brukerconverter - npm Package Compare versions

Comparing version 1.1.2 to 2.0.0

bower.json

 {
   "name": "brukerconverter",
-  "version": "1.1.2",
+  "version": "2.0.0",
   "main": "build/brukerconverter.js",
@@ -5,0 +5,0 @@ "homepage": "https://github.com/cheminfo-js/brukerconverter",

package.json

 {
   "name": "brukerconverter",
-  "version": "1.1.2",
+  "version": "2.0.0",
   "description": "Parse and convert Bruker raw data",
@@ -30,15 +30,17 @@ "main": "./src/brukerconverter.js",
     "cheminfo-tools": "1.23.3",
-    "eslint": "^5.16.0 ",
-    "eslint-config-cheminfo": "^1.20.1",
-    "eslint-plugin-import": "^2.17.3",
-    "eslint-plugin-jest": "^22.6.4",
-    "jest": "^21.0.0",
-    "npm-run-all": "^4.1.5"
+    "eslint": "^6.8.0",
+    "eslint-config-cheminfo": "^2.0.4",
+    "eslint-plugin-import": "^2.20.1",
+    "eslint-plugin-jest": "^23.7.0",
+    "eslint-plugin-prettier": "^3.1.2",
+    "jest": "^25.1.0",
+    "npm-run-all": "^4.1.5",
+    "prettier": "^1.19.1"
   },
   "dependencies": {
-    "@babel/preset-env": "^7.4.5",
-    "iobuffer": "^4.0.1",
-    "jcampconverter": "^3.0.2",
-    "jszip": "^3.2.1"
+    "@babel/preset-env": "^7.8.4",
+    "iobuffer": "^5.0.2",
+    "jcampconverter": "^5.0.2",
+    "jszip": "^3.2.2"
   }
 }

src/brukerconverter.js

@@ -22,5 +22,6 @@ const Converter = require('jcampconverter');
       '1i': BINARY,
-      '2rr': BINARY
+      '2rr': BINARY,
     };
-    let folders = zip.filter(function (relativePath) {
+    let folders = zip.filter(function(relativePath) {
+      if (relativePath.match('__MACOSX')) return false;
       if (
@@ -36,11 +37,11 @@ relativePath.endsWith('ser') ||
     });
-    var spectra = new Array(folders.length);
+    let spectra = new Array(folders.length);
 
     for (let i = 0; i < folders.length; ++i) {
-      var promises = [];
-      var name = folders[i].name;
+      let promises = [];
+      let name = folders[i].name;
       name = name.substr(0, name.lastIndexOf('/') + 1);
       promises.push(name);
-      var currFolder = zip.folder(name);
-      var currFiles = currFolder.filter(function (relativePath) {
+      let currFolder = zip.folder(name);
+      let currFiles = currFolder.filter(function(relativePath) {
         return files[relativePath] ? true : false;
@@ -51,8 +52,8 @@ });
         promises.push(
-          zip.file(name.replace(/pdata\/[0-9]+\//, 'acqus')).async('string')
+          zip.file(name.replace(/pdata\/[0-9]+\//, 'acqus')).async('string'),
         );
       }
-      for (var j = 0; j < currFiles.length; ++j) {
-        var idx = currFiles[j].name.lastIndexOf('/');
-        var name = currFiles[j].name.substr(idx + 1);
+      for (let j = 0; j < currFiles.length; ++j) {
+        let idx = currFiles[j].name.lastIndexOf('/');
+        name = currFiles[j].name.substr(idx + 1);
         promises.push(name);
@@ -67,5 +68,5 @@ if (files[name] === BINARY) {
         let brukerFiles = {};
-        for (let i = 1; i < result.length; i += 2) {
-          let name = result[i];
-          brukerFiles[name] = result[i + 1];
+        for (let k = 1; k < result.length; k += 2) {
+          name = result[k];
+          brukerFiles[name] = result[k + 1];
         }
@@ -81,4 +82,4 @@ return { filename: result[0], value: convert(brukerFiles, options) };
   options = options || {};
-  var start = new Date();
-  var result;
+  let start = new Date();
+  let result;
   if (brukerFiles.ser || brukerFiles['2rr']) {
@@ -91,3 +92,2 @@ result = convert2D(brukerFiles, options);
   }
-
   if (result.twoD && !options.noContours) {
@@ -98,3 +98,3 @@ add2D(result);
         action: 'Finished countour plot calculation',
-        time: new Date() - start
+        time: new Date() - start,
       });
@@ -107,21 +107,19 @@ }
 
-  var spectra = result.spectra;
+  let spectra = result.spectra;
   if (options.xy) {
-    // the spectraData should not be a oneD array but an object with x and y
+    //the spectraData should not be a oneD array but an object with x and y
     if (spectra.length > 0) {
-      for (var i = 0; i < spectra.length; i++) {
-        var spectrum = spectra[i];
-        if (spectrum.data.length > 0) {
-          for (var j = 0; j < spectrum.data.length; j++) {
-            var data = spectrum.data[j];
-            var newData = {
-              x: new Array(data.length / 2),
-              y: new Array(data.length / 2)
-            };
-            for (var k = 0; k < data.length; k = k + 2) {
-              newData.x[k / 2] = data[k];
-              newData.y[k / 2] = data[k + 1];
-            }
-            spectrum.data[j] = newData;
+      for (let i = 0; i < spectra.length; i++) {
+        let spectrum = spectra[i];
+        if (spectrum.data.length) {
+          let data = spectrum.data;
+          let newData = {
+            x: new Array(data.length / 2),
+            y: new Array(data.length / 2),
+          };
+          for (let k = 0; k < data.length; k = k + 2) {
+            newData.x[k / 2] = data[k];
+            newData.y[k / 2] = data[k + 1];
           }
+          spectrum.data = newData;
         }
@@ -136,8 +134,8 @@ }
 function convert1D(files, options) {
-  var result = parseData(files.procs || '', options);
-  var temp = parseData(files.acqus || '', options);
-
-  var keys = Object.keys(temp.info);
-  for (var i = 0; i < keys.length; i++) {
-    var currKey = keys[i];
+  let result = parseData(files.procs || '', options);
+  let temp = parseData(files.acqus || '', options);
+  let keys = Object.keys(temp.info || {});
+  if (!result.info) result = temp;
+  for (let i = 0; i < keys.length; i++) {
+    let currKey = keys[i];
     if (result.info[currKey] === undefined) {
@@ -147,3 +145,2 @@ result.info[currKey] = temp.info[currKey];
   }
-
   if (files['1r'] || files['1i']) {
@@ -164,10 +161,9 @@ if (files['1r']) {
 function convert2D(files, options) {
-  var sf, swP, offset;
+  let sf, swP, offset, result, temp;
   if (files['2rr']) {
-    var result = parseData(files.procs, options);
-    var temp = parseData(files.acqus, options);
-
-    var keys = Object.keys(temp.info);
-    for (var i = 0; i < keys.length; i++) {
-      var currKey = keys[i];
+    result = parseData(files.procs, options);
+    temp = parseData(files.acqus, options);
+    let keys = Object.keys(temp.info);
+    for (let i = 0; i < keys.length; i++) {
+      let currKey = keys[i];
       if (result.info[currKey] === undefined) {
@@ -177,5 +173,4 @@ result.info[currKey] = temp.info[currKey];
     }
-
     temp = parseData(files.proc2s, options);
-    result.info.nbSubSpectra = temp.info.$SI = parseInt(temp.info.$SI);
+    result.info.nbSubSpectra = temp.info.$SI = parseInt(temp.info.$SI, 10);
     sf = temp.info.$SF = parseFloat(temp.info.$SF);
@@ -187,4 +182,4 @@ swP = temp.info.$SWP = parseFloat(temp.info.$SWP);
     temp = parseData(files.acqu2s, options);
-    result.info.nbSubSpectra = temp.info.$SI = parseInt(temp.info.$TD);
-    result.info.$SI = parseInt(result.info.$TD);
+    result.info.nbSubSpectra = temp.info.$SI = parseInt(temp.info.$TD, 10);
+    result.info.$SI = parseInt(result.info.$TD, 10);
     // SW_p = temp.info['$SWH'] = parseFloat(temp.info['$SWH']);
@@ -209,5 +204,5 @@
 
-  var nbSubSpectra = result.info.nbSubSpectra;
-  var pageValue = result.info.firstY;
-  var deltaY = (result.info.lastY - result.info.firstY) / (nbSubSpectra - 1);
+  let nbSubSpectra = result.info.nbSubSpectra;
+  let pageValue = result.info.firstY;
+  let deltaY = (result.info.lastY - result.info.firstY) / (nbSubSpectra - 1);
 
@@ -241,10 +236,10 @@ if (files['2rr']) {
   file = ensureIOBuffer(file);
-  var td = (spectra.info.$SI = parseInt(spectra.info.$SI));
+  let td = (spectra.info.$SI = parseInt(spectra.info.$SI, 10));
 
-  var swP = parseFloat(spectra.info.$SWP);
-  var sf = parseFloat(spectra.info.$SF);
-  var bf = sf;
+  let swP = parseFloat(spectra.info.$SWP);
+  let sf = parseFloat(spectra.info.$SF);
+  let bf = sf;
 
   // var BF = parseFloat(spectra.info["$BF1"]);
-  var offset = spectra.shiftOffsetVal || parseFloat(spectra.info.$OFFSET);
+  let offset = spectra.shiftOffsetVal || parseFloat(spectra.info.$OFFSET);
 
@@ -255,8 +250,9 @@ spectra.info.observeFrequency = sf;
   spectra.info.brukerReference = bf;
+  spectra.info.DATATYPE = 'NMR Spectrum';
 
-  var endian = parseInt(spectra.info.$BYTORDP);
+  let endian = parseInt(spectra.info.$BYTORDP, 10);
   endian = endian ? 0 : 1;
 
   // number of spectras
-  var nbSubSpectra = spectra.info.nbSubSpectra ? spectra.info.nbSubSpectra : 1;
+  let nbSubSpectra = spectra.info.nbSubSpectra ? spectra.info.nbSubSpectra : 1;
 
@@ -269,4 +265,4 @@ if (endian) {
 
-  for (var i = 0; i < nbSubSpectra; i++) {
-    var toSave = {
+  for (let i = 0; i < nbSubSpectra; i++) {
+    let toSave = {
       dataType: 'NMR Spectrum',
@@ -279,21 +275,18 @@ dataTable: '(X++(R..R))',
       yUnit: 'Arbitrary',
-      data: [new Array(td * 2)], // [{x:new Array(td),y:new Array(td)}],
+      data: new Array(td * 2), // [{x:new Array(td),y:new Array(td)}],
       isXYdata: true,
       observeFrequency: sf,
       title: spectra.info.TITLE,
-      deltaX: -(swP / sf) / (td - 1)
+      deltaX: -(swP / sf) / (td - 1),
     };
 
-    var x = offset;
-    var deltaX = toSave.deltaX;
+    let x = offset;
+    let deltaX = toSave.deltaX;
 
     if (real) {
-      for (var k = 0; k < td; ++k) {
-        toSave.data[0][2 * k] = x;
-        toSave.data[0][2 * k + 1] = file.readInt32();
-        if (
-          toSave.data[0][2 * k + 1] === null ||
-          isNaN(toSave.data[0][2 * k + 1])
-        ) {
-          toSave.data[0][2 * k + 1] = 0;
+      for (let k = 0; k < td; ++k) {
+        toSave.data[2 * k] = x;
+        toSave.data[2 * k + 1] = file.readInt32();
+        if (toSave.data[2 * k + 1] === null || isNaN(toSave.data[2 * k + 1])) {
+          toSave.data[2 * k + 1] = 0;
         }
@@ -303,10 +296,7 @@ x += deltaX;
     } else {
-      for (k = td - 1; k >= 0; --k) {
-        toSave.data[0][2 * k] = x;
-        toSave.data[0][2 * k + 1] = file.readInt32();
-        if (
-          toSave.data[0][2 * k + 1] === null ||
-          isNaN(toSave.data[0][2 * k + 1])
-        ) {
-          toSave.data[0][2 * k + 1] = 0;
+      for (let k = td - 1; k >= 0; --k) {
+        toSave.data[2 * k] = x;
+        toSave.data[2 * k + 1] = file.readInt32();
+        if (toSave.data[2 * k + 1] === null || isNaN(toSave.data[2 * k + 1])) {
+          toSave.data[2 * k + 1] = 0;
         }
@@ -322,7 +312,9 @@ x += deltaX;
 function parseData(file, options) {
-  var keepRecordsRegExp = /.*/;
+  let keepRecordsRegExp = /.*/;
   if (options.keepRecordsRegExp) keepRecordsRegExp = options.keepRecordsRegExp;
-  return Converter.convert(file, {
-    keepRecordsRegExp: keepRecordsRegExp
+  let result = Converter.convert(file, {
+    keepRecordsRegExp: keepRecordsRegExp,
   });
+
+  return result.flatten.length === 0 ? {} : result.flatten[0];
 }
@@ -332,16 +324,17 @@
   file = ensureIOBuffer(file);
-  var td = (spectra.info.$TD = parseInt(spectra.info.$TD));
+  let td = (spectra.info.$TD = parseInt(spectra.info.$TD, 10));
 
-  var SW = (spectra.info.$SW = parseFloat(spectra.info.$SW));
+  let SW = (spectra.info.$SW = parseFloat(spectra.info.$SW));
 
-  var SF = (spectra.info.$SFO1 = parseFloat(spectra.info.$SFO1));
-  var BF = parseFloat(spectra.info.$BF1);
+  let SF = (spectra.info.$SFO1 = parseFloat(spectra.info.$SFO1));
+  let BF = parseFloat(spectra.info.$BF1);
   spectra.info.$BF1 = BF;
+  spectra.info.DATATYPE = 'NMR FID';
 
   // var DW = 1 / (2 * SW_h);
   // var AQ = td * DW;
-  var AQ = SW;
-  var DW = AQ / (td - 1);
+  let AQ = SW;
+  let DW = AQ / (td - 1);
 
-  var endian = parseInt(spectra.info.$BYTORDP);
+  let endian = parseInt(spectra.info.$BYTORDP, 10);
   endian = endian ? 0 : 1;
@@ -355,7 +348,7 @@
 
-  var nbSubSpectra = spectra.info.nbSubSpectra ? spectra.info.nbSubSpectra : 1;
+  let nbSubSpectra = spectra.info.nbSubSpectra ? spectra.info.nbSubSpectra : 1;
   spectra.spectra = new Array(nbSubSpectra);
 
-  for (var j = 0; j < nbSubSpectra / 2; j++) {
-    var toSave = {
+  for (let j = 0; j < nbSubSpectra / 2; j++) {
+    let toSave = {
       dataType: 'NMR FID',
@@ -373,3 +366,3 @@ dataTable: '(X++(R..R))',
       title: spectra.info.TITLE,
-      deltaX: DW
+      deltaX: DW,
     };
@@ -387,13 +380,13 @@ spectra.spectra[j * 2] = toSave;
       yUnit: 'Arbitrary',
-      data: [new Array(2 * td)], // [{x:new Array(td),y:new Array(td)}],
+      data: new Array(2 * td), // [{x:new Array(td),y:new Array(td)}],
       isXYdata: true,
       observeFrequency: SF,
       title: spectra.info.TITLE,
-      deltaX: DW
+      deltaX: DW,
     };
     spectra.spectra[j * 2 + 1] = toSave;
 
-    var x = 0;
-    var y;
-    for (var i = 0; file.available(8) && i < td; i++, x = i * DW) {
+    let x = 0;
+    let y, i;
+    for (i = 0; file.available(8) && i < td; i++, x = i * DW) {
       y = file.readInt32();
@@ -403,4 +396,4 @@ if (y === null || isNaN(y)) {
       }
-      spectra.spectra[j * 2].data[0][2 * i + 1] = y;
-      spectra.spectra[j * 2].data[0][2 * i] = x;
+      spectra.spectra[j * 2].data[2 * i + 1] = y;
+      spectra.spectra[j * 2].data[2 * i] = x;
       y = file.readInt32();
@@ -410,11 +403,11 @@ if (y === null || isNaN(y)) {
       }
-      spectra.spectra[j * 2 + 1].data[0][2 * i + 1] = y;
-      spectra.spectra[j * 2 + 1].data[0][2 * i] = x;
+      spectra.spectra[j * 2 + 1].data[2 * i + 1] = y;
+      spectra.spectra[j * 2 + 1].data[2 * i] = x;
     }
 
     for (; i < td; i++, x = i * DW) {
-      spectra.spectra[j * 2].data[0][2 * i + 1] = 0;
-      spectra.spectra[j * 2].data[0][2 * i] = x;
-      spectra.spectra[j * 2 + 1].data[0][2 * i + 1] = 0;
-      spectra.spectra[j * 2 + 1].data[0][2 * i] = x;
+      spectra.spectra[j * 2].data[2 * i + 1] = 0;
+      spectra.spectra[j * 2].data[2 * i] = x;
+      spectra.spectra[j * 2 + 1].data[2 * i + 1] = 0;
+      spectra.spectra[j * 2 + 1].data[2 * i] = x;
     }
@@ -431,14 +424,14 @@ }
 function convertTo3DZ(spectra) {
-  var noise = 0;
-  var minZ = spectra[0].data[0][0];
-  var maxZ = minZ;
-  var ySize = spectra.length;
-  var xSize = spectra[0].data[0].length / 2;
-  var z = new Array(ySize);
-  for (var i = 0; i < ySize; i++) {
+  let noise = 0;
+  let minZ = spectra[0].data[0];
+  let maxZ = minZ;
+  let ySize = spectra.length;
+  let xSize = spectra[0].data.length / 2;
+  let z = new Array(ySize);
+  for (let i = 0; i < ySize; i++) {
     z[i] = new Array(xSize);
-    for (var j = 0; j < xSize; j++) {
-      z[i][j] = spectra[i].data[0][j * 2 + 1];
-      if (z[i][j] < minZ) minZ = spectra[i].data[0][j * 2 + 1];
-      if (z[i][j] > maxZ) maxZ = spectra[i].data[0][j * 2 + 1];
+    for (let j = 0; j < xSize; j++) {
+      z[i][j] = spectra[i].data[j * 2 + 1];
+      if (z[i][j] < minZ) minZ = spectra[i].data[j * 2 + 1];
+      if (z[i][j] > maxZ) maxZ = spectra[i].data[j * 2 + 1];
       if (i !== 0 && j !== 0) {
@@ -452,4 +445,4 @@ noise +=
     z: z,
-    minX: spectra[0].data[0][0],
-    maxX: spectra[0].data[0][spectra[0].data[0].length - 2],
+    minX: spectra[0].data[0],
+    maxX: spectra[0].data[spectra[0].data.length - 2],
     minY: spectra[0].pageValue,
@@ -459,3 +452,3 @@ maxY: spectra[ySize - 1].pageValue,
     maxZ: maxZ,
-    noise: noise / ((ySize - 1) * (xSize - 1) * 2)
+    noise: noise / ((ySize - 1) * (xSize - 1) * 2),
   };
@@ -465,3 +458,3 @@ }
 function add2D(result) {
-  var zData = convertTo3DZ(result.spectra);
+  let zData = convertTo3DZ(result.spectra);
   result.contourLines = generateContourLines(zData);
@@ -473,20 +466,20 @@ delete zData.z;
 function generateContourLines(zData) {
-  var noise = zData.noise;
-  var z = zData.z;
-  var contourLevels = [];
-  var nbLevels = 7;
-  var povarHeight = new Float32Array(4);
-  var isOver = [];
-  var nbSubSpectra = z.length;
-  var nbPovars = z[0].length;
-  var pAx, pAy, pBx, pBy;
+  let noise = zData.noise;
+  let z = zData.z;
+  let contourLevels = [];
+  let nbLevels = 7;
+  let povarHeight = new Float32Array(4);
+  let isOver = [];
+  let nbSubSpectra = z.length;
+  let nbPovars = z[0].length;
+  let pAx, pAy, pBx, pBy;
 
-  var x0 = zData.minX;
-  var xN = zData.maxX;
-  var dx = (xN - x0) / (nbPovars - 1);
-  var y0 = zData.minY;
-  var yN = zData.maxY;
-  var dy = (yN - y0) / (nbSubSpectra - 1);
-  var minZ = zData.minZ;
-  var maxZ = zData.maxZ;
+  let x0 = zData.minX;
+  let xN = zData.maxX;
+  let dx = (xN - x0) / (nbPovars - 1);
+  let y0 = zData.minY;
+  let yN = zData.maxY;
+  let dy = (yN - y0) / (nbSubSpectra - 1);
+  let minZ = zData.minZ;
+  let maxZ = zData.maxZ;
 
@@ -504,8 +497,8 @@ // System.out.prvarln('y0 '+y0+' yN '+yN);
 
-  var lineZValue;
-  for (var level = 0; level < nbLevels * 2; level++) {
+  let lineZValue;
+  for (let level = 0; level < nbLevels * 2; level++) {
     // multiply by 2 for positif and negatif
-    var contourLevel = {};
+    let contourLevel = {};
     contourLevels.push(contourLevel);
-    var side = level % 2;
+    let side = level % 2;
     if (side === 0) {
@@ -518,3 +511,3 @@ lineZValue =
     }
-    var lines = [];
+    let lines = [];
     contourLevel.zValue = lineZValue;
@@ -525,4 +518,4 @@ contourLevel.lines = lines;
 
-    for (var iSubSpectra = 0; iSubSpectra < nbSubSpectra - 1; iSubSpectra++) {
-      for (var povar = 0; povar < nbPovars - 1; povar++) {
+    for (let iSubSpectra = 0; iSubSpectra < nbSubSpectra - 1; iSubSpectra++) {
+      for (let povar = 0; povar < nbPovars - 1; povar++) {
         povarHeight[0] = z[iSubSpectra][povar];
@@ -533,3 +526,3 @@ povarHeight[1] = z[iSubSpectra][povar + 1];
 
-        for (var i = 0; i < 4; i++) {
+        for (let i = 0; i < 4; i++) {
           isOver[i] = povarHeight[i] > lineZValue;
@@ -554,3 +547,3 @@ }
             pBx * dx + x0,
-            pBy * dy + y0
+            pBy * dy + y0,
           );
@@ -573,3 +566,3 @@ }
             pBx * dx + x0,
-            pBy * dy + y0
+            pBy * dy + y0,
           );
@@ -596,3 +589,3 @@ }
               pBx * dx + x0,
-              pBy * dy + y0
+              pBy * dy + y0,
             );
@@ -610,3 +603,3 @@ }
               pBx * dx + x0,
-              pBy * dy + y0
+              pBy * dy + y0,
             );
@@ -623,3 +616,3 @@ }
               pBx * dx + x0,
-              pBy * dy + y0
+              pBy * dy + y0,
             );
@@ -636,3 +629,3 @@ }
               pBx * dx + x0,
-              pBy * dy + y0
+              pBy * dy + y0,
             );
@@ -650,3 +643,3 @@ }
     maxY: zData.maxY,
-    segments: contourLevels
+    segments: contourLevels,
   };
@@ -667,3 +660,3 @@ }
   convertZip: readZIP,
-  convertFolder: convert
+  convertFolder: convert,
 };

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Major refactor

Supply chain risk

Package has recently undergone a major refactor. It may be unstable or indicate significant internal changes. Use caution when updating to versions that include significant changes.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

210507

increased by855.42%

Number of package files

20

increased by185.71%

Lines of code

1285

increased by118.17%

Worsened metrics

Dev dependency count

9

increased by28.57%

Dependency changes

• + Addediobuffer@5.3.2(transitive)

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

• + Addedjcampconverter@5.0.2(transitive)

• + Addedmedian-quickselect@1.0.1(transitive)

• + Addedml-array-median@1.1.6(transitive)

• - Removed@types/utf8@2.1.6(transitive)

• - Removediobuffer@4.0.1(transitive)

• - Removedjcampconverter@3.0.4(transitive)

• - Removedutf8@3.0.0(transitive)

• Updated@babel/preset-env@^7.8.4

• Updatediobuffer@^5.0.2

• Updatedjcampconverter@^5.0.2

• Updatedjszip@^3.2.2