nmr-processing 8.7.2 → 9.0.2
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/lib/peaks/peakToXY.d.ts +3 -3
- package/lib/peaks/peakToXY.js +1 -1
- package/lib/peaks/peakToXY.js.map +1 -1
- package/lib/peaks/peaksToRanges.d.ts +1 -1
- package/lib/peaks/peaksToRanges.js +14 -16
- package/lib/peaks/peaksToRanges.js.map +1 -1
- package/lib/peaks/peaksToXY.d.ts +21 -2
- package/lib/peaks/peaksToXY.js +22 -5
- package/lib/peaks/peaksToXY.js.map +1 -1
- package/lib/peaks/util/convertWidth.d.ts +14 -0
- package/lib/peaks/util/convertWidth.js +34 -0
- package/lib/peaks/util/convertWidth.js.map +1 -0
- package/lib/peaks/util/convertWidthToHz.d.ts +4 -0
- package/lib/peaks/util/convertWidthToHz.js +9 -0
- package/lib/peaks/util/convertWidthToHz.js.map +1 -0
- package/lib/peaks/util/convertWidthToPPM.d.ts +3 -0
- package/lib/peaks/util/convertWidthToPPM.js +9 -0
- package/lib/peaks/util/convertWidthToPPM.js.map +1 -0
- package/lib/{peaks/util → ranges/utils}/joinRanges.d.ts +0 -0
- package/lib/{peaks/util → ranges/utils}/joinRanges.js +0 -0
- package/lib/ranges/utils/joinRanges.js.map +1 -0
- package/lib/{peaks/util → signals/utils}/jAnalyzer.d.ts +1 -1
- package/lib/{peaks/util → signals/utils}/jAnalyzer.js +2 -1
- package/lib/signals/utils/jAnalyzer.js.map +1 -0
- package/lib/xy/xyAutoPeaksPicking.d.ts +9 -1
- package/lib/xy/xyAutoPeaksPicking.js +9 -8
- package/lib/xy/xyAutoPeaksPicking.js.map +1 -1
- package/lib/xy/xyAutoRangesPicking.d.ts +2 -2
- package/lib/xy/xyAutoRangesPicking.js +1 -1
- package/lib/xy/xyAutoRangesPicking.js.map +1 -1
- package/lib/xy/xyPeaksOptimization.d.ts +7 -1
- package/lib/xy/xyPeaksOptimization.js +9 -1
- package/lib/xy/xyPeaksOptimization.js.map +1 -1
- package/lib/xyz/xyzJResAnalyzer.d.ts +1 -1
- package/lib/xyz/xyzJResAnalyzer.js +3 -2
- package/lib/xyz/xyzJResAnalyzer.js.map +1 -1
- package/lib-esm/peaks/peakToXY.js +1 -1
- package/lib-esm/peaks/peakToXY.js.map +1 -1
- package/lib-esm/peaks/peaksToRanges.js +14 -16
- package/lib-esm/peaks/peaksToRanges.js.map +1 -1
- package/lib-esm/peaks/peaksToXY.js +22 -5
- package/lib-esm/peaks/peaksToXY.js.map +1 -1
- package/lib-esm/peaks/util/convertWidth.js +30 -0
- package/lib-esm/peaks/util/convertWidth.js.map +1 -0
- package/lib-esm/peaks/util/convertWidthToHz.js +5 -0
- package/lib-esm/peaks/util/convertWidthToHz.js.map +1 -0
- package/lib-esm/peaks/util/convertWidthToPPM.js +5 -0
- package/lib-esm/peaks/util/convertWidthToPPM.js.map +1 -0
- package/lib-esm/{peaks/util → ranges/utils}/joinRanges.js +0 -0
- package/lib-esm/ranges/utils/joinRanges.js.map +1 -0
- package/lib-esm/{peaks/util → signals/utils}/jAnalyzer.js +2 -1
- package/lib-esm/signals/utils/jAnalyzer.js.map +1 -0
- package/lib-esm/xy/xyAutoPeaksPicking.js +9 -8
- package/lib-esm/xy/xyAutoPeaksPicking.js.map +1 -1
- package/lib-esm/xy/xyAutoRangesPicking.js +1 -1
- package/lib-esm/xy/xyAutoRangesPicking.js.map +1 -1
- package/lib-esm/xy/xyPeaksOptimization.js +9 -1
- package/lib-esm/xy/xyPeaksOptimization.js.map +1 -1
- package/lib-esm/xyz/xyzJResAnalyzer.js +3 -2
- package/lib-esm/xyz/xyzJResAnalyzer.js.map +1 -1
- package/package.json +2 -2
- package/src/peaks/peakToXY.ts +3 -5
- package/src/peaks/peaksToRanges.ts +15 -19
- package/src/peaks/peaksToXY.ts +53 -6
- package/src/peaks/util/convertWidth.ts +47 -0
- package/src/peaks/util/convertWidthToHz.ts +9 -0
- package/src/peaks/util/convertWidthToPPM.ts +8 -0
- package/src/ranges/markSolventSignal.ts +1 -1
- package/src/{peaks/util → ranges/utils}/joinRanges.ts +0 -0
- package/src/{peaks/util → signals/utils}/jAnalyzer.ts +3 -2
- package/src/xy/xyAutoPeaksPicking.ts +23 -10
- package/src/xy/xyAutoRangesPicking.ts +2 -2
- package/src/xy/xyPeaksOptimization.ts +17 -2
- package/src/xyz/xyzJResAnalyzer.ts +4 -3
- package/lib/peaks/util/jAnalyzer.js.map +0 -1
- package/lib/peaks/util/joinRanges.js.map +0 -1
- package/lib-esm/peaks/util/jAnalyzer.js.map +0 -1
- package/lib-esm/peaks/util/joinRanges.js.map +0 -1
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{"version":3,"file":"peakToXY.js","sourceRoot":"","sources":["../../src/peaks/peakToXY.ts"],"names":[],"mappings":"
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{"version":3,"file":"peakToXY.js","sourceRoot":"","sources":["../../src/peaks/peakToXY.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,SAAS,EAAoB,MAAM,aAAa,CAAC;AAE1D,MAAM,UAAU,QAAQ,CAAC,IAAe,EAAE,OAAyB;IACjE,OAAO,SAAS,CAAC,CAAC,IAAI,CAAC,EAAE,OAAO,CAAC,CAAC;AACpC,CAAC"}
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import { xyIntegration } from 'ml-spectra-processing';
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import { joinRanges } from '../ranges/utils/joinRanges';
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import jAnalyzer from '../signals/utils/jAnalyzer';
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function checkSignalAfterCompilePattern(signal) {
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// if (!signal.symRank)
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// throw new Error('Internal error, symRank was not calculated');
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from: peak.x - (peak.width * 3) / frequency,
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to: peak.x + (peak.width * 3) / frequency,
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value: 0,
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peaks: [
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for (let j = signal.maskPattern.length - 1; j >= 0; j--) {
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if (!signal.maskPattern[j]) {
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}
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}
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if (peaksO.length > 0) {
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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.width;
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let tmp = peak.x + peak.width / frequency;
|
|
196
196
|
signal1D.stopX = Math.max(signal1D.stopX, tmp);
|
|
197
197
|
signal1D.startX = Math.min(signal1D.startX, tmp);
|
|
198
198
|
signal1D.nbPeaks++;
|
|
@@ -201,8 +201,8 @@ export function detectSignals(data, peakList, options = {}) {
|
|
|
201
201
|
intensity: peak.y,
|
|
202
202
|
width: peak.width,
|
|
203
203
|
});
|
|
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|
-
signal1D.integralData.from = Math.min(signal1D.integralData.from, peak.x - peak.width * 3);
|
|
205
|
-
signal1D.integralData.to = Math.max(signal1D.integralData.to, peak.x + peak.width * 3);
|
|
204
|
+
signal1D.integralData.from = Math.min(signal1D.integralData.from, peak.x - (peak.width * 3) / frequency);
|
|
205
|
+
signal1D.integralData.to = Math.max(signal1D.integralData.to, peak.x + (peak.width * 3) / frequency);
|
|
206
206
|
if (peak.kind)
|
|
207
207
|
signal1D.kind = peak.kind;
|
|
208
208
|
}
|
|
@@ -214,7 +214,7 @@ export function detectSignals(data, peakList, options = {}) {
|
|
|
214
214
|
let chemicalShift = 0;
|
|
215
215
|
let integralPeaks = 0;
|
|
216
216
|
for (const peak of peaks) {
|
|
217
|
-
let area = computeArea(peak);
|
|
217
|
+
let area = computeArea(peak, frequency);
|
|
218
218
|
chemicalShift += peak.x * area;
|
|
219
219
|
integralPeaks += area;
|
|
220
220
|
}
|
|
@@ -241,11 +241,9 @@ export function detectSignals(data, peakList, options = {}) {
|
|
|
241
241
|
}
|
|
242
242
|
/**
|
|
243
243
|
* Return the area of a Lorentzian function
|
|
244
|
-
* @param {object} peak - object with peak information
|
|
245
|
-
* @return {Number}
|
|
246
244
|
* @private
|
|
247
245
|
*/
|
|
248
|
-
function computeArea(peak) {
|
|
249
|
-
return Math.abs(peak.intensity * peak.width * 1.57); // todo add an option with this value: 1.772453851
|
|
246
|
+
function computeArea(peak, frequency) {
|
|
247
|
+
return Math.abs(((peak.intensity * peak.width) / frequency) * 1.57); // todo add an option with this value: 1.772453851
|
|
250
248
|
}
|
|
251
249
|
//# sourceMappingURL=peaksToRanges.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"peaksToRanges.js","sourceRoot":"","sources":["../../src/peaks/peaksToRanges.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,aAAa,EAAE,MAAM,uBAAuB,CAAC;
|
|
1
|
+
{"version":3,"file":"peaksToRanges.js","sourceRoot":"","sources":["../../src/peaks/peaksToRanges.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,aAAa,EAAE,MAAM,uBAAuB,CAAC;AAEtD,OAAO,EAAE,UAAU,EAAE,MAAM,4BAA4B,CAAC;AAExD,OAAO,SAAS,MAAM,4BAA4B,CAAC;AAqEnD,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,IAAqB,EACrB,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,GAAG,SAAS;QACvC,KAAK,EAAE,IAAI,CAAC,CAAC,GAAG,IAAI,CAAC,KAAK,GAAG,SAAS;QACtC,OAAO,EAAE,SAAS;QAClB,OAAO;QACP,YAAY,EAAE;YACZ,IAAI,EAAE,IAAI,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,SAAS;YAC3C,EAAE,EAAE,IAAI,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,SAAS;YACzC,KAAK,EAAE,CAAC;SACT;QACD,KAAK,EAAE;YACL;gBACE,CAAC,EAAE,IAAI,CAAC,CAAC;gBACT,SAAS,EAAE,IAAI,CAAC,CAAC;gBACjB,KAAK,EAAE,IAAI,CAAC,KAAK;aAClB;SACF;KACF,CAAC;AACJ,CAAC,CAAC;AACF;;GAEG;AAEH,MAAM,UAAU,aAAa,CAC3B,IAAY,EACZ,QAA2B,EAC3B,UAAgC,EAAE;IAElC,IAAI,EACF,cAAc,GAAG,GAAG,EACpB,iBAAiB,GAAG,IAAI,EACxB,KAAK,GAAG,GAAG,EACX,OAAO,GAAG,IAAI,EACd,YAAY,GAAG,KAAK,EACpB,SAAS,GAAG,GAAG,EACf,gBAAgB,GAAG,EAAE,EACrB,SAAS,GAAG,KAAK,EACjB,OAAO,GAAG,IAAI,GACf,GAAG,OAAO,CAAC;IAEZ,IAAI,aAAa,GAAG;QAClB,cAAc;QACd,YAAY;QACZ,gBAAgB;QAChB,SAAS;QACT,OAAO;KACR,CAAC;IAEF,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO,EAAE,CAAC;IAErC,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE;QACzB,IAAI,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC;QAC1B,IAAI,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC;KAC3B;IAED,IAAI,OAAO,GAAG,aAAa,CAAC,IAAI,EAAE,QAAQ,EAAE,aAAa,CAAC,CAAC;IAC3D,IAAI,KAAK,EAAE;QACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACvC,IAAI,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,YAAY,CAAC,KAAK,CAAC,GAAG,KAAK,EAAE;gBACnD,OAAO,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;aACtB;SACF;KACF;IAED,IAAI,OAAO,EAAE;QACX,IAAI,GAAG,EAAE,GAAG,CAAC;QACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACvC,OAAO,CAAC,CAAC,CAAC,GAAG,SAAS,CAAC,cAAc,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC;YAClD,IAAI,MAAM,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC;YACxB,IACE,MAAM,CAAC,WAAW;gBAClB,MAAM,CAAC,YAAY,KAAK,GAAG;gBAC3B,MAAM,CAAC,YAAY,KAAK,EAAE,EAC1B;gBACA,8BAA8B,CAAC,MAAM,CAAC,CAAC;gBACvC,6CAA6C;gBAC7C,GAAG,GAAG,CAAC,CAAC;gBACR,GAAG,GAAG,CAAC,CAAC;gBACR,IAAI,MAAM,GAAG,EAAE,CAAC;gBAChB,KAAK,IAAI,CAAC,GAAG,MAAM,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE;oBACvD,GAAG,IAAI,WAAW,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,SAAS,CAAC,CAAC;oBAC/C,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,EAAE;wBAC1B,IAAI,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;wBACzC,MAAM,CAAC,IAAI,CAAC;4BACV,CAAC,EAAE,KAAK,CAAC,CAAC;4BACV,CAAC,EAAE,KAAK,CAAC,SAAS;4BAClB,KAAK,EAAE,KAAK,CAAC,KAAK;yBACnB,CAAC,CAAC;wBACH,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;wBACzB,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;wBAC1B,MAAM,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;wBAChC,MAAM,CAAC,OAAO,EAAE,CAAC;wBACjB,GAAG,IAAI,WAAW,CAAC,KAAK,EAAE,SAAS,CAAC,CAAC;qBACtC;iBACF;gBACD,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE;oBACrB,GAAG,GAAG,CAAC,GAAG,GAAG,MAAM,CAAC,YAAY,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC;oBAC9C,MAAM,CAAC,YAAY,CAAC,KAAK,IAAI,GAAG,CAAC;oBACjC,IAAI,MAAM,GAAG,EAAE,CAAC;oBAChB,KAAK,IAAI,CAAC,GAAG,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE;wBAC3C,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC;qBACxB;oBACD,aAAa,CAAC,cAAc,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;oBAC7C,IAAI,MAAM,GAAG,aAAa,CAAC,IAAI,EAAE,MAAM,EAAE,aAAa,CAAC,CAAC;oBAExD,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE;wBAC1B,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;qBACrB;iBACF;aACF;SACF;QACD,qCAAqC;QACrC,IAAI,WAAW,GAAG,CAAC,CAAC;QACpB,IAAI,WAAW,GAAG,CAAC,CAAC;QACpB,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;YAC5B,WAAW,IAAI,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC;SAChE;QACD,IAAI,WAAW,KAAK,cAAc,EAAE;YAClC,WAAW,GAAG,cAAc,GAAG,WAAW,CAAC;YAC3C,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;gBAC5B,MAAM,CAAC,YAAY,CAAC,KAAK,IAAI,WAAW,CAAC;aAC1C;SACF;KACF;IAED,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;QACpB,OAAO,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC;IAC3B,CAAC,CAAC,CAAC;IAEH,IAAI,KAAK,EAAE;QACT,KAAK,IAAI,CAAC,GAAG,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE;YAC5C,IAAI,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,YAAY,CAAC,KAAK,CAAC,GAAG,KAAK,EAAE;gBACnD,OAAO,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;aACtB;SACF;KACF;IACD,IAAI,MAAM,GAAe,EAAE,CAAC;IAC5B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACvC,IAAI,MAAM,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC;QACxB,MAAM,KAAK,GAAa;YACtB,IAAI,EAAE,MAAM,CAAC,YAAY,CAAC,IAAI;YAC9B,EAAE,EAAE,MAAM,CAAC,YAAY,CAAC,EAAE;YAC1B,WAAW,EAAE,MAAM,CAAC,YAAY,CAAC,KAAK;SACvC,CAAC;QACF,MAAM,YAAY,GAAgB;YAChC,KAAK,EAAE,MAAM,CAAC,KAAK;YACnB,IAAI,EAAE,MAAM,CAAC,IAAI,IAAI,QAAQ;YAC7B,YAAY,EAAE,MAAM,CAAC,YAAY;YACjC,WAAW,EAAE,MAAM,CAAC,YAAY,CAAC,KAAK;SACvC,CAAC;QACF,IAAI,SAAS,EAAE;YACb,YAAY,CAAC,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE;gBAC7C,MAAM,SAAS,GAAQ;oBACrB,CAAC,EAAE,IAAI,CAAC,SAAS;oBACjB,GAAG,IAAI;iBACR,CAAC;gBACF,OAAO,SAAS,CAAC,SAAS,CAAC;gBAC3B,OAAO,SAAsB,CAAC;YAChC,CAAC,CAAC,CAAC;SACJ;QACD,IAAI,MAAM,CAAC,KAAK,EAAE;YAChB,YAAY,CAAC,EAAE,GAAG,MAAM,CAAC,KAAK,CAAC;SAChC;QAED,KAAK,CAAC,OAAO,GAAG,CAAC,YAAY,CAAC,CAAC;QAC/B,MAAM,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC;KACnB;IAED,IAAI,iBAAiB;QAAE,MAAM,GAAG,UAAU,CAAC,MAAM,CAAC,CAAC;IACnD,OAAO,MAAM,CAAC;AAChB,CAAC;AAED;;;;;;;;;;;;;GAaG;AAEH,MAAM,UAAU,aAAa,CAC3B,IAAY,EACZ,QAA2B,EAC3B,UAAgC,EAAE;IAElC,IAAI,EACF,cAAc,GAAG,GAAG,EACpB,YAAY,GAAG,KAAK,EACpB,gBAAgB,GAAG,EAAE,EACrB,SAAS,GAAG,GAAG,EACf,OAAO,GAAG,IAAI,GACf,GAAG,OAAO,CAAC;IAEZ,IAAI,QAAQ,GAAiB,YAAY,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,SAAS,EAAE,OAAO,CAAC,CAAC;IAC3E,IAAI,KAAK,CAAC;IACV,IAAI,OAAO,GAAG,EAAE,CAAC;IACjB,IAAI,QAAQ,GAAG,EAAE,CAAC,EAAE,MAAM,CAAC,gBAAgB,EAAE,CAAC;IAC9C,IAAI,gBAAgB,GAAG,CAAC,CAAC;IACzB,gBAAgB,IAAI,SAAS,CAAC;IAC9B,KAAK,MAAM,IAAI,IAAI,QAAQ,EAAE;QAC3B,IAAI,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,GAAG,gBAAgB,EAAE;YACpD,QAAQ,GAAG,YAAY,CAAC,IAAI,EAAE,SAAS,EAAE,OAAO,CAAC,CAAC;YAClD,IAAI,IAAI,CAAC,IAAI;gBAAE,QAAQ,CAAC,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC;YACzC,OAAO,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;SACxB;aAAM;YACL,IAAI,GAAG,GAAG,IAAI,CAAC,CAAC,GAAG,IAAI,CAAC,KAAK,GAAG,SAAS,CAAC;YAC1C,QAAQ,CAAC,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC;YAC/C,QAAQ,CAAC,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC;YACjD,QAAQ,CAAC,OAAO,EAAE,CAAC;YACnB,QAAQ,CAAC,KAAK,CAAC,IAAI,CAAC;gBAClB,CAAC,EAAE,IAAI,CAAC,CAAC;gBACT,SAAS,EAAE,IAAI,CAAC,CAAC;gBACjB,KAAK,EAAE,IAAI,CAAC,KAAK;aAClB,CAAC,CAAC;YACH,QAAQ,CAAC,YAAY,CAAC,IAAI,GAAG,IAAI,CAAC,GAAG,CACnC,QAAQ,CAAC,YAAY,CAAC,IAAI,EAC1B,IAAI,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,SAAS,CACtC,CAAC;YACF,QAAQ,CAAC,YAAY,CAAC,EAAE,GAAG,IAAI,CAAC,GAAG,CACjC,QAAQ,CAAC,YAAY,CAAC,EAAE,EACxB,IAAI,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,SAAS,CACtC,CAAC;YACF,IAAI,IAAI,CAAC,IAAI;gBAAE,QAAQ,CAAC,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC;SAC1C;QACD,QAAQ,GAAG,IAAI,CAAC;KACjB;IACD,KAAK,IAAI,MAAM,IAAI,OAAO,EAAE;QAC1B,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC;QACrB,IAAI,WAAW,GAAG,MAAM,CAAC,YAAY,CAAC;QACtC,IAAI,aAAa,GAAG,CAAC,CAAC;QACtB,IAAI,aAAa,GAAG,CAAC,CAAC;QAEtB,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE;YACxB,IAAI,IAAI,GAAG,WAAW,CAAC,IAAI,EAAE,SAAS,CAAC,CAAC;YACxC,aAAa,IAAI,IAAI,CAAC,CAAC,GAAG,IAAI,CAAC;YAC/B,aAAa,IAAI,IAAI,CAAC;SACvB;QACD,MAAM,CAAC,KAAK,GAAG,aAAa,GAAG,aAAa,CAAC;QAE7C,IAAI,YAAY,KAAK,KAAK,EAAE;YAC1B,WAAW,CAAC,KAAK,GAAG,aAAa,CAAC,IAAI,EAAE;gBACtC,IAAI,EAAE,WAAW,CAAC,IAAI;gBACtB,EAAE,EAAE,WAAW,CAAC,EAAE;aACnB,CAAC,CAAC;SACJ;aAAM;YACL,WAAW,CAAC,KAAK,GAAG,aAAa,CAAC;SACnC;QACD,gBAAgB,IAAI,WAAW,CAAC,KAAK,CAAC;KACvC;IAED,IAAI,cAAc,GAAG,CAAC,EAAE;QACtB,IAAI,cAAc,GAAG,cAAc,GAAG,gBAAgB,CAAC;QACvD,KAAK,IAAI,MAAM,IAAI,OAAO,EAAE;YAC1B,IAAI,WAAW,GAAG,MAAM,CAAC,YAAY,CAAC;YACtC,WAAW,CAAC,KAAK,IAAI,cAAc,CAAC;SACrC;KACF;IAED,OAAO,OAAO,CAAC;AACjB,CAAC;AAED;;;GAGG;AACH,SAAS,WAAW,CAAC,IAAkB,EAAE,SAAiB;IACxD,OAAO,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,SAAS,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,SAAS,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,kDAAkD;AACzH,CAAC"}
|
|
@@ -1,13 +1,30 @@
|
|
|
1
1
|
import { generateSpectrum } from 'spectrum-generator';
|
|
2
|
-
|
|
3
|
-
|
|
4
|
-
|
|
2
|
+
import { convertWidthToPPM } from './util/convertWidthToPPM';
|
|
3
|
+
export function peaksToXY(peaks, options) {
|
|
4
|
+
const { frequency, nbPoints = 1024, shape } = options;
|
|
5
|
+
const newPeaks = convertWidthToPPM(peaks, { frequency });
|
|
6
|
+
return generateSpectrum(newPeaks, {
|
|
5
7
|
generator: {
|
|
6
|
-
|
|
7
|
-
to,
|
|
8
|
+
...getFromTo(newPeaks, options),
|
|
8
9
|
nbPoints,
|
|
9
10
|
shape,
|
|
10
11
|
},
|
|
11
12
|
});
|
|
12
13
|
}
|
|
14
|
+
function getFromTo(newPeaks, options) {
|
|
15
|
+
if ('to' in options && 'from' in options) {
|
|
16
|
+
return {
|
|
17
|
+
from: options.from,
|
|
18
|
+
to: options.to,
|
|
19
|
+
};
|
|
20
|
+
}
|
|
21
|
+
newPeaks.sort((a, b) => a.x - b.x);
|
|
22
|
+
const firstPeak = newPeaks[0];
|
|
23
|
+
const lastPeak = newPeaks[newPeaks.length - 1];
|
|
24
|
+
const { from = firstPeak.x - firstPeak.width * 2, to = lastPeak.x + lastPeak.width * 2, } = options;
|
|
25
|
+
return {
|
|
26
|
+
from,
|
|
27
|
+
to,
|
|
28
|
+
};
|
|
29
|
+
}
|
|
13
30
|
//# sourceMappingURL=peaksToXY.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"peaksToXY.js","sourceRoot":"","sources":["../../src/peaks/peaksToXY.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"peaksToXY.js","sourceRoot":"","sources":["../../src/peaks/peaksToXY.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,gBAAgB,EAAe,MAAM,oBAAoB,CAAC;AAGnE,OAAO,EAAE,iBAAiB,EAAE,MAAM,0BAA0B,CAAC;AAuB7D,MAAM,UAAU,SAAS,CAAC,KAAkB,EAAE,OAAyB;IACrE,MAAM,EAAE,SAAS,EAAE,QAAQ,GAAG,IAAI,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC;IACtD,MAAM,QAAQ,GAAG,iBAAiB,CAAC,KAAK,EAAE,EAAE,SAAS,EAAE,CAAC,CAAC;IAEzD,OAAO,gBAAgB,CAAC,QAAQ,EAAE;QAChC,SAAS,EAAE;YACT,GAAG,SAAS,CAAC,QAAQ,EAAE,OAAO,CAAC;YAC/B,QAAQ;YACR,KAAK;SACN;KACF,CAAC,CAAC;AACL,CAAC;AAED,SAAS,SAAS,CAAC,QAAqB,EAAE,OAAyB;IACjE,IAAI,IAAI,IAAI,OAAO,IAAI,MAAM,IAAI,OAAO,EAAE;QACxC,OAAO;YACL,IAAI,EAAE,OAAO,CAAC,IAAI;YAClB,EAAE,EAAE,OAAO,CAAC,EAAE;SACf,CAAC;KACH;IAED,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;IACnC,MAAM,SAAS,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC;IAC9B,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;IAE/C,MAAM,EACJ,IAAI,GAAG,SAAS,CAAC,CAAC,GAAG,SAAS,CAAC,KAAK,GAAG,CAAC,EACxC,EAAE,GAAG,QAAQ,CAAC,CAAC,GAAG,QAAQ,CAAC,KAAK,GAAG,CAAC,GACrC,GAAG,OAAO,CAAC;IAEZ,OAAO;QACL,IAAI;QACJ,EAAE;KACH,CAAC;AACJ,CAAC"}
|
|
@@ -0,0 +1,30 @@
|
|
|
1
|
+
/**
|
|
2
|
+
* convert width and fwhm to ppm
|
|
3
|
+
*/
|
|
4
|
+
export function convertWidth(peaks, options) {
|
|
5
|
+
const { frequency, convertTo, output = JSON.parse(JSON.stringify(peaks)), } = options;
|
|
6
|
+
const convert = getConverter(convertTo, frequency);
|
|
7
|
+
for (const peak of output) {
|
|
8
|
+
peak.width = convert(peak.width);
|
|
9
|
+
if (hasShape(peak)) {
|
|
10
|
+
if (peak.shape.fwhm) {
|
|
11
|
+
peak.shape.fwhm = convert(peak.shape.fwhm);
|
|
12
|
+
}
|
|
13
|
+
}
|
|
14
|
+
}
|
|
15
|
+
return output;
|
|
16
|
+
}
|
|
17
|
+
function hasShape(peak) {
|
|
18
|
+
return 'shape' in peak;
|
|
19
|
+
}
|
|
20
|
+
function getConverter(convertTo, frequency) {
|
|
21
|
+
switch (convertTo) {
|
|
22
|
+
case 'ppm':
|
|
23
|
+
return (x) => x / frequency;
|
|
24
|
+
case 'hz':
|
|
25
|
+
return (x) => x * frequency;
|
|
26
|
+
default:
|
|
27
|
+
throw new Error(`Does not support convert to ${convertTo}`);
|
|
28
|
+
}
|
|
29
|
+
}
|
|
30
|
+
//# sourceMappingURL=convertWidth.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"convertWidth.js","sourceRoot":"","sources":["../../../src/peaks/util/convertWidth.ts"],"names":[],"mappings":"AAUA;;GAEG;AACH,MAAM,UAAU,YAAY,CAAC,KAAkB,EAAE,OAA4B;IAC3E,MAAM,EACJ,SAAS,EACT,SAAS,EACT,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,GAC3C,GAAG,OAAO,CAAC;IAEZ,MAAM,OAAO,GAAG,YAAY,CAAC,SAAS,EAAE,SAAS,CAAC,CAAC;IAEnD,KAAK,MAAM,IAAI,IAAI,MAAM,EAAE;QACzB,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;QACjC,IAAI,QAAQ,CAAC,IAAI,CAAC,EAAE;YAClB,IAAI,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE;gBACnB,IAAI,CAAC,KAAK,CAAC,IAAI,GAAG,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;aAC5C;SACF;KACF;IACD,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,SAAS,QAAQ,CAAC,IAAe;IAC/B,OAAO,OAAO,IAAI,IAAI,CAAC;AACzB,CAAC;AAED,SAAS,YAAY,CAAC,SAAiB,EAAE,SAAiB;IACxD,QAAQ,SAAS,EAAE;QACjB,KAAK,KAAK;YACR,OAAO,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAAG,SAAS,CAAC;QACtC,KAAK,IAAI;YACP,OAAO,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAAG,SAAS,CAAC;QACtC;YACE,MAAM,IAAI,KAAK,CAAC,+BAA+B,SAAS,EAAE,CAAC,CAAC;KAC/D;AACH,CAAC"}
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"convertWidthToHz.js","sourceRoot":"","sources":["../../../src/peaks/util/convertWidthToHz.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,YAAY,EAAuB,MAAM,gBAAgB,CAAC;AAInE,MAAM,UAAU,gBAAgB,CAAC,KAAkB,EAAE,OAAuB;IAC1E,OAAO,YAAY,CAAC,KAAK,EAAE,EAAE,GAAG,OAAO,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;AAC9D,CAAC"}
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"convertWidthToPPM.js","sourceRoot":"","sources":["../../../src/peaks/util/convertWidthToPPM.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,YAAY,EAAE,MAAM,gBAAgB,CAAC;AAG9C,MAAM,UAAU,iBAAiB,CAAC,KAAkB,EAAE,OAAuB;IAC3E,OAAO,YAAY,CAAC,KAAK,EAAE,EAAE,GAAG,OAAO,EAAE,SAAS,EAAE,KAAK,EAAE,CAAC,CAAC;AAC/D,CAAC"}
|
|
File without changes
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"joinRanges.js","sourceRoot":"","sources":["../../../src/ranges/utils/joinRanges.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,UAAU,CAAC,MAAkB;IAC3C,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;IAEvC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;QAC1C,MAAM,YAAY,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC;QAC/B,MAAM,SAAS,GAAG,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;QAEhC,IAAI,YAAY,CAAC,EAAE,GAAG,SAAS,CAAC,IAAI,EAAE;YACpC,YAAY,CAAC,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,EAAE,YAAY,CAAC,EAAE,CAAC,CAAC;YAC1D,IAAI,YAAY,CAAC,OAAO,IAAI,SAAS,CAAC,OAAO,EAAE;gBAC7C,YAAY,CAAC,OAAO,GAAG,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,CAAC;aACvE;YACD,IAAI,YAAY,CAAC,WAAW,KAAK,SAAS,EAAE;gBAC1C,YAAY,CAAC,WAAW,IAAI,SAAS,CAAC,WAAW,IAAI,CAAC,CAAC;aACxD;YACD,MAAM,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC;YACxB,CAAC,EAAE,CAAC;SACL;KACF;IAED,OAAO,MAAM,CAAC;AAChB,CAAC"}
|
|
@@ -137,6 +137,7 @@ export default {
|
|
|
137
137
|
// Before to return, change the units of peaksComp from Hz to PPM again
|
|
138
138
|
for (let peakComp of signal.peaksComp) {
|
|
139
139
|
peakComp.x /= signal.observe;
|
|
140
|
+
peakComp.width *= signal.observe;
|
|
140
141
|
}
|
|
141
142
|
return signal;
|
|
142
143
|
},
|
|
@@ -375,7 +376,7 @@ function symmetrize(signalInput, maxError, iteration, key) {
|
|
|
375
376
|
peaks[i] = {
|
|
376
377
|
x: peak[jAxis] * newSignal.observe,
|
|
377
378
|
intensity: peak[intensity],
|
|
378
|
-
width: peak.width,
|
|
379
|
+
width: peak.width / newSignal.observe,
|
|
379
380
|
};
|
|
380
381
|
}
|
|
381
382
|
// Join the peaks that are closer than 0.25 Hz
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
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@@ -1,7 +1,8 @@
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1
1
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import { gsd, optimizePeaks, joinBroadPeaks } from 'ml-gsd';
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2
2
|
import { xyExtract, xNoiseSanPlot, xAbsoluteMedian, } from 'ml-spectra-processing';
|
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3
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-
|
|
4
|
-
|
|
3
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+
import { convertWidthToHz } from '../peaks/util/convertWidthToHz';
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4
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+
export function xyAutoPeaksPicking(data, options) {
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5
|
+
const { from, to, frequency, noiseLevel, thresholdFactor = 3, minMaxRatio = 0.05, broadRatio = 0.00025, useSanPlot = false, smoothY = true, optimize = false, factorLimits = 4, realTopDetection = true, shape = { kind: 'gaussian' }, optimization = { kind: 'lm' }, broadWidth = 0.25, sgOptions = {}, direction = 'positive', } = options;
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|
5
6
|
const { windowSize = 9, polynomial = 3 } = sgOptions;
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|
6
7
|
if (data.x.length < windowSize)
|
|
7
8
|
return [];
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@@ -11,6 +12,7 @@ export function xyAutoPeaksPicking(data, options = {}) {
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|
11
12
|
const cutOff = getCutOff(data.y, { noiseLevel, useSanPlot, thresholdFactor });
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12
13
|
let getPeakOptions = {
|
|
13
14
|
shape,
|
|
15
|
+
frequency,
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14
16
|
broadWidth,
|
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15
17
|
optimize,
|
|
16
18
|
factorLimits,
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@@ -49,7 +51,7 @@ function getNegativePeaks(data, cutOff, getPeakOptions) {
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|
|
49
51
|
return getPeakList(data, getPeakOptions);
|
|
50
52
|
}
|
|
51
53
|
function getPeakList(data, options) {
|
|
52
|
-
const { shape, broadWidth, optimize, maxCriteria, factorLimits, sgOptions, minMaxRatio, broadRatio, noiseLevel, smoothY, optimization, realTopDetection, } = options;
|
|
54
|
+
const { shape, frequency, broadWidth, optimize, maxCriteria, factorLimits, sgOptions, minMaxRatio, broadRatio, noiseLevel, smoothY, optimization, realTopDetection, } = options;
|
|
53
55
|
let peakList = gsd(data, {
|
|
54
56
|
shape,
|
|
55
57
|
sgOptions,
|
|
@@ -67,14 +69,13 @@ function getPeakList(data, options) {
|
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|
optimization,
|
|
68
70
|
});
|
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69
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|
}
|
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-
|
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|
-
|
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+
return convertWidthToHz(optimize
|
|
73
|
+
? optimizePeaks(data, peakList, {
|
|
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|
shape,
|
|
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|
factorLimits,
|
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|
optimization,
|
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75
|
-
})
|
|
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-
|
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|
-
return peakList;
|
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|
+
})
|
|
78
|
+
: peakList, { frequency });
|
|
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79
|
}
|
|
79
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|
function getCutOff(data, options) {
|
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80
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|
const { noiseLevel, useSanPlot, thresholdFactor } = options;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"xyAutoPeaksPicking.js","sourceRoot":"","sources":["../../src/xy/xyAutoPeaksPicking.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,GAAG,EAAE,aAAa,EAAE,cAAc,EAAE,MAAM,QAAQ,CAAC;AAM5D,OAAO,EACL,SAAS,EACT,aAAa,EACb,eAAe,GAChB,MAAM,uBAAuB,CAAC;
|
|
1
|
+
{"version":3,"file":"xyAutoPeaksPicking.js","sourceRoot":"","sources":["../../src/xy/xyAutoPeaksPicking.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,GAAG,EAAE,aAAa,EAAE,cAAc,EAAE,MAAM,QAAQ,CAAC;AAM5D,OAAO,EACL,SAAS,EACT,aAAa,EACb,eAAe,GAChB,MAAM,uBAAuB,CAAC;AAG/B,OAAO,EAAE,gBAAgB,EAAE,MAAM,gCAAgC,CAAC;AA4DlE,MAAM,UAAU,kBAAkB,CAChC,IAAY,EACZ,OAAkC;IAElC,MAAM,EACJ,IAAI,EACJ,EAAE,EACF,SAAS,EACT,UAAU,EACV,eAAe,GAAG,CAAC,EACnB,WAAW,GAAG,IAAI,EAClB,UAAU,GAAG,OAAO,EACpB,UAAU,GAAG,KAAK,EAClB,OAAO,GAAG,IAAI,EACd,QAAQ,GAAG,KAAK,EAChB,YAAY,GAAG,CAAC,EAChB,gBAAgB,GAAG,IAAI,EACvB,KAAK,GAAG,EAAE,IAAI,EAAE,UAAU,EAAE,EAC5B,YAAY,GAAG,EAAE,IAAI,EAAE,IAAI,EAAE,EAC7B,UAAU,GAAG,IAAI,EACjB,SAAS,GAAG,EAAE,EACd,SAAS,GAAG,UAAU,GACvB,GAAG,OAAO,CAAC;IAEZ,MAAM,EAAE,UAAU,GAAG,CAAC,EAAE,UAAU,GAAG,CAAC,EAAE,GAAG,SAAS,CAAC;IAErD,IAAI,IAAI,CAAC,CAAC,CAAC,MAAM,GAAG,UAAU;QAAE,OAAO,EAAE,CAAC;IAE1C,IAAI,IAAI,KAAK,SAAS,IAAI,EAAE,KAAK,SAAS,EAAE;QAC1C,IAAI,GAAG,SAAS,CAAC,IAAI,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,CAAC;KACnD;IAED,MAAM,MAAM,GAAG,SAAS,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,UAAU,EAAE,UAAU,EAAE,eAAe,EAAE,CAAC,CAAC;IAE9E,IAAI,cAAc,GAAuB;QACvC,KAAK;QACL,SAAS;QACT,UAAU;QACV,QAAQ;QACR,YAAY;QACZ,WAAW,EAAE,IAAI;QACjB,SAAS,EAAE,EAAE,UAAU,EAAE,UAAU,EAAE;QACrC,WAAW;QACX,UAAU;QACV,UAAU,EAAE,MAAM,CAAC,QAAQ;QAC3B,OAAO;QACP,YAAY;QACZ,gBAAgB;KACjB,CAAC;IAEF,QAAQ,SAAS,EAAE;QACjB,KAAK,UAAU,CAAC,CAAC;YACf,OAAO,WAAW,CAAC,IAAI,EAAE,cAAc,CAAC,CAAC;SAC1C;QACD,KAAK,UAAU,CAAC,CAAC;YACf,OAAO,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,cAAc,CAAC,CAAC;SACvD;QACD,KAAK,MAAM,CAAC,CAAC;YACX,OAAO;gBACL,GAAG,WAAW,CAAC,IAAI,EAAE,cAAc,CAAC;gBACpC,GAAG,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,cAAc,CAAC;aAClD,CAAC;SACH;QACD,OAAO,CAAC,CAAC;YACP,MAAM,SAAS,GAAU,SAAS,CAAC;YACnC,4EAA4E;YAC5E,MAAM,KAAK,CAAC,wBAAwB,SAAS,EAAE,CAAC,CAAC;SAClD;KACF;AACH,CAAC;AAED,SAAS,gBAAgB,CACvB,IAAY,EACZ,MAA4B,EAC5B,cAAkC;IAElC,cAAc,CAAC,UAAU,GAAG,MAAM,CAAC,QAAQ,CAAC;IAC5C,cAAc,CAAC,WAAW,GAAG,KAAK,CAAC;IACnC,OAAO,WAAW,CAAC,IAAI,EAAE,cAAc,CAAC,CAAC;AAC3C,CAAC;AAED,SAAS,WAAW,CAAC,IAAY,EAAE,OAA2B;IAC5D,MAAM,EACJ,KAAK,EACL,SAAS,EACT,UAAU,EACV,QAAQ,EACR,WAAW,EACX,YAAY,EACZ,SAAS,EACT,WAAW,EACX,UAAU,EACV,UAAU,EACV,OAAO,EACP,YAAY,EACZ,gBAAgB,GACjB,GAAG,OAAO,CAAC;IAEZ,IAAI,QAAQ,GAAG,GAAG,CAAC,IAAI,EAAE;QACvB,KAAK;QACL,SAAS;QACT,WAAW;QACX,WAAW;QACX,UAAU;QACV,OAAO;QACP,gBAAgB;KACjB,CAAC,CAAC;IAEH,IAAI,UAAU,EAAE;QACd,QAAQ,GAAG,cAAc,CAAC,QAAQ,EAAE;YAClC,UAAU;YACV,UAAU;YACV,KAAK;YACL,YAAY;SACb,CAAC,CAAC;KACJ;IAED,OAAO,gBAAgB,CACrB,QAAQ;QACN,CAAC,CAAC,aAAa,CAAC,IAAI,EAAE,QAAQ,EAAE;YAC5B,KAAK;YACL,YAAY;YACZ,YAAY;SACb,CAAC;QACJ,CAAC,CAAC,QAAQ,EACZ,EAAE,SAAS,EAAE,CACd,CAAC;AACJ,CAAC;AAED,SAAS,SAAS,CAAC,IAA6B,EAAE,OAAyB;IACzE,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,eAAe,EAAE,GAAG,OAAO,CAAC;IAE5D,MAAM,YAAY,GAAG,CAAC,UAAkB,EAAE,EAAE,CAC1C,OAAO,UAAU,KAAK,QAAQ;QAC5B,CAAC,CAAC,EAAE,QAAQ,EAAE,UAAU,EAAE,QAAQ,EAAE,CAAC,UAAU,EAAE;QACjD,CAAC,CAAC,UAAU,CAAC;IAEjB,IAAI,UAAU,EAAE;QACd,OAAO,YAAY,CAAC,UAAU,CAAC,CAAC;KACjC;SAAM;QACL,OAAO,UAAU;YACf,CAAC,CAAC,aAAa,CAAC,IAAI,EAAE,EAAE,SAAS,EAAE,eAAe,EAAE,CAAC;YACrD,CAAC,CAAC,YAAY,CAAC,eAAe,CAAC,IAAI,CAAC,GAAG,eAAe,CAAC,CAAC;KAC3D;AACH,CAAC"}
|
|
@@ -4,7 +4,7 @@ import { xyAutoPeaksPicking } from './xyAutoPeaksPicking';
|
|
|
4
4
|
/**
|
|
5
5
|
* Detect peaks, optimize parameters and compile multiplicity if required.
|
|
6
6
|
*/
|
|
7
|
-
export function xyAutoRangesPicking(data, options
|
|
7
|
+
export function xyAutoRangesPicking(data, options) {
|
|
8
8
|
let peaks = xyAutoPeaksPicking(data, options.peakPicking);
|
|
9
9
|
peaks = peaksFilterImpurities(peaks, options.impurities);
|
|
10
10
|
return peaksToRanges(data, peaks, options.ranges);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"xyAutoRangesPicking.js","sourceRoot":"","sources":["../../src/xy/xyAutoRangesPicking.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,qBAAqB,EAAE,MAAM,gCAAgC,CAAC;AAEvE,OAAO,EAAwB,aAAa,EAAE,MAAM,wBAAwB,CAAC;AAE7E,OAAO,EAAE,kBAAkB,EAAE,MAAM,sBAAsB,CAAC;AAS1D;;GAEG;AACH,MAAM,UAAU,mBAAmB,CACjC,IAAY,EACZ,
|
|
1
|
+
{"version":3,"file":"xyAutoRangesPicking.js","sourceRoot":"","sources":["../../src/xy/xyAutoRangesPicking.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,qBAAqB,EAAE,MAAM,gCAAgC,CAAC;AAEvE,OAAO,EAAwB,aAAa,EAAE,MAAM,wBAAwB,CAAC;AAE7E,OAAO,EAAE,kBAAkB,EAAE,MAAM,sBAAsB,CAAC;AAS1D;;GAEG;AACH,MAAM,UAAU,mBAAmB,CACjC,IAAY,EACZ,OAAmC;IAEnC,IAAI,KAAK,GAAG,kBAAkB,CAAC,IAAI,EAAE,OAAO,CAAC,WAAW,CAAC,CAAC;IAC1D,KAAK,GAAG,qBAAqB,CAAC,KAAK,EAAE,OAAO,CAAC,UAAU,CAAC,CAAC;IACzD,OAAO,aAAa,CAAC,IAAI,EAAE,KAAK,EAAE,OAAO,CAAC,MAAM,CAAC,CAAC;AACpD,CAAC"}
|
|
@@ -1,5 +1,13 @@
|
|
|
1
1
|
import { optimizePeaks } from 'ml-gsd';
|
|
2
|
+
import { convertWidthToHz } from '../peaks/util/convertWidthToHz';
|
|
3
|
+
import { convertWidthToPPM } from '../peaks/util/convertWidthToPPM';
|
|
2
4
|
export function xyPeaksOptimization(data, peaks, options) {
|
|
3
|
-
|
|
5
|
+
const { frequency } = options;
|
|
6
|
+
const newPeaks = convertWidthToPPM(peaks, { frequency });
|
|
7
|
+
const optimizedPeaks = optimizePeaks(data, newPeaks, options);
|
|
8
|
+
return convertWidthToHz(optimizedPeaks, {
|
|
9
|
+
frequency,
|
|
10
|
+
output: optimizedPeaks,
|
|
11
|
+
});
|
|
4
12
|
}
|
|
5
13
|
//# sourceMappingURL=xyPeaksOptimization.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"xyPeaksOptimization.js","sourceRoot":"","sources":["../../src/xy/xyPeaksOptimization.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,aAAa,EAAwB,MAAM,QAAQ,CAAC;AAE7D,MAAM,UAAU,mBAAmB,CACjC,IAAY,EACZ,KAAoB,EACpB,
|
|
1
|
+
{"version":3,"file":"xyPeaksOptimization.js","sourceRoot":"","sources":["../../src/xy/xyPeaksOptimization.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,aAAa,EAAwB,MAAM,QAAQ,CAAC;AAE7D,OAAO,EAAE,gBAAgB,EAAE,MAAM,gCAAgC,CAAC;AAClE,OAAO,EAAE,iBAAiB,EAAE,MAAM,iCAAiC,CAAC;AAQpE,MAAM,UAAU,mBAAmB,CACjC,IAAY,EACZ,KAAoB,EACpB,OAAmC;IAEnC,MAAM,EAAE,SAAS,EAAE,GAAG,OAAO,CAAC;IAC9B,MAAM,QAAQ,GAAG,iBAAiB,CAAC,KAAK,EAAE,EAAE,SAAS,EAAE,CAAC,CAAC;IACzD,MAAM,cAAc,GAAG,aAAa,CAAC,IAAI,EAAE,QAAQ,EAAE,OAAO,CAAC,CAAC;IAC9D,OAAO,gBAAgB,CAAC,cAAc,EAAE;QACtC,SAAS;QACT,MAAM,EAAE,cAAc;KACvB,CAAC,CAAC;AACL,CAAC"}
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import simpleClustering from 'ml-simple-clustering';
|
|
2
|
-
import jAnalyzer from '../
|
|
2
|
+
import jAnalyzer from '../signals/utils/jAnalyzer';
|
|
3
3
|
import { formatZones } from './util/formatZone';
|
|
4
4
|
export function xyzJResAnalyzer(signals, options = {}) {
|
|
5
5
|
let { reference = 0, getZones = false, referenceMaxShiftError = 0.08, tolerances = [10, 100], nuclei = ['1H', '1H'], observedFrequencies = [400, 400], jAnalyzer = {
|
|
@@ -30,6 +30,7 @@ function compilePattern(signals, options) {
|
|
|
30
30
|
dx: signals[0].x.resolution,
|
|
31
31
|
dy: signals[0].y.resolution,
|
|
32
32
|
};
|
|
33
|
+
const defaultWidth = 0.02 * observedFrequencies[0];
|
|
33
34
|
const newSignals = JSON.parse(JSON.stringify(signals));
|
|
34
35
|
//adapt to 1D jAnalyzer
|
|
35
36
|
for (const signal of newSignals) {
|
|
@@ -45,7 +46,7 @@ function compilePattern(signals, options) {
|
|
|
45
46
|
};
|
|
46
47
|
for (const peak of peaks) {
|
|
47
48
|
if (!peak.width)
|
|
48
|
-
peak.width =
|
|
49
|
+
peak.width = defaultWidth;
|
|
49
50
|
}
|
|
50
51
|
peaks.sort((a, b) => a.y - b.y);
|
|
51
52
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"xyzJResAnalyzer.js","sourceRoot":"","sources":["../../src/xyz/xyzJResAnalyzer.ts"],"names":[],"mappings":"AACA,OAAO,gBAAgB,MAAM,sBAAsB,CAAC;AAGpD,OAAO,SAAS,MAAM,
|
|
1
|
+
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package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "nmr-processing",
|
|
3
|
-
"version": "
|
|
3
|
+
"version": "9.0.2",
|
|
4
4
|
"description": "Pure functions allowing to process NMR spectra.",
|
|
5
5
|
"main": "./lib/index.js",
|
|
6
6
|
"module": "./lib-esm/index.js",
|
|
@@ -69,7 +69,7 @@
|
|
|
69
69
|
"ml-matrix": "^6.10.2",
|
|
70
70
|
"ml-matrix-convolution": "^1.0.0",
|
|
71
71
|
"ml-matrix-peaks-finder": "^1.0.0",
|
|
72
|
-
"ml-peak-shape-generator": "^4.1.
|
|
72
|
+
"ml-peak-shape-generator": "^4.1.2",
|
|
73
73
|
"ml-simple-clustering": "^0.1.0",
|
|
74
74
|
"ml-sparse-matrix": "^2.1.0",
|
|
75
75
|
"ml-spectra-processing": "^11.12.0",
|
package/src/peaks/peakToXY.ts
CHANGED
|
@@ -1,8 +1,6 @@
|
|
|
1
|
-
import {
|
|
2
|
-
import {
|
|
1
|
+
import { NMRPeak1D } from './NMRPeak1D';
|
|
2
|
+
import { peaksToXY, PeaksToXYOptions } from './peaksToXY';
|
|
3
3
|
|
|
4
|
-
|
|
5
|
-
|
|
6
|
-
export function peakToXY(peak: PeakXYWidth, options: OptionsSG1D = {}) {
|
|
4
|
+
export function peakToXY(peak: NMRPeak1D, options: PeaksToXYOptions) {
|
|
7
5
|
return peaksToXY([peak], options);
|
|
8
6
|
}
|