ir-spectrum 3.2.1 → 4.0.0

package/lib/convertPeak.d.ts

@@ -0,0 +1,22 @@
+import type { MeasurementXY } from 'cheminfo-types';
+export interface ConvertedPeak {
+    wavenumber: number;
+    absorbance: number;
+    transmittance: number;
+    kind: string;
+}
+interface SpectrumPeak {
+    x: number;
+    a: number;
+    t: number;
+    [key: string]: number;
+}
+/**
+ * Converts a peak from common-spectrum format to IR-specific format.
+ * @param peak - Peak object with x, a, t properties.
+ * @param spectrum - Spectrum containing variable metadata.
+ * @returns Converted peak with wavenumber, absorbance, transmittance, and kind.
+ */
+export declare function convertPeak(peak: SpectrumPeak, spectrum: MeasurementXY): ConvertedPeak;
+export {};
+//# sourceMappingURL=convertPeak.d.ts.map

package/lib/convertPeak.d.ts.map

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package/lib/convertPeak.js

@@ -0,0 +1,26 @@
+/**
+ * Converts a peak from common-spectrum format to IR-specific format.
+ * @param peak - Peak object with x, a, t properties.
+ * @param spectrum - Spectrum containing variable metadata.
+ * @returns Converted peak with wavenumber, absorbance, transmittance, and kind.
+ */
+export function convertPeak(peak, spectrum) {
+    const tVariable = spectrum.variables.t;
+    return {
+        wavenumber: peak.x,
+        absorbance: peak.a,
+        transmittance: peak.t / 100,
+        kind: getPeakKind(peak.t, tVariable?.min ?? 0, tVariable?.max ?? 100),
+    };
+}
+function getPeakKind(transmittance, minTransmittance, maxTransmittance) {
+    const position = (maxTransmittance - transmittance) / (maxTransmittance - minTransmittance);
+    if (position < 0.33) {
+        return 'w';
+    }
+    else if (position < 0.66) {
+        return 'm';
+    }
+    return 'S';
+}
+//# sourceMappingURL=convertPeak.js.map

package/lib/convertPeak.js.map

@@ -0,0 +1 @@
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package/lib/from/fromJcamp.d.ts

@@ -0,0 +1,19 @@
+import type { MeasurementXYVariables, TextData } from 'cheminfo-types';
+import type { Analysis } from 'common-spectrum';
+interface FromJcampOptions {
+    /** Unique identifier for the analysis. */
+    id?: string;
+    /** Human-readable label for the analysis. */
+    label?: string;
+    /** Custom callback to apply on variables when creating a spectrum. Defaults to adding absorbance/transmittance variables. */
+    spectrumCallback?: (variables: MeasurementXYVariables) => MeasurementXYVariables;
+}
+/**
+ * Creates a new Analysis from a JCAMP string or buffer.
+ * @param jcamp - JCAMP data as a string or ArrayBuffer.
+ * @param options - Options for the analysis.
+ * @returns New Analysis element with the given data.
+ */
+export declare function fromJcamp(jcamp: TextData, options?: FromJcampOptions): Analysis;
+export {};
+//# sourceMappingURL=fromJcamp.d.ts.map

package/lib/from/fromJcamp.d.ts.map

@@ -0,0 +1 @@
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package/lib/from/fromJcamp.js

@@ -0,0 +1,13 @@
+import { fromJcamp as commonFromJcamp } from 'common-spectrum';
+import { spectrumCallback as defaultSpectrumCallback } from "./utils/spectrumCallback.js";
+/**
+ * Creates a new Analysis from a JCAMP string or buffer.
+ * @param jcamp - JCAMP data as a string or ArrayBuffer.
+ * @param options - Options for the analysis.
+ * @returns New Analysis element with the given data.
+ */
+export function fromJcamp(jcamp, options = {}) {
+    const { spectrumCallback = defaultSpectrumCallback, ...rest } = options;
+    return commonFromJcamp(jcamp, { ...rest, spectrumCallback });
+}
+//# sourceMappingURL=fromJcamp.js.map

package/lib/from/fromJcamp.js.map

@@ -0,0 +1 @@
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package/lib/from/fromSPC.d.ts

@@ -0,0 +1,20 @@
+import type { MeasurementXYVariables } from 'cheminfo-types';
+import { Analysis } from 'common-spectrum';
+import type { InputData } from 'spc-parser';
+interface FromSPCOptions {
+    /** Unique identifier for the analysis. */
+    id?: string;
+    /** Human-readable label for the analysis. */
+    label?: string;
+    /** Custom callback to apply on variables when creating a spectrum. Defaults to adding absorbance/transmittance variables. */
+    spectrumCallback?: (variables: MeasurementXYVariables) => MeasurementXYVariables;
+}
+/**
+ * Creates a new Analysis from an SPC buffer.
+ * @param buffer - SPC file buffer.
+ * @param options - Options for the analysis.
+ * @returns New Analysis element with the given data.
+ */
+export declare function fromSPC(buffer: InputData, options?: FromSPCOptions): Analysis;
+export {};
+//# sourceMappingURL=fromSPC.d.ts.map

package/lib/from/fromSPC.d.ts.map

@@ -0,0 +1 @@
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package/lib/from/fromSPC.js

@@ -0,0 +1,25 @@
+import { Analysis } from 'common-spectrum';
+import { parse } from 'spc-parser';
+import { spectrumCallback as defaultSpectrumCallback } from "./utils/spectrumCallback.js";
+/**
+ * Creates a new Analysis from an SPC buffer.
+ * @param buffer - SPC file buffer.
+ * @param options - Options for the analysis.
+ * @returns New Analysis element with the given data.
+ */
+export function fromSPC(buffer, options = {}) {
+    const { spectrumCallback = defaultSpectrumCallback, ...rest } = options;
+    const analysis = new Analysis({ ...rest, spectrumCallback });
+    const result = parse(buffer);
+    const { parameters: _resultParameters, ...resultMeta } = result.meta;
+    for (const spectrum of result.spectra) {
+        const { parameters: _spectrumParameters, ...spectrumMeta } = spectrum.meta ?? {};
+        analysis.pushSpectrum(spectrum.variables, {
+            dataType: 'IR SPECTRUM',
+            title: '',
+            meta: { ...resultMeta, ...spectrumMeta },
+        });
+    }
+    return analysis;
+}
+//# sourceMappingURL=fromSPC.js.map

package/lib/from/fromSPC.js.map

@@ -0,0 +1 @@
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package/lib/from/utils/spectrumCallback.d.ts

@@ -0,0 +1,9 @@
+import type { MeasurementXYVariables } from 'cheminfo-types';
+/**
+ * Callback that adds absorbance (a) and transmittance (t) variables to the spectrum.
+ * If the y variable is absorbance, transmittance is computed and vice versa.
+ * @param variables - Spectrum variables with at least x and y defined.
+ * @returns The modified variables with a and t added.
+ */
+export declare function spectrumCallback(variables: MeasurementXYVariables): MeasurementXYVariables;
+//# sourceMappingURL=spectrumCallback.d.ts.map

package/lib/from/utils/spectrumCallback.d.ts.map

@@ -0,0 +1 @@
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package/lib/from/utils/spectrumCallback.js

@@ -0,0 +1,55 @@
+/**
+ * Callback that adds absorbance (a) and transmittance (t) variables to the spectrum.
+ * If the y variable is absorbance, transmittance is computed and vice versa.
+ * @param variables - Spectrum variables with at least x and y defined.
+ * @returns The modified variables with a and t added.
+ */
+export function spectrumCallback(variables) {
+    // we add missing absorbance / transmittance
+    // variable a = absorbance
+    // variable t = transmittance
+    const yVariable = variables.y;
+    let isAbsorbance = true;
+    if (yVariable.label.toLowerCase().includes('trans')) {
+        isAbsorbance = false;
+    }
+    if (isAbsorbance) {
+        variables.a = {
+            ...yVariable,
+            symbol: 'a',
+            data: yVariable.data.slice(),
+        };
+        variables.t = {
+            data: yVariable.data.map((absorbance) => 10 ** -absorbance * 100),
+            label: 'Transmittance (%)',
+            symbol: 't',
+            units: '',
+        };
+    }
+    else {
+        const factor = yVariable.label.includes('%') ||
+            yVariable.label.toLowerCase().includes('percent')
+            ? 100
+            : 1;
+        variables.a = {
+            data: yVariable.data.map((transmittance) => -Math.log10(transmittance / factor)),
+            symbol: 'a',
+            label: 'Absorbance',
+            units: '',
+        };
+        if (factor === 100) {
+            variables.t = { ...yVariable, symbol: 't' };
+            variables.t.data = variables.t.data.slice();
+        }
+        else {
+            variables.t = {
+                units: '',
+                label: 'Transmittance (%)',
+                symbol: 't',
+                data: yVariable.data.map((transmittance) => transmittance * 100),
+            };
+        }
+    }
+    return variables;
+}
+//# sourceMappingURL=spectrumCallback.js.map

package/lib/from/utils/spectrumCallback.js.map

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package/lib/index.d.ts

@@ -0,0 +1,28 @@
+import type { MeasurementXY } from 'cheminfo-types';
+import type { AutoPeakPickingOptions, PeakPickingOptions } from 'common-spectrum';
+import { JSGraph as OriginalJSGraph } from 'common-spectrum';
+import type { ConvertedPeak } from './convertPeak.ts';
+import { getAnnotations } from './jsgraph/getAnnotations.ts';
+export type { ConvertedPeak } from './convertPeak.ts';
+export { AnalysesManager, Analysis, toJcamp } from 'common-spectrum';
+/**
+ * Picks a single peak closest to the given target wavenumber.
+ * @param spectrum - The spectrum to pick from.
+ * @param target - Target wavenumber value.
+ * @param options - Peak picking options.
+ * @returns The converted peak or undefined if no peak is found.
+ */
+export declare function peakPicking(spectrum: MeasurementXY, target: number, options?: PeakPickingOptions): ConvertedPeak | undefined;
+/**
+ * Automatically picks all peaks in the spectrum.
+ * @param spectrum - The spectrum to pick from.
+ * @param options - Auto peak picking options.
+ * @returns Array of converted peaks.
+ */
+export declare function autoPeakPicking(spectrum: MeasurementXY, options?: AutoPeakPickingOptions): ConvertedPeak[];
+export { fromJcamp } from './from/fromJcamp.ts';
+export { fromSPC } from './from/fromSPC.ts';
+export declare const JSGraph: typeof OriginalJSGraph & {
+    getAnnotations: typeof getAnnotations;
+};
+//# sourceMappingURL=index.d.ts.map

package/lib/index.d.ts.map

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package/lib/index.js

@@ -0,0 +1,33 @@
+import { JSGraph as OriginalJSGraph, autoPeakPicking as originalAutoPeakPicking, peakPicking as originalPeakPicking, } from 'common-spectrum';
+import { convertPeak } from "./convertPeak.js";
+import { getAnnotations } from "./jsgraph/getAnnotations.js";
+export { AnalysesManager, Analysis, toJcamp } from 'common-spectrum';
+/**
+ * Picks a single peak closest to the given target wavenumber.
+ * @param spectrum - The spectrum to pick from.
+ * @param target - Target wavenumber value.
+ * @param options - Peak picking options.
+ * @returns The converted peak or undefined if no peak is found.
+ */
+export function peakPicking(spectrum, target, options) {
+    const peak = originalPeakPicking(spectrum, target, options);
+    if (!peak)
+        return undefined;
+    return convertPeak(peak, spectrum);
+}
+/**
+ * Automatically picks all peaks in the spectrum.
+ * @param spectrum - The spectrum to pick from.
+ * @param options - Auto peak picking options.
+ * @returns Array of converted peaks.
+ */
+export function autoPeakPicking(spectrum, options) {
+    const peaks = originalAutoPeakPicking(spectrum, options);
+    if (!peaks)
+        return [];
+    return peaks.map((peak) => convertPeak(peak, spectrum));
+}
+export { fromJcamp } from "./from/fromJcamp.js";
+export { fromSPC } from "./from/fromSPC.js";
+export const JSGraph = { ...OriginalJSGraph, getAnnotations };
+//# sourceMappingURL=index.js.map

package/lib/index.js.map

@@ -0,0 +1 @@
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package/lib/jsgraph/getAnnotations.d.ts

@@ -0,0 +1,59 @@
+interface AnnotationPeak {
+    wavenumber: number;
+    transmittance: number;
+    absorbance: number;
+    kind: string;
+    assignment?: string;
+}
+interface AnnotationLabel {
+    text: string;
+    size: string;
+    anchor: string;
+    color: string;
+    angle?: number;
+    position: {
+        x: number;
+        y: number;
+        dy: string;
+    };
+}
+interface AnnotationPosition {
+    x: number;
+    y: number;
+    dy: string;
+    dx: string;
+}
+interface Annotation {
+    line: number;
+    type: string;
+    strokeColor: string;
+    strokeWidth: number;
+    fillColor: string;
+    labels?: AnnotationLabel[];
+    position?: AnnotationPosition[];
+}
+interface GetAnnotationsOptions {
+    /** Fill color for annotation rectangles. */
+    fillColor?: string;
+    /** Stroke color for annotation rectangles. */
+    strokeColor?: string;
+    /** Display the kind ('m', 'w', 'S'). */
+    showKind?: boolean;
+    /** Display the assignment. */
+    showAssignment?: boolean;
+    /** Callback allowing to add properties to an annotation. */
+    creationFct?: (annotation: Annotation, peak: AnnotationPeak) => void;
+    /** 't100'=transmittance in %, 't'=transmittance, 'a'=absorbance. */
+    mode?: 'a' | 't' | 't100';
+    /** Angle for assignment labels in absorbance mode. */
+    assignmentAngle?: number;
+}
+/**
+ * Creates annotations for jsgraph that allows to display the result of peak picking.
+ * @param peaks - Array of peaks with wavenumber, transmittance, absorbance, kind.
+ * @param options - Display options for the annotations.
+ * @returns Array of annotation objects for jsgraph.
+ */
+export declare function getAnnotations(peaks: AnnotationPeak[], options?: GetAnnotationsOptions): Annotation[];
+export {};
+//# sourceMappingURL=getAnnotations.d.ts.map

package/lib/jsgraph/getAnnotations.d.ts.map

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package/lib/jsgraph/getAnnotations.js

@@ -0,0 +1,133 @@
+/**
+ * Creates annotations for jsgraph that allows to display the result of peak picking.
+ * @param peaks - Array of peaks with wavenumber, transmittance, absorbance, kind.
+ * @param options - Display options for the annotations.
+ * @returns Array of annotation objects for jsgraph.
+ */
+export function getAnnotations(peaks, options = {}) {
+    const { fillColor = 'green', strokeColor = 'red', creationFct, mode = 't100', } = options;
+    const annotations = peaks.map((peak) => {
+        const annotation = {
+            line: 1,
+            type: 'rect',
+            strokeColor,
+            strokeWidth: 0,
+            fillColor,
+        };
+        if (creationFct) {
+            creationFct(annotation, peak);
+        }
+        switch (mode) {
+            case 'a':
+                annotationAbsorbance(annotation, peak, options);
+                break;
+            case 't':
+                annotationTransmittance(annotation, peak, 1, options);
+                break;
+            case 't100':
+                annotationTransmittance(annotation, peak, 100, options);
+                break;
+            default:
+        }
+        return annotation;
+    });
+    return annotations;
+}
+function annotationTransmittance(annotation, peak, factor = 1, options = {}) {
+    const { showKind = true, showAssignment = true } = options;
+    const labels = [];
+    let line = 0;
+    if (showKind) {
+        labels.push({
+            text: peak.kind,
+            size: '18px',
+            anchor: 'middle',
+            color: 'red',
+            position: {
+                x: peak.wavenumber,
+                y: peak.transmittance * factor,
+                dy: `${23 + line * 14}px`,
+            },
+        });
+        line++;
+    }
+    if (showAssignment) {
+        labels.push({
+            text: peak.assignment ?? '',
+            size: '18px',
+            anchor: 'middle',
+            color: 'darkred',
+            position: {
+                x: peak.wavenumber,
+                y: peak.transmittance * factor,
+                dy: `${23 + line * 14}px`,
+            },
+        });
+        line++;
+    }
+    annotation.labels = labels;
+    annotation.position = [
+        {
+            x: peak.wavenumber,
+            y: peak.transmittance * factor,
+            dy: '10px',
+            dx: '-1px',
+        },
+        {
+            x: peak.wavenumber,
+            y: peak.transmittance * factor,
+            dy: '5px',
+            dx: '1px',
+        },
+    ];
+}
+function annotationAbsorbance(annotation, peak, options = {}) {
+    const { showKind = true, showAssignment = true, assignmentAngle = -45, } = options;
+    const labels = [];
+    let line = 0;
+    if (showKind) {
+        labels.push({
+            text: peak.kind,
+            size: '18px',
+            anchor: 'middle',
+            color: 'red',
+            position: {
+                x: peak.wavenumber,
+                y: peak.absorbance,
+                dy: `${-15 - line * 14}px`,
+            },
+        });
+        line++;
+    }
+    if (showAssignment) {
+        labels.push({
+            text: peak.assignment ?? '',
+            size: '18px',
+            angle: assignmentAngle,
+            anchor: 'left',
+            color: 'darkred',
+            position: {
+                x: peak.wavenumber,
+                y: peak.absorbance,
+                dy: `${-15 - line * 14}px`,
+            },
+        });
+        line++;
+    }
+    annotation.labels = labels;
+    annotation.position = [
+        {
+            x: peak.wavenumber,
+            y: peak.absorbance,
+            dy: '-10px',
+            dx: '-1px',
+        },
+        {
+            x: peak.wavenumber,
+            y: peak.absorbance,
+            dy: '-5px',
+            dx: '1px',
+        },
+    ];
+}
+//# sourceMappingURL=getAnnotations.js.map

package/lib/jsgraph/getAnnotations.js.map

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package/package.json

@@ -1,22 +1,28 @@
 {
   "name": "ir-spectrum",
-  "version": "3.2.1",
+  "version": "4.0.0",
   "description": "Package used to handle IR spectra in SciPeaks.",
   "type": "module",
-  "exports": "./src/index.js",
+  "exports": {
+    ".": "./lib/index.js"
+  },
   "files": [
+    "lib",
     "src"
   ],
   "scripts": {
-    "build": "cheminfo-build  --entry src/index.js --root IRSpectrum",
-    "build-doc": "cheminfo doc",
+    "build": "npm run tsc && cheminfo-build --entry lib/index.js --root IRSpectrum",
+    "check-types": "tsc --noEmit",
+    "clean": "rimraf lib",
     "eslint": "eslint src",
     "eslint-fix": "npm run eslint -- --fix",
+    "prepack": "npm run tsc",
     "prettier": "prettier --check src",
     "prettier-write": "prettier --write src",
-    "test": "npm run test-only && npm run eslint && npm run prettier",
+    "test": "npm run test-only && npm run check-types && npm run eslint && npm run prettier",
     "test-only": "vitest run --coverage",
-    "test-import": "node -e \"import('file://' + process.cwd() + '/src/index.js').then(console.log)\""
+    "tsc": "npm run clean && npm run tsc-build",
+    "tsc-build": "tsc --project tsconfig.build.json"
   },
   "repository": {
     "type": "git",
@@ -29,22 +35,23 @@
     "url": "https://github.com/cheminfo/ir-spectrum/issues"
   },
   "homepage": "https://github.com/cheminfo/ir-spectrum#readme",
+  "dependencies": {
+    "common-spectrum": "3.1.0",
+    "ml-gsd": "^13.1.1",
+    "spc-parser": "^1.0.0"
+  },
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.27.1",
-    "@vitest/coverage-v8": "^3.2.4",
-    "cheminfo-build": "^1.2.1",
-    "eslint": "^9.32.0",
-    "eslint-config-cheminfo": "^15.0.1",
-    "esm": "^3.2.25",
+    "@types/node": "^25.3.0",
+    "@vitest/coverage-v8": "^4.0.18",
+    "@zakodium/tsconfig": "^1.0.2",
+    "cheminfo-build": "^1.3.2",
+    "eslint": "^9.39.2",
+    "eslint-config-cheminfo-typescript": "^21.1.0",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "prettier": "^3.6.2",
-    "vitest": "^3.2.4"
-  },
-  "dependencies": {
-    "common-spectrum": "2.12.0",
-    "ml-gsd": "^13.0.1",
-    "spc-parser": "^1.0.0",
-    "uninstall": "^0.0.0"
+    "prettier": "^3.8.1",
+    "rimraf": "^6.1.3",
+    "typescript": "^5.9.3",
+    "vitest": "^4.0.18"
   },
   "info": {
     "logo": "https://raw.githubusercontent.com/cheminfo/font/master/src/ir/assignment.svg",

package/src/convertPeak.ts

@@ -0,0 +1,49 @@
+import type { MeasurementXY } from 'cheminfo-types';
+
+export interface ConvertedPeak {
+  wavenumber: number;
+  absorbance: number;
+  transmittance: number;
+  kind: string;
+}
+
+interface SpectrumPeak {
+  x: number;
+  a: number;
+  t: number;
+  [key: string]: number;
+}
+
+/**
+ * Converts a peak from common-spectrum format to IR-specific format.
+ * @param peak - Peak object with x, a, t properties.
+ * @param spectrum - Spectrum containing variable metadata.
+ * @returns Converted peak with wavenumber, absorbance, transmittance, and kind.
+ */
+export function convertPeak(
+  peak: SpectrumPeak,
+  spectrum: MeasurementXY,
+): ConvertedPeak {
+  const tVariable = spectrum.variables.t;
+  return {
+    wavenumber: peak.x,
+    absorbance: peak.a,
+    transmittance: peak.t / 100,
+    kind: getPeakKind(peak.t, tVariable?.min ?? 0, tVariable?.max ?? 100),
+  };
+}
+
+function getPeakKind(
+  transmittance: number,
+  minTransmittance: number,
+  maxTransmittance: number,
+): string {
+  const position =
+    (maxTransmittance - transmittance) / (maxTransmittance - minTransmittance);
+  if (position < 0.33) {
+    return 'w';
+  } else if (position < 0.66) {
+    return 'm';
+  }
+  return 'S';
+}

package/src/from/fromJcamp.ts

@@ -0,0 +1,30 @@
+import type { MeasurementXYVariables, TextData } from 'cheminfo-types';
+import type { Analysis } from 'common-spectrum';
+import { fromJcamp as commonFromJcamp } from 'common-spectrum';
+
+import { spectrumCallback as defaultSpectrumCallback } from './utils/spectrumCallback.ts';
+
+interface FromJcampOptions {
+  /** Unique identifier for the analysis. */
+  id?: string;
+  /** Human-readable label for the analysis. */
+  label?: string;
+  /** Custom callback to apply on variables when creating a spectrum. Defaults to adding absorbance/transmittance variables. */
+  spectrumCallback?: (
+    variables: MeasurementXYVariables,
+  ) => MeasurementXYVariables;
+}
+
+/**
+ * Creates a new Analysis from a JCAMP string or buffer.
+ * @param jcamp - JCAMP data as a string or ArrayBuffer.
+ * @param options - Options for the analysis.
+ * @returns New Analysis element with the given data.
+ */
+export function fromJcamp(
+  jcamp: TextData,
+  options: FromJcampOptions = {},
+): Analysis {
+  const { spectrumCallback = defaultSpectrumCallback, ...rest } = options;
+  return commonFromJcamp(jcamp, { ...rest, spectrumCallback });
+}

package/src/from/fromSPC.ts

@@ -0,0 +1,45 @@
+import type { MeasurementXYVariables } from 'cheminfo-types';
+import { Analysis } from 'common-spectrum';
+import type { InputData } from 'spc-parser';
+import { parse } from 'spc-parser';
+
+import { spectrumCallback as defaultSpectrumCallback } from './utils/spectrumCallback.ts';
+
+interface FromSPCOptions {
+  /** Unique identifier for the analysis. */
+  id?: string;
+  /** Human-readable label for the analysis. */
+  label?: string;
+  /** Custom callback to apply on variables when creating a spectrum. Defaults to adding absorbance/transmittance variables. */
+  spectrumCallback?: (
+    variables: MeasurementXYVariables,
+  ) => MeasurementXYVariables;
+}
+
+/**
+ * Creates a new Analysis from an SPC buffer.
+ * @param buffer - SPC file buffer.
+ * @param options - Options for the analysis.
+ * @returns New Analysis element with the given data.
+ */
+export function fromSPC(
+  buffer: InputData,
+  options: FromSPCOptions = {},
+): Analysis {
+  const { spectrumCallback = defaultSpectrumCallback, ...rest } = options;
+  const analysis = new Analysis({ ...rest, spectrumCallback });
+  const result = parse(buffer);
+
+  const { parameters: _resultParameters, ...resultMeta } = result.meta;
+
+  for (const spectrum of result.spectra) {
+    const { parameters: _spectrumParameters, ...spectrumMeta } =
+      spectrum.meta ?? {};
+    analysis.pushSpectrum(spectrum.variables, {
+      dataType: 'IR SPECTRUM',
+      title: '',
+      meta: { ...resultMeta, ...spectrumMeta },
+    });
+  }
+  return analysis;
+}

package/src/from/utils/spectrumCallback.ts

@@ -0,0 +1,64 @@
+import type { MeasurementXYVariables } from 'cheminfo-types';
+
+/**
+ * Callback that adds absorbance (a) and transmittance (t) variables to the spectrum.
+ * If the y variable is absorbance, transmittance is computed and vice versa.
+ * @param variables - Spectrum variables with at least x and y defined.
+ * @returns The modified variables with a and t added.
+ */
+export function spectrumCallback(
+  variables: MeasurementXYVariables,
+): MeasurementXYVariables {
+  // we add missing absorbance / transmittance
+  // variable a = absorbance
+  // variable t = transmittance
+  const yVariable = variables.y;
+  let isAbsorbance = true;
+  if (yVariable.label.toLowerCase().includes('trans')) {
+    isAbsorbance = false;
+  }
+  if (isAbsorbance) {
+    variables.a = {
+      ...yVariable,
+      symbol: 'a',
+      data: yVariable.data.slice() as number[],
+    };
+    variables.t = {
+      data: (yVariable.data as number[]).map(
+        (absorbance: number) => 10 ** -absorbance * 100,
+      ),
+      label: 'Transmittance (%)',
+      symbol: 't',
+      units: '',
+    };
+  } else {
+    const factor =
+      yVariable.label.includes('%') ||
+      yVariable.label.toLowerCase().includes('percent')
+        ? 100
+        : 1;
+
+    variables.a = {
+      data: (yVariable.data as number[]).map(
+        (transmittance: number) => -Math.log10(transmittance / factor),
+      ),
+      symbol: 'a',
+      label: 'Absorbance',
+      units: '',
+    };
+    if (factor === 100) {
+      variables.t = { ...yVariable, symbol: 't' };
+      variables.t.data = variables.t.data.slice() as number[];
+    } else {
+      variables.t = {
+        units: '',
+        label: 'Transmittance (%)',
+        symbol: 't',
+        data: (yVariable.data as number[]).map(
+          (transmittance: number) => transmittance * 100,
+        ),
+      };
+    }
+  }
+  return variables;
+}

package/src/index.ts

@@ -0,0 +1,64 @@
+import type { MeasurementXY } from 'cheminfo-types';
+import type {
+  AutoPeakPickingOptions,
+  PeakPickingOptions,
+} from 'common-spectrum';
+import {
+  JSGraph as OriginalJSGraph,
+  autoPeakPicking as originalAutoPeakPicking,
+  peakPicking as originalPeakPicking,
+} from 'common-spectrum';
+
+import type { ConvertedPeak } from './convertPeak.ts';
+import { convertPeak } from './convertPeak.ts';
+import { getAnnotations } from './jsgraph/getAnnotations.ts';
+
+export type { ConvertedPeak } from './convertPeak.ts';
+export { AnalysesManager, Analysis, toJcamp } from 'common-spectrum';
+
+/**
+ * Picks a single peak closest to the given target wavenumber.
+ * @param spectrum - The spectrum to pick from.
+ * @param target - Target wavenumber value.
+ * @param options - Peak picking options.
+ * @returns The converted peak or undefined if no peak is found.
+ */
+export function peakPicking(
+  spectrum: MeasurementXY,
+  target: number,
+  options?: PeakPickingOptions,
+): ConvertedPeak | undefined {
+  const peak = originalPeakPicking(spectrum, target, options);
+  if (!peak) return undefined;
+  return convertPeak(
+    peak as { x: number; a: number; t: number; [key: string]: number },
+    spectrum,
+  );
+}
+
+/**
+ * Automatically picks all peaks in the spectrum.
+ * @param spectrum - The spectrum to pick from.
+ * @param options - Auto peak picking options.
+ * @returns Array of converted peaks.
+ */
+export function autoPeakPicking(
+  spectrum: MeasurementXY,
+  options?: AutoPeakPickingOptions,
+): ConvertedPeak[] {
+  const peaks = originalAutoPeakPicking(spectrum, options);
+  if (!peaks) return [];
+  return peaks.map((peak) =>
+    convertPeak(
+      peak as { x: number; a: number; t: number; [key: string]: number },
+      spectrum,
+    ),
+  );
+}
+
+export { fromJcamp } from './from/fromJcamp.ts';
+export { fromSPC } from './from/fromSPC.ts';
+
+export const JSGraph: typeof OriginalJSGraph & {
+  getAnnotations: typeof getAnnotations;
+} = { ...OriginalJSGraph, getAnnotations };

package/src/jsgraph/{getAnnotations.js → getAnnotations.ts}

@@ -1,34 +1,76 @@
-/**
- * @typedef {object} Peak
- * @property {number} wavenumber
- * @property {number} transmittance
- * @property {number} absorbance
- * @property {number} kind
- * @property {number} assignment
- */
+interface AnnotationPeak {
+  wavenumber: number;
+  transmittance: number;
+  absorbance: number;
+  kind: string;
+  assignment?: string;
+}
+
+interface AnnotationLabel {
+  text: string;
+  size: string;
+  anchor: string;
+  color: string;
+  angle?: number;
+  position: {
+    x: number;
+    y: number;
+    dy: string;
+  };
+}
+
+interface AnnotationPosition {
+  x: number;
+  y: number;
+  dy: string;
+  dx: string;
+}
+
+interface Annotation {
+  line: number;
+  type: string;
+  strokeColor: string;
+  strokeWidth: number;
+  fillColor: string;
+  labels?: AnnotationLabel[];
+  position?: AnnotationPosition[];
+}
+
+interface GetAnnotationsOptions {
+  /** Fill color for annotation rectangles. */
+  fillColor?: string;
+  /** Stroke color for annotation rectangles. */
+  strokeColor?: string;
+  /** Display the kind ('m', 'w', 'S'). */
+  showKind?: boolean;
+  /** Display the assignment. */
+  showAssignment?: boolean;
+  /** Callback allowing to add properties to an annotation. */
+  creationFct?: (annotation: Annotation, peak: AnnotationPeak) => void;
+  /** 't100'=transmittance in %, 't'=transmittance, 'a'=absorbance. */
+  mode?: 'a' | 't' | 't100';
+  /** Angle for assignment labels in absorbance mode. */
+  assignmentAngle?: number;
+}
 
 /**
- * Creates annotations for jsgraph that allows to display the result of peak picking
- * @param {Array<Peak>} peaks
- * @param {object} [options={}]
- * @param {string} [options.fillColor='green']
- * @param {string} [options.strokeColor='red']
- * @param {string} [options.showKind=true] - Display the kind, 'm', 'w', 'S'
- * @param {string} [options.showAssignment=true] - Display the assignment
- * @param {Function} [options.createFct] - (annotation, peak) => {}: callback allowing to add properties
- * @param {string} [options.mode='t100'] - 't100'=transmittance in %, 't'=transmittance, 'a'=absorbance
- * @returns array
+ * Creates annotations for jsgraph that allows to display the result of peak picking.
+ * @param peaks - Array of peaks with wavenumber, transmittance, absorbance, kind.
+ * @param options - Display options for the annotations.
+ * @returns Array of annotation objects for jsgraph.
  */
-
-export function getAnnotations(peaks, options = {}) {
+export function getAnnotations(
+  peaks: AnnotationPeak[],
+  options: GetAnnotationsOptions = {},
+): Annotation[] {
   const {
     fillColor = 'green',
     strokeColor = 'red',
     creationFct,
     mode = 't100',
   } = options;
-  let annotations = peaks.map((peak) => {
-    let annotation = {
+  const annotations = peaks.map((peak) => {
+    const annotation: Annotation = {
       line: 1,
       type: 'rect',
       strokeColor,
@@ -55,9 +97,14 @@ export function getAnnotations(peaks, options = {}) {
   return annotations;
 }
 
-function annotationTransmittance(annotation, peak, factor = 1, options = {}) {
+function annotationTransmittance(
+  annotation: Annotation,
+  peak: AnnotationPeak,
+  factor = 1,
+  options: GetAnnotationsOptions = {},
+): void {
   const { showKind = true, showAssignment = true } = options;
-  let labels = [];
+  const labels: AnnotationLabel[] = [];
   let line = 0;
 
   if (showKind) {
@@ -77,7 +124,7 @@ function annotationTransmittance(annotation, peak, factor = 1, options = {}) {
 
   if (showAssignment) {
     labels.push({
-      text: peak.assignment,
+      text: peak.assignment ?? '',
       size: '18px',
       anchor: 'middle',
       color: 'darkred',
@@ -107,13 +154,17 @@ function annotationTransmittance(annotation, peak, factor = 1, options = {}) {
   ];
 }
 
-function annotationAbsorbance(annotation, peak, options = {}) {
+function annotationAbsorbance(
+  annotation: Annotation,
+  peak: AnnotationPeak,
+  options: GetAnnotationsOptions = {},
+): void {
   const {
     showKind = true,
     showAssignment = true,
     assignmentAngle = -45,
   } = options;
-  let labels = [];
+  const labels: AnnotationLabel[] = [];
   let line = 0;
 
   if (showKind) {
@@ -133,7 +184,7 @@ function annotationAbsorbance(annotation, peak, options = {}) {
 
   if (showAssignment) {
     labels.push({
-      text: peak.assignment,
+      text: peak.assignment ?? '',
       size: '18px',
       angle: assignmentAngle,
       anchor: 'left',

package/src/convertPeak.js

@@ -1,23 +0,0 @@
-export function convertPeak(peak, spectrum) {
-  return {
-    wavenumber: peak.x,
-    absorbance: peak.a,
-    transmittance: peak.t / 100,
-    kind: getPeakKind(
-      peak.t,
-      spectrum.variables.t.min,
-      spectrum.variables.t.max,
-    ),
-  };
-}
-
-function getPeakKind(transmittance, minTransmittance, maxTransmittance) {
-  let position =
-    (maxTransmittance - transmittance) / (maxTransmittance - minTransmittance);
-  if (position < 0.33) {
-    return 'w';
-  } else if (position < 0.66) {
-    return 'm';
-  }
-  return 'S';
-}

package/src/from/fromJcamp.js

@@ -1,16 +0,0 @@
-import { fromJcamp as commonFromJcamp } from 'common-spectrum';
-
-import { spectrumCallback } from './utils/spectrumCallback.js';
-
-/**
- * Creates a new Analysis from a SPC buffer
- * @param {ArrayBuffer|string} jcamp
- * @param {object} [options={}]
- * @param {string|number} [options.id=Math.random()]
- * @param {string} [options.label=options.id] - human redeable label
- * @param {string} [options.spectrumCallback] - a callback to apply on variables when creating spectrum. Default will add a and t
- * @returns {Analysis} - New class element with the given data
- */
-export function fromJcamp(jcamp, options = {}) {
-  return commonFromJcamp(jcamp, { ...options, spectrumCallback });
-}

package/src/from/fromSPC.js

@@ -1,31 +0,0 @@
-import { Analysis } from 'common-spectrum';
-import { parse } from 'spc-parser';
-
-import { spectrumCallback } from './utils/spectrumCallback.js';
-
-/**
- * Creates a new Analysis from a SPC buffer
- * @param {ArrayBuffer} buffer
- * @param {object} [options={}]
- * @param {object} [options.id=Math.random()]
- * @param {string} [options.label=options.id] - human redeable label
- * @param {string} [options.spectrumCallback] - a callback to apply on variables when creating spectrum. Default will add a and t
- * @returns {Analysis} - New class element with the given data
- */
-
-export function fromSPC(buffer, options = {}) {
-  let analysis = new Analysis({ ...options, spectrumCallback });
-  let result = parse(buffer);
-
-  if (result.meta) delete result.meta.parameters;
-
-  for (let spectrum of result.spectra) {
-    if (spectrum.meta) delete spectrum.meta.parameters;
-    analysis.pushSpectrum(spectrum.variables, {
-      dataType: 'IR SPECTRUM',
-      title: '',
-      meta: { ...result.meta, ...spectrum.meta },
-    });
-  }
-  return analysis;
-}

package/src/from/utils/spectrumCallback.js

@@ -1,45 +0,0 @@
-export function spectrumCallback(variables) {
-  // we add missing absorbance / transmittance
-  // variable a = absorbance
-  // variable t = transmittance
-  let yVariable = variables.y;
-  let absorbance = true;
-  if (yVariable.label.toLowerCase().includes('trans')) {
-    absorbance = false;
-  }
-  if (absorbance) {
-    variables.a = { ...yVariable, symbol: 'a', data: yVariable.data.slice() };
-    variables.t = {
-      data: yVariable.data.map((absorbance) => 10 ** -absorbance * 100),
-      label: 'Transmittance (%)',
-      symbol: 't',
-      units: '',
-    };
-  } else {
-    const factor =
-      yVariable.label.includes('%') ||
-      yVariable.label.toLowerCase().includes('percent')
-        ? 100
-        : 1;
-
-    variables.a = {
-      data: yVariable.data.map(
-        (transmittance) => -Math.log10(transmittance / factor),
-      ),
-      symbol: 'a',
-      label: 'Absorbance',
-      units: '',
-    };
-    if (factor === 100) {
-      variables.t = { ...yVariable, symbol: 't' };
-      variables.t.data = variables.t.data.slice();
-    } else {
-      variables.t = {
-        units: '',
-        label: 'Transmittance (%)',
-        symbol: 't',
-        data: yVariable.data.map((transmittance) => transmittance * 100),
-      };
-    }
-  }
-}

package/src/index.js

@@ -1,27 +0,0 @@
-import {
-  JSGraph as OriginalJSGraph,
-  autoPeakPicking as originalAutoPeakPicking,
-  peakPicking as originalPeakPicking,
-} from 'common-spectrum';
-
-import { convertPeak } from './convertPeak.js';
-import { getAnnotations } from './jsgraph/getAnnotations.js';
-
-export { AnalysesManager, Analysis, toJcamp } from 'common-spectrum';
-
-export function peakPicking(spectrum, target, options) {
-  const peak = originalPeakPicking(spectrum, target, options);
-  if (!peak) return undefined;
-  return convertPeak(peak, spectrum);
-}
-
-export function autoPeakPicking(spectrum, options) {
-  const peaks = originalAutoPeakPicking(spectrum, options);
-  if (!peaks) return [];
-  return peaks.map((peak) => convertPeak(peak, spectrum));
-}
-
-export { fromJcamp } from './from/fromJcamp.js';
-export { fromSPC } from './from/fromSPC.js';
-
-export const JSGraph = { ...OriginalJSGraph, getAnnotations };