brukerconverter - npm Package Compare versions

Comparing version 5.0.3 to 6.0.0

brukerconverter.d.ts

 import { DoubleArray } from 'cheminfo-types';
 import type { FileCollectionItem, FileCollection } from 'filelist-utils';
-import { DoubleMatrix } from 'ml-spectra-processing';
 
@@ -72,3 +71,3 @@ type FirstLevelKeys =
   expno: number;
-  fileCollection: FileCollection;
+  fileCollectionItems: FileCollectionItem[];
   processedData?: ProcessedData;
@@ -136,4 +135,4 @@ is2D?: boolean;
 
-export interface MinMax {
-  z: DoubleMatrix;
+export interface MinMaxContent {
+  z: DoubleArray[];
   minZ: number;
@@ -146,2 +145,4 @@ maxZ: number;
 }
+export type MinMax = Record<string, MinMaxContent>;
+
 export interface SpectraData2D {
@@ -148,0 +149,0 @@ spectra: Spectrum2D[];

lib/index.js

@@ -227,2 +227,4 @@ 'use strict';
 
+const QSEQ = 2;
+
 async function setFIDSpectrumData(file, spectra) {
@@ -238,11 +240,10 @@ let td = parseInt(spectra.meta.TD[0], 10);
 
-  let SW_H = Number(spectra.meta.SW_h[0]);
+  const SW_H = Number(spectra.meta.SW_h[0]);
 
-  let SF = Number(spectra.meta.SFO1[0]);
+  const SF = Number(spectra.meta.SFO1[0]);
 
   spectra.meta.DATATYPE = 'NMR FID';
 
-  let DW = 1 / (2 * SW_H);
-  let AQ = td * DW;
-
+  const DW = 1 / (2 * SW_H);
+  const AQ = td * DW;
   let endian = parseInt(spectra.meta.BYTORDA, 10);
@@ -263,3 +264,6 @@ endian = endian ? 0 : 1;
 
-  const stopReading = td / 2;
+  const aqMode = spectra.meta.AQ_mod;
+  const deltaX = aqMode === QSEQ ? DW : 2 * DW;
+  const nbPoints = aqMode === QSEQ ? td : (td / 2) >> 0;
+
   for (let j = 0; j < nbSubSpectra; j++) {
@@ -269,3 +273,3 @@ let toSave = {
       dataTable: '(X++(R..R))',
-      nbPoints: td,
+      nbPoints,
       firstX: 0,
@@ -277,16 +281,24 @@ lastX: AQ,
       data: {
-        x: mlSpectraProcessing.createStepArray({ length: td, step: DW }),
-        re: new Float64Array(td),
-        im: new Float64Array(td),
+        x: mlSpectraProcessing.createStepArray({ length: nbPoints, step: deltaX }),
+        re: new Float64Array(nbPoints),
+        im: new Float64Array(nbPoints),
       },
       isXYdata: true,
+      isFID: true,
       observeFrequency: SF,
       title: spectra.meta.TITLE,
-      deltaX: DW,
+      deltaX,
     };
     spectra.spectra[j] = toSave;
 
-    for (let i = 0; i < stopReading; i++) {
-      spectra.spectra[j].data.re[i] = ioBuffer.readInt32();
-      spectra.spectra[j].data.im[i] = ioBuffer.readInt32();
+    // const dtypa = spectra.meta.DTYPA;// we should use it for float or double FID data;
+    if (aqMode === QSEQ) {
+      for (let i = 0; i < nbPoints; i++) {
+        spectra.spectra[j].data.re[i] = ioBuffer.readInt32();
+      }
+    } else {
+      for (let i = 0; i < nbPoints; i++) {
+        spectra.spectra[j].data.re[i] = ioBuffer.readInt32();
+        spectra.spectra[j].data.im[i] = ioBuffer.readInt32();
+      }
     }
@@ -296,7 +308,9 @@ }
 
-async function setXYSpectrumData(file, spectra) {
-  let ioBufferReal = file.re ? new iobuffer.IOBuffer(await file.re.arrayBuffer()) : null;
-  let ioBufferImaginary = file.im
-    ? new iobuffer.IOBuffer(await file.im.arrayBuffer())
-    : null;
+async function setProcessedSpectrumData(files, spectra) {
+  const buffers = {};
+  for (const key in files) {
+    if (!files[key]) continue;
+    buffers[key] = new iobuffer.IOBuffer(await files[key].arrayBuffer());
+  }
+
   let td = getDirectParameter(spectra.meta.SI);
@@ -317,8 +331,7 @@ let swP = getDirectParameter(spectra.meta.SW_p);
   let nbSubSpectra = spectra.meta.nbSubSpectra ? spectra.meta.nbSubSpectra : 1;
+
   if (endian) {
-    if (file.re) ioBufferReal.setLittleEndian();
-    if (file.im) ioBufferImaginary.setLittleEndian();
+    for (const key in buffers) buffers[key].setLittleEndian();
   } else {
-    if (file.re) ioBufferReal.setBigEndian();
-    if (file.im) ioBufferImaginary.setBigEndian();
+    for (const key in buffers) buffers[key].setBigEndian();
   }
@@ -335,2 +348,3 @@
       isXYdata: true,
+      isFT: true,
       nucleus: spectra.meta.NUC1,
@@ -342,21 +356,15 @@ observeFrequency: sf,
 
-    let deltaX = toSave.deltaX;
-    let x = new Float64Array(td);
-    let re = new Float64Array(td);
-    let im = file.im ? new Float64Array(td) : null;
-
-    if (im) {
+    const deltaX = toSave.deltaX;
+    const x = mlSpectraProcessing.xSequentialFill({ from: offset, step: deltaX, size: td });
+    const datum = {};
+    for (const key in buffers) {
+      const buffer = buffers[key];
+      const data = new Float64Array(td);
       for (let k = 0; k < td; ++k) {
-        x[k] = offset + k * deltaX;
-        re[k] = ioBufferReal.readInt32();
-        im[k] = ioBufferImaginary.readInt32();
+        data[k] = buffer.readInt32();
       }
-    } else {
-      for (let k = 0; k < td; ++k) {
-        x[k] = offset + k * deltaX;
-        re[k] = ioBufferReal.readInt32();
-      }
+      datum[key] = data;
     }
 
-    toSave.data = im ? { x, re, im } : { x, re };
+    toSave.data = { ...datum, x };
 
@@ -377,3 +385,3 @@ spectra.spectra.push(toSave);
   if (files['1r'] || files['1i']) {
-    await setXYSpectrumData(
+    await setProcessedSpectrumData(
       {
@@ -419,3 +427,5 @@ re: files['1r'],
 
-  result.meta.nbSubSpectra = files['2rr']
+  result.meta.nbSubSpectra = ['2rr', '2ri', '2ir', '2ii'].some(
+    (key) => key in files,
+  )
     ? parseInt(result.meta.SI[1], 10)
@@ -442,3 +452,11 @@ : parseInt(result.meta.TD[1], 10);
     result.meta.lastY = lastY;
-    await setXYSpectrumData({ re: files['2rr'] }, result);
+    await setProcessedSpectrumData(
+      {
+        rr: files['2rr'],
+        ri: files['2ri'],
+        ir: files['2ir'],
+        ii: files['2ii'],
+      },
+      result,
+    );
   } else if (files.ser) {
@@ -484,13 +502,15 @@ firstY = 0;
  * @param spectra
- * @returns {{z: Array, minX: *, maxX: *, minY: *, maxY: *, minZ: *, maxZ: *, noise: number}}
+ * @returns {{z: Array<Array<number>>, minX: *, maxX: *, minY: *, maxY: *, minZ: *, maxZ: *}}
  */
 
-function convertTo3DZ(spectra) {
+function convertTo3DZ(datum) {
+  const spectra = datum.spectra;
+
+  // if (fileKeys.length === 0) {
+  //   throw new Error('There is not data to extract');
+  // }
+
   let ySize = spectra.length;
-  let xSize = spectra[0].data.re.length;
-  let z = new Array(ySize);
+  let xSize = spectra[0].data.x.length;
 
-  for (let i = 0; i < ySize; i++) {
-    z[i] = new Float64Array(spectra[i].data.re);
-  }
   const firstX = spectra[0].data.x[0];
@@ -501,2 +521,27 @@ const lastX = spectra[0].data.x[xSize - 1];
 
+  const minMax = {};
+  const keyFiles = Object.keys(spectra[0].data).filter((key) => key !== 'x');
+  for (const keyFile of keyFiles) {
+    minMax[keyFile] = extractZMatrix(datum, {
+      keyFile,
+      ySize,
+      firstX,
+      lastX,
+      firstY,
+      lastY,
+    });
+  }
+  return minMax;
+}
+
+function extractZMatrix(datum, options) {
+  const spectra = datum.spectra;
+
+  const { keyFile, ySize, firstX, lastX, firstY, lastY } = options;
+  let z = new Array(ySize);
+
+  for (let i = 0; i < ySize; i++) {
+    z[i] = new Float64Array(spectra[i].data[keyFile]);
+  }
+
   // Because the min / max value are the only information about the matrix if we invert
@@ -545,3 +590,3 @@ // min and max we need to invert the array
   let result;
-  if (brukerFiles.ser || brukerFiles['2rr']) {
+  if (['ser', '2rr', '2ri', '2ir', '2ii'].some((key) => key in brukerFiles)) {
     result = await convert2D(brukerFiles, options);
@@ -586,3 +631,3 @@ } else if (brukerFiles['1r'] || brukerFiles['1i'] || brukerFiles.fid) {
   if (result.twoD) {
-    result.minMax = convertTo3DZ(result.spectra);
+    result.minMax = convertTo3DZ(result);
 
@@ -589,0 +634,0 @@ if (!options.keepSpectra) {

package.json

 {
   "name": "brukerconverter",
-  "version": "5.0.3",
+  "version": "6.0.0",
   "description": "Parse and convert Bruker raw data",
@@ -5,0 +5,0 @@ "main": "lib/index.js",

src/__tests__/convertFileList.test.js

@@ -39,3 +39,3 @@ import { getCoffee } from 'bruker-data-test';
         dataTable: '(X++(R..R))',
-        nbPoints: 65536,
+        nbPoints: 32768,
         firstX: 0,
@@ -42,0 +42,0 @@ lastX: 3.984588800000003,

src/__tests__/convertZip.test.js

@@ -34,4 +34,4 @@ import { getData } from 'bruker-data-test';
     expect(metadataFt.SI[1]).toBe(1024);
-    expect(minMaxFt.z).toHaveLength(1024);
-    expect(minMaxFt.z[0]).toHaveLength(1024);
+    expect(minMaxFt.rr.z).toHaveLength(1024);
+    expect(minMaxFt.rr.z[0]).toHaveLength(1024);
 
@@ -43,5 +43,5 @@ let minMaxSer = result[0].minMax;
     expect(metadataSer.TD[1]).toBe(128);
-    expect(minMaxSer.z).toHaveLength(64);
-    expect(minMaxSer.z[0]).toHaveLength(4096);
+    expect(minMaxSer.re.z).toHaveLength(64);
+    expect(minMaxSer.re.z[0]).toHaveLength(2048);
   });
 });

src/util/convert1D.js

 import { joinInfoMeta } from './joinMetaInfo.js';
 import { parseData } from './parseData';
 import { setFIDSpectrumData } from './setFIDSpectrumData';
-import { setXYSpectrumData } from './setXYSpectrumData';
+import { setProcessedSpectrumData } from './setProcessedSpectrumData';
 
@@ -12,3 +12,3 @@ export async function convert1D(files, options) {
   if (files['1r'] || files['1i']) {
-    await setXYSpectrumData(
+    await setProcessedSpectrumData(
       {
@@ -15,0 +15,0 @@ re: files['1r'],

src/util/convert2D.js

@@ -5,3 +5,3 @@ import { joinInfoMeta } from './joinMetaInfo.js';
 import { setFIDSpectrumData } from './setFIDSpectrumData';
-import { setXYSpectrumData } from './setXYSpectrumData';
+import { setProcessedSpectrumData } from './setProcessedSpectrumData';
 
@@ -21,3 +21,5 @@ export async function convert2D(files, options) {
 
-  result.meta.nbSubSpectra = files['2rr']
+  result.meta.nbSubSpectra = ['2rr', '2ri', '2ir', '2ii'].some(
+    (key) => key in files,
+  )
     ? parseInt(result.meta.SI[1], 10)
@@ -44,3 +46,11 @@ : parseInt(result.meta.TD[1], 10);
     result.meta.lastY = lastY;
-    await setXYSpectrumData({ re: files['2rr'] }, result, true);
+    await setProcessedSpectrumData(
+      {
+        rr: files['2rr'],
+        ri: files['2ri'],
+        ir: files['2ir'],
+        ii: files['2ii'],
+      },
+      result,
+    );
   } else if (files.ser) {
@@ -59,3 +69,3 @@ firstY = 0;
       yTransmitterFrequencyOffset / yTransmitterFrequency + yWindowSize / 2;
-    await setFIDSpectrumData(files.ser, result);
+    await setFIDSpectrumData(files.ser, result, true);
   }
@@ -62,0 +72,0 @@

src/util/convertOneExperiment.js

@@ -17,3 +17,3 @@ import { convert1D } from './convert1D';
   let result;
-  if (brukerFiles.ser || brukerFiles['2rr']) {
+  if (['ser', '2rr', '2ri', '2ir', '2ii'].some((key) => key in brukerFiles)) {
     result = await convert2D(brukerFiles, options);
@@ -58,3 +58,3 @@ } else if (brukerFiles['1r'] || brukerFiles['1i'] || brukerFiles.fid) {
   if (result.twoD) {
-    result.minMax = convertTo3DZ(result.spectra);
+    result.minMax = convertTo3DZ(result);
 
@@ -61,0 +61,0 @@ if (!options.keepSpectra) {

src/util/convertTo3DZ.js

@@ -5,13 +5,15 @@ import { matrixMinMaxZ } from 'ml-spectra-processing';
  * @param spectra
- * @returns {{z: Array, minX: *, maxX: *, minY: *, maxY: *, minZ: *, maxZ: *, noise: number}}
+ * @returns {{z: Array<Array<number>>, minX: *, maxX: *, minY: *, maxY: *, minZ: *, maxZ: *}}
  */
 
-export default function convertTo3DZ(spectra) {
+export default function convertTo3DZ(datum) {
+  const spectra = datum.spectra;
+
+  // if (fileKeys.length === 0) {
+  //   throw new Error('There is not data to extract');
+  // }
+
   let ySize = spectra.length;
-  let xSize = spectra[0].data.re.length;
-  let z = new Array(ySize);
+  let xSize = spectra[0].data.x.length;
 
-  for (let i = 0; i < ySize; i++) {
-    z[i] = new Float64Array(spectra[i].data.re);
-  }
   const firstX = spectra[0].data.x[0];
@@ -22,2 +24,27 @@ const lastX = spectra[0].data.x[xSize - 1];
 
+  const minMax = {};
+  const keyFiles = Object.keys(spectra[0].data).filter((key) => key !== 'x');
+  for (const keyFile of keyFiles) {
+    minMax[keyFile] = extractZMatrix(datum, {
+      keyFile,
+      ySize,
+      firstX,
+      lastX,
+      firstY,
+      lastY,
+    });
+  }
+  return minMax;
+}
+
+function extractZMatrix(datum, options) {
+  const spectra = datum.spectra;
+
+  const { keyFile, ySize, firstX, lastX, firstY, lastY } = options;
+  let z = new Array(ySize);
+
+  for (let i = 0; i < ySize; i++) {
+    z[i] = new Float64Array(spectra[i].data[keyFile]);
+  }
+
   // Because the min / max value are the only information about the matrix if we invert
@@ -24,0 +51,0 @@ // min and max we need to invert the array

src/util/setFIDSpectrumData.js

 import { IOBuffer } from 'iobuffer';
 import { createStepArray } from 'ml-spectra-processing';
 
+import * as aqModeDirect from '../constants/acquisitionModeDirect';
+
 export async function setFIDSpectrumData(file, spectra) {
@@ -14,11 +16,10 @@ let td = parseInt(spectra.meta.TD[0], 10);
 
-  let SW_H = Number(spectra.meta.SW_h[0]);
+  const SW_H = Number(spectra.meta.SW_h[0]);
 
-  let SF = Number(spectra.meta.SFO1[0]);
+  const SF = Number(spectra.meta.SFO1[0]);
 
   spectra.meta.DATATYPE = 'NMR FID';
 
-  let DW = 1 / (2 * SW_H);
-  let AQ = td * DW;
-
+  const DW = 1 / (2 * SW_H);
+  const AQ = td * DW;
   let endian = parseInt(spectra.meta.BYTORDA, 10);
@@ -39,3 +40,6 @@ endian = endian ? 0 : 1;
 
-  const stopReading = td / 2;
+  const aqMode = spectra.meta.AQ_mod;
+  const deltaX = aqMode === aqModeDirect.QSEQ ? DW : 2 * DW;
+  const nbPoints = aqMode === aqModeDirect.QSEQ ? td : (td / 2) >> 0;
+
   for (let j = 0; j < nbSubSpectra; j++) {
@@ -45,3 +49,3 @@ let toSave = {
       dataTable: '(X++(R..R))',
-      nbPoints: td,
+      nbPoints,
       firstX: 0,
@@ -53,18 +57,26 @@ lastX: AQ,
       data: {
-        x: createStepArray({ length: td, step: DW }),
-        re: new Float64Array(td),
-        im: new Float64Array(td),
+        x: createStepArray({ length: nbPoints, step: deltaX }),
+        re: new Float64Array(nbPoints),
+        im: new Float64Array(nbPoints),
       },
       isXYdata: true,
+      isFID: true,
       observeFrequency: SF,
       title: spectra.meta.TITLE,
-      deltaX: DW,
+      deltaX,
     };
     spectra.spectra[j] = toSave;
 
-    for (let i = 0; i < stopReading; i++) {
-      spectra.spectra[j].data.re[i] = ioBuffer.readInt32();
-      spectra.spectra[j].data.im[i] = ioBuffer.readInt32();
+    // const dtypa = spectra.meta.DTYPA;// we should use it for float or double FID data;
+    if (aqMode === aqModeDirect.QSEQ) {
+      for (let i = 0; i < nbPoints; i++) {
+        spectra.spectra[j].data.re[i] = ioBuffer.readInt32();
+      }
+    } else {
+      for (let i = 0; i < nbPoints; i++) {
+        spectra.spectra[j].data.re[i] = ioBuffer.readInt32();
+        spectra.spectra[j].data.im[i] = ioBuffer.readInt32();
+      }
     }
   }
 }

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Improved metrics

Total package byte prevSize

53288

increased by4.79%

Number of package files

23

increased by9.52%

Lines of code

1515

increased by5.94%

No dependency changes