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feat: importation and exportation of nmredata (#989)
* fix: nmredata exportation of 2D signals close #980 * feat: prepare to import nmredata * feat: nmredata importation and ranges assigned * feat(nmredata): 2D signals assign completed * feat: use nmredata 0.2.0 * chore: fix eslint * chore: use node 14
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,132 @@ | ||
| import { NmrRecord, parseSDF } from 'nmredata'; | ||
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| import { addBruker, addJcamp } from '../../data/SpectraManager'; | ||
| import { detectRanges, mapRanges } from '../../data/data1d/Datum1D'; | ||
| import { detectZones } from '../../data/data2d/Datum2D'; | ||
|
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||
| const computeDistance = (s1, s2) => | ||
| ['x', 'y'].reduce( | ||
| (dist, axis) => Math.pow(s2[axis].delta - s1[axis].delta, 2) + dist, | ||
| 0, | ||
| ); | ||
|
|
||
| export async function nmredataToNmrium(zipFilesValues) { | ||
| let files = {}; | ||
| for (const file of zipFilesValues) files[file.name] = file; | ||
| const sdfFiles = await getSDF(files); | ||
| const jsonData = await NmrRecord.toJSON({ | ||
| sdf: sdfFiles[0], | ||
| zipFiles: files, | ||
| }); | ||
|
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| let { spectra, molecules = [] } = jsonData; | ||
|
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| let nmrium = { | ||
| spectra: [], | ||
| molecules, | ||
| }; | ||
|
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| for (const data of spectra) { | ||
| const { zip, jcamp } = data.source; | ||
|
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||
| let spectrum = zip | ||
| ? await addBruker({ xy: true, noContours: true }, zip) | ||
| : (spectrum = addJcamp({}, jcamp)); | ||
|
|
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| const { info } = spectrum[0]; | ||
| if (info.dimension > 1) { | ||
| detectZones(spectrum[0], {}); | ||
| assignZones(spectrum[0], data.signals); | ||
| } else { | ||
| detectRanges(spectrum[0], {}); | ||
| assignRanges(spectrum[0], data.signals); | ||
| } | ||
| nmrium.spectra.push(...spectrum); | ||
| } | ||
|
|
||
| return nmrium; | ||
| } | ||
|
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||
| async function getSDF(zipFiles) { | ||
| let result = []; | ||
| for (const file in zipFiles) { | ||
| const pathFile = file.split('/'); | ||
| if (pathFile[pathFile.length - 1].match(/^[^.].+sdf$/)) { | ||
| const filename = pathFile[pathFile.length - 1].replace(/\.sdf/, ''); | ||
| const root = pathFile.slice(0, pathFile.length - 1).join('/'); | ||
| const sdf = await zipFiles[file].async('string'); | ||
| let parserResult = parseSDF(`${sdf}`, { mixedEOL: true }); | ||
| parserResult.filename = filename; | ||
| parserResult.root = root !== '' ? `${root}/` : ''; | ||
| result.push(parserResult); | ||
| } | ||
| } | ||
| return result; | ||
| } | ||
|
|
||
| function assignZones(datum, eSignals) { | ||
| let zones = datum.zones.values; | ||
| let signals = eSignals.slice(); | ||
| for (let zone of zones) { | ||
| let signalsInside = []; | ||
| for (let i = 0; i < signals.length; i++) { | ||
| let isInside = 0; | ||
| let signal = signals[i]; | ||
| for (let axis of ['x', 'y']) { | ||
| let { from, to } = zone[axis]; | ||
| let deltaIn = signal[axis].delta; | ||
| if (deltaIn >= from && deltaIn <= to) isInside++; | ||
| } | ||
| if (isInside > 1) { | ||
| signalsInside.push(signal); | ||
| signals.splice(i, 1); | ||
| i--; | ||
| } | ||
| } | ||
| if (signalsInside.length > 0) { | ||
| for (let signal of signalsInside) { | ||
| for (let axis of ['x', 'y']) { | ||
| if (!signal[axis].diaID) continue; | ||
| let index = closeSignalIndex(signal, zone); | ||
| zone.signal[index][axis].diaID = signal[axis].diaID; | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
|
|
||
| function closeSignalIndex(signal, zone) { | ||
| const signals = zone.signal; | ||
| if (signals.length === 1) return 0; | ||
|
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||
| let index = 0; | ||
| let distance = computeDistance(signals[0], signal); | ||
| for (let i = 0; i < signals.length; i++) { | ||
| let currentDistance = computeDistance(signals[i], signal); | ||
| if (currentDistance < distance) { | ||
| index = i; | ||
| distance = currentDistance; | ||
| } | ||
| } | ||
| return index; | ||
| } | ||
|
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||
| function assignRanges(datum, signals) { | ||
| let ranges = datum.ranges.values.slice(); | ||
| ranges.sort((a, b) => a.from - b.from); | ||
| signals.sort((a, b) => a.delta - b.delta); | ||
| for (let range of ranges) { | ||
| let { from, to } = range; | ||
| let signalsInside = []; | ||
| for (let signal of signals) { | ||
| if (signal.delta >= from && signal.delta <= to) { | ||
| let { jCoupling: j, delta, diaID = [], multiplicity } = signal; | ||
| signalsInside.push({ j, delta, diaID, multiplicity }); | ||
| } | ||
| if (signal.delta > to) break; | ||
| } | ||
| if (signalsInside.length > 0) range.signal = signalsInside; | ||
| } | ||
| datum.ranges.values = []; | ||
| datum.ranges.values = mapRanges(ranges, datum); | ||
| } |
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