jcampconverter 9.2.0 → 9.2.2

package/src/parse/parsePeakTable.js

@@ -1,69 +0,0 @@
-const removeCommentRegExp = /\$\$.*/;
-const peakTableSplitRegExp = /[,\t ]+/;
-
-export default function parsePeakTable(spectrum, value, result) {
-  spectrum.isPeaktable = true;
-
-  if (!spectrum.variables || Object.keys(spectrum.variables) === 2) {
-    parseXY(spectrum, value, result);
-  } else {
-    parseXYZ(spectrum, value, result);
-  }
-
-  // we will add the data in the variables
-  if (spectrum.variables) {
-    for (let key in spectrum.variables) {
-      spectrum.variables[key].data = spectrum.data[key];
-    }
-  }
-}
-
-function parseXY(spectrum, value, result) {
-  let currentData = { x: [], y: [] };
-  spectrum.data = currentData;
-
-  // counts for around 20% of the time
-  let lines = value.split(/,? *,?[;\r\n]+ */);
-
-  for (let i = 1; i < lines.length; i++) {
-    let values = lines[i]
-      .trim()
-      .replace(removeCommentRegExp, '')
-      .split(peakTableSplitRegExp);
-    if (values.length % 2 === 0) {
-      for (let j = 0; j < values.length; j = j + 2) {
-        // takes around 40% of the time to add and parse the 2 values nearly exclusively because of Number
-        currentData.x.push(Number(values[j]) * spectrum.xFactor);
-        currentData.y.push(Number(values[j + 1]) * spectrum.yFactor);
-      }
-    } else {
-      result.logs.push(`Format error: ${values}`);
-    }
-  }
-}
-
-function parseXYZ(spectrum, value, result) {
-  let currentData = {};
-  let variables = Object.keys(spectrum.variables);
-  let numberOfVariables = variables.length;
-  variables.forEach((variable) => (currentData[variable] = []));
-  spectrum.data = currentData;
-
-  // counts for around 20% of the time
-  let lines = value.split(/,? *,?[;\r\n]+ */);
-
-  for (let i = 1; i < lines.length; i++) {
-    let values = lines[i]
-      .trim()
-      .replace(removeCommentRegExp, '')
-      .split(peakTableSplitRegExp);
-    if (values.length % numberOfVariables === 0) {
-      for (let j = 0; j < values.length; j++) {
-        // todo should try to find a xFactor (y, ...)
-        currentData[variables[j % numberOfVariables]].push(Number(values[j]));
-      }
-    } else {
-      result.logs.push(`Format error: ${values}`);
-    }
-  }
-}

package/src/parse/parseXYA.js

@@ -1,50 +0,0 @@
-/*
-(5.4.4) ##РЕАК ASSIGNMENTS= (STRING). List
-of peak assignments for components or functional groups
-in the forms ##РЕАК ASSIGNMENTS= (ХУА),
-(XYW А), (ХУМА), (XYMW А). Each entry is surrounded Ьу parentheses and starts а new line. У, W (peak
-width), and М (multiplicity) values are optional. The
-symbol А stands for а string detailing the assignment
-and must Ье enclosed Ьу angle brackets. If the peak width
-value is included, then the function used to calculate the
-peak width must Ье detailed in а $$ comment on the
-line(s) below ##PEAKASSIGNMENTS=. Priority OPTIONAL. N.B.: ##РЕАК ASSIGNMENTS= is the preferred method of transmitting peak information when
-the assignments are known.
- */
-
-export default function parseXYA(spectrum, value) {
-  spectrum.isXYAdata = true;
-  const currentData = {};
-  spectrum.data = currentData;
-
-  let lines = value.split(/\r?\n/);
-  const variables = lines[0]
-    .replace(/^.*?([A-Z]+).*$/, '$1')
-    .split('')
-    .map((variable) => variable.toLowerCase());
-
-  for (let i = 1; i < lines.length; i++) {
-    const fields = lines[i].replace(/^\((.*)\)$/, '$1').split(/ *, */);
-    for (let j = 0; j < variables.length; j++) {
-      let value = fields[j];
-      switch (variables[j]) {
-        case 'x':
-        case 'y':
-        case 'w':
-          value = Number.parseFloat(value);
-          break;
-        case 'a':
-          value = value.replace(/^<(.*)>$/, '$1');
-          break;
-        case 'm':
-          break;
-        default:
-          continue;
-      }
-      if (!currentData[variables[j]]) {
-        currentData[variables[j]] = [];
-      }
-      currentData[variables[j]].push(value);
-    }
-  }
-}

package/src/postProcessing.js

@@ -1,93 +0,0 @@
-import { parseString } from 'dynamic-typing';
-
-import add2D from './2d/add2D';
-import { complexChromatogram } from './complexChromatogram';
-import postProcessingNMR from './postProcessingNMR';
-import profiling from './profiling';
-import simpleChromatogram from './simpleChromatogram';
-
-export default function postProcessing(entriesFlat, result, options) {
-  // converting Hz to ppm
-  postProcessingNMR(entriesFlat);
-
-  createArray(entriesFlat, options);
-
-  for (let entry of entriesFlat) {
-    if (Object.keys(entry.ntuples).length > 0) {
-      let newNtuples = [];
-      let keys = Object.keys(entry.ntuples);
-      for (let i = 0; i < keys.length; i++) {
-        let key = keys[i];
-        let values = entry.ntuples[key];
-        for (let j = 0; j < values.length; j++) {
-          if (!newNtuples[j]) newNtuples[j] = {};
-          newNtuples[j][key] = values[j];
-        }
-      }
-      entry.ntuples = newNtuples;
-    }
-
-    if (entry.twoD && options.wantXY) {
-      add2D(entry, options);
-
-      profiling(result, 'Finished countour plot calculation', options);
-
-      if (!options.keepSpectra) {
-        delete entry.spectra;
-      }
-    }
-
-    // maybe it is a GC (HPLC) / MS. In this case we add a new format
-    if (options.chromatogram) {
-      if (entry.spectra.length > 1) {
-        complexChromatogram(entry);
-      } else {
-        simpleChromatogram(entry);
-      }
-      profiling(result, 'Finished chromatogram calculation', options);
-    }
-
-    delete entry.tmp;
-  }
-}
-
-function createArray(entriesFlat, options) {
-  for (const entry of entriesFlat) {
-    for (const key in entry.meta) {
-      const value = entry.meta[key];
-      if (typeof value === 'string') {
-        if (value[0] === '{') {
-          // could be an array
-          if (value[value.length - 1] === '}') {
-            const array = value
-              .slice(1, -1)
-              .split(/[,; ]+/)
-              .filter((e) => e);
-            for (let i = 0; i < array.length; i++) {
-              entry.meta[key + String(i)] = options.dynamicTyping
-                ? parseString(array[i])
-                : array[i];
-            }
-          }
-        } else if (value[0] === '(') {
-          const lines = value.split(/\r?\n/);
-          const regexp = /^\((?<from>\d+)\.\.(?<to>\d+)\)$/;
-          if (regexp.test(lines[0])) {
-            // parsing  '(0..63)'
-            const [from, to] = lines[0].match(regexp).slice(1).map(Number);
-            const array = lines
-              .slice(1)
-              .join(' ')
-              .split(/[,; ]+/)
-              .filter((e) => e);
-            for (let i = from; i <= to; i++) {
-              entry.meta[key + String(i)] = options.dynamicTyping
-                ? parseString(array[i - from])
-                : array[i - from];
-            }
-          }
-        }
-      }
-    }
-  }
-}

package/src/postProcessingNMR.js

@@ -1,99 +0,0 @@
-import { gyromagneticRatio } from 'gyromagnetic-ratio';
-
-export default function postProcessingNMR(entriesFlat) {
-  // specific NMR functions
-
-  for (let entry of entriesFlat) {
-    let observeFrequency = 0;
-    let shiftOffsetVal = 0;
-    for (let spectrum of entry.spectra) {
-      if (entry.ntuples && entry.ntuples.symbol) {
-        if (!observeFrequency && spectrum.observeFrequency) {
-          observeFrequency = spectrum.observeFrequency;
-        }
-        if (!shiftOffsetVal && spectrum.shiftOffsetVal) {
-          shiftOffsetVal = spectrum.shiftOffsetVal;
-        }
-      } else {
-        observeFrequency = spectrum.observeFrequency;
-        shiftOffsetVal = spectrum.shiftOffsetVal;
-      }
-
-      if (observeFrequency) {
-        if (spectrum.xUnits && spectrum.xUnits.toUpperCase().includes('HZ')) {
-          spectrum.xUnits = 'PPM';
-          spectrum.xFactor = spectrum.xFactor / observeFrequency;
-          spectrum.firstX = spectrum.firstX / observeFrequency;
-          spectrum.lastX = spectrum.lastX / observeFrequency;
-          spectrum.deltaX = spectrum.deltaX / observeFrequency;
-          for (let i = 0; i < spectrum.data.x.length; i++) {
-            spectrum.data.x[i] /= observeFrequency;
-          }
-        }
-      }
-      if (shiftOffsetVal && spectrum.xUnits.toLowerCase().includes('ppm')) {
-        let shift = spectrum.firstX - shiftOffsetVal;
-        spectrum.firstX = spectrum.firstX - shift;
-        spectrum.lastX = spectrum.lastX - shift;
-        for (let i = 0; i < spectrum.data.x.length; i++) {
-          spectrum.data.x[i] -= shift;
-        }
-      }
-
-      // we will check if some nucleus are missing ...
-      if (entry.ntuples && entry.ntuples.nucleus && entry.ntuples.symbol) {
-        for (let i = 0; i < entry.ntuples.nucleus.length; i++) {
-          let symbol = entry.ntuples.symbol[i];
-          let nucleus = entry.ntuples.nucleus[i];
-          if (symbol.match(/^[F|T]/) && !nucleus) {
-            if (symbol.match(/[F|T]1/)) {
-              // if F1 is defined we will use F2
-              if (entry.tmp.$NUC2) {
-                entry.ntuples.nucleus[i] = entry.tmp.$NUC2;
-              } else {
-                let f2index = entry.ntuples.symbol.indexOf(
-                  symbol.replace(/^([F|T]).*/, '$12'),
-                );
-                if (f2index && entry.ntuples.nucleus[f2index]) {
-                  entry.ntuples.nucleus[i] = entry.ntuples.nucleus[f2index];
-                }
-              }
-            }
-            if (symbol.match(/[F|T]2/)) {
-              entry.ntuples.nucleus[i] = entry.tmp.$NUC1;
-            }
-          }
-          if (symbol.match(/[F|T]2/)) {
-            entry.yType = entry.ntuples.nucleus[0];
-          }
-        }
-      }
-
-      if (
-        observeFrequency &&
-        entry.ntuples &&
-        entry.ntuples.symbol &&
-        entry.ntuples.nucleus
-      ) {
-        let unit = '';
-        let pageSymbolIndex = entry.ntuples.symbol.indexOf(spectrum.pageSymbol);
-        if (entry.ntuples.units && entry.ntuples.units[pageSymbolIndex]) {
-          unit = entry.ntuples.units[pageSymbolIndex];
-        }
-        if (unit !== 'PPM') {
-          if (pageSymbolIndex !== 0) {
-            throw Error('Not sure about this ntuples format');
-          }
-
-          let ratio0 = gyromagneticRatio[entry.ntuples.nucleus[0]];
-          let ratio1 = gyromagneticRatio[entry.ntuples.nucleus[1]];
-          if (!ratio0 || !ratio1) {
-            throw Error('Problem with determination of gyromagnetic ratio');
-          }
-          let ratio = (ratio0 / ratio1) * observeFrequency;
-          spectrum.pageValue /= ratio;
-        }
-      }
-    }
-  }
-}

package/src/prepareNtuplesDatatable.js

@@ -1,85 +0,0 @@
-export default function prepareNtuplesDatatable(currentEntry, spectrum, kind) {
-  let xIndex = -1;
-  let yIndex = -1;
-  let firstVariable = '';
-  let secondVariable = '';
-  if (kind.indexOf('++') > 0) {
-    firstVariable = kind.replace(/.*\(([a-zA-Z0-9]+)\+\+.*/, '$1');
-    secondVariable = kind.replace(/.*\.\.([a-zA-Z0-9]+).*/, '$1');
-  } else {
-    kind = kind.replace(/[^a-zA-Z]/g, '');
-    firstVariable = kind.charAt(0);
-    secondVariable = kind.charAt(1);
-    spectrum.variables = {};
-    for (let symbol of kind) {
-      let lowerCaseSymbol = symbol.toLowerCase();
-      let index = currentEntry.ntuples.symbol.indexOf(symbol);
-      if (index === -1) throw Error(`Symbol undefined: ${symbol}`);
-      spectrum.variables[lowerCaseSymbol] = {};
-      for (let key in currentEntry.ntuples) {
-        if (currentEntry.ntuples[key][index]) {
-          spectrum.variables[lowerCaseSymbol][key.replace(/^var/, '')] =
-            currentEntry.ntuples[key][index];
-        }
-      }
-    }
-  }
-  xIndex = currentEntry.ntuples.symbol.indexOf(firstVariable);
-  yIndex = currentEntry.ntuples.symbol.indexOf(secondVariable);
-
-  if (xIndex === -1) xIndex = 0;
-  if (yIndex === -1) yIndex = 0;
-
-  if (currentEntry.ntuples.first) {
-    if (currentEntry.ntuples.first.length > xIndex) {
-      spectrum.firstX = currentEntry.ntuples.first[xIndex];
-    }
-    if (currentEntry.ntuples.first.length > yIndex) {
-      spectrum.firstY = currentEntry.ntuples.first[yIndex];
-    }
-  }
-  if (currentEntry.ntuples.last) {
-    if (currentEntry.ntuples.last.length > xIndex) {
-      spectrum.lastX = currentEntry.ntuples.last[xIndex];
-    }
-    if (currentEntry.ntuples.last.length > yIndex) {
-      spectrum.lastY = currentEntry.ntuples.last[yIndex];
-    }
-  }
-  if (
-    currentEntry.ntuples.vardim &&
-    currentEntry.ntuples.vardim.length > xIndex
-  ) {
-    spectrum.nbPoints = currentEntry.ntuples.vardim[xIndex];
-  }
-  if (currentEntry.ntuples.factor) {
-    if (currentEntry.ntuples.factor.length > xIndex) {
-      spectrum.xFactor = currentEntry.ntuples.factor[xIndex];
-    }
-    if (currentEntry.ntuples.factor.length > yIndex) {
-      spectrum.yFactor = currentEntry.ntuples.factor[yIndex];
-    }
-  }
-  if (currentEntry.ntuples.units) {
-    if (currentEntry.ntuples.units.length > xIndex) {
-      if (
-        currentEntry.ntuples.varname &&
-        currentEntry.ntuples.varname[xIndex]
-      ) {
-        spectrum.xUnits = `${currentEntry.ntuples.varname[xIndex]} [${currentEntry.ntuples.units[xIndex]}]`;
-      } else {
-        spectrum.xUnits = currentEntry.ntuples.units[xIndex];
-      }
-    }
-    if (currentEntry.ntuples.units.length > yIndex) {
-      if (
-        currentEntry.ntuples.varname &&
-        currentEntry.ntuples.varname[yIndex]
-      ) {
-        spectrum.yUnits = `${currentEntry.ntuples.varname[yIndex]} [${currentEntry.ntuples.units[yIndex]}]`;
-      } else {
-        spectrum.yUnits = currentEntry.ntuples.units[yIndex];
-      }
-    }
-  }
-}

package/src/prepareSpectrum.js

@@ -1,4 +0,0 @@
-export default function prepareSpectrum(spectrum) {
-  if (!spectrum.xFactor) spectrum.xFactor = 1;
-  if (!spectrum.yFactor) spectrum.yFactor = 1;
-}

package/src/profiling.js

@@ -1,9 +0,0 @@
-export default function profiling(result, action, options = {}) {
-  options.logger?.trace(action);
-  if (result.profiling) {
-    result.profiling.push({
-      action,
-      time: Date.now() - options.start,
-    });
-  }
-}

package/src/simpleChromatogram.js

@@ -1,12 +0,0 @@
-export default function simpleChromatogram(result) {
-  let data = result.spectra[0].data;
-  result.chromatogram = {
-    times: data.x.slice(),
-    series: {
-      intensity: {
-        dimension: 1,
-        data: data.y.slice(),
-      },
-    },
-  };
-}