brukerconverter - npm Package Compare versions

Comparing version 6.2.3 to 6.2.4-pre.1694336922

lib/index.js

@@ -217,2 +217,19 @@ 'use strict';
 
+function getValueFct(results) {
+  const getIndex = getIndexFct(results);
+  return (name) => {
+    const index = getIndex(name);
+    if (index > 0 && results[index].status === 'fulfilled') {
+      return results[index].value;
+    }
+  };
+}
+
+function getIndexFct(results) {
+  return (name) => {
+    const index = results.findIndex((r) => r.value === name);
+    return index > -1 ? index + 1 : null;
+  };
+}
+
 function joinInfoMeta(target, toAppend) {
@@ -283,5 +300,5 @@ for (let key in toAppend.meta) {
 
-async function setFIDSpectrumData(file, spectra) {
+function setFIDSpectrumData(file, spectra) {
   let td = parseInt(spectra.meta.TD[0], 10);
-  let ioBuffer = new iobuffer.IOBuffer(await file.arrayBuffer());
+  let ioBuffer = new iobuffer.IOBuffer(file);
 
@@ -359,7 +376,7 @@ if (td * spectra.meta.nbSubSpectra * 4 > ioBuffer.length) {
 
-async function setProcessedSpectrumData(files, spectra) {
+function setProcessedSpectrumData(files, spectra) {
   const buffers = {};
   for (const key in files) {
     if (!files[key]) continue;
-    buffers[key] = new iobuffer.IOBuffer(await files[key].arrayBuffer());
+    buffers[key] = new iobuffer.IOBuffer(files[key]);
   }
@@ -428,19 +445,45 @@
 async function convert1D(files, options) {
-  const result = await parseData(files.procs, options);
-  const acqus = await parseData(files.acqus, options);
-  joinInfoMeta(result, acqus);
+  const promises = [];
+  promises.push('procs', parseData(files.procs, options));
+  promises.push('acqus', parseData(files.acqus, options));
 
-  if (files.quantFactorSample) addEreticFactor(result, files);
-  if (files.integrals) result.integrals = await parseIntegrals(files);
+  if (files.quantFactorSample) {
+    promises.push('ereticFactor', getEreticFactor(files));
+  }
+  if (files.integrals) {
+    promises.push('integrals', parseIntegrals(files));
+  }
 
-  if (files['1r'] || files['1i']) {
-    await setProcessedSpectrumData(
+  const filesToRead = files['1r'] || files['1i'] ? ['1r', '1i'] : ['fid'];
+  for (const key of filesToRead) {
+    if (!files[key]) continue;
+    promises.push(key, files[key].arrayBuffer());
+  }
+
+  return Promise.allSettled(promises).then(formatSpectrum$1);
+}
+
+function formatSpectrum$1(results) {
+  const getValue = getValueFct(results);
+
+  const result = getValue('procs');
+  joinInfoMeta(result, getValue('acqus'));
+
+  const getIndex = getIndexFct(results);
+  if (getIndex('integrals')) {
+    result.integrals = getValue('integrals');
+  }
+  if (getIndex('ereticFactor')) {
+    result.info.ereticFactor = getValue('ereticFactor');
+  }
+  if (getIndex('1r') || getIndex('1i')) {
+    setProcessedSpectrumData(
       {
-        re: files['1r'],
-        im: files['1i'],
+        re: getValue('1r'),
+        im: getValue('1i'),
       },
       result,
     );
-  } else if (files.fid) {
-    await setFIDSpectrumData(files.fid, result);
+  } else if (getIndex('fid')) {
+    setFIDSpectrumData(getValue('fid'), result);
   }
@@ -451,9 +494,7 @@
 
-async function addEreticFactor(result, files) {
+async function getEreticFactor(files) {
   const quantFactorSample = (await files.quantFactorSample.text()).match(
     /<Application[\w\W]+<Eretic_Factor>(?<ereticFactor>[\d.]+)/,
   );
-  if (quantFactorSample) {
-    result.info.ereticFactor = Number(quantFactorSample.groups.ereticFactor);
-  }
+  return Number(quantFactorSample.groups.ereticFactor);
 }
@@ -476,20 +517,26 @@
 async function convert2D(files, options) {
-  const result = mergeMetadata(
-    await parseData(files.procs, options),
-    await parseData(files.proc2s, options),
-  );
+  const promises = [];
+  promises.push('procs', parseData(files.procs, options));
+  promises.push('proc2s', parseData(files.proc2s, options));
+  promises.push('acqus', parseData(files.acqus, options));
+  promises.push('acqu2s', parseData(files.acqu2s, options));
 
-  const acqus = mergeMetadata(
-    await parseData(files.acqus, options),
-    await parseData(files.acqu2s, options),
-  );
+  const filesToRead = ['2rr', '2ri', '2ir', '2ii', 'ser'];
+  for (const key of filesToRead) {
+    if (!files[key]) continue;
+    promises.push(key, files[key].arrayBuffer());
+  }
 
+  return Promise.allSettled(promises).then(formatSpectrum);
+}
+
+function formatSpectrum(results) {
+  const getIndex = getIndexFct(results);
+  const getValue = getValueFct(results);
+  const result = mergeMetadata(getValue('procs'), getValue('proc2s'));
+
+  const acqus = mergeMetadata(getValue('acqus'), getValue('acqu2s'));
+
   joinInfoMeta(result, acqus);
 
-  result.meta.nbSubSpectra = ['2rr', '2ri', '2ir', '2ii'].some(
-    (key) => key in files,
-  )
-    ? parseInt(result.meta.SI[1], 10)
-    : parseInt(result.meta.TD[1], 10);
-
   if (!result.meta.SW_p) {
@@ -503,4 +550,9 @@ // eslint-disable-next-line camelcase
 
+  const isFft = ['2rr', '2ri', '2ir', '2ii'].some((key) => getIndex(key) > 0);
+  result.meta.nbSubSpectra = isFft
+    ? parseInt(result.meta.SI[1], 10)
+    : parseInt(result.meta.TD[1], 10);
+
   let firstY, lastY, xOffset, yOffset;
-  if (files['2rr']) {
+  if (isFft) {
     let sf = Number(result.meta.SF[1]);
@@ -514,12 +566,12 @@ let swP = Number(result.meta.SW_p[1] || result.meta.SW[1]);
     result.meta.lastY = lastY;
-    await setProcessedSpectrumData(
+    setProcessedSpectrumData(
       {
-        rr: files['2rr'],
-        ri: files['2ri'],
-        ir: files['2ir'],
-        ii: files['2ii'],
+        rr: getValue('2rr'),
+        ri: getValue('2ri'),
+        ir: getValue('2ir'),
+        ii: getValue('2ii'),
       },
       result,
     );
-  } else if (files.ser) {
+  } else if (getIndex('ser')) {
     firstY = 0;
@@ -537,7 +589,7 @@ lastY = result.meta.nbSubSpectra;
       yTransmitterFrequencyOffset / yTransmitterFrequency + yWindowSize / 2;
-    await setFIDSpectrumData(files.ser, result);
+    setFIDSpectrumData(getValue('ser'), result);
   }
 
   let pageValue = firstY;
-  let nbSubSpectra = result.meta.nbSubSpectra / (files['2rr'] ? 1 : 2);
+  let nbSubSpectra = result.meta.nbSubSpectra / (isFft ? 1 : 2);
   let deltaY = (lastY - firstY) / (nbSubSpectra - 1);
@@ -544,0 +596,0 @@ for (let i = 0; i < nbSubSpectra; i++) {

package.json

 {
   "name": "brukerconverter",
-  "version": "6.2.3",
+  "version": "6.2.4-pre.1694336922",
   "description": "Parse and convert Bruker raw data",
@@ -5,0 +5,0 @@ "main": "lib/index.js",

src/util/convert1D.js

@@ -0,1 +1,2 @@
+import { getIndexFct, getValueFct } from './getValueFct.js';
 import { joinInfoMeta } from './joinMetaInfo.js';
@@ -8,19 +9,45 @@ import { parseData } from './parseData';
 export async function convert1D(files, options) {
-  const result = await parseData(files.procs, options);
-  const acqus = await parseData(files.acqus, options);
-  joinInfoMeta(result, acqus);
+  const promises = [];
+  promises.push('procs', parseData(files.procs, options));
+  promises.push('acqus', parseData(files.acqus, options));
 
-  if (files.quantFactorSample) addEreticFactor(result, files);
-  if (files.integrals) result.integrals = await parseIntegrals(files);
+  if (files.quantFactorSample) {
+    promises.push('ereticFactor', getEreticFactor(files));
+  }
+  if (files.integrals) {
+    promises.push('integrals', parseIntegrals(files));
+  }
 
-  if (files['1r'] || files['1i']) {
-    await setProcessedSpectrumData(
+  const filesToRead = files['1r'] || files['1i'] ? ['1r', '1i'] : ['fid'];
+  for (const key of filesToRead) {
+    if (!files[key]) continue;
+    promises.push(key, files[key].arrayBuffer());
+  }
+
+  return Promise.allSettled(promises).then(formatSpectrum);
+}
+
+function formatSpectrum(results) {
+  const getValue = getValueFct(results);
+
+  const result = getValue('procs');
+  joinInfoMeta(result, getValue('acqus'));
+
+  const getIndex = getIndexFct(results);
+  if (getIndex('integrals')) {
+    result.integrals = getValue('integrals');
+  }
+  if (getIndex('ereticFactor')) {
+    result.info.ereticFactor = getValue('ereticFactor');
+  }
+  if (getIndex('1r') || getIndex('1i')) {
+    setProcessedSpectrumData(
       {
-        re: files['1r'],
-        im: files['1i'],
+        re: getValue('1r'),
+        im: getValue('1i'),
       },
       result,
     );
-  } else if (files.fid) {
-    await setFIDSpectrumData(files.fid, result);
+  } else if (getIndex('fid')) {
+    setFIDSpectrumData(getValue('fid'), result);
   }
@@ -31,9 +58,7 @@
 
-async function addEreticFactor(result, files) {
+async function getEreticFactor(files) {
   const quantFactorSample = (await files.quantFactorSample.text()).match(
     /<Application[\w\W]+<Eretic_Factor>(?<ereticFactor>[\d.]+)/,
   );
-  if (quantFactorSample) {
-    result.info.ereticFactor = Number(quantFactorSample.groups.ereticFactor);
-  }
+  return Number(quantFactorSample.groups.ereticFactor);
 }

src/util/convert2D.js

@@ -6,22 +6,29 @@ import { joinInfoMeta } from './joinMetaInfo.js';
 import { setProcessedSpectrumData } from './setProcessedSpectrumData';
+import { getIndexFct, getValueFct } from './getValueFct.js';
 
 export async function convert2D(files, options) {
-  const result = mergeMetadata(
-    await parseData(files.procs, options),
-    await parseData(files.proc2s, options),
-  );
+  const promises = [];
+  promises.push('procs', parseData(files.procs, options));
+  promises.push('proc2s', parseData(files.proc2s, options));
+  promises.push('acqus', parseData(files.acqus, options));
+  promises.push('acqu2s', parseData(files.acqu2s, options));
 
-  const acqus = mergeMetadata(
-    await parseData(files.acqus, options),
-    await parseData(files.acqu2s, options),
-  );
+  const filesToRead = ['2rr', '2ri', '2ir', '2ii', 'ser'];
+  for (const key of filesToRead) {
+    if (!files[key]) continue;
+    promises.push(key, files[key].arrayBuffer());
+  }
 
+  return Promise.allSettled(promises).then(formatSpectrum);
+}
+
+function formatSpectrum(results) {
+  const getIndex = getIndexFct(results);
+  const getValue = getValueFct(results);
+  const result = mergeMetadata(getValue('procs'), getValue('proc2s'));
+
+  const acqus = mergeMetadata(getValue('acqus'), getValue('acqu2s'));
+
   joinInfoMeta(result, acqus);
 
-  result.meta.nbSubSpectra = ['2rr', '2ri', '2ir', '2ii'].some(
-    (key) => key in files,
-  )
-    ? parseInt(result.meta.SI[1], 10)
-    : parseInt(result.meta.TD[1], 10);
-
   if (!result.meta.SW_p) {
@@ -35,4 +42,9 @@ // eslint-disable-next-line camelcase
 
+  const isFft = ['2rr', '2ri', '2ir', '2ii'].some((key) => getIndex(key) > 0);
+  result.meta.nbSubSpectra = isFft
+    ? parseInt(result.meta.SI[1], 10)
+    : parseInt(result.meta.TD[1], 10);
+
   let firstY, lastY, xOffset, yOffset;
-  if (files['2rr']) {
+  if (isFft) {
     let sf = Number(result.meta.SF[1]);
@@ -46,12 +58,12 @@ let swP = Number(result.meta.SW_p[1] || result.meta.SW[1]);
     result.meta.lastY = lastY;
-    await setProcessedSpectrumData(
+    setProcessedSpectrumData(
       {
-        rr: files['2rr'],
-        ri: files['2ri'],
-        ir: files['2ir'],
-        ii: files['2ii'],
+        rr: getValue('2rr'),
+        ri: getValue('2ri'),
+        ir: getValue('2ir'),
+        ii: getValue('2ii'),
       },
       result,
     );
-  } else if (files.ser) {
+  } else if (getIndex('ser')) {
     firstY = 0;
@@ -69,7 +81,7 @@ lastY = result.meta.nbSubSpectra;
       yTransmitterFrequencyOffset / yTransmitterFrequency + yWindowSize / 2;
-    await setFIDSpectrumData(files.ser, result, true);
+    setFIDSpectrumData(getValue('ser'), result, true);
   }
 
   let pageValue = firstY;
-  let nbSubSpectra = result.meta.nbSubSpectra / (files['2rr'] ? 1 : 2);
+  let nbSubSpectra = result.meta.nbSubSpectra / (isFft ? 1 : 2);
   let deltaY = (lastY - firstY) / (nbSubSpectra - 1);
@@ -76,0 +88,0 @@ for (let i = 0; i < nbSubSpectra; i++) {

src/util/setFIDSpectrumData.js

@@ -6,5 +6,5 @@ import { IOBuffer } from 'iobuffer';
 
-export async function setFIDSpectrumData(file, spectra) {
+export function setFIDSpectrumData(file, spectra) {
   let td = parseInt(spectra.meta.TD[0], 10);
-  let ioBuffer = new IOBuffer(await file.arrayBuffer());
+  let ioBuffer = new IOBuffer(file);
 
@@ -11,0 +11,0 @@ if (td * spectra.meta.nbSubSpectra * 4 > ioBuffer.length) {

src/util/setProcessedSpectrumData.js

@@ -5,7 +5,7 @@ import { IOBuffer } from 'iobuffer';
 
-export async function setProcessedSpectrumData(files, spectra) {
+export function setProcessedSpectrumData(files, spectra) {
   const buffers = {};
   for (const key in files) {
     if (!files[key]) continue;
-    buffers[key] = new IOBuffer(await files[key].arrayBuffer());
+    buffers[key] = new IOBuffer(files[key]);
   }
@@ -12,0 +12,0 @@

New alerts

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This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

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Quality

Package is not semver >=1. This means it is not stable and does not support ^ ranges.

Found 1 instance in 1 package

Fixed alerts

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Improved metrics

Total package byte prevSize

1731574

increased by0.18%

Number of package files

50

increased by2.04%

Lines of code

1966

increased by4.69%

Worsened metrics

Number of low quality alerts

2

increased by100%

No dependency changes