feat: peak picking returns id and keep id if it exists (#108)

* chore: initial steps to keep id property * feat(broadenPeaks): conditional type * chore(joinBroadPeaks): conditional type * feat(setShape): generic function n output option pure function now * chore(gsd): peaks with id * chore: refactor broadenPeaks * chore(joinBroadPeaks): refactor * chore(joinBroadPeaks): remove conditional type * chore(optimizePeaks): conditional types * fix(addMissingShape): convert to pure * fix(optimizePeaks): convert to generic n conditional types * feat: addMissingIDs
mljs · Aug 27, 2022 · f22f5a5 · f22f5a5
1 parent 928ea11
commit f22f5a5
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Showing 21 changed files with 234 additions and 101 deletions.
diff --git a/package.json b/package.json
@@ -79,10 +79,11 @@
     "xy-parser": "^5.0.2"
   },
   "dependencies": {
+    "@lukeed/uuid": "^2.0.0",
     "cheminfo-types": "^1.1.0",
     "ml-peak-shape-generator": "^4.1.1",
     "ml-savitzky-golay-generalized": "^4.0.1",
-    "ml-spectra-fitting": "^4.1.0",
+    "ml-spectra-fitting": "^4.1.1",
     "ml-spectra-processing": "^11.6.0"
   }
 }
diff --git a/src/GSDBroadenPeak.ts b/src/GSDBroadenPeak.ts
@@ -1,7 +1,11 @@
+import { Shape1D } from 'ml-peak-shape-generator';
+
 export interface GSDBroadenPeak {
+  id?: string;
   x: number;
   y: number;
   width: number;
+  shape?: Shape1D;
   index: number;
   from: { x: number };
   to: { x: number };

diff --git a/src/GSDPeak.ts b/src/GSDPeak.ts
@@ -1,6 +1,7 @@
 import { Shape1D } from 'ml-peak-shape-generator';
 
 export interface GSDPeak {
+  id?: string;
   x: number;
   y: number;
   /**

diff --git a/src/GSDPeakOptimized.ts b/src/GSDPeakOptimized.ts
@@ -1,6 +1,7 @@
 import { Shape1D } from 'ml-peak-shape-generator';
 
 export interface GSDPeakOptimized {
+  id?: string;
   x: number;
   y: number;
   width: number;

diff --git a/src/__tests__/gaussian-smooth.test.ts b/src/__tests__/gaussian-smooth.test.ts
@@ -33,6 +33,7 @@ describe('gaussian simulated peaks', () => {
     });
     expect(peakList).toBeDeepCloseTo([
       {
+        id: peakList[0].id,
         x: -0.5,
         y: 0.6945098953985852,
         ddY: -259.83290100626783,
@@ -48,6 +49,7 @@ describe('gaussian simulated peaks', () => {
         },
       },
       {
+        id: peakList[1].id,
         x: 0.5,
         y: 0.6945098953985852,
         ddY: -259.83290100626783,

diff --git a/src/__tests__/gaussian.test.ts b/src/__tests__/gaussian.test.ts
@@ -63,7 +63,7 @@ describe('smooth:false option', () => {
         },
       },
     ];
-    expect(peakList).toBeDeepCloseTo(expected);
+    expect(peakList).toBeDeepCloseTo(addMissingID(peakList, expected));
   });
 
   it('negative maxima peaks', () => {
@@ -101,7 +101,7 @@ describe('smooth:false option', () => {
         },
       },
     ];
-    expect(peakList).toBeDeepCloseTo(expected);
+    expect(peakList).toBeDeepCloseTo(addMissingID(peakList, expected));
   });
 
   it('Negative peaks', () => {
@@ -143,7 +143,7 @@ describe('smooth:false option', () => {
       },
     ];
 
-    expect(peakList).toBeDeepCloseTo(expected);
+    expect(peakList).toBeDeepCloseTo(addMissingID(peakList, expected));
   });
 
   it('minima peaks', () => {
@@ -185,7 +185,7 @@ describe('smooth:false option', () => {
       },
     ];
 
-    expect(peakList).toBeDeepCloseTo(expected);
+    expect(peakList).toBeDeepCloseTo(addMissingID(peakList, expected));
   });
 
   it('negative peaks with maxCriteria true', () => {
@@ -196,3 +196,10 @@ describe('smooth:false option', () => {
     expect(peakList).toHaveLength(0);
   });
 });
+
+function addMissingID(peaks, expected) {
+  for (let i = 0; i < expected.length; i++) {
+    expected[i].id = peaks[i].id;
+  }
+  return expected;
+}
diff --git a/src/__tests__/power.test.ts b/src/__tests__/power.test.ts
@@ -51,6 +51,7 @@ describe('power', () => {
     let peakList = gsd(data);
     let expected = [
       {
+        id: peakList[0].id,
         x: 5,
         y: 10000,
         width: 0.3,
@@ -77,6 +78,7 @@ describe('power', () => {
     // This shape is anyway quite strange
     const expected = [
       {
+        id: peakList[0].id,
         x: 4.45,
         y: 7921,
         width: 0.05,
@@ -92,6 +94,7 @@ describe('power', () => {
         },
       },
       {
+        id: peakList[1].id,
         x: 5,
         y: 10000,
         width: 0.2,
@@ -107,6 +110,7 @@ describe('power', () => {
         },
       },
       {
+        id: peakList[2].id,
         x: 5.55,
         y: 7921,
         width: 0.05,

diff --git a/src/__tests__/ubiquitin.test.ts b/src/__tests__/ubiquitin.test.ts
@@ -22,7 +22,9 @@ describe('Global spectra deconvolution ubiquitin', () => {
       realTopDetection: true,
       sgOptions: { windowSize: 7, polynomial: 3 },
     });
+
     expect(peaks[0]).toBeDeepCloseTo({
+      id: peaks[0].id,
       x: 200.05527917306466,
       y: 28.795378784444413,
       ddY: -15468134.039875854,

diff --git a/src/gsd.ts b/src/gsd.ts
@@ -1,3 +1,4 @@
+import { v4 as generateID } from '@lukeed/uuid';
 import type { DataXY } from 'cheminfo-types';
 import { Shape1D } from 'ml-peak-shape-generator';
 import { sgg, SGGOptions } from 'ml-savitzky-golay-generalized';
@@ -10,6 +11,8 @@ import {
 } from 'ml-spectra-processing';
 
 import { GSDPeak } from './GSDPeak';
+import { MakeMandatory } from './utils/MakeMandatory';
+import { MakeOptional } from './utils/MakeOptional';
 import { optimizeTop } from './utils/optimizeTop';
 import { setShape } from './utils/setShape';
 
@@ -52,7 +55,8 @@ export interface GSDOptions {
    */
   shape?: Shape1D;
 }
-
+export type GSDPeakID = MakeMandatory<GSDPeak, 'id'>;
+export type GSDPeakIDOptionalShape = MakeOptional<GSDPeak, 'shape'>;
 /**
  * Global spectra deconvolution
  * @param  data - Object data with x and y arrays. Values in x has to be growing
@@ -61,7 +65,7 @@ export interface GSDOptions {
 
  */
 
-export function gsd(data: DataXY, options: GSDOptions = {}): GSDPeak[] {
+export function gsd(data: DataXY, options: GSDOptions = {}): GSDPeakID[] {
   let {
     sgOptions = {
       windowSize: 9,
@@ -217,7 +221,7 @@ export function gsd(data: DataXY, options: GSDOptions = {}): GSDPeak[] {
 
   let lastK = -1;
 
-  const peaks: GSDPeak[] = [];
+  const peaks: GSDPeakIDOptionalShape[] = [];
   for (const minddYIndex of minddY) {
     let deltaX = x[minddYIndex];
     let possible = -1;
@@ -245,6 +249,7 @@ export function gsd(data: DataXY, options: GSDOptions = {}): GSDPeak[] {
       if (yData[minddYIndex] > yThreshold) {
         let width = Math.abs(intervalR[possible].x - intervalL[possible].x);
         peaks.push({
+          id: generateID(),
           x: deltaX,
           y: yData[minddYIndex],
           width,
@@ -254,7 +259,7 @@ export function gsd(data: DataXY, options: GSDOptions = {}): GSDPeak[] {
             from: intervalL[possible],
             to: intervalR[possible],
           },
-        } as GSDPeak);
+        });
       }
     }
   }
@@ -274,5 +279,5 @@ export function gsd(data: DataXY, options: GSDOptions = {}): GSDPeak[] {
     return a.x - b.x;
   });
 
-  return setShape(peaks, { shape });
+  return setShape(peaks, { shape }) as GSDPeakID[];
 }
diff --git a/src/post/__tests__/broadenPeaks.test.ts b/src/post/__tests__/broadenPeaks.test.ts
@@ -300,6 +300,7 @@ describe('broadenPeaks', () => {
     let result = broadenPeaks(
       [
         {
+          id: '1',
           x: -0.5,
           y: 1,
           ddY: 0,
@@ -327,6 +328,7 @@ describe('broadenPeaks', () => {
           ddY: 0,
           width: 0.08,
           index: 575,
+          shape: { kind: 'gaussian' },
           inflectionPoints: {
             from: { index: 573, x: 10.46 },
             to: { index: 577, x: 10.54 },
@@ -335,31 +337,36 @@ describe('broadenPeaks', () => {
       ],
       { factor: 20 },
     );
-    expect(result).toBeDeepCloseTo([
-      {
-        x: -0.5,
-        y: 1,
-        index: 25,
-        width: 1.3,
-        from: { x: -1.3 },
-        to: { x: 0 },
-      },
-      {
-        x: 0.5,
-        y: 1,
-        index: 75,
-        width: 1.3,
-        from: { x: 0 },
-        to: { x: 1.3 },
-      },
-      {
-        x: 10.5,
-        y: 1,
-        index: 575,
-        width: 1.6,
-        from: { x: 9.7 },
-        to: { x: 11.3 },
-      },
-    ]);
+    expect(result).toBeDeepCloseTo(
+      [
+        {
+          id: '1',
+          x: -0.5,
+          y: 1,
+          index: 25,
+          width: 1.3,
+          from: { x: -1.3 },
+          to: { x: 0 },
+        },
+        {
+          x: 0.5,
+          y: 1,
+          index: 75,
+          width: 1.3,
+          from: { x: 0 },
+          to: { x: 1.3 },
+        },
+        {
+          x: 10.5,
+          y: 1,
+          index: 575,
+          shape: { kind: 'gaussian' },
+          width: 1.6,
+          from: { x: 9.7 },
+          to: { x: 11.3 },
+        },
+      ],
+      1,
+    );
   });
 });
diff --git a/src/post/__tests__/joinBroadPeaks.test.ts b/src/post/__tests__/joinBroadPeaks.test.ts
@@ -26,7 +26,6 @@ describe('joinBroadPeaks', () => {
       broadRatio: 0.03,
       broadWidth: 0.25,
     });
-
     expect(peaks.length).toBeGreaterThan(3);
     expect(newPeaks).toHaveLength(3);
   });