nmr-processing 11.10.1 → 11.11.1-pre.1709824354

package/nmr-processing.d.ts

@@ -8,7 +8,7 @@ import { GSDPeakOptimized } from 'ml-gsd';
 import { GSDPeakOptimizedID } from 'ml-gsd';
 import { JoinBroadPeaksOptions } from 'ml-gsd';
 import { Logger } from 'cheminfo-types';
-import type { Matrix } from 'ml-matrix';
+import { Matrix } from 'ml-matrix';
 import * as matrixPeakFinders from 'ml-matrix-peaks-finder';
 import { Molecule } from 'openchemlib/full';
 import { NmrData1D } from 'cheminfo-types';
@@ -187,6 +187,10 @@ declare interface BooleanField extends Field<boolean> {
     type: 'boolean';
 }
 
+declare interface CalculateT1Options {
+    optimization?: any;
+}
+
 export declare const carbonImpurities: DatabaseNMREntry[];
 
 /**
@@ -291,6 +295,13 @@ export declare const DatumKind: {
 
 declare function deleteFilter(datum: Entry1D | Entry2D, id?: string): void;
 
+export declare interface DirectDimensionOptions {
+    acquisitionScheme?: string;
+    reverse?: boolean;
+    digitalFilterValue?: number;
+    phaseCorrection?: PhaseCorrection;
+}
+
 declare function enableFilter(datum: Entry1D | Entry2D, id: string | null, checked: boolean | null, filters?: Filter[]): void;
 
 declare type Entry = Entry1D | Entry2D;
@@ -346,6 +357,19 @@ declare interface ExponentialOptions {
     dw: number;
 }
 
+export declare function fftDirectDimension(data: {
+    re: DoubleArray[];
+    im: DoubleArray[];
+}, options?: DirectDimensionOptions): {
+    re: Matrix;
+    im: Matrix;
+};
+
+export declare function fftIndirectDimension(data: {
+    re: DoubleArray[] | Matrix;
+    im: DoubleArray[] | Matrix;
+}, options: IndirectDimensionOptions): Record<string, Matrix>;
+
 declare interface Field<T> extends BaseField {
     default: T;
 }
@@ -401,7 +425,7 @@ export { FiltersManager }
  */
 export declare function findMultiplet(name: string): MultipletDefinition | undefined;
 
-declare type FlexibleWindowFunctions = Exponential<Partial<ExponentialOptions>> | LorentToGauss<Partial<LorentzToGaussOptions>> | SineBell<Partial<SineBellOptions>> | Traf<Partial<TrafOptions>>;
+export declare type FlexibleWindowFunctions = Exponential<Partial<ExponentialOptions>> | LorentToGauss<Partial<LorentzToGaussOptions>> | SineBell<Partial<SineBellOptions>> | Traf<Partial<TrafOptions>> | ModifiedGaussian<Partial<ModifiedGaussianOptions>>;
 
 export declare interface ForwardLPOptions {
     /**
@@ -599,6 +623,11 @@ export declare interface GetPeakListOptions extends GSDOptions, OptimizePeaksOpt
      * frequency used to convert width and fwhm to Hz
      */
     frequency: number;
+    /**
+     * maximum absolute value of the second derivative of the intensity array, if it is not passed
+     * the function will calculate it.
+     */
+    maxAbsDdY?: number;
 }
 
 export declare function getShiftX(spectrum: Entry1D): number;
@@ -2120,6 +2149,12 @@ export declare interface ImpuritySignal {
     shift: number;
 }
 
+export declare interface IndirectDimensionOptions {
+    acquisitionScheme?: string;
+    reverse?: boolean;
+    phaseCorrection?: PhaseCorrection_2;
+}
+
 declare interface Info {
     isFid: boolean;
     phc1?: number;
@@ -2408,6 +2443,32 @@ export declare interface MatrixOptions {
 
 declare type MatrixProperties = Record<string, Properties>;
 
+declare interface ModifiedGaussian<ShapeOption = ModifiedGaussianOptions> {
+    kind: 'modifiedGaussian';
+    options: ShapeOption;
+}
+
+declare interface ModifiedGaussianOptions {
+    /**
+     * line broadening value in Hz, a negative value will invert the shape
+     * @default -0.01
+     */
+    lineBroadening?: number;
+    /**
+     * ModifiedGaussian Broadening, (0 - 1] define the position of the top of the gaussian shape.
+     * @default 0.01
+     */
+    gaussianBroadening?: number;
+    /**
+     * increment value in time or the independent value
+     */
+    dwellTime: number;
+    /**
+     * size of the shape function
+     */
+    length: number;
+}
+
 export declare interface MultipletDefinition {
     label: string;
     value: string;
@@ -2783,6 +2844,18 @@ export declare interface PeaksToXYOptions extends OptionsSG1D {
 
 export declare function peakToXY(peak: NMRPeak1D, options: PeaksToXYOptions): DataXY<Float64Array>;
 
+declare interface PhaseCorrection {
+    mode?: string;
+    ph0?: number;
+    ph1?: number;
+}
+
+declare interface PhaseCorrection_2 {
+    mode?: string;
+    ph0?: number;
+    ph1?: number;
+}
+
 declare interface PhaseCorrectionHorizontalOptions {
     ph0: number;
     ph1: number;
@@ -3055,7 +3128,7 @@ export declare function rangeFromSignal(signal: NMRSignal1D, options?: RangeFrom
 export declare interface RangeFromSignalOptions {
     /**
      * nucleus
-     * @default '1h'
+     * @default '1H'
      */
     nucleus?: string;
     /**
@@ -3064,7 +3137,7 @@ export declare interface RangeFromSignalOptions {
      */
     frequency?: number;
     /**
-     * tolerance to the halfWidth, default depends of the nucleus
+     * tolerance to the halfWidth, default depends on the nucleus
      */
     tolerance?: number;
 }
@@ -3111,11 +3184,21 @@ export declare interface RangesToACSOptions {
     solvent?: string;
 }
 
-export declare function rangesToXY(ranges: NMRRange[], options?: any): {
-    x: DoubleArray;
+export declare function rangesToXY(ranges: NMRRange[], options?: RangesToXYOptions): {
+    x: Float64Array;
     y: Float64Array;
 };
 
+export declare interface RangesToXYOptions {
+    nucleus?: string;
+    frequency?: number;
+    nbPoints?: number;
+    lineWidth?: number;
+    shape?: Shape1D;
+    from?: number;
+    to?: number;
+}
+
 export declare interface RangeToXYOptions {
     /**
      * frequency observed
@@ -3338,7 +3421,11 @@ export declare function signalsToFID(signals: NMRSignal1D[], options: SignalsToF
     re: DoubleArray;
     im: DoubleArray;
 } | {
-    re: DoubleArray;
+    re: DoubleArray; /**
+    * at the end of the superposition of all component, an exponential apodization will be applied
+    * in order to have FID like shape.
+    * @default 1
+    */
     im: DoubleArray;
 };
 
@@ -3646,7 +3733,7 @@ declare function unlink(range: Range_2, options?: UnlinkOptions): Range_2;
 
  export declare function updateRangesRelativeValues(spectrum: Entry1D, forceCalculateIntegral?: boolean): void;
 
- declare type WindowFunctions = Exponential | LorentToGauss | SineBell | Traf;
+ export declare type WindowFunctions = Exponential | LorentToGauss | SineBell | Traf | ModifiedGaussian;
 
  /**
   * Predict back points by singular value decomposition.
@@ -3666,7 +3753,7 @@ declare function unlink(range: Range_2, options?: UnlinkOptions): Range_2;
      predicted: Float64Array;
  };
 
- export declare function xyAutoPeaksPicking(data: DataXY, options: OptionsXYAutoPeaksPicking): NMRPeak1DWithShapeID[];
+ export declare function xyAutoPeaksPicking(data: DataXY<Float64Array>, options: OptionsXYAutoPeaksPicking): NMRPeak1DWithShapeID[];
 
  /**
   * error for default windowSize computation
@@ -3680,7 +3767,12 @@ declare function unlink(range: Range_2, options?: UnlinkOptions): Range_2;
  /**
   * Detect peaks, optimize parameters and compile multiplicity if required.
   */
- export declare function xyAutoRangesPicking(data: DataXY, options: OptionsXYAutoRangesPicking): NMRRange[];
+ export declare function xyAutoRangesPicking(data: DataXY<Float64Array>, options: OptionsXYAutoRangesPicking): NMRRange[];
+
+ export declare function xyCalculateT1(data: DataXY, options?: CalculateT1Options): {
+     relaxationT1: number;
+     fullMagnetization: number;
+ };
 
  export declare function xyPeaksOptimization<T extends PeakXYWidth>(data: DataXY, peaks: T[], options: XYPeaksOptimizationOptions): (T extends {
      id: string;