nmr-processing 9.5.0 → 9.5.1-pre.1684857934

package/lib-esm/filters/ExclusionZone.js.map

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

package/lib-esm/filters/Filters.js

@@ -0,0 +1,21 @@
+import * as apodization from './filter1d/apodization';
+import * as baselineCorrection from './filter1d/baselineCorrection';
+import * as digitalFilter from './filter1d/digitalFilter';
+import * as fft from './filter1d/fft';
+import * as phaseCorrection from './filter1d/phaseCorrection';
+import * as shiftX from './filter1d/shiftX';
+import * as zeroFilling from './filter1d/zeroFilling';
+import * as shift2DX from './filter2d/shiftX';
+import * as shift2DY from './filter2d/shiftY';
+export const filters = {
+    apodization,
+    baselineCorrection,
+    digitalFilter,
+    fft,
+    phaseCorrection,
+    shiftX,
+    zeroFilling,
+    shift2DX,
+    shift2DY,
+};
+//# sourceMappingURL=Filters.js.map

package/lib-esm/filters/Filters.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"Filters.js","sourceRoot":"","sources":["../../src/filters/Filters.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,WAAW,MAAM,wBAAwB,CAAC;AACtD,OAAO,KAAK,kBAAkB,MAAM,+BAA+B,CAAC;AACpE,OAAO,KAAK,aAAa,MAAM,0BAA0B,CAAC;AAC1D,OAAO,KAAK,GAAG,MAAM,gBAAgB,CAAC;AACtC,OAAO,KAAK,eAAe,MAAM,4BAA4B,CAAC;AAC9D,OAAO,KAAK,MAAM,MAAM,mBAAmB,CAAC;AAC5C,OAAO,KAAK,WAAW,MAAM,wBAAwB,CAAC;AACtD,OAAO,KAAK,QAAQ,MAAM,mBAAmB,CAAC;AAC9C,OAAO,KAAK,QAAQ,MAAM,mBAAmB,CAAC;AAE9C,MAAM,CAAC,MAAM,OAAO,GAGhB;IACF,WAAW;IACX,kBAAkB;IAClB,aAAa;IACb,GAAG;IACH,eAAe;IACf,MAAM;IACN,WAAW;IACX,QAAQ;IACR,QAAQ;CACT,CAAC"}

package/lib-esm/filters/FiltersManager.js

@@ -0,0 +1,124 @@
+import { v4 } from '@lukeed/uuid';
+import { cloneData1D } from '../utilities/cloneData1D';
+import { cloneData2D } from '../utilities/cloneData2D';
+import { filters as Filters } from './Filters';
+function resetDataToOrigin(datum) {
+    datum.data =
+        datum.info.dimension === 1
+            ? cloneData1D(datum.originalData)
+            : cloneData2D(datum.originalData);
+    datum.info = { ...datum.originalInfo };
+}
+/***
+ * @param {object} Filters [{name:'',options:{}},{...}]
+ */
+function applyFilter(datum, filters = [], forceReapply = false) {
+    let isReduced = false;
+    for (let filter of filters) {
+        const filterOption = {
+            name: filter.name,
+            label: Filters[filter.name].name,
+            value: filter.options,
+        };
+        const previousFilter = lookupForFilter(datum, filter.name);
+        if (previousFilter) {
+            const reduceResult = Filters[filter.name].reduce(previousFilter.value, filterOption.value);
+            if (reduceResult.once) {
+                if (!isReduced) {
+                    isReduced = true;
+                }
+                if (reduceResult.reduce != null && reduceResult.reduce !== undefined) {
+                    replaceFilter(datum, previousFilter.id, reduceResult.reduce);
+                }
+            }
+            else {
+                addFilter(datum, filterOption, Object.prototype.hasOwnProperty.call(filter, 'isDeleteAllow')
+                    ? filter.isDeleteAllow
+                    : true);
+            }
+        }
+        else {
+            addFilter(datum, filterOption, Object.prototype.hasOwnProperty.call(filter, 'isDeleteAllow')
+                ? filter.isDeleteAllow
+                : true);
+        }
+    }
+    if (forceReapply) {
+        reapplyFilters(datum);
+    }
+    else if (isReduced) {
+        if (filters.length === 1 && isLastFilter(datum, filters[0].name)) {
+            Filters[filters[0].name].apply(datum, filters[0].options);
+        }
+        else {
+            reapplyFilters(datum);
+        }
+    }
+    else {
+        for (let filter of filters) {
+            Filters[filter.name].apply(datum, filter.options);
+        }
+    }
+}
+function isLastFilter(datum, id) {
+    const index = datum.filters.findIndex((f) => f.name === id);
+    if (datum.filters.length === index + 1) {
+        return true;
+    }
+    return false;
+}
+function lookupForFilter(datum, filterName) {
+    return datum.filters.find((f) => f.name === filterName);
+}
+function reapplyFilters(datum, filters = null) {
+    const _filters = filters || datum.filters;
+    enableFilter(datum, null, null, _filters);
+}
+// id filter id
+function enableFilter(datum, id, checked, filters = null) {
+    datum.filters = datum.filters.slice(0);
+    if (id) {
+        datum.filters = datum.filters.map((filter) => {
+            return { ...filter, flag: filter.id === id ? checked : filter.flag };
+        });
+    }
+    resetDataToOrigin(datum);
+    const _filters = filters || datum.filters;
+    for (let filterIndex = 0; filterIndex < _filters.length; filterIndex++) {
+        const filter = datum.filters[filterIndex];
+        datum.filters[filterIndex] = {
+            ...datum.filters[filterIndex],
+        };
+        if (filter.flag) {
+            try {
+                Filters[filter.name].apply(datum, filter.value);
+            }
+            catch (error) {
+                datum.filters[filterIndex] = {
+                    ...datum.filters[filterIndex],
+                    error: error.message,
+                };
+            }
+        }
+    }
+}
+function addFilter(datum, filter, isDeleteAllow = true) {
+    const id = v4();
+    datum.filters = datum.filters.slice(0);
+    datum.filters.push({
+        ...filter,
+        id,
+        flag: true,
+        isDeleteAllow,
+    });
+}
+function replaceFilter(datum, filterID, value) {
+    // datum.filters = datum.filters.slice(0);
+    const index = datum.filters.findIndex((f) => f.id === filterID);
+    datum.filters[index] = {
+        ...datum.filters[index],
+        value,
+    };
+}
+export { applyFilter, reapplyFilters, enableFilter, addFilter };
+//# sourceMappingURL=FiltersManager.js.map

package/lib-esm/filters/FiltersManager.js.map

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

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=MatrixFilter.js.map

package/lib-esm/filters/MatrixFilter.js.map

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

package/lib-esm/filters/MatrixOptions.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=MatrixOptions.js.map

package/lib-esm/filters/MatrixOptions.js.map

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

package/lib-esm/filters/filter1d/apodization.js

@@ -0,0 +1,70 @@
+import { apodization } from '../../apodization/apodization';
+export const id = 'apodization';
+export const name = 'Apodization';
+export const DOMAIN_UPDATE_RULES = {
+    updateXDomain: true,
+    updateYDomain: false,
+};
+export const defaultApodizationOptions = {
+    lineBroadening: 1,
+    gaussBroadening: 0,
+    lineBroadeningCenter: 0,
+};
+export function apply(datum1D, options) {
+    const newData = apodizationFilter(datum1D, options);
+    datum1D.data = {
+        ...datum1D.data,
+        re: newData.re,
+        im: newData.im,
+    };
+}
+export function isApplicable(datum1D) {
+    if (datum1D.info.isComplex && datum1D.info.isFid)
+        return true;
+    return false;
+}
+export function reduce(previousValue, newValue) {
+    return {
+        once: true,
+        reduce: newValue,
+    };
+}
+export function apodizationFilter(datum1D, options) {
+    var _a;
+    const { lineBroadening, gaussBroadening, lineBroadeningCenter } = options;
+    let grpdly = ((_a = datum1D.info) === null || _a === void 0 ? void 0 : _a.digitalFilter) || 0;
+    let pointsToShift;
+    if (grpdly > 0) {
+        pointsToShift = Math.floor(grpdly);
+    }
+    else {
+        pointsToShift = 0;
+    }
+    const re = datum1D.data.re;
+    const im = datum1D.data.im;
+    const t = datum1D.data.x;
+    const length = re.length;
+    const dw = (t[length - 1] - t[0]) / (length - 1); //REPLACE CONSTANT with calculated value... : for this we need AQ or DW to set it right...
+    return apodization({ re, im }, {
+        pointsToShift,
+        compose: {
+            length,
+            shapes: [
+                {
+                    start: 0,
+                    shape: {
+                        kind: 'lorentzToGauss',
+                        options: {
+                            length,
+                            dw,
+                            exponentialHz: gaussBroadening > 0 ? lineBroadening : -lineBroadening,
+                            gaussianHz: gaussBroadening,
+                            center: lineBroadeningCenter,
+                        },
+                    },
+                },
+            ],
+        },
+    });
+}
+//# sourceMappingURL=apodization.js.map

package/lib-esm/filters/filter1d/apodization.js.map

@@ -0,0 +1 @@
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package/lib-esm/filters/filter1d/baselineCorrection.js

@@ -0,0 +1,52 @@
+import airPLS from 'ml-airpls';
+import baselineRegression from 'ml-baseline-correction-regression';
+import { xyEquallySpaced } from 'ml-spectra-processing';
+export const id = 'baselineCorrection';
+export const name = 'Baseline correction';
+export const DOMAIN_UPDATE_RULES = {
+    updateXDomain: false,
+    updateYDomain: true,
+};
+export function apply(datum1D, options) {
+    if (!isApplicable(datum1D)) {
+        throw new Error('baselineCorrection not applicable on this data');
+    }
+    const { algorithm } = options;
+    let { x, re } = datum1D.data;
+    let corrected;
+    switch (algorithm) {
+        case 'airpls':
+            corrected = airPLS(x, re, options).corrected;
+            break;
+        case 'polynomial':
+            {
+                const { degree, zones } = options;
+                let reduced = xyEquallySpaced({ x, y: re }, { numberOfPoints: 4096, zones });
+                let result = baselineRegression(reduced.x, reduced.y, {
+                    regressionOptions: degree,
+                });
+                let { regression } = result;
+                corrected = new Float64Array(x.length);
+                for (let i = 0; i < re.length; i++) {
+                    corrected[i] = re[i] - regression.predict(x[i]);
+                }
+            }
+            break;
+        default:
+            // eslint-disable-next-line @typescript-eslint/restrict-template-expressions
+            throw new Error(`baselineCorrection: algorithm unknown: ${algorithm}`);
+    }
+    Object.assign(datum1D.data, { re: corrected });
+}
+export function isApplicable(datum1D) {
+    if (!datum1D.info.isFid)
+        return true;
+    return false;
+}
+export function reduce(previousValue, newValue) {
+    return {
+        once: true,
+        reduce: newValue,
+    };
+}
+//# sourceMappingURL=baselineCorrection.js.map

package/lib-esm/filters/filter1d/baselineCorrection.js.map

@@ -0,0 +1 @@
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package/lib-esm/filters/filter1d/digitalFilter.js

@@ -0,0 +1,41 @@
+export const id = 'digitalFilter';
+export const name = 'Digital Filter';
+export const DOMAIN_UPDATE_RULES = {
+    updateXDomain: true,
+    updateYDomain: true,
+};
+/**
+ * Move points from the beginning to the end of FID and performs a first order phase correction
+ * @param {Datum1d} datum1d
+ */
+export function apply(datum1D, options = {}) {
+    if (!isApplicable(datum1D)) {
+        throw new Error('Digital Filter is not applicable on this data');
+    }
+    let { digitalFilterValue = 0 } = options;
+    let re = new Float64Array(datum1D.data.re);
+    let im = new Float64Array(datum1D.data.im);
+    let pointsToShift = Math.floor(digitalFilterValue);
+    const skip = 0;
+    pointsToShift += 0;
+    const newRe = new Float64Array(re.length);
+    const newIm = new Float64Array(im.length);
+    newRe.set(re.slice(pointsToShift));
+    newRe.set(re.slice(skip, pointsToShift), re.length - pointsToShift);
+    newIm.set(im.slice(pointsToShift));
+    newIm.set(im.slice(skip, pointsToShift), im.length - pointsToShift);
+    datum1D.data.re = newRe;
+    datum1D.data.im = newIm;
+}
+export function isApplicable(datum1D) {
+    if (datum1D.info.isComplex && datum1D.info.isFid)
+        return true;
+    return false;
+}
+export function reduce() {
+    return {
+        once: true,
+        reduce: undefined,
+    };
+}
+//# sourceMappingURL=digitalFilter.js.map

package/lib-esm/filters/filter1d/digitalFilter.js.map

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package/lib-esm/filters/filter1d/equallySpaced.js

@@ -0,0 +1,49 @@
+import { xyEquallySpaced } from 'ml-spectra-processing';
+export const id = 'equallySpaced';
+export const name = 'Equally spaced';
+/**
+ * Equally Spaced
+ * **
+ * Function that returns a Number array of equally spaced numberOfPoints
+ * containing a representation of intensities of the spectra arguments x
+ * and y.
+ *
+ * The options parameter contains an object in the following form:
+ * from: starting point
+ * to: last point
+ * numberOfPoints: number of points between from and to
+ * variant: "slot" or "smooth" - smooth is the default option
+ *
+ * The slot variant consist that each point in the new array is calculated
+ * averaging the existing points between the slot that belongs to the current
+ * value. The smooth variant is the same but takes the integral of the range
+ * of the slot and divide by the step size between two points in the new array.
+ *
+ * @param {Array<{from:number;to:number}>} options.exclusions
+ */
+export function apply(spectrum, options = {}) {
+    if (!isApplicable(spectrum)) {
+        throw new Error('Equally Spaced is not applicable on this data');
+    }
+    const { from, to, numberOfPoints, exclusions } = options;
+    const { x, re, im } = spectrum.data;
+    const XREdata = xyEquallySpaced({ x, y: re }, { from, to, numberOfPoints, exclusions });
+    spectrum.data.x = XREdata.x;
+    spectrum.data.re = XREdata.y;
+    if (im) {
+        const XIMdata = xyEquallySpaced({ x, y: re }, { from, to, numberOfPoints, exclusions });
+        spectrum.data.im = XIMdata.y;
+    }
+}
+export function isApplicable(spectrum) {
+    if (spectrum.info.isComplex && !spectrum.info.isFid)
+        return true;
+    return false;
+}
+export function reduce() {
+    return {
+        once: false,
+        reduce: null,
+    };
+}
+//# sourceMappingURL=equallySpaced.js.map

package/lib-esm/filters/filter1d/equallySpaced.js.map

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package/lib-esm/filters/filter1d/exclusionZones.js

@@ -0,0 +1,29 @@
+import { xySetYValue, zonesNormalize } from 'ml-spectra-processing';
+export const id = 'exclusionZones';
+export const name = 'Exclusion zones';
+export const DOMAIN_UPDATE_RULES = {
+    updateXDomain: false,
+    updateYDomain: false,
+};
+export function apply(spectrum, zones = []) {
+    if (!isApplicable(spectrum)) {
+        throw new Error('Exclusion Zones filter not applicable on this data');
+    }
+    const { x, re, im } = spectrum.data;
+    spectrum.data.re = Float64Array.from(xySetYValue({ x, y: re }, { zones }).y);
+    spectrum.data.im = im
+        ? Float64Array.from(xySetYValue({ x, y: re }, { zones }).y)
+        : im;
+}
+export function isApplicable(spectrum) {
+    if (spectrum.info.isFt)
+        return true;
+    return false;
+}
+export function reduce(previousValue, newValue) {
+    return {
+        once: true,
+        reduce: zonesNormalize(previousValue.concat(newValue)),
+    };
+}
+//# sourceMappingURL=exclusionZones.js.map

package/lib-esm/filters/filter1d/exclusionZones.js.map

@@ -0,0 +1 @@
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package/lib-esm/filters/filter1d/fft.js

@@ -0,0 +1,88 @@
+import { reimFFT, reimPhaseCorrection, xMean, } from 'ml-spectra-processing';
+import { padDataToNextPowerOfTwo } from './utils/padDataToNextPowerOfTwo';
+export const id = 'fft';
+export const name = 'FFT';
+export const DOMAIN_UPDATE_RULES = {
+    updateXDomain: true,
+    updateYDomain: true,
+};
+export function apply(datum1D) {
+    if (!isApplicable(datum1D)) {
+        throw new Error('fft not applicable on this data');
+    }
+    checkSameLength(datum1D);
+    let digitalFilterApplied = datum1D.filters.some((e) => e.name === 'digitalFilter' && e.flag);
+    const { info: { aqMod }, } = datum1D;
+    if (aqMod === 1) {
+        removeDCOffset(datum1D, digitalFilterApplied);
+    }
+    if (!isPowerOfTwo(datum1D.data.x.length)) {
+        padDataToNextPowerOfTwo(datum1D, digitalFilterApplied);
+    }
+    const { data, info } = datum1D;
+    Object.assign(data, reimFFT({
+        re: data.re,
+        im: data.im,
+    }, { applyZeroShift: true }));
+    if (digitalFilterApplied) {
+        let { digitalFilter = 0 } = info;
+        let ph1 = (digitalFilter - Math.floor(digitalFilter)) * Math.PI * 2;
+        Object.assign(data, reimPhaseCorrection(data, 0, -ph1, { reverse: true }));
+    }
+    datum1D.data.x = generateXAxis(datum1D);
+    datum1D.info = { ...datum1D.info, isFid: false, isFt: true };
+}
+export function isApplicable(datum1D) {
+    if (datum1D.info.isComplex && datum1D.info.isFid)
+        return true;
+    return false;
+}
+export function reduce() {
+    return {
+        once: true,
+        reduce: undefined,
+    };
+}
+function generateXAxis(datum1D) {
+    const info = datum1D.info;
+    const baseFrequency = Number.parseFloat(info.baseFrequency);
+    const frequencyOffset = Number.parseFloat(info.frequencyOffset);
+    const spectralWidth = Number.parseFloat(info.spectralWidth);
+    const offset = frequencyOffset / baseFrequency;
+    let spectralHalfWidth = 0.5 * spectralWidth;
+    let nbPoints = datum1D.data.x.length;
+    let firstPoint = offset - spectralHalfWidth;
+    let dx = spectralWidth / (nbPoints - 1);
+    const xAxis = new Float64Array(nbPoints);
+    for (let i = 0; i < nbPoints; i++) {
+        xAxis[i] = firstPoint;
+        firstPoint += dx;
+    }
+    return xAxis;
+}
+function isPowerOfTwo(n) {
+    return n !== 0 && (n & (n - 1)) === 0;
+}
+function removeDCOffset(spectrum, digitalFilterApplied) {
+    let { digitalFilter = 0 } = digitalFilterApplied ? spectrum.info : {};
+    const data = spectrum.data;
+    const nbPoints = data.re.length;
+    const newRe = new Float64Array(data.re);
+    const newIm = new Float64Array(data.im);
+    const averageRe = xMean(data.re.slice((nbPoints * 0.75) >> 0, nbPoints - digitalFilter));
+    const averageIm = xMean(data.im.slice((nbPoints * 0.75) >> 0, nbPoints - digitalFilter));
+    for (let i = digitalFilterApplied ? 0 : digitalFilter; i < nbPoints - digitalFilter; i++) {
+        newRe[i] -= averageRe;
+        newIm[i] -= averageIm;
+    }
+    Object.assign(spectrum.data, { re: newRe, im: newIm });
+    return spectrum;
+}
+function checkSameLength(spectrum) {
+    var _a;
+    const { data } = spectrum;
+    if (data.x.length !== data.re.length || data.x.length !== ((_a = data.im) === null || _a === void 0 ? void 0 : _a.length)) {
+        throw new Error('The length of data should be equal');
+    }
+}
+//# sourceMappingURL=fft.js.map

package/lib-esm/filters/filter1d/fft.js.map

@@ -0,0 +1 @@
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package/lib-esm/filters/filter1d/phaseCorrection.js

@@ -0,0 +1,75 @@
+import { reimAbsolute, reimAutoPhaseCorrection, reimPhaseCorrection, } from 'ml-spectra-processing';
+export const id = 'phaseCorrection';
+export const name = 'Phase correction';
+export const DOMAIN_UPDATE_RULES = {
+    updateXDomain: false,
+    updateYDomain: false,
+};
+/**
+ *
+ * @param {Datum1d} datum1d
+ * @param {Object} [options={}]
+ * @param {number} [options.ph0=0]
+ * @param {number} [options.ph1=0]
+ */
+export function apply(datum1D, options = {}) {
+    var _a;
+    if (!isApplicable(datum1D)) {
+        throw new Error('phaseCorrection not applicable on this data');
+    }
+    const { absolute = false } = options;
+    const filter = (_a = datum1D.filters) === null || _a === void 0 ? void 0 : _a.find((filter) => filter.name === id);
+    if (absolute) {
+        const { re, im } = datum1D.data;
+        datum1D.data.re = reimAbsolute({ re, im });
+        datum1D.data.im = new Float64Array(0);
+        if (filter) {
+            filter.value = { ...filter.value, ph0: 0, ph1: 0, absolute };
+        }
+    }
+    else if ('ph0' in options && 'ph1' in options) {
+        let { ph0, ph1 } = options;
+        phaseCorrection(datum1D, { ph0, ph1 });
+        if (filter) {
+            filter.value = { ...filter.value, absolute };
+        }
+    }
+    else {
+        let { ph0, ph1 } = autoPhaseCorrection(datum1D);
+        phaseCorrection(datum1D, { ph0, ph1 });
+        if (filter) {
+            filter.value = { ...filter.value, absolute, ph0, ph1 };
+        }
+    }
+}
+function phaseCorrection(spectrum, phaseValues) {
+    let { ph0, ph1 } = phaseValues;
+    ph0 *= Math.PI / 180;
+    ph1 *= Math.PI / 180;
+    spectrum.data = {
+        ...spectrum.data,
+        ...reimPhaseCorrection(spectrum.data, ph0, ph1, { reverse: true }),
+    };
+}
+function autoPhaseCorrection(spectrum, options = {}) {
+    const { minRegSize = 5, maxDistanceToJoin = 128, magnitudeMode = true, factorNoise = 5, reverse = true, } = options;
+    return reimAutoPhaseCorrection(spectrum.data, {
+        minRegSize,
+        maxDistanceToJoin,
+        magnitudeMode,
+        factorNoise,
+        reverse,
+    });
+}
+export function isApplicable(spectrum) {
+    if (spectrum.info.isComplex && !spectrum.info.isFid)
+        return true;
+    return false;
+}
+export function reduce(previousValue, newValue) {
+    return {
+        once: true,
+        reduce: newValue,
+    };
+}
+//# sourceMappingURL=phaseCorrection.js.map

package/lib-esm/filters/filter1d/phaseCorrection.js.map

@@ -0,0 +1 @@
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package/lib-esm/filters/filter1d/shiftX.js

@@ -0,0 +1,24 @@
+/**
+ *
+ * @param {Object} datum1d
+ * @param {number} [shiftValue=0]
+ */
+export const id = 'shiftX';
+export const name = 'Shift X';
+export const DOMAIN_UPDATE_RULES = {
+    updateXDomain: true,
+    updateYDomain: false,
+};
+export function apply(datum1D, shiftValue = 0) {
+    datum1D.data.x = datum1D.data.x.map((val) => val + shiftValue);
+}
+export function isApplicable() {
+    return true;
+}
+export function reduce(previousValue, newValue) {
+    return {
+        once: true,
+        reduce: previousValue + newValue,
+    };
+}
+//# sourceMappingURL=shiftX.js.map