fix: getPeaks heightFilter is based on the median of Y

examples/full.js

@@ -0,0 +1,16 @@
+import { SpectrumGenerator } from 'spectrum-generator';
+import { Chromatogram } from '../src';
+let spectrumGenerator = new SpectrumGenerator({ start: 0, end: 1000 });
+
+spectrumGenerator.addPeak([100, 100]);
+spectrumGenerator.addPeak([200, 20]);
+spectrumGenerator.addPeak([300, 30]);
+spectrumGenerator.addPeak([400, 40]);
+spectrumGenerator.addPeak([500, 50]);
+
+const { x, y } = spectrumGenerator.getSpectrum();
+
+const chromatogram = new Chromatogram(x, { tic: y });
+
+const peaks = chromatogram.getPeaks({ heightFilter: 2 });
+console.log(peaks);

package.json

@@ -47,7 +47,8 @@
     "jest": "^25.1.0",
     "jest-matcher-deep-close-to": "^1.3.0",
     "prettier": "^1.19.1",
-    "rollup": "^1.31.1"
+    "rollup": "^1.31.1",
+    "spectrum-generator": "^3.1.0"
   },
   "dependencies": {
     "binary-search": "^1.3.6",
@@ -57,6 +58,7 @@
     "mf-parser": "^0.13.1",
     "ml-array-max": "^1.1.2",
     "ml-array-mean": "^1.1.2",
+    "ml-array-median": "^1.1.2",
     "ml-array-sum": "^1.1.2",
     "ml-gsd": "^2.0.7",
     "ml-regression-polynomial": "^2.1.0",

src/util/getPeaks.js

@@ -1,5 +1,5 @@
 import { gsd, post } from 'ml-gsd';
-
+import median from 'ml-array-median';
 /**
  * Apply the GSD peak picking algorithm
  * @param {Chromatogram} chromatogram - GC/MS chromatogram where make the peak picking
@@ -58,7 +58,8 @@ export function getPeaks(chromatogram, options = {}) {
   peakList.sort((a, b) => a.height - b.height);
 
   // filter height by factor
-  let medianHeight = peakList[Math.floor((peakList.length - 1) / 2)].height;
+  let medianHeight = median(serie);
+
   peakList = peakList.filter((val) => val.height > medianHeight * heightFilter);
 
   let { factor = 1, overlap = false } = broadenPeaks;