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feat: add shape to gsd result (#102)
* feat: add shape to gsd result adapt to new version of ml-spectra * chore: remove support for node 12 * chore: reverse change in test case
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‎.github/workflows/nodejs-ts.yml‎

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@@ -11,5 +11,5 @@ jobs:
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# Documentation: https://github.com/zakodium/workflows#nodejs-ci
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uses: zakodium/workflows/.github/workflows/nodejs.yml@nodejs-v1
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with:
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node-version-matrix: '[12, 14, 16, 18]'
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node-version-matrix: '[14, 16, 18]'
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lint-check-types: true

‎package.json‎

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@@ -82,7 +82,7 @@
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"cheminfo-types": "^1.1.0",
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"ml-peak-shape-generator": "^4.1.1",
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"ml-savitzky-golay-generalized": "4.0.1",
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"ml-spectra-fitting": "4.0.2",
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"ml-spectra-fitting": "4.1.0",
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"ml-spectra-processing": "^11.6.0"
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}
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}

‎src/GSDPeak.ts‎

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@@ -1,3 +1,5 @@
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import { Shape1D } from 'ml-peak-shape-generator';
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export interface GSDPeak {
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x: number;
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y: number;
@@ -14,6 +16,9 @@ export interface GSDPeak {
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* This allows to determine if a peak is soft or not
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*/
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ddY: number;
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shape: Shape1D;
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inflectionPoints: {
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from: { x: number; index: number };
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to: { x: number; index: number };

‎src/__tests__/gaussian-smooth.test.ts‎

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@@ -38,6 +38,10 @@ describe('gaussian simulated peaks', () => {
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ddY: -259.83290100626783,
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width: 0.08,
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index: 25,
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shape: {
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fwhm: 0.09419280180123805,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { x: -0.54, index: 23 },
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to: { x: -0.46, index: 27 },
@@ -49,6 +53,10 @@ describe('gaussian simulated peaks', () => {
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ddY: -259.83290100626783,
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width: 0.08,
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index: 75,
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shape: {
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fwhm: 0.09419280180123805,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { x: 0.46, index: 73 },
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to: { x: 0.54, index: 77 },

‎src/__tests__/gaussian.test.ts‎

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@@ -38,6 +38,10 @@ describe('smooth:false option', () => {
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ddY: -259.83290100626783,
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width: 0.08,
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index: 25,
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shape: {
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fwhm: 0.09419280180123805,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { index: 23, x: -0.54 },
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to: { index: 27, x: -0.46 },
@@ -49,6 +53,10 @@ describe('smooth:false option', () => {
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ddY: -259.83290100626783,
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width: 0.08,
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index: 75,
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shape: {
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fwhm: 0.09419280180123805,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { index: 73, x: 0.46 },
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to: { index: 77, x: 0.54 },
@@ -68,6 +76,10 @@ describe('smooth:false option', () => {
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ddY: -259.83290100626783,
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width: 0.08,
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index: 25,
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shape: {
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fwhm: 0.09419280180123805,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { index: 23, x: -0.54 },
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to: { index: 27, x: -0.46 },
@@ -79,6 +91,10 @@ describe('smooth:false option', () => {
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ddY: -259.83290100626783,
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width: 0.08,
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index: 75,
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shape: {
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fwhm: 0.09419280180123805,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { index: 73, x: 0.46 },
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to: { index: 77, x: 0.54 },
@@ -101,6 +117,10 @@ describe('smooth:false option', () => {
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ddY: 259.83290100626783,
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width: 0.08,
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index: 25,
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shape: {
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fwhm: 0.09419280180123805,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { index: 23, x: -0.54 },
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to: { index: 27, x: -0.46 },
@@ -112,6 +132,10 @@ describe('smooth:false option', () => {
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ddY: 259.83290100626783,
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width: 0.08,
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index: 75,
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shape: {
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fwhm: 0.09419280180123805,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { index: 73, x: 0.46 },
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to: { index: 77, x: 0.54 },
@@ -135,6 +159,10 @@ describe('smooth:false option', () => {
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ddY: 259.83290100626783,
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width: 0.08,
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index: 25,
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shape: {
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fwhm: 0.09419280180123805,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { index: 23, x: -0.54 },
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to: { index: 27, x: -0.46 },
@@ -146,6 +174,10 @@ describe('smooth:false option', () => {
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ddY: 259.83290100626783,
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width: 0.08,
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index: 75,
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shape: {
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fwhm: 0.09419280180123805,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { index: 73, x: 0.46 },
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to: { index: 77, x: 0.54 },

‎src/__tests__/power.test.ts‎

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@@ -56,6 +56,10 @@ describe('power', () => {
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width: 0.3,
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index: 100,
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ddY: -33832.03463203485,
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shape: {
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fwhm: 0.35322300675464324,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { x: 4.85, index: 97 },
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to: { x: 5.15, index: 103 },
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width: 0.05,
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index: 89,
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ddY: 800,
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shape: {
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fwhm: 0.05887050112577352,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { x: 4.4, index: 88 },
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to: { x: 4.45, index: 89 },
@@ -89,6 +97,10 @@ describe('power', () => {
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width: 0.2,
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index: 100,
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ddY: -44914.28571428623,
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shape: {
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fwhm: 0.2354820045030941,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { x: 4.9, index: 98 },
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to: { x: 5.1, index: 102 },
@@ -100,6 +112,10 @@ describe('power', () => {
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width: 0.05,
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index: 111,
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ddY: 800,
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shape: {
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fwhm: 0.05887050112577352,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { x: 5.55, index: 111 },
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to: { x: 5.6, index: 112 },

‎src/__tests__/ubiquitin.test.ts‎

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@@ -28,6 +28,10 @@ describe('Global spectra deconvolution ubiquitin', () => {
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ddY: -15468134.039875854,
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width: 0.002420000000000755,
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index: 11,
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shape: {
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fwhm: 0.0028493322544883375,
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kind: 'gaussian',
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},
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inflectionPoints: {
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from: { x: 200.054133, index: 9 },
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to: { x: 200.056553, index: 13 },

‎src/gsd.ts‎

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@@ -1,4 +1,5 @@
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import type { DataXY } from 'cheminfo-types';
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import { Shape1D } from 'ml-peak-shape-generator';
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import { sgg, SGGOptions } from 'ml-savitzky-golay-generalized';
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import {
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xIsEquallySpaced,
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} from 'ml-spectra-processing';
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import { GSDPeak } from './GSDPeak';
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import { appendShapeAndFWHM } from './utils/appendShapeAndFWHM';
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import { optimizeTop } from './utils/optimizeTop';
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export interface GSDOptions {
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* @default false
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*/
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realTopDetection?: boolean;
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/**
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* Shape used to add FWHM property in the peaks
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* @default {kind:'gaussian'}
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*/
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shape?: Shape1D;
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}
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/**
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windowSize: 9,
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polynomial: 3,
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},
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shape,
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noiseLevel,
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smoothY = false,
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maxCriteria = true,
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peaks.push({
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x: deltaX,
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y: yData[minddYIndex],
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width: width,
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width,
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index: minddYIndex,
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ddY: ddY[minddYIndex],
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inflectionPoints: {
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from: intervalL[possible],
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to: intervalR[possible],
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},
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});
257+
} as GSDPeak);
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}
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}
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}
@@ -266,5 +274,5 @@ export function gsd(data: DataXY, options: GSDOptions = {}): GSDPeak[] {
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return a.x - b.x;
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});
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return peaks;
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return appendShapeAndFWHM(peaks, { shape });
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}

‎src/post/__tests__/optimizePeaksWithLogs.test.ts‎

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@@ -30,7 +30,7 @@ describe('optimizePeaksWithLogs', () => {
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expect(result.logs).toMatchObject([
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{
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iterations: 100,
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error: 0.000017852930772995625,
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error: 0.000017852931247867768,
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parameters: { kind: 'lm', options: { timeout: 10 } },
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message: 'optimization successful',
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groupSize: 1,

‎src/post/broadenPeaks.ts‎

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@@ -10,7 +10,7 @@ import { GSDPeak } from '../GSDPeak';
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*/
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export function broadenPeaks(
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peakList: GSDPeak[],
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peakList: Omit<GSDPeak, 'shape'>[],
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options: {
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/**
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* @default 2

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