brukerconverter - npm Package Compare versions

Comparing version 6.0.8 to 6.0.9-pre.1677169339

brukerconverter.d.ts

@@ -31,22 +31,12 @@ import { DoubleArray } from 'cheminfo-types';
   /**
-   * should we ignore fid
-   * @default false
+   * should we keep 1D spectra
+   * @default true
    */
-  ignoreFID?: boolean;
+  keep1D?: boolean;
   /**
-   * should we ignore the ft transformed fid
-   * @default false
+   * should we keep 2D spectra
+   * @default true
    */
-  ignoreFT?: boolean;
+  keep2D?: boolean;
   /**
-   * should we ignore 1D spectra
-   * @default false
-   */
-  ignore1D?: boolean;
-  /**
-   * should we ignore 2D spectra
-   * @default false
-   */
-  ignore2D?: boolean;
-  /**
    * should we take only the first processed data (procno).
@@ -56,2 +46,8 @@ * @default true
   onlyFirstProcessedData?: boolean;
+  /**
+   * allow filter by only processed (FT) or raw data (FID), set a preference for 
+   * FT or FID if both exists, or always load both.
+   * @default 'both'
+   */
+  dataSelection?: 'ft' | 'fid' | 'both' | 'preferFT' | 'preferFID';
 }
@@ -121,7 +117,7 @@
 
-export interface Files {
-  relativePath: string;
+export interface File {
+  relativePath?: string;
   name: string;
   lastModified: number;
-  size: number;
+  size?: number;
 }
@@ -137,3 +133,3 @@
   shiftOffsetNum: 0;
-  source: BrukerSource & {
+  source: GeneralBrukerSource & {
     is1D: boolean;
@@ -171,3 +167,3 @@ };
   isFID: boolean;
-  files?: Files;
+  files?: File[];
 }
@@ -184,3 +180,3 @@
   shiftOffsetNum: 0;
-  source: BrukerSource & { is2D: boolean };
+  source: GeneralBrukerSource & { is2D: boolean };
 }
@@ -187,0 +183,0 @@

lib/index.js

@@ -11,8 +11,6 @@ 'use strict';
  * Retrieve the list of files for further process
- * @param {FileCollection[]} fileCollection
+ * @param {FileCollection} fileCollection
  * @param {object} [options={}]
  * @param {number[]} [options.processingNumbers] - processing number to select, default the smallest number
  * @param {number[]} [options.experimentNumbers] - experiment number to select, default all
- * @param {boolean} [options.keepFID=true] - should we keep fid
- * @param {boolean} [options.keepFT=true] - should we keep the ft transformed fid
  * @param {boolean} [options.keep1D=true] - should we keep 1D spectra
@@ -27,4 +25,3 @@ * @param {boolean} [options.keep2D=true] - should we keep 2D spectra
     experimentNumbers,
-    keepFID = true,
-    keepFT = true,
+    dataSelection = 'both',
     keep1D = true,
@@ -36,2 +33,3 @@ keep2D = true,
   const experiments = {};
+  const fileList = fileCollection.files.map((file) => file.relativePath);
   for (let file of fileCollection) {
@@ -51,3 +49,3 @@ let procno;
       id = parts.slice(0, -3).join('/');
-    } else if (file.name.match(/^(ser|fid|acqus|acqu2s)$/)) {
+    } else if (isRawOrAcquisitionFile(file, fileList)) {
       const firstLevel = parts.indexOf(file.name);
@@ -143,11 +141,18 @@ expno = Number(parts[firstLevel - 1]);
     const { processedData: processed, ...experiment } = { ...experiments[key] };
-    if (experiment.ser || experiment.fid) {
-      if (Object.keys(processed).length > 0) {
-        const firstProcessed = processed[Object.keys(processed)[0]];
+
+    const processedKeys = Object.keys(processed);
+    const hasRawData = experiment.ser || experiment.fid;
+
+    if (
+      (hasRawData && dataSelection !== 'ft' && dataSelection !== 'preferFT') ||
+      (dataSelection === 'preferFT' && !processedKeys.length)
+    ) {
+      if (processedKeys.length > 0) {
+        const firstProcessed = processed[processedKeys[0]];
         if (firstProcessed.procs) {
-          experiment.fileCollectionItems.push(firstProcessed.procs); //seems useless
+          experiment.fileCollectionItems.push(firstProcessed.procs);
           experiment.procs = firstProcessed.procs;
         }
         if (firstProcessed.proc2s) {
-          // experiment.fileCollectionItems.push(firstProcessed.proc2s); //seems useless
+          experiment.fileCollectionItems.push(firstProcessed.proc2s);
           experiment.proc2s = firstProcessed.proc2s;
@@ -158,2 +163,9 @@ }
     }
+
+    if (
+      dataSelection === 'fid' ||
+      (dataSelection === 'preferFID' && hasRawData)
+    ) {
+      continue;
+    }
     for (let processedKey in processed) {
@@ -177,8 +189,2 @@ const oneProcessed = processed[processedKey];
   // we can not easily filter
-  if (!keepFID) {
-    experimentsArray = experimentsArray.filter((item) => !item.isFID);
-  }
-  if (!keepFT) {
-    experimentsArray = experimentsArray.filter((item) => !item.isFT);
-  }
   if (!keep1D) {
@@ -194,2 +200,10 @@ experimentsArray = experimentsArray.filter((item) => !item.is1D);
 
+function isRawOrAcquisitionFile(file, fileList) {
+  return (
+    file.name.match(/^(ser|acqus|acqu2s)$/) ||
+    (file.name.match(/^(fid)$/) &&
+      fileList.includes(file.relativePath.replace(/fid$/, 'acqus')))
+  );
+}
+
 function joinInfoMeta(target, toAppend) {
@@ -597,4 +611,2 @@ for (let key in toAppend.meta) {
     }
-    // todo we could as well keep the FileList at this level if
-    // we want to keep the original data
   }
@@ -601,0 +613,0 @@

package.json

 {
   "name": "brukerconverter",
-  "version": "6.0.8",
+  "version": "6.0.9-pre.1677169339",
   "description": "Parse and convert Bruker raw data",
@@ -47,3 +47,3 @@ "main": "lib/index.js",
     "cheminfo-types": "^1.4.0",
-    "filelist-utils": "^1.7.0",
+    "filelist-utils": "^1.7.0-pre.1676560930",
     "iobuffer": "^5.3.2",
@@ -54,2 +54,2 @@ "is-any-array": "^2.0.0",
   }
-}
+}

src/__tests__/convertFileList.test.js

@@ -37,2 +37,39 @@ import { join } from 'path';
   });
+  it('keep only fid', async () => {
+    const fileCollection = await fileCollectionFromPath(
+      join(__dirname, 'data/withoutExpno'),
+    );
+    const results = await convertFileCollection(fileCollection, {
+      converter: { keepFiles: true },
+      filter: { dataSelection: 'fid' },
+    });
+
+    expect(results).toHaveLength(1);
+    expect(results[0].source).toMatchCloseTo({
+      name: 'withoutExpno',
+      expno: 0,
+      is1D: true,
+      isFID: true,
+    });
+    expect(results[0].spectra[0].data.re).toHaveLength(65536 / 2);
+  });
+  it('keep only ft', async () => {
+    const fileCollection = await fileCollectionFromPath(
+      join(__dirname, 'data/withoutExpno'),
+    );
+    const results = await convertFileCollection(fileCollection, {
+      converter: { keepFiles: true },
+      filter: { dataSelection: 'ft' },
+    });
+
+    expect(results).toHaveLength(1);
+    expect(results[0].source).toMatchCloseTo({
+      name: 'withoutExpno',
+      expno: 0,
+      procno: 1,
+      is1D: true,
+      isFT: true,
+    });
+    expect(results[0].spectra[0].data.re).toHaveLength(65536 / 2);
+  });
   it('advanced example', async () => {
@@ -39,0 +76,0 @@ const fileCollection = await getCoffee();

src/__tests__/groupByExperiments.test.js

@@ -32,2 +32,61 @@ import { join } from 'path';
 
+describe('dataSelection', () => {
+  it('priorize FT', async () => {
+    const fileCollection = await fileCollectionFromPath(
+      join(__dirname, 'data/10'),
+    );
+    const results = groupByExperiments(fileCollection, {
+      dataSelection: 'preferFT',
+    });
+    expect(results).toHaveLength(1);
+    expect(results[0].expno).toBe(10);
+    expect(results[0].procno).toBe(1);
+  });
+  it('priorize FID', async () => {
+    const fileCollection = await fileCollectionFromPath(
+      join(__dirname, 'data/10'),
+    );
+    const results = groupByExperiments(fileCollection, {
+      dataSelection: 'preferFID',
+    });
+    expect(results).toHaveLength(1);
+    expect(results[0].expno).toBe(10);
+    expect(results[0]).not.toHaveProperty('procno');
+  });
+  it('keep both', async () => {
+    const fileCollection = await fileCollectionFromPath(
+      join(__dirname, 'data/10'),
+    );
+    const results = groupByExperiments(fileCollection, {
+      dataSelection: 'both',
+    });
+    expect(results).toHaveLength(2);
+    expect(results[0].expno).toBe(10);
+    expect(results[0].name).toBe('10');
+    expect(results[1].expno).toBe(10);
+    expect(results[1].name).toBe('10');
+  });
+  it('keep only ft', async () => {
+    const fileCollection = await fileCollectionFromPath(
+      join(__dirname, 'data/10'),
+    );
+    const results = groupByExperiments(fileCollection, {
+      dataSelection: 'ft',
+    });
+    expect(results).toHaveLength(1);
+    expect(results[0].expno).toBe(10);
+    expect(results[0].procno).toBe(1);
+  });
+  it('keep only FID', async () => {
+    const fileCollection = await fileCollectionFromPath(
+      join(__dirname, 'data/10'),
+    );
+    const results = groupByExperiments(fileCollection, {
+      dataSelection: 'fid',
+    });
+    expect(results).toHaveLength(1);
+    expect(results[0].expno).toBe(10);
+    expect(results[0]).not.toHaveProperty('procno');
+  });
+});
 describe('groupByExperiments', () => {
@@ -43,3 +102,3 @@ it('no options', async () => {
       keep2D: false,
-      keepFID: false,
+      dataSelection: 'ft',
     });
@@ -60,3 +119,3 @@ expect(results).toHaveLength(8);
       keep2D: false,
-      keepFT: false,
+      dataSelection: 'fid',
     });
@@ -77,3 +136,3 @@ expect(results).toHaveLength(7);
       keep1D: false,
-      keepFID: false,
+      dataSelection: 'ft',
     });
@@ -86,3 +145,3 @@ expect(results).toHaveLength(1);
       keep1D: false,
-      keepFT: false,
+      dataSelection: 'fid',
     });
@@ -102,3 +161,3 @@ expect(results).toHaveLength(2);
       onlyFirstProcessedData: false,
-      keepFID: false,
+      dataSelection: 'ft',
     });
@@ -111,3 +170,3 @@ expect(results).toHaveLength(9);
       processingNumbers: [2],
-      keepFID: false,
+      dataSelection: 'ft',
     });
@@ -120,3 +179,3 @@ expect(results).toHaveLength(0);
       processingNumbers: [1],
-      keepFID: false,
+      dataSelection: 'ft',
     });
@@ -123,0 +182,0 @@ expect(results).toHaveLength(9);

src/groupByExperiments.js

 /**
  * Retrieve the list of files for further process
- * @param {FileCollection[]} fileCollection
+ * @param {FileCollection} fileCollection
  * @param {object} [options={}]
  * @param {number[]} [options.processingNumbers] - processing number to select, default the smallest number
  * @param {number[]} [options.experimentNumbers] - experiment number to select, default all
- * @param {boolean} [options.keepFID=true] - should we keep fid
- * @param {boolean} [options.keepFT=true] - should we keep the ft transformed fid
  * @param {boolean} [options.keep1D=true] - should we keep 1D spectra
@@ -18,4 +16,3 @@ * @param {boolean} [options.keep2D=true] - should we keep 2D spectra
     experimentNumbers,
-    keepFID = true,
-    keepFT = true,
+    dataSelection = 'both',
     keep1D = true,
@@ -27,2 +24,3 @@ keep2D = true,
   const experiments = {};
+  const fileList = fileCollection.files.map((file) => file.relativePath);
   for (let file of fileCollection) {
@@ -42,3 +40,3 @@ let procno;
       id = parts.slice(0, -3).join('/');
-    } else if (file.name.match(/^(ser|fid|acqus|acqu2s)$/)) {
+    } else if (isRawOrAcquisitionFile(file, fileList)) {
       const firstLevel = parts.indexOf(file.name);
@@ -134,11 +132,18 @@ expno = Number(parts[firstLevel - 1]);
     const { processedData: processed, ...experiment } = { ...experiments[key] };
-    if (experiment.ser || experiment.fid) {
-      if (Object.keys(processed).length > 0) {
-        const firstProcessed = processed[Object.keys(processed)[0]];
+
+    const processedKeys = Object.keys(processed);
+    const hasRawData = experiment.ser || experiment.fid;
+
+    if (
+      (hasRawData && dataSelection !== 'ft' && dataSelection !== 'preferFT') ||
+      (dataSelection === 'preferFT' && !processedKeys.length)
+    ) {
+      if (processedKeys.length > 0) {
+        const firstProcessed = processed[processedKeys[0]];
         if (firstProcessed.procs) {
-          experiment.fileCollectionItems.push(firstProcessed.procs); //seems useless
+          experiment.fileCollectionItems.push(firstProcessed.procs);
           experiment.procs = firstProcessed.procs;
         }
         if (firstProcessed.proc2s) {
-          // experiment.fileCollectionItems.push(firstProcessed.proc2s); //seems useless
+          experiment.fileCollectionItems.push(firstProcessed.proc2s);
           experiment.proc2s = firstProcessed.proc2s;
@@ -149,2 +154,9 @@ }
     }
+
+    if (
+      dataSelection === 'fid' ||
+      (dataSelection === 'preferFID' && hasRawData)
+    ) {
+      continue;
+    }
     for (let processedKey in processed) {
@@ -168,8 +180,2 @@ const oneProcessed = processed[processedKey];
   // we can not easily filter
-  if (!keepFID) {
-    experimentsArray = experimentsArray.filter((item) => !item.isFID);
-  }
-  if (!keepFT) {
-    experimentsArray = experimentsArray.filter((item) => !item.isFT);
-  }
   if (!keep1D) {
@@ -184,1 +190,9 @@ experimentsArray = experimentsArray.filter((item) => !item.is1D);
 }
+
+function isRawOrAcquisitionFile(file, fileList) {
+  return (
+    file.name.match(/^(ser|acqus|acqu2s)$/) ||
+    (file.name.match(/^(fid)$/) &&
+      fileList.includes(file.relativePath.replace(/fid$/, 'acqus')))
+  );
+}

src/util/convertOneExperiment.js

@@ -31,4 +31,2 @@ import { convert1D } from './convert1D';
     }
-    // todo we could as well keep the FileList at this level if
-    // we want to keep the original data
   }
@@ -35,0 +33,0 @@

New alerts

No v1

Quality

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

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

1153987

0.29%

Lines of code

1714

6.59%

Worsened metrics

Number of low quality alerts

2

100%

Dependency changes

• Updated

  filelist-utils@^1.7.0-pre.1676560930