nmr-processing 9.5.1 → 9.5.2-pre.1685982544

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

@@ -0,0 +1,55 @@
+export const id = 'zeroFilling';
+export const name = 'Zero Filling';
+export const DOMAIN_UPDATE_RULES = {
+    updateXDomain: true,
+    updateYDomain: false,
+};
+export function apply(datum1D, options) {
+    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);
+    const grpdly = datum1D.info?.digitalFilter || 0;
+    const pointsToShift = digitalFilterApplied && grpdly > 0 ? Math.floor(grpdly) : 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

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

@@ -0,0 +1 @@
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package/lib-esm/datum/data1d/utils/RangeUtilities.js

@@ -0,0 +1,69 @@
+import { v4 as generateID } from '@lukeed/uuid';
+import omit from 'lodash/omit';
+import { DatumKind } from '../../../constants/SignalsKinds';
+export function getDiaIDs(range) {
+    return [].concat(range.diaIDs || [], range.signals
+        ? range.signals.flatMap((_signal) => _signal.diaIDs || [])
+        : []);
+}
+export function getNbAtoms(range, signalIndex) {
+    if (signalIndex === undefined) {
+        let sum = 0;
+        if (range.signals) {
+            for (const signal of range.signals) {
+                sum += signal.nbAtoms || 0;
+            }
+        }
+        return sum;
+    }
+    return range.signals[signalIndex].nbAtoms || 0;
+}
+export function setNbAtoms(range, signalIndex) {
+    range.nbAtoms = getNbAtoms(range, signalIndex);
+    if (range.nbAtoms === 0) {
+        delete range.nbAtoms;
+    }
+}
+export function resetDiaIDs(range) {
+    const deletedKeys = ['diaIDs', 'nbAtoms'];
+    range = omit(range, deletedKeys);
+    range.signals = range.signals.map((signal) => {
+        return omit(signal, deletedKeys);
+    });
+}
+export function unlink(range, options = {}) {
+    const { unlinkType = 'both', signalIndex = -1 } = options;
+    const keys = ['diaIDs', 'nbAtoms'];
+    switch (unlinkType) {
+        case 'both':
+            resetDiaIDs(range);
+            break;
+        case 'range':
+            range = omit(range, keys);
+            break;
+        case 'signal':
+            if (signalIndex !== -1) {
+                range.signals[signalIndex] = omit(range.signals[signalIndex], keys);
+            }
+            break;
+        default:
+            break;
+    }
+    return range;
+}
+export function addDefaultSignal(range) {
+    range.signals.push({
+        id: generateID(),
+        multiplicity: 'm',
+        kind: 'signal',
+        js: [],
+        delta: (range.to + range.from) / 2,
+    });
+}
+export function checkRangeKind(range) {
+    return range.kind === DatumKind.signal;
+}
+export function checkSignalKinds(range, kinds) {
+    return !range.signals.some((_signal) => _signal.kind === undefined || !kinds.includes(_signal.kind));
+}
+//# sourceMappingURL=RangeUtilities.js.map

package/lib-esm/datum/data1d/utils/RangeUtilities.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data1d/utils/checkIntegralKind.js

@@ -0,0 +1,10 @@
+import { SignalKindsToInclude } from '../../../constants/SignalsKinds';
+/**
+ * check whether integral based on its kind can be included in another operation or not
+ * @param integral  integral
+ * @returns {boolean}
+ */
+export function checkIntegralKind(integral) {
+    return SignalKindsToInclude.includes(integral.kind);
+}
+//# sourceMappingURL=checkIntegralKind.js.map

package/lib-esm/datum/data1d/utils/checkIntegralKind.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data1d/utils/checkRangeKind.js

@@ -0,0 +1,6 @@
+import { SignalKindsToInclude } from '../../../constants/SignalsKinds';
+import { checkSignalKinds } from './RangeUtilities';
+export function checkRangeKind(range) {
+    return range.signals && checkSignalKinds(range, SignalKindsToInclude);
+}
+//# sourceMappingURL=checkRangeKind.js.map

package/lib-esm/datum/data1d/utils/checkRangeKind.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data1d/utils/getShiftX.js

@@ -0,0 +1,7 @@
+import { Filters } from '../../Filters';
+export function getShiftX(spectrum) {
+    const filter = spectrum?.filters &&
+        spectrum?.filters.find((filter) => filter.name === Filters.shiftX.id);
+    return filter?.flag ? filter.value.shift : 0;
+}
+//# sourceMappingURL=getShiftX.js.map

package/lib-esm/datum/data1d/utils/getShiftX.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data1d/utils/getSpectrumErrorValue.js

@@ -0,0 +1,5 @@
+export function getSpectrumErrorValue(spectrum) {
+    const { x } = spectrum.data;
+    return (x[x.length - 1] - x[0]) / 10000;
+}
+//# sourceMappingURL=getSpectrumErrorValue.js.map

package/lib-esm/datum/data1d/utils/getSpectrumErrorValue.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data1d/utils/mapIntegrals.js

@@ -0,0 +1,37 @@
+import { v4 } from '@lukeed/uuid';
+import { xyIntegration } from 'ml-spectra-processing';
+import { getShiftX } from './getShiftX';
+function getRange(integral, shiftTarget, shift) {
+    const { originFrom, originTo, from, to } = integral;
+    if (shiftTarget === 'origin') {
+        return {
+            originFrom: from - shift,
+            originTo: to - shift,
+            from,
+            to,
+        };
+    }
+    else {
+        return {
+            originFrom,
+            originTo,
+            from: originFrom + shift,
+            to: originTo + shift,
+        };
+    }
+}
+export function mapIntegrals(integrals, spectrum, shiftTarget = 'origin') {
+    const { x, re } = spectrum.data;
+    const shiftX = getShiftX(spectrum);
+    return integrals.map((integral) => {
+        const integralBoundary = getRange(integral, shiftTarget, shiftX);
+        const absolute = xyIntegration({ x, y: re }, { from: integralBoundary.from, to: integralBoundary.to, reverse: true });
+        return {
+            ...integral,
+            id: integral.id || v4(),
+            ...integralBoundary,
+            absolute,
+        };
+    });
+}
+//# sourceMappingURL=mapIntegrals.js.map

package/lib-esm/datum/data1d/utils/mapIntegrals.js.map

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package/lib-esm/datum/data1d/utils/mapPeaks.js

@@ -0,0 +1,46 @@
+import { v4 } from '@lukeed/uuid';
+import { getShiftX } from './getShiftX';
+import { getSpectrumErrorValue } from './getSpectrumErrorValue';
+function isExists(peak, spectrum, error) {
+    // check if the Peak is already exists
+    for (const { x } of spectrum.peaks?.values || []) {
+        if (Math.abs(peak.x - x) < error) {
+            return true;
+        }
+    }
+    return false;
+}
+function getPeakDelta(peak, shiftTarget, shift) {
+    const { originalX = 0, x } = peak;
+    if (shiftTarget === 'origin') {
+        return {
+            originalX: x - shift,
+            x,
+        };
+    }
+    else {
+        return {
+            originalX,
+            x: originalX + shift,
+        };
+    }
+}
+export function mapPeaks(peaks, spectrum, options = {}) {
+    const { checkIsExisting = true, shiftTarget = 'origin' } = options;
+    const shiftX = getShiftX(spectrum);
+    const error = getSpectrumErrorValue(spectrum);
+    let newPeaks = [];
+    for (const peak of peaks) {
+        const peakDelta = getPeakDelta(peak, shiftTarget, shiftX);
+        if (!checkIsExisting ||
+            (checkIsExisting && !isExists(peak, spectrum, error))) {
+            newPeaks.push({
+                ...peak,
+                id: peak?.id || v4(),
+                ...peakDelta,
+            });
+        }
+    }
+    return newPeaks;
+}
+//# sourceMappingURL=mapPeaks.js.map

package/lib-esm/datum/data1d/utils/mapPeaks.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data1d/utils/mapRanges.js

@@ -0,0 +1,79 @@
+import { v4 } from '@lukeed/uuid';
+import { xyIntegration } from 'ml-spectra-processing';
+import { DatumKind } from '../../../constants/SignalsKinds';
+import { getShiftX } from './getShiftX';
+import { getSpectrumErrorValue } from './getSpectrumErrorValue';
+function checkRange(range, spectrum, error) {
+    // check if the range is already exists
+    for (const { from, to } of spectrum.ranges?.values || []) {
+        if (Math.abs(range.from - from) < error &&
+            Math.abs(range.to - to) < error) {
+            return true;
+        }
+    }
+}
+function getRange(range, shiftTarget, shift) {
+    const { originFrom, originTo, from, to } = range;
+    if (shiftTarget === 'origin') {
+        return {
+            originFrom: from - shift,
+            originTo: to - shift,
+            from,
+            to,
+        };
+    }
+    else {
+        return {
+            originFrom,
+            originTo,
+            from: (originFrom || 0) + shift,
+            to: (originTo || 0) + shift,
+        };
+    }
+}
+function getSignalDelta(signal, shiftTarget, shift) {
+    const { delta, originDelta } = signal;
+    if (shiftTarget === 'origin') {
+        return {
+            originDelta: delta - shift,
+            delta,
+        };
+    }
+    else {
+        return {
+            originDelta,
+            delta: (originDelta || 0) + shift,
+        };
+    }
+}
+export function mapRanges(ranges, spectrum, options = {}) {
+    const { checkIsExisting = true, shiftTarget = 'origin' } = options;
+    const { x, re } = spectrum.data;
+    const shiftX = getShiftX(spectrum);
+    const error = getSpectrumErrorValue(spectrum);
+    if (checkIsExisting) {
+        ranges = ranges.filter((r) => (checkIsExisting && !checkRange(r, spectrum, error)) || r.id === 'new');
+    }
+    return ranges.map((range) => {
+        const rangeBoundary = getRange(range, shiftTarget, shiftX);
+        const absolute = xyIntegration({ x, y: re }, { from: rangeBoundary.from, to: rangeBoundary.to, reverse: true });
+        const signals = range.signals.map((signal) => {
+            const { kind = null, id, ...resSignal } = signal;
+            return {
+                kind: kind || 'signal',
+                id: id || v4(),
+                ...resSignal,
+                ...getSignalDelta(signal, shiftTarget, shiftX),
+            };
+        });
+        return {
+            ...range,
+            id: range.id || v4(),
+            kind: signals?.[0].kind || DatumKind.signal,
+            ...rangeBoundary,
+            absolute,
+            signals,
+        };
+    });
+}
+//# sourceMappingURL=mapRanges.js.map

package/lib-esm/datum/data1d/utils/mapRanges.js.map

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package/lib-esm/datum/data1d/utils/mapValues.js

@@ -0,0 +1,11 @@
+export function mapValues(values, key, factor, check) {
+    return values.map((value) => {
+        return {
+            ...value,
+            ...(check(value) && {
+                [key]: value.absolute * factor,
+            }),
+        };
+    });
+}
+//# sourceMappingURL=mapValues.js.map

package/lib-esm/datum/data1d/utils/mapValues.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data1d/utils/updateIntegrals.js

@@ -0,0 +1,7 @@
+import { mapIntegrals } from './mapIntegrals';
+import { updateIntegralsRelativeValues } from './updateIntegralsRelativeValues';
+export function updateIntegrals(spectrum) {
+    spectrum.integrals.values = mapIntegrals(spectrum.integrals.values, spectrum, 'current');
+    updateIntegralsRelativeValues(spectrum, true);
+}
+//# sourceMappingURL=updateIntegrals.js.map

package/lib-esm/datum/data1d/utils/updateIntegrals.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data1d/utils/updateIntegralsRelativeValues.js

@@ -0,0 +1,22 @@
+import { getSum } from '../../../utilities/getSum';
+import { checkIntegralKind } from './checkIntegralKind';
+import { mapValues } from './mapValues';
+export function updateIntegralsRelativeValues(spectrum, forceCalculateIntegral = false) {
+    const { values, options } = spectrum.integrals;
+    const currentSum = getSum(values, 'absolute', checkIntegralKind);
+    let factor = 0;
+    if (options?.sum) {
+        if (options.isSumConstant || forceCalculateIntegral) {
+            factor = currentSum > 0 ? options.sum / currentSum : 0;
+        }
+        else if (values?.[0]) {
+            const item = values[0];
+            factor = (item.integral || options.sum) / item.absolute;
+        }
+    }
+    spectrum.integrals.values = mapValues(values, 'integral', factor, checkIntegralKind);
+    if (!options.isSumConstant && !forceCalculateIntegral) {
+        options.sum = getSum(values, 'integral', checkIntegralKind);
+    }
+}
+//# sourceMappingURL=updateIntegralsRelativeValues.js.map

package/lib-esm/datum/data1d/utils/updateIntegralsRelativeValues.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data1d/utils/updatePeaks.js

@@ -0,0 +1,8 @@
+import { mapPeaks } from './mapPeaks';
+export function updatePeaks(spectrum) {
+    spectrum.peaks.values = mapPeaks(spectrum.peaks.values, spectrum, {
+        checkIsExisting: false,
+        shiftTarget: 'current',
+    });
+}
+//# sourceMappingURL=updatePeaks.js.map

package/lib-esm/datum/data1d/utils/updatePeaks.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data1d/utils/updateRanges.js

@@ -0,0 +1,10 @@
+import { mapRanges } from './mapRanges';
+import { updateRangesRelativeValues } from './updateRangesRelativeValues';
+export function updateRanges(spectrum) {
+    spectrum.ranges.values = mapRanges(spectrum.ranges.values, spectrum, {
+        checkIsExisting: false,
+        shiftTarget: 'current',
+    });
+    updateRangesRelativeValues(spectrum, true);
+}
+//# sourceMappingURL=updateRanges.js.map

package/lib-esm/datum/data1d/utils/updateRanges.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data1d/utils/updateRangesRelativeValues.js

@@ -0,0 +1,22 @@
+import { getSum } from '../../../utilities/getSum';
+import { checkRangeKind } from './checkRangeKind';
+import { mapValues } from './mapValues';
+export function updateRangesRelativeValues(spectrum, forceCalculateIntegral = false) {
+    const { values, options } = spectrum.ranges;
+    const currentSum = getSum(values, 'absolute', checkRangeKind);
+    let factor = 0;
+    if (options?.sum) {
+        if (options.isSumConstant || forceCalculateIntegral) {
+            factor = currentSum > 0 ? options.sum / currentSum : 0;
+        }
+        else if (values?.[0]) {
+            const item = values[0];
+            factor = (item.integration || options.sum) / item.absolute;
+        }
+    }
+    spectrum.ranges.values = mapValues(values, 'integration', factor, checkRangeKind);
+    if (!options.isSumConstant && !forceCalculateIntegral) {
+        options.sum = getSum(values, 'integration', checkRangeKind);
+    }
+}
+//# sourceMappingURL=updateRangesRelativeValues.js.map

package/lib-esm/datum/data1d/utils/updateRangesRelativeValues.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data2d/Entry2D.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=Entry2D.js.map

package/lib-esm/datum/data2d/Entry2D.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"Entry2D.js","sourceRoot":"","sources":["../../../src/datum/data2d/Entry2D.ts"],"names":[],"mappings":""}

package/lib-esm/datum/data2d/filter2d/shiftX.js

@@ -0,0 +1,28 @@
+export const id = 'shift2DX';
+export const name = 'Shift 2D X';
+export const DOMAIN_UPDATE_RULES = {
+    updateXDomain: true,
+    updateYDomain: false,
+};
+/**
+ *
+ * @param {Object} datum2d
+ * @param {number} [shiftValue=0]
+ */
+export function apply(datum2D, shiftValue = 0) {
+    const data = { ...datum2D.data };
+    for (const key in data) {
+        data[key].minX += shiftValue;
+        data[key].maxX += 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/data2d/filter2d/shiftX.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data2d/filter2d/shiftY.js

@@ -0,0 +1,28 @@
+export const id = 'shift2DY';
+export const name = 'Shift 2D Y';
+export const DOMAIN_UPDATE_RULES = {
+    updateXDomain: false,
+    updateYDomain: true,
+};
+/**
+ *
+ * @param {Object} datum2d
+ * @param {number} [shiftValue=0]
+ */
+export function apply(datum2D, shiftValue = 0) {
+    const data = { ...datum2D.data };
+    for (const key in data) {
+        data[key].minY += shiftValue;
+        data[key].maxY += shiftValue;
+    }
+}
+export function isApplicable() {
+    return true;
+}
+export function reduce(previousValue, newValue) {
+    return {
+        once: true,
+        reduce: previousValue + newValue,
+    };
+}
+//# sourceMappingURL=shiftY.js.map

package/lib-esm/datum/data2d/filter2d/shiftY.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data2d/utils/get2DSpectrumErrorValue.js

@@ -0,0 +1,10 @@
+export function get2DSpectrumErrorValue(spectrum) {
+    const { data, info } = spectrum;
+    const { minX, maxX, minY, maxY } = info.isFid
+        ? data.re
+        : data.rr;
+    const x = Math.abs(maxX - minX) / 10000;
+    const y = Math.abs(maxY - minY) / 10000;
+    return { x, y };
+}
+//# sourceMappingURL=get2DSpectrumErrorValue.js.map

package/lib-esm/datum/data2d/utils/get2DSpectrumErrorValue.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data2d/utils/getShift.js

@@ -0,0 +1,16 @@
+import { Filters } from '../../Filters';
+export function getShift(spectrum) {
+    let shift = { x: 0, y: 0 };
+    if (spectrum?.filters) {
+        for (const filter of spectrum.filters) {
+            if (filter.name === Filters.shift2DX.id) {
+                shift.x = filter?.flag ? filter.value.shift : 0;
+            }
+            if (filter.name === Filters.shift2DY.id) {
+                shift.y = filter?.flag ? filter.value.shift : 0;
+            }
+        }
+    }
+    return shift;
+}
+//# sourceMappingURL=getShift.js.map

package/lib-esm/datum/data2d/utils/getShift.js.map

@@ -0,0 +1 @@
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package/lib-esm/datum/data2d/utils/isZoneExists.js

@@ -0,0 +1,16 @@
+export function isZoneExists(zone, spectrum, error) {
+    const newXRange = zone.x || { from: 0, to: 0 };
+    const newYRange = zone.y || { from: 0, to: 0 };
+    if (!spectrum.zones?.values)
+        return false;
+    for (const { x, y } of spectrum.zones.values) {
+        if (Math.abs(newXRange.from - x.from) < error.x &&
+            Math.abs(newXRange.to - x.to) < error.x &&
+            Math.abs(newYRange.from - y.from) < error.y &&
+            Math.abs(newYRange.to - y.to) < error.y) {
+            return true;
+        }
+    }
+    return false;
+}
+//# sourceMappingURL=isZoneExists.js.map

package/lib-esm/datum/data2d/utils/isZoneExists.js.map

@@ -0,0 +1 @@
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