jcampconverter 9.2.0 → 9.2.2

package/lib/prepareNtuplesDatatable.js

@@ -1,87 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-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];
-            }
-        }
-    }
-}
-exports.default = prepareNtuplesDatatable;
-//# sourceMappingURL=prepareNtuplesDatatable.js.map

package/lib/prepareNtuplesDatatable.js.map

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package/lib/prepareSpectrum.d.ts

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

package/lib/prepareSpectrum.d.ts.map

@@ -1 +0,0 @@
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package/lib/prepareSpectrum.js

@@ -1,10 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-function prepareSpectrum(spectrum) {
-    if (!spectrum.xFactor)
-        spectrum.xFactor = 1;
-    if (!spectrum.yFactor)
-        spectrum.yFactor = 1;
-}
-exports.default = prepareSpectrum;
-//# sourceMappingURL=prepareSpectrum.js.map

package/lib/prepareSpectrum.js.map

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

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

package/lib/profiling.d.ts.map

@@ -1 +0,0 @@
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package/lib/profiling.js

@@ -1,13 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-function profiling(result, action, options = {}) {
-    options.logger?.trace(action);
-    if (result.profiling) {
-        result.profiling.push({
-            action,
-            time: Date.now() - options.start,
-        });
-    }
-}
-exports.default = profiling;
-//# sourceMappingURL=profiling.js.map

package/lib/profiling.js.map

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package/lib/simpleChromatogram.d.ts

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

package/lib/simpleChromatogram.d.ts.map

@@ -1 +0,0 @@
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package/lib/simpleChromatogram.js

@@ -1,16 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-function simpleChromatogram(result) {
-    let data = result.spectra[0].data;
-    result.chromatogram = {
-        times: data.x.slice(),
-        series: {
-            intensity: {
-                dimension: 1,
-                data: data.y.slice(),
-            },
-        },
-    };
-}
-exports.default = simpleChromatogram;
-//# sourceMappingURL=simpleChromatogram.js.map

package/lib/simpleChromatogram.js.map

@@ -1 +0,0 @@
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package/lib-esm/2d/add2D.d.ts

@@ -1,2 +0,0 @@
-export default function add2D(result: any, options: any): void;
-//# sourceMappingURL=add2D.d.ts.map

package/lib-esm/2d/add2D.d.ts.map

@@ -1 +0,0 @@
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package/lib-esm/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;
-}
-//# sourceMappingURL=add2D.js.map

package/lib-esm/2d/add2D.js.map

@@ -1 +0,0 @@
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package/lib-esm/2d/convertTo3DZ.d.ts

@@ -1,11 +0,0 @@
-export default function convertTo3DZ(spectra: any): {
-    z: any[];
-    minX: number;
-    maxX: number;
-    minY: number;
-    maxY: number;
-    minZ: any;
-    maxZ: any;
-    noise: number;
-};
-//# sourceMappingURL=convertTo3DZ.d.ts.map

package/lib-esm/2d/convertTo3DZ.d.ts.map

@@ -1 +0,0 @@
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package/lib-esm/2d/convertTo3DZ.js

@@ -1,53 +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,
-    };
-}
-//# sourceMappingURL=convertTo3DZ.js.map

package/lib-esm/2d/convertTo3DZ.js.map

@@ -1 +0,0 @@
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package/lib-esm/2d/generateContourLines.d.ts

@@ -1,8 +0,0 @@
-export default function generateContourLines(zData: any, options: any): {
-    minX: any;
-    maxX: any;
-    minY: any;
-    maxY: any;
-    segments: any[];
-};
-//# sourceMappingURL=generateContourLines.d.ts.map

package/lib-esm/2d/generateContourLines.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"generateContourLines.d.ts","sourceRoot":"","sources":["../../src/2d/generateContourLines.js"],"names":[],"mappings":"AAAA;;;;;;EAqKC"}

package/lib-esm/2d/generateContourLines.js

@@ -1,160 +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,
-    };
-}
-//# sourceMappingURL=generateContourLines.js.map

package/lib-esm/2d/generateContourLines.js.map

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package/lib-esm/complexChromatogram.d.ts

@@ -1,4 +0,0 @@
-export function complexChromatogram(result: any): void;
-export function isMSField(canonicDataLabel: any): boolean;
-export function convertMSFieldToLabel(value: any): any;
-//# sourceMappingURL=complexChromatogram.d.ts.map

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

@@ -1 +0,0 @@
-{"version":3,"file":"complexChromatogram.d.ts","sourceRoot":"","sources":["../src/complexChromatogram.js"],"names":[],"mappings":"AAEA,uDAsCC;AAED,0DAEC;AAED,uDAEC"}

package/lib-esm/complexChromatogram.js

@@ -1,43 +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, '');
-}
-//# sourceMappingURL=complexChromatogram.js.map

package/lib-esm/complexChromatogram.js.map

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