nmr-processing 8.3.1 → 8.5.1
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/xy/xyAutoPeaksPicking.d.ts +3 -3
- package/lib/xy/xyAutoPeaksPicking.js +26 -9
- package/lib/xy/xyAutoPeaksPicking.js.map +1 -1
- package/lib-esm/xy/xyAutoPeaksPicking.js +26 -9
- package/lib-esm/xy/xyAutoPeaksPicking.js.map +1 -1
- package/package.json +9 -9
- package/src/xy/xyAutoPeaksPicking.ts +35 -12
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@@ -23,10 +23,10 @@ export interface OptionsXYAutoPeaksPicking extends Partial<GetPeakListOptions> {
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*/
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thresholdFactor?: number;
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/**
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*
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* @default
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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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-
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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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* @default false
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@@ -4,13 +4,13 @@ exports.xyAutoPeaksPicking = void 0;
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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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shape,
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@@ -26,15 +26,32 @@ function xyAutoPeaksPicking(data, options = {}) {
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optimization,
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realTopDetection,
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};
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-
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-
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-
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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) {
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getPeakOptions.noiseLevel = cutOff.negative;
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getPeakOptions.maxCriteria = false;
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return getPeakList(data, getPeakOptions);
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}
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function getPeakList(data, options) {
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const { shape, broadWidth, optimize, maxCriteria, factorLimits, sgOptions, minMaxRatio, broadRatio, noiseLevel, smoothY, optimization, realTopDetection, } = options;
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let peakList = (0, ml_gsd_1.gsd)(data, {
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@@ -1 +1 @@
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-
{"version":3,"file":"xyAutoPeaksPicking.js","sourceRoot":"","sources":["../../src/xy/xyAutoPeaksPicking.ts"],"names":[],"mappings":";;;AACA,mCAAgF;AAMhF,iEAI+B;
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{"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"}
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@@ -1,13 +1,13 @@
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import { gsd, optimizePeaks, joinBroadPeaks, appendShapeAndFWHM } from 'ml-gsd';
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import { xyExtract, xNoiseSanPlot, xAbsoluteMedian, } from 'ml-spectra-processing';
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export 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 = 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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shape,
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@@ -23,13 +23,30 @@ export function xyAutoPeaksPicking(data, options = {}) {
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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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}
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function getNegativePeaks(data, cutOff, getPeakOptions) {
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getPeakOptions.noiseLevel = cutOff.negative;
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getPeakOptions.maxCriteria = false;
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return getPeakList(data, getPeakOptions);
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}
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function getPeakList(data, options) {
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const { shape, broadWidth, optimize, maxCriteria, factorLimits, sgOptions, minMaxRatio, broadRatio, noiseLevel, smoothY, optimization, realTopDetection, } = options;
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{"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;
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+
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "nmr-processing",
|
|
3
|
-
"version": "8.
|
|
3
|
+
"version": "8.5.1",
|
|
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": {
|
|
@@ -65,7 +65,7 @@
|
|
|
65
65
|
"ml-array-rescale": "^1.3.7",
|
|
66
66
|
"ml-array-sequential-fill": "^1.1.8",
|
|
67
67
|
"ml-array-sum": "^1.1.6",
|
|
68
|
-
"ml-gsd": "^11.
|
|
68
|
+
"ml-gsd": "^11.3.0",
|
|
69
69
|
"ml-hclust": "^3.1.0",
|
|
70
70
|
"ml-levenberg-marquardt": "^4.1.0",
|
|
71
71
|
"ml-matrix": "^6.10.2",
|
|
@@ -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
|
}
|
|
@@ -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) {
|