nmr-processing 9.5.0 → 9.5.1-pre.1685396168

package/lib-esm/datum/data1d/filter1d/apodization.js

@@ -0,0 +1,68 @@
+import { apodization } from '../../../apodization/apodization';
+export const id = 'apodization';
+export const name = 'Apodization';
+export const DOMAIN_UPDATE_RULES = {
+    updateXDomain: true,
+    updateYDomain: false,
+};
+export function apply(datum1D, options) {
+    if (!isApplicable(datum1D)) {
+        throw new Error('apodization not applicable on this data');
+    }
+    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/datum/data1d/filter1d/apodization.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data1d/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/datum/data1d/filter1d/baselineCorrection.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data1d/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/datum/data1d/filter1d/digitalFilter.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data1d/filter1d/equallySpaced.js

@@ -0,0 +1,49 @@
+import { xEnsureFloat64, 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 = xEnsureFloat64(XREdata.x);
+    spectrum.data.re = xEnsureFloat64(XREdata.y);
+    if (im) {
+        const XIMdata = xyEquallySpaced({ x, y: re }, { from, to, numberOfPoints, exclusions });
+        spectrum.data.im = xEnsureFloat64(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/datum/data1d/filter1d/equallySpaced.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data1d/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/datum/data1d/filter1d/exclusionZones.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data1d/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/datum/data1d/filter1d/fft.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data1d/filter1d/phaseCorrection.js

@@ -0,0 +1,78 @@
+import { reimAbsolute, reimAutoPhaseCorrection, reimPhaseCorrection, xEnsureFloat64, } 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;
+    const { re, im } = spectrum.data;
+    const phased = reimPhaseCorrection({ re, im }, (ph0 * Math.PI) / 180, (ph1 * Math.PI) / 180, { reverse: true });
+    spectrum.data = {
+        ...spectrum.data,
+        ...{
+            re: xEnsureFloat64(phased.re),
+            im: xEnsureFloat64(phased.im),
+        },
+    };
+}
+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/datum/data1d/filter1d/phaseCorrection.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data1d/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

package/lib-esm/datum/data1d/filter1d/shiftX.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data1d/filter1d/signalProcessing.js

@@ -0,0 +1,58 @@
+import * as Filters from 'ml-signal-processing';
+export const id = 'signalProcessing';
+export const name = 'Signal processing';
+export const DOMAIN_UPDATE_RULES = {
+    updateXDomain: true,
+    updateYDomain: true,
+};
+export function apply(spectrum, options) {
+    if (!isApplicable(spectrum)) {
+        throw new Error('Signal Processing is not applicable on this data');
+    }
+    spectrum.data = filterXY(spectrum, options);
+}
+export function isApplicable(spectrum) {
+    if (spectrum.info.isFt)
+        return true;
+    return false;
+}
+export function reduce(previousValue, newValue) {
+    return {
+        once: true,
+        reduce: newValue,
+    };
+}
+export function filterXY(spectrum, options) {
+    var _a;
+    let x = spectrum.data.x.slice(0);
+    let cloneX = spectrum.data.x.slice(0);
+    let re = spectrum.data.re.slice(0);
+    let im = (_a = spectrum.data.im) === null || _a === void 0 ? void 0 : _a.slice(0);
+    const filters = options.filters.slice();
+    const { range: { from, to }, numberOfPoints, exclusionsZones: exclusions, } = options;
+    filters.push({
+        name: 'equallySpaced',
+        options: { from, to, numberOfPoints, exclusions },
+        properties: {},
+    });
+    for (const filter of filters) {
+        // eslint-disable-next-line import/namespace
+        const filterFunction = Filters[filter.name];
+        if (!filterFunction) {
+            throw new Error(`Unknown filter: ${filter.name}`);
+        }
+        const filterOptions = (filter === null || filter === void 0 ? void 0 : filter.options) || {};
+        // @ts-expect-error some method have options and some other ones don't have any options
+        const realResult = filterFunction({ x, y: re }, filterOptions);
+        x = realResult.data.x;
+        re = realResult.data.y;
+        if (im) {
+            const imaginaryResult = filterFunction({ x: cloneX, y: im }, 
+            // @ts-expect-error some method have options and some other ones don't have any options
+            filterOptions);
+            im = imaginaryResult.data.y;
+        }
+    }
+    return { x, re, im };
+}
+//# sourceMappingURL=signalProcessing.js.map

package/lib-esm/datum/data1d/filter1d/signalProcessing.js.map

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package/lib-esm/datum/data1d/filter1d/utils/padDataToNextPowerOfTwo.js

@@ -0,0 +1,37 @@
+import { xSequentialFill } from 'ml-spectra-processing';
+export function padDataToNextPowerOfTwo(datum1D, digitalFilterApplied) {
+    const { x, re, im } = datum1D.data;
+    const size = nextPowerOfTwo(x.length);
+    let newRE = new Float64Array(size);
+    let newIM = new Float64Array(size);
+    const pointsToShift = getPointsToShift(datum1D);
+    newRE.set(re.slice(0, size - pointsToShift));
+    newIM.set(im.slice(0, size - pointsToShift));
+    if (pointsToShift > 0 && digitalFilterApplied) {
+        newRE.set(re.slice(re.length - pointsToShift), size - pointsToShift);
+        newIM.set(im.slice(re.length - pointsToShift), size - pointsToShift);
+    }
+    const newX = xSequentialFill({
+        from: x[0],
+        size,
+        step: x[1] - x[0],
+    });
+    datum1D.data = { ...datum1D.data, re: newRE, im: newIM, x: newX };
+}
+function getPointsToShift(datum1D) {
+    var _a;
+    let grpdly = ((_a = datum1D.info) === null || _a === void 0 ? void 0 : _a.digitalFilter) || 0;
+    return grpdly > 0 ? Math.floor(grpdly) : 0;
+}
+function nextPowerOfTwo(n) {
+    if (n === 0)
+        return 1;
+    n--;
+    n |= n >> 1;
+    n |= n >> 2;
+    n |= n >> 4;
+    n |= n >> 8;
+    n |= n >> 16;
+    return n + 1;
+}
+//# sourceMappingURL=padDataToNextPowerOfTwo.js.map

package/lib-esm/datum/data1d/filter1d/utils/padDataToNextPowerOfTwo.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data1d/filter1d/zeroFilling.js

@@ -0,0 +1,62 @@
+export const id = 'zeroFilling';
+export const name = 'Zero Filling';
+export const DOMAIN_UPDATE_RULES = {
+    updateXDomain: true,
+    updateYDomain: false,
+};
+export function apply(datum1D, options) {
+    var _a;
+    if (!isApplicable(datum1D)) {
+        throw new Error('zeroFilling not applicable on this data');
+    }
+    let { nbPoints, factor = 2 } = options;
+    if (!nbPoints) {
+        nbPoints = 2 ** Math.round(Math.log2(datum1D.data.x.length * factor));
+        const filter = datum1D.filters.find((filter) => filter.name === id);
+        if (filter) {
+            filter.value = { nbPoints };
+        }
+    }
+    let digitalFilterApplied = datum1D.filters.some((e) => e.name === 'digitalFilter' && e.flag);
+    let grpdly = ((_a = datum1D.info) === null || _a === void 0 ? void 0 : _a.digitalFilter) || 0;
+    let pointsToShift;
+    if (grpdly > 0 && digitalFilterApplied) {
+        pointsToShift = Math.floor(grpdly);
+    }
+    else {
+        pointsToShift = 0;
+    }
+    const { re, im, x } = datum1D.data;
+    let newRE = new Float64Array(nbPoints);
+    let newIM = new Float64Array(nbPoints);
+    let newX = new Float64Array(nbPoints);
+    const length = Math.min(nbPoints, re.length);
+    newRE.set(re.slice(0, length - pointsToShift));
+    newIM.set(im.slice(0, length - pointsToShift));
+    newX.set(x.slice(0, length - pointsToShift));
+    let diff = x[1] - x[0];
+    let currentX = x[length - pointsToShift - 1];
+    for (let i = length - pointsToShift; i < nbPoints; i++) {
+        currentX += diff;
+        newX[i] = currentX;
+    }
+    if (pointsToShift > 0 && pointsToShift < nbPoints) {
+        newRE.set(re.slice(re.length - pointsToShift), nbPoints - pointsToShift);
+        newIM.set(im.slice(re.length - pointsToShift), nbPoints - pointsToShift);
+    }
+    datum1D.data = { ...datum1D.data, re: newRE, im: newIM, x: newX };
+}
+export function isApplicable(datum1D) {
+    if (datum1D.info.isComplex && datum1D.info.isFid) {
+        return true;
+    }
+    return false;
+}
+export function reduce(_previousValue, newValue) {
+    delete newValue.factor;
+    return {
+        once: true,
+        reduce: newValue,
+    };
+}
+//# sourceMappingURL=zeroFilling.js.map