nmr-processing - npm Package Compare versions

Comparing version 0.2.1 to 0.2.3

package.json

 {
   "name": "nmr-processing",
-  "version": "0.2.1",
+  "version": "0.2.3",
   "description": "",
@@ -42,12 +42,12 @@ "main": "lib/index.js",
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.10.1",
+    "@babel/plugin-transform-modules-commonjs": "^7.10.4",
     "@types/jest": "^25.2.1",
     "cheminfo-build": "^1.1.1",
-    "eslint": "^7.2.0",
+    "eslint": "^7.4.0",
     "eslint-config-cheminfo": "^3.0.0",
-    "eslint-plugin-import": "^2.21.2",
-    "eslint-plugin-jest": "^23.13.2",
+    "eslint-plugin-import": "^2.22.0",
+    "eslint-plugin-jest": "^23.18.0",
     "eslint-plugin-prettier": "^3.1.4",
     "esm": "^3.2.25",
-    "jest": "^26.0.1",
+    "jest": "^26.1.0",
     "jest-matcher-deep-close-to": "^2.0.1",
@@ -57,3 +57,3 @@ "ml-array-median": "^1.1.3",
     "prettier": "^2.0.5",
-    "rollup": "^2.17.0"
+    "rollup": "^2.21.0"
   },
@@ -63,3 +63,3 @@ "dependencies": {
     "ml-gsd": "^5.0.1",
-    "ml-matrix-peaks-finder": "^0.2.1",
+    "ml-matrix-peaks-finder": "^0.2.2",
     "ml-simple-clustering": "^0.1.0",
@@ -66,0 +66,0 @@ "ml-spectra-processing": "^4.0.0"

src/constants/gyromagneticRatio.js

@@ -1,3 +0,6 @@
-// source: https://en.wikipedia.org/wiki/Gyromagnetic_ratio
+// sources:
+// https://en.wikipedia.org/wiki/Gyromagnetic_ratio
 
+// TODO: can we have a better source and more digits ? @jwist
+
 export const gyromagneticRatio = {
@@ -4,0 +7,0 @@ '1H': 267.52218744e6,

src/xyz/xyzAutoPeaksPicking.js

@@ -20,3 +20,11 @@ import { FFTUtils } from 'ml-fft';
 export function xyzAutoPeaksPicking(spectraData, options = {}) {
-  let { thresholdFactor = 0.5, isHomoNuclear, nucleus, sfo1 } = options;
+  let {
+    thresholdFactor = 0.5,
+    isHomoNuclear,
+    nucleus = ['1H', '1H'],
+    observeFrequencies,
+    enhanceSymmetry = false,
+    clean = true,
+    maxPercentCutOff = 0.03,
+  } = options;
 
@@ -48,11 +56,13 @@ if (thresholdFactor === 0) {
   let [nucleusX, nucleusY] = nucleus;
-  let [observeFrequencyX, observeFrequencyY] = sfo1;
+  let [observeFrequencyX, observeFrequencyY] = observeFrequencies;
 
+  let convolutedSpectrum = FFTUtils.convolute(
+    data,
+    smallFilter,
+    nbSubSpectra,
+    nbPoints,
+  );
+
+  let signals = [];
   if (isHomoNuclear) {
-    let convolutedSpectrum = FFTUtils.convolute(
-      data,
-      smallFilter,
-      nbSubSpectra,
-      nbPoints,
-    );
     let peaksMC1 = matrixPeakFinders.findPeaks2DRegion(data, {
@@ -63,3 +73,4 @@ filteredData: convolutedSpectrum,
       nStdDev: nStdDev * thresholdFactor,
-    }); // )1.5);
+    });
+
     let peaksMax1 = matrixPeakFinders.findPeaks2DMax(data, {
@@ -70,22 +81,20 @@ filteredData: convolutedSpectrum,
       nStdDev: (nStdDev + 0.5) * thresholdFactor,
-    }); // 2.0);
+    });
+
     for (let i = 0; i < peaksMC1.length; i++) {
       peaksMax1.push(peaksMC1[i]);
     }
-    return PeakOptimizer.enhanceSymmetry(
-      createSignals2D(peaksMax1, spectraData, {
-        tolerance: 24,
-        nucleusX,
-        nucleusY,
-        observeFrequencyX,
-        observeFrequencyY,
-      }),
-    );
+
+    signals = createSignals2D(peaksMax1, spectraData, {
+      tolerance: 24,
+      nucleusX,
+      nucleusY,
+      observeFrequencyX,
+      observeFrequencyY,
+    });
+
+    if (enhanceSymmetry) {
+      signals = PeakOptimizer.enhanceSymmetry(signals);
+    }
   } else {
-    let convolutedSpectrum = FFTUtils.convolute(
-      data,
-      smallFilter,
-      nbSubSpectra,
-      nbPoints,
-    );
     let peaksMC1 = matrixPeakFinders.findPeaks2DRegion(data, {
@@ -98,5 +107,8 @@ filteredData: convolutedSpectrum,
 
-    // Peak2D[] peaksMC1 = matrixPeakFinders.findPeaks2DMax(data, nbSubSpectra, nbPoints, (nStdDev+0.5)*thresholdFactor);
-    // Remove peaks with less than 3% of the intensity of the highest peak
-    return createSignals2D(PeakOptimizer.clean(peaksMC1, 0.03), spectraData, {
+    if (clean) {
+      // Remove peaks with less than x% of the intensity of the highest peak
+      peaksMC1 = PeakOptimizer.clean(peaksMC1, maxPercentCutOff);
+    }
+
+    signals = createSignals2D(peaksMC1, spectraData, {
       tolerance: 24,
@@ -109,2 +121,4 @@ nucleusX,
   }
+
+  return signals;
 }
@@ -140,4 +154,5 @@
 
-  let dy = (lastY - firstY) / (spectraData.z[0].length - 1); //@TODO: check the dimensionality
-  let dx = (lastX - firstX) / (spectraData.z.length - 1);
+  let dy = (lastY - firstY) / (spectraData.z.length - 1); //@TODO: check the dimensionality
+  let dx = (lastX - firstX) / (spectraData.z[0].length - 1);
+
   for (let i = peaks.length - 1; i >= 0; i--) {
@@ -144,0 +159,0 @@ peaks[i].x = firstX + dx * peaks[i].x;

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Improved metrics

Total package byte prevSize

228805

increased by0.08%

Lines of code

9797

increased by0.18%

Dependency changes

• Updatedml-matrix-peaks-finder@^0.2.2