feat: expose options for automatic processing and range/zone detection

Author: hamed-musallam

app/scripts/nmr-cli/src/index.ts

@@ -1,6 +1,6 @@
 #!/usr/bin/env node
 import yargs, { type Argv, type CommandModule, type Options } from 'yargs'
-import { loadSpectrumFromURL, loadSpectrumFromFilePath } from './prase-spectra'
+import { loadSpectrumFromURL, loadSpectrumFromFilePath } from './parse/prase-spectra'
 import { generateSpectrumFromPublicationString } from './publication-string'
 import { parsePredictionCommand } from './prediction/parsePredictionCommand'
 import { hideBin } from 'yargs/helpers'
@@ -14,18 +14,14 @@ Commands:
   predict                      Predict spectrum from Mol 
 
 Options for 'parse-spectra' command:
-  -u, --url           File URL
-  -p, --path          Directory path
-  -s, --capture-snapshot   Capture snapshot
+  -u, --url                File URL  
+  -dir, --dir-path         Directory path  
+  -s, --capture-snapshot   Capture snapshot  
+  -p, --auto-processing    Automatic processing of spectrum (FID → FT spectra).
+  -d, --auto-detection     Enable ranges and zones automatic detection.
 
 Arguments for 'parse-publication-string' command:
   publicationString   Publication string
-
-Options for 'parse-spectra' command:
-  -u, --url           File URL
-  -p, --path          Directory path
-  -s, --capture-snapshot   Capture snapshot
-
  
 Options for 'predict' command:
   -ps,--peakShape     Peak shape algorithm (default: "lorentzian") choices: ["gaussian", "lorentzian"]
@@ -46,16 +42,43 @@ Options for 'predict' command:
 
 Examples:
   nmr-cli  parse-spectra -u file-url -s                                   // Process spectra files from a URL and capture an image for the spectra
-  nmr-cli  parse-spectra -p directory-path -s                             // process a spectra files from a directory and capture an image for the spectra
+  nmr-cli  parse-spectra -dir directory-path -s                             // process a spectra files from a directory and capture an image for the spectra
   nmr-cli  parse-spectra -u file-url                                      // Process spectra files from a URL 
-  nmr-cli  parse-spectra -p directory-path                                // Process spectra files from a directory 
+  nmr-cli  parse-spectra -dir directory-path                                // Process spectra files from a directory 
   nmr-cli  parse-publication-string "your publication string"
 `
 
-interface FileOptionsArgs {
-  u?: string
-  p?: string
-  s?: boolean
+export interface FileOptionsArgs {
+  /**  
+   * -u, --url  
+   * File URL to load remote spectra or data.
+   */
+  u?: string;
+
+  /**  
+   * -dir, --dir-path  
+   * Local directory path for file input or output.
+   */
+  dir?: string;
+
+  /**  
+   * -s, --capture-snapshot  
+   * Capture a visual snapshot of the current state or spectrum.
+   */
+  s?: boolean;
+
+  /**  
+   * -p, --auto-processing  
+   * Automatically process spectrum from FID to FT spectra.  
+   * Mandatory when automatic detection (`--auto-detection`) is enabled.
+   */
+  p?: boolean;
+
+  /**  
+   * -d, --auto-detection  
+   * Perform automatic ranges and zones detection.
+   */
+  d?: boolean;
 }
 
 // Define options for parsing a spectra file
@@ -66,8 +89,8 @@ const fileOptions: { [key in keyof FileOptionsArgs]: Options } = {
     type: 'string',
     nargs: 1,
   },
-  p: {
-    alias: 'path',
+  dir: {
+    alias: 'dir-path',
     describe: 'Directory path',
     type: 'string',
     nargs: 1,
@@ -77,6 +100,16 @@ const fileOptions: { [key in keyof FileOptionsArgs]: Options } = {
     describe: 'Capture snapshot',
     type: 'boolean',
   },
+  p: {
+    alias: 'auto-processing',
+    describe: 'Auto processing',
+    type: 'boolean',
+  },
+  d: {
+    alias: 'auto-detection',
+    describe: 'Ranges and zones auto detection',
+    type: 'boolean',
+  },
 } as const
 
 const parseFileCommand: CommandModule<{}, FileOptionsArgs> = {
@@ -85,21 +118,25 @@ const parseFileCommand: CommandModule<{}, FileOptionsArgs> = {
   builder: yargs => {
     return yargs
       .options(fileOptions)
-      .conflicts('u', 'p') as Argv<FileOptionsArgs>
+      .conflicts('u', 'dir') as Argv<FileOptionsArgs>
   },
   handler: argv => {
+
+    const { u, dir } = argv;
     // Handle parsing the spectra file logic based on argv options
-    if (argv?.u) {
-      loadSpectrumFromURL(argv.u, argv.s).then(result => {
+    if (u) {
+      loadSpectrumFromURL({ u, ...argv }).then(result => {
         console.log(JSON.stringify(result))
       })
     }
 
-    if (argv?.p) {
-      loadSpectrumFromFilePath(argv.p, argv.s).then(result => {
+
+    if (dir) {
+      loadSpectrumFromFilePath({ dir, ...argv }).then(result => {
         console.log(JSON.stringify(result))
       })
     }
+
   },
 }
 

app/scripts/nmr-cli/src/parse/prase-spectra.ts

@@ -1,8 +1,23 @@
 import { join, isAbsolute } from 'path'
-import { type NmriumState } from '@zakodium/nmrium-core'
+import { NmriumData, ParsingOptions, type NmriumState } from '@zakodium/nmrium-core'
 import init from '@zakodium/nmrium-core-plugins'
 import playwright from 'playwright'
 import { FileCollection } from 'file-collection'
+import { FileOptionsArgs } from '..'
+import { isSpectrum2D } from './data/data2d/isSpectrum2D'
+import { initiateDatum2D } from './data/data2d/initiateDatum2D'
+import { initiateDatum1D } from './data/data1D/initiateDatum1D'
+import { detectZones } from './data/data2d/detectZones'
+import { detectRanges } from './data/data1D/detectRanges'
+import { Filters1DManager, Filters2DManager } from 'nmr-processing'
+
+type RequiredKey<T, K extends keyof T> = Omit<T, K> & Required<Pick<T, K>>;
+
+const parsingOptions: ParsingOptions = {
+  onLoadProcessing: { autoProcessing: true },
+  sourceSelector: { general: { dataSelection: 'preferFT' } },
+  experimentalFeatures: true
+};
 
 interface Snapshot {
   image: string
@@ -79,9 +94,39 @@ async function captureSpectraViewAsBase64(nmriumState: Partial<NmriumState>) {
   await browser.close()
 
   return snapshots
+
+}
+
+interface ProcessSpectraOptions {
+  autoDetection: boolean; autoProcessing: boolean;
 }
 
-async function loadSpectrumFromURL(url: string, enableSnapshot = false) {
+function processSpectra(data: NmriumData, options: ProcessSpectraOptions) {
+
+  const { autoDetection = false, autoProcessing = false } = options
+
+  for (let index = 0; index < data.spectra.length; index++) {
+    const inputSpectrum = data.spectra[index]
+    const is2D = isSpectrum2D(inputSpectrum);
+    const spectrum = is2D ? initiateDatum2D(inputSpectrum) : initiateDatum1D(inputSpectrum);
+
+    if (autoProcessing) {
+      isSpectrum2D(spectrum) ? Filters2DManager.reapplyFilters(spectrum) : Filters1DManager.reapplyFilters(spectrum)
+    }
+
+    if (autoDetection && spectrum.info.isFt) {
+      isSpectrum2D(spectrum) ? detectZones(spectrum) : detectRanges(spectrum);
+    }
+
+    data.spectra[index] = spectrum;
+  }
+
+
+}
+
+async function loadSpectrumFromURL(options: RequiredKey<FileOptionsArgs, 'u'>) {
+  const { u: url, s: enableSnapshot = false, p: autoProcessing = false, d: autoDetection = false } = options;
+
   const { pathname: relativePath, origin: baseURL } = new URL(url)
   const source = {
     entries: [
@@ -92,11 +137,16 @@ async function loadSpectrumFromURL(url: string, enableSnapshot = false) {
     baseURL,
   }
 
-  const [nmriumState] = await core.readFromWebSource(source);
+  const [nmriumState] = await core.readFromWebSource(source, parsingOptions);
   const {
     data, version
   } = nmriumState;
 
+
+  if (data) {
+    processSpectra(data, { autoDetection, autoProcessing });
+  }
+
   let images: Snapshot[] = []
 
   if (enableSnapshot) {
@@ -106,7 +156,9 @@ async function loadSpectrumFromURL(url: string, enableSnapshot = false) {
   return { data, version, images }
 }
 
-async function loadSpectrumFromFilePath(path: string, enableSnapshot = false) {
+async function loadSpectrumFromFilePath(options: RequiredKey<FileOptionsArgs, 'dir'>) {
+  const { dir: path, s: enableSnapshot = false, p: autoProcessing = false, d: autoDetection = false } = options;
+
   const dirPath = isAbsolute(path) ? path : join(process.cwd(), path)
 
   const fileCollection = await FileCollection.fromPath(dirPath, {
@@ -115,7 +167,12 @@ async function loadSpectrumFromFilePath(path: string, enableSnapshot = false) {
 
   const {
     nmriumState: { data, version },
-  } = await core.read(fileCollection)
+  } = await core.read(fileCollection, parsingOptions)
+
+
+  if (data) {
+    processSpectra(data, { autoDetection, autoProcessing })
+  }
 
   let images: Snapshot[] = []