nmr-processing 22.21.0 → 22.22.1

package/dist/nmr-processing.d.ts

@@ -18,7 +18,7 @@ import type { BaselineCorrectionFilterOptions } from '@zakodium/nmr-types';
 import type { BaselineCorrectionOptions } from '@zakodium/nmr-types';
 import type { BaselineCorrectionZone } from '@zakodium/nmr-types';
 import { BaseRegression } from 'ml-regression-base';
-import type { DataReIm } from 'ml-spectra-processing';
+import { DataReIm } from 'ml-spectra-processing';
 import type { DataReImMatrix } from 'ml-spectra-processing';
 import type { DataXReIm } from 'ml-spectra-processing';
 import { DataXY } from 'cheminfo-types';
@@ -69,6 +69,7 @@ import type { NmrData2DContent } from 'cheminfo-types';
 import type { NmrData2DFt } from 'cheminfo-types';
 import type { NMRPeak1D } from '@zakodium/nmr-types';
 import { NMRRange } from '@zakodium/nmr-types';
+import type { NMRShape1D } from '@zakodium/nmr-types';
 import type { NMRSignal1D } from '@zakodium/nmr-types';
 import type { NumberArray } from 'cheminfo-types';
 import type { NUSDimension2Options } from '@zakodium/nmr-types';
@@ -88,7 +89,6 @@ import type { PhaseCorrectionTwoDOptions } from '@zakodium/nmr-types';
 import { PointXY } from 'cheminfo-types';
 import type { Range as Range_2 } from '@zakodium/nmr-types';
 import type { Ranges } from '@zakodium/nmr-types';
-import type { Shape1D } from 'ml-peak-shape-generator';
 import type { Shape1DWithFWHM } from '@zakodium/nmr-types';
 import type { Shapes } from '@zakodium/nmr-types';
 import type { Shift2DXFilterOptions } from '@zakodium/nmr-types';
@@ -224,6 +224,12 @@ declare interface AtomOutput {
 
 declare type AtomTypes = 'H' | 'C';
 
+export declare function autoPhaseCorrection(spectrum: Entry1D, options?: AutoPhaseCorrectionOptions): {
+    data: DataReIm;
+    ph0: number;
+    ph1: number;
+};
+
 export declare interface AutoPhaseCorrectionOptions {
     minRegSize?: number;
     maxDistanceToJoin?: number;
@@ -962,7 +968,7 @@ export declare function getPeakDelta(peak: Peak1D | NMRPeak1D, shiftTarget: Shif
     x: number;
 };
 
-export declare interface GetPeakListOptions extends GSDOptions, OptimizePeaksOptions, JoinBroadPeaksOptions {
+export declare interface GetPeakListOptions extends GSDOptions, OptimizeNMRPeaksOptions, JoinBroadNMRPeaksOptions {
     smoothedY: NumberArray;
     /**
      * If it is true, the peaks parameters will be optimized.
@@ -1023,6 +1029,10 @@ declare function getShifts(s: ShiftInput[]): ShiftOutput[];
 
 export declare function getShiftX(spectrum: Entry1D): number;
 
+declare type GSDNMRPeakOptimizedID = Omit<GSDPeakOptimizedID, 'shape'> & {
+    shape: NMRShape1D;
+};
+
 declare interface HOSEPrediction {
     /**
      * In case the prediction is based on HOSE codes, this is the sphere
@@ -1047,6 +1057,10 @@ export declare function isZoneExists(zone: Pick<Zone, 'x' | 'y'>, spectrum: Entr
 
 declare type JcouplingFromPrediction = MakeMandatory<Jcoupling, 'multiplicity' | 'diaIDs' | 'pathLength'>;
 
+declare type JoinBroadNMRPeaksOptions = Omit<JoinBroadPeaksOptions, 'shape'> & {
+    shape?: NMRShape1D;
+};
+
 declare type LevenbergMarquardtOptimizationOptionsDefaultsKeys = Extract<'minValues' | 'maxValues' | 'initialValues' | 'gradientDifference' | keyof typeof defaultLMOptimizationOptions, keyof LevenbergMarquardtOptions>;
 
 declare type LevenbergMarquardtOptionsDefault = Pick<LevenbergMarquardtOptions, LevenbergMarquardtOptionsWithDefaultKeys>;
@@ -1263,11 +1277,15 @@ declare interface OneDOptions {
 
 export declare type OneLetterMultiplet = 's' | 'd' | 't' | 'q' | 'i' | 'h' | 'p' | 'o' | 'n' | 'm';
 
+declare type OptimizeNMRPeaksOptions = Omit<OptimizePeaksOptions, 'shape'> & {
+    shape?: NMRShape1D;
+};
+
 export declare function optimizeSignals(data: DataXY, signals: Signal[], options: OptimizeSignalsOptions): {
     delta: number;
     js: Jcoupling[];
     shape: {
-        kind: "gaussian" | "lorentzian" | "pseudoVoigt" | "lorentzianDispersive" | "generalizedLorentzian" | "pseudoVoigtTCH";
+        kind: "gaussian" | "lorentzian" | "pseudoVoigt" | "generalizedLorentzian";
         fwhm: number;
     };
     intensity: number;
@@ -1284,7 +1302,7 @@ export declare interface OptimizeSignalsOptions {
      * @default 'min intensity value'
      */
     baseline?: number;
-    shape?: Shape1D;
+    shape?: NMRShape1D;
     parameters?: ParametersFromOptions;
     optimization?: OptimizeSignalsOptionsOptimization;
     simulation: SignalsToPointXYOptions;
@@ -1312,7 +1330,7 @@ declare interface OptionsPeaksToRanges {
      * Peak shape used to reconstruct additional or filtered peaks when compiling patterns.
      * @default { kind: 'gaussian' }
      */
-    shape?: Shape1D;
+    shape?: NMRShape1D;
     /**
      * if it is true, it will join any overlaped ranges.
      * @default true
@@ -1378,7 +1396,7 @@ export declare interface OptionsSignalsToXY extends Partial<Simulate1DOptions> {
     /**
      * Shape options for ml-spectrum-generator
      */
-    shape?: Shape1D;
+    shape?: NMRShape1D;
     /**
      * The linewidth of the output spectrum, expresed in Hz.
      * @default 1
@@ -1468,7 +1486,7 @@ declare type Parameter = 'delta' | 'intensity' | 'fwhm' | 'mu' | 'coupling' | 'g
 
 declare type ParametersFromOptions = Record<Parameter, Record<string, number | ((options?: {
     signal?: Signal;
-    shape?: Shape1D;
+    shape?: NMRShape1D;
     index?: number;
     jCoupling?: Jcoupling;
 }) => number)>>;
@@ -1999,7 +2017,7 @@ export declare interface RangesToXYOptions {
     frequency?: number;
     nbPoints?: number;
     lineWidth?: number;
-    shape?: Shape1D;
+    shape?: NMRShape1D;
     from?: number;
     to?: number;
 }
@@ -2033,7 +2051,7 @@ export declare interface RangeToXYOptions {
     /**
      * options of signals.  default { kind: 'gaussian' }
      */
-    shape: Shape1D;
+    shape: NMRShape1D;
 }
 
 export declare namespace RangeUtilities {
@@ -2147,7 +2165,7 @@ declare type ShiftX = FilterFactory<Entry1D, ShiftXOptions> & Pick<ShiftXFilterO
 
 export declare interface Signal extends NMRSignal1D {
     intensity?: number;
-    shape?: Shape1D;
+    shape?: NMRShape1D;
     parameters?: ParametersFromSignal;
 }
 
@@ -2376,7 +2394,7 @@ export declare interface Simulate1DOptions extends SimulateXYPeaksOptions {
      * Shape options
      * @default {kind:'gaussian'}
      */
-    shape?: Shape1D;
+    shape?: NMRShape1D;
     /**
      * Function to generate or add a baseline
      */
@@ -2742,7 +2760,7 @@ export declare function xyPeaksOptimization<T extends PeakXYWidth>(data: DataXY,
     id: string;
 } ? GSDPeakOptimizedID : GSDPeakOptimized)[];
 
-export declare function xyPeaksOptimizationByStages(data: DataXY, peaks: PeakXYWidth[], options: XYPeaksOptimizationOptionsByStages): GSDPeakOptimizedID[];
+export declare function xyPeaksOptimizationByStages(data: DataXY, peaks: PeakXYWidth[], options: XYPeaksOptimizationOptionsByStages): GSDNMRPeakOptimizedID[];
 
 export declare interface XYPeaksOptimizationOptions extends OptimizePeaksOptions {
     /**