nmr-processing 8.3.0 → 8.5.0
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/README.md +23 -3
- package/lib/index.d.ts +0 -1
- package/lib/index.js +0 -1
- package/lib/index.js.map +1 -1
- package/lib/signals/signalsJoin.js +4 -3
- package/lib/signals/signalsJoin.js.map +1 -1
- package/lib/xy/xyAutoPeaksPicking.d.ts +3 -3
- package/lib/xy/xyAutoPeaksPicking.js +26 -9
- package/lib/xy/xyAutoPeaksPicking.js.map +1 -1
- package/lib-esm/index.js +0 -1
- package/lib-esm/index.js.map +1 -1
- package/lib-esm/signals/signalsJoin.js +4 -3
- package/lib-esm/signals/signalsJoin.js.map +1 -1
- package/lib-esm/xy/xyAutoPeaksPicking.js +26 -9
- package/lib-esm/xy/xyAutoPeaksPicking.js.map +1 -1
- package/package.json +8 -8
- package/src/index.ts +0 -1
- package/src/signals/signalsJoin.ts +5 -7
- package/src/xy/xyAutoPeaksPicking.ts +35 -12
package/README.md
CHANGED
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@@ -5,7 +5,25 @@
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[![Test coverage][codecov-image]][codecov-url]
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[![npm download][download-image]][download-url]
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-
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## Introduction
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The goal is to have [pure functions](https://medium.com/@jamesjefferyuk/javascript-what-are-pure-functions-4d4d5392d49c) allowing to process NMR spectra.
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All the functions use only native javascript object and will not use any classes.
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The functions are sorted by category on which they apply. Currently the categories are:
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- xy
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- xyz
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- peaks
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- signals
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- ranges
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- prediction
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- assignment
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## Debug
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A viewer for xy data is available in `/web`
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## Installation
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@@ -14,12 +32,14 @@
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## Usage
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```js
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import {
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import { library } from 'nmr-processing';
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const result =
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const result = library(args);
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// result is ...
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```
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## [API Documentation](https://cheminfo.github.io/nmr-processing/)
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## License
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[MIT](./LICENSE)
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package/lib/index.d.ts
CHANGED
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@@ -30,7 +30,6 @@ export * from './databases/protonImpurities';
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export * from './peaks/solventSuppression';
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export * from './ranges/markSolventSignal';
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export * from './apodization/apodization';
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export * from './apodization/compose';
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export type { NMRSignal1D } from './signals/NMRSignal1D';
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export type { NMRSignal2D, Signal2DProjection } from './xyz/NMRSignal2D';
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export type { NMRRange } from './xy/NMRRange';
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package/lib/index.js
CHANGED
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@@ -46,5 +46,4 @@ __exportStar(require("./databases/protonImpurities"), exports);
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__exportStar(require("./peaks/solventSuppression"), exports);
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__exportStar(require("./ranges/markSolventSignal"), exports);
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__exportStar(require("./apodization/apodization"), exports);
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__exportStar(require("./apodization/compose"), exports);
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//# sourceMappingURL=index.js.map
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package/lib/index.js.map
CHANGED
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@@ -1 +1 @@
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;AAAA,qDAAmC;AACnC,yDAAuC;AACvC,+DAA6C;AAE7C,gEAA8C;AAE9C,6DAA2C;AAC3C,6DAA2C;AAC3C,2DAAyC;AACzC,2DAAyC;AACzC,2DAAyC;AACzC,0DAAwC;AACxC,iEAA+C;AAE/C,gEAA8C;AAC9C,iEAA+C;AAC/C,8DAA4C;AAE5C,uDAAqC;AACrC,sDAAoC;AAEpC,4DAA0C;AAC1C,wDAAsC;AACtC,yDAAuC;AAEvC,wDAAsC;AACtC,8DAA4C;AAC5C,2DAAyC;AAEzC,0DAAwC;AACxC,2DAAyC;AAEzC,4DAA0C;AAC1C,wDAAsC;AAEtC,0DAAwC;AACxC,+DAA6C;AAC7C,+DAA6C;AAE7C,6DAA2C;AAC3C,6DAA2C;AAE3C,4DAA0C"}
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@@ -85,9 +85,10 @@ function signalsJoin(signals, options = {}) {
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ignoreDiaIDs,
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});
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if (newSignal.js) {
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newSignal.multiplicity =
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newSignal.multiplicity =
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newSignal.js.length > 0
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? newSignal.js.map((j) => j.multiplicity).join('')
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: 's';
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}
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return newSignal;
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})
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{"version":3,"file":"signalsJoin.js","sourceRoot":"","sources":["../../src/signals/signalsJoin.ts"],"names":[],"mappings":";;;;;;AAAA,kEAAiC;AACjC,gEAA+B;AAE/B,uEAAoE;AAwBpE,MAAM,aAAa,GAAG,CAAC,CAAS,EAAE,CAAS,EAAE,EAAE,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC;AACnE,MAAM,0BAA0B,GAAG,CACjC,CAA0B,EAC1B,CAA0B,EAC1B,EAAE;IACF,MAAM,EAAE,GAAG,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,UAAU,EAAE,CAAC;IAClD,MAAM,EAAE,GAAG,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,UAAU,EAAE,CAAC;IAClD,OAAO,aAAa,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC;AAC/B,CAAC,CAAC;AACF,SAAS,iBAAiB,CACxB,OAAsB;IAEtB,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;QAC5B,IAAI,CAAC,MAAM,CAAC,EAAE;YAAE,MAAM,IAAI,KAAK,CAAC,iBAAiB,CAAC,CAAC;QACnD,IAAI,CAAC,MAAM,CAAC,MAAM;YAAE,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAC;QAC3D,KAAK,MAAM,SAAS,IAAI,MAAM,CAAC,EAAE,EAAE;YACjC,IAAI,CAAC,SAAS,CAAC,MAAM;gBAAE,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAC;YAC9D,IAAI,CAAC,SAAS,CAAC,UAAU;gBAAE,MAAM,IAAI,KAAK,CAAC,yBAAyB,CAAC,CAAC;SACvE;KACF;AACH,CAAC;AACD;;GAEG;AACH,SAAgB,WAAW,CACzB,OAAsB,EACtB,UAA8B,EAAE;IAEhC,iBAAiB,CAAC,OAAO,CAAC,CAAC;IAC3B,MAAM,EAAE,aAAa,GAAG,EAAE,EAAE,GAAG,OAAO,CAAC;IACvC,MAAM,EAAE,SAAS,EAAE,YAAY,EAAE,GAAG,aAAa,CAAC;IAClD,0BAA0B;IAE1B,MAAM,WAAW,GAA8B,IAAI,CAAC,KAAK,CACvD,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,CACxB,CAAC;IAEF,MAAM,cAAc,GAA8C,EAAE,CAAC;IAErE,KAAK,IAAI,MAAM,IAAI,WAAW,EAAE;QAC9B,MAAM,CAAC,EAAE,GAAG,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC,0BAA0B,CAAC,CAAC;QACvD,MAAM,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;QAC1C,IAAI,EAAE,GAAG,GAAG,SAAS,IAAI,MAAM,CAAC,EAAE;aAC/B,GAAG,CACF,CAAC,CAA0B,EAAE,EAAE,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,UAAU,EAAE,CACxE;aACA,IAAI,CAAC,aAAa,CAAC;aACnB,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;QACf,IAAI,CAAC,cAAc,CAAC,EAAE,CAAC,EAAE;YACvB,cAAc,CAAC,EAAE,CAAC,GAAG,EAAE,CAAC;SACzB;QACD,cAAc,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;KACjC;IACD,sEAAsE;IACtE,IAAI,UAAU,GAA8B,EAAE,CAAC;IAC/C,MAAM,CAAC,MAAM,CAAC,cAAc,CAAC,CAAC,OAAO,CAAC,CAAC,KAAK,EAAE,EAAE;QAC9C,2DAA2D;QAC3D,IAAI,EAAE,GAA8B,EAAE,CAAC;QACvC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC3C,MAAM,QAAQ,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;YAChC,EAAE,CAAC,IAAI,CAAC;gBACN,MAAM,EAAE,QAAQ,CAAC,MAAM;gBACvB,UAAU,EAAE,QAAQ,CAAC,UAAU;gBAC/B,YAAY,EAAE,QAAQ,CAAC,YAAY;gBACnC,QAAQ,EAAE,IAAA,uBAAI,EAAC,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC;aACzD,CAAC,CAAC;SACJ;QACD,IAAI,MAAM,GAA4B;YACpC,OAAO,EAAE,IAAA,sBAAG,EAAC,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,OAAO,IAAI,CAAC,CAAC,CAAC;YACpD,KAAK,EAAE,IAAA,uBAAI,EAAC,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;YAC5C,MAAM,EAAE,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM;YACvB,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,KAAK,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE;YACnD,EAAE;SACH,CAAC;QAEF,MAAM,UAAU,GAAG,KAAK;aACrB,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,UAAU,CAAC;aAC9B,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC;aACtB,IAAI,CAAC,GAAG,CAAC,CAAC;QAEb,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC;YAAE,MAAM,CAAC,UAAU,GAAG,UAAU,CAAC;QAE1D,UAAU,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;IAC1B,CAAC,CAAC,CAAC;IAEH,UAAU,GAAG,UAAU;SACpB,GAAG,CAAC,CAAC,MAAM,EAAE,EAAE;QACd,IAAI,SAAS,GAAG,IAAA,yCAAmB,EAAC,MAAM,EAAE;YAC1C,SAAS;YACT,YAAY;SACb,CAA4B,CAAC;QAC9B,IAAI,SAAS,CAAC,EAAE,EAAE;YAChB,SAAS,CAAC,YAAY;gBACpB,SAAS,CAAC,EAAE,CAAC,MAAM,GAAG,CAAC;oBACrB,CAAC,CAAC,SAAS,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC;oBAClD,CAAC,CAAC,GAAG,CAAC;SACX;QACD,OAAO,SAAS,CAAC;IACnB,CAAC,CAAC;SACD,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC;IAErC,OAAO,UAAU,CAAC;AACpB,CAAC;AA9ED,kCA8EC"}
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*/
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thresholdFactor?: number;
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/**
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*
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* look for peaks in negative, positive or both sense
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* @default 'positive'
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*/
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direction?: 'negative' | 'positive' | 'both';
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/**
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* If it is true, it calculate the noise level by sanPlot method.
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const ml_gsd_1 = require("ml-gsd");
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const ml_spectra_processing_1 = require("ml-spectra-processing");
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function xyAutoPeaksPicking(data, options = {}) {
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const { from, to, 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 = {},
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const { from, to, 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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const { windowSize = 9, polynomial = 3 } = sgOptions;
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if (data.x.length < windowSize)
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return [];
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if (from !== undefined && to !== undefined) {
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data = (0, ml_spectra_processing_1.xyExtract)(data, { zones: [{ from, to }] });
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}
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if (data.x.length < windowSize)
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return [];
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const cutOff = getCutOff(data.y, { noiseLevel, useSanPlot, thresholdFactor });
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let getPeakOptions = {
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optimization,
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realTopDetection,
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};
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switch (direction) {
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case 'positive': {
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return getPeakList(data, getPeakOptions);
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}
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case 'negative': {
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return getNegativePeaks(data, cutOff, getPeakOptions);
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}
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case 'both': {
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return [
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...getPeakList(data, getPeakOptions),
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...getNegativePeaks(data, cutOff, getPeakOptions),
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];
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}
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default: {
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const unHandled = direction;
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// eslint-disable-next-line @typescript-eslint/restrict-template-expressions
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throw Error(`Unknown distribution ${unHandled}`);
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}
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}
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return peaks;
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}
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exports.xyAutoPeaksPicking = xyAutoPeaksPicking;
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+
function getNegativePeaks(data, cutOff, getPeakOptions) {
|
|
51
|
+
getPeakOptions.noiseLevel = cutOff.negative;
|
|
52
|
+
getPeakOptions.maxCriteria = false;
|
|
53
|
+
return getPeakList(data, getPeakOptions);
|
|
54
|
+
}
|
|
38
55
|
function getPeakList(data, options) {
|
|
39
56
|
const { shape, broadWidth, optimize, maxCriteria, factorLimits, sgOptions, minMaxRatio, broadRatio, noiseLevel, smoothY, optimization, realTopDetection, } = options;
|
|
40
57
|
let peakList = (0, ml_gsd_1.gsd)(data, {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"xyAutoPeaksPicking.js","sourceRoot":"","sources":["../../src/xy/xyAutoPeaksPicking.ts"],"names":[],"mappings":";;;AACA,mCAAgF;AAMhF,iEAI+B;
|
|
1
|
+
{"version":3,"file":"xyAutoPeaksPicking.js","sourceRoot":"","sources":["../../src/xy/xyAutoPeaksPicking.ts"],"names":[],"mappings":";;;AACA,mCAAgF;AAMhF,iEAI+B;AAsD/B,SAAgB,kBAAkB,CAChC,IAAY,EACZ,UAAqC,EAAE;IAEvC,MAAM,EACJ,IAAI,EACJ,EAAE,EACF,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,IAAA,iCAAS,EAAC,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,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;AAnED,gDAmEC;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,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,IAAA,YAAG,EAAC,IAAI,EAAE;QACvB,SAAS;QACT,WAAW;QACX,WAAW;QACX,UAAU;QACV,OAAO;QACP,gBAAgB;KACjB,CAAC,CAAC;IAEH,IAAI,UAAU,EAAE;QACd,QAAQ,GAAG,IAAA,uBAAc,EAAC,QAAQ,EAAE;YAClC,UAAU;YACV,UAAU;YACV,KAAK;YACL,YAAY;SACb,CAAC,CAAC;KACJ;IAED,IAAI,QAAQ,EAAE;QACZ,OAAO,IAAA,sBAAa,EAAC,IAAI,EAAE,QAAQ,EAAE;YACnC,KAAK;YACL,YAAY;YACZ,YAAY;SACb,CAAC,CAAC;KACJ;IAED,OAAO,IAAA,2BAAkB,EAAC,QAAQ,EAAE,EAAE,KAAK,EAAE,CAAC,CAAC;AACjD,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,IAAA,qCAAa,EAAC,IAAI,EAAE,EAAE,SAAS,EAAE,eAAe,EAAE,CAAC;YACrD,CAAC,CAAC,YAAY,CAAC,IAAA,uCAAe,EAAC,IAAI,CAAC,GAAG,eAAe,CAAC,CAAC;KAC3D;AACH,CAAC"}
|
package/lib-esm/index.js
CHANGED
package/lib-esm/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,cAAc,oBAAoB,CAAC;AACnC,cAAc,wBAAwB,CAAC;AACvC,cAAc,8BAA8B,CAAC;AAE7C,cAAc,+BAA+B,CAAC;AAE9C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,gCAAgC,CAAC;AAE/C,cAAc,+BAA+B,CAAC;AAC9C,cAAc,gCAAgC,CAAC;AAC/C,cAAc,6BAA6B,CAAC;AAE5C,cAAc,sBAAsB,CAAC;AACrC,cAAc,qBAAqB,CAAC;AAEpC,cAAc,2BAA2B,CAAC;AAC1C,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AAEvC,cAAc,uBAAuB,CAAC;AACtC,cAAc,6BAA6B,CAAC;AAC5C,cAAc,0BAA0B,CAAC;AAEzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,0BAA0B,CAAC;AAEzC,cAAc,2BAA2B,CAAC;AAC1C,cAAc,uBAAuB,CAAC;AAEtC,cAAc,yBAAyB,CAAC;AACxC,cAAc,8BAA8B,CAAC;AAC7C,cAAc,8BAA8B,CAAC;AAE7C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAE3C,cAAc,2BAA2B,CAAC
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,cAAc,oBAAoB,CAAC;AACnC,cAAc,wBAAwB,CAAC;AACvC,cAAc,8BAA8B,CAAC;AAE7C,cAAc,+BAA+B,CAAC;AAE9C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,gCAAgC,CAAC;AAE/C,cAAc,+BAA+B,CAAC;AAC9C,cAAc,gCAAgC,CAAC;AAC/C,cAAc,6BAA6B,CAAC;AAE5C,cAAc,sBAAsB,CAAC;AACrC,cAAc,qBAAqB,CAAC;AAEpC,cAAc,2BAA2B,CAAC;AAC1C,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AAEvC,cAAc,uBAAuB,CAAC;AACtC,cAAc,6BAA6B,CAAC;AAC5C,cAAc,0BAA0B,CAAC;AAEzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,0BAA0B,CAAC;AAEzC,cAAc,2BAA2B,CAAC;AAC1C,cAAc,uBAAuB,CAAC;AAEtC,cAAc,yBAAyB,CAAC;AACxC,cAAc,8BAA8B,CAAC;AAC7C,cAAc,8BAA8B,CAAC;AAE7C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAE3C,cAAc,2BAA2B,CAAC"}
|
|
@@ -79,9 +79,10 @@ export function signalsJoin(signals, options = {}) {
|
|
|
79
79
|
ignoreDiaIDs,
|
|
80
80
|
});
|
|
81
81
|
if (newSignal.js) {
|
|
82
|
-
newSignal.multiplicity =
|
|
83
|
-
|
|
84
|
-
|
|
82
|
+
newSignal.multiplicity =
|
|
83
|
+
newSignal.js.length > 0
|
|
84
|
+
? newSignal.js.map((j) => j.multiplicity).join('')
|
|
85
|
+
: 's';
|
|
85
86
|
}
|
|
86
87
|
return newSignal;
|
|
87
88
|
})
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"signalsJoin.js","sourceRoot":"","sources":["../../src/signals/signalsJoin.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,eAAe,CAAC;AACjC,OAAO,GAAG,MAAM,cAAc,CAAC;AAE/B,OAAO,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AAwBpE,MAAM,aAAa,GAAG,CAAC,CAAS,EAAE,CAAS,EAAE,EAAE,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC;AACnE,MAAM,0BAA0B,GAAG,CACjC,CAA0B,EAC1B,CAA0B,EAC1B,EAAE;IACF,MAAM,EAAE,GAAG,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,UAAU,EAAE,CAAC;IAClD,MAAM,EAAE,GAAG,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,UAAU,EAAE,CAAC;IAClD,OAAO,aAAa,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC;AAC/B,CAAC,CAAC;AACF,SAAS,iBAAiB,CACxB,OAAsB;IAEtB,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;QAC5B,IAAI,CAAC,MAAM,CAAC,EAAE;YAAE,MAAM,IAAI,KAAK,CAAC,iBAAiB,CAAC,CAAC;QACnD,IAAI,CAAC,MAAM,CAAC,MAAM;YAAE,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAC;QAC3D,KAAK,MAAM,SAAS,IAAI,MAAM,CAAC,EAAE,EAAE;YACjC,IAAI,CAAC,SAAS,CAAC,MAAM;gBAAE,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAC;YAC9D,IAAI,CAAC,SAAS,CAAC,UAAU;gBAAE,MAAM,IAAI,KAAK,CAAC,yBAAyB,CAAC,CAAC;SACvE;KACF;AACH,CAAC;AACD;;GAEG;AACH,MAAM,UAAU,WAAW,CACzB,OAAsB,EACtB,UAA8B,EAAE;IAEhC,iBAAiB,CAAC,OAAO,CAAC,CAAC;IAC3B,MAAM,EAAE,aAAa,GAAG,EAAE,EAAE,GAAG,OAAO,CAAC;IACvC,MAAM,EAAE,SAAS,EAAE,YAAY,EAAE,GAAG,aAAa,CAAC;IAClD,0BAA0B;IAE1B,MAAM,WAAW,GAA8B,IAAI,CAAC,KAAK,CACvD,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,CACxB,CAAC;IAEF,MAAM,cAAc,
|
|
1
|
+
{"version":3,"file":"signalsJoin.js","sourceRoot":"","sources":["../../src/signals/signalsJoin.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,eAAe,CAAC;AACjC,OAAO,GAAG,MAAM,cAAc,CAAC;AAE/B,OAAO,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AAwBpE,MAAM,aAAa,GAAG,CAAC,CAAS,EAAE,CAAS,EAAE,EAAE,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC;AACnE,MAAM,0BAA0B,GAAG,CACjC,CAA0B,EAC1B,CAA0B,EAC1B,EAAE;IACF,MAAM,EAAE,GAAG,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,UAAU,EAAE,CAAC;IAClD,MAAM,EAAE,GAAG,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,UAAU,EAAE,CAAC;IAClD,OAAO,aAAa,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC;AAC/B,CAAC,CAAC;AACF,SAAS,iBAAiB,CACxB,OAAsB;IAEtB,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;QAC5B,IAAI,CAAC,MAAM,CAAC,EAAE;YAAE,MAAM,IAAI,KAAK,CAAC,iBAAiB,CAAC,CAAC;QACnD,IAAI,CAAC,MAAM,CAAC,MAAM;YAAE,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAC;QAC3D,KAAK,MAAM,SAAS,IAAI,MAAM,CAAC,EAAE,EAAE;YACjC,IAAI,CAAC,SAAS,CAAC,MAAM;gBAAE,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAC;YAC9D,IAAI,CAAC,SAAS,CAAC,UAAU;gBAAE,MAAM,IAAI,KAAK,CAAC,yBAAyB,CAAC,CAAC;SACvE;KACF;AACH,CAAC;AACD;;GAEG;AACH,MAAM,UAAU,WAAW,CACzB,OAAsB,EACtB,UAA8B,EAAE;IAEhC,iBAAiB,CAAC,OAAO,CAAC,CAAC;IAC3B,MAAM,EAAE,aAAa,GAAG,EAAE,EAAE,GAAG,OAAO,CAAC;IACvC,MAAM,EAAE,SAAS,EAAE,YAAY,EAAE,GAAG,aAAa,CAAC;IAClD,0BAA0B;IAE1B,MAAM,WAAW,GAA8B,IAAI,CAAC,KAAK,CACvD,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,CACxB,CAAC;IAEF,MAAM,cAAc,GAA8C,EAAE,CAAC;IAErE,KAAK,IAAI,MAAM,IAAI,WAAW,EAAE;QAC9B,MAAM,CAAC,EAAE,GAAG,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC,0BAA0B,CAAC,CAAC;QACvD,MAAM,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;QAC1C,IAAI,EAAE,GAAG,GAAG,SAAS,IAAI,MAAM,CAAC,EAAE;aAC/B,GAAG,CACF,CAAC,CAA0B,EAAE,EAAE,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,UAAU,EAAE,CACxE;aACA,IAAI,CAAC,aAAa,CAAC;aACnB,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;QACf,IAAI,CAAC,cAAc,CAAC,EAAE,CAAC,EAAE;YACvB,cAAc,CAAC,EAAE,CAAC,GAAG,EAAE,CAAC;SACzB;QACD,cAAc,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;KACjC;IACD,sEAAsE;IACtE,IAAI,UAAU,GAA8B,EAAE,CAAC;IAC/C,MAAM,CAAC,MAAM,CAAC,cAAc,CAAC,CAAC,OAAO,CAAC,CAAC,KAAK,EAAE,EAAE;QAC9C,2DAA2D;QAC3D,IAAI,EAAE,GAA8B,EAAE,CAAC;QACvC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC3C,MAAM,QAAQ,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;YAChC,EAAE,CAAC,IAAI,CAAC;gBACN,MAAM,EAAE,QAAQ,CAAC,MAAM;gBACvB,UAAU,EAAE,QAAQ,CAAC,UAAU;gBAC/B,YAAY,EAAE,QAAQ,CAAC,YAAY;gBACnC,QAAQ,EAAE,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC;aACzD,CAAC,CAAC;SACJ;QACD,IAAI,MAAM,GAA4B;YACpC,OAAO,EAAE,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,OAAO,IAAI,CAAC,CAAC,CAAC;YACpD,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;YAC5C,MAAM,EAAE,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM;YACvB,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,KAAK,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE;YACnD,EAAE;SACH,CAAC;QAEF,MAAM,UAAU,GAAG,KAAK;aACrB,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,UAAU,CAAC;aAC9B,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC;aACtB,IAAI,CAAC,GAAG,CAAC,CAAC;QAEb,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC;YAAE,MAAM,CAAC,UAAU,GAAG,UAAU,CAAC;QAE1D,UAAU,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;IAC1B,CAAC,CAAC,CAAC;IAEH,UAAU,GAAG,UAAU;SACpB,GAAG,CAAC,CAAC,MAAM,EAAE,EAAE;QACd,IAAI,SAAS,GAAG,mBAAmB,CAAC,MAAM,EAAE;YAC1C,SAAS;YACT,YAAY;SACb,CAA4B,CAAC;QAC9B,IAAI,SAAS,CAAC,EAAE,EAAE;YAChB,SAAS,CAAC,YAAY;gBACpB,SAAS,CAAC,EAAE,CAAC,MAAM,GAAG,CAAC;oBACrB,CAAC,CAAC,SAAS,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC;oBAClD,CAAC,CAAC,GAAG,CAAC;SACX;QACD,OAAO,SAAS,CAAC;IACnB,CAAC,CAAC;SACD,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC;IAErC,OAAO,UAAU,CAAC;AACpB,CAAC"}
|
|
@@ -1,13 +1,13 @@
|
|
|
1
1
|
import { gsd, optimizePeaks, joinBroadPeaks, appendShapeAndFWHM } from 'ml-gsd';
|
|
2
2
|
import { xyExtract, xNoiseSanPlot, xAbsoluteMedian, } from 'ml-spectra-processing';
|
|
3
3
|
export function xyAutoPeaksPicking(data, options = {}) {
|
|
4
|
-
const { from, to, 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 = {},
|
|
4
|
+
const { from, to, 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;
|
|
5
5
|
const { windowSize = 9, polynomial = 3 } = sgOptions;
|
|
6
|
+
if (data.x.length < windowSize)
|
|
7
|
+
return [];
|
|
6
8
|
if (from !== undefined && to !== undefined) {
|
|
7
9
|
data = xyExtract(data, { zones: [{ from, to }] });
|
|
8
10
|
}
|
|
9
|
-
if (data.x.length < windowSize)
|
|
10
|
-
return [];
|
|
11
11
|
const cutOff = getCutOff(data.y, { noiseLevel, useSanPlot, thresholdFactor });
|
|
12
12
|
let getPeakOptions = {
|
|
13
13
|
shape,
|
|
@@ -23,13 +23,30 @@ export function xyAutoPeaksPicking(data, options = {}) {
|
|
|
23
23
|
optimization,
|
|
24
24
|
realTopDetection,
|
|
25
25
|
};
|
|
26
|
-
|
|
27
|
-
|
|
28
|
-
|
|
29
|
-
|
|
30
|
-
|
|
26
|
+
switch (direction) {
|
|
27
|
+
case 'positive': {
|
|
28
|
+
return getPeakList(data, getPeakOptions);
|
|
29
|
+
}
|
|
30
|
+
case 'negative': {
|
|
31
|
+
return getNegativePeaks(data, cutOff, getPeakOptions);
|
|
32
|
+
}
|
|
33
|
+
case 'both': {
|
|
34
|
+
return [
|
|
35
|
+
...getPeakList(data, getPeakOptions),
|
|
36
|
+
...getNegativePeaks(data, cutOff, getPeakOptions),
|
|
37
|
+
];
|
|
38
|
+
}
|
|
39
|
+
default: {
|
|
40
|
+
const unHandled = direction;
|
|
41
|
+
// eslint-disable-next-line @typescript-eslint/restrict-template-expressions
|
|
42
|
+
throw Error(`Unknown distribution ${unHandled}`);
|
|
43
|
+
}
|
|
31
44
|
}
|
|
32
|
-
|
|
45
|
+
}
|
|
46
|
+
function getNegativePeaks(data, cutOff, getPeakOptions) {
|
|
47
|
+
getPeakOptions.noiseLevel = cutOff.negative;
|
|
48
|
+
getPeakOptions.maxCriteria = false;
|
|
49
|
+
return getPeakList(data, getPeakOptions);
|
|
33
50
|
}
|
|
34
51
|
function getPeakList(data, options) {
|
|
35
52
|
const { shape, broadWidth, optimize, maxCriteria, factorLimits, sgOptions, minMaxRatio, broadRatio, noiseLevel, smoothY, optimization, realTopDetection, } = 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,kBAAkB,EAAE,MAAM,QAAQ,CAAC;AAMhF,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,kBAAkB,EAAE,MAAM,QAAQ,CAAC;AAMhF,OAAO,EACL,SAAS,EACT,aAAa,EACb,eAAe,GAChB,MAAM,uBAAuB,CAAC;AAsD/B,MAAM,UAAU,kBAAkB,CAChC,IAAY,EACZ,UAAqC,EAAE;IAEvC,MAAM,EACJ,IAAI,EACJ,EAAE,EACF,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,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,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,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,IAAI,QAAQ,EAAE;QACZ,OAAO,aAAa,CAAC,IAAI,EAAE,QAAQ,EAAE;YACnC,KAAK;YACL,YAAY;YACZ,YAAY;SACb,CAAC,CAAC;KACJ;IAED,OAAO,kBAAkB,CAAC,QAAQ,EAAE,EAAE,KAAK,EAAE,CAAC,CAAC;AACjD,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"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "nmr-processing",
|
|
3
|
-
"version": "8.
|
|
3
|
+
"version": "8.5.0",
|
|
4
4
|
"description": "Pure functions allowing to process NMR spectra.",
|
|
5
5
|
"main": "./lib/index.js",
|
|
6
6
|
"module": "./lib-esm/index.js",
|
|
@@ -38,12 +38,12 @@
|
|
|
38
38
|
},
|
|
39
39
|
"homepage": "https://github.com/cheminfo/nmr-processing#readme",
|
|
40
40
|
"devDependencies": {
|
|
41
|
-
"@types/jest": "^28.1.
|
|
41
|
+
"@types/jest": "^28.1.6",
|
|
42
42
|
"cheminfo-build": "^1.1.11",
|
|
43
|
-
"cheminfo-types": "^1.
|
|
44
|
-
"eslint": "^8.
|
|
43
|
+
"cheminfo-types": "^1.4.0",
|
|
44
|
+
"eslint": "^8.21.0",
|
|
45
45
|
"eslint-config-cheminfo-typescript": "^11.0.1",
|
|
46
|
-
"jest": "^28.1.
|
|
46
|
+
"jest": "^28.1.3",
|
|
47
47
|
"jest-matcher-deep-close-to": "^3.0.2",
|
|
48
48
|
"md5": "^2.3.0",
|
|
49
49
|
"ml-array-median": "^1.1.6",
|
|
@@ -51,7 +51,7 @@
|
|
|
51
51
|
"openchemlib": "^7.4.3",
|
|
52
52
|
"prettier": "^2.7.1",
|
|
53
53
|
"rimraf": "^3.0.2",
|
|
54
|
-
"ts-jest": "^28.0.
|
|
54
|
+
"ts-jest": "^28.0.7",
|
|
55
55
|
"typescript": "^4.7.4"
|
|
56
56
|
},
|
|
57
57
|
"dependencies": {
|
|
@@ -74,9 +74,9 @@
|
|
|
74
74
|
"ml-peak-shape-generator": "^4.1.1",
|
|
75
75
|
"ml-simple-clustering": "^0.1.0",
|
|
76
76
|
"ml-sparse-matrix": "^2.1.0",
|
|
77
|
-
"ml-spectra-processing": "^11.
|
|
77
|
+
"ml-spectra-processing": "^11.12.0",
|
|
78
78
|
"ml-tree-set": "^0.1.1",
|
|
79
|
-
"nmr-correlation": "^2.3.
|
|
79
|
+
"nmr-correlation": "^2.3.3",
|
|
80
80
|
"openchemlib-utils": "^1.11.0",
|
|
81
81
|
"spectrum-generator": "^8.0.2"
|
|
82
82
|
}
|
package/src/index.ts
CHANGED
|
@@ -41,7 +41,6 @@ export * from './peaks/solventSuppression';
|
|
|
41
41
|
export * from './ranges/markSolventSignal';
|
|
42
42
|
|
|
43
43
|
export * from './apodization/apodization';
|
|
44
|
-
export * from './apodization/compose';
|
|
45
44
|
|
|
46
45
|
export type { NMRSignal1D } from './signals/NMRSignal1D';
|
|
47
46
|
export type { NMRSignal2D, Signal2DProjection } from './xyz/NMRSignal2D';
|
|
@@ -62,7 +62,7 @@ export function signalsJoin(
|
|
|
62
62
|
JSON.stringify(signals),
|
|
63
63
|
);
|
|
64
64
|
|
|
65
|
-
const groupedSignals:
|
|
65
|
+
const groupedSignals: Record<string, Signal1DWidthJsAndDiaID[]> = {};
|
|
66
66
|
|
|
67
67
|
for (let signal of copySignals) {
|
|
68
68
|
signal.js = signal.js.sort(localeCompareJcouplingKeys);
|
|
@@ -117,12 +117,10 @@ export function signalsJoin(
|
|
|
117
117
|
ignoreDiaIDs,
|
|
118
118
|
}) as Signal1DWidthJsAndDiaID;
|
|
119
119
|
if (newSignal.js) {
|
|
120
|
-
newSignal.multiplicity =
|
|
121
|
-
|
|
122
|
-
|
|
123
|
-
|
|
124
|
-
'',
|
|
125
|
-
);
|
|
120
|
+
newSignal.multiplicity =
|
|
121
|
+
newSignal.js.length > 0
|
|
122
|
+
? newSignal.js.map((j) => j.multiplicity).join('')
|
|
123
|
+
: 's';
|
|
126
124
|
}
|
|
127
125
|
return newSignal;
|
|
128
126
|
})
|
|
@@ -36,6 +36,7 @@ export interface GetPeakListOptions
|
|
|
36
36
|
*/
|
|
37
37
|
optimize: boolean;
|
|
38
38
|
}
|
|
39
|
+
|
|
39
40
|
export interface OptionsXYAutoPeaksPicking extends Partial<GetPeakListOptions> {
|
|
40
41
|
/**
|
|
41
42
|
* Low limit value in the x axis to extract a sub set of points from the input data.
|
|
@@ -51,10 +52,10 @@ export interface OptionsXYAutoPeaksPicking extends Partial<GetPeakListOptions> {
|
|
|
51
52
|
*/
|
|
52
53
|
thresholdFactor?: number;
|
|
53
54
|
/**
|
|
54
|
-
*
|
|
55
|
-
* @default
|
|
55
|
+
* look for peaks in negative, positive or both sense
|
|
56
|
+
* @default 'positive'
|
|
56
57
|
*/
|
|
57
|
-
|
|
58
|
+
direction?: 'negative' | 'positive' | 'both';
|
|
58
59
|
/**
|
|
59
60
|
* If it is true, it calculate the noise level by sanPlot method.
|
|
60
61
|
* @default false
|
|
@@ -82,15 +83,16 @@ export function xyAutoPeaksPicking(
|
|
|
82
83
|
optimization = { kind: 'lm' },
|
|
83
84
|
broadWidth = 0.25,
|
|
84
85
|
sgOptions = {},
|
|
85
|
-
|
|
86
|
+
direction = 'positive',
|
|
86
87
|
} = options;
|
|
87
88
|
|
|
88
89
|
const { windowSize = 9, polynomial = 3 } = sgOptions;
|
|
89
90
|
|
|
91
|
+
if (data.x.length < windowSize) return [];
|
|
92
|
+
|
|
90
93
|
if (from !== undefined && to !== undefined) {
|
|
91
94
|
data = xyExtract(data, { zones: [{ from, to }] });
|
|
92
95
|
}
|
|
93
|
-
if (data.x.length < windowSize) return [];
|
|
94
96
|
|
|
95
97
|
const cutOff = getCutOff(data.y, { noiseLevel, useSanPlot, thresholdFactor });
|
|
96
98
|
|
|
@@ -109,14 +111,35 @@ export function xyAutoPeaksPicking(
|
|
|
109
111
|
realTopDetection,
|
|
110
112
|
};
|
|
111
113
|
|
|
112
|
-
|
|
113
|
-
|
|
114
|
-
|
|
115
|
-
|
|
116
|
-
|
|
117
|
-
|
|
114
|
+
switch (direction) {
|
|
115
|
+
case 'positive': {
|
|
116
|
+
return getPeakList(data, getPeakOptions);
|
|
117
|
+
}
|
|
118
|
+
case 'negative': {
|
|
119
|
+
return getNegativePeaks(data, cutOff, getPeakOptions);
|
|
120
|
+
}
|
|
121
|
+
case 'both': {
|
|
122
|
+
return [
|
|
123
|
+
...getPeakList(data, getPeakOptions),
|
|
124
|
+
...getNegativePeaks(data, cutOff, getPeakOptions),
|
|
125
|
+
];
|
|
126
|
+
}
|
|
127
|
+
default: {
|
|
128
|
+
const unHandled: never = direction;
|
|
129
|
+
// eslint-disable-next-line @typescript-eslint/restrict-template-expressions
|
|
130
|
+
throw Error(`Unknown distribution ${unHandled}`);
|
|
131
|
+
}
|
|
118
132
|
}
|
|
119
|
-
|
|
133
|
+
}
|
|
134
|
+
|
|
135
|
+
function getNegativePeaks(
|
|
136
|
+
data: DataXY,
|
|
137
|
+
cutOff: { negative: number },
|
|
138
|
+
getPeakOptions: GetPeakListOptions,
|
|
139
|
+
) {
|
|
140
|
+
getPeakOptions.noiseLevel = cutOff.negative;
|
|
141
|
+
getPeakOptions.maxCriteria = false;
|
|
142
|
+
return getPeakList(data, getPeakOptions);
|
|
120
143
|
}
|
|
121
144
|
|
|
122
145
|
function getPeakList(data: DataXY, options: GetPeakListOptions) {
|