nmr-processing 3.4.1 → 4.0.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CHANGELOG.md +11 -0
- package/lib/peaks/peaksFilterImpurities.js +1 -1
- package/lib/peaks/peaksFilterImpurities.js.map +1 -1
- package/lib/peaks/peaksToRanges.js +11 -17
- package/lib/peaks/peaksToRanges.js.map +1 -1
- package/lib/peaks/util/determineRealTop.js +3 -2
- package/lib/peaks/util/determineRealTop.js.map +1 -1
- package/lib/peaks/util/jAnalyzer.js +9 -11
- package/lib/peaks/util/jAnalyzer.js.map +1 -1
- package/lib/ranges/rangesToXY.d.ts +2 -2
- package/lib/ranges/rangesToXY.js.map +1 -1
- package/lib/signals/signalsToXY.d.ts +2 -2
- package/lib/signals/simulation/simulate1D.d.ts +4 -3
- package/lib/signals/simulation/simulate1D.js.map +1 -1
- package/lib/types/NMRPeak1D.d.ts +2 -9
- package/lib/xy/xyAutoPeaksPicking.d.ts +4 -60
- package/lib/xy/xyAutoPeaksPicking.js +3 -3
- package/lib/xy/xyAutoPeaksPicking.js.map +1 -1
- package/lib-esm/peaks/peaksFilterImpurities.js +1 -1
- package/lib-esm/peaks/peaksFilterImpurities.js.map +1 -1
- package/lib-esm/peaks/peaksToRanges.js +11 -17
- package/lib-esm/peaks/peaksToRanges.js.map +1 -1
- package/lib-esm/peaks/util/determineRealTop.js +4 -3
- package/lib-esm/peaks/util/determineRealTop.js.map +1 -1
- package/lib-esm/peaks/util/jAnalyzer.js +9 -11
- package/lib-esm/peaks/util/jAnalyzer.js.map +1 -1
- package/lib-esm/ranges/rangesToXY.js.map +1 -1
- package/lib-esm/signals/simulation/simulate1D.js.map +1 -1
- package/lib-esm/xy/xyAutoPeaksPicking.js +3 -3
- package/lib-esm/xy/xyAutoPeaksPicking.js.map +1 -1
- package/package.json +4 -4
- package/src/peaks/peaksFilterImpurities.ts +1 -1
- package/src/peaks/peaksToRanges.ts +11 -17
- package/src/peaks/util/determineRealTop.ts +4 -6
- package/src/peaks/util/jAnalyzer.ts +10 -12
- package/src/ranges/rangesToXY.ts +2 -2
- package/src/signals/signalsToXY.ts +2 -2
- package/src/signals/simulation/simulate1D.ts +4 -3
- package/src/types/NMRPeak1D.ts +3 -9
- package/src/xy/xyAutoPeaksPicking.ts +19 -58
- package/src/types/ml-gsd/index.d.ts +0 -164
package/CHANGELOG.md
CHANGED
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@@ -1,5 +1,16 @@
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# Changelog
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## [4.0.0](https://www.github.com/cheminfo/nmr-processing/compare/v3.4.1...v4.0.0) (2021-11-23)
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### ⚠ BREAKING CHANGES
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* change shape1D n NMRPeak1D structure (#119)
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### Features
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* change shape1D n NMRPeak1D structure ([#119](https://www.github.com/cheminfo/nmr-processing/issues/119)) ([0255510](https://www.github.com/cheminfo/nmr-processing/commit/02555100407fe2ff80a4c41fff1ddd66d97fbaef))
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### [3.4.1](https://www.github.com/cheminfo/nmr-processing/compare/v3.4.0...v3.4.1) (2021-11-06)
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@@ -33,7 +33,7 @@ function checkImpurity(peakList, impurity, options) {
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while (i--) {
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j = peakList.length;
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while (j--) {
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tolerance = error + peakList[j].
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tolerance = error + peakList[j].width;
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difference = Math.abs(impurity[i].shift - peakList[j].x);
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if (difference < tolerance) {
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// && (impurity[i].multiplicity === '' || (impurity[i].multiplicity.indexOf(peakList[j].multiplicity)) { // some impurities has multiplicities like 'bs' but at presents it is unsupported
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{"version":3,"file":"peaksFilterImpurities.js","sourceRoot":"","sources":["../../src/peaks/peaksFilterImpurities.ts"],"names":[],"mappings":";;;AAAA,wDAAqD;AAIrD,MAAM,OAAO,GAAG,CAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC,CAAC;AA2B1C;;GAEG;AAEH,SAAgB,qBAAqB,CACnC,QAAqB,EACrB,UAAwC,EAAE;IAE1C,IAAI,EAAE,OAAO,EAAE,KAAK,GAAG,KAAK,EAAE,MAAM,GAAG,KAAK,EAAE,GAAG,OAAO,CAAC;IAEzD,IAAI,OAAO,EAAE;QACX,IAAI,OAAO,KAAK,UAAU;YAAE,OAAO,GAAG,MAAM,CAAC;QAC7C,IAAI,OAAO,KAAK,MAAM;YAAE,OAAO,GAAG,OAAO,CAAC;QAC1C,IAAI,iBAAiB,GAAG,uBAAU,CAAC,OAAO,CAAC,CAAC;QAC5C,KAAK,IAAI,QAAQ,IAAI,OAAO,EAAE;YAC5B,IAAI,cAAc,GAAG,iBAAiB,CAAC,QAAQ,CAAC,CAAC;YACjD,aAAa,CAAC,QAAQ,EAAE,cAAc,EAAE;gBACtC,KAAK;gBACL,MAAM;gBACN,IAAI,EAAE,QAAQ;aACf,CAAC,CAAC;SACJ;KACF;IACD,OAAO,QAAQ,CAAC;AAClB,CAAC;AApBD,sDAoBC;AAED,SAAS,aAAa,CACpB,QAAqB,EACrB,QAA0B,EAC1B,OAA6B;IAE7B,IAAI,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC;IACtC,IAAI,CAAC,EAAE,SAAS,EAAE,UAAU,CAAC;IAC7B,IAAI,CAAC,GAAG,QAAQ,CAAC,MAAM,CAAC;IACxB,OAAO,CAAC,EAAE,EAAE;QACV,CAAC,GAAG,QAAQ,CAAC,MAAM,CAAC;QACpB,OAAO,CAAC,EAAE,EAAE;YACV,SAAS,GAAG,KAAK,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC
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{"version":3,"file":"peaksFilterImpurities.js","sourceRoot":"","sources":["../../src/peaks/peaksFilterImpurities.ts"],"names":[],"mappings":";;;AAAA,wDAAqD;AAIrD,MAAM,OAAO,GAAG,CAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC,CAAC;AA2B1C;;GAEG;AAEH,SAAgB,qBAAqB,CACnC,QAAqB,EACrB,UAAwC,EAAE;IAE1C,IAAI,EAAE,OAAO,EAAE,KAAK,GAAG,KAAK,EAAE,MAAM,GAAG,KAAK,EAAE,GAAG,OAAO,CAAC;IAEzD,IAAI,OAAO,EAAE;QACX,IAAI,OAAO,KAAK,UAAU;YAAE,OAAO,GAAG,MAAM,CAAC;QAC7C,IAAI,OAAO,KAAK,MAAM;YAAE,OAAO,GAAG,OAAO,CAAC;QAC1C,IAAI,iBAAiB,GAAG,uBAAU,CAAC,OAAO,CAAC,CAAC;QAC5C,KAAK,IAAI,QAAQ,IAAI,OAAO,EAAE;YAC5B,IAAI,cAAc,GAAG,iBAAiB,CAAC,QAAQ,CAAC,CAAC;YACjD,aAAa,CAAC,QAAQ,EAAE,cAAc,EAAE;gBACtC,KAAK;gBACL,MAAM;gBACN,IAAI,EAAE,QAAQ;aACf,CAAC,CAAC;SACJ;KACF;IACD,OAAO,QAAQ,CAAC;AAClB,CAAC;AApBD,sDAoBC;AAED,SAAS,aAAa,CACpB,QAAqB,EACrB,QAA0B,EAC1B,OAA6B;IAE7B,IAAI,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC;IACtC,IAAI,CAAC,EAAE,SAAS,EAAE,UAAU,CAAC;IAC7B,IAAI,CAAC,GAAG,QAAQ,CAAC,MAAM,CAAC;IACxB,OAAO,CAAC,EAAE,EAAE;QACV,CAAC,GAAG,QAAQ,CAAC,MAAM,CAAC;QACpB,OAAO,CAAC,EAAE,EAAE;YACV,SAAS,GAAG,KAAK,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC;YACtC,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YACzD,IAAI,UAAU,GAAG,SAAS,EAAE;gBAC1B,0LAA0L;gBAC1L,IAAI,MAAM,EAAE;oBACV,QAAQ,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;iBACvB;qBAAM;oBACL,QAAQ,CAAC,CAAC,CAAC,CAAC,IAAI,GAAG,IAAI,CAAC;iBACzB;aACF;SACF;KACF;AACH,CAAC"}
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@@ -23,22 +23,20 @@ const assignSignal = (peak, frequency, nucleus) => {
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delta: NaN,
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nbPeaks: 1,
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kind: 'signal',
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startX: peak.x - peak.
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stopX: peak.x + peak.
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startX: peak.x - peak.width,
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stopX: peak.x + peak.width,
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observe: frequency,
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nucleus,
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integralData: {
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from: peak.x - peak.
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to: peak.x + peak.
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from: peak.x - peak.width * 3,
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to: peak.x + peak.width * 3,
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value: 0,
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},
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peaks: [
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{
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x: peak.x,
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intensity: peak.y,
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width: peak.shape.width,
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},
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width: peak.width,
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},
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],
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};
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peaksO.push({
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x: peakR.x,
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y: peakR.intensity,
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width: peakR.shape.width,
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},
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width: peakR.width,
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});
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signal.mask.splice(j, 1);
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signal.mask2.splice(j, 1);
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signals.push(signal1D);
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}
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else {
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let tmp = peak.x + peak.
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let tmp = peak.x + peak.width;
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signal1D.stopX = Math.max(signal1D.stopX, tmp);
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signal1D.startX = Math.min(signal1D.startX, tmp);
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signal1D.nbPeaks++;
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signal1D.peaks.push({
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x: peak.x,
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intensity: peak.y,
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width: peak.shape.width,
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},
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width: peak.width,
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});
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signal1D.integralData.from = Math.min(signal1D.integralData.from, peak.x - peak.
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signal1D.integralData.to = Math.max(signal1D.integralData.to, peak.x + peak.
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signal1D.integralData.from = Math.min(signal1D.integralData.from, peak.x - peak.width * 3);
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signal1D.integralData.to = Math.max(signal1D.integralData.to, peak.x + peak.width * 3);
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if (peak.kind)
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signal1D.kind = peak.kind;
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}
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* @private
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*/
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function computeArea(peak) {
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return Math.abs(peak.intensity * peak.
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return Math.abs(peak.intensity * peak.width * 1.57); // todo add an option with this value: 1.772453851
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}
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//# sourceMappingURL=peaksToRanges.js.map
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{"version":3,"file":"peaksToRanges.js","sourceRoot":"","sources":["../../src/peaks/peaksToRanges.ts"],"names":[],"mappings":";;;;;;AACA,iEAAsD;AAOtD,iEAAyC;AAEzC,kDAA+C;AA8D/C,SAAS,8BAA8B,CACrC,MAAoB;IAEpB,uBAAuB;IACvB,mEAAmE;IACnE,IAAI,CAAC,MAAM,CAAC,IAAI;QAAE,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAC;IACxE,IAAI,CAAC,MAAM,CAAC,KAAK;QAAE,MAAM,IAAI,KAAK,CAAC,qCAAqC,CAAC,CAAC;IAC1E,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE;QACvB,MAAM,IAAI,KAAK,CAAC,2CAA2C,CAAC,CAAC;KAC9D;AACH,CAAC;AAED,MAAM,YAAY,GAAG,CACnB,IAAe,EACf,SAAiB,EACjB,OAAe,EACD,EAAE;IAChB,OAAO;QACL,KAAK,EAAE,GAAG;QACV,OAAO,EAAE,CAAC;QACV,IAAI,EAAE,QAAQ;QACd,MAAM,EAAE,IAAI,CAAC,CAAC,GAAG,IAAI,CAAC,KAAK
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@@ -6,7 +6,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
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6
6
|
exports.determineRealTop = void 0;
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7
7
|
const ml_levenberg_marquardt_1 = __importDefault(require("ml-levenberg-marquardt"));
|
|
8
8
|
const ml_peak_shape_generator_1 = require("ml-peak-shape-generator");
|
|
9
|
-
const { fct: gaussian2DFct } = ml_peak_shape_generator_1.gaussian2D;
|
|
10
9
|
const direction8X = [-1, -1, -1, 0, 0, 1, 1, 1];
|
|
11
10
|
const direction8Y = [-1, 0, 1, -1, 1, -1, 0, 1];
|
|
12
11
|
const direction16X = [-2, -2, -2, -2, -2, -1, -1, 0, 0, 1, 1, 2, 2, 2, 2, 2];
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|
@@ -113,6 +112,7 @@ function fitGaussian(data, options) {
|
|
|
113
112
|
};
|
|
114
113
|
}
|
|
115
114
|
function paramGaussian2D(intervalX, intervalY, nCols) {
|
|
115
|
+
const gaussian2D = new ml_peak_shape_generator_1.Gaussian2D();
|
|
116
116
|
return (p) => {
|
|
117
117
|
return (t) => {
|
|
118
118
|
let nL = p.length / 5;
|
|
@@ -120,9 +120,10 @@ function paramGaussian2D(intervalX, intervalY, nCols) {
|
|
|
120
120
|
let xIndex = t % nCols;
|
|
121
121
|
let yIndex = (t - xIndex) / nCols;
|
|
122
122
|
for (let i = 0; i < nL; i++) {
|
|
123
|
+
gaussian2D.fwhm = { x: p[i + 3 * nL], y: p[i + 4 * nL] };
|
|
123
124
|
result +=
|
|
124
125
|
p[i + 2 * nL] *
|
|
125
|
-
|
|
126
|
+
gaussian2D.fct((xIndex - p[i]) * intervalX, (yIndex - p[i + nL]) * intervalY);
|
|
126
127
|
}
|
|
127
128
|
return result;
|
|
128
129
|
};
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
{"version":3,"file":"determineRealTop.js","sourceRoot":"","sources":["../../../src/peaks/util/determineRealTop.ts"],"names":[],"mappings":";;;;;;AAAA,oFAAwC;AACxC,qEAAqD;AAIrD,MAAM,WAAW,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC;AAChD,MAAM,WAAW,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC;AAChD,MAAM,YAAY,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC;AAC7E,MAAM,YAAY,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC;AAI7E,SAAgB,gBAAgB,CAAC,KAAgB,EAAE,OAAY;IAC7D,IAAI,EAAE,KAAK,EAAE,YAAY,EAAE,YAAY,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,OAAO,CAAC;IAC5E,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACrC,IAAI,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QACpC,IAAI,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QAEpC,IAAI,YAAY,GAAG,MAAM,GAAG,MAAM,GAAG,KAAK,CAAC;QAC3C,IAAI,EAAE,KAAK,EAAE,KAAK,EAAE,GAAG,YAAY,CAAC,YAAY,EAAE;YAChD,MAAM;YACN,MAAM;YACN,KAAK;YACL,KAAK,EAAE,CAAC;SACT,CAAC,CAAC;QACH,YAAY,GAAG,KAAK;YAClB,CAAC,CAAC,KAAK;YACP,CAAC,CAAC,YAAY,CAAC,YAAY,EAAE;gBACzB,MAAM;gBACN,MAAM;gBACN,KAAK;gBACL,KAAK,EAAE,CAAC;aACT,CAAC,CAAC,KAAK,CAAC;QAEb,IAAI,kBAAkB,GAAG,WAAW,CAAC,YAAY,EAAE;YACjD,KAAK;YACL,KAAK,EAAE,YAAY;YACnB,IAAI;YACJ,IAAI;YACJ,IAAI;YACJ,IAAI;SACL,CAAC,CAAC;QAEH,KAAK,CAAC,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,kBAAkB,CAAC,CAAC;KACxD;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AAlCD,4CAkCC;AAED,SAAS,YAAY,CACnB,IAAU,EACV,OAAyE;IAEzE,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC;IAC/C,IAAI,YAAY,GAAG,MAAM,GAAG,MAAM,GAAG,KAAK,CAAC;IAC3C,IAAI,CAAC,UAAU,EAAE,UAAU,CAAC,GAC1B,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,YAAY,EAAE,YAAY,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,WAAW,CAAC,CAAC;IAExE,IAAI,KAAK,GAAG,KAAK,CAAC;IAClB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QAC1C,IAAI,CAAC,GAAG,MAAM,GAAG,UAAU,CAAC,CAAC,CAAC,CAAC;QAC/B,IAAI,CAAC,GAAG,MAAM,GAAG,UAAU,CAAC,CAAC,CAAC,CAAC;QAC/B,IAAI,IAAI,CAAC,CAAC,GAAG,CAAC,GAAG,KAAK,CAAC,IAAI,IAAI,CAAC,YAAY,CAAC,EAAE;YAC7C,KAAK,GAAG,IAAI,CAAC;YACb,IAAI,cAAc,GAAG,CAAC,GAAG,CAAC,GAAG,KAAK,CAAC;YACnC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBAC3C,IAAI,EAAE,GAAG,CAAC,GAAG,WAAW,CAAC,CAAC,CAAC,CAAC;gBAC5B,IAAI,EAAE,GAAG,CAAC,GAAG,WAAW,CAAC,CAAC,CAAC,CAAC;gBAC5B,IAAI,IAAI,CAAC,EAAE,GAAG,EAAE,GAAG,KAAK,CAAC,GAAG,IAAI,CAAC,cAAc,CAAC,EAAE;oBAChD,KAAK,GAAG,KAAK,CAAC;oBACd,MAAM;iBACP;aACF;YACD,IAAI,KAAK,EAAE;gBACT,YAAY,GAAG,cAAc,CAAC;aAC/B;SACF;KACF;IAED,OAAO,EAAE,KAAK,EAAE,YAAY,EAAE,KAAK,EAAE,CAAC;AACxC,CAAC;AAED,SAAS,WAAW,CAClB,IAA6B,EAC7B,OAOC;IAED,IAAI,EAAE,KAAK,EAAE,KAAK,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,OAAO,CAAC;IAEvD,IAAI,KAAK,GAAG,IAAI,CAAC,MAAM,GAAG,KAAK,CAAC;IAEhC,IAAI,SAAS,GAAG,CAAC,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC;IAC5C,IAAI,SAAS,GAAG,CAAC,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC;IAE5C,IAAI,GAAG,GAAG,KAAK,GAAG,KAAK,CAAC;IACxB,IAAI,GAAG,GAAG,CAAC,KAAK,GAAG,GAAG,CAAC,GAAG,KAAK,CAAC;IAEhC,IAAI,MAAM,GAAG,CAAC,CAAC;IACf,IAAI,MAAM,GAAG,CAAC,CAAC;IAEf,IAAI,GAAG,GAAG,MAAM,CAAC,gBAAgB,CAAC;IAClC,IAAI,CAAC,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;IAC1C,IAAI,KAAK,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;IAC9C,KAAK,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;QACnC,KAAK,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,KAAK,CAAC,EAAE,CAAC,GAAG,EAAE,EAAE,EAAE;YAC7C,IAAI,KAAK,GAAG,IAAI,CAAC,GAAG,GAAG,CAAC,GAAG,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,KAAK,CAAC,CAAC;YAC9C,IAAI,GAAG,GAAG,KAAK;gBAAE,GAAG,GAAG,KAAK,CAAC;YAC7B,CAAC,CAAC,MAAM,GAAG,CAAC,GAAG,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,KAAK,CAAC;SAC1C;KACF;IAED,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,CAAC,EAAE;QAAE,CAAC,CAAC,CAAC,CAAC,IAAI,GAAG,CAAC;IAE/C,IAAI,SAAS,GAAG,CAAC,MAAM,GAAG,CAAC,EAAE,MAAM,GAAG,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC;IACpD,IAAI,SAAS,GAAG,CAAC,MAAM,GAAG,CAAC,EAAE,MAAM,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,KAAK,EAAE,KAAK,CAAC,CAAC;IAC7D,IAAI,aAAa,GAAG,CAAC,MAAM,EAAE,MAAM,EAAE,CAAC,CAAC,MAAM,GAAG,MAAM,GAAG,CAAC,CAAC,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC;IACvE,IAAI,kBAAkB,GAAG,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,CAAC;IACxD,IAAI,IAAI,GAAG,eAAe,CAAC,SAAS,EAAE,SAAS,EAAE,CAAC,CAAC,CAAC;IAEpD,IAAI,IAAI,GAAG,IAAA,gCAAE,EAAC,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE,IAAI,EAAE;QACtC,OAAO,EAAE,GAAG;QACZ,aAAa,EAAE,GAAG;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa;QACb,kBAAkB;QAClB,SAAS;QACT,SAAS;KACV,CAAC,CAAC,eAAe,CAAC;IAEnB,OAAO;QACL,CAAC,EAAE,IAAI,CAAC,CAAC,C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@@ -152,13 +152,13 @@ function updateSignal(signal, jCouplings) {
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152
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// Update the limits of the signal
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153
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let peaks = signal.peaksComp; // Always in Hz
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154
154
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let nbPeaks = peaks.length;
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155
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-
signal.startX = peaks[0].x / signal.observe - peaks[0].
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155
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+
signal.startX = peaks[0].x / signal.observe - peaks[0].width;
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156
156
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signal.stopX =
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157
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-
peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].
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157
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+
peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].width;
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158
158
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signal.integralData.from =
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159
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-
peaks[0].x / signal.observe - peaks[0].
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159
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+
peaks[0].x / signal.observe - peaks[0].width * 3;
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160
160
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signal.integralData.to =
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161
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-
peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].
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161
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+
peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].width * 3;
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162
162
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// Compile the pattern and format the constant couplings
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163
163
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signal.maskPattern = signal.mask2;
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164
164
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signal.multiplicity = abstractPattern(signal, jCouplings);
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@@ -377,9 +377,7 @@ function symmetrize(signalInput, maxError, iteration, key) {
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377
377
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peaks[i] = {
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378
378
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x: peak[jAxis] * newSignal.observe,
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379
379
|
intensity: peak[intensity],
|
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380
|
-
|
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381
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-
width: peak.shape.width,
|
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382
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-
},
|
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380
|
+
width: peak.width,
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383
381
|
};
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384
382
|
}
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385
383
|
// Join the peaks that are closer than 0.25 Hz
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@@ -391,7 +389,7 @@ function symmetrize(signalInput, maxError, iteration, key) {
|
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|
391
389
|
peaks[i].intensity = peaks[i].intensity + peaks[i + 1].intensity;
|
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392
390
|
peaks[i].x /= peaks[i].intensity;
|
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393
391
|
peaks[i].intensity /= 2;
|
|
394
|
-
peaks[i].
|
|
392
|
+
peaks[i].width += peaks[i + 1].width;
|
|
395
393
|
peaks.splice(i + 1, 1);
|
|
396
394
|
}
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|
397
395
|
}
|
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@@ -439,9 +437,9 @@ function symmetrize(signalInput, maxError, iteration, key) {
|
|
|
439
437
|
let diffR = Math.abs(peaks[right].x - cs);
|
|
440
438
|
if (Math.abs(diffL - diffR) < maxError) {
|
|
441
439
|
avg = Math.min(peaks[left].intensity, peaks[right].intensity);
|
|
442
|
-
avgWidth = Math.min(peaks[left].
|
|
440
|
+
avgWidth = Math.min(peaks[left].width, peaks[right].width);
|
|
443
441
|
peaks[left].intensity = peaks[right].intensity = avg;
|
|
444
|
-
peaks[left].
|
|
442
|
+
peaks[left].width = peaks[right].width = avgWidth;
|
|
445
443
|
middle = [
|
|
446
444
|
middle[0] + (peaks[right].x + peaks[left].x) / 2,
|
|
447
445
|
middle[1] + 1,
|
|
@@ -618,6 +616,6 @@ function chemicalShift(peaks, mask = []) {
|
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|
618
616
|
* @private
|
|
619
617
|
*/
|
|
620
618
|
function getArea(peak) {
|
|
621
|
-
return Math.abs(peak.intensity * peak.
|
|
619
|
+
return Math.abs(peak.intensity * peak.width * 1.57); // 1.772453851);
|
|
622
620
|
}
|
|
623
621
|
//# sourceMappingURL=jAnalyzer.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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@@ -1,4 +1,4 @@
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|
|
1
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-
import type {
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1
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+
import type { Shape1D } from 'ml-peak-shape-generator';
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|
2
2
|
import type { NMRRange } from '../types/NMRRange';
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3
3
|
export interface RangeToXYOptions {
|
|
4
4
|
/**
|
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@@ -30,7 +30,7 @@ export interface RangeToXYOptions {
|
|
|
30
30
|
* options of signals.
|
|
31
31
|
* @default { kind: 'gaussian' }
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|
32
32
|
*/
|
|
33
|
-
shape:
|
|
33
|
+
shape: Shape1D;
|
|
34
34
|
}
|
|
35
35
|
export declare function rangesToXY(ranges: NMRRange[], options?: any): {
|
|
36
36
|
x: number[];
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"rangesToXY.js","sourceRoot":"","sources":["../../src/ranges/rangesToXY.ts"],"names":[],"mappings":";;;;;;AACA,wFAA2D;
|
|
1
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+
{"version":3,"file":"rangesToXY.js","sourceRoot":"","sources":["../../src/ranges/rangesToXY.ts"],"names":[],"mappings":";;;;;;AACA,wFAA2D;AAE3D,2DAAuD;AAEvD,gEAA6D;AAuC7D,SAAS,eAAe,CACtB,MAAkB;IAElB,KAAK,IAAI,KAAK,IAAI,MAAM,EAAE;QACxB,IAAI,CAAC,KAAK,CAAC,OAAO;YAAE,MAAM,IAAI,KAAK,CAAC,uBAAuB,CAAC,CAAC;KAC9D;AACH,CAAC;AACD,SAAgB,UAAU,CAAC,MAAkB,EAAE,UAAe,EAAE;IAC9D,eAAe,CAAC,MAAM,CAAC,CAAC;IACxB,IAAI,EACF,SAAS,GAAG,GAAG,EACf,SAAS,GAAG,CAAC,EACb,IAAI,GAAG,CAAC,EACR,EAAE,GAAG,EAAE,EACP,QAAQ,GAAG,EAAE,GAAG,IAAI,EACpB,KAAK,GAAG,EAAE,IAAI,EAAE,UAAU,EAAE,GAC7B,GAAG,OAAO,CAAC;IAEZ,MAAM,WAAW,GAAG,CAAC,CAAc,EAAE,CAAc,EAAE,EAAE;QACrD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE;YACjC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;SACd;IACH,CAAC,CAAC;IAEF,MAAM,eAAe,GAAG;QACtB,IAAI;QACJ,EAAE;QACF,QAAQ;QACR,KAAK;QACL,SAAS;QACT,SAAS;KACV,CAAC;IAEF,IAAI,QAAQ,GAAgB,IAAI,YAAY,CAAC,QAAQ,CAAC,CAAC;IACvD,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE;QAC1B,MAAM,EAAE,WAAW,EAAE,OAAO,GAAG,EAAE,EAAE,GAAG,KAAK,CAAC;QAC5C,MAAM,EAAE,YAAY,EAAE,eAAe,GAAG,EAAE,EAAE,GAAG,KAAK,CAAC;QACrD,IAAI,eAAe,KAAK,GAAG,IAAI,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE;YACjD,MAAM,EAAE,IAAI,EAAE,EAAE,EAAE,GAAG,KAAK,CAAC;YAC3B,OAAO,CAAC,IAAI,CAAC;gBACX,KAAK,EAAE,CAAC,IAAI,GAAG,EAAE,CAAC,GAAG,CAAC;gBACtB,YAAY,EAAE,GAAG;aAClB,CAAC,CAAC;SACJ;QACD,IAAI,aAAa,GAAgB,IAAI,YAAY,CAAC,QAAQ,CAAC,CAAC;QAC5D,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;YAC5B,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,CAAC;YAChC,IAAI,cAAc,GAChB,YAAY,KAAK,GAAG,IAAI,YAAY,KAAK,GAAG,IAAI,YAAY,KAAK,MAAM;gBACrE,CAAC,CAAC,4BAA4B,CAAC,CAAC,MAAM,CAAC,EAAE,eAAe,CAAC,CAAC,CAAC;gBAC3D,CAAC,CAAC,IAAA,iCAAe,EAAC,CAAC,MAAM,CAAC,EAAE,eAAe,CAAC,CAAC,CAAC,CAAC;YACnD,iBAAiB,CAAC,cAAc,EAAE,CAAC,MAAM,CAAC,CAAC,CAAC;YAC5C,WAAW,CAAC,aAAa,EAAE,cAAc,CAAC,CAAC;SAC5C;QACD,IAAI,KAAK,CAAC,WAAW,EAAE;YACrB,iBAAiB,CAAC,aAAa,EAAE,OAAO,EAAE,EAAE,WAAW,EAAE,CAAC,CAAC;SAC5D;QACD,WAAW,CAAC,QAAQ,EAAE,aAAa,CAAC,CAAC;KACtC;IAED,OAAO;QACL,CAAC,EAAE,IAAA,kCAAmB,EAAC,EAAE,IAAI,EAAE,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,CAAC;QACpD,CAAC,EAAE,QAAQ;KACZ,CAAC;AACJ,CAAC;AAzDD,gCAyDC;AAED,SAAS,4BAA4B,CACnC,OAAsB,EACtB,UAAe,EAAE;IAEjB,MAAM,EAAE,SAAS,EAAE,SAAS,EAAE,GAAG,OAAO,CAAC;IACzC,MAAM,iBAAiB,GAAG,IAAI,sCAAiB,CAAC,OAAO,CAAC,CAAC;IAEzD,MAAM,UAAU,GAAG,CAAC,SAAS,GAAG,CAAC,CAAC,GAAG,SAAS,CAAC;IAC/C,KAAK,IAAI,MAAM,IAAI,OAAO,EAAE;QAC1B,MAAM,EAAE,YAAY,EAAE,KAAK,EAAE,WAAW,GAAG,CAAC,EAAE,GAAG,MAAM,CAAC;QACxD,IAAI,YAAY,KAAK,GAAG,IAAI,YAAY,KAAK,MAAM,EAAE;YACnD,iBAAiB,CAAC,OAAO,CAAC;gBACxB,CAAC,EAAE,KAAK;gBACR,CAAC,EAAE,WAAW;gBACd,KAAK,EAAE,UAAU;aAClB,CAAC,CAAC;SACJ;aAAM;YACL,MAAM,KAAK,GAAG,gBAAgB,CAAC,KAAK,EAAE;gBACpC,SAAS;gBACT,SAAS;aACV,CAAC,CAAC;YACH,iBAAiB,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC;SACnC;KACF;IACD,OAAO,iBAAiB,CAAC,WAAW,EAAE,CAAC;AACzC,CAAC;AAED,SAAS,gBAAgB,CAAC,KAAa,EAAE,OAAY;IACnD,MAAM,EACJ,SAAS,EACT,SAAS,EACT,WAAW,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,GAC1C,GAAG,OAAO,CAAC;IAEZ,MAAM,YAAY,GAAG,SAAS,GAAG,SAAS,CAAC;IAC3C,MAAM,iBAAiB,GAAG,YAAY,GAAG,GAAG,CAAC;IAE7C,MAAM,KAAK,GAAG,EAAE,CAAC;IACjB,MAAM,iBAAiB,GACrB,KAAK,GAAG,CAAC,iBAAiB,GAAG,WAAW,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;IACvD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QAC3C,KAAK,CAAC,IAAI,CAAC;YACT,CAAC,EAAE,iBAAiB,GAAG,iBAAiB,GAAG,CAAC;YAC5C,CAAC,EAAE,WAAW,CAAC,CAAC,CAAC;YACjB,KAAK,EAAE,YAAY;SACpB,CAAC,CAAC;KACJ;IAED,OAAO,KAAK,CAAC;AACf,CAAC;AAED,SAAS,iBAAiB,CACxB,QAAqB,EACrB,OAAsB,EACtB,UAAe,EAAE;IAEjB,MAAM,EACJ,WAAW,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,GAAG,EAAE,MAAM,EAAE,EAAE;QAC3C,MAAM,EAAE,WAAW,GAAG,CAAC,EAAE,GAAG,MAAM,CAAC;QACnC,OAAO,GAAG,GAAG,WAAW,CAAC;IAC3B,CAAC,EAAE,CAAC,CAAC,GACN,GAAG,OAAO,CAAC;IACZ,MAAM,GAAG,GAAI,QAAyB,CAAC,MAAM,CAC3C,CAAC,GAAW,EAAE,OAAe,EAAE,EAAE,CAAC,GAAG,GAAG,OAAO,EAC/C,CAAC,CACF,CAAC;IAEF,IAAI,GAAG,KAAK,CAAC,EAAE;QACb,MAAM,KAAK,GAAG,CAAC,WAAW,GAAG,GAAG,CAAC,GAAG,GAAG,CAAC;QACxC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACxC,QAAQ,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC;SACtB;KACF;AACH,CAAC"}
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@@ -1,4 +1,4 @@
|
|
|
1
|
-
import type {
|
|
1
|
+
import type { Shape1D } from 'ml-peak-shape-generator';
|
|
2
2
|
import type { NMRSignal1D } from '../types/NMRSignal1D';
|
|
3
3
|
export interface OptionsSignalsToXY {
|
|
4
4
|
frequency?: number;
|
|
@@ -15,7 +15,7 @@ export interface OptionsSignalsToXY {
|
|
|
15
15
|
/**
|
|
16
16
|
* Shape options for ml-spectrum-generator
|
|
17
17
|
*/
|
|
18
|
-
shape?:
|
|
18
|
+
shape?: Shape1D;
|
|
19
19
|
/**
|
|
20
20
|
* The linewidth of the output spectrum, expresed in Hz.
|
|
21
21
|
* @default 1
|
|
@@ -1,4 +1,5 @@
|
|
|
1
|
-
import
|
|
1
|
+
import { DataXY } from 'cheminfo-types';
|
|
2
|
+
import type { Shape1D } from 'ml-peak-shape-generator';
|
|
2
3
|
import type { SpinSystem } from '../../types/spinSystem';
|
|
3
4
|
interface Simulate1DOptions {
|
|
4
5
|
/**
|
|
@@ -35,7 +36,7 @@ interface Simulate1DOptions {
|
|
|
35
36
|
* Shape options
|
|
36
37
|
* @default {kind:'gaussian'}
|
|
37
38
|
*/
|
|
38
|
-
shape?:
|
|
39
|
+
shape?: Shape1D;
|
|
39
40
|
}
|
|
40
41
|
/**
|
|
41
42
|
* 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).
|
|
@@ -44,5 +45,5 @@ export default function simulate1D(
|
|
|
44
45
|
/**
|
|
45
46
|
* The SpinSystem object to be simulated
|
|
46
47
|
*/
|
|
47
|
-
spinSystem: SpinSystem, options?: Simulate1DOptions):
|
|
48
|
+
spinSystem: SpinSystem, options?: Simulate1DOptions): DataXY;
|
|
48
49
|
export {};
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"simulate1D.js","sourceRoot":"","sources":["../../../src/signals/simulation/simulate1D.ts"],"names":[],"mappings":";;;;;AAAA,kEAAyC;
|
|
1
|
+
{"version":3,"file":"simulate1D.js","sourceRoot":"","sources":["../../../src/signals/simulation/simulate1D.ts"],"names":[],"mappings":";;;;;AAAA,kEAAyC;AAEzC,yCAAwC;AAGxC,uDAAgD;AAChD,2DAAuD;AAIvD,sEAA8C;AAE9C,MAAM,UAAU,GAAG,IAAI,CAAC;AAwCxB;;GAEG;AAEH,SAAwB,UAAU;AAChC;;GAEG;AACH,UAAsB,EACtB,UAA6B,EAAE;IAE/B,IAAI,EACF,SAAS,GAAG,CAAC,EACb,cAAc,GAAG,CAAC,EAClB,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,IAAI,iBAAiB,GAAG,IAAI,sCAAiB,CAAC;QAC5C,IAAI;QACJ,EAAE;QACF,QAAQ;QACR,KAAK;QACL,YAAY,EAAE,GAAG,EAAE,CAAC,SAAS;KAC9B,CAAC,CAAC;IAEH,MAAM,cAAc,GAAG,UAAU,CAAC,cAAc,CAAC,KAAK,EAAE,CAAC;IACzD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,cAAc,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QAC9C,cAAc,CAAC,CAAC,CAAC,GAAG,cAAc,CAAC,CAAC,CAAC,GAAG,YAAY,CAAC;KACtD;IAED,MAAM,YAAY,GAAG,UAAU,CAAC,YAAY,CAAC;IAC7C,KAAK,MAAM,OAAO,IAAI,UAAU,CAAC,QAAQ,EAAE;QACzC,IAAI,WAAW,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,OAAO,EAAE,EAAE,CACxC,OAAO,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CACrC,CAAC;QAEF,IAAI,MAAM,GAAG,CAAC,CAAC;QACf,IAAI,IAAI,GAAG,CAAC,CAAC;QACb,IAAI,WAAW,GAAa,EAAE,CAAC;QAC/B,IAAI,WAAW,GAAa,EAAE,CAAC;QAC/B,IAAI,OAAO,CAAC,MAAM,GAAG,cAAc,EAAE;YACnC,6EAA6E;YAC7E,2CAA2C;YAC3C,uEAAuE;YACvE,IAAI,KAAK,GAAG,CAAC,CAAC;YACd,OAAO,OAAO,CAAC,KAAK,EAAE,CAAC,GAAG,CAAC;gBAAC,CAAC;YAC7B,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC;YAC3B,WAAW,CAAC,IAAI,CAAC,CAAC,cAAc,CAAC,KAAK,CAAC,CAAC,CAAC;YACzC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACvC,IAAI,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE;oBAClB,IAAI,EAAE,GAAG,UAAU,CAAC,iBAAiB,CAAC,GAAG,CAAC,KAAK,EAAE,WAAW,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;oBACrE,IAAI,WAAW,GAAG,WAAW,CAAC,MAAM,CAAC;oBACrC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE;wBACpC,WAAW,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC;wBACtC,WAAW,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;qBACtB;iBACF;aACF;YAED,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;YAClC,IAAI,GAAG,WAAW,CAAC,MAAM,CAAC;YAC1B,MAAM,GAAG,CAAC,CAAC;YAEX,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE;gBAC7B,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;aACrB;SACF;aAAM;YACL,MAAM,WAAW,GAAG,cAAc,CAChC,cAAc,EACd,UAAU,CAAC,iBAAiB,EAC5B,YAAY,EACZ,UAAU,CAAC,YAAY,EACvB,WAAW,CACZ,CAAC;YACF,MAAM,OAAO,GAAG,WAAW,CAAC,IAAI,CAAC;YACjC,kBAAkB;YAClB,MAAM,GAAG,GAAG,IAAI,eAAG,CAAC,WAAW,CAAC,CAAC;YACjC,MAAM,CAAC,GAAG,GAAG,CAAC,iBAAiB,CAAC;YAChC,MAAM,KAAK,GAAG,GAAG,CAAC,eAAe,CAAC;YAClC,MAAM,gBAAgB,GAAG,IAAI,+BAAY,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;YAC5D,MAAM,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC;YAC/B,MAAM,GAAG,CAAC,CAAC;YACX,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,EAAE,CAAC,EAAE,EAAE;gBAChC,MAAM,CAAC,GAAG,IAAA,wBAAc,EAAC,YAAY,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;gBAEvD,IAAI,IAAI,GAAG,CAAC,CAAC;gBACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;oBAC1B,IAAI,IAAI,YAAY,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC;iBACtC;gBACD,MAAM,CAAC,GAAG,+BAAY,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;gBAEjC,IAAI,GAAG,CAAC,CAAC;gBACT,KAAK,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,EAAE,CAAC,EAAE,EAAE;oBACpC,IAAI,IAAI,YAAY,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC;iBACtC;gBACD,MAAM,CAAC,GAAG,+BAAY,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;gBACjC,MAAM,OAAO,GAAG,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,CAAC;gBAC5D,IAAI,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE;oBACnB,gBAAgB,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;oBAClD,MAAM,EAAE,CAAC;iBACV;qBAAM;oBACL,gBAAgB,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;iBAC/C;aACF;YAED,IAAI,KAAK,GAAG,kBAAM,CAAC,KAAK,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;YAC3C,gBAAgB,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE;gBAC1C,IAAI,CAAC,GAAG,CAAC,EAAE;oBACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,EAAE,CAAC,EAAE,EAAE;wBAClC,IAAI,OAAO,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;wBAC1B,IAAI,OAAO,KAAK,CAAC,EAAE;4BACjB,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC;yBAC5C;qBACF;iBACF;gBACD,OAAO,CAAC,CAAC;YACX,CAAC,CAAC,CAAC;YAEH,IAAI,MAAM,GAAG,KAAK,CAAC,KAAK,EAAE,CAAC;YAC3B,gBAAgB,CAAC,cAAc,CAAC,CAAC,CAAS,EAAE,CAAS,EAAE,CAAS,EAAE,EAAE;gBAClE,IAAI,CAAC,GAAG,CAAC,EAAE;oBACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,EAAE,CAAC,EAAE,EAAE;wBAClC,IAAI,OAAO,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;wBAC1B,IAAI,OAAO,KAAK,CAAC,EAAE;4BACjB,MAAM,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC;yBAC9C;qBACF;iBACF;gBACD,OAAO,CAAC,CAAC;YACX,CAAC,CAAC,CAAC;YACH,MAAM,EAAE,GAAG,CAAC,CAAC,SAAS,EAAE,CAAC;YAEzB,KAAK,GAAG,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;YACvB,MAAM,WAAW,GAAG,IAAI,+BAAY,CAAC,KAAK,CAAC,SAAS,EAAE,EAAE;gBACtD,SAAS,EAAE,UAAU;aACtB,CAAC,CAAC;YACH,YAAY,CAAC,WAAW,EAAE,UAAU,CAAC,CAAC;YAEtC,MAAM,GAAG,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;YACzB,MAAM,YAAY,GAAG,IAAI,+BAAY,CAAC,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package/lib/types/NMRPeak1D.d.ts
CHANGED
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@@ -1,68 +1,13 @@
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|
|
1
1
|
import { DataXY } from 'cheminfo-types';
|
|
2
|
-
import type {
|
|
3
|
-
interface
|
|
4
|
-
/**
|
|
5
|
-
* Noise threshold in spectrum y units. Default is three/thresholdFactor times the absolute median of data.y.
|
|
6
|
-
* @default `median(data.y) * (options.thresholdFactor || 3)`
|
|
7
|
-
*/
|
|
8
|
-
noiseLevel?: number;
|
|
9
|
-
/**
|
|
10
|
-
* Threshold to determine if a given peak should be considered as a noise, bases on its relative height compared to the highest peak.
|
|
11
|
-
* @default 0.01
|
|
12
|
-
*/
|
|
13
|
-
minMaxRatio: number;
|
|
14
|
-
/**
|
|
15
|
-
* If broadRatio is higher than 0, then all the peaks which second derivative smaller than broadRatio * maxAbsSecondDerivative will be marked with the soft mask equal to true.
|
|
16
|
-
* @default 0.00025
|
|
17
|
-
*/
|
|
18
|
-
broadRatio: number;
|
|
19
|
-
/**
|
|
20
|
-
* Select the peak intensities from a smoothed version of the independent variables.
|
|
21
|
-
* @default true
|
|
22
|
-
*/
|
|
23
|
-
smoothY: boolean;
|
|
2
|
+
import type { Peak1D, IGSDOptions, IOptimizePeaksOptions, IJoinBroadPeaksOptions } from 'ml-gsd';
|
|
3
|
+
export interface IGetPeakListOptions extends IGSDOptions, IOptimizePeaksOptions, IJoinBroadPeaksOptions {
|
|
24
4
|
/**
|
|
25
5
|
* If it is true, the peaks parameters will be optimized.
|
|
26
6
|
* @default false
|
|
27
7
|
*/
|
|
28
8
|
optimize: boolean;
|
|
29
|
-
/**
|
|
30
|
-
* factor to determine the width at the moment to group the peaks in signals in 'GSD.optimizePeaks' function.
|
|
31
|
-
* @default 4
|
|
32
|
-
*/
|
|
33
|
-
factorWidth: number;
|
|
34
|
-
/**
|
|
35
|
-
* if it is true, it optimizes the x and intensity by extrapolation.
|
|
36
|
-
*/
|
|
37
|
-
realTopDetection: boolean;
|
|
38
|
-
/**
|
|
39
|
-
* options to shape used to adapt the FWHM
|
|
40
|
-
* @default {kind:'gaussian'}
|
|
41
|
-
*/
|
|
42
|
-
shape: {
|
|
43
|
-
kind: string;
|
|
44
|
-
};
|
|
45
|
-
/**
|
|
46
|
-
* options for optimization step, kind represent the algorithm
|
|
47
|
-
* @default {kind:'lm'}
|
|
48
|
-
*/
|
|
49
|
-
optimization: {
|
|
50
|
-
kind: string;
|
|
51
|
-
};
|
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52
|
-
/**
|
|
53
|
-
* Threshold to determine if some peak is candidate to clustering into range.
|
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54
|
-
* @default 0.25
|
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55
|
-
*/
|
|
56
|
-
broadWidth: number;
|
|
57
|
-
/**
|
|
58
|
-
* Options for savitz Golay
|
|
59
|
-
*/
|
|
60
|
-
sgOptions: {
|
|
61
|
-
windowSize: number;
|
|
62
|
-
polynomial: number;
|
|
63
|
-
};
|
|
64
9
|
}
|
|
65
|
-
export interface OptionsXYAutoPeaksPicking extends Partial<
|
|
10
|
+
export interface OptionsXYAutoPeaksPicking extends Partial<IGetPeakListOptions> {
|
|
66
11
|
/**
|
|
67
12
|
* Low limit value in the x axis to extract a sub set of points from the input data.
|
|
68
13
|
*/
|
|
@@ -87,5 +32,4 @@ export interface OptionsXYAutoPeaksPicking extends Partial<OptionsGetPeakList> {
|
|
|
87
32
|
*/
|
|
88
33
|
useSanPlot?: boolean;
|
|
89
34
|
}
|
|
90
|
-
export declare function xyAutoPeaksPicking(data: DataXY, options?: OptionsXYAutoPeaksPicking):
|
|
91
|
-
export {};
|
|
35
|
+
export declare function xyAutoPeaksPicking(data: DataXY, options?: OptionsXYAutoPeaksPicking): Peak1D[];
|
|
@@ -36,14 +36,14 @@ function getPeakList(data, options) {
|
|
|
36
36
|
shape,
|
|
37
37
|
sgOptions,
|
|
38
38
|
minMaxRatio,
|
|
39
|
-
broadRatio,
|
|
40
39
|
noiseLevel,
|
|
41
40
|
smoothY,
|
|
42
41
|
realTopDetection,
|
|
43
42
|
});
|
|
44
43
|
if (broadWidth) {
|
|
45
|
-
peakList = (0, ml_gsd_1.joinBroadPeaks)(peakList, {
|
|
46
|
-
|
|
44
|
+
peakList = (0, ml_gsd_1.joinBroadPeaks)(data, peakList, {
|
|
45
|
+
broadRatio,
|
|
46
|
+
broadWidth,
|
|
47
47
|
shape,
|
|
48
48
|
optimization,
|
|
49
49
|
});
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"xyAutoPeaksPicking.js","sourceRoot":"","sources":["../../src/xy/xyAutoPeaksPicking.ts"],"names":[],"mappings":";;;AACA,mCAA4D;
|
|
1
|
+
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|