nmr-processing 9.7.8 → 9.8.0

package/lib/xyz/xyzAutoSignalsPicking.js

@@ -48,7 +48,8 @@ const smallFilter = [
     [0, 0, 1, 2, 2, 2, 1, 0, 0],
 ];
 function xyzAutoSignalsPicking(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;
+    const { sizeToPad = 14, realTopDetection = true, nuclei = ['1H', '1H'], observedFrequencies, enhanceSymmetry = false, clean = true, maxPercentCutOff = 0.03, tolerances = [24, 24], convolutionByFFT = true, kernel: kernelOptions, } = options;
+    let { thresholdFactor = 0.5 } = options;
     if (!Array.isArray(observedFrequencies) &&
         !ArrayBuffer.isView(observedFrequencies)) {
         throw new Error('observedFrequencies is mandatory');
@@ -61,18 +62,18 @@ function xyzAutoSignalsPicking(spectraData, options) {
         nbPoints = spectraData.z[0].length;
         nbSubSpectra = spectraData.z.length;
     }
-    let absoluteData = new Float64Array(nbPoints * nbSubSpectra);
-    let originalData = new Float64Array(nbPoints * nbSubSpectra);
+    const absoluteData = new Float64Array(nbPoints * nbSubSpectra);
+    const originalData = new Float64Array(nbPoints * nbSubSpectra);
     for (let iSubSpectra = 0; iSubSpectra < nbSubSpectra; iSubSpectra++) {
-        let spectrum = spectraData.z[iSubSpectra];
+        const spectrum = spectraData.z[iSubSpectra];
         for (let iCol = 0; iCol < nbPoints; iCol++) {
-            let index = iSubSpectra * nbPoints + iCol;
+            const index = iSubSpectra * nbPoints + iCol;
             absoluteData[index] = Math.abs(spectrum[iCol]);
             originalData[index] = spectrum[iCol]; //@todo pensar si se puede evitar originalData
         }
     }
     const kernel = kernelOptions ? (0, getKernel_1.getKernel)(kernelOptions) : smallFilter;
-    let convolutedSpectrum = convolutionByFFT
+    const convolutedSpectrum = convolutionByFFT
         ? convolution.fft(absoluteData, kernel, {
             rows: nbSubSpectra,
             cols: nbPoints,
@@ -113,12 +114,12 @@ function xyzAutoSignalsPicking(spectraData, options) {
 }
 exports.xyzAutoSignalsPicking = xyzAutoSignalsPicking;
 function createSignals2D(peaks, options) {
-    let { nCols, nRows, absoluteData, originalData, observedFrequencies, tolerances, nuclei, realTopDetection, minY, maxY, minX, maxX, } = options;
-    let [nucleusX, nucleusY] = nuclei;
-    let [toleranceX, toleranceY] = tolerances;
-    let [observeFrequencyX, observeFrequencyY] = observedFrequencies;
-    let dy = (maxY - minY) / (nRows - 1);
-    let dx = (maxX - minX) / (nCols - 1);
+    const { nCols, nRows, absoluteData, originalData, observedFrequencies, tolerances, nuclei, realTopDetection, minY, maxY, minX, maxX, } = options;
+    const [nucleusX, nucleusY] = nuclei;
+    const [toleranceX, toleranceY] = tolerances;
+    const [observeFrequencyX, observeFrequencyY] = observedFrequencies;
+    const dy = (maxY - minY) / (nRows - 1);
+    const dx = (maxX - minX) / (nCols - 1);
     if (realTopDetection) {
         peaks = (0, determineRealTop_1.determineRealTop)(peaks, {
             nCols,
@@ -131,7 +132,7 @@ function createSignals2D(peaks, options) {
         });
     }
     for (let i = peaks.length - 1; i >= 0; i--) {
-        let { x, y } = peaks[i];
+        const { x, y } = peaks[i];
         peaks[i].x = minX + dx * x;
         peaks[i].y = minY + dy * y;
         peaks[i].minX = minX + dx * peaks[i].minX;
@@ -142,7 +143,7 @@ function createSignals2D(peaks, options) {
     }
     // The connectivity matrix is an square and symmetric matrix, so we'll only store the upper diagonal in an
     // array like form
-    let connectivity = [];
+    const connectivity = [];
     for (let i = 0; i < peaks.length; i++) {
         for (let j = i; j < peaks.length; j++) {
             if (Math.abs(peaks[i].x - peaks[j].x) * observeFrequencyX < toleranceX &&
@@ -155,11 +156,11 @@ function createSignals2D(peaks, options) {
             }
         }
     }
-    let clusters = (0, ml_simple_clustering_1.default)(connectivity);
-    let signals = [];
+    const clusters = (0, ml_simple_clustering_1.default)(connectivity);
+    const signals = [];
     if (clusters) {
         for (const cluster of clusters) {
-            let signal = {
+            const signal = {
                 id: (0, uuid_1.v4)(),
                 x: {
                     delta: 0,
@@ -172,7 +173,7 @@ function createSignals2D(peaks, options) {
                     resolution: dy,
                 },
             };
-            let peaks2D = [];
+            const peaks2D = [];
             let sumZ = 0;
             for (let jPeak = 0; jPeak < cluster.length; jPeak++) {
                 if (cluster[jPeak] === 1) {

package/lib/xyz/xyzAutoSignalsPicking.js.map

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+{"version":3,"file":"xyzAutoSignalsPicking.js","sourceRoot":"","sources":["../../src/xyz/xyzAutoSignalsPicking.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,uCAAgD;AAEhD,mEAAqD;AACrD,0EAA4D;AAE5D,gFAAoD;AAEpD,+DAA4D;AAC5D,qEAAkE;AAClE,uDAAoD;AAEpD,2EAA6D;AAI7D,4CAAyC;AAEzC,MAAM,WAAW,GAAG;IAClB,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC;IAC3B,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC;IAC3B,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC;IAC3B,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC;IACjC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC;IACjC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC;IACjC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC;IAC3B,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC;IAC3B,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC;CAC5B,CAAC;AA+DF,SAAgB,qBAAqB,CACnC,WAA6B,EAC7B,OAAqC;IAErC,MAAM,EACJ,SAAS,GAAG,EAAE,EACd,gBAAgB,GAAG,IAAI,EACvB,MAAM,GAAG,CAAC,IAAI,EAAE,IAAI,CAAC,EACrB,mBAAmB,EACnB,eAAe,GAAG,KAAK,EACvB,KAAK,GAAG,IAAI,EACZ,gBAAgB,GAAG,IAAI,EACvB,UAAU,GAAG,CAAC,EAAE,EAAE,EAAE,CAAC,EACrB,gBAAgB,GAAG,IAAI,EACvB,MAAM,EAAE,aAAa,GACtB,GAAG,OAAO,CAAC;IAEZ,IAAI,EAAE,eAAe,GAAG,GAAG,EAAE,GAAG,OAAO,CAAC;IAExC,IACE,CAAC,KAAK,CAAC,OAAO,CAAC,mBAAmB,CAAC;QACnC,CAAC,WAAW,CAAC,MAAM,CAAC,mBAAmB,CAAC,EACxC;QACA,MAAM,IAAI,KAAK,CAAC,kCAAkC,CAAC,CAAC;KACrD;IAED,eAAe,GAAG,eAAe,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,eAAe,CAAC,CAAC;IAExE,IAAI,QAAQ,GAAG,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC;IACvC,IAAI,YAAY,GAAG,WAAW,CAAC,CAAC,CAAC,MAAM,CAAC;IAExC,IAAI,YAAY,GAAG,SAAS,EAAE;QAC5B,WAAW,GAAG,IAAA,iBAAO,EAAC,WAAW,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,CAAC,CAAC;QACzD,QAAQ,GAAG,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC;QACnC,YAAY,GAAG,WAAW,CAAC,CAAC,CAAC,MAAM,CAAC;KACrC;IAED,MAAM,YAAY,GAAG,IAAI,YAAY,CAAC,QAAQ,GAAG,YAAY,CAAC,CAAC;IAC/D,MAAM,YAAY,GAAG,IAAI,YAAY,CAAC,QAAQ,GAAG,YAAY,CAAC,CAAC;IAE/D,KAAK,IAAI,WAAW,GAAG,CAAC,EAAE,WAAW,GAAG,YAAY,EAAE,WAAW,EAAE,EAAE;QACnE,MAAM,QAAQ,GAAG,WAAW,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC;QAC5C,KAAK,IAAI,IAAI,GAAG,CAAC,EAAE,IAAI,GAAG,QAAQ,EAAE,IAAI,EAAE,EAAE;YAC1C,MAAM,KAAK,GAAG,WAAW,GAAG,QAAQ,GAAG,IAAI,CAAC;YAC5C,YAAY,CAAC,KAAK,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC;YAC/C,YAAY,CAAC,KAAK,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,8CAA8C;SACrF;KACF;IAED,MAAM,MAAM,GAAG,aAAa,CAAC,CAAC,CAAC,IAAA,qBAAS,EAAC,aAAa,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC;IAEtE,MAAM,kBAAkB,GAAG,gBAAgB;QACzC,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,YAAY,EAAE,MAAM,EAAE;YACpC,IAAI,EAAE,YAAY;YAClB,IAAI,EAAE,QAAQ;SACf,CAAC;QACJ,CAAC,CAAC,WAAW,CAAC,MAAM,CAAC,YAAY,EAAE,MAAM,EAAE;YACvC,IAAI,EAAE,YAAY;YAClB,IAAI,EAAE,QAAQ;SACf,CAAC,CAAC;IAEP,IAAI,QAAQ,GAAG,iBAAiB,CAAC,iBAAiB,CAAC,YAAY,EAAE;QAC/D,YAAY;QACZ,YAAY,EAAE,kBAAkB;QAChC,IAAI,EAAE,YAAY;QAClB,IAAI,EAAE,QAAQ;QACd,OAAO,EAAE,eAAe;KACzB,CAAC,CAAC;IAEH,IAAI,KAAK,EAAE;QACT,sEAAsE;QACtE,QAAQ,GAAG,aAAa,CAAC,KAAK,CAAC,QAAQ,EAAE,gBAAgB,CAAC,CAAC;KAC5D;IAED,IAAI,OAAO,GAAG,eAAe,CAAC,IAAA,6BAAa,EAAC,QAAQ,CAAC,EAAE;QACrD,KAAK,EAAE,YAAY;QACnB,KAAK,EAAE,QAAQ;QACf,IAAI,EAAE,WAAW,CAAC,IAAI;QACtB,IAAI,EAAE,WAAW,CAAC,IAAI;QACtB,IAAI,EAAE,WAAW,CAAC,IAAI;QACtB,IAAI,EAAE,WAAW,CAAC,IAAI;QACtB,YAAY;QACZ,YAAY;QACZ,UAAU;QACV,MAAM;QACN,mBAAmB;QACnB,gBAAgB;KACjB,CAAC,CAAC;IAEH,IAAI,eAAe,EAAE;QACnB,OAAO,GAAG,aAAa,CAAC,eAAe,CAAC,OAAO,CAAC,CAAC;KAClD;IAED,OAAO,OAAO,CAAC;AACjB,CAAC;AA9FD,sDA8FC;AAuBD,SAAS,eAAe,CACtB,KAAU,EACV,OAA+B;IAE/B,MAAM,EACJ,KAAK,EACL,KAAK,EACL,YAAY,EACZ,YAAY,EACZ,mBAAmB,EACnB,UAAU,EACV,MAAM,EACN,gBAAgB,EAChB,IAAI,EACJ,IAAI,EACJ,IAAI,EACJ,IAAI,GACL,GAAG,OAAO,CAAC;IAEZ,MAAM,CAAC,QAAQ,EAAE,QAAQ,CAAC,GAAG,MAAM,CAAC;IACpC,MAAM,CAAC,UAAU,EAAE,UAAU,CAAC,GAAG,UAAU,CAAC;IAC5C,MAAM,CAAC,iBAAiB,EAAE,iBAAiB,CAAC,GAAG,mBAAmB,CAAC;IAEnE,MAAM,EAAE,GAAG,CAAC,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC;IACvC,MAAM,EAAE,GAAG,CAAC,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC;IAEvC,IAAI,gBAAgB,EAAE;QACpB,KAAK,GAAG,IAAA,mCAAgB,EAAC,KAAK,EAAE;YAC9B,KAAK;YACL,YAAY;YACZ,YAAY;YACZ,IAAI;YACJ,IAAI;YACJ,IAAI;YACJ,IAAI;SACL,CAAC,CAAC;KACJ;IAED,KAAK,IAAI,CAAC,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE;QAC1C,MAAM,EAAE,CAAC,EAAE,CAAC,EAAE,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC;QAC1B,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,GAAG,EAAE,GAAG,CAAC,CAAC;QAC3B,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,GAAG,EAAE,GAAG,CAAC,CAAC;QAC3B,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,GAAG,IAAI,GAAG,EAAE,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;QAC1C,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,GAAG,IAAI,GAAG,EAAE,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;QAC1C,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,GAAG,IAAI,GA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package/lib/xyz/xyzBidimensionalFFT.js

@@ -4,6 +4,7 @@ exports.xyzBidimensionalFFT = void 0;
 const quadrature_1 = require("./quadrature");
 const fftDirectDimension_1 = require("./util/fft2d/fftDirectDimension");
 const fftIndirectDimension_1 = require("./util/fft2d/fftIndirectDimension");
+const getMinMaxXY_1 = require("./util/getMinMaxXY");
 function xyzBidimensionalFFT(data, options) {
     ensureData2DFid(data);
     const { info, fnMode, digitalFilterValue = 0, zeroFilling: zeroFillingGeneral, } = options;
@@ -29,7 +30,7 @@ function xyzBidimensionalFFT(data, options) {
         fnMode,
         zeroFilling: { nbPoints: nbPointsF1 },
     });
-    const minMaxXY = getMinMaxXY(info);
+    const minMaxXY = (0, getMinMaxXY_1.getMinMaxXY)(info);
     return {
         re: {
             z: convertToDoubleArray(reResult),
@@ -58,22 +59,4 @@ function convertToDoubleArray(data) {
     }
     return result;
 }
-function getMinMaxXY(info) {
-    const min = [];
-    const max = [];
-    for (let i = 0; i < info.baseFrequency.length; i++) {
-        const baseFrequency = Number.parseFloat(info.baseFrequency[i]);
-        const frequencyOffset = Number.parseFloat(info.frequencyOffset[i]);
-        const spectralWidth = Number.parseFloat(info.spectralWidth[i]);
-        const offset = frequencyOffset / baseFrequency;
-        min.push(offset - spectralWidth * 0.5);
-        max.push(offset + spectralWidth * 0.5);
-    }
-    return {
-        minX: min[0],
-        maxX: max[0],
-        minY: min[1],
-        maxY: max[1],
-    };
-}
 //# sourceMappingURL=xyzBidimensionalFFT.js.map

package/lib/xyz/xyzBidimensionalFFT.js.map

@@ -1 +1 @@
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package/lib/xyz/xyzJResAnalyzer.js

@@ -11,10 +11,10 @@ const jAnalyzer_1 = __importDefault(require("../signals/utils/jAnalyzer"));
 const formatZone_1 = require("./util/formatZone");
 const { parse, stringify } = JSON;
 function xyzJResAnalyzer(signals, options = {}) {
-    let { reference = 0, getZones = false, referenceMaxShiftError = 0.08, tolerances = [10, 100], nuclei = ['1H', '1H'], observedFrequencies = [400, 400], jAnalyzer = {
+    const { 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, {
+    const temporalSignals = compilePattern(signals, {
         observedFrequencies,
         tolerances,
         nuclei,
@@ -23,7 +23,7 @@ function xyzJResAnalyzer(signals, options = {}) {
     //check if the signal are symmetric around the reference
     let signals2D = [];
     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);
@@ -33,8 +33,8 @@ function xyzJResAnalyzer(signals, options = {}) {
 }
 exports.xyzJResAnalyzer = xyzJResAnalyzer;
 function compilePattern(signals, options) {
-    let { observedFrequencies, tolerances, nuclei, jAnalyzer: jAnalyzerOptions, } = options;
-    let signalOptions = {
+    const { observedFrequencies, tolerances, nuclei, jAnalyzer: jAnalyzerOptions, } = options;
+    const signalOptions = {
         observedFrequencies,
         tolerances,
         nuclei,
@@ -45,7 +45,7 @@ function compilePattern(signals, options) {
     const newSignals = [];
     //adapt to 1D jAnalyzer
     for (const signal of signals) {
-        let peaks = [];
+        const peaks = [];
         for (const peak of signal.peaks || []) {
             peaks.push({
                 ...peak,
@@ -75,10 +75,10 @@ function compilePattern(signals, options) {
             signal.multiplicity !== 'm' &&
             signal.multiplicity !== '') {
             // Create a new signal with the removed peaks
-            let peaksO = [];
+            const peaksO = [];
             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);
@@ -88,7 +88,7 @@ function compilePattern(signals, options) {
             }
             if (peaksO.length > 0) {
                 peaksO.reverse();
-                let signals2D = createSignals2D(peaksO, signalOptions);
+                const signals2D = createSignals2D(peaksO, signalOptions);
                 for (const signal of signals2D) {
                     newSignals.push(signal);
                 }
@@ -101,14 +101,14 @@ function compilePattern(signals, options) {
     return signals;
 }
 function createSignals2D(peaksInput, options) {
-    let { observedFrequencies, tolerances, nuclei, dx, dy } = options;
+    const { observedFrequencies, tolerances, nuclei, dx, dy } = options;
     const peaks = 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 = [];
+    const connectivity = [];
     for (let i = 0; i < peaks.length; i++) {
         for (let j = i; j < peaks.length; j++) {
             if (Math.abs(peaks[i].x - peaks[j].x) * observeFrequencyX < toleranceX &&
@@ -121,11 +121,11 @@ function createSignals2D(peaksInput, options) {
             }
         }
     }
-    let clusters = (0, ml_simple_clustering_1.default)(connectivity);
-    let signals = [];
+    const clusters = (0, ml_simple_clustering_1.default)(connectivity);
+    const signals = [];
     if (clusters) {
-        for (let cluster of clusters) {
-            let signal = {
+        for (const cluster of clusters) {
+            const signal = {
                 id: (0, uuid_1.v4)(),
                 nucleusX,
                 nucleusY,
@@ -142,9 +142,9 @@ function createSignals2D(peaksInput, options) {
                 shiftX: 0,
                 shiftY: 0,
             };
-            let peaks2D = [];
-            let minMax1 = [Number.MAX_VALUE, 0];
-            let minMax2 = [Number.MAX_VALUE, 0];
+            const peaks2D = [];
+            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/lib/xyz/xyzJResAnalyzer.js.map

@@ -1 +1 @@
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package/lib/xyz/xyzPhaseCorrectionDirectDimension.d.ts

@@ -0,0 +1,16 @@
+import { NmrData2DFt } from 'cheminfo-types';
+import Matrix from 'ml-matrix';
+interface ReimMatrix {
+    re: Matrix;
+    im: Matrix;
+}
+export interface PhaseCorrectionOptions {
+    ph0: number;
+    ph1: number;
+    applyPhaseCorrection: (d: ReimMatrix, o: {
+        ph0: number;
+        ph1: number;
+    }) => ReimMatrix;
+}
+export declare function xyzPhaseCorrectionDirectDimension(data: NmrData2DFt, options: PhaseCorrectionOptions): NmrData2DFt;
+export {};

package/lib/xyz/xyzPhaseCorrectionDirectDimension.js

@@ -0,0 +1,30 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.xyzPhaseCorrectionDirectDimension = void 0;
+const degreeToRadians_1 = require("../constants/degreeToRadians");
+const ml_spectra_processing_1 = require("ml-spectra-processing");
+const applyOverImag_1 = require("./util/phaseCorrection/applyOverImag");
+const applyOverReal_1 = require("./util/phaseCorrection/applyOverReal");
+function xyzPhaseCorrectionDirectDimension(data, options) {
+    (0, applyOverReal_1.applyOverReal)(data, { ...options, applyPhaseCorrection });
+    if ('ri' in data && 'ii' in data) {
+        (0, applyOverImag_1.applyOverImag)(data, { ...options, applyPhaseCorrection });
+    }
+    return data;
+}
+exports.xyzPhaseCorrectionDirectDimension = xyzPhaseCorrectionDirectDimension;
+function applyPhaseCorrection(data, options) {
+    const ph0 = options.ph0 * degreeToRadians_1.degreeToRadians;
+    const ph1 = options.ph1 * degreeToRadians_1.degreeToRadians;
+    const nbRows = data.re.rows;
+    for (let i = 0; i < nbRows; i++) {
+        const { re, im } = (0, ml_spectra_processing_1.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;
+}
+//# sourceMappingURL=xyzPhaseCorrectionDirectDimension.js.map

package/lib/xyz/xyzPhaseCorrectionDirectDimension.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"xyzPhaseCorrectionDirectDimension.js","sourceRoot":"","sources":["../../src/xyz/xyzPhaseCorrectionDirectDimension.ts"],"names":[],"mappings":";;;AACA,kEAA+D;AAE/D,iEAA4D;AAC5D,wEAAqE;AACrE,wEAAqE;AAerE,SAAgB,iCAAiC,CAC/C,IAAiB,EACjB,OAA+B;IAE/B,IAAA,6BAAa,EAAC,IAAI,EAAE,EAAE,GAAG,OAAO,EAAE,oBAAoB,EAAE,CAAC,CAAC;IAC1D,IAAI,IAAI,IAAI,IAAI,IAAI,IAAI,IAAI,IAAI,EAAE;QAChC,IAAA,6BAAa,EAAC,IAAI,EAAE,EAAE,GAAG,OAAO,EAAE,oBAAoB,EAAE,CAAC,CAAC;KAC3D;IACD,OAAO,IAAI,CAAC;AACd,CAAC;AATD,8EASC;AAED,SAAS,oBAAoB,CAC3B,IAAgC,EAChC,OAAqC;IAErC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,GAAG,iCAAe,CAAC;IAC1C,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,GAAG,iCAAe,CAAC;IAC1C,MAAM,MAAM,GAAG,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC;IAC5B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE;QAC/B,MAAM,EAAE,EAAE,EAAE,EAAE,EAAE,GAAG,IAAA,2CAAmB,EACpC;YACE,EAAE,EAAE,IAAI,CAAC,EAAE,CAAC,MAAM,CAAC,CAAC,CAAC;YACrB,EAAE,EAAE,IAAI,CAAC,EAAE,CAAC,MAAM,CAAC,CAAC,CAAC;SACtB,EACD,GAAG,EACH,GAAG,CACJ,CAAC;QACF,IAAI,CAAC,EAAE,CAAC,MAAM,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;QACtB,IAAI,CAAC,EAAE,CAAC,MAAM,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;KACvB;IACD,OAAO,IAAI,CAAC;AACd,CAAC"}

package/lib/xyz/xyzPhaseCorrectionIndirectDimension.d.ts

@@ -0,0 +1,25 @@
+import { NmrData2DFt } from 'cheminfo-types';
+import { PhaseCorrectionOptions } from './xyzPhaseCorrectionDirectDimension';
+export type PhaseCorrectionIndirectDimensionOptions = PhaseCorrectionOptions & {
+    quad: 'imag' | 'real';
+};
+export declare function xyzPhaseCorrectionIndirectDimension(data: NmrData2DFt, options: PhaseCorrectionIndirectDimensionOptions): (NmrData2DFt & {
+    rr: {
+        z: Float64Array[];
+        maxZ: number;
+        minZ: number;
+        minY: number;
+        maxY: number;
+        minX: number;
+        maxX: number;
+    };
+    ir: {
+        z: Float64Array[];
+        maxZ: number;
+        minZ: number;
+        minY: number;
+        maxY: number;
+        minX: number;
+        maxX: number;
+    };
+}) | undefined;

package/lib/xyz/xyzPhaseCorrectionIndirectDimension.js

@@ -0,0 +1,32 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.xyzPhaseCorrectionIndirectDimension = void 0;
+const degreeToRadians_1 = require("../constants/degreeToRadians");
+const ml_spectra_processing_1 = require("ml-spectra-processing");
+const applyOverImag_1 = require("./util/phaseCorrection/applyOverImag");
+const applyOverReal_1 = require("./util/phaseCorrection/applyOverReal");
+function xyzPhaseCorrectionIndirectDimension(data, options) {
+    const { quad } = options;
+    if (quad === 'real') {
+        return (0, applyOverReal_1.applyOverReal)(data, { ...options, applyPhaseCorrection });
+    }
+    else if (quad === 'imag') {
+        return (0, applyOverImag_1.applyOverImag)(data, { ...options, applyPhaseCorrection });
+    }
+}
+exports.xyzPhaseCorrectionIndirectDimension = xyzPhaseCorrectionIndirectDimension;
+function applyPhaseCorrection(data, options) {
+    const ph0 = options.ph0 * degreeToRadians_1.degreeToRadians;
+    const ph1 = options.ph1 * degreeToRadians_1.degreeToRadians;
+    const nbColumns = data.re.columns;
+    for (let i = 0; i < nbColumns; i++) {
+        const { re, im } = (0, ml_spectra_processing_1.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;
+}
+//# sourceMappingURL=xyzPhaseCorrectionIndirectDimension.js.map

package/lib/xyz/xyzPhaseCorrectionIndirectDimension.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"xyzPhaseCorrectionIndirectDimension.js","sourceRoot":"","sources":["../../src/xyz/xyzPhaseCorrectionIndirectDimension.ts"],"names":[],"mappings":";;;AACA,kEAA+D;AAE/D,iEAA4D;AAC5D,wEAAqE;AAErE,wEAAqE;AAMrE,SAAgB,mCAAmC,CACjD,IAAiB,EACjB,OAAgD;IAEhD,MAAM,EAAE,IAAI,EAAE,GAAG,OAAO,CAAC;IACzB,IAAI,IAAI,KAAK,MAAM,EAAE;QACnB,OAAO,IAAA,6BAAa,EAAC,IAAI,EAAE,EAAE,GAAG,OAAO,EAAE,oBAAoB,EAAE,CAAC,CAAC;KAClE;SAAM,IAAI,IAAI,KAAK,MAAM,EAAE;QAC1B,OAAO,IAAA,6BAAa,EAAC,IAAI,EAAE,EAAE,GAAG,OAAO,EAAE,oBAAoB,EAAE,CAAC,CAAC;KAClE;AACH,CAAC;AAVD,kFAUC;AAED,SAAS,oBAAoB,CAC3B,IAAgC,EAChC,OAAqC;IAErC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,GAAG,iCAAe,CAAC;IAC1C,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,GAAG,iCAAe,CAAC;IAC1C,MAAM,SAAS,GAAG,IAAI,CAAC,EAAE,CAAC,OAAO,CAAC;IAClC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,EAAE,CAAC,EAAE,EAAE;QAClC,MAAM,EAAE,EAAE,EAAE,EAAE,EAAE,GAAG,IAAA,2CAAmB,EACpC;YACE,EAAE,EAAE,IAAI,CAAC,EAAE,CAAC,SAAS,CAAC,CAAC,CAAC;YACxB,EAAE,EAAE,IAAI,CAAC,EAAE,CAAC,SAAS,CAAC,CAAC,CAAC;SACzB,EACD,GAAG,EACH,GAAG,CACJ,CAAC;QACF,IAAI,CAAC,EAAE,CAAC,SAAS,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;QACzB,IAAI,CAAC,EAAE,CAAC,SAAS,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;KAC1B;IACD,OAAO,IAAI,CAAC;AACd,CAAC"}

package/lib-esm/apodization/compose.js

@@ -3,7 +3,7 @@ import { getFunction } from './getFunction';
 import { getData } from './utils/getData';
 export function compose(shapeOptions) {
     const { length: dataLength, shapes = [] } = shapeOptions;
-    let data = new Float64Array(dataLength).fill(1);
+    const data = new Float64Array(dataLength).fill(1);
     shapes.forEach((options) => {
         const { shape, start = 0 } = options;
         const { options: shapeOptions } = shape;

package/lib-esm/apodization/compose.js.map

@@ -1 +1 @@
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+{"version":3,"file":"compose.js","sourceRoot":"","sources":["../../src/apodization/compose.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC;AAC5C,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC;AAE5C,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAC;AAyB1C,MAAM,UAAU,OAAO,CAAC,YAA0B;IAChD,MAAM,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,GAAG,EAAE,EAAE,GAAG,YAAY,CAAC;IACzD,MAAM,IAAI,GAAG,IAAI,YAAY,CAAC,UAAU,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClD,MAAM,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,EAAE;QACzB,MAAM,EAAE,KAAK,EAAE,KAAK,GAAG,CAAC,EAAE,GAAG,OAAO,CAAC;QACrC,MAAM,EAAE,OAAO,EAAE,YAAY,EAAE,GAAG,KAAK,CAAC;QACxC,MAAM,MAAM,GACV,QAAQ,IAAI,YAAY,CAAC,CAAC,CAAC,YAAY,CAAC,MAAM,CAAC,CAAC,CAAC,UAAU,GAAG,KAAK,CAAC;QAEtE,MAAM,UAAU,GAAG,OAAO,CAAC,WAAW,CAAC,KAAK,CAAC,EAAE,MAAM,CAAC,CAAC;QAEvD,WAAW,CAAC,IAAI,EAAE;YAChB,UAAU;YACV,MAAM;YACN,KAAK;YACL,MAAM,EAAE,IAAI;SACb,CAAC,CAAC;IACL,CAAC,CAAC,CAAC;IACH,OAAO,IAAI,CAAC;AACd,CAAC"}

package/lib-esm/assignment/get13CAssignments.js

@@ -1,7 +1,7 @@
 import { v4 as generateID } from '@lukeed/uuid';
 import { addDiastereotopicMissingChirality } from 'openchemlib-utils';
 import { predictCarbon, } from '../prediction/predictCarbon';
-import { buildAssignments } from './utils/buildAssignments';
+import { buildAssignments, } from './utils/oneDimensionalAssignment/buildAssignments';
 function checkAtomsAndDiaIDs(signals) {
     for (const signal of signals) {
         if (!signal.atoms)
@@ -13,14 +13,14 @@ function checkAtomsAndDiaIDs(signals) {
     }
 }
 function checkIntegration(ranges) {
-    for (let range of ranges) {
+    for (const range of ranges) {
         if (range.integration === undefined)
             range.integration = 0;
     }
     return ranges;
 }
 export async function get13CAssignments(ranges, molecule, options = {}) {
-    let { restrictionByCS = {}, minScore = 1, maxSolutions = 10, nbAllowedUnAssigned = 0, timeout = 6000, predictionOptions = {}, } = options;
+    const { restrictionByCS = {}, minScore = 1, maxSolutions = 10, nbAllowedUnAssigned = 0, timeout = 6000, predictionOptions = {}, } = options;
     if (!molecule) {
         throw new Error('It is needed a OCL molecule instance to assign');
     }

package/lib-esm/assignment/get13CAssignments.js.map

@@ -1 +1 @@
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package/lib-esm/assignment/get1HAssignments.js

@@ -1,7 +1,7 @@
 import { v4 as generateID } from '@lukeed/uuid';
 import { addDiastereotopicMissingChirality } from 'openchemlib-utils';
 import { predictProton, } from '../prediction/predictProton';
-import { buildAssignments } from './utils/buildAssignments';
+import { buildAssignments, } from './utils/oneDimensionalAssignment/buildAssignments';
 function checkAtomsAndDiaIDs(signals) {
     for (const signal of signals) {
         if (!signal.atoms)
@@ -13,14 +13,14 @@ function checkAtomsAndDiaIDs(signals) {
     }
 }
 function checkForIntegration(ranges) {
-    for (let range of ranges) {
+    for (const range of ranges) {
         if (range.integration === undefined) {
             throw new Error('ranges has not integration property');
         }
     }
 }
 export async function get1HAssignments(ranges, molecule, options = {}) {
-    let { restrictionByCS, minScore = 1, maxSolutions = 10, nbAllowedUnAssigned = 0, timeout = 6000, predictionOptions = {}, } = options;
+    const { restrictionByCS, minScore = 1, maxSolutions = 10, nbAllowedUnAssigned = 0, timeout = 6000, predictionOptions = {}, } = options;
     if (!molecule) {
         throw new Error('It is needed a OCL molecule instance to assign');
     }

package/lib-esm/assignment/get1HAssignments.js.map

@@ -1 +1 @@
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package/lib-esm/assignment/getAssignments.js

@@ -1,10 +1,10 @@
 import { addDiastereotopicMissingChirality } from 'openchemlib-utils';
-import { buildAssignments, } from './utils/getAssignment/buildAssignments';
-import { checkIDs } from './utils/getAssignment/checkIDs';
-import { getTargetsAndCorrelations } from './utils/getAssignment/getTargetsAndCorrelations';
-import getWorkFlow from './utils/getAssignment/getWorkFlow';
+import { buildAssignments, } from './utils/generalAssignment/buildAssignments';
+import { checkIDs } from './utils/generalAssignment/checkIDs';
+import { getTargetsAndCorrelations } from './utils/generalAssignment/getTargetsAndCorrelations';
+import getWorkFlow from './utils/generalAssignment/getWorkFlow';
 export async function getAssignments(input, options = {}) {
-    let { restrictionByCS = {}, justAssign, minScore = 0.01, maxSolutions = 10, nbAllowedUnAssigned, timeout = 6000, predictionOptions = {}, predictions = {}, correlation: correlationOptions = {}, } = options;
+    const { restrictionByCS = {}, justAssign, minScore = 0.01, maxSolutions = 10, nbAllowedUnAssigned, timeout = 6000, predictionOptions = {}, predictions = {}, correlation: correlationOptions = {}, } = options;
     const { tolerance = { H: 0.2, C: 1 }, useChemicalShiftScore = false, chemicalShiftRestriction = true, } = restrictionByCS;
     const molecule = input.molecule;
     if (!molecule)

package/lib-esm/assignment/getAssignments.js.map

@@ -1 +1 @@
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package/lib-esm/assignment/utils/addSolution.js

@@ -0,0 +1,25 @@
+export function addSolution(store, props) {
+    const { score, maxSolutions, partial, predictions } = props;
+    store.nSolutions++;
+    const solution = {
+        assignment: JSON.parse(JSON.stringify(partial)),
+        score: score / doubleAssignmentPenalty(partial, predictions),
+    };
+    if (store.nSolutions >= maxSolutions) {
+        if (solution.score > store.solutions.last().score) {
+            store.solutions.pollLast();
+            store.solutions.add(solution);
+        }
+    }
+    else {
+        store.solutions.add(solution);
+        store.nSolutions++;
+    }
+}
+function doubleAssignmentPenalty(partial, predictions) {
+    const nbSources = Object.keys(predictions).length;
+    const assignments = new Set(partial);
+    const nbDoubleAssignment = nbSources - assignments.size;
+    return nbDoubleAssignment > 0 ? 2 * nbDoubleAssignment : 1;
+}
+//# sourceMappingURL=addSolution.js.map

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

@@ -0,0 +1 @@
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