ml-spectra-processing - npm Package Compare versions

Comparing version 0.4.0 to 0.5.0

lib/index.js

@@ -491,2 +491,124 @@ 'use strict';
 
+/**
+ * Finds all the max values
+ * If the values are equal the middle
+ * of the equal part will be the position of the signal!
+ *
+ * @param {object} [points={}] - Object of points contains property x (an ordered increasing array) and y (an array)
+ * @return {Array} Array of points
+ */
+
+function maximaY(points = {}) {
+  check(points);
+  const { x, y } = points;
+  if (x.length < 3) return [];
+  let maxima = [];
+  let startEqualIndex = -1;
+  for (let i = 1; i < x.length - 1; i++) {
+    if (y[i - 1] < y[i] && y[i + 1] < y[i]) {
+      maxima.push({ x: x[i], y: y[i], index: i });
+    } else if (y[i - 1] < y[i] && y[i + 1] === y[i]) {
+      startEqualIndex = i;
+    } else if (y[i - 1] === y[i] && y[i + 1] < y[i]) {
+      let index = ((i + startEqualIndex) / 2) >> 0;
+      maxima.push({ x: x[index], y: y[index], index });
+    }
+  }
+  return maxima;
+}
+
+/**
+ * Finds all the min values
+ * If the values are equal the middle
+ * of the equal part will be the position of the signal!
+ *
+ * @param {object} [points={}] - Object of points contains property x (an ordered increasing array) and y (an array)
+ * @return {Array} Array of points
+ */
+
+function minimaY(points = {}) {
+  check(points);
+  const { x, y } = points;
+  if (x.length < 3) return [];
+  let maxima = [];
+  let startEqualIndex = -1;
+  for (let i = 1; i < x.length - 1; i++) {
+    if (y[i - 1] > y[i] && y[i + 1] > y[i]) {
+      maxima.push({ x: x[i], y: y[i], index: i });
+    } else if (y[i - 1] > y[i] && y[i + 1] === y[i]) {
+      startEqualIndex = i;
+    } else if (y[i - 1] === y[i] && y[i + 1] > y[i]) {
+      let index = ((i + startEqualIndex) / 2) >> 0;
+      maxima.push({ x: x[index], y: y[index], index });
+    }
+  }
+  return maxima;
+}
+
+/**
+ * Returns an information about a signal
+ *
+ * We expect ordered data and equidistant X axis
+ * You can use the method helper if required:
+ * ML.ArrayXY.uniqueX
+ * ML.ArrayXY.sortX
+ * ML.ArrayXY.equallySpaced
+ *
+ * @param {object} [points={}] - Object of points contains property x (an ordered increasing array) and y (an array)
+ * @param {object} [options={}]
+ * @param {number} [options.target]
+ * @param {number} [options.targetIndex]
+ * @return {object} Information about signal
+ */
+
+function peakInfo(points = {}, options = {}) {
+  check(points);
+  const { x, y } = points;
+  if (x.length < 3) return undefined;
+  let { targetIndex, target } = options;
+  if (targetIndex === undefined) {
+    if (target !== undefined) {
+      targetIndex = findClosestIndex(x, target);
+    }
+  }
+
+  if (targetIndex === undefined) {
+    throw new Error('peakInfo: need to specify target or targetIndex');
+  }
+
+  let i = targetIndex;
+  let currentDiff = y[i] - y[i + 1];
+
+  let multiplier = currentDiff < 0 ? -1 : 1;
+  currentDiff *= multiplier;
+  while (i < x.length - 1) {
+    i++;
+    let newDiff = (y[i] - y[i + 1]) * multiplier;
+    if (newDiff < currentDiff) break;
+    currentDiff = newDiff;
+  }
+  let after = { x: x[i], y: y[i] };
+
+  i = targetIndex;
+  currentDiff = (y[i] - y[i - 1]) * multiplier;
+  while (i > 1) {
+    i--;
+    let newDiff = (y[i] - y[i - 1]) * multiplier;
+    if (newDiff < currentDiff) break;
+    currentDiff = newDiff;
+  }
+  let before = { x: x[i], y: y[i] };
+
+  return {
+    inflectionBefore: before,
+    inflectionAfter: after,
+    extrema: { x: x[targetIndex], y: y[targetIndex] },
+    inflectionMiddle: {
+      x: (before.x + after.x) / 2,
+      y: (before.y + after.y) / 2,
+    },
+    width: Math.abs(before.x - after.x),
+  };
+}
+
 const XY = {
@@ -497,3 +619,5 @@ check,
   maxY,
+  maximaY,
   maxYPoint,
+  minimaY,
   minYPoint,
@@ -506,2 +630,3 @@ reduce,
   realMinYPoint,
+  peakInfo,
 };
@@ -523,3 +648,3 @@
       re: data.re.slice(0, zeroFilling),
-      im: data.im.slice(0, zeroFilling)
+      im: data.im.slice(0, zeroFilling),
     };
@@ -549,3 +674,3 @@ }
     re: newRE,
-    im: newIM
+    im: newIM,
   };
@@ -649,3 +774,5 @@ }
   if (Array.isArray(array2)) {
-    if (array1.length !== array2.length) throw new Error('sub: size of array1 and array2 must be identical');
+    if (array1.length !== array2.length) {
+      throw new Error('sub: size of array1 and array2 must be identical');
+    }
   } else {
@@ -678,7 +805,16 @@ isConstant = true;
   if (array.length < 5) {
-    throw Error('boxPlot: can not calculate info if array contains less than 3 elements');
+    throw Error(
+      'boxPlot: can not calculate info if array contains less than 3 elements',
+    );
   }
-  let info = { Q1: 0.0, Q2: 0.0, Q3: 0.0, min: array[0], max: array[array.length - 1] };
+  let info = {
+    Q1: 0.0,
+    Q2: 0.0,
+    Q3: 0.0,
+    min: array[0],
+    max: array[array.length - 1],
+  };
   let q1max, q3min;
-  if (array.length % 2 === 1) { // odd
+  if (array.length % 2 === 1) {
+    // odd
     let middle = (array.length - 1) / 2;
@@ -688,3 +824,4 @@ info.Q2 = array[middle];
     q3min = middle + 1;
-  } else { // even
+  } else {
+    // even
     q3min = array.length / 2;
@@ -717,3 +854,5 @@ q1max = q3min - 1;
   if (Array.isArray(array2)) {
-    if (array1.length !== array2.length) throw new Error('sub: size of array1 and array2 must be identical');
+    if (array1.length !== array2.length) {
+      throw new Error('sub: size of array1 and array2 must be identical');
+    }
   } else {
@@ -750,3 +889,5 @@ isConstant = true;
   if (Array.isArray(array2)) {
-    if (array1.length !== array2.length) throw new Error('sub: size of array1 and array2 must be identical');
+    if (array1.length !== array2.length) {
+      throw new Error('sub: size of array1 and array2 must be identical');
+    }
   } else {
@@ -783,3 +924,5 @@ isConstant = true;
   if (shift < 0) shift += array.length;
-  return array.slice(array.length - shift).concat(array.slice(0, array.length - shift));
+  return array
+    .slice(array.length - shift)
+    .concat(array.slice(0, array.length - shift));
 }
@@ -797,3 +940,5 @@
   if (Array.isArray(array2)) {
-    if (array1.length !== array2.length) throw new Error('sub: size of array1 and array2 must be identical');
+    if (array1.length !== array2.length) {
+      throw new Error('sub: size of array1 and array2 must be identical');
+    }
   } else {
@@ -818,2 +963,34 @@ isConstant = true;
 
+/**
+
+/**
+ * Calculates the correlation between 2 vectors
+ * https://en.wikipedia.org/wiki/Correlation_and_dependence
+ *
+ * @param {Array} [A] - the array that will be rotated
+ * @param {Array} [B]
+ * @return {Array}
+ */
+function correlation(A, B) {
+  let n = A.length;
+  let sumA = 0;
+  let sumA2 = 0;
+  let sumB = 0;
+  let sumB2 = 0;
+  let sumAB = 0;
+  for (let i = 0; i < n; i++) {
+    let a = A[i];
+    let b = B[i];
+    sumA += a;
+    sumA2 += a ** 2;
+    sumB += b;
+    sumB2 += b ** 2;
+    sumAB += a * b;
+  }
+  return (
+    (n * sumAB - sumA * sumB) /
+    (Math.sqrt(n * sumA2 - sumA ** 2) * Math.sqrt(n * sumB2 - sumB ** 2))
+  );
+}
+
 const X = {
@@ -828,2 +1005,3 @@ add,
   subtract,
+  correlation,
 };
@@ -830,0 +1008,0 @@

package.json

 {
   "name": "ml-spectra-processing",
-  "version": "0.4.0",
+  "version": "0.5.0",
   "description": "Various method to process spectra",
@@ -12,2 +12,3 @@ "main": "lib/index.js",
   "scripts": {
+    "build": "rollup -c && cheminfo-build --root SpectraProcessing",
     "eslint": "eslint src",
@@ -43,10 +44,13 @@ "eslint-fix": "npm run eslint -- --fix",
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.5.0",
-    "eslint": "^6.0.1",
-    "eslint-config-cheminfo": "^1.20.1",
-    "eslint-plugin-import": "^2.18.0",
-    "eslint-plugin-jest": "^22.7.1",
+    "@babel/plugin-transform-modules-commonjs": "^7.6.0",
+    "cheminfo-build": "^1.0.3",
+    "eslint": "^6.5.1",
+    "eslint-config-cheminfo": "^2.0.3",
+    "eslint-plugin-import": "^2.18.2",
+    "eslint-plugin-jest": "^22.17.0",
+    "eslint-plugin-prettier": "^3.1.1",
     "esm": "^3.2.25",
-    "jest": "^24.8.0",
-    "rollup": "^1.16.7"
+    "jest": "^24.9.0",
+    "prettier": "^1.18.2",
+    "rollup": "^1.23.1"
   },
@@ -53,0 +57,0 @@ "dependencies": {

src/x/add.js

@@ -13,3 +13,5 @@ /**
   if (Array.isArray(array2)) {
-    if (array1.length !== array2.length) throw new Error('sub: size of array1 and array2 must be identical');
+    if (array1.length !== array2.length) {
+      throw new Error('sub: size of array1 and array2 must be identical');
+    }
   } else {
@@ -33,2 +35,1 @@ isConstant = true;
 }
-

src/x/boxPlot.js

@@ -9,7 +9,16 @@ /**
   if (array.length < 5) {
-    throw Error('boxPlot: can not calculate info if array contains less than 3 elements');
+    throw Error(
+      'boxPlot: can not calculate info if array contains less than 3 elements',
+    );
   }
-  let info = { Q1: 0.0, Q2: 0.0, Q3: 0.0, min: array[0], max: array[array.length - 1] };
+  let info = {
+    Q1: 0.0,
+    Q2: 0.0,
+    Q3: 0.0,
+    min: array[0],
+    max: array[array.length - 1],
+  };
   let q1max, q3min;
-  if (array.length % 2 === 1) { // odd
+  if (array.length % 2 === 1) {
+    // odd
     let middle = (array.length - 1) / 2;
@@ -19,3 +28,4 @@ info.Q2 = array[middle];
     q3min = middle + 1;
-  } else { // even
+  } else {
+    // even
     q3min = array.length / 2;
@@ -35,2 +45,1 @@ q1max = q3min - 1;
 }
-

src/x/divide.js

@@ -13,3 +13,5 @@ /**
   if (Array.isArray(array2)) {
-    if (array1.length !== array2.length) throw new Error('sub: size of array1 and array2 must be identical');
+    if (array1.length !== array2.length) {
+      throw new Error('sub: size of array1 and array2 must be identical');
+    }
   } else {
@@ -33,2 +35,1 @@ isConstant = true;
 }
-

src/x/index.js

@@ -9,2 +9,3 @@ import { add } from './add';
 import { subtract } from './subtract';
+import { correlation } from './correlation';
 
@@ -20,2 +21,3 @@ export const X = {
   subtract,
+  correlation,
 };

src/x/multiply.js

@@ -13,3 +13,5 @@ /**
   if (Array.isArray(array2)) {
-    if (array1.length !== array2.length) throw new Error('sub: size of array1 and array2 must be identical');
+    if (array1.length !== array2.length) {
+      throw new Error('sub: size of array1 and array2 must be identical');
+    }
   } else {
@@ -33,2 +35,1 @@ isConstant = true;
 }
-

src/x/rotate.js

@@ -13,4 +13,5 @@ /**
   if (shift < 0) shift += array.length;
-  return array.slice(array.length - shift).concat(array.slice(0, array.length - shift));
+  return array
+    .slice(array.length - shift)
+    .concat(array.slice(0, array.length - shift));
 }
-

src/x/subtract.js

@@ -11,3 +11,5 @@ /**
   if (Array.isArray(array2)) {
-    if (array1.length !== array2.length) throw new Error('sub: size of array1 and array2 must be identical');
+    if (array1.length !== array2.length) {
+      throw new Error('sub: size of array1 and array2 must be identical');
+    }
   } else {
@@ -31,2 +33,1 @@ isConstant = true;
 }
-

src/xreim/zeroFilling.js

@@ -15,3 +15,3 @@ /**
       re: data.re.slice(0, zeroFilling),
-      im: data.im.slice(0, zeroFilling)
+      im: data.im.slice(0, zeroFilling),
     };
@@ -41,5 +41,4 @@ }
     re: newRE,
-    im: newIM
+    im: newIM,
   };
 }
-

src/xy/index.js

@@ -13,2 +13,5 @@ import { check } from './check';
 import { realMaxYPoint } from './realMaxYPoint';
+import { maximaY } from './maximaY';
+import { minimaY } from './minimaY';
+import { peakInfo } from './peakInfo';
 
@@ -20,3 +23,5 @@ export const XY = {
   maxY,
+  maximaY,
   maxYPoint,
+  minimaY,
   minYPoint,
@@ -29,2 +34,3 @@ reduce,
   realMinYPoint,
+  peakInfo,
 };

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Improved metrics

Total package byte prevSize

61886

increased by17.11%

Number of package files

39

increased by11.43%

Lines of code

1807

increased by23.01%

Worsened metrics

Dev dependency count

11

increased by37.5%

No dependency changes