nmr-processing 8.3.1 → 8.4.0
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/lib/xy/xyAutoPeaksPicking.d.ts +5 -0
- package/lib/xy/xyAutoPeaksPicking.js +9 -4
- package/lib/xy/xyAutoPeaksPicking.js.map +1 -1
- package/lib-esm/xy/xyAutoPeaksPicking.js +9 -4
- package/lib-esm/xy/xyAutoPeaksPicking.js.map +1 -1
- package/package.json +1 -1
- package/src/xy/xyAutoPeaksPicking.ts +14 -2
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@@ -22,6 +22,11 @@ export interface OptionsXYAutoPeaksPicking extends Partial<GetPeakListOptions> {
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* @default 3
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*/
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thresholdFactor?: number;
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/**
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* If it is true, it check for negative peaks.
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* @default true
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*/
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lookPositive?: boolean;
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/**
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* If it is true, it check for negative peaks.
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* @default false
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@@ -4,13 +4,15 @@ 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 = {}, lookNegative = false, } = 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 = {}, lookPositive = true, lookNegative = false, } = options;
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const { windowSize = 9, polynomial = 3 } = sgOptions;
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9
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if (data.x.length < windowSize)
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return [];
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if (!lookPositive && !lookNegative)
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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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@@ -26,7 +28,10 @@ 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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const peaks = [];
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if (lookPositive) {
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peaks.push(...getPeakList(data, getPeakOptions));
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}
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if (lookNegative) {
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getPeakOptions.noiseLevel = cutOff.negative;
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getPeakOptions.maxCriteria = false;
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@@ -1 +1 @@
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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;AA0D/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,YAAY,GAAG,IAAI,EACnB,YAAY,GAAG,KAAK,GACrB,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,CAAC,YAAY,IAAI,CAAC,YAAY;QAAE,OAAO,EAAE,CAAC;IAE9C,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,MAAM,KAAK,GAAG,EAAE,CAAC;IACjB,IAAI,YAAY,EAAE;QAChB,KAAK,CAAC,IAAI,CAAC,GAAG,WAAW,CAAC,IAAI,EAAE,cAAc,CAAC,CAAC,CAAC;KAClD;IAED,IAAI,YAAY,EAAE;QAChB,cAAc,CAAC,UAAU,GAAG,MAAM,CAAC,QAAQ,CAAC;QAC5C,cAAc,CAAC,WAAW,GAAG,KAAK,CAAC;QACnC,KAAK,CAAC,IAAI,CAAC,GAAG,WAAW,CAAC,IAAI,EAAE,cAAc,CAAC,CAAC,CAAC;KAClD;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AA9DD,gDA8DC;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 +1,15 @@
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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 = {}, lookNegative = false, } = 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 = {}, lookPositive = true, lookNegative = false, } = 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 (!lookPositive && !lookNegative)
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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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@@ -23,7 +25,10 @@ export function xyAutoPeaksPicking(data, options = {}) {
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optimization,
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realTopDetection,
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};
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const peaks = [];
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if (lookPositive) {
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peaks.push(...getPeakList(data, getPeakOptions));
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}
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if (lookNegative) {
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getPeakOptions.noiseLevel = cutOff.negative;
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getPeakOptions.maxCriteria = false;
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@@ -1 +1 @@
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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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{"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;AA0D/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,YAAY,GAAG,IAAI,EACnB,YAAY,GAAG,KAAK,GACrB,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,CAAC,YAAY,IAAI,CAAC,YAAY;QAAE,OAAO,EAAE,CAAC;IAE9C,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,MAAM,KAAK,GAAG,EAAE,CAAC;IACjB,IAAI,YAAY,EAAE;QAChB,KAAK,CAAC,IAAI,CAAC,GAAG,WAAW,CAAC,IAAI,EAAE,cAAc,CAAC,CAAC,CAAC;KAClD;IAED,IAAI,YAAY,EAAE;QAChB,cAAc,CAAC,UAAU,GAAG,MAAM,CAAC,QAAQ,CAAC;QAC5C,cAAc,CAAC,WAAW,GAAG,KAAK,CAAC;QACnC,KAAK,CAAC,IAAI,CAAC,GAAG,WAAW,CAAC,IAAI,EAAE,cAAc,CAAC,CAAC,CAAC;KAClD;IACD,OAAO,KAAK,CAAC;AACf,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"}
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package/package.json
CHANGED
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@@ -50,6 +50,11 @@ export interface OptionsXYAutoPeaksPicking extends Partial<GetPeakListOptions> {
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* @default 3
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*/
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thresholdFactor?: number;
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/**
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* If it is true, it check for negative peaks.
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* @default true
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*/
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lookPositive?: boolean;
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/**
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* If it is true, it check for negative peaks.
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* @default false
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@@ -82,15 +87,19 @@ export function xyAutoPeaksPicking(
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optimization = { kind: 'lm' },
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broadWidth = 0.25,
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sgOptions = {},
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lookPositive = true,
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lookNegative = false,
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} = options;
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const { windowSize = 9, polynomial = 3 } = sgOptions;
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if (data.x.length < windowSize) return [];
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if (!lookPositive && !lookNegative) 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) return [];
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const cutOff = getCutOff(data.y, { noiseLevel, useSanPlot, thresholdFactor });
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@@ -109,7 +118,10 @@ export function xyAutoPeaksPicking(
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realTopDetection,
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};
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const peaks = [];
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if (lookPositive) {
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peaks.push(...getPeakList(data, getPeakOptions));
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}
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if (lookNegative) {
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getPeakOptions.noiseLevel = cutOff.negative;
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