@zakodium/nmr-types 0.5.8 → 0.5.10

package/dist/nmr-types.d.ts

@@ -1,15 +1,25 @@
 import type * as Filters from 'ml-signal-processing';
 import type { FilterXYType } from 'ml-signal-processing';
 import type { FromTo } from 'cheminfo-types';
+import type { Logger } from 'cheminfo-types';
+import type { NumberArray } from 'cheminfo-types';
 import type { PeakXYWidth } from 'cheminfo-types';
 import type { Shape1D } from 'ml-peak-shape-generator';
 import type { XYEquallySpacedOptions } from 'ml-spectra-processing';
 
 export declare interface AirplsOptions {
-    zones: BaselineCorrectionZone[];
     algorithm: 'airpls';
+    lambda?: number;
+    /**
+     * Array of x positions (anchors) where the baseline will be estimated.
+     * When provided only the x positions are needed; the corresponding y
+     * values are computed internally using a median window around each x.
+     * @default undefined
+     */
+    anchors?: NumberArray;
     maxIterations: number;
     tolerance: number;
+    autoDownsample?: boolean;
 }
 
 export declare interface Apodization1DFilterOptions extends BaseFilter {
@@ -112,12 +122,47 @@ export declare interface BasePeak {
 }
 
 export declare interface BernsteinOptions {
-    algorithm: 'bernstein';
     degree: number;
+    algorithm: 'bernstein';
+    /**
+     * Array of x positions (anchors) where the baseline will be estimated.
+     * When provided only the x positions are needed; the corresponding y
+     * values are computed internally using a median window around each x.
+     * @default undefined
+     */
+    anchors?: NumberArray;
+    /**
+     * Median window size (in number of points) used to compute anchor y
+     * values from the input `data` when `anchors` (x positions) are
+     * provided. If omitted a sensible default is used by `getAnchors`.
+     * @default undefined
+     */
+    medianWindow?: number;
+    /**
+     * Maximum number of iterations to perform.
+     * @default 100
+     */
     maxIterations?: number;
+    /**
+     * Tolerance level for convergence.
+     * The algorithm stops if the change between iterations is below this value.
+     * @default 1e-6
+     */
     tolerance?: number;
+    /**
+     * Factor to scale the residuals.
+     * @default 1.0
+     */
     factorStd?: number;
+    /**
+     * Learning rate for the iterative updates.
+     * @default 0.01
+     */
     learningRate?: number;
+    /**
+     * Logger instance for logging the progress and debug information.
+     */
+    logger?: Logger;
 }
 
 declare interface BooleanField extends Field<boolean> {
@@ -128,12 +173,46 @@ declare type CommonField = SelectField | StringField | NumberField | BooleanFiel
 
 export declare interface CubicOptions {
     algorithm: 'cubic';
-    numAnchors?: number;
+    /**
+     * Array of x positions (anchors) where the baseline will be estimated.
+     * When provided only the x positions are needed; the corresponding y
+     * values are computed internally using a median window around each x.
+     * @default []
+     */
+    anchors?: NumberArray;
+    /**
+     * Noise threshold multiplier.  An anchor is clipped when
+     *   signal[anchor] > baseline[anchor] + noiseThreshold * σ_noise
+     * Smaller → more aggressive clipping (may clip baseline regions too).
+     * Larger  → less clipping (may leave some signal contamination).
+     * Default: 1.0
+     */
     noiseThreshold?: number;
+    /**
+     * Maximum number of clipping iterations.
+     * Default: 20
+     */
     maxIterations?: number;
+    /**
+     * Stop iterating when RMS change in baseline between iterations
+     * falls below tolerance * σ_noise.
+     * Default: 0.001
+     */
     tolerance?: number;
+    /**
+     * Override the automatic noise estimate with a fixed value.
+     * Useful when you know your instrument's noise floor.
+     */
     noiseLevel?: number;
+    /**
+     * Percentile (0–100) used to estimate noise from |diff(signal)|.
+     * Default: 10 (lower 10th percentile of first differences).
+     */
     noisePercentile?: number;
+    /** Median window size (number of points) passed to `getAnchors` when
+     * `anchors` is supplied. Default: Math.max(1, Math.floor(data.y.length/100)).
+     */
+    medianWindow?: number;
 }
 
 export declare interface DigitalFilter2DOptions extends BaseFilter {
@@ -292,6 +371,7 @@ export declare interface Info {
     solvent?: string;
     pulseSequence?: string;
     name: string;
+    spectrumSource?: SpectrumSource;
 }
 
 export declare interface Info1D extends Info {
@@ -528,7 +608,13 @@ export declare interface PhaseCorrectionVerticalOptions extends PhaseCorrectionH
 }
 
 export declare interface PolynomialOptions {
-    zones: BaselineCorrectionZone[];
+    /**
+     * Array of x positions (anchors) where the baseline will be estimated.
+     * When provided only the x positions are needed; the corresponding y
+     * values are computed internally using a median window around each x.
+     * @default undefined
+     */
+    anchors?: NumberArray;
     algorithm: 'polynomial';
     degree: number;
 }
@@ -639,6 +725,8 @@ export declare interface SineBellOptions {
 
 export declare type SineSquareOptions = Omit<SineBellOptions, 'exponent'>;
 
+export declare type SpectrumSource = 'prediction' | 'database' | 'unknown';
+
 declare interface StringField extends Field<string> {
     type: 'string';
 }
@@ -723,8 +811,35 @@ export declare interface TrimOptions {
 
 export declare interface WhittakerOptions {
     algorithm: 'whittaker';
+    /**
+     * Value between [0-1] that indicates how much the initial weight will be updated relative to the absolute
+     * value of an approximation of the standard deviation of the difference between
+     * the baseline and the original signal.
+     * @default 0.2
+     */
+    learningRate?: number;
+    /**
+     * Smoothing parameter. Factor of weights matrix in -> [I + lambda D'D]z = x.
+     * @default 2000
+     */
     lambda?: number;
+    /**
+     * Maximal number of iterations if the method does not reach the stop criterion.
+     * @default 100
+     */
     maxIterations?: number;
+    /**
+     * Tolerance for convergence. The process stops if the change in baseline is less than this value.
+     * @default 1e-3
+     */
+    tolerance?: number;
+    /**
+     * Array of x positions (anchors) where the baseline will be estimated.
+     * When provided only the x positions are needed; the corresponding y
+     * values are computed internally using a median window around each x.
+     * @default undefined
+     */
+    anchors?: NumberArray;
 }
 
 export declare interface ZeroFillingDimension1Options extends BaseFilter {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@zakodium/nmr-types",
-  "version": "0.5.8",
+  "version": "0.5.10",
   "description": "Types related to NMR data processing.",
   "author": "Zakodium Sàrl",
   "license": "CC-BY-NC-SA-4.0",
@@ -38,5 +38,5 @@
   "volta": {
     "extends": "../../../package.json"
   },
-  "gitHead": "433002a53e8ad5b8b3743ae5762c1d4a4b8fc85a"
+  "gitHead": "33548bbb69c0f3d6eb5ded49caf404d5f53cf7ac"
 }