nmr-processing - npm Package Compare versions

Comparing version 0.1.0 to 0.1.1

package.json

 {
   "name": "nmr-processing",
-  "version": "0.1.0",
+  "version": "0.1.1",
   "description": "",
@@ -12,2 +12,3 @@ "main": "lib/index.js",
   "scripts": {
+    "build": "rollup -c && cheminfo-build --root NMRProcessing",
     "eslint": "eslint src",
@@ -44,2 +45,3 @@ "eslint-fix": "npm run eslint -- --fix",
     "@types/jest": "^25.2.1",
+    "cheminfo-build": "^1.1.1",
     "eslint": "^7.0.0",
@@ -46,0 +48,0 @@ "eslint-config-cheminfo": "^3.0.0",

src/peaks/peaksToRanges.js

 import round from 'lodash.round';
 
-import { peaksFilterImpurities } from './peaksFilterImpurities';
+// import { Ranges } from 'spectra-data-ranges';
+import { xyGetArea } from '../xy/xyGetArea';
+
 import jAnalyzer from './util/jAnalyzer';
+import { joinRanges } from './util/joinRanges';
 
@@ -13,2 +16,3 @@ const defaultOptions = {
   optimize: true,
+  joinOverlapRanges: true,
   frequencyCluster: 16,
@@ -20,3 +24,3 @@ keepPeaks: false,
  * This function clustering peaks and calculate the integral value for each range from the peak list returned from extractPeaks function.
- * @param {SD} spectrum - SD instance
+ * @param {Object} data - spectra data
  * @param {Object} peakList - nmr signals
@@ -35,12 +39,11 @@ * @param {Object} options - options object with some parameter for GSD, detectSignal functions.
 
-export function peaksToRanges(peakList, options) {
+export function peaksToRanges(data, peakList, options = {}) {
   options = Object.assign({}, defaultOptions, options);
-  let i, j;
-  let nH = options.nH;
-  peakList = peaksFilterImpurities(peakList, options.removeImpurity);
-  let signals = detectSignals(peakList, options);
+  let { nH, joinOverlapRanges, clean, compile } = options;
 
-  if (options.clean) {
-    for (i = 0; i < signals.length; i++) {
-      if (signals[i].integralData.value < options.clean) {
+  let signals = detectSignals(data, peakList, options);
+
+  if (clean) {
+    for (let i = 0; i < signals.length; i++) {
+      if (signals[i].integralData.value < clean) {
         signals.splice(i, 1);
@@ -51,5 +54,5 @@ }
 
-  if (options.compile) {
+  if (compile) {
     let nHi, sum;
-    for (i = 0; i < signals.length; i++) {
+    for (let i = 0; i < signals.length; i++) {
       jAnalyzer.compilePattern(signals[i]);
@@ -66,3 +69,3 @@
         let peaksO = [];
-        for (j = signals[i].maskPattern.length - 1; j >= 0; j--) {
+        for (let j = signals[i].maskPattern.length - 1; j >= 0; j--) {
           sum += computeArea(signals[i].peaks[j]);
@@ -83,9 +86,9 @@ if (signals[i].maskPattern[j] === false) {
           let peaks1 = [];
-          for (j = peaksO.length - 1; j >= 0; j--) {
+          for (let j = peaksO.length - 1; j >= 0; j--) {
             peaks1.push(peaksO[j]);
           }
           options.nH = nHi;
-          let ranges = detectSignals(peaks1, options);
+          let ranges = detectSignals(data, peaks1, options);
 
-          for (j = 0; j < ranges.length; j++) {
+          for (let j = 0; j < ranges.length; j++) {
             signals.push(ranges[j]);
@@ -99,3 +102,3 @@ }
     let sumObserved = 0;
-    for (i = 0; i < signals.length; i++) {
+    for (let i = 0; i < signals.length; i++) {
       sumObserved += Math.round(signals[i].integralData.value);
@@ -105,3 +108,3 @@ }
       sumIntegral = nH / sumObserved;
-      for (i = 0; i < signals.length; i++) {
+      for (let i = 0; i < signals.length; i++) {
         signals[i].integralData.value *= sumIntegral;
@@ -112,9 +115,9 @@ }
 
-  signals.sort(function (a, b) {
+  signals.sort((a, b) => {
     return b.delta1 - a.delta1;
   });
 
-  if (options.clean) {
-    for (i = signals.length - 1; i >= 0; i--) {
-      if (signals[i].integralData.value < options.clean) {
+  if (clean) {
+    for (let i = signals.length - 1; i >= 0; i--) {
+      if (signals[i].integralData.value < clean) {
         signals.splice(i, 1);
@@ -125,4 +128,4 @@ }
 
-  let ranges = new Array(signals.length);
-  for (i = 0; i < signals.length; i++) {
+  let ranges = []; //new Array(signals.length);
+  for (let i = 0; i < signals.length; i++) {
     let signal = signals[i];
@@ -150,2 +153,5 @@ ranges[i] = {
 
+  if (joinOverlapRanges) ranges = joinRanges(ranges);
+
+  // return new Ranges(ranges);
   return ranges;
@@ -156,3 +162,3 @@ }
  * Extract the signals from the peakList and the given spectrum.
- * @param {object} spectrum - spectra data
+ * @param {object} data - spectra data
  * @param {object} peakList - nmr signals
@@ -167,3 +173,3 @@ * @param {object} options
  */
-function detectSignals(peakList, options = {}) {
+function detectSignals(data, peakList, options = {}) {
   let {
@@ -177,3 +183,3 @@ nH = 100,
 
-  let i, j, signal1D, peaks;
+  let signal1D, peaks;
   let signals = [];
@@ -183,3 +189,3 @@ let prevPeak = { x: 100000 };
   frequencyCluster /= frequency;
-  for (i = 0; i < peakList.length; i++) {
+  for (let i = 0; i < peakList.length; i++) {
     if (Math.abs(peakList[i].x - prevPeak.x) > frequencyCluster) {
@@ -230,3 +236,3 @@ signal1D = {
 
-  for (i = 0; i < signals.length; i++) {
+  for (let i = 0; i < signals.length; i++) {
     peaks = signals[i].peaks;
@@ -237,3 +243,3 @@ let integral = signals[i].integralData;
 
-    for (j = 0; j < peaks.length; j++) {
+    for (let j = 0; j < peaks.length; j++) {
       let area = computeArea(peaks[j]);
@@ -246,3 +252,6 @@ chemicalShift += peaks[j].x * area;
     if (integralType === 'sum') {
-      integral.value = 10; //spectrum.getArea(integral.from, integral.to); //@TODO
+      integral.value = xyGetArea(data, {
+        from: integral.from,
+        to: integral.to,
+      });
     } else {
@@ -256,3 +265,3 @@ integral.value = integralPeaks;
     let integralFactor = nH / spectrumIntegral;
-    for (i = 0; i < signals.length; i++) {
+    for (let i = 0; i < signals.length; i++) {
       let integral = signals[i].integralData;
@@ -259,0 +268,0 @@ integral.value *= integralFactor;

src/xy/xyAutoRangesPicking.js

@@ -9,5 +9,5 @@ import { peaksFilterImpurities } from '../peaks/peaksFilterImpurities';
   peaks = peaksFilterImpurities(peaks, options.impurities);
-  let ranges = peaksToRanges(peaks, options.ranges);
+  let ranges = peaksToRanges(data, peaks, options.peakPicking);
 
   return ranges;
 }

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Improved metrics

Total package byte prevSize

196890

increased by0.98%

Number of package files

20

increased by11.11%

Lines of code

8781

increased by0.62%

Worsened metrics

Dev dependency count

15

increased by7.14%

Number of medium supply chain risk alerts

1

increased byInfinity%

No dependency changes