ir-spectrum 1.0.2 → 2.0.0

package/CHANGELOG.md

@@ -1,5 +1,42 @@
 # 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)
 
 

package/README.md

@@ -4,8 +4,6 @@
 [![Test coverage][codecov-image]][codecov-url]
 [![npm download][download-image]][download-url]
 
-.
-
 ## Installation
 
 `$ npm install --save ir-spectrum`

package/lib/index.js

@@ -3,6 +3,7 @@
 Object.defineProperty(exports, '__esModule', { value: true });
 
 var commonSpectrum = require('common-spectrum');
+var spcParser = require('spc-parser');
 
 /**
  * @typedef {Object} Peak
@@ -170,10 +171,6 @@ function annotationAbsorbance(annotation, peak, options = {}) {
   ];
 }
 
-function fromJcamp(jcamp, options) {
-  return commonSpectrum.fromJcamp(jcamp, { ...options, spectrumCallback });
-}
-
 function spectrumCallback(variables) {
   // we add missing absorbance / transmittance
   // variable a = absorbance
@@ -218,37 +215,68 @@ function spectrumCallback(variables) {
   }
 }
 
+/**
+ * Creates a new Analysis from a SPC buffer
+ * @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
+ */
+function fromJcamp(jcamp, options = {}) {
+  return commonSpectrum.fromJcamp(jcamp, { ...options, spectrumCallback });
+}
+
+/**
+ * Creates a new Analysis from a SPC buffer
+ * @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
+ */
+
+function fromSPC(buffer, options = {}) {
+  let analysis = new commonSpectrum.Analysis({ ...options, spectrumCallback });
+  let result = spcParser.parse(buffer);
+
+  if (result.meta) delete result.meta.parameters;
+
+  for (let spectrum of result.spectra) {
+    if (spectrum.meta) delete spectrum.meta.parameters;
+    analysis.pushSpectrum(spectrum.variables, {
+      dataType: 'IR SPECTRUM',
+      title: '',
+      meta: { ...result.meta, ...spectrum.meta },
+    });
+  }
+  return analysis;
+}
+
 const JSGraph = { ...commonSpectrum.JSGraph, getAnnotations };
 
 Object.defineProperty(exports, 'AnalysesManager', {
   enumerable: true,
-  get: function () {
-    return commonSpectrum.AnalysesManager;
-  }
+  get: function () { return commonSpectrum.AnalysesManager; }
 });
 Object.defineProperty(exports, 'Analysis', {
   enumerable: true,
-  get: function () {
-    return commonSpectrum.Analysis;
-  }
+  get: function () { return commonSpectrum.Analysis; }
 });
 Object.defineProperty(exports, 'autoPeakPicking', {
   enumerable: true,
-  get: function () {
-    return commonSpectrum.autoPeakPicking;
-  }
+  get: function () { return commonSpectrum.autoPeakPicking; }
 });
 Object.defineProperty(exports, 'peakPicking', {
   enumerable: true,
-  get: function () {
-    return commonSpectrum.peakPicking;
-  }
+  get: function () { return commonSpectrum.peakPicking; }
 });
 Object.defineProperty(exports, 'toJcamp', {
   enumerable: true,
-  get: function () {
-    return commonSpectrum.toJcamp;
-  }
+  get: function () { return commonSpectrum.toJcamp; }
 });
 exports.JSGraph = JSGraph;
 exports.fromJcamp = fromJcamp;
+exports.fromSPC = fromSPC;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "ir-spectrum",
-  "version": "1.0.2",
+  "version": "2.0.0",
   "description": "",
   "main": "lib/index.js",
   "module": "src/index.js",
@@ -14,6 +14,8 @@
     "eslint": "eslint src",
     "eslint-fix": "npm run eslint -- --fix",
     "prepublishOnly": "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"
@@ -33,23 +35,46 @@
     "testEnvironment": "node"
   },
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.13.8",
-    "@types/jest": "^26.0.22",
-    "cheminfo-build": "^1.1.10",
-    "codecov": "^3.8.1",
-    "eslint": "^7.22.0",
-    "eslint-config-cheminfo": "^5.2.3",
-    "eslint-plugin-import": "^2.22.1",
-    "eslint-plugin-jest": "^24.3.2",
-    "eslint-plugin-prettier": "^3.3.1",
+    "@babel/plugin-transform-modules-commonjs": "^7.17.9",
+    "@types/jest": "^27.5.0",
+    "cheminfo-build": "^1.1.11",
+    "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",
     "esm": "^3.2.25",
-    "jest": "^26.6.3",
-    "jest-matcher-deep-close-to": "^2.0.1",
-    "prettier": "^2.2.1",
-    "rollup": "^2.42.4"
+    "jest": "^28.0.3",
+    "jest-matcher-deep-close-to": "^3.0.2",
+    "prettier": "^2.6.2",
+    "rollup": "^2.72.0"
   },
   "dependencies": {
-    "common-spectrum": "0.30.1",
-    "ml-gsd": "^6.6.1"
+    "common-spectrum": "1.0.2",
+    "ml-gsd": "^11.2.0",
+    "spc-parser": "^0.5.2"
+  },
+  "info": {
+    "logo": "https://raw.githubusercontent.com/cheminfo/font/master/src/ir/assignment.svg",
+    "domain": [
+      "Physical Chemistry",
+      "Materials Science",
+      "Organic Chemistry"
+    ],
+    "technique": {
+      "name": "IR",
+      "chmo": "0000630",
+      "iupac": "https://goldbook.iupac.org/terms/view/IT07399"
+    },
+    "functionality": {
+      "fileTypes": [
+        {
+          "extension": "jdx",
+          "manufacturer": "IUPAC",
+          "example": "https://raw.githubusercontent.com/cheminfo/ir-spectrum/master/testFiles/absorbance.jdx"
+        }
+      ]
+    }
   }
 }

package/src/from/fromJcamp.js

@@ -1,49 +1,16 @@
 import { fromJcamp as commonFromJcamp } from 'common-spectrum';
 
-export function fromJcamp(jcamp, options) {
-  return commonFromJcamp(jcamp, { ...options, spectrumCallback });
-}
+import { spectrumCallback } from './utils/spectrumCallback';
 
-function spectrumCallback(variables) {
-  // we add missing absorbance / transmittance
-  // variable a = absorbance
-  // variable t = transmittance
-  let yVariable = variables.y;
-  let absorbance = true;
-  if (yVariable.label.toLowerCase().includes('trans')) {
-    absorbance = false;
-  }
-
-  if (absorbance) {
-    variables.a = { ...yVariable };
-    variables.a.data = variables.a.data.slice();
-    variables.t = {
-      data: yVariable.data.map((absorbance) => 10 ** -absorbance * 100),
-      label: 'Transmittance (%)',
-      units: '',
-    };
-  } else {
-    const factor =
-      yVariable.label.includes('%') ||
-      yVariable.label.toLowerCase().includes('percent')
-        ? 100
-        : 1;
-    variables.a = {
-      data: yVariable.data.map(
-        (transmittance) => -Math.log10(transmittance / factor),
-      ),
-      label: 'Absorbance',
-      units: '',
-    };
-    if (factor === 100) {
-      variables.t = { ...yVariable };
-      variables.t.data = variables.t.data.slice();
-    } else {
-      variables.t = {
-        units: '',
-        label: 'Transmittance (%)',
-        data: yVariable.data.map((transmittance) => transmittance * 100),
-      };
-    }
-  }
+/**
+ * Creates a new Analysis from a SPC buffer
+ * @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
+ */
+export function fromJcamp(jcamp, options = {}) {
+  return commonFromJcamp(jcamp, { ...options, spectrumCallback });
 }

package/src/from/fromSPC.js

@@ -0,0 +1,31 @@
+import { Analysis } from 'common-spectrum';
+import { parse } from 'spc-parser';
+
+import { spectrumCallback } from './utils/spectrumCallback';
+
+/**
+ * Creates a new Analysis from a SPC buffer
+ * @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
+ */
+
+export function fromSPC(buffer, options = {}) {
+  let analysis = new Analysis({ ...options, spectrumCallback });
+  let result = parse(buffer);
+
+  if (result.meta) delete result.meta.parameters;
+
+  for (let spectrum of result.spectra) {
+    if (spectrum.meta) delete spectrum.meta.parameters;
+    analysis.pushSpectrum(spectrum.variables, {
+      dataType: 'IR SPECTRUM',
+      title: '',
+      meta: { ...result.meta, ...spectrum.meta },
+    });
+  }
+  return analysis;
+}

package/src/from/utils/spectrumCallback.js

@@ -0,0 +1,43 @@
+export function spectrumCallback(variables) {
+  // we add missing absorbance / transmittance
+  // variable a = absorbance
+  // variable t = transmittance
+  let yVariable = variables.y;
+  let absorbance = true;
+  if (yVariable.label.toLowerCase().includes('trans')) {
+    absorbance = false;
+  }
+
+  if (absorbance) {
+    variables.a = { ...yVariable };
+    variables.a.data = variables.a.data.slice();
+    variables.t = {
+      data: yVariable.data.map((absorbance) => 10 ** -absorbance * 100),
+      label: 'Transmittance (%)',
+      units: '',
+    };
+  } else {
+    const factor =
+      yVariable.label.includes('%') ||
+      yVariable.label.toLowerCase().includes('percent')
+        ? 100
+        : 1;
+    variables.a = {
+      data: yVariable.data.map(
+        (transmittance) => -Math.log10(transmittance / factor),
+      ),
+      label: 'Absorbance',
+      units: '',
+    };
+    if (factor === 100) {
+      variables.t = { ...yVariable };
+      variables.t.data = variables.t.data.slice();
+    } else {
+      variables.t = {
+        units: '',
+        label: 'Transmittance (%)',
+        data: yVariable.data.map((transmittance) => transmittance * 100),
+      };
+    }
+  }
+}

package/src/index.js

@@ -11,5 +11,6 @@ export {
 } from 'common-spectrum';
 
 export { fromJcamp } from './from/fromJcamp';
+export { fromSPC } from './from/fromSPC';
 
 export const JSGraph = { ...OriginalJSGraph, getAnnotations };