Merge branch 'main' of https://github.com/cheminfo/mass-tools

cheminfo · Oct 13, 2023 · 72471e2 · 72471e2
2 parents b7177e3 + 9167b72
commit 72471e2
Show file tree

Hide file tree

Showing 3 changed files with 45 additions and 7 deletions.
diff --git a/packages/mfs-deconvolution/package.json b/packages/mfs-deconvolution/package.json
@@ -20,6 +20,7 @@
   },
   "homepage": "https://github.com/cheminfo/mass-tools/tree/main/packages/emdb#readme",
   "dependencies": {
+    "@lukeed/uuid": "^2.0.1",
     "cheminfo-types": "^1.7.2",
     "isotopic-distribution": "^3.0.1",
     "mf-generator": "^3.0.2",

diff --git a/packages/mfs-deconvolution/src/__tests__/mfsDeconvolution.test.js b/packages/mfs-deconvolution/src/__tests__/mfsDeconvolution.test.js
@@ -121,12 +121,17 @@ describe('mfsDeconvolution', () => {
     const logger = new FifoLogger();
     const text = readFileSync(join(__dirname, './data/isotopic.txt'));
     const spectrum = new Spectrum(parseXY(text));
-    const { mfs, reconstructed, matchingScore, difference } =
-      await mfsDeconvolution(spectrum, ['HValOH', '([13C]C-1)0-10,Br'], {
-        ionizations: 'H+',
-        logger,
-        peakWidthFct: (em) => em / 1000,
-      });
+    const {
+      mfs,
+      reconstructed,
+      matchingScore,
+      difference,
+      getFilteredReconstructed,
+    } = await mfsDeconvolution(spectrum, ['HValOH', '([13C]C-1)0-10,Br'], {
+      ionizations: 'H+',
+      logger,
+      peakWidthFct: (em) => em / 1000,
+    });
     expect(matchingScore).toBeCloseTo(1);
     const absoluteQuantities = mfs.map((mf) => mf.absoluteQuantity);
     expect(absoluteQuantities).toBeDeepCloseTo([100, 50, 20, 10, 0, 0, 0], 3);
@@ -142,5 +147,20 @@ describe('mfsDeconvolution', () => {
     expect(difference.x).toHaveLength(19);
     expect(difference.y).toHaveLength(19);
     expect(logger.getLogs()).toHaveLength(5);
+
+    const filteredReconstructed = getFilteredReconstructed();
+    expect(filteredReconstructed).toStrictEqual(reconstructed);
+
+    const reallyFilteredReconstructed = getFilteredReconstructed(
+      mfs.slice(2, 4).map((mf) => mf.id),
+    );
+    expect(reallyFilteredReconstructed.x).toStrictEqual(
+      filteredReconstructed.x,
+    );
+    expect(reallyFilteredReconstructed.y).toBeDeepCloseTo([
+      0, 0, 19.174220339122392, 10.423872010621597, 0.35511193913682987,
+      0.04532585451294238, 0.0012090061609091609, 0.00005384872306899919,
+      0.0000010912189424224057, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+    ]);
   });
 });
diff --git a/packages/mfs-deconvolution/src/mfsDeconvolution.js b/packages/mfs-deconvolution/src/mfsDeconvolution.js
@@ -1,3 +1,4 @@
+import { v4 } from '@lukeed/uuid';
 import { IsotopicDistribution } from 'isotopic-distribution';
 import { generateMFs } from 'mf-generator';
 import { fcnnlsVector } from 'ml-fcnnls';
@@ -48,8 +49,10 @@ export async function mfsDeconvolution(spectrum, ranges, options = {}) {
 
   const peakWidthFct = getPeakWidthFct(options);
   const centroids = getCentroids(spectrum, { threshold });
-
   let mfs = await generateMFs(ranges, { filter, ionizations });
+  mfs.forEach((mf) => {
+    mf.id = v4();
+  });
   mfs = addIsotopicDistributionAndCheckMF(mfs, { logger, peakWidthFct });
 
   mfs.sort((mf1, mf2) => mf1.ms.em - mf2.ms.em);
@@ -116,7 +119,21 @@ export async function mfsDeconvolution(spectrum, ranges, options = {}) {
     },
     mfs,
     matchingScore,
+    getFilteredReconstructed,
   };
+
+  function getFilteredReconstructed(ids = mfs.map((mf) => mf.id)) {
+    const filteredW = W.clone();
+    for (let i = 0; i < mfs.length; i++) {
+      if (ids.includes(mfs[i].id)) continue;
+      filteredW.set(0, i, 0);
+    }
+    const filteredReconstructed = filteredW.mmul(A).getRow(0);
+    return {
+      x: combined.x,
+      y: filteredReconstructed,
+    };
+  }
 }
 
 /**