nmr-processing 9.3.7 → 9.3.8-pre.1681135907

package/lib/xyz/xyzBidimensionalFFT.d.ts

@@ -0,0 +1,41 @@
+import { DoubleArray } from 'cheminfo-types';
+import { ApodizationOptions } from '../apodization/apodization';
+import { Data2D } from './Data2D';
+import { DirectDimensionOptions } from './util/fft2d/fftDirectDimension';
+import { IndirectDimensionOptions } from './util/fft2d/fftIndirectDimension';
+import { ZeroFillingOptions } from './util/fft2d/zeroFilling';
+type Info2D = any;
+interface BidimensionalFFTOptions {
+    fnMode: string;
+    info: Info2D;
+    zeroFilling?: ZeroFillingOptions;
+    phaseCorrection?: {
+        ph0: number;
+        ph1: number;
+    };
+    digitalFilterValue?: number;
+    apodization?: ApodizationOptions;
+    indirect?: IndirectDimensionOptions;
+    direct?: DirectDimensionOptions;
+}
+export declare function xyzBidimensionalFFT(data: Data2D, options: BidimensionalFFTOptions): {
+    re: {
+        minX: number;
+        maxX: number;
+        minY: number;
+        maxY: number;
+        z: DoubleArray[];
+        maxZ: number;
+        minZ: number;
+    };
+    im: {
+        minX: number;
+        maxX: number;
+        minY: number;
+        maxY: number;
+        z: DoubleArray[];
+        maxZ: number;
+        minZ: number;
+    };
+};
+export {};

package/lib/xyz/xyzBidimensionalFFT.js

@@ -0,0 +1,79 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.xyzBidimensionalFFT = void 0;
+const quadrature_1 = require("./quadrature");
+const fftDirectDimension_1 = require("./util/fft2d/fftDirectDimension");
+const fftIndirectDimension_1 = require("./util/fft2d/fftIndirectDimension");
+function xyzBidimensionalFFT(data, options) {
+    ensureData2DFid(data);
+    const { info, fnMode, digitalFilterValue = 0, zeroFilling: zeroFillingGeneral, } = options;
+    const orderedData = (0, quadrature_1.quadrature)(data, { fnMode });
+    const { re: reData } = orderedData;
+    const nbRows = reData.length;
+    const nbColumns = reData[0].length;
+    const { direct = {}, indirect = {} } = options;
+    const { zeroFilling: zeroFillingF2 = zeroFillingGeneral } = direct;
+    const { factor: f2Factor = 2 } = zeroFillingF2 || {};
+    const nbPointsF2 = (zeroFillingF2 === null || zeroFillingF2 === void 0 ? void 0 : zeroFillingF2.nbPoints) || 2 ** Math.round(Math.log2(nbColumns * f2Factor));
+    const transformed = (0, fftDirectDimension_1.fftDirectDimension)(orderedData, {
+        ...direct,
+        fnMode,
+        digitalFilterValue,
+        zeroFilling: { nbPoints: nbPointsF2 },
+    });
+    const { zeroFilling: zeroFillingF1 } = options;
+    const { factor: f1Factor = 2 } = zeroFillingF1 || {};
+    const nbPointsF1 = (zeroFillingF1 === null || zeroFillingF1 === void 0 ? void 0 : zeroFillingF1.nbPoints) || 2 ** Math.round(Math.log2(nbRows * f1Factor));
+    const { re: reResult, im: imResult } = (0, fftIndirectDimension_1.fftIndirectDimension)(transformed, {
+        ...indirect,
+        fnMode,
+        zeroFilling: { nbPoints: nbPointsF1 },
+    });
+    const minMaxXY = getMinMaxXY(info);
+    return {
+        re: {
+            z: convertToDoubleArray(reResult),
+            maxZ: reResult.max(),
+            minZ: reResult.min(),
+            ...minMaxXY,
+        },
+        im: {
+            z: convertToDoubleArray(imResult),
+            maxZ: imResult.max(),
+            minZ: imResult.min(),
+            ...minMaxXY,
+        },
+    };
+}
+exports.xyzBidimensionalFFT = xyzBidimensionalFFT;
+function ensureData2DFid(data) {
+    if (!('re' in data)) {
+        throw new Error('bidimensional FFT only can be applied to raw data');
+    }
+}
+function convertToDoubleArray(data) {
+    const result = new Array(data.rows);
+    for (let i = 0; i < data.rows; i++) {
+        result[i] = new Float64Array(data.getRow(i));
+    }
+    return result;
+}
+function getMinMaxXY(info) {
+    const min = [];
+    const max = [];
+    for (let i = 0; i < info.baseFrequency.length; i++) {
+        const baseFrequency = Number.parseFloat(info.baseFrequency[i]);
+        const frequencyOffset = Number.parseFloat(info.frequencyOffset[i]);
+        const spectralWidth = Number.parseFloat(info.spectralWidth[i]);
+        const offset = frequencyOffset / baseFrequency;
+        min.push(offset - spectralWidth * 0.5);
+        max.push(offset + spectralWidth * 0.5);
+    }
+    return {
+        minX: min[0],
+        maxX: max[0],
+        minY: min[1],
+        maxY: max[1],
+    };
+}
+//# sourceMappingURL=xyzBidimensionalFFT.js.map

package/lib/xyz/xyzBidimensionalFFT.js.map

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

@@ -1,7 +1,9 @@
 import { applyWindow } from './applyWindow';
 import { compose } from './compose';
-export function apodization(data, options) {
+export function apodization(data, options = {}) {
     const { compose: composeOptions, pointsToShift } = options;
+    if (!composeOptions)
+        return { ...data, windowData: [] };
     const windowData = compose(composeOptions);
     const applyWindowOptions = {
         windowData,

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

@@ -1 +1 @@
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+{"version":3,"file":"apodization.js","sourceRoot":"","sources":["../../src/apodization/apodization.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC;AAC5C,OAAO,EAAE,OAAO,EAAgB,MAAM,WAAW,CAAC;AAiBlD,MAAM,UAAU,WAAW,CAAC,IAAc,EAAE,UAA8B,EAAE;IAC1E,MAAM,EAAE,OAAO,EAAE,cAAc,EAAE,aAAa,EAAE,GAAG,OAAO,CAAC;IAE3D,IAAI,CAAC,cAAc;QAAE,OAAO,EAAE,GAAG,IAAI,EAAE,UAAU,EAAE,EAAE,EAAE,CAAC;IAExD,MAAM,UAAU,GAAG,OAAO,CAAC,cAAc,CAAC,CAAC;IAE3C,MAAM,kBAAkB,GAAG;QACzB,UAAU;QACV,aAAa;KACd,CAAC;IACF,MAAM,EAAE,GAAG,WAAW,CAAC,IAAI,CAAC,EAAE,EAAE,kBAAkB,CAAC,CAAC;IACpD,MAAM,EAAE,GAAG,WAAW,CAAC,IAAI,CAAC,EAAE,EAAE,kBAAkB,CAAC,CAAC;IAEpD,OAAO,EAAE,EAAE,EAAE,EAAE,EAAE,UAAU,EAAE,CAAC;AAChC,CAAC"}

package/lib-esm/apodization/applyWindow.js.map

@@ -1 +1 @@
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+{"version":3,"file":"applyWindow.js","sourceRoot":"","sources":["../../src/apodization/applyWindow.ts"],"names":[],"mappings":"AA0BA;;GAEG;AACH,MAAM,UAAU,WAAW,CAAC,IAAiB,EAAE,OAA2B;IACxE,MAAM,UAAU,GAAG,IAAI,CAAC,MAAM,CAAC;IAE/B,MAAM,EACJ,UAAU,EACV,KAAK,GAAG,CAAC,EACT,MAAM,GAAG,UAAU,EACnB,aAAa,GAAG,CAAC,EACjB,MAAM,GAAG,IAAI,YAAY,CAAC,IAAI,CAAC,GAChC,GAAG,OAAO,CAAC;IAEZ,MAAM,aAAa,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,MAAM,EAAE,UAAU,GAAG,aAAa,CAAC,CAAC;IAC3E,KAAK,IAAI,CAAC,GAAG,KAAK,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,aAAa,EAAE,CAAC,EAAE,EAAE;QACjD,MAAM,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC,CAAC,EAAE,CAAC,CAAC;KAC9B;IACD,KAAK,IAAI,CAAC,GAAG,UAAU,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,GAAG,aAAa,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;QAC3E,MAAM,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC,CAAC,EAAE,CAAC,CAAC;KAC9B;IAED,OAAO,MAAM,CAAC;AAChB,CAAC"}

package/lib-esm/apodization/compose.js.map

@@ -1 +1 @@
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+{"version":3,"file":"compose.js","sourceRoot":"","sources":["../../src/apodization/compose.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC;AAC5C,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC;AAE5C,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAC;AAyB1C,MAAM,UAAU,OAAO,CAAC,YAA0B;IAChD,MAAM,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,GAAG,EAAE,EAAE,GAAG,YAAY,CAAC;IACzD,IAAI,IAAI,GAAG,IAAI,YAAY,CAAC,UAAU,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAChD,MAAM,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,EAAE;QACzB,MAAM,EAAE,KAAK,EAAE,KAAK,GAAG,CAAC,EAAE,GAAG,OAAO,CAAC;QACrC,MAAM,EAAE,OAAO,EAAE,YAAY,EAAE,GAAG,KAAK,CAAC;QACxC,MAAM,MAAM,GACV,QAAQ,IAAI,YAAY,CAAC,CAAC,CAAC,YAAY,CAAC,MAAM,CAAC,CAAC,CAAC,UAAU,GAAG,KAAK,CAAC;QAEtE,MAAM,UAAU,GAAG,OAAO,CAAC,WAAW,CAAC,KAAK,CAAC,EAAE,MAAM,CAAC,CAAC;QAEvD,WAAW,CAAC,IAAI,EAAE;YAChB,UAAU;YACV,MAAM;YACN,KAAK;YACL,MAAM,EAAE,IAAI;SACb,CAAC,CAAC;IACL,CAAC,CAAC,CAAC;IACH,OAAO,IAAI,CAAC;AACd,CAAC"}

package/lib-esm/apodization/getFunction.js

@@ -1,5 +1,6 @@
 import { exponential } from './shapes/exponential';
 import { lorentzToGauss } from './shapes/lorentzToGauss';
+import { sineBell } from './shapes/sineBell';
 export function getFunction(shape) {
     const { kind, options } = shape;
     switch (kind) {
@@ -7,6 +8,8 @@ export function getFunction(shape) {
             return exponential(options);
         case 'lorentzToGauss':
             return lorentzToGauss(options);
+        case 'sineBell':
+            return sineBell(options);
         default:
             throw Error(`Unknown distribution ${kind}`);
     }

package/lib-esm/apodization/getFunction.js.map

@@ -1 +1 @@
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+{"version":3,"file":"getFunction.js","sourceRoot":"","sources":["../../src/apodization/getFunction.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAC;AACnD,OAAO,EAAE,cAAc,EAAE,MAAM,yBAAyB,CAAC;AACzD,OAAO,EAAE,QAAQ,EAAE,MAAM,mBAAmB,CAAC;AAE7C,MAAM,UAAU,WAAW,CAAC,KAAsB;IAChD,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,KAAK,CAAC;IAChC,QAAQ,IAAI,EAAE;QACZ,KAAK,aAAa;YAChB,OAAO,WAAW,CAAC,OAAO,CAAC,CAAC;QAC9B,KAAK,gBAAgB;YACnB,OAAO,cAAc,CAAC,OAAO,CAAC,CAAC;QACjC,KAAK,UAAU;YACb,OAAO,QAAQ,CAAC,OAAO,CAAC,CAAC;QAC3B;YACE,MAAM,KAAK,CAAC,wBAAwB,IAAc,EAAE,CAAC,CAAC;KACzD;AACH,CAAC"}

package/lib-esm/apodization/shapes/sineBell.js

@@ -0,0 +1,13 @@
+export function sineBell(options) {
+    const { exponent = 1, offset = 0, end = 1, length } = options;
+    if (length === undefined) {
+        throw new Error('length options should exists for sineBell shape');
+    }
+    if (end < 0 || end > 1) {
+        throw new Error(`the end parameter should be [0-1]`);
+    }
+    const c1 = Math.PI * offset;
+    const c2 = (Math.PI * (end - offset)) / (length - 1);
+    return (i) => Math.pow(Math.sin(c1 + c2 * i), exponent);
+}
+//# sourceMappingURL=sineBell.js.map

package/lib-esm/apodization/shapes/sineBell.js.map

@@ -0,0 +1 @@
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package/lib-esm/apodization/utils/getData.js.map

@@ -1 +1 @@
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+{"version":3,"file":"getData.js","sourceRoot":"","sources":["../../../src/apodization/utils/getData.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,MAAM,UAAU,OAAO,CAAC,IAA2B,EAAE,MAAc;IACjE,MAAM,IAAI,GAAG,IAAI,YAAY,CAAC,MAAM,CAAC,CAAC;IACtC,IAAI,GAAG,GAAG,MAAM,CAAC,gBAAgB,CAAC;IAClC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE;QAC/B,MAAM,KAAK,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;QACtB,IAAI,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC;QAChB,IAAI,KAAK,GAAG,GAAG;YAAE,GAAG,GAAG,KAAK,CAAC;KAC9B;IACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE;QAAE,IAAI,CAAC,CAAC,CAAC,IAAI,GAAG,CAAC;IAChD,OAAO,IAAI,CAAC;AACd,CAAC"}

package/lib-esm/utilities/checkData2DFid.js

@@ -0,0 +1,6 @@
+export function checkData2DFid(data) {
+    if (!('re' in data && 'im' in data)) {
+        throw new Error('imaginary (im) data should exists');
+    }
+}
+//# sourceMappingURL=checkData2DFid.js.map

package/lib-esm/utilities/checkData2DFid.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"checkData2DFid.js","sourceRoot":"","sources":["../../src/utilities/checkData2DFid.ts"],"names":[],"mappings":"AAGA,MAAM,UAAU,cAAc,CAC5B,IAAY;IAEZ,IAAI,CAAC,CAAC,IAAI,IAAI,IAAI,IAAI,IAAI,IAAI,IAAI,CAAC,EAAE;QACnC,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAC;KACtD;AACH,CAAC"}

package/lib-esm/xyz/Data2D.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=Data2D.js.map

package/lib-esm/xyz/Data2D.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"Data2D.js","sourceRoot":"","sources":["../../src/xyz/Data2D.ts"],"names":[],"mappings":""}

package/lib-esm/xyz/quadrature.js

@@ -0,0 +1,50 @@
+import { xAdd, xMultiply, xSubtract } from 'ml-spectra-processing';
+import { checkData2DFid } from '../utilities/checkData2DFid';
+export function quadrature(data, options) {
+    checkData2DFid(data);
+    const { fnMode } = options;
+    switch (fnMode) {
+        case 'ttpi':
+            return ttpiQuadrature(data);
+        case 'states':
+            return shrQuadrature(data);
+        case 'echo':
+            return echoQuadrature(data);
+        default:
+            return {
+                re: data.re.z,
+                im: data.im.z,
+            };
+    }
+}
+function echoQuadrature(data) {
+    const { re: { z: reMatrix }, im: { z: imMatrix }, } = data;
+    const newRe = [];
+    const newIm = [];
+    for (let i = 0; i < reMatrix.length; i += 2) {
+        let reCosine = reMatrix[i];
+        let imCosine = imMatrix[i];
+        let reSine = reMatrix[i + 1];
+        let imSine = imMatrix[i + 1];
+        newRe.push(xSubtract(xMultiply(imSine, -1), imCosine));
+        newRe.push(xSubtract(reSine, reCosine));
+        newIm.push(xAdd(reSine, reCosine));
+        newIm.push(xSubtract(imSine, imCosine));
+    }
+    return { re: newRe, im: newIm };
+}
+function shrQuadrature(data) {
+    const { re, im } = data;
+    return { re: re.z, im: im.z };
+}
+function ttpiQuadrature(data) {
+    const newRe = [];
+    const newIm = [];
+    const { re: { z: reMatrix }, im: { z: imMatrix }, } = data;
+    for (let i = 0; i < reMatrix.length; i++) {
+        newRe.push(i % 2 ? reMatrix[i].slice() : xMultiply(reMatrix[i], -1));
+        newIm.push(i % 2 ? imMatrix[i].slice() : xMultiply(imMatrix[i], -1));
+    }
+    return { re: newRe, im: newIm };
+}
+//# sourceMappingURL=quadrature.js.map

package/lib-esm/xyz/quadrature.js.map

@@ -0,0 +1 @@
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package/lib-esm/xyz/util/fft2d/digitalFilter.js

@@ -0,0 +1,16 @@
+export function digitalFilter(data, options) {
+    let { digitalFilterValue = 0 } = options;
+    let re = new Float64Array(data.re);
+    let im = new Float64Array(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);
+    return { re: newRe, im: newIm };
+}
+//# sourceMappingURL=digitalFilter.js.map

package/lib-esm/xyz/util/fft2d/digitalFilter.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"digitalFilter.js","sourceRoot":"","sources":["../../../../src/xyz/util/fft2d/digitalFilter.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,aAAa,CAC3B,IAAc,EACd,OAAuC;IAEvC,IAAI,EAAE,kBAAkB,GAAG,CAAC,EAAE,GAAG,OAAO,CAAC;IACzC,IAAI,EAAE,GAAG,IAAI,YAAY,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACnC,IAAI,EAAE,GAAG,IAAI,YAAY,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IAEnC,IAAI,aAAa,GAAG,IAAI,CAAC,KAAK,CAAC,kBAAkB,CAAC,CAAC;IAEnD,MAAM,IAAI,GAAG,CAAC,CAAC;IACf,aAAa,IAAI,CAAC,CAAC;IAEnB,MAAM,KAAK,GAAG,IAAI,YAAY,CAAC,EAAE,CAAC,MAAM,CAAC,CAAC;IAC1C,MAAM,KAAK,GAAG,IAAI,YAAY,CAAC,EAAE,CAAC,MAAM,CAAC,CAAC;IAC1C,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,aAAa,CAAC,CAAC,CAAC;IACnC,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,IAAI,EAAE,aAAa,CAAC,EAAE,EAAE,CAAC,MAAM,GAAG,aAAa,CAAC,CAAC;IACpE,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,aAAa,CAAC,CAAC,CAAC;IACnC,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,IAAI,EAAE,aAAa,CAAC,EAAE,EAAE,CAAC,MAAM,GAAG,aAAa,CAAC,CAAC;IAEpE,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC;AAClC,CAAC"}

package/lib-esm/xyz/util/fft2d/fftDirectDimension.js

@@ -0,0 +1,50 @@
+import Matrix from 'ml-matrix';
+import { reimAutoPhaseCorrection, reimFFT, reimPhaseCorrection, } from 'ml-spectra-processing';
+import { apodization, } from '../../../apodization/apodization';
+import { digitalFilter } from './digitalFilter';
+import { removeDCOffset } from './removeDCOffset';
+import { zeroFilling } from './zeroFilling';
+export function fftDirectDimension(data, options) {
+    const { re: reData, im: imData } = data;
+    const nbRows = reData.length;
+    const nbColumns = reData[0].length;
+    const { zeroFilling: zeroFillingF2, digitalFilterValue = 0 } = options;
+    const { factor: f2Factor = 2 } = zeroFillingF2 || {};
+    const nbPointsF2 = (zeroFillingF2 === null || zeroFillingF2 === void 0 ? void 0 : zeroFillingF2.nbPoints) || 2 ** Math.round(Math.log2(nbColumns * f2Factor));
+    const reFFT = new Matrix(nbRows, nbPointsF2);
+    const imFFT = new Matrix(nbRows, nbPointsF2);
+    const { apodization: apodizationF2 } = options;
+    let { ph0: ph0F2, ph1: ph1F2, mode: pcModeF2 = 'no', } = (options === null || options === void 0 ? void 0 : options.phaseCorrection) || {};
+    for (let i = 0; i < nbRows; i++) {
+        const newData = digitalFilter({ re: reData[i], im: imData[i] }, { digitalFilterValue });
+        Object.assign(newData, removeDCOffset(newData, { digitalFilterValue }));
+        if (apodizationF2) {
+            const { re: aRe, im: aIm } = apodization(newData, apodizationF2);
+            Object.assign(newData, { re: aRe, im: aIm });
+        }
+        Object.assign(newData, zeroFilling(newData, { digitalFilterValue, nbPoints: nbPointsF2 }));
+        Object.assign(newData, reimFFT(newData, { applyZeroShift: true }));
+        const dfResidual = (digitalFilterValue - Math.round(digitalFilterValue)) * Math.PI * 2;
+        if (dfResidual > 0) {
+            Object.assign(newData, reimPhaseCorrection(newData, 0, -dfResidual));
+        }
+        if (i === 0 &&
+            pcModeF2 === 'pk' &&
+            ph0F2 === undefined &&
+            ph1F2 === undefined) {
+            const phased = reimAutoPhaseCorrection(newData, { magnitudeMode: false });
+            ph0F2 = phased.ph0;
+            ph1F2 = phased.ph1;
+        }
+        if (pcModeF2 === 'pk' && ph0F2 !== undefined && ph1F2 !== undefined) {
+            Object.assign(newData, reimPhaseCorrection(newData, (ph0F2 * Math.PI) / 180, (ph1F2 * Math.PI) / 180));
+        }
+        reFFT.setRow(i, newData.re);
+        imFFT.setRow(i, newData.im);
+    }
+    return {
+        re: reFFT,
+        im: imFFT,
+    };
+}
+//# sourceMappingURL=fftDirectDimension.js.map

package/lib-esm/xyz/util/fft2d/fftDirectDimension.js.map

@@ -0,0 +1 @@
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package/lib-esm/xyz/util/fft2d/fftIndirectDimension.js

@@ -0,0 +1,65 @@
+import Matrix from 'ml-matrix';
+import { reimAbsolute, reimAutoPhaseCorrection, reimFFT, reimPhaseCorrection, } from 'ml-spectra-processing';
+import { apodization, } from '../../../apodization/apodization';
+import { zeroFilling } from './zeroFilling';
+export function fftIndirectDimension(data, options) {
+    var _a;
+    const reData = Matrix.checkMatrix(data.re);
+    const imData = Matrix.checkMatrix(data.im);
+    const nbRows = reData.rows;
+    const nbColumns = reData.columns;
+    const { zeroFilling: zeroFillingF1 } = options;
+    const { factor: f1Factor = 2 } = zeroFillingF1 || {};
+    const nbPointsF1 = (zeroFillingF1 === null || zeroFillingF1 === void 0 ? void 0 : zeroFillingF1.nbPoints) || 2 ** Math.round(Math.log2(nbRows * f1Factor));
+    const { apodization: apodizationF1 } = options;
+    let { ph0: ph0F1, ph1: ph1F1, mode: pcModeF1, } = options.phaseCorrection || {};
+    const reResult = new Matrix(nbPointsF1, nbColumns);
+    const imResult = new Matrix(nbPointsF1, nbColumns);
+    for (let i = 0; i < nbColumns; i++) {
+        const { re: aRe, im: aIm } = apodization({
+            re: reData.getColumn(i),
+            im: imData.getColumn(i),
+        }, apodizationF1);
+        const newRe = [];
+        const newIm = [];
+        if (options.fnMode === 'echo') {
+            for (let j = 0; j < aRe.length; j += 2) {
+                newRe.push(aRe[j]);
+                newIm.push(aRe[j + 1]);
+            }
+        }
+        else {
+            for (let j = 0; j < aRe.length; j++) {
+                newRe.push(aRe[j]);
+                newIm.push(-aIm[j]);
+            }
+        }
+        let transformed = reimFFT(zeroFilling({
+            re: newRe,
+            im: newIm,
+        }, { digitalFilterValue: 0, nbPoints: nbPointsF1 }), { applyZeroShift: true });
+        let { re, im } = transformed;
+        if (((_a = options.phaseCorrection) === null || _a === void 0 ? void 0 : _a.mode) === 'mc') {
+            re = reimAbsolute({ re, im });
+            im = new Float64Array(im.length);
+        }
+        if (pcModeF1 === 'pk') {
+            if (i === 0 && ph0F1 === undefined && ph1F1 === undefined) {
+                //here we can improve it by checking if the experiment is phase sensitive.
+                const phased = reimAutoPhaseCorrection({ re, im }, { magnitudeMode: false });
+                ph0F1 = phased.ph0;
+                ph1F1 = phased.ph1;
+            }
+            if (ph0F1 !== undefined && ph1F1 !== undefined) {
+                Object.assign(transformed, reimPhaseCorrection(transformed, (ph0F1 * Math.PI) / 180, (ph1F1 * Math.PI) / 180));
+            }
+        }
+        reResult.setColumn(i, re);
+        imResult.setColumn(i, im);
+    }
+    return {
+        re: reResult,
+        im: imResult,
+    };
+}
+//# sourceMappingURL=fftIndirectDimension.js.map

package/lib-esm/xyz/util/fft2d/fftIndirectDimension.js.map

@@ -0,0 +1 @@
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package/lib-esm/xyz/util/fft2d/removeDCOffset.js

@@ -0,0 +1,15 @@
+import { xMean } from 'ml-spectra-processing';
+export function removeDCOffset(data, options) {
+    let { digitalFilterValue = 0 } = options;
+    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 - digitalFilterValue));
+    const averageIm = xMean(data.im.slice((nbPoints * 0.75) >> 0, nbPoints - digitalFilterValue));
+    for (let i = digitalFilterValue; i < nbPoints - digitalFilterValue; i++) {
+        newRe[i] -= averageRe;
+        newIm[i] -= averageIm;
+    }
+    return { re: newRe, im: newIm };
+}
+//# sourceMappingURL=removeDCOffset.js.map

package/lib-esm/xyz/util/fft2d/removeDCOffset.js.map

@@ -0,0 +1 @@
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package/lib-esm/xyz/util/fft2d/zeroFilling.js

@@ -0,0 +1,25 @@
+export function zeroFilling(data, options) {
+    let { nbPoints, factor = 2, digitalFilterValue: grpdly = 0 } = options;
+    if (!nbPoints) {
+        nbPoints = 2 ** Math.round(Math.log2(data.re.length * factor));
+    }
+    let pointsToShift;
+    if (grpdly > 0) {
+        pointsToShift = Math.floor(grpdly);
+    }
+    else {
+        pointsToShift = 0;
+    }
+    const { re, im } = data;
+    let newRE = new Float64Array(nbPoints);
+    let newIM = new Float64Array(nbPoints);
+    const length = Math.min(nbPoints, re.length);
+    newRE.set(re.slice(0, length - pointsToShift));
+    newIM.set(im.slice(0, length - pointsToShift));
+    if (pointsToShift > 0 && pointsToShift < nbPoints) {
+        newRE.set(re.slice(re.length - pointsToShift), nbPoints - pointsToShift);
+        newIM.set(im.slice(re.length - pointsToShift), nbPoints - pointsToShift);
+    }
+    return { re: newRE, im: newIM };
+}
+//# sourceMappingURL=zeroFilling.js.map

package/lib-esm/xyz/util/fft2d/zeroFilling.js.map

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

@@ -0,0 +1,75 @@
+import { quadrature } from './quadrature';
+import { fftDirectDimension, } from './util/fft2d/fftDirectDimension';
+import { fftIndirectDimension, } from './util/fft2d/fftIndirectDimension';
+export function xyzBidimensionalFFT(data, options) {
+    ensureData2DFid(data);
+    const { info, fnMode, digitalFilterValue = 0, zeroFilling: zeroFillingGeneral, } = options;
+    const orderedData = quadrature(data, { fnMode });
+    const { re: reData } = orderedData;
+    const nbRows = reData.length;
+    const nbColumns = reData[0].length;
+    const { direct = {}, indirect = {} } = options;
+    const { zeroFilling: zeroFillingF2 = zeroFillingGeneral } = direct;
+    const { factor: f2Factor = 2 } = zeroFillingF2 || {};
+    const nbPointsF2 = (zeroFillingF2 === null || zeroFillingF2 === void 0 ? void 0 : zeroFillingF2.nbPoints) || 2 ** Math.round(Math.log2(nbColumns * f2Factor));
+    const transformed = fftDirectDimension(orderedData, {
+        ...direct,
+        fnMode,
+        digitalFilterValue,
+        zeroFilling: { nbPoints: nbPointsF2 },
+    });
+    const { zeroFilling: zeroFillingF1 } = options;
+    const { factor: f1Factor = 2 } = zeroFillingF1 || {};
+    const nbPointsF1 = (zeroFillingF1 === null || zeroFillingF1 === void 0 ? void 0 : zeroFillingF1.nbPoints) || 2 ** Math.round(Math.log2(nbRows * f1Factor));
+    const { re: reResult, im: imResult } = fftIndirectDimension(transformed, {
+        ...indirect,
+        fnMode,
+        zeroFilling: { nbPoints: nbPointsF1 },
+    });
+    const minMaxXY = getMinMaxXY(info);
+    return {
+        re: {
+            z: convertToDoubleArray(reResult),
+            maxZ: reResult.max(),
+            minZ: reResult.min(),
+            ...minMaxXY,
+        },
+        im: {
+            z: convertToDoubleArray(imResult),
+            maxZ: imResult.max(),
+            minZ: imResult.min(),
+            ...minMaxXY,
+        },
+    };
+}
+function ensureData2DFid(data) {
+    if (!('re' in data)) {
+        throw new Error('bidimensional FFT only can be applied to raw data');
+    }
+}
+function convertToDoubleArray(data) {
+    const result = new Array(data.rows);
+    for (let i = 0; i < data.rows; i++) {
+        result[i] = new Float64Array(data.getRow(i));
+    }
+    return result;
+}
+function getMinMaxXY(info) {
+    const min = [];
+    const max = [];
+    for (let i = 0; i < info.baseFrequency.length; i++) {
+        const baseFrequency = Number.parseFloat(info.baseFrequency[i]);
+        const frequencyOffset = Number.parseFloat(info.frequencyOffset[i]);
+        const spectralWidth = Number.parseFloat(info.spectralWidth[i]);
+        const offset = frequencyOffset / baseFrequency;
+        min.push(offset - spectralWidth * 0.5);
+        max.push(offset + spectralWidth * 0.5);
+    }
+    return {
+        minX: min[0],
+        maxX: max[0],
+        minY: min[1],
+        maxY: max[1],
+    };
+}
+//# sourceMappingURL=xyzBidimensionalFFT.js.map

package/lib-esm/xyz/xyzBidimensionalFFT.js.map

@@ -0,0 +1 @@
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