jcampconverter 8.2.2 → 8.2.3

package/lib/profiling.js

@@ -0,0 +1,12 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+function profiling(result, action, options) {
+    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

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

package/lib/simpleChromatogram.d.ts.map

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

package/lib/simpleChromatogram.js

@@ -0,0 +1,16 @@
+"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

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

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

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

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+{"version":3,"file":"add2D.d.ts","sourceRoot":"","sources":["../../src/2d/add2D.js"],"names":[],"mappings":"AAGA,+DAOC"}

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

@@ -0,0 +1,11 @@
+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

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

@@ -0,0 +1,11 @@
+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

@@ -0,0 +1 @@
+{"version":3,"file":"convertTo3DZ.d.ts","sourceRoot":"","sources":["../../src/2d/convertTo3DZ.js"],"names":[],"mappings":"AAEA;;;;;;;;;EAoDC"}

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

@@ -0,0 +1,53 @@
+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: z,
+        minX: Math.min(firstX, lastX),
+        maxX: Math.max(firstX, lastX),
+        minY: Math.min(firstY, lastY),
+        maxY: Math.max(firstY, lastY),
+        minZ: minZ,
+        maxZ: maxZ,
+        noise: median,
+    };
+}
+//# sourceMappingURL=convertTo3DZ.js.map

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

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

@@ -0,0 +1,8 @@
+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

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

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

@@ -0,0 +1,160 @@
+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

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

@@ -0,0 +1,4 @@
+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

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

@@ -0,0 +1,43 @@
+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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package/lib-esm/convert.d.ts

@@ -0,0 +1,139 @@
+/**
+ *
+ * @typedef {object} ConvertOptions
+ * @property {RegExp} [options.keepRecordsRegExp=/^$/] - By default we don't keep meta information.
+ * @property {boolean} [options.canonicDataLabels=true] - Canonize the Labels (uppercase without symbol).
+ * @property {boolean} [options.canonicMetadataLabels=false] - Canonize the metadata Labels (uppercase without symbol).
+ * @property {boolean} [options.dynamicTyping=false] - Convert numbers to Number.
+ * @property {boolean} [options.withoutXY=false] - Remove the XY data.
+ * @property {boolean} [options.chromatogram=false] - Special post-processing for GC / HPLC / MS.
+ * @property {boolean} [options.keepSpectra=false] - Force to keep the spectra in case of 2D.
+ * @property {boolean} [options.noContour=false] - Don't calculate countour in case of 2D.
+ * @property {number} [options.nbContourLevels=7] - Number of positive / negative contour levels to calculate.
+ * @property {number} [options.noiseMultiplier=5] - Define for 2D the level as 5 times the median as default.
+ * @property {boolean} [options.profiling=false] - Add profiling information.
+ */
+/**
+ *
+ * @typedef {object} Ntuples
+ * @property {string[]} [varname]
+ * @property {string[]} [symbol]
+ * @property {string[]} [vartype]
+ * @property {string[]} [varform]
+ * @property {number[]} [vardim]
+ * @property {string[]} [units]
+ * @property {number[]} [factor]
+ * @property {number[]} [first]
+ * @property {number[]} [last]
+ * @property {number[]} [min]
+ * @property {number[]} [max]
+ * @property {string[]} [nucleus]
+ */
+/**
+ *
+ * @typedef { object } Entry
+ * @property {Spectrum[]} spectra
+ * @property {Ntuples} ntuples
+ * @property {object} meta
+ * @property {object} tmp
+ * @property {string} [title]
+ * @property {string} [dataType]
+ * @property {string} [dataClass]
+ * @property {boolean} [twoD]
+ */
+/**
+ *
+ * @typedef { object } ConvertResult
+ * @property { object[] | boolean } profiling
+ * @property { string[] } logs
+ * @property { object[] } entries
+ * @property { Entry[] } flatten
+ */
+/**
+ * Parse a jcamp.
+ *
+ * @param {string|ArrayBuffer|Uint8Array} jcamp
+ * @param {ConvertOptions} [options]
+ * @returns {ConvertResult}
+ */
+export function convert(jcamp: string | ArrayBuffer | Uint8Array, options?: ConvertOptions | undefined): ConvertResult;
+export type ConvertOptions = {
+    /**
+     * - By default we don't keep meta information.
+     */
+    keepRecordsRegExp?: RegExp | undefined;
+    /**
+     * - Canonize the Labels (uppercase without symbol).
+     */
+    canonicDataLabels?: boolean | undefined;
+    /**
+     * - Canonize the metadata Labels (uppercase without symbol).
+     */
+    canonicMetadataLabels?: boolean | undefined;
+    /**
+     * - Convert numbers to Number.
+     */
+    dynamicTyping?: boolean | undefined;
+    /**
+     * - Remove the XY data.
+     */
+    withoutXY?: boolean | undefined;
+    /**
+     * - Special post-processing for GC / HPLC / MS.
+     */
+    chromatogram?: boolean | undefined;
+    /**
+     * - Force to keep the spectra in case of 2D.
+     */
+    keepSpectra?: boolean | undefined;
+    /**
+     * - Don't calculate countour in case of 2D.
+     */
+    noContour?: boolean | undefined;
+    /**
+     * - Number of positive / negative contour levels to calculate.
+     */
+    nbContourLevels?: number | undefined;
+    /**
+     * - Define for 2D the level as 5 times the median as default.
+     */
+    noiseMultiplier?: number | undefined;
+    /**
+     * - Add profiling information.
+     */
+    profiling?: boolean | undefined;
+};
+export type Ntuples = {
+    varname?: string[] | undefined;
+    symbol?: string[] | undefined;
+    vartype?: string[] | undefined;
+    varform?: string[] | undefined;
+    vardim?: number[] | undefined;
+    units?: string[] | undefined;
+    factor?: number[] | undefined;
+    first?: number[] | undefined;
+    last?: number[] | undefined;
+    min?: number[] | undefined;
+    max?: number[] | undefined;
+    nucleus?: string[] | undefined;
+};
+export type Entry = {
+    spectra: Spectrum[];
+    ntuples: Ntuples;
+    meta: object;
+    tmp: object;
+    title?: string | undefined;
+    dataType?: string | undefined;
+    dataClass?: string | undefined;
+    twoD?: boolean | undefined;
+};
+export type ConvertResult = {
+    profiling: object[] | boolean;
+    logs: string[];
+    entries: object[];
+    flatten: Entry[];
+};
+declare class Spectrum {
+}
+export {};
+//# sourceMappingURL=convert.d.ts.map

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

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