feat: added timeout option to avoid long executions. close #37 (#47)

* feat: add default value of timeout to avoid long executions

* feat: update opmitization package

* chore: improve jsdoc

* feat: add default value of timeout to avoid long executions

* feat: update opmitization package

Co-authored-by: Luc Patiny <[email protected]>

Author: jobo322

package.json

@@ -77,7 +77,7 @@
   "dependencies": {
     "ml-peak-shape-generator": "^0.12.0",
     "ml-savitzky-golay-generalized": "2.0.3",
-    "ml-spectra-fitting": "0.10.0",
+    "ml-spectra-fitting": "^0.11.0",
     "ml-spectra-processing": "^4.10.0"
   }
 }

src/post/__tests__/optimizePeaks.test.js

@@ -0,0 +1,30 @@
+import { generateSpectrum } from 'spectrum-generator';
+
+import { optimizePeaks } from '../optimizePeaks';
+
+describe('optimizePeaks', () => {
+  it('Should throw because execution time is over timeout', () => {
+    const peaks = [{ x: 0, y: 1, width: 0.12 }];
+
+    const data = generateSpectrum(peaks, {
+      from: -0.5,
+      to: 0.5,
+      nbPoints: 101,
+      shape: {
+        kind: 'gaussian',
+      },
+    });
+
+    const options = {
+      optimization: {
+        kind: 'lm',
+        options: {
+          timeout: 0,
+        },
+      },
+    };
+    expect(() =>
+      optimizePeaks(data, [{ x: 0.1, y: 0.9, width: 0.11 }], options),
+    ).toThrow('The execution time is over to 0 seconds');
+  });
+});

src/post/joinBroadPeaks.js

@@ -9,13 +9,14 @@ import { optimize } from 'ml-spectra-fitting';
  * @param {string} [options.shape.kind = 'gaussian'] - kind of shape; lorentzian, gaussian and pseudovoigt are supported.
  * @param {object} [options.optimization = {}] - it's specify the kind and options of the algorithm use to optimize parameters.
  * @param {string} [options.optimization.kind = 'lm'] - kind of algorithm. By default it's levenberg-marquardt.
+ * @param {number} [options.optimization.options.timeout = 10] - maximum time running before break in seconds.
  * @param {object} [options.optimization.options = {}] - options for the specific kind of algorithm.
  */
 export function joinBroadPeaks(peakList, options = {}) {
   let {
     width = 0.25,
     shape = { kind: 'gaussian' },
-    optimization = { kind: 'lm' },
+    optimization = { kind: 'lm', timeout: 10 },
   } = options;
   let broadLines = [];
   // Optimize the possible broad lines

src/post/optimizePeaks.js

@@ -13,9 +13,9 @@ import { groupPeaks } from './groupPeaks';
  * @param {number} [options.factorLimits = 2] - times of width to use to optimize peaks
  * @param {object} [options.shape={}] - it's specify the kind of shape used to fitting.
  * @param {string} [options.shape.kind='gaussian'] - kind of shape; lorentzian, gaussian and pseudovoigt are supported.
- * @param {string} [options.shape.options] - kind of shape; lorentzian, gaussian and pseudovoigt are supported.
  * @param {object} [options.optimization={}] - it's specify the kind and options of the algorithm use to optimize parameters.
  * @param {string} [options.optimization.kind='lm'] - kind of algorithm. By default it's levenberg-marquardt.
+ * @param {number} [options.optimization.options.timeout=10] - maximum time running before break in seconds.
  * @param {object} [options.optimization.options={}] - options for the specific kind of algorithm.
  */
 
@@ -28,6 +28,9 @@ export function optimizePeaks(data, peakList, options = {}) {
     },
     optimization = {
       kind: 'lm',
+      options: {
+        timeout: 10,
+      },
     },
   } = options;