ir-spectrum 4.2.0 → 4.2.1

package/README.md

@@ -12,21 +12,26 @@
 ## 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();
 ```
 
+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            |
+| 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            |
 
-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.
+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.
 
 ### Selector for visualization
 

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

@@ -1 +1 @@
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+{"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/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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+{"version":3,"file":"spectrumCallback.js","sourceRoot":"","sources":["../../../src/from/utils/spectrumCallback.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,SAAS,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAC;AAElE;;;;;GAKG;AACH,MAAM,UAAU,gBAAgB,CAC9B,SAAiC;IAEjC,4CAA4C;IAC5C,0BAA0B;IAC1B,6BAA6B;IAC7B,MAAM,SAAS,GAAG,SAAS,CAAC,CAAC,CAAC;IAC9B,IAAI,CAAC,eAAe,CAAC,SAAS,CAAC,EAAE,CAAC;QAChC,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,GAAG,SAAS,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;QAE9C,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,MAAM,EAAE,KAAK,EAAE,KAAK,EAAE,IAAI,EAAE,GAAG,SAAS,CAAC;QACzC,IAAI,SAAS,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC;YAChC,SAAS,CAAC,CAAC,GAAG,EAAE,GAAG,SAAS,EAAE,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,IAAI,CAAC,KAAK,EAAE,EAAE,CAAC;QAClE,CAAC;aAAM,CAAC;YACN,SAAS,CAAC,CAAC,GAAG;gBACZ,KAAK,EAAE,EAAE;gBACT,KAAK,EAAE,mBAAmB;gBAC1B,MAAM,EAAE,GAAG;gBACX,IAAI,EACF,MAAM,KAAK,GAAG;oBACZ,CAAC,CAAC,IAAI,CAAC,KAAK,EAAE;oBACd,CAAC,CAAE,IAAiB,CAAC,GAAG,CACpB,CAAC,aAAqB,EAAE,EAAE,CAAC,aAAa,GAAG,GAAG,CAC/C;aACR,CAAC;QACJ,CAAC;IACH,CAAC;IACD,OAAO,SAAS,CAAC;AACnB,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "ir-spectrum",
-  "version": "4.2.0",
+  "version": "4.2.1",
   "description": "Package used to handle IR spectra in SciPeaks.",
   "type": "module",
   "exports": {
@@ -14,11 +14,11 @@
     "build": "npm run tsc && cheminfo-build --entry lib/index.js --root IRSpectrum",
     "check-types": "tsc --noEmit",
     "clean": "rimraf coverage lib",
-    "eslint": "eslint src",
-    "eslint-fix": "eslint src --fix",
+    "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",
@@ -36,26 +36,27 @@
   },
   "homepage": "https://github.com/cheminfo/ir-spectrum#readme",
   "dependencies": {
-    "common-spectrum": "3.2.0",
-    "ml-gsd": "^13.1.1",
-    "spc-parser": "^2.0.0",
+    "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": "^25.6.0",
-    "@vitest/coverage-v8": "^4.1.5",
+    "@types/node": "^26.6.1",
+    "@vitest/coverage-v8": "^4.1.11",
     "@zakodium/tsconfig": "^1.0.5",
-    "cheminfo-build": "^1.3.2",
+    "cheminfo-build": "^1.4.0",
     "eslint": "^9.39.2",
     "eslint-config-cheminfo-typescript": "^22.0.0",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "prettier": "^3.8.3",
+    "prettier": "^3.9.8",
     "rimraf": "^6.1.3",
     "typescript": "^6.0.3",
-    "vitest": "^4.1.5"
+    "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",
@@ -71,7 +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/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();
+    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,
+              ),
       };
     }
   }