brukerconverter - npm Package Compare versions

Comparing version 2.1.2 to 3.0.0

bower.json

 {
   "name": "brukerconverter",
-  "version": "2.1.2",
+  "version": "3.0.0",
   "main": "build/brukerconverter.js",
@@ -5,0 +5,0 @@ "homepage": "https://github.com/cheminfo-js/brukerconverter",

lib/index.js

@@ -11,2 +11,55 @@ 'use strict';
 
+/**
+ * Those functions should disappear if add2D becomes accessible in jcampconvert
+ * @param spectra
+ * @returns {{z: Array, minX: *, maxX: *, minY: *, maxY: *, minZ: *, maxZ: *, noise: number}}
+ */
+
+function convertTo3DZ(spectra) {
+  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 (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) {
+        noise +=
+          Math.abs(z[i][j] - z[i][j - 1]) + Math.abs(z[i][j] - z[i - 1][j]);
+      }
+    }
+  }
+  const firstX = spectra[0].data[0];
+  const lastX = spectra[0].data[spectra[0].data.length - 2]; // has to be -2 because it is a 1D array [x,y,x,y,...]
+  const firstY = spectra[0].pageValue;
+  const lastY = spectra[ySize - 1].pageValue;
+
+  // Because the min / max value are the only information about the matrix if we invert
+  // min and max we need to invert the array
+  if (firstX > lastX) {
+    for (let spectrum of z) {
+      spectrum.reverse();
+    }
+  }
+  if (firstY > lastY) {
+    z.reverse();
+  }
+
+  return {
+    z,
+    minX: Math.min(firstX, lastX),
+    maxX: Math.max(firstX, lastX),
+    minY: Math.min(firstY, lastY),
+    maxY: Math.max(firstY, lastY),
+    minZ: minZ,
+    maxZ: maxZ,
+    noise: noise / ((ySize - 1) * (xSize - 1) * 2),
+  };
+}
+
 function generateContourLines(zData) {
@@ -183,55 +236,2 @@ let noise = zData.noise;
 
-/**
- * Those functions should disappear if add2D becomes accessible in jcampconvert
- * @param spectra
- * @returns {{z: Array, minX: *, maxX: *, minY: *, maxY: *, minZ: *, maxZ: *, noise: number}}
- */
-
-function convertTo3DZ(spectra) {
-  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 (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) {
-        noise +=
-          Math.abs(z[i][j] - z[i][j - 1]) + Math.abs(z[i][j] - z[i - 1][j]);
-      }
-    }
-  }
-  const firstX = spectra[0].data[0];
-  const lastX = spectra[0].data[spectra[0].data.length - 2]; // has to be -2 because it is a 1D array [x,y,x,y,...]
-  const firstY = spectra[0].pageValue;
-  const lastY = spectra[ySize - 1].pageValue;
-
-  // Because the min / max value are the only information about the matrix if we invert
-  // min and max we need to invert the array
-  if (firstX > lastX) {
-    for (let spectrum of z) {
-      spectrum.reverse();
-    }
-  }
-  if (firstY > lastY) {
-    z.reverse();
-  }
-
-  return {
-    z,
-    minX: Math.min(firstX, lastX),
-    maxX: Math.max(firstX, lastX),
-    minY: Math.min(firstY, lastY),
-    maxY: Math.max(firstY, lastY),
-    minZ: minZ,
-    maxZ: maxZ,
-    noise: noise / ((ySize - 1) * (xSize - 1) * 2),
-  };
-}
-
 const BINARY = 1;
@@ -283,2 +283,7 @@ const TEXT = 2;
         );
+        let acqu2s = zip.file(name.replace(/pdata\/[0-9]+\//, 'acqu2s'));
+        if (acqu2s) {
+          promises.push('acqu2s');
+          promises.push(acqu2s.async('string'));
+        }
       }
@@ -322,2 +327,27 @@ for (let j = 0; j < currFiles.length; ++j) {
   }
+  //normalizing info
+  result.info.$DATE = parseFloat(result.info.$DATE);
+  if (result.info.$GRPDLY) {
+    result.info.$GRPDLY = parseFloat(result.info.$GRPDLY[0]);
+    result.info.$DSPFVS = parseFloat(result.info.$DSPFVS[0]);
+    result.info.$DECIM = parseFloat(result.info.$DECIM[0]);
+  }
+
+  for (let key in result.info) {
+    if (!Array.isArray(result.info[key])) continue;
+
+    if (key.indexOf('$') > -1) {
+      if (result.info[key].length === 1) {
+        result.info[key] = result.info[key][0];
+      } else if (
+        typeof result.info[key][0] === 'string' &&
+        result.info[key][0].indexOf('(0..') > -1
+      ) {
+        result.info[key] = result.info[key][0];
+      }
+    } else {
+      result.info[key] = result.info[key][0];
+    }
+  }
+
   if (result.twoD) {
@@ -365,10 +395,14 @@ add2D(result, 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 (!Object.keys(result).length) result = temp;
+
+  for (let key in result.info) {
+    result.info[key] = [result.info[key]];
+  }
+
+  for (let currKey in temp.info) {
     if (result.info[currKey] === undefined) {
-      result.info[currKey] = temp.info[currKey];
+      result.info[currKey] = [temp.info[currKey]];
     }
   }
+
   if (files['1r'] || files['1i']) {
@@ -389,40 +423,57 @@ if (files['1r']) {
 function convert2D(files, options) {
-  let sf, swP, offset, result, temp;
-  if (files['2rr']) {
+  let sf, swP, offset, temp, temp2, result;
+  if (files.proc2s && files.procs) {
     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) {
-        result.info[currKey] = temp.info[currKey];
+    temp = parseData(files.proc2s, options);
+    for (let key in temp.info) {
+      if (result.info[key]) {
+        if (!Array.isArray(result.info[key])) {
+          result.info[key] = [result.info[key]];
+        }
+        result.info[key].push(temp.info[key]);
+      } else if (result.info[key] === undefined) {
+        result.info[key] = [temp.info[key]];
       }
     }
-    temp = parseData(files.proc2s, options);
-    result.info.nbSubSpectra = temp.info.$SI = parseInt(temp.info.$SI, 10);
-    sf = temp.info.$SF = parseFloat(temp.info.$SF);
-    swP = temp.info.$SWP = parseFloat(temp.info.$SWP);
-    offset = temp.info.$OFFSET = parseFloat(temp.info.$OFFSET);
-  } else if (files.ser) {
-    result = parseData(files.acqus, options);
-    temp = parseData(files.acqu2s, options);
-    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']);
+  }
 
-    swP = temp.info.$SW;
+  temp = parseData(files.acqus, options);
+  temp2 = parseData(files.acqu2s, options);
+  for (let key in temp2.info) {
+    if (temp.info[key]) {
+      if (!Array.isArray(temp.info[key])) {
+        temp.info[key] = [temp.info[key]];
+      }
+      temp.info[key].push(temp2.info[key]);
+    } else if (temp.info[key] === undefined) {
+      temp.info[key] = [temp2.info[key]];
+    }
+  }
 
-    result.info.$SWP = result.info.$SWH;
-    result.info.$SF = parseFloat(temp.info.$SFO1);
-    result.info.$OFFSET = 0;
-    sf = temp.info.$SFO1 = parseFloat(temp.info.$SFO1);
-    offset = 0;
-    result.info.$AXNUC = result.info.$NUC1;
-    temp.info.$AXNUC = temp.info.$NUC1;
+  if (!result) result = temp;
+  for (let key in temp.info) {
+    if (result.info[key] === undefined) {
+      result.info[key] = temp.info[key];
+    }
   }
 
+  for (let key in result.info) {
+    if (!Array.isArray(result.info[key])) {
+      result.info[key] = [result.info[key]];
+    }
+  }
+
+  result.info.nbSubSpectra = files['2rr']
+    ? parseInt(result.info.$SI[1], 10)
+    : parseInt(result.info.$TD[1], 10);
+
+  if (result.info.$SWP) result.info.$SWP = result.info.$SWH;
+  if (!result.info.$SF) result.info.$SF = result.info.$SFO1;
+  if (!result.info.$OFFSET) result.info.$OFFSET = 0;
+
+  sf = parseFloat(result.info.$SF);
+  swP = parseFloat(result.info.$SWP || result.info.$SW);
+  offset = parseFloat(result.info.$OFFSET);
   result.info.firstY = offset;
   result.info.lastY = offset - swP / sf;
-  result.info.$BF2 = sf;
-  result.info.$SFO1 = sf;
 
@@ -444,6 +495,4 @@ let nbSubSpectra = result.info.nbSubSpectra;
 
-  // var dataType = files.ser ? 'TYPE_2DNMR_FID' : 'TYPE_2DNMR_SPECTRUM';
-
-  result.info['2D_Y_NUCLEUS'] = temp.info.$AXNUC;
-  result.info['2D_X_NUCLEUS'] = result.info.$AXNUC;
+  result.info['2D_Y_NUCLEUS'] = result.info.$NUC1[1];
+  result.info['2D_X_NUCLEUS'] = result.info.$NUC1[0];
   result.info['2D_Y_FRECUENCY'] = sf;
@@ -453,5 +502,4 @@ result.info['2D_Y_OFFSET'] = offset;
   result.info['2D_X_OFFSET'] = result.info.$OFFSET;
+  result.info.twoD = result.twoD = true;
 
-  result.twoD = true;
-
   return result;
@@ -462,4 +510,4 @@ }
   file = ensureIOBuffer(file);
-  let td = (spectra.info.$SI = parseInt(spectra.info.$SI, 10));
 
+  let td = parseInt(spectra.info.$SI[0], 10);
   let swP = parseFloat(spectra.info.$SWP);
@@ -469,8 +517,5 @@ let sf = parseFloat(spectra.info.$SF);
 
-  // var BF = parseFloat(spectra.info["$BF1"]);
   let offset = spectra.shiftOffsetVal || parseFloat(spectra.info.$OFFSET);
 
   spectra.info.observeFrequency = sf;
-  spectra.info.$BF1 = bf;
-  spectra.info.$SFO1 = sf;
   spectra.info.brukerReference = bf;
@@ -482,3 +527,2 @@ spectra.info.DATATYPE = 'NMR Spectrum';
 
-  // number of spectras
   let nbSubSpectra = spectra.info.nbSubSpectra ? spectra.info.nbSubSpectra : 1;
@@ -541,3 +585,2 @@
   });
-
   return result.flatten.length === 0 ? {} : result.flatten[0];
@@ -548,8 +591,7 @@ }
   file = ensureIOBuffer(file);
-  let td = (spectra.info.$TD = parseInt(spectra.info.$TD, 10));
+  let td = (spectra.info.$TD[0] = parseInt(spectra.info.$TD[0], 10));
+  let SW_H = (spectra.info.$SWH[0] = parseFloat(spectra.info.$SWH[0]));
 
-  let SW_H = (spectra.info.$SWH = parseFloat(spectra.info.$SWH));
-
-  let SF = (spectra.info.$SFO1 = parseFloat(spectra.info.$SFO1));
-  let BF = parseFloat(spectra.info.$BF1);
+  let SF = (spectra.info.$SFO1[0] = parseFloat(spectra.info.$SFO1[0]));
+  let BF = parseFloat(spectra.info.$BF1[0]);
   spectra.info.$BF1 = BF;
@@ -600,5 +642,5 @@ spectra.info.DATATYPE = 'NMR FID';
       yUnit: 'Arbitrary',
-      data: new Array(2 * td), // [{x:new Array(td),y:new Array(td)}],
+      data: new Array(2 * td),
       isXYdata: true,
-      observeFrequency: SF,
+      directFrequency: SF,
       title: spectra.info.TITLE,
@@ -605,0 +647,0 @@ deltaX: DW,

package.json

 {
   "name": "brukerconverter",
-  "version": "2.1.2",
+  "version": "3.0.0",
   "description": "Parse and convert Bruker raw data",
@@ -35,15 +35,14 @@ "main": "lib/index.js",
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.9.6",
-    "@types/jest": "^25.2.1",
+    "@babel/plugin-transform-modules-commonjs": "^7.10.4",
+    "@types/jest": "^25.2.3",
     "cheminfo-build": "^1.1.1",
-    "cheminfo-tools": "1.23.3",
     "eslint": "^6.8.0",
     "eslint-config-cheminfo": "^3.0.0",
-    "eslint-plugin-import": "^2.20.2",
-    "eslint-plugin-jest": "^23.8.2",
-    "eslint-plugin-prettier": "^3.1.3",
-    "jest": "^25.5.2",
+    "eslint-plugin-import": "^2.22.0",
+    "eslint-plugin-jest": "^23.18.0",
+    "eslint-plugin-prettier": "^3.1.4",
+    "jest": "^25.5.4",
     "npm-run-all": "^4.1.5",
     "prettier": "^2.0.5",
-    "rollup": "^2.7.3"
+    "rollup": "^2.19.0"
   },
@@ -53,4 +52,4 @@ "dependencies": {
     "jcampconverter": "^5.0.2",
-    "jszip": "^3.4.0"
+    "jszip": "^3.5.0"
   }
 }

src/index.js

 import { IOBuffer } from 'iobuffer';
 import { convert as convertJcamp } from 'jcampconverter';
 import JSZip from 'jszip/dist/jszip';
+
+import convertTo3DZ from './convertTo3DZ';
 import generateContourLines from './generateContourLines';
-import convertTo3DZ from './convertTo3DZ';
 
@@ -53,2 +54,7 @@ const BINARY = 1;
         );
+        let acqu2s = zip.file(name.replace(/pdata\/[0-9]+\//, 'acqu2s'));
+        if (acqu2s) {
+          promises.push('acqu2s');
+          promises.push(acqu2s.async('string'));
+        }
       }
@@ -92,2 +98,27 @@ for (let j = 0; j < currFiles.length; ++j) {
   }
+  //normalizing info
+  result.info.$DATE = parseFloat(result.info.$DATE);
+  if (result.info.$GRPDLY) {
+    result.info.$GRPDLY = parseFloat(result.info.$GRPDLY[0]);
+    result.info.$DSPFVS = parseFloat(result.info.$DSPFVS[0]);
+    result.info.$DECIM = parseFloat(result.info.$DECIM[0]);
+  }
+
+  for (let key in result.info) {
+    if (!Array.isArray(result.info[key])) continue;
+
+    if (key.indexOf('$') > -1) {
+      if (result.info[key].length === 1) {
+        result.info[key] = result.info[key][0];
+      } else if (
+        typeof result.info[key][0] === 'string' &&
+        result.info[key][0].indexOf('(0..') > -1
+      ) {
+        result.info[key] = result.info[key][0];
+      }
+    } else {
+      result.info[key] = result.info[key][0];
+    }
+  }
+
   if (result.twoD) {
@@ -135,10 +166,14 @@ add2D(result, 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 (!Object.keys(result).length) result = temp;
+
+  for (let key in result.info) {
+    result.info[key] = [result.info[key]];
+  }
+
+  for (let currKey in temp.info) {
     if (result.info[currKey] === undefined) {
-      result.info[currKey] = temp.info[currKey];
+      result.info[currKey] = [temp.info[currKey]];
     }
   }
+
   if (files['1r'] || files['1i']) {
@@ -159,40 +194,57 @@ if (files['1r']) {
 function convert2D(files, options) {
-  let sf, swP, offset, result, temp;
-  if (files['2rr']) {
+  let sf, swP, offset, temp, temp2, result;
+  if (files.proc2s && files.procs) {
     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) {
-        result.info[currKey] = temp.info[currKey];
+    temp = parseData(files.proc2s, options);
+    for (let key in temp.info) {
+      if (result.info[key]) {
+        if (!Array.isArray(result.info[key])) {
+          result.info[key] = [result.info[key]];
+        }
+        result.info[key].push(temp.info[key]);
+      } else if (result.info[key] === undefined) {
+        result.info[key] = [temp.info[key]];
       }
     }
-    temp = parseData(files.proc2s, options);
-    result.info.nbSubSpectra = temp.info.$SI = parseInt(temp.info.$SI, 10);
-    sf = temp.info.$SF = parseFloat(temp.info.$SF);
-    swP = temp.info.$SWP = parseFloat(temp.info.$SWP);
-    offset = temp.info.$OFFSET = parseFloat(temp.info.$OFFSET);
-  } else if (files.ser) {
-    result = parseData(files.acqus, options);
-    temp = parseData(files.acqu2s, options);
-    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']);
+  }
 
-    swP = temp.info.$SW;
+  temp = parseData(files.acqus, options);
+  temp2 = parseData(files.acqu2s, options);
+  for (let key in temp2.info) {
+    if (temp.info[key]) {
+      if (!Array.isArray(temp.info[key])) {
+        temp.info[key] = [temp.info[key]];
+      }
+      temp.info[key].push(temp2.info[key]);
+    } else if (temp.info[key] === undefined) {
+      temp.info[key] = [temp2.info[key]];
+    }
+  }
 
-    result.info.$SWP = result.info.$SWH;
-    result.info.$SF = parseFloat(temp.info.$SFO1);
-    result.info.$OFFSET = 0;
-    sf = temp.info.$SFO1 = parseFloat(temp.info.$SFO1);
-    offset = 0;
-    result.info.$AXNUC = result.info.$NUC1;
-    temp.info.$AXNUC = temp.info.$NUC1;
+  if (!result) result = temp;
+  for (let key in temp.info) {
+    if (result.info[key] === undefined) {
+      result.info[key] = temp.info[key];
+    }
   }
 
+  for (let key in result.info) {
+    if (!Array.isArray(result.info[key])) {
+      result.info[key] = [result.info[key]];
+    }
+  }
+
+  result.info.nbSubSpectra = files['2rr']
+    ? parseInt(result.info.$SI[1], 10)
+    : parseInt(result.info.$TD[1], 10);
+
+  if (result.info.$SWP) result.info.$SWP = result.info.$SWH;
+  if (!result.info.$SF) result.info.$SF = result.info.$SFO1;
+  if (!result.info.$OFFSET) result.info.$OFFSET = 0;
+
+  sf = parseFloat(result.info.$SF);
+  swP = parseFloat(result.info.$SWP || result.info.$SW);
+  offset = parseFloat(result.info.$OFFSET);
   result.info.firstY = offset;
   result.info.lastY = offset - swP / sf;
-  result.info.$BF2 = sf;
-  result.info.$SFO1 = sf;
 
@@ -214,6 +266,4 @@ let nbSubSpectra = result.info.nbSubSpectra;
 
-  // var dataType = files.ser ? 'TYPE_2DNMR_FID' : 'TYPE_2DNMR_SPECTRUM';
-
-  result.info['2D_Y_NUCLEUS'] = temp.info.$AXNUC;
-  result.info['2D_X_NUCLEUS'] = result.info.$AXNUC;
+  result.info['2D_Y_NUCLEUS'] = result.info.$NUC1[1];
+  result.info['2D_X_NUCLEUS'] = result.info.$NUC1[0];
   result.info['2D_Y_FRECUENCY'] = sf;
@@ -223,5 +273,4 @@ result.info['2D_Y_OFFSET'] = offset;
   result.info['2D_X_OFFSET'] = result.info.$OFFSET;
+  result.info.twoD = result.twoD = true;
 
-  result.twoD = true;
-
   return result;
@@ -232,4 +281,4 @@ }
   file = ensureIOBuffer(file);
-  let td = (spectra.info.$SI = parseInt(spectra.info.$SI, 10));
 
+  let td = parseInt(spectra.info.$SI[0], 10);
   let swP = parseFloat(spectra.info.$SWP);
@@ -239,8 +288,5 @@ let sf = parseFloat(spectra.info.$SF);
 
-  // var BF = parseFloat(spectra.info["$BF1"]);
   let offset = spectra.shiftOffsetVal || parseFloat(spectra.info.$OFFSET);
 
   spectra.info.observeFrequency = sf;
-  spectra.info.$BF1 = bf;
-  spectra.info.$SFO1 = sf;
   spectra.info.brukerReference = bf;
@@ -252,3 +298,2 @@ spectra.info.DATATYPE = 'NMR Spectrum';
 
-  // number of spectras
   let nbSubSpectra = spectra.info.nbSubSpectra ? spectra.info.nbSubSpectra : 1;
@@ -311,3 +356,2 @@
   });
-
   return result.flatten.length === 0 ? {} : result.flatten[0];
@@ -318,8 +362,7 @@ }
   file = ensureIOBuffer(file);
-  let td = (spectra.info.$TD = parseInt(spectra.info.$TD, 10));
+  let td = (spectra.info.$TD[0] = parseInt(spectra.info.$TD[0], 10));
+  let SW_H = (spectra.info.$SWH[0] = parseFloat(spectra.info.$SWH[0]));
 
-  let SW_H = (spectra.info.$SWH = parseFloat(spectra.info.$SWH));
-
-  let SF = (spectra.info.$SFO1 = parseFloat(spectra.info.$SFO1));
-  let BF = parseFloat(spectra.info.$BF1);
+  let SF = (spectra.info.$SFO1[0] = parseFloat(spectra.info.$SFO1[0]));
+  let BF = parseFloat(spectra.info.$BF1[0]);
   spectra.info.$BF1 = BF;
@@ -370,5 +413,5 @@ spectra.info.DATATYPE = 'NMR FID';
       yUnit: 'Arbitrary',
-      data: new Array(2 * td), // [{x:new Array(td),y:new Array(td)}],
+      data: new Array(2 * td),
       isXYdata: true,
-      observeFrequency: SF,
+      directFrequency: SF,
       title: spectra.info.TITLE,
@@ -375,0 +418,0 @@ deltaX: DW,

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Fixed alerts

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Major refactor

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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.

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Improved metrics

Total package byte prevSize

160153

increased by1.28%

Dev dependency count

12

decreased by-7.69%

Lines of code

1787

increased by4.32%

Number of medium supply chain risk alerts

0

decreased by-100%

Dependency changes

• Updatedjszip@^3.5.0