brukerconverter - npm Package Compare versions

Comparing version 5.0.1 to 5.0.2-pre.1667228020

brukerconverter.d.ts

@@ -72,3 +72,3 @@ import { DoubleArray } from 'cheminfo-types';
   expno: number;
-  fileCollection: FileCollection;
+  fileCollectionItems: FileCollectionItem[];
   processedData?: ProcessedData;
@@ -164,5 +164,5 @@ is2D?: boolean;
 
-export function convertFileList(
+export function convertFileCollection(
   fileCollection: FileCollection,
   options?: ConvertFileListOptions,
 ): Promise<SpectraData[]>;

lib/index.js

@@ -11,3 +11,3 @@ 'use strict';
  * Retrieve the list of files for further process
- * @param {FileCollection[]} fileList
+ * @param {FileCollection[]} fileCollection
  * @param {object} [options={}]
@@ -22,3 +22,3 @@ * @param {number|number[]} [options.processingNumber] - processing number to select, default the smallest number
  */
-function groupByExperiments(fileList, options = {}) {
+function groupByExperiments(fileCollection, options = {}) {
   let {
@@ -41,3 +41,3 @@ processingNumber,
   const experiments = {};
-  for (let file of fileList) {
+  for (let file of fileCollection) {
     let currentProcessingNo;
@@ -71,3 +71,3 @@ let currentExperimentNo;
         processedData: {},
-        fileList: [],
+        fileCollectionItems: [],
       };
@@ -79,3 +79,3 @@ }
         experiment.processedData[currentProcessingNo] = {
-          fileList: [],
+          fileCollectionItems: [],
           name,
@@ -86,3 +86,3 @@ expno: currentExperimentNo,
       const processedData = experiment.processedData[currentProcessingNo];
-      processedData.fileList.push(file);
+      processedData.fileCollectionItems.push(file);
       if (file.name.match(/^(1r|1i|2rr|procs|proc2s)$/)) {
@@ -100,3 +100,3 @@ processedData[file.name] = file;
     } else {
-      experiment.fileList.push(file);
+      experiment.fileCollectionItems.push(file);
       if (file.name.match(/^(ser|fid|acqus|acqu2s)$/)) {
@@ -152,7 +152,7 @@ experiment[file.name] = file;
         if (firstProcessed.procs) {
-          experiment.fileList.push(firstProcessed.procs);
+          experiment.fileCollectionItems.push(firstProcessed.procs);
           experiment.procs = firstProcessed.procs;
         }
         if (firstProcessed.proc2s) {
-          experiment.fileList.push(firstProcessed.proc2s);
+          experiment.fileCollectionItems.push(firstProcessed.proc2s);
           experiment.proc2s = firstProcessed.proc2s;
@@ -167,6 +167,6 @@ }
         if (experiment.acqus) {
-          oneProcessed.fileList.push(experiment.acqus);
+          oneProcessed.fileCollectionItems.push(experiment.acqus);
         }
         if (experiment.acqu2s) {
-          oneProcessed.fileList.push(experiment.acqu2s);
+          oneProcessed.fileCollectionItems.push(experiment.acqu2s);
         }
@@ -236,2 +236,4 @@ experimentsArray.push({
 
+const QSEQ = 2;
+
 async function setFIDSpectrumData(file, spectra) {
@@ -247,11 +249,10 @@ 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);
@@ -272,3 +273,6 @@ 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++) {
@@ -278,3 +282,3 @@ let toSave = {
       dataTable: '(X++(R..R))',
-      nbPoints: td,
+      nbPoints,
       firstX: 0,
@@ -286,16 +290,24 @@ 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();
+      }
     }
@@ -305,7 +317,9 @@ }
 
-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);
@@ -326,8 +340,7 @@ 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();
   }
@@ -344,2 +357,3 @@
       isXYdata: true,
+      isFT: true,
       nucleus: spectra.meta.NUC1,
@@ -351,21 +365,15 @@ 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 });
+    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 };
 
@@ -386,3 +394,3 @@ spectra.spectra.push(toSave);
   if (files['1r'] || files['1i']) {
-    await setXYSpectrumData(
+    await setProcessedSpectrumData(
       {
@@ -428,3 +436,5 @@ 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)
@@ -451,3 +461,11 @@ : 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) {
@@ -493,13 +511,15 @@ 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];
@@ -510,2 +530,27 @@ 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
@@ -554,3 +599,3 @@ // 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);
@@ -595,3 +640,3 @@ } else if (brukerFiles['1r'] || brukerFiles['1i'] || brukerFiles.fid) {
   if (result.twoD) {
-    result.minMax = convertTo3DZ(result.spectra);
+    result.minMax = convertTo3DZ(result);
 
@@ -598,0 +643,0 @@ if (!options.keepSpectra) {

package.json

 {
   "name": "brukerconverter",
-  "version": "5.0.1",
+  "version": "5.0.2-pre.1667228020",
   "description": "Parse and convert Bruker raw data",
@@ -53,2 +53,2 @@ "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/groupByExperiments.js

 /**
  * Retrieve the list of files for further process
- * @param {FileCollection[]} fileList
+ * @param {FileCollection[]} fileCollection
  * @param {object} [options={}]
@@ -13,3 +13,3 @@ * @param {number|number[]} [options.processingNumber] - processing number to select, default the smallest number
  */
-export function groupByExperiments(fileList, options = {}) {
+export function groupByExperiments(fileCollection, options = {}) {
   let {
@@ -32,3 +32,3 @@ processingNumber,
   const experiments = {};
-  for (let file of fileList) {
+  for (let file of fileCollection) {
     let currentProcessingNo;
@@ -62,3 +62,3 @@ let currentExperimentNo;
         processedData: {},
-        fileList: [],
+        fileCollectionItems: [],
       };
@@ -70,3 +70,3 @@ }
         experiment.processedData[currentProcessingNo] = {
-          fileList: [],
+          fileCollectionItems: [],
           name,
@@ -77,3 +77,3 @@ expno: currentExperimentNo,
       const processedData = experiment.processedData[currentProcessingNo];
-      processedData.fileList.push(file);
+      processedData.fileCollectionItems.push(file);
       if (file.name.match(/^(1r|1i|2rr|procs|proc2s)$/)) {
@@ -91,3 +91,3 @@ processedData[file.name] = file;
     } else {
-      experiment.fileList.push(file);
+      experiment.fileCollectionItems.push(file);
       if (file.name.match(/^(ser|fid|acqus|acqu2s)$/)) {
@@ -143,7 +143,7 @@ experiment[file.name] = file;
         if (firstProcessed.procs) {
-          experiment.fileList.push(firstProcessed.procs);
+          experiment.fileCollectionItems.push(firstProcessed.procs);
           experiment.procs = firstProcessed.procs;
         }
         if (firstProcessed.proc2s) {
-          experiment.fileList.push(firstProcessed.proc2s);
+          experiment.fileCollectionItems.push(firstProcessed.proc2s);
           experiment.proc2s = firstProcessed.proc2s;
@@ -158,6 +158,6 @@ }
         if (experiment.acqus) {
-          oneProcessed.fileList.push(experiment.acqus);
+          oneProcessed.fileCollectionItems.push(experiment.acqus);
         }
         if (experiment.acqu2s) {
-          oneProcessed.fileList.push(experiment.acqu2s);
+          oneProcessed.fileCollectionItems.push(experiment.acqu2s);
         }
@@ -164,0 +164,0 @@ experimentsArray.push({

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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