multiplet-analysis - npm Package Compare versions

Comparing version 2.1.2 to 2.1.3

lib/index.js

 'use strict';
 
-var maxY = require('ml-array-xy-max-y');
+var mlSpectraProcessing = require('ml-spectra-processing');
 var FFT = require('fft.js');
@@ -242,3 +242,2 @@
   sign, // sign of the split 1: ++ -1: +-
-  chopTail, // 1: cut tail
   multiplicity,
@@ -468,8 +467,8 @@ incrementForSpeed,
 
+/**@typedef {import('../multiplet-analysis').AnalizeMultipletOptions} AnalizeMultipletOptions */
+/**@typedef {import('cheminfo-types').DataXY} DataXY */
 /**
  * Analyse a multiplet
- * @param {object} [data] object of the kind {x:[], y:[]} containing the multiplet
- * @param {object} [options={}]
- * @param {number} [options.frequency=400] frequency
- * @param {boolean} [options.debug=false] generate debug information if true
+ * @param {DataXY} [data] xy data containing the multiplet.
+ * @param {AnalizeMultipletOptions} [options]
  */
@@ -512,9 +511,2 @@
 
-  let factorResolution = resolutionHz / minimalResolution;
-
-  let nextPowerTwo = 2 ** Math.ceil(Math.log2(x.length * factorResolution));
-  let nextPowerTwoInital = 2 ** Math.ceil(Math.log2(x.length));
-
-  let integerFactorResolution = nextPowerTwo / nextPowerTwoInital;
-
   let scale;
@@ -538,3 +530,7 @@ let spectrum;
   if (resolutionHz > minimalResolution) {
-    // need increase resolution
+    const nextPoTwoInital = mlSpectraProcessing.nextPowerOfTwo(x.length);
+    const factorResolution = resolutionHz / minimalResolution;
+    const nextPofTwo = mlSpectraProcessing.nextPowerOfTwo(x.length * factorResolution);
+    const integerFactorResolution = nextPofTwo / nextPoTwoInital;
+
     let returned = trigInterpolate(
@@ -555,9 +551,9 @@ x,
     spectrum = y;
-  } //satnoeuhs
+  }
 
+  [spectrum, scale] = removeShift(spectrum, scale, 95);
   if (checkSymmetryFirst) {
-    const result = removeShift(spectrum, scale, 95);
-    let symFactor = getSymFactor(result.spectrum);
+    let symFactor = getSymFactor(spectrum);
     if (symFactor < 0.98) {
-      let maxAmplitudePosition = maxY({ x: scale, y: spectrum });
+      let maxAmplitudePosition = mlSpectraProcessing.xyMaxYPoint({ x: scale, y: spectrum });
       return {
@@ -568,6 +564,10 @@ chemShift: scale[maxAmplitudePosition.index],
     } else {
-      scale = result.scale;
-      spectrum = symmetrize(result.spectrum);
+      spectrum = symmetrize(spectrum);
     }
   }
+
+  let incrementForSpeed = 1;
+  let curIncrementForSpeed;
+  incrementForSpeed = (1 + 0.3 / minimalResolution) | 0; // 1 could be set better (according to line widht ?!)
+
   resolutionPpm =
@@ -578,3 +578,3 @@ Math.abs(scale[0] - scale[scale.length - 1]) / (scale.length - 1);
 
-  let minTestedPt = Math.trunc(minTestedJ / resolutionHz) + 1;
+  let minTestedPt = Math.trunc(minTestedJ / resolutionHz) - incrementForSpeed;
   // will find center of symmetry of the multiplet
@@ -586,5 +586,2 @@ // add zeroes as to make it symetrical if requested... and needed
 
-  let incrementForSpeed = 1;
-  let curIncrementForSpeed;
-  incrementForSpeed = (1 + 0.3 / minimalResolution) | 0; // 1 could be set better (according to line widht ?!)
   for (
@@ -597,13 +594,13 @@ let loopoverJvalues = 1;
     let jStarArray = [];
-    for (let jStar = 0; jStar < minTestedPt; jStar++) {
+    for (let jStar = 0; jStar < minTestedPt + incrementForSpeed; jStar++) {
       jStarArray[jStar] = jStar * resolutionHz;
       scalProd[jStar] = 0;
     }
+
     let beforeSymSpe = new Float64Array(spectrum.length);
 
+    //symmetrize if requested to
     if (symmetrizeEachStep === true) {
-      //symmetrize if requested to
-      const result = removeShift(spectrum, scale, 95);
-      scale = result.scale;
-      spectrum = result.spectrum;
+      [spectrum, scale] = removeShift(spectrum, scale, 95);
+
       if (debug) {
@@ -636,3 +633,7 @@ // save this to plot it as well
     let jStarFine;
-    for (let jStar = minTestedPt; jStar < maxTestedPt; jStar++) {
+    for (
+      let jStar = minTestedPt + incrementForSpeed;
+      jStar < maxTestedPt;
+      jStar++
+    ) {
       jStarArray[jStar] = jStar * resolutionHz;
@@ -650,8 +651,7 @@ scalProd[jStar] = -1;
         sign,
-        chopTail,
         multiplicity,
         curIncrementForSpeed,
       );
+      jStarArray[jStar] = jStar * resolutionHz;
 
-      jStarArray[jStar] = jStar * resolutionHz;
       if (!gotJValue) {
@@ -686,3 +686,2 @@ if (scalProd[jStar] > topValue) {
                   sign,
-                  chopTail,
                   multiplicity,
@@ -762,3 +761,3 @@ curIncrementForSpeed,
       ); // for next step
-      if (chopTail) {
+      if (chopTail || takeBestPartMultiplet) {
         let remove = 0.5 * topPosJ * (2 * multiplicity);
@@ -774,3 +773,3 @@ scale = scale.slice(remove, scale.length - remove);
 
-  let maxAmplitudePosition = maxY({ x: scale, y: spectrum });
+  let maxAmplitudePosition = mlSpectraProcessing.xyMaxYPoint({ x: scale, y: spectrum });
   result.chemShift = scale[maxAmplitudePosition.index];
@@ -930,5 +929,5 @@ return result;
   }
-  return { spectrum, scale };
+  return [spectrum, scale];
 }
 
 exports.analyseMultiplet = analyseMultiplet;

package.json

 {
   "name": "multiplet-analysis",
-  "version": "2.1.2",
+  "version": "2.1.3",
   "description": "Extract coupling constants from a complex NMR multiiplet",
   "main": "lib/index.js",
+  "types": "multiplet-analysis.d.ts",
   "module": "src/index.js",
@@ -12,10 +13,11 @@ "files": [
   "scripts": {
+    "build": "cheminfo-build --entry src/index.js --root AirPLS",
+    "compile": "rollup -c",
+    "prepack": "npm run compile",
     "eslint": "eslint src",
     "eslint-fix": "npm run eslint -- --fix",
-    "prepack": "rollup -c",
     "prettier": "prettier --check src",
     "prettier-write": "prettier --write src",
-    "test": "npm run test-coverage && npm run eslint && npm run prettier",
-    "test-coverage": "jest --coverage",
-    "test-only": "jest"
+    "test": "npm run test-only && npm run eslint && npm run prettier",
+    "test-only": "jest --coverage"
   },
@@ -50,2 +52,3 @@ "repository": {
     "jest-matcher-deep-close-to": "^3.0.2",
+    "nmr-processing": "^14.0.5",
     "nmr-simulation": "^1.0.21",
@@ -56,5 +59,7 @@ "prettier": "^2.8.8",
   "dependencies": {
+    "cheminfo-types": "^1.8.1",
     "fft.js": "^4.0.4",
-    "ml-array-xy-max-y": "^1.0.2"
+    "ml-airpls": "^2.0.0",
+    "ml-spectra-processing": "^14.7.0"
   }
 }

src/index.js

@@ -8,3 +8,3 @@ /**
 
-import maxY from 'ml-array-xy-max-y';
+import { nextPowerOfTwo, xyMaxYPoint } from 'ml-spectra-processing';
 
@@ -19,8 +19,8 @@ import { appendDebug } from './appendDebug';
 
+/**@typedef {import('../multiplet-analysis').AnalizeMultipletOptions} AnalizeMultipletOptions */
+/**@typedef {import('cheminfo-types').DataXY} DataXY */
 /**
  * Analyse a multiplet
- * @param {object} [data] object of the kind {x:[], y:[]} containing the multiplet
- * @param {object} [options={}]
- * @param {number} [options.frequency=400] frequency
- * @param {boolean} [options.debug=false] generate debug information if true
+ * @param {DataXY} [data] xy data containing the multiplet.
+ * @param {AnalizeMultipletOptions} [options]
  */
@@ -63,9 +63,2 @@
 
-  let factorResolution = resolutionHz / minimalResolution;
-
-  let nextPowerTwo = 2 ** Math.ceil(Math.log2(x.length * factorResolution));
-  let nextPowerTwoInital = 2 ** Math.ceil(Math.log2(x.length));
-
-  let integerFactorResolution = nextPowerTwo / nextPowerTwoInital;
-
   let scale;
@@ -89,3 +82,7 @@ let spectrum;
   if (resolutionHz > minimalResolution) {
-    // need increase resolution
+    const nextPoTwoInital = nextPowerOfTwo(x.length);
+    const factorResolution = resolutionHz / minimalResolution;
+    const nextPofTwo = nextPowerOfTwo(x.length * factorResolution);
+    const integerFactorResolution = nextPofTwo / nextPoTwoInital;
+
     let returned = trigInterpolate(
@@ -106,9 +103,9 @@ x,
     spectrum = y;
-  } //satnoeuhs
+  }
 
+  [spectrum, scale] = removeShift(spectrum, scale, 95);
   if (checkSymmetryFirst) {
-    const result = removeShift(spectrum, scale, 95);
-    let symFactor = getSymFactor(result.spectrum);
+    let symFactor = getSymFactor(spectrum);
     if (symFactor < 0.98) {
-      let maxAmplitudePosition = maxY({ x: scale, y: spectrum });
+      let maxAmplitudePosition = xyMaxYPoint({ x: scale, y: spectrum });
       return {
@@ -119,6 +116,10 @@ chemShift: scale[maxAmplitudePosition.index],
     } else {
-      scale = result.scale;
-      spectrum = symmetrize(result.spectrum);
+      spectrum = symmetrize(spectrum);
     }
   }
+
+  let incrementForSpeed = 1;
+  let curIncrementForSpeed;
+  incrementForSpeed = (1 + 0.3 / minimalResolution) | 0; // 1 could be set better (according to line widht ?!)
+
   resolutionPpm =
@@ -129,3 +130,3 @@ Math.abs(scale[0] - scale[scale.length - 1]) / (scale.length - 1);
 
-  let minTestedPt = Math.trunc(minTestedJ / resolutionHz) + 1;
+  let minTestedPt = Math.trunc(minTestedJ / resolutionHz) - incrementForSpeed;
   // will find center of symmetry of the multiplet
@@ -137,5 +138,2 @@ // add zeroes as to make it symetrical if requested... and needed
 
-  let incrementForSpeed = 1;
-  let curIncrementForSpeed;
-  incrementForSpeed = (1 + 0.3 / minimalResolution) | 0; // 1 could be set better (according to line widht ?!)
   for (
@@ -148,13 +146,13 @@ let loopoverJvalues = 1;
     let jStarArray = [];
-    for (let jStar = 0; jStar < minTestedPt; jStar++) {
+    for (let jStar = 0; jStar < minTestedPt + incrementForSpeed; jStar++) {
       jStarArray[jStar] = jStar * resolutionHz;
       scalProd[jStar] = 0;
     }
+
     let beforeSymSpe = new Float64Array(spectrum.length);
 
+    //symmetrize if requested to
     if (symmetrizeEachStep === true) {
-      //symmetrize if requested to
-      const result = removeShift(spectrum, scale, 95);
-      scale = result.scale;
-      spectrum = result.spectrum;
+      [spectrum, scale] = removeShift(spectrum, scale, 95);
+
       if (debug) {
@@ -187,3 +185,7 @@ // save this to plot it as well
     let jStarFine;
-    for (let jStar = minTestedPt; jStar < maxTestedPt; jStar++) {
+    for (
+      let jStar = minTestedPt + incrementForSpeed;
+      jStar < maxTestedPt;
+      jStar++
+    ) {
       jStarArray[jStar] = jStar * resolutionHz;
@@ -201,8 +203,7 @@ scalProd[jStar] = -1;
         sign,
-        chopTail,
         multiplicity,
         curIncrementForSpeed,
       );
+      jStarArray[jStar] = jStar * resolutionHz;
 
-      jStarArray[jStar] = jStar * resolutionHz;
       if (!gotJValue) {
@@ -237,3 +238,2 @@ if (scalProd[jStar] > topValue) {
                   sign,
-                  chopTail,
                   multiplicity,
@@ -313,3 +313,3 @@ curIncrementForSpeed,
       ); // for next step
-      if (chopTail) {
+      if (chopTail || takeBestPartMultiplet) {
         let remove = 0.5 * topPosJ * (2 * multiplicity);
@@ -325,3 +325,3 @@ scale = scale.slice(remove, scale.length - remove);
 
-  let maxAmplitudePosition = maxY({ x: scale, y: spectrum });
+  let maxAmplitudePosition = xyMaxYPoint({ x: scale, y: spectrum });
   result.chemShift = scale[maxAmplitudePosition.index];
@@ -481,3 +481,3 @@ return result;
   }
-  return { spectrum, scale };
+  return [spectrum, scale];
 }

src/measureDeco.js

@@ -8,3 +8,2 @@ import { decofast1, decofast2 } from './deco';
   sign, // sign of the split 1: ++ -1: +-
-  chopTail, // 1: cut tail
   multiplicity,
@@ -11,0 +10,0 @@ incrementForSpeed,

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Improved metrics

Total package byte prevSize

61235

increased by0.49%

Number of package files

14

increased by7.69%

Lines of code

1724

increased by0.23%

Worsened metrics

Dependency count

4

increased by100%

Dev dependency count

10

increased by11.11%

Dependency changes

• + Addedcheminfo-types@^1.8.1

• + Addedml-airpls@^2.0.0

• + Addedml-spectra-processing@^14.7.0

• + Addedcheminfo-types@1.8.1(transitive)

• + Addedcuthill-mckee@1.0.0(transitive)

• + Addedd3-array@0.7.1(transitive)

• + Addedis-any-array@2.0.1(transitive)

• + Addedml-airpls@2.0.0(transitive)

• + Addedml-array-max@1.2.4(transitive)

• + Addedml-array-min@1.2.3(transitive)

• + Addedml-array-rescale@1.3.7(transitive)

• + Addedml-matrix@6.12.0(transitive)

• + Addedml-spectra-processing@14.9.1(transitive)

• + Addedml-xsadd@3.0.1(transitive)

• + Addedspline-interpolator@1.0.0(transitive)

• - Removedml-array-xy-max-y@^1.0.2

• - Removedml-array-xy-max-y@1.0.2(transitive)

• - Removednum-sort@2.1.0(transitive)