utils/getAssignment/groupCarbonTargetByIntegrationZone.js.map

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package/lib-esm/assignment/utils/getAssignment/isSpectraData1D.js.map

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package/lib-esm/assignment/utils/getAssignment/partialScore.js.map

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package/lib-esm/assignment/utils/getAssignment/searchIndices.js.map

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package/lib-esm/assignment/utils/partialScore.js.map

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