ml-gsd - npm Package Compare versions

Comparing version 6.6.2 to 6.6.3

CHANGELOG.md

 # Changelog
 
+### [6.6.3](https://www.github.com/mljs/global-spectral-deconvolution/compare/v6.6.2...v6.6.3) (2021-06-18)
+
+
+### Bug Fixes
+
+* maxCriteria=false gives more consistent results ([2652ec2](https://www.github.com/mljs/global-spectral-deconvolution/commit/2652ec265193207ff128348c8d0207d74e1b0c0c))
+
 ### [6.6.2](https://www.github.com/mljs/global-spectral-deconvolution/compare/v6.6.1...v6.6.2) (2021-05-11)
@@ -4,0 +11,0 @@

lib/index.js

@@ -60,17 +60,14 @@ 'use strict';
 
+  if (maxCriteria === false) {
+    for (let i = 0; i < y.length; i++) {
+      y[i] *= -1;
+    }
+  }
+
   if (noiseLevel === undefined) {
     noiseLevel = equalSpaced ? getNoiseLevel(y) : 0;
   }
-
-  const yCorrection = { m: 1, b: noiseLevel };
-
-  if (!maxCriteria) {
-    yCorrection.m = -1;
-    yCorrection.b *= -1;
-  }
-
   for (let i = 0; i < y.length; i++) {
-    y[i] = yCorrection.m * y[i] - yCorrection.b;
+    y[i] -= noiseLevel;
   }
-
   for (let i = 0; i < y.length; i++) {
@@ -224,3 +221,5 @@ if (y[i] < 0) {
           x: frequency,
-          y: (yData[minddY[j]] + yCorrection.b) / yCorrection.m,
+          y: maxCriteria
+            ? yData[minddY[j]] + noiseLevel
+            : -yData[minddY[j]] - noiseLevel,
           width: widthProcessor(width),
@@ -227,0 +226,0 @@ soft: broadMask[j],

package.json

 {
   "name": "ml-gsd",
-  "version": "6.6.2",
+  "version": "6.6.3",
   "description": "Global Spectra Deconvolution",
@@ -61,6 +61,6 @@ "main": "lib/index.js",
     "cheminfo-build": "^1.1.10",
-    "eslint": "^7.26.0",
+    "eslint": "^7.27.0",
     "eslint-config-cheminfo": "^5.2.4",
     "esm": "^3.2.25",
-    "jest": "^26.6.3",
+    "jest": "^27.0.1",
     "jest-matcher-deep-close-to": "^2.0.1",
@@ -71,3 +71,3 @@ "mf-global": "^1.3.6",
     "prettier": "^2.3.0",
-    "rollup": "^2.47.0",
+    "rollup": "^2.50.1",
     "spectrum-generator": "^4.7.1",
@@ -80,4 +80,4 @@ "xy-parser": "^3.1.1"
     "ml-spectra-fitting": "^1.0.0",
-    "ml-spectra-processing": "^6.5.0"
+    "ml-spectra-processing": "^6.6.0"
   }
 }

src/__tests__/simple.js

@@ -10,9 +10,13 @@ import { toMatchCloseTo } from 'jest-matcher-deep-close-to';
   let y = [];
+  let negY = [];
   for (let i = 0; i < 10; i++) {
     x.push(x.length);
     y.push(0);
+    negY.push(0);
   }
   for (let i = 0; i <= 10; i++) {
     x.push(x.length);
-    y.push(i > 5 ? 10 - i : i);
+    let newY = i > 5 ? 10 - i : i;
+    y.push(newY);
+    negY.push(-newY);
   }
@@ -22,2 +26,3 @@ for (let i = 0; i < 10; i++) {
     y.push(0);
+    negY.push(0);
   }
@@ -43,2 +48,20 @@
 
+  it('gsd negative peak', () => {
+    let peaks = gsd(
+      { x, y: negY },
+      {
+        realTopDetection: false,
+        maxCriteria: false,
+        smoothY: true,
+        sgOptions: {
+          windowSize: 5,
+          polynomial: 3,
+        },
+      },
+    );
+    expect(peaks[0].y).toBeCloseTo(-4.657, 3);
+    expect(peaks[0].base).toBeCloseTo(1.1956, 3);
+    expect(peaks[0].x).toStrictEqual(15);
+  });
+
   it('gsd not realtop asymetric', () => {
@@ -45,0 +68,0 @@ let Y2 = y.slice(0);

src/gsd.js

@@ -50,17 +50,14 @@ import { getShapeGenerator } from 'ml-peak-shape-generator';
 
+  if (maxCriteria === false) {
+    for (let i = 0; i < y.length; i++) {
+      y[i] *= -1;
+    }
+  }
+
   if (noiseLevel === undefined) {
     noiseLevel = equalSpaced ? getNoiseLevel(y) : 0;
   }
-
-  const yCorrection = { m: 1, b: noiseLevel };
-
-  if (!maxCriteria) {
-    yCorrection.m = -1;
-    yCorrection.b *= -1;
-  }
-
   for (let i = 0; i < y.length; i++) {
-    y[i] = yCorrection.m * y[i] - yCorrection.b;
+    y[i] -= noiseLevel;
   }
-
   for (let i = 0; i < y.length; i++) {
@@ -214,3 +211,5 @@ if (y[i] < 0) {
           x: frequency,
-          y: (yData[minddY[j]] + yCorrection.b) / yCorrection.m,
+          y: maxCriteria
+            ? yData[minddY[j]] + noiseLevel
+            : -yData[minddY[j]] - noiseLevel,
           width: widthProcessor(width),
@@ -217,0 +216,0 @@ soft: broadMask[j],

src/post/__tests__/optimizePeaks.test.js

@@ -0,1 +1,2 @@
+import { toMatchCloseTo } from 'jest-matcher-deep-close-to';
 import { generateSpectrum } from 'spectrum-generator';
@@ -5,2 +6,4 @@
 
+expect.extend({ toMatchCloseTo });
+
 describe('optimizePeaks', () => {
@@ -19,2 +22,12 @@ it('Should throw because execution time is over timeout', () => {
 
+    let result = optimizePeaks(data, [{ x: 0.01, y: 0.9, width: 0.11 }]);
+    expect(result).toMatchCloseTo([
+      {
+        x: -3.419674049814014e-8,
+        y: 0.999994064595118,
+        width: 0.12000070163648587,
+        group: 0,
+      },
+    ]);
+
     const options = {
@@ -21,0 +34,0 @@ optimization: {

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Found 1 instance in 1 package

Fixed alerts

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Improved metrics

Total package byte prevSize

5869127

increased by0.05%

Number of package files

32

increased by3.23%

Lines of code

1894

increased by6.17%

Dependency changes

• - Removedcheminfo-types@0.5.0(transitive)

• - Removedml-gsd@6.9.2(transitive)

• - Removedml-peak-shape-generator@2.0.2(transitive)

• Updatedml-spectra-processing@^6.6.0