ir-spectrum 2.0.0 → 3.1.0

package/README.md

@@ -3,6 +3,7 @@
 [![NPM version][npm-image]][npm-url]
 [![Test coverage][codecov-image]][codecov-url]
 [![npm download][download-image]][download-url]
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5482831.svg)](https://doi.org/10.5281/zenodo.5482831)
 
 ## Installation
 

package/lib/index.js

@@ -1,12 +1,34 @@
 'use strict';
 
-Object.defineProperty(exports, '__esModule', { value: true });
-
 var commonSpectrum = require('common-spectrum');
 var spcParser = require('spc-parser');
 
+function convertPeak(peak, spectrum) {
+  return {
+    wavenumber: peak.x,
+    absorbance: peak.a,
+    transmittance: peak.t / 100,
+    kind: getPeakKind(
+      peak.t,
+      spectrum.variables.t.min,
+      spectrum.variables.t.max,
+    ),
+  };
+}
+
+function getPeakKind(transmittance, minTransmittance, maxTransmittance) {
+  let position =
+    (maxTransmittance - transmittance) / (maxTransmittance - minTransmittance);
+  if (position < 0.33) {
+    return 'w';
+  } else if (position < 0.66) {
+    return 'm';
+  }
+  return 'S';
+}
+
 /**
- * @typedef {Object} Peak
+ * @typedef {object} Peak
  * @property {number} wavenumber
  * @property {number} transmittance
  * @property {number} absorbance
@@ -16,14 +38,14 @@ var spcParser = require('spc-parser');
 
 /**
  * Creates annotations for jsgraph that allows to display the result of peak picking
- * @param {array<Peak>} peaks
+ * @param {Array<Peak>} peaks
  * @param {object} [options={}]
  * @param {string} [options.fillColor='green']
  * @param {string} [options.strokeColor='red']
- * @param {string} [options.showKind=true] Display the kind, 'm', 'w', 'S'
- * @param {string} [options.showAssignment=true] Display the assignment
- * @param {function} [options.createFct] (annotation, peak) => {}: callback allowing to add properties
- * @param {string} [options.mode='t100'] 't100'=transmittance in %, 't'=transmittance, 'a'=absorbance
+ * @param {string} [options.showKind=true] - Display the kind, 'm', 'w', 'S'
+ * @param {string} [options.showAssignment=true] - Display the assignment
+ * @param {Function} [options.createFct] - (annotation, peak) => {}: callback allowing to add properties
+ * @param {string} [options.mode='t100'] - 't100'=transmittance in %, 't'=transmittance, 'a'=absorbance
  * @returns array
  */
 
@@ -38,9 +60,9 @@ function getAnnotations(peaks, options = {}) {
     let annotation = {
       line: 1,
       type: 'rect',
-      strokeColor: strokeColor,
+      strokeColor,
       strokeWidth: 0,
-      fillColor: fillColor,
+      fillColor,
     };
     if (creationFct) {
       creationFct(annotation, peak);
@@ -180,13 +202,12 @@ function spectrumCallback(variables) {
   if (yVariable.label.toLowerCase().includes('trans')) {
     absorbance = false;
   }
-
   if (absorbance) {
-    variables.a = { ...yVariable };
-    variables.a.data = variables.a.data.slice();
+    variables.a = { ...yVariable, symbol: 'a', data: yVariable.data.slice() };
     variables.t = {
       data: yVariable.data.map((absorbance) => 10 ** -absorbance * 100),
       label: 'Transmittance (%)',
+      symbol: 't',
       units: '',
     };
   } else {
@@ -195,20 +216,23 @@ function spectrumCallback(variables) {
       yVariable.label.toLowerCase().includes('percent')
         ? 100
         : 1;
+
     variables.a = {
       data: yVariable.data.map(
         (transmittance) => -Math.log10(transmittance / factor),
       ),
+      symbol: 'a',
       label: 'Absorbance',
       units: '',
     };
     if (factor === 100) {
-      variables.t = { ...yVariable };
+      variables.t = { ...yVariable, symbol: 't' };
       variables.t.data = variables.t.data.slice();
     } else {
       variables.t = {
         units: '',
         label: 'Transmittance (%)',
+        symbol: 't',
         data: yVariable.data.map((transmittance) => transmittance * 100),
       };
     }
@@ -220,9 +244,9 @@ function spectrumCallback(variables) {
  * @param {ArrayBuffer|string} jcamp
  * @param {object} [options={}]
  * @param {string|number} [options.id=Math.random()]
- * @param {string} [options.label=options.id] human redeable label
- * @param {string} [options.spectrumCallback] a callback to apply on variables when creating spectrum. Default will add a and t
- * @return {Analysis} - New class element with the given data
+ * @param {string} [options.label=options.id] - human redeable label
+ * @param {string} [options.spectrumCallback] - a callback to apply on variables when creating spectrum. Default will add a and t
+ * @returns {Analysis} - New class element with the given data
  */
 function fromJcamp(jcamp, options = {}) {
   return commonSpectrum.fromJcamp(jcamp, { ...options, spectrumCallback });
@@ -233,9 +257,9 @@ function fromJcamp(jcamp, options = {}) {
  * @param {ArrayBuffer} buffer
  * @param {object} [options={}]
  * @param {object} [options.id=Math.random()]
- * @param {string} [options.label=options.id] human redeable label
- * @param {string} [options.spectrumCallback] a callback to apply on variables when creating spectrum. Default will add a and t
- * @return {Analysis} - New class element with the given data
+ * @param {string} [options.label=options.id] - human redeable label
+ * @param {string} [options.spectrumCallback] - a callback to apply on variables when creating spectrum. Default will add a and t
+ * @returns {Analysis} - New class element with the given data
  */
 
 function fromSPC(buffer, options = {}) {
@@ -255,28 +279,34 @@ function fromSPC(buffer, options = {}) {
   return analysis;
 }
 
+function peakPicking(spectrum, target, options) {
+  const peak = commonSpectrum.peakPicking(spectrum, target, options);
+  if (!peak) return undefined;
+  return convertPeak(peak, spectrum);
+}
+
+function autoPeakPicking(spectrum, options) {
+  const peaks = commonSpectrum.autoPeakPicking(spectrum, options);
+  if (!peaks) return [];
+  return peaks.map((peak) => convertPeak(peak, spectrum));
+}
+
 const JSGraph = { ...commonSpectrum.JSGraph, getAnnotations };
 
-Object.defineProperty(exports, 'AnalysesManager', {
+Object.defineProperty(exports, "AnalysesManager", {
   enumerable: true,
   get: function () { return commonSpectrum.AnalysesManager; }
 });
-Object.defineProperty(exports, 'Analysis', {
+Object.defineProperty(exports, "Analysis", {
   enumerable: true,
   get: function () { return commonSpectrum.Analysis; }
 });
-Object.defineProperty(exports, 'autoPeakPicking', {
-  enumerable: true,
-  get: function () { return commonSpectrum.autoPeakPicking; }
-});
-Object.defineProperty(exports, 'peakPicking', {
-  enumerable: true,
-  get: function () { return commonSpectrum.peakPicking; }
-});
-Object.defineProperty(exports, 'toJcamp', {
+Object.defineProperty(exports, "toJcamp", {
   enumerable: true,
   get: function () { return commonSpectrum.toJcamp; }
 });
 exports.JSGraph = JSGraph;
+exports.autoPeakPicking = autoPeakPicking;
 exports.fromJcamp = fromJcamp;
 exports.fromSPC = fromSPC;
+exports.peakPicking = peakPicking;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "ir-spectrum",
-  "version": "2.0.0",
+  "version": "3.1.0",
   "description": "",
   "main": "lib/index.js",
   "module": "src/index.js",
@@ -13,12 +13,12 @@
     "build-doc": "cheminfo doc",
     "eslint": "eslint src",
     "eslint-fix": "npm run eslint -- --fix",
-    "prepublishOnly": "rollup -c",
+    "prepack": "rollup -c",
     "prettier": "prettier --check src",
     "prettier-write": "prettier --write src",
-    "test": "npm run test-coverage && npm run eslint",
-    "test-coverage": "jest --coverage",
-    "test-only": "jest"
+    "test": "npm run test-coverage && npm run eslint && npm run prettier",
+    "test-coverage": "vitest run --coverage",
+    "test-only": "vitest run"
   },
   "repository": {
     "type": "git",
@@ -35,25 +35,23 @@
     "testEnvironment": "node"
   },
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.17.9",
-    "@types/jest": "^27.5.0",
-    "cheminfo-build": "^1.1.11",
+    "@babel/plugin-transform-modules-commonjs": "^7.25.9",
+    "@vitest/coverage-v8": "^2.1.5",
+    "cheminfo-build": "^1.2.0",
     "codecov": "^3.8.3",
-    "eslint": "^8.14.0",
-    "eslint-config-cheminfo": "^7.3.0",
-    "eslint-plugin-import": "^2.26.0",
-    "eslint-plugin-jest": "^26.1.5",
-    "eslint-plugin-prettier": "^4.0.0",
+    "eslint": "^9.14.0",
+    "eslint-config-cheminfo": "^12.0.1",
     "esm": "^3.2.25",
-    "jest": "^28.0.3",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "prettier": "^2.6.2",
-    "rollup": "^2.72.0"
+    "prettier": "^3.3.3",
+    "rollup": "^4.26.0",
+    "vitest": "^2.1.5"
   },
   "dependencies": {
-    "common-spectrum": "1.0.2",
-    "ml-gsd": "^11.2.0",
-    "spc-parser": "^0.5.2"
+    "common-spectrum": "2.12.0",
+    "ml-gsd": "^12.1.8",
+    "spc-parser": "^1.0.0",
+    "uninstall": "^0.0.0"
   },
   "info": {
     "logo": "https://raw.githubusercontent.com/cheminfo/font/master/src/ir/assignment.svg",

package/src/convertPeak.js

@@ -0,0 +1,23 @@
+export function convertPeak(peak, spectrum) {
+  return {
+    wavenumber: peak.x,
+    absorbance: peak.a,
+    transmittance: peak.t / 100,
+    kind: getPeakKind(
+      peak.t,
+      spectrum.variables.t.min,
+      spectrum.variables.t.max,
+    ),
+  };
+}
+
+function getPeakKind(transmittance, minTransmittance, maxTransmittance) {
+  let position =
+    (maxTransmittance - transmittance) / (maxTransmittance - minTransmittance);
+  if (position < 0.33) {
+    return 'w';
+  } else if (position < 0.66) {
+    return 'm';
+  }
+  return 'S';
+}

package/src/from/fromJcamp.js

@@ -7,9 +7,9 @@ import { spectrumCallback } from './utils/spectrumCallback';
  * @param {ArrayBuffer|string} jcamp
  * @param {object} [options={}]
  * @param {string|number} [options.id=Math.random()]
- * @param {string} [options.label=options.id] human redeable label
- * @param {string} [options.spectrumCallback] a callback to apply on variables when creating spectrum. Default will add a and t
- * @return {Analysis} - New class element with the given data
+ * @param {string} [options.label=options.id] - human redeable label
+ * @param {string} [options.spectrumCallback] - a callback to apply on variables when creating spectrum. Default will add a and t
+ * @returns {Analysis} - New class element with the given data
  */
 export function fromJcamp(jcamp, options = {}) {
   return commonFromJcamp(jcamp, { ...options, spectrumCallback });

package/src/from/fromSPC.js

@@ -8,9 +8,9 @@ import { spectrumCallback } from './utils/spectrumCallback';
  * @param {ArrayBuffer} buffer
  * @param {object} [options={}]
  * @param {object} [options.id=Math.random()]
- * @param {string} [options.label=options.id] human redeable label
- * @param {string} [options.spectrumCallback] a callback to apply on variables when creating spectrum. Default will add a and t
- * @return {Analysis} - New class element with the given data
+ * @param {string} [options.label=options.id] - human redeable label
+ * @param {string} [options.spectrumCallback] - a callback to apply on variables when creating spectrum. Default will add a and t
+ * @returns {Analysis} - New class element with the given data
  */
 
 export function fromSPC(buffer, options = {}) {

package/src/from/utils/spectrumCallback.js

@@ -7,13 +7,12 @@ export function spectrumCallback(variables) {
   if (yVariable.label.toLowerCase().includes('trans')) {
     absorbance = false;
   }
-
   if (absorbance) {
-    variables.a = { ...yVariable };
-    variables.a.data = variables.a.data.slice();
+    variables.a = { ...yVariable, symbol: 'a', data: yVariable.data.slice() };
     variables.t = {
       data: yVariable.data.map((absorbance) => 10 ** -absorbance * 100),
       label: 'Transmittance (%)',
+      symbol: 't',
       units: '',
     };
   } else {
@@ -22,20 +21,23 @@ export function spectrumCallback(variables) {
       yVariable.label.toLowerCase().includes('percent')
         ? 100
         : 1;
+
     variables.a = {
       data: yVariable.data.map(
         (transmittance) => -Math.log10(transmittance / factor),
       ),
+      symbol: 'a',
       label: 'Absorbance',
       units: '',
     };
     if (factor === 100) {
-      variables.t = { ...yVariable };
+      variables.t = { ...yVariable, symbol: 't' };
       variables.t.data = variables.t.data.slice();
     } else {
       variables.t = {
         units: '',
         label: 'Transmittance (%)',
+        symbol: 't',
         data: yVariable.data.map((transmittance) => transmittance * 100),
       };
     }

package/src/index.js

@@ -1,14 +1,25 @@
-import { JSGraph as OriginalJSGraph } from 'common-spectrum';
+import {
+  JSGraph as OriginalJSGraph,
+  autoPeakPicking as originalAutoPeakPicking,
+  peakPicking as originalPeakPicking,
+} from 'common-spectrum';
 
+import { convertPeak } from './convertPeak.js';
 import { getAnnotations } from './jsgraph/getAnnotations';
 
-export {
-  Analysis,
-  AnalysesManager,
-  toJcamp,
-  peakPicking,
-  autoPeakPicking,
-} from 'common-spectrum';
+export { Analysis, AnalysesManager, toJcamp } from 'common-spectrum';
+
+export function peakPicking(spectrum, target, options) {
+  const peak = originalPeakPicking(spectrum, target, options);
+  if (!peak) return undefined;
+  return convertPeak(peak, spectrum);
+}
+
+export function autoPeakPicking(spectrum, options) {
+  const peaks = originalAutoPeakPicking(spectrum, options);
+  if (!peaks) return [];
+  return peaks.map((peak) => convertPeak(peak, spectrum));
+}
 
 export { fromJcamp } from './from/fromJcamp';
 export { fromSPC } from './from/fromSPC';

package/src/jsgraph/getAnnotations.js

@@ -1,5 +1,5 @@
 /**
- * @typedef {Object} Peak
+ * @typedef {object} Peak
  * @property {number} wavenumber
  * @property {number} transmittance
  * @property {number} absorbance
@@ -9,14 +9,14 @@
 
 /**
  * Creates annotations for jsgraph that allows to display the result of peak picking
- * @param {array<Peak>} peaks
+ * @param {Array<Peak>} peaks
  * @param {object} [options={}]
  * @param {string} [options.fillColor='green']
  * @param {string} [options.strokeColor='red']
- * @param {string} [options.showKind=true] Display the kind, 'm', 'w', 'S'
- * @param {string} [options.showAssignment=true] Display the assignment
- * @param {function} [options.createFct] (annotation, peak) => {}: callback allowing to add properties
- * @param {string} [options.mode='t100'] 't100'=transmittance in %, 't'=transmittance, 'a'=absorbance
+ * @param {string} [options.showKind=true] - Display the kind, 'm', 'w', 'S'
+ * @param {string} [options.showAssignment=true] - Display the assignment
+ * @param {Function} [options.createFct] - (annotation, peak) => {}: callback allowing to add properties
+ * @param {string} [options.mode='t100'] - 't100'=transmittance in %, 't'=transmittance, 'a'=absorbance
  * @returns array
  */
 
@@ -31,9 +31,9 @@ export function getAnnotations(peaks, options = {}) {
     let annotation = {
       line: 1,
       type: 'rect',
-      strokeColor: strokeColor,
+      strokeColor,
       strokeWidth: 0,
-      fillColor: fillColor,
+      fillColor,
     };
     if (creationFct) {
       creationFct(annotation, peak);

package/CHANGELOG.md

@@ -1,61 +0,0 @@
-# Changelog
-
-## [2.0.0](https://www.github.com/cheminfo/ir-spectrum/compare/v1.1.0...v2.0.0) (2022-05-05)
-
-
-### ⚠ BREAKING CHANGES
-
-* remove node 12 compatibility
-* update dependencies to use new ml-signal-processing package
-
-### Features
-
-* update dependencies to use new ml-signal-processing package ([41e89c2](https://www.github.com/cheminfo/ir-spectrum/commit/41e89c29fec7d228fd9c65828b471cde15af5a9c))
-
-
-### Miscellaneous Chores
-
-* remove node 12 compatibility ([fd426fc](https://www.github.com/cheminfo/ir-spectrum/commit/fd426fce70fcf8260de58a49224e6b66b07641e8))
-
-## [1.1.0](https://www.github.com/cheminfo/ir-spectrum/compare/v1.0.3...v1.1.0) (2021-09-07)
-
-
-### Features
-
-* add fromSPC ([d9eacf4](https://www.github.com/cheminfo/ir-spectrum/commit/d9eacf4cc3d4338ad630f7ee4798c3a168ead34f))
-
-
-### Bug Fixes
-
-* remove compatibility with node 10.x ([08ed76c](https://www.github.com/cheminfo/ir-spectrum/commit/08ed76c47905625822272eb6e9831ba57f6b777f))
-
-### [1.0.3](https://www.github.com/cheminfo/ir-spectrum/compare/v1.0.2...v1.0.3) (2021-07-06)
-
-
-### Bug Fixes
-
-* dot in README ([dac6c63](https://www.github.com/cheminfo/ir-spectrum/commit/dac6c63f88399c1e87f10dd6dbb163b9c149e9b9))
-* iupac link for technique ([b67a76d](https://www.github.com/cheminfo/ir-spectrum/commit/b67a76d98e494655f037a43915aea29ad00eb5ff))
-
-### [1.0.2](https://www.github.com/cheminfo/ir-spectrum/compare/v1.0.1...v1.0.2) (2021-04-14)
-
-
-### Bug Fixes
-
-* double reverse because same variable (pointer) ([208bcf9](https://www.github.com/cheminfo/ir-spectrum/commit/208bcf9c04d1dcd5f9875d773f5bb201f26d2c56))
-
-### [1.0.1](https://www.github.com/cheminfo/ir-spectrum/compare/v1.0.0...v1.0.1) (2021-03-29)
-
-
-### Bug Fixes
-
-* use wavenumber and not wavelength ([66b6b51](https://www.github.com/cheminfo/ir-spectrum/commit/66b6b51a7c92c424183c4b34865bd21d0d714848))
-
-## 1.0.0 (2021-03-26)
-
-
-### Features
-
-* add getAnnotations ([e3f8b63](https://www.github.com/cheminfo/ir-spectrum/commit/e3f8b631f74fbb4bcdcebab7f1b6666e9695b722))
-* add peakPicking and autoPeakPicking ([a950e2d](https://www.github.com/cheminfo/ir-spectrum/commit/a950e2d7a4c02009f6b3c5c82f9f264193f25345))
-* fromJcamp adds a and t ([b3c8d77](https://www.github.com/cheminfo/ir-spectrum/commit/b3c8d77404d49415f594ec94ba92009877fc81a4))