ir-spectrum 4.0.0 → 4.2.0

package/README.md

@@ -17,14 +17,25 @@ import IRSpectrum from 'ir-spectrum';
 let analysis = IRSpectrum.fromJcamp(jcamp);
 ```
 
-When loading an IRSpectrum from Jcamp we will systamatically add 2 new variables:
+When loading an IR spectrum from JCAMP or SPC, two additional variables are systematically added:
 
-- a: containing the absorbance
-- t: containing the percent transmittance
+| Key | Label              | Units | Description                      | Always present |
+| --- | ------------------ | ----- | -------------------------------- | -------------- |
+| x   | Wavenumber         | cm⁻¹  | Infrared wavenumber              | Yes            |
+| y   | (from source file) |       | Original y-axis data             | Yes            |
+| a   | Absorbance         |       | Absorbance values                | Yes            |
+| t   | Transmittance      | %     | Percent transmittance values     | Yes            |
 
-In order to calculate those 2 variables we will check the Y label. If it contains
-transmittance we calculate absorbance, if it contains absorbance we calculate transmittance.
-For transmittance we also check for the presence of a '%' sign.:w
+The conversion is automatic: if the original y label contains "transmittance", absorbance is calculated; if it contains "absorbance", transmittance is calculated. For transmittance, the presence of '%' or 'percent' in the label is used to determine the scaling factor.
+
+### Selector for visualization
+
+```html
+<select name="selector.variables">
+  <option value="a vs x">Absorbance versus wavenumber</option>
+  <option value="t vs x">Transmittance versus wavenumber</option>
+</select>
+```
 
 ## [API Documentation](https://cheminfo.github.io/ir-spectrum/)
 

package/lib/from/fromText.d.ts

@@ -0,0 +1,18 @@
+import type { TextData } from 'cheminfo-types';
+import type { FromTextOptions as CommonFromTextOptions } from 'common-spectrum';
+import { Analysis } from 'common-spectrum';
+interface FromTextOptions extends CommonFromTextOptions {
+    /** Unique identifier for the analysis. */
+    id?: string;
+    /** Human-readable label for the analysis. */
+    label?: string;
+}
+/**
+ * Creates a new Analysis from text data (CSV, TSV, etc.).
+ * @param data - Text data containing x,y values.
+ * @param options - Options for parsing and analysis creation.
+ * @returns New Analysis element with the given data.
+ */
+export declare function fromText(data: TextData, options?: FromTextOptions): Analysis;
+export {};
+//# sourceMappingURL=fromText.d.ts.map

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

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

@@ -0,0 +1,28 @@
+import { Analysis } from 'common-spectrum';
+import { parseXYAndKeepInfo } from 'xy-parser';
+/**
+ * Creates a new Analysis from text data (CSV, TSV, etc.).
+ * @param data - Text data containing x,y values.
+ * @param options - Options for parsing and analysis creation.
+ * @returns New Analysis element with the given data.
+ */
+export function fromText(data, options = {}) {
+    const { info = {}, parser = {}, dataType = 'IR spectrum', title = '', ...rest } = options;
+    const analysis = new Analysis(rest);
+    const parsed = parseXYAndKeepInfo(data, parser);
+    const variables = {
+        x: {
+            data: parsed.data.x,
+            units: info.xUnits || '',
+            label: info.xLabel || '',
+        },
+        y: {
+            data: parsed.data.y,
+            units: info.yUnits || '',
+            label: info.yLabel || '',
+        },
+    };
+    analysis.pushSpectrum(variables, { dataType, title });
+    return analysis;
+}
+//# sourceMappingURL=fromText.js.map

package/lib/from/fromText.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"spectrumCallback.js","sourceRoot":"","sources":["../../../src/from/utils/spectrumCallback.ts"],"names":[],"mappings":"AAEA;;;;;GAKG;AACH,MAAM,UAAU,gBAAgB,CAC9B,SAAiC;IAEjC,4CAA4C;IAC5C,0BAA0B;IAC1B,6BAA6B;IAC7B,MAAM,SAAS,GAAG,SAAS,CAAC,CAAC,CAAC;IAC9B,IAAI,YAAY,GAAG,IAAI,CAAC;IACxB,IAAI,SAAS,CAAC,KAAK,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,OAAO,CAAC,EAAE,CAAC;QACpD,YAAY,GAAG,KAAK,CAAC;IACvB,CAAC;IACD,IAAI,YAAY,EAAE,CAAC;QACjB,SAAS,CAAC,CAAC,GAAG;YACZ,GAAG,SAAS;YACZ,MAAM,EAAE,GAAG;YACX,IAAI,EAAE,SAAS,CAAC,IAAI,CAAC,KAAK,EAAc;SACzC,CAAC;QACF,SAAS,CAAC,CAAC,GAAG;YACZ,IAAI,EAAG,SAAS,CAAC,IAAiB,CAAC,GAAG,CACpC,CAAC,UAAkB,EAAE,EAAE,CAAC,EAAE,IAAI,CAAC,UAAU,GAAG,GAAG,CAChD;YACD,KAAK,EAAE,mBAAmB;YAC1B,MAAM,EAAE,GAAG;YACX,KAAK,EAAE,EAAE;SACV,CAAC;IACJ,CAAC;SAAM,CAAC;QACN,MAAM,MAAM,GACV,SAAS,CAAC,KAAK,CAAC,QAAQ,CAAC,GAAG,CAAC;YAC7B,SAAS,CAAC,KAAK,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,SAAS,CAAC;YAC/C,CAAC,CAAC,GAAG;YACL,CAAC,CAAC,CAAC,CAAC;QAER,SAAS,CAAC,CAAC,GAAG;YACZ,IAAI,EAAG,SAAS,CAAC,IAAiB,CAAC,GAAG,CACpC,CAAC,aAAqB,EAAE,EAAE,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,aAAa,GAAG,MAAM,CAAC,CAC/D;YACD,MAAM,EAAE,GAAG;YACX,KAAK,EAAE,YAAY;YACnB,KAAK,EAAE,EAAE;SACV,CAAC;QACF,IAAI,MAAM,KAAK,GAAG,EAAE,CAAC;YACnB,SAAS,CAAC,CAAC,GAAG,EAAE,GAAG,SAAS,EAAE,MAAM,EAAE,GAAG,EAAE,CAAC;YAC5C,SAAS,CAAC,CAAC,CAAC,IAAI,GAAG,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC;QAC9C,CAAC;aAAM,CAAC;YACN,SAAS,CAAC,CAAC,GAAG;gBACZ,KAAK,EAAE,EAAE;gBACT,KAAK,EAAE,mBAAmB;gBAC1B,MAAM,EAAE,GAAG;gBACX,IAAI,EAAG,SAAS,CAAC,IAAiB,CAAC,GAAG,CACpC,CAAC,aAAqB,EAAE,EAAE,CAAC,aAAa,GAAG,GAAG,CAC/C;aACF,CAAC;QACJ,CAAC;IACH,CAAC;IACD,OAAO,SAAS,CAAC;AACnB,CAAC"}

package/lib/index.d.ts

@@ -22,6 +22,7 @@ export declare function peakPicking(spectrum: MeasurementXY, target: number, opt
 export declare function autoPeakPicking(spectrum: MeasurementXY, options?: AutoPeakPickingOptions): ConvertedPeak[];
 export { fromJcamp } from './from/fromJcamp.ts';
 export { fromSPC } from './from/fromSPC.ts';
+export { fromText } from './from/fromText.ts';
 export declare const JSGraph: typeof OriginalJSGraph & {
     getAnnotations: typeof getAnnotations;
 };

package/lib/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,gBAAgB,CAAC;AACpD,OAAO,KAAK,EACV,sBAAsB,EACtB,kBAAkB,EACnB,MAAM,iBAAiB,CAAC;AACzB,OAAO,EACL,OAAO,IAAI,eAAe,EAG3B,MAAM,iBAAiB,CAAC;AAEzB,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AAEtD,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAC;AAE7D,YAAY,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AACtD,OAAO,EAAE,eAAe,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAC;AAErE;;;;;;GAMG;AACH,wBAAgB,WAAW,CACzB,QAAQ,EAAE,aAAa,EACvB,MAAM,EAAE,MAAM,EACd,OAAO,CAAC,EAAE,kBAAkB,GAC3B,aAAa,GAAG,SAAS,CAO3B;AAED;;;;;GAKG;AACH,wBAAgB,eAAe,CAC7B,QAAQ,EAAE,aAAa,EACvB,OAAO,CAAC,EAAE,sBAAsB,GAC/B,aAAa,EAAE,CASjB;AAED,OAAO,EAAE,SAAS,EAAE,MAAM,qBAAqB,CAAC;AAChD,OAAO,EAAE,OAAO,EAAE,MAAM,mBAAmB,CAAC;AAE5C,eAAO,MAAM,OAAO,EAAE,OAAO,eAAe,GAAG;IAC7C,cAAc,EAAE,OAAO,cAAc,CAAC;CACE,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,gBAAgB,CAAC;AACpD,OAAO,KAAK,EACV,sBAAsB,EACtB,kBAAkB,EACnB,MAAM,iBAAiB,CAAC;AACzB,OAAO,EACL,OAAO,IAAI,eAAe,EAG3B,MAAM,iBAAiB,CAAC;AAEzB,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AAEtD,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAC;AAE7D,YAAY,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AACtD,OAAO,EAAE,eAAe,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAC;AAErE;;;;;;GAMG;AACH,wBAAgB,WAAW,CACzB,QAAQ,EAAE,aAAa,EACvB,MAAM,EAAE,MAAM,EACd,OAAO,CAAC,EAAE,kBAAkB,GAC3B,aAAa,GAAG,SAAS,CAO3B;AAED;;;;;GAKG;AACH,wBAAgB,eAAe,CAC7B,QAAQ,EAAE,aAAa,EACvB,OAAO,CAAC,EAAE,sBAAsB,GAC/B,aAAa,EAAE,CASjB;AAED,OAAO,EAAE,SAAS,EAAE,MAAM,qBAAqB,CAAC;AAChD,OAAO,EAAE,OAAO,EAAE,MAAM,mBAAmB,CAAC;AAC5C,OAAO,EAAE,QAAQ,EAAE,MAAM,oBAAoB,CAAC;AAE9C,eAAO,MAAM,OAAO,EAAE,OAAO,eAAe,GAAG;IAC7C,cAAc,EAAE,OAAO,cAAc,CAAC;CACE,CAAC"}

package/lib/index.js

@@ -29,5 +29,6 @@ export function autoPeakPicking(spectrum, options) {
 }
 export { fromJcamp } from "./from/fromJcamp.js";
 export { fromSPC } from "./from/fromSPC.js";
+export { fromText } from "./from/fromText.js";
 export const JSGraph = { ...OriginalJSGraph, getAnnotations };
 //# sourceMappingURL=index.js.map

package/lib/index.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "ir-spectrum",
-  "version": "4.0.0",
+  "version": "4.2.0",
   "description": "Package used to handle IR spectra in SciPeaks.",
   "type": "module",
   "exports": {
@@ -13,9 +13,9 @@
   "scripts": {
     "build": "npm run tsc && cheminfo-build --entry lib/index.js --root IRSpectrum",
     "check-types": "tsc --noEmit",
-    "clean": "rimraf lib",
+    "clean": "rimraf coverage lib",
     "eslint": "eslint src",
-    "eslint-fix": "npm run eslint -- --fix",
+    "eslint-fix": "eslint src --fix",
     "prepack": "npm run tsc",
     "prettier": "prettier --check src",
     "prettier-write": "prettier --write src",
@@ -36,22 +36,23 @@
   },
   "homepage": "https://github.com/cheminfo/ir-spectrum#readme",
   "dependencies": {
-    "common-spectrum": "3.1.0",
+    "common-spectrum": "3.2.0",
     "ml-gsd": "^13.1.1",
-    "spc-parser": "^1.0.0"
+    "spc-parser": "^2.0.0",
+    "xy-parser": "^6.0.1"
   },
   "devDependencies": {
-    "@types/node": "^25.3.0",
-    "@vitest/coverage-v8": "^4.0.18",
-    "@zakodium/tsconfig": "^1.0.2",
+    "@types/node": "^25.6.0",
+    "@vitest/coverage-v8": "^4.1.5",
+    "@zakodium/tsconfig": "^1.0.5",
     "cheminfo-build": "^1.3.2",
     "eslint": "^9.39.2",
-    "eslint-config-cheminfo-typescript": "^21.1.0",
+    "eslint-config-cheminfo-typescript": "^22.0.0",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "prettier": "^3.8.1",
+    "prettier": "^3.8.3",
     "rimraf": "^6.1.3",
-    "typescript": "^5.9.3",
-    "vitest": "^4.0.18"
+    "typescript": "^6.0.3",
+    "vitest": "^4.1.5"
   },
   "info": {
     "logo": "https://raw.githubusercontent.com/cheminfo/font/master/src/ir/assignment.svg",

package/src/from/fromText.ts

@@ -0,0 +1,50 @@
+import type { TextData } from 'cheminfo-types';
+import type { FromTextOptions as CommonFromTextOptions } from 'common-spectrum';
+import { Analysis } from 'common-spectrum';
+import { parseXYAndKeepInfo } from 'xy-parser';
+
+interface FromTextOptions extends CommonFromTextOptions {
+  /** Unique identifier for the analysis. */
+  id?: string;
+  /** Human-readable label for the analysis. */
+  label?: string;
+}
+
+/**
+ * Creates a new Analysis from text data (CSV, TSV, etc.).
+ * @param data - Text data containing x,y values.
+ * @param options - Options for parsing and analysis creation.
+ * @returns New Analysis element with the given data.
+ */
+export function fromText(
+  data: TextData,
+  options: FromTextOptions = {},
+): Analysis {
+  const {
+    info = {},
+    parser = {},
+    dataType = 'IR spectrum',
+    title = '',
+    ...rest
+  } = options;
+
+  const analysis = new Analysis(rest);
+
+  const parsed = parseXYAndKeepInfo(data, parser);
+  const variables = {
+    x: {
+      data: parsed.data.x,
+      units: info.xUnits || '',
+      label: info.xLabel || '',
+    },
+    y: {
+      data: parsed.data.y,
+      units: info.yUnits || '',
+      label: info.yLabel || '',
+    },
+  };
+
+  analysis.pushSpectrum(variables, { dataType, title });
+
+  return analysis;
+}

package/src/from/utils/spectrumCallback.ts

@@ -48,7 +48,7 @@ export function spectrumCallback(
     };
     if (factor === 100) {
       variables.t = { ...yVariable, symbol: 't' };
-      variables.t.data = variables.t.data.slice() as number[];
+      variables.t.data = variables.t.data.slice();
     } else {
       variables.t = {
         units: '',

package/src/index.ts

@@ -58,6 +58,7 @@ export function autoPeakPicking(
 
 export { fromJcamp } from './from/fromJcamp.ts';
 export { fromSPC } from './from/fromSPC.ts';
+export { fromText } from './from/fromText.ts';
 
 export const JSGraph: typeof OriginalJSGraph & {
   getAnnotations: typeof getAnnotations;