ir-spectrum 4.1.0 → 4.2.1

package/README.md

@@ -12,19 +12,35 @@
 ## Usage
 
 ```js
-import IRSpectrum from 'ir-spectrum';
+import { readFileSync } from 'node:fs';
 
-let analysis = IRSpectrum.fromJcamp(jcamp);
+import { fromJcamp } from 'ir-spectrum';
+
+const analysis = fromJcamp(readFileSync('absorbance.jdx', 'utf8'));
+const spectrum = analysis.getSpectrum();
 ```
 
-When loading an IRSpectrum from Jcamp we will systamatically add 2 new variables:
+Other loaders are `fromSPC` (SPC files) and `fromText` (CSV, TSV and other x,y text). `peakPicking` and `autoPeakPicking` return peaks with their wavenumber, absorbance and transmittance.
+
+When loading an IR spectrum from JCAMP or SPC, two additional variables are systematically added:
+
+| 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            |
 
-- a: containing the absorbance
-- t: containing the percent transmittance
+The conversion is automatic: if the y label or units name a transmittance ("Transmittance", "Transmission", "%T", "T"), absorbance is calculated; otherwise y is taken as an absorbance and transmittance is calculated. A transmittance is read as a percentage when its label or units contain '%' or 'percent', or, failing that, when its values go above 2.
 
-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
+### 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/fromSPC.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"fromSPC.d.ts","sourceRoot":"","sources":["../../src/from/fromSPC.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,sBAAsB,EAAE,MAAM,gBAAgB,CAAC;AAC7D,OAAO,EAAE,QAAQ,EAAE,MAAM,iBAAiB,CAAC;AAC3C,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,YAAY,CAAC;AAK5C,UAAU,cAAc;IACtB,0CAA0C;IAC1C,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,6CAA6C;IAC7C,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,6HAA6H;IAC7H,gBAAgB,CAAC,EAAE,CACjB,SAAS,EAAE,sBAAsB,KAC9B,sBAAsB,CAAC;CAC7B;AAED;;;;;GAKG;AACH,wBAAgB,OAAO,CACrB,MAAM,EAAE,SAAS,EACjB,OAAO,GAAE,cAAmB,GAC3B,QAAQ,CAiBV"}
+{"version":3,"file":"fromSPC.d.ts","sourceRoot":"","sources":["../../src/from/fromSPC.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,sBAAsB,EAAE,MAAM,gBAAgB,CAAC;AAC7D,OAAO,EAAE,QAAQ,EAAE,MAAM,iBAAiB,CAAC;AAC3C,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,YAAY,CAAC;AAK5C,UAAU,cAAc;IACtB,0CAA0C;IAC1C,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,6CAA6C;IAC7C,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,6HAA6H;IAC7H,gBAAgB,CAAC,EAAE,CACjB,SAAS,EAAE,sBAAsB,KAC9B,sBAAsB,CAAC;CAC7B;AAED;;;;;GAKG;AACH,wBAAgB,OAAO,CACrB,MAAM,EAAE,SAAS,EACjB,OAAO,GAAE,cAAmB,GAC3B,QAAQ,CAkBV"}

package/lib/from/fromSPC.js

@@ -11,7 +11,8 @@ 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;
+    const resultMeta = { ...result.meta };
+    delete resultMeta.parameters;
     for (const spectrum of result.spectra) {
         const { parameters: _spectrumParameters, ...spectrumMeta } = spectrum.meta ?? {};
         analysis.pushSpectrum(spectrum.variables, {

package/lib/from/fromSPC.js.map

@@ -1 +1 @@
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+{"version":3,"file":"fromSPC.js","sourceRoot":"","sources":["../../src/from/fromSPC.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,QAAQ,EAAE,MAAM,iBAAiB,CAAC;AAE3C,OAAO,EAAE,KAAK,EAAE,MAAM,YAAY,CAAC;AAEnC,OAAO,EAAE,gBAAgB,IAAI,uBAAuB,EAAE,MAAM,6BAA6B,CAAC;AAa1F;;;;;GAKG;AACH,MAAM,UAAU,OAAO,CACrB,MAAiB,EACjB,UAA0B,EAAE;IAE5B,MAAM,EAAE,gBAAgB,GAAG,uBAAuB,EAAE,GAAG,IAAI,EAAE,GAAG,OAAO,CAAC;IACxE,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,EAAE,GAAG,IAAI,EAAE,gBAAgB,EAAE,CAAC,CAAC;IAC7D,MAAM,MAAM,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC;IAE7B,MAAM,UAAU,GAA4B,EAAE,GAAG,MAAM,CAAC,IAAI,EAAE,CAAC;IAC/D,OAAO,UAAU,CAAC,UAAU,CAAC;IAE7B,KAAK,MAAM,QAAQ,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;QACtC,MAAM,EAAE,UAAU,EAAE,mBAAmB,EAAE,GAAG,YAAY,EAAE,GACxD,QAAQ,CAAC,IAAI,IAAI,EAAE,CAAC;QACtB,QAAQ,CAAC,YAAY,CAAC,QAAQ,CAAC,SAAS,EAAE;YACxC,QAAQ,EAAE,aAAa;YACvB,KAAK,EAAE,EAAE;YACT,IAAI,EAAE,EAAE,GAAG,UAAU,EAAE,GAAG,YAAY,EAAE;SACzC,CAAC,CAAC;IACL,CAAC;IACD,OAAO,QAAQ,CAAC;AAClB,CAAC"}

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 @@
+{"version":3,"file":"fromText.d.ts","sourceRoot":"","sources":["../../src/from/fromText.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,gBAAgB,CAAC;AAC/C,OAAO,KAAK,EAAE,eAAe,IAAI,qBAAqB,EAAE,MAAM,iBAAiB,CAAC;AAChF,OAAO,EAAE,QAAQ,EAAE,MAAM,iBAAiB,CAAC;AAG3C,UAAU,eAAgB,SAAQ,qBAAqB;IACrD,0CAA0C;IAC1C,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,6CAA6C;IAC7C,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED;;;;;GAKG;AACH,wBAAgB,QAAQ,CACtB,IAAI,EAAE,QAAQ,EACd,OAAO,GAAE,eAAoB,GAC5B,QAAQ,CA4BV"}

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/isTransmittance.d.ts

@@ -0,0 +1,20 @@
+import type { MeasurementVariable, NumberArray } from 'cheminfo-types';
+/**
+ * Checks whether a variable holds a transmittance rather than an absorbance.
+ * Spectrometers spell the unit in many ways and `%T` is as common as
+ * `TRANSMITTANCE`, so both the label and the units are tested.
+ * @param variable - Variable to inspect, usually the y of an IR spectrum.
+ * @returns True when the data is a transmittance.
+ */
+export declare function isTransmittance(variable: Pick<MeasurementVariable, 'label' | 'units'>): boolean;
+/**
+ * Checks whether a transmittance is expressed as a percentage rather than as a
+ * fraction of 1. The label and the units are tested first; when neither says
+ * so, the data decides, since a fraction never goes much above 1.
+ * @param variable - Variable known to hold a transmittance.
+ * @returns True when the data runs from 0 to 100.
+ */
+export declare function isPercent(variable: Pick<MeasurementVariable, 'label' | 'units'> & {
+    data?: NumberArray;
+}): boolean;
+//# sourceMappingURL=isTransmittance.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"isTransmittance.d.ts","sourceRoot":"","sources":["../../../src/from/utils/isTransmittance.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,mBAAmB,EAAE,WAAW,EAAE,MAAM,gBAAgB,CAAC;AAQvE;;;;;;GAMG;AACH,wBAAgB,eAAe,CAC7B,QAAQ,EAAE,IAAI,CAAC,mBAAmB,EAAE,OAAO,GAAG,OAAO,CAAC,GACrD,OAAO,CAOT;AAED;;;;;;GAMG;AACH,wBAAgB,SAAS,CACvB,QAAQ,EAAE,IAAI,CAAC,mBAAmB,EAAE,OAAO,GAAG,OAAO,CAAC,GAAG;IACvD,IAAI,CAAC,EAAE,WAAW,CAAC;CACpB,GACA,OAAO,CAST"}

package/lib/from/utils/isTransmittance.js

@@ -0,0 +1,41 @@
+import { xMaxValue } from 'ml-spectra-processing';
+/** Any spelling built on the word itself: `TRANSMITTANCE`, `%Transmission`. */
+const spelledOut = /trans/i;
+/** The abbreviated forms, which share no substring with `transmittance`. */
+const abbreviated = /^\s*%?\s*t\s*%?\s*$/i;
+/**
+ * Checks whether a variable holds a transmittance rather than an absorbance.
+ * Spectrometers spell the unit in many ways and `%T` is as common as
+ * `TRANSMITTANCE`, so both the label and the units are tested.
+ * @param variable - Variable to inspect, usually the y of an IR spectrum.
+ * @returns True when the data is a transmittance.
+ */
+export function isTransmittance(variable) {
+    const { label, units } = variable;
+    for (const value of [label, units]) {
+        if (!value)
+            continue;
+        if (spelledOut.test(value) || abbreviated.test(value))
+            return true;
+    }
+    return false;
+}
+/**
+ * Checks whether a transmittance is expressed as a percentage rather than as a
+ * fraction of 1. The label and the units are tested first; when neither says
+ * so, the data decides, since a fraction never goes much above 1.
+ * @param variable - Variable known to hold a transmittance.
+ * @returns True when the data runs from 0 to 100.
+ */
+export function isPercent(variable) {
+    const { label, units, data } = variable;
+    for (const value of [label, units]) {
+        if (!value)
+            continue;
+        if (value.includes('%') || value.toLowerCase().includes('percent')) {
+            return true;
+        }
+    }
+    return data !== undefined && data.length > 0 && xMaxValue(data) > 2;
+}
+//# sourceMappingURL=isTransmittance.js.map

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

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

@@ -1 +1 @@
-{"version":3,"file":"spectrumCallback.d.ts","sourceRoot":"","sources":["../../../src/from/utils/spectrumCallback.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,sBAAsB,EAAE,MAAM,gBAAgB,CAAC;AAE7D;;;;;GAKG;AACH,wBAAgB,gBAAgB,CAC9B,SAAS,EAAE,sBAAsB,GAChC,sBAAsB,CAqDxB"}
+{"version":3,"file":"spectrumCallback.d.ts","sourceRoot":"","sources":["../../../src/from/utils/spectrumCallback.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,sBAAsB,EAAE,MAAM,gBAAgB,CAAC;AAI7D;;;;;GAKG;AACH,wBAAgB,gBAAgB,CAC9B,SAAS,EAAE,sBAAsB,GAChC,sBAAsB,CAgDxB"}

package/lib/from/utils/spectrumCallback.js

@@ -1,3 +1,4 @@
+import { isPercent, isTransmittance } from "./isTransmittance.js";
 /**
  * Callback that adds absorbance (a) and transmittance (t) variables to the spectrum.
  * If the y variable is absorbance, transmittance is computed and vice versa.
@@ -9,11 +10,7 @@ export function spectrumCallback(variables) {
     // variable a = absorbance
     // variable t = transmittance
     const yVariable = variables.y;
-    let isAbsorbance = true;
-    if (yVariable.label.toLowerCase().includes('trans')) {
-        isAbsorbance = false;
-    }
-    if (isAbsorbance) {
+    if (!isTransmittance(yVariable)) {
         variables.a = {
             ...yVariable,
             symbol: 'a',
@@ -27,26 +24,25 @@ export function spectrumCallback(variables) {
         };
     }
     else {
-        const factor = yVariable.label.includes('%') ||
-            yVariable.label.toLowerCase().includes('percent')
-            ? 100
-            : 1;
+        const factor = isPercent(yVariable) ? 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();
+        const { label, units, data } = yVariable;
+        if (isPercent({ label, units })) {
+            variables.t = { ...yVariable, symbol: 't', data: data.slice() };
         }
         else {
             variables.t = {
                 units: '',
                 label: 'Transmittance (%)',
                 symbol: 't',
-                data: yVariable.data.map((transmittance) => transmittance * 100),
+                data: factor === 100
+                    ? data.slice()
+                    : data.map((transmittance) => transmittance * 100),
             };
         }
     }

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

@@ -1 +1 @@
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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 @@
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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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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAKA,OAAO,EACL,OAAO,IAAI,eAAe,EAC1B,eAAe,IAAI,uBAAuB,EAC1C,WAAW,IAAI,mBAAmB,GACnC,MAAM,iBAAiB,CAAC;AAGzB,OAAO,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAC;AAC/C,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAC;AAG7D,OAAO,EAAE,eAAe,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAC;AAErE;;;;;;GAMG;AACH,MAAM,UAAU,WAAW,CACzB,QAAuB,EACvB,MAAc,EACd,OAA4B;IAE5B,MAAM,IAAI,GAAG,mBAAmB,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,CAAC,CAAC;IAC5D,IAAI,CAAC,IAAI;QAAE,OAAO,SAAS,CAAC;IAC5B,OAAO,WAAW,CAChB,IAAkE,EAClE,QAAQ,CACT,CAAC;AACJ,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,eAAe,CAC7B,QAAuB,EACvB,OAAgC;IAEhC,MAAM,KAAK,GAAG,uBAAuB,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;IACzD,IAAI,CAAC,KAAK;QAAE,OAAO,EAAE,CAAC;IACtB,OAAO,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CACxB,WAAW,CACT,IAAkE,EAClE,QAAQ,CACT,CACF,CAAC;AACJ,CAAC;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,MAAM,CAAC,MAAM,OAAO,GAEhB,EAAE,GAAG,eAAe,EAAE,cAAc,EAAE,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "ir-spectrum",
-  "version": "4.1.0",
+  "version": "4.2.1",
   "description": "Package used to handle IR spectra in SciPeaks.",
   "type": "module",
   "exports": {
@@ -13,12 +13,12 @@
   "scripts": {
     "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",
+    "clean": "rimraf coverage lib",
+    "eslint": "eslint .",
+    "eslint-fix": "eslint . --fix",
     "prepack": "npm run tsc",
-    "prettier": "prettier --check src",
-    "prettier-write": "prettier --write src",
+    "prettier": "prettier --check .",
+    "prettier-write": "prettier --write .",
     "test": "npm run test-only && npm run check-types && npm run eslint && npm run prettier",
     "test-only": "vitest run --coverage",
     "tsc": "npm run clean && npm run tsc-build",
@@ -36,25 +36,27 @@
   },
   "homepage": "https://github.com/cheminfo/ir-spectrum#readme",
   "dependencies": {
-    "common-spectrum": "3.1.0",
-    "ml-gsd": "^13.1.1",
-    "spc-parser": "^1.0.0"
+    "common-spectrum": "4.0.1",
+    "ml-gsd": "^14.3.0",
+    "ml-spectra-processing": "^14.35.1",
+    "spc-parser": "^2.1.1",
+    "xy-parser": "^6.0.1"
   },
   "devDependencies": {
-    "@types/node": "^25.3.0",
-    "@vitest/coverage-v8": "^4.0.18",
-    "@zakodium/tsconfig": "^1.0.2",
-    "cheminfo-build": "^1.3.2",
+    "@types/node": "^26.6.1",
+    "@vitest/coverage-v8": "^4.1.11",
+    "@zakodium/tsconfig": "^1.0.5",
+    "cheminfo-build": "^1.4.0",
     "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": "^3.9.8",
     "rimraf": "^6.1.3",
-    "typescript": "^5.9.3",
-    "vitest": "^4.0.18"
+    "typescript": "^6.0.3",
+    "vitest": "^4.1.11"
   },
   "info": {
-    "logo": "https://raw.githubusercontent.com/cheminfo/font/master/src/ir/assignment.svg",
+    "logo": "https://raw.githubusercontent.com/cheminfo/font/main/src/ir/assignment.svg",
     "domain": [
       "Physical Chemistry",
       "Materials Science",
@@ -70,7 +72,7 @@
         {
           "extension": "jdx",
           "manufacturer": "IUPAC",
-          "example": "https://raw.githubusercontent.com/cheminfo/ir-spectrum/master/testFiles/absorbance.jdx"
+          "example": "https://raw.githubusercontent.com/cheminfo/ir-spectrum/main/src/from/__tests__/data/absorbance.jdx"
         }
       ]
     }

package/src/from/fromSPC.ts

@@ -30,7 +30,8 @@ export function fromSPC(
   const analysis = new Analysis({ ...rest, spectrumCallback });
   const result = parse(buffer);
 
-  const { parameters: _resultParameters, ...resultMeta } = result.meta;
+  const resultMeta: Record<string, unknown> = { ...result.meta };
+  delete resultMeta.parameters;
 
   for (const spectrum of result.spectra) {
     const { parameters: _spectrumParameters, ...spectrumMeta } =

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/isTransmittance.ts

@@ -0,0 +1,47 @@
+import type { MeasurementVariable, NumberArray } from 'cheminfo-types';
+import { xMaxValue } from 'ml-spectra-processing';
+
+/** Any spelling built on the word itself: `TRANSMITTANCE`, `%Transmission`. */
+const spelledOut = /trans/i;
+/** The abbreviated forms, which share no substring with `transmittance`. */
+const abbreviated = /^\s*%?\s*t\s*%?\s*$/i;
+
+/**
+ * Checks whether a variable holds a transmittance rather than an absorbance.
+ * Spectrometers spell the unit in many ways and `%T` is as common as
+ * `TRANSMITTANCE`, so both the label and the units are tested.
+ * @param variable - Variable to inspect, usually the y of an IR spectrum.
+ * @returns True when the data is a transmittance.
+ */
+export function isTransmittance(
+  variable: Pick<MeasurementVariable, 'label' | 'units'>,
+): boolean {
+  const { label, units } = variable;
+  for (const value of [label, units]) {
+    if (!value) continue;
+    if (spelledOut.test(value) || abbreviated.test(value)) return true;
+  }
+  return false;
+}
+
+/**
+ * Checks whether a transmittance is expressed as a percentage rather than as a
+ * fraction of 1. The label and the units are tested first; when neither says
+ * so, the data decides, since a fraction never goes much above 1.
+ * @param variable - Variable known to hold a transmittance.
+ * @returns True when the data runs from 0 to 100.
+ */
+export function isPercent(
+  variable: Pick<MeasurementVariable, 'label' | 'units'> & {
+    data?: NumberArray;
+  },
+): boolean {
+  const { label, units, data } = variable;
+  for (const value of [label, units]) {
+    if (!value) continue;
+    if (value.includes('%') || value.toLowerCase().includes('percent')) {
+      return true;
+    }
+  }
+  return data !== undefined && data.length > 0 && xMaxValue(data) > 2;
+}

package/src/from/utils/spectrumCallback.ts

@@ -1,5 +1,7 @@
 import type { MeasurementXYVariables } from 'cheminfo-types';
 
+import { isPercent, isTransmittance } from './isTransmittance.ts';
+
 /**
  * Callback that adds absorbance (a) and transmittance (t) variables to the spectrum.
  * If the y variable is absorbance, transmittance is computed and vice versa.
@@ -13,11 +15,7 @@ export function spectrumCallback(
   // variable a = absorbance
   // variable t = transmittance
   const yVariable = variables.y;
-  let isAbsorbance = true;
-  if (yVariable.label.toLowerCase().includes('trans')) {
-    isAbsorbance = false;
-  }
-  if (isAbsorbance) {
+  if (!isTransmittance(yVariable)) {
     variables.a = {
       ...yVariable,
       symbol: 'a',
@@ -32,11 +30,7 @@ export function spectrumCallback(
       units: '',
     };
   } else {
-    const factor =
-      yVariable.label.includes('%') ||
-      yVariable.label.toLowerCase().includes('percent')
-        ? 100
-        : 1;
+    const factor = isPercent(yVariable) ? 100 : 1;
 
     variables.a = {
       data: (yVariable.data as number[]).map(
@@ -46,17 +40,20 @@ export function spectrumCallback(
       label: 'Absorbance',
       units: '',
     };
-    if (factor === 100) {
-      variables.t = { ...yVariable, symbol: 't' };
-      variables.t.data = variables.t.data.slice() as number[];
+    const { label, units, data } = yVariable;
+    if (isPercent({ label, units })) {
+      variables.t = { ...yVariable, symbol: 't', data: data.slice() };
     } else {
       variables.t = {
         units: '',
         label: 'Transmittance (%)',
         symbol: 't',
-        data: (yVariable.data as number[]).map(
-          (transmittance: number) => transmittance * 100,
-        ),
+        data:
+          factor === 100
+            ? data.slice()
+            : (data as number[]).map(
+                (transmittance: number) => transmittance * 100,
+              ),
       };
     }
   }

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;