jcampconverter 9.2.0 → 9.2.2

package/lib-esm/postProcessingNMR.js

@@ -1,92 +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;
-                }
-            }
-        }
-    }
-}
-//# sourceMappingURL=postProcessingNMR.js.map

package/lib-esm/postProcessingNMR.js.map

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package/lib-esm/prepareNtuplesDatatable.d.ts

@@ -1,2 +0,0 @@
-export default function prepareNtuplesDatatable(currentEntry: any, spectrum: any, kind: any): void;
-//# sourceMappingURL=prepareNtuplesDatatable.d.ts.map

package/lib-esm/prepareNtuplesDatatable.d.ts.map

@@ -1 +0,0 @@
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package/lib-esm/prepareNtuplesDatatable.js

@@ -1,84 +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];
-            }
-        }
-    }
-}
-//# sourceMappingURL=prepareNtuplesDatatable.js.map

package/lib-esm/prepareNtuplesDatatable.js.map

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package/lib-esm/prepareSpectrum.d.ts

@@ -1,2 +0,0 @@
-export default function prepareSpectrum(spectrum: any): void;
-//# sourceMappingURL=prepareSpectrum.d.ts.map

package/lib-esm/prepareSpectrum.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"prepareSpectrum.d.ts","sourceRoot":"","sources":["../src/prepareSpectrum.js"],"names":[],"mappings":"AAAA,6DAGC"}

package/lib-esm/prepareSpectrum.js

@@ -1,7 +0,0 @@
-export default function prepareSpectrum(spectrum) {
-    if (!spectrum.xFactor)
-        spectrum.xFactor = 1;
-    if (!spectrum.yFactor)
-        spectrum.yFactor = 1;
-}
-//# sourceMappingURL=prepareSpectrum.js.map

package/lib-esm/prepareSpectrum.js.map

@@ -1 +0,0 @@
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package/lib-esm/profiling.d.ts

@@ -1,2 +0,0 @@
-export default function profiling(result: any, action: any, options?: {}): void;
-//# sourceMappingURL=profiling.d.ts.map

package/lib-esm/profiling.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"profiling.d.ts","sourceRoot":"","sources":["../src/profiling.js"],"names":[],"mappings":"AAAA,gFAQC"}

package/lib-esm/profiling.js

@@ -1,10 +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,
-        });
-    }
-}
-//# sourceMappingURL=profiling.js.map

package/lib-esm/profiling.js.map

@@ -1 +0,0 @@
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package/lib-esm/simpleChromatogram.d.ts

@@ -1,2 +0,0 @@
-export default function simpleChromatogram(result: any): void;
-//# sourceMappingURL=simpleChromatogram.d.ts.map

package/lib-esm/simpleChromatogram.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"simpleChromatogram.d.ts","sourceRoot":"","sources":["../src/simpleChromatogram.js"],"names":[],"mappings":"AAAA,8DAWC"}

package/lib-esm/simpleChromatogram.js

@@ -1,13 +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(),
-            },
-        },
-    };
-}
-//# sourceMappingURL=simpleChromatogram.js.map

package/lib-esm/simpleChromatogram.js.map

@@ -1 +0,0 @@
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package/src/2d/add2D.js

@@ -1,11 +0,0 @@
-import convertTo3DZ from './convertTo3DZ';
-import generateContourLines from './generateContourLines';
-
-export default function add2D(result, options) {
-  let zData = convertTo3DZ(result.spectra);
-  if (!options.noContour) {
-    result.contourLines = generateContourLines(zData, options);
-    delete zData.z;
-  }
-  result.minMax = zData;
-}

package/src/2d/convertTo3DZ.js

@@ -1,55 +0,0 @@
-import getMedian from 'ml-array-median';
-
-export default function convertTo3DZ(spectra) {
-  let minZ = spectra[0].data.y[0];
-  let maxZ = minZ;
-  let ySize = spectra.length;
-  let xSize = spectra[0].data.x.length;
-
-  let z = new Array(ySize);
-  for (let i = 0; i < ySize; i++) {
-    z[i] = spectra[i].data.y;
-    for (let j = 0; j < xSize; j++) {
-      let value = z[i][j];
-      if (value < minZ) minZ = value;
-      if (value > maxZ) maxZ = value;
-    }
-  }
-
-  const firstX = spectra[0].data.x[0];
-  const lastX = spectra[0].data.x[spectra[0].data.x.length - 1]; // has to be -2 because it is a 1D array [x,y,x,y,...]
-  const firstY = spectra[0].pageValue;
-  const lastY = spectra[ySize - 1].pageValue;
-
-  // Because the min / max value are the only information about the matrix if we invert
-  // min and max we need to invert the array
-  if (firstX > lastX) {
-    for (let spectrum of z) {
-      spectrum.reverse();
-    }
-  }
-  if (firstY > lastY) {
-    z.reverse();
-  }
-
-  const medians = [];
-  for (let i = 0; i < z.length; i++) {
-    const row = Float64Array.from(z[i]);
-    for (let i = 0; i < row.length; i++) {
-      if (row[i] < 0) row[i] = -row[i];
-    }
-    medians.push(getMedian(row));
-  }
-  const median = getMedian(medians);
-
-  return {
-    z,
-    minX: Math.min(firstX, lastX),
-    maxX: Math.max(firstX, lastX),
-    minY: Math.min(firstY, lastY),
-    maxY: Math.max(firstY, lastY),
-    minZ,
-    maxZ,
-    noise: median,
-  };
-}

package/src/2d/generateContourLines.js

@@ -1,166 +0,0 @@
-export default function generateContourLines(zData, options) {
-  let noise = zData.noise;
-  let z = zData.z;
-  let povarHeight0, povarHeight1, povarHeight2, povarHeight3;
-  let isOver0, isOver1, isOver2, isOver3;
-  let nbSubSpectra = z.length;
-  let nbPovars = z[0].length;
-  let pAx, pAy, pBx, pBy;
-
-  let x0 = zData.minX;
-  let xN = zData.maxX;
-  let dx = (xN - x0) / (nbPovars - 1);
-  let y0 = zData.minY;
-  let yN = zData.maxY;
-  let dy = (yN - y0) / (nbSubSpectra - 1);
-  let minZ = zData.minZ;
-  let maxZ = zData.maxZ;
-
-  // System.out.prvarln('y0 '+y0+' yN '+yN);
-  // -------------------------
-  // Povars attribution
-  //
-  // 0----1
-  // |  / |
-  // | /  |
-  // 2----3
-  //
-  // ---------------------d------
-
-  let iter = options.nbContourLevels * 2;
-  let contourLevels = new Array(iter);
-  let lineZValue;
-  for (let level = 0; level < iter; level++) {
-    // multiply by 2 for positif and negatif
-    let contourLevel = {};
-    contourLevels[level] = contourLevel;
-    let side = level % 2;
-    let factor =
-      (maxZ - options.noiseMultiplier * noise) *
-      Math.exp((level >> 1) - options.nbContourLevels);
-    if (side === 0) {
-      lineZValue = factor + options.noiseMultiplier * noise;
-    } else {
-      lineZValue = 0 - factor - options.noiseMultiplier * noise;
-    }
-    let lines = [];
-    contourLevel.zValue = lineZValue;
-    contourLevel.lines = lines;
-
-    if (lineZValue <= minZ || lineZValue >= maxZ) continue;
-
-    for (let iSubSpectra = 0; iSubSpectra < nbSubSpectra - 1; iSubSpectra++) {
-      let subSpectra = z[iSubSpectra];
-      let subSpectraAfter = z[iSubSpectra + 1];
-      for (let povar = 0; povar < nbPovars - 1; povar++) {
-        povarHeight0 = subSpectra[povar];
-        povarHeight1 = subSpectra[povar + 1];
-        povarHeight2 = subSpectraAfter[povar];
-        povarHeight3 = subSpectraAfter[povar + 1];
-
-        isOver0 = povarHeight0 > lineZValue;
-        isOver1 = povarHeight1 > lineZValue;
-        isOver2 = povarHeight2 > lineZValue;
-        isOver3 = povarHeight3 > lineZValue;
-
-        // Example povar0 is over the plane and povar1 and
-        // povar2 are below, we find the varersections and add
-        // the segment
-        if (isOver0 !== isOver1 && isOver0 !== isOver2) {
-          pAx =
-            povar + (lineZValue - povarHeight0) / (povarHeight1 - povarHeight0);
-          pAy = iSubSpectra;
-          pBx = povar;
-          pBy =
-            iSubSpectra +
-            (lineZValue - povarHeight0) / (povarHeight2 - povarHeight0);
-          lines.push(pAx * dx + x0);
-          lines.push(pAy * dy + y0);
-          lines.push(pBx * dx + x0);
-          lines.push(pBy * dy + y0);
-        }
-        // remove push does not help !!!!
-        if (isOver3 !== isOver1 && isOver3 !== isOver2) {
-          pAx = povar + 1;
-          pAy =
-            iSubSpectra +
-            1 -
-            (lineZValue - povarHeight3) / (povarHeight1 - povarHeight3);
-          pBx =
-            povar +
-            1 -
-            (lineZValue - povarHeight3) / (povarHeight2 - povarHeight3);
-          pBy = iSubSpectra + 1;
-          lines.push(pAx * dx + x0);
-          lines.push(pAy * dy + y0);
-          lines.push(pBx * dx + x0);
-          lines.push(pBy * dy + y0);
-        }
-        // test around the diagonal
-        if (isOver1 !== isOver2) {
-          pAx =
-            (povar +
-              1 -
-              (lineZValue - povarHeight1) / (povarHeight2 - povarHeight1)) *
-              dx +
-            x0;
-          pAy =
-            (iSubSpectra +
-              (lineZValue - povarHeight1) / (povarHeight2 - povarHeight1)) *
-              dy +
-            y0;
-          if (isOver1 !== isOver0) {
-            pBx =
-              povar +
-              1 -
-              (lineZValue - povarHeight1) / (povarHeight0 - povarHeight1);
-            pBy = iSubSpectra;
-            lines.push(pAx);
-            lines.push(pAy);
-            lines.push(pBx * dx + x0);
-            lines.push(pBy * dy + y0);
-          }
-          if (isOver2 !== isOver0) {
-            pBx = povar;
-            pBy =
-              iSubSpectra +
-              1 -
-              (lineZValue - povarHeight2) / (povarHeight0 - povarHeight2);
-            lines.push(pAx);
-            lines.push(pAy);
-            lines.push(pBx * dx + x0);
-            lines.push(pBy * dy + y0);
-          }
-          if (isOver1 !== isOver3) {
-            pBx = povar + 1;
-            pBy =
-              iSubSpectra +
-              (lineZValue - povarHeight1) / (povarHeight3 - povarHeight1);
-            lines.push(pAx);
-            lines.push(pAy);
-            lines.push(pBx * dx + x0);
-            lines.push(pBy * dy + y0);
-          }
-          if (isOver2 !== isOver3) {
-            pBx =
-              povar +
-              (lineZValue - povarHeight2) / (povarHeight3 - povarHeight2);
-            pBy = iSubSpectra + 1;
-            lines.push(pAx);
-            lines.push(pAy);
-            lines.push(pBx * dx + x0);
-            lines.push(pBy * dy + y0);
-          }
-        }
-      }
-    }
-  }
-
-  return {
-    minX: zData.minX,
-    maxX: zData.maxX,
-    minY: zData.minY,
-    maxY: zData.maxY,
-    segments: contourLevels,
-  };
-}

package/src/complexChromatogram.js

@@ -1,49 +0,0 @@
-const GC_MS_FIELDS = ['TIC', '.RIC', 'SCANNUMBER'];
-
-export function complexChromatogram(result) {
-  let spectra = result.spectra;
-  let length = spectra.length;
-  let chromatogram = {
-    times: new Array(length),
-    series: {
-      ms: {
-        dimension: 2,
-        data: new Array(length),
-      },
-    },
-  };
-
-  let existingGCMSFields = [];
-  for (let i = 0; i < GC_MS_FIELDS.length; i++) {
-    let label = convertMSFieldToLabel(GC_MS_FIELDS[i]);
-    if (spectra[0][label]) {
-      existingGCMSFields.push(label);
-      chromatogram.series[label] = {
-        dimension: 1,
-        data: new Array(length),
-      };
-    }
-  }
-
-  for (let i = 0; i < length; i++) {
-    let spectrum = spectra[i];
-    chromatogram.times[i] = spectrum.pageValue;
-    for (let j = 0; j < existingGCMSFields.length; j++) {
-      chromatogram.series[existingGCMSFields[j]].data[i] = Number(
-        spectrum[existingGCMSFields[j]],
-      );
-    }
-    if (spectrum.data) {
-      chromatogram.series.ms.data[i] = [spectrum.data.x, spectrum.data.y];
-    }
-  }
-  result.chromatogram = chromatogram;
-}
-
-export function isMSField(canonicDataLabel) {
-  return GC_MS_FIELDS.indexOf(canonicDataLabel) !== -1;
-}
-
-export function convertMSFieldToLabel(value) {
-  return value.toLowerCase().replace(/[^a-z0-9]/g, '');
-}