react-cheminfo 0.28.0 → 0.29.0

package/lib/ir/core/irState.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"irState.js","sourceRoot":"","sources":["../../../src/ir/core/irState.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAuEH,6EAA6E;AAC7E,MAAM,CAAC,MAAM,kBAAkB,GAAkB,SAAS,CAAC;AAE3D;;;;;;GAMG;AACH,MAAM,CAAC,MAAM,mBAAmB,GAAoB,CAAC,SAAS,EAAE,OAAO,CAAC,CAAC;AAEzE,iEAAiE;AACjE,MAAM,CAAC,MAAM,mBAAmB,GAAG,GAAG,CAAC;AAEvC,2CAA2C;AAC3C,MAAM,CAAC,MAAM,mBAAmB,GAAG,EAAE,CAAC;AAEtC,0DAA0D;AAC1D,MAAM,CAAC,MAAM,eAAe,GAAqB;IAC/C,iBAAiB,EAAE,IAAI;IACvB,YAAY,EAAE,CAAC;CAChB,CAAC;AAEF,gDAAgD;AAChD,MAAM,CAAC,MAAM,gBAAgB,GAAe;IAC1C,IAAI,EAAE,eAAe;IACrB,SAAS,EAAE,IAAI;IACf,OAAO,EAAE,eAAe;IACxB,eAAe,EAAE,KAAK;IACtB,UAAU,EAAE,mBAAmB;IAC/B,mBAAmB,EAAE,CAAC;CACvB,CAAC;AAEF;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,eAAe,CAC7B,OAAmB,EACnB,SAA8B,EAAE;IAEhC,MAAM,KAAK,GAAG,MAAM,CAAC,UAAU,IAAI,OAAO,CAAC,UAAU,CAAC;IACtD,MAAM,SAAS,GAAG,MAAM,CAAC,mBAAmB,IAAI,OAAO,CAAC,mBAAmB,CAAC;IAC5E,OAAO;QACL,GAAG,OAAO;QACV,GAAG,MAAM;QACT,OAAO,EAAE,EAAE,GAAG,OAAO,CAAC,OAAO,EAAE,GAAG,MAAM,CAAC,OAAO,EAAE;QAClD,UAAU,EAAE,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC;YAChC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,mBAAmB,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC;YAC/D,CAAC,CAAC,OAAO,CAAC,UAAU;QACtB,mBAAmB,EACjB,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,IAAI,SAAS,IAAI,CAAC;YAC1C,CAAC,CAAC,SAAS;YACX,CAAC,CAAC,OAAO,CAAC,mBAAmB;KAClC,CAAC;AACJ,CAAC;AAED;;;;;;;;;GASG;AACH,MAAM,UAAU,UAAU,CAAC,MAAgB;IACzC,OAAO,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;AAClD,CAAC;AAED;;;;GAIG;AACH,SAAS,QAAQ,CAAC,MAAwB;IACxC,MAAM,CAAC,IAAI,EAAE,EAAE,CAAC,GAAG,MAAM,CAAC;IAC1B,OAAO,MAAM,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,IAAI,IAAI,GAAG,EAAE,CAAC;AACnE,CAAC"}

package/lib/ir/core/loadIrSpectra.d.ts

@@ -0,0 +1,36 @@
+/**
+ * One entry point for whatever was dropped, opened or pasted.
+ *
+ * The format is decided from the bytes and the right reader is called, so a
+ * caller hands over a file and gets spectra back without knowing what it turned
+ * out to be. Each reader is imported only once the bytes turn out to need it, so
+ * a page that never opens an SPC never downloads its parser.
+ */
+import type { LoadedIrSpectrum } from './analysisSpectra.ts';
+import type { IrOrigin } from './irSpectrum.ts';
+/** How a file is read. */
+export interface LoadIrSpectraOptions {
+    /**
+     * The file's name, which decides the reader when the content is silent and is
+     * carried onto every spectrum read out of it.
+     * @default undefined
+     */
+    fileName?: string;
+}
+/** What a file turned out to hold. */
+export interface LoadIrSpectraResult {
+    /** The spectra it held, in the order the file wrote them. */
+    spectra: LoadedIrSpectrum[];
+    /** What it turned out to be. */
+    format: IrOrigin['format'];
+}
+/**
+ * Read every infrared spectrum a file holds.
+ * @param data - The file, as bytes, or the pasted text.
+ * @param options - The file's name.
+ * @returns The spectra, and the format they were read from.
+ * @throws {Error} When nothing in the file names a format this can read, or when
+ * the reader for that format gave up on it.
+ */
+export declare function loadIrSpectra(data: Uint8Array | string, options?: LoadIrSpectraOptions): Promise<LoadIrSpectraResult>;
+//# sourceMappingURL=loadIrSpectra.d.ts.map

package/lib/ir/core/loadIrSpectra.d.ts.map

@@ -0,0 +1 @@
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package/lib/ir/core/loadIrSpectra.js

@@ -0,0 +1,44 @@
+/**
+ * One entry point for whatever was dropped, opened or pasted.
+ *
+ * The format is decided from the bytes and the right reader is called, so a
+ * caller hands over a file and gets spectra back without knowing what it turned
+ * out to be. Each reader is imported only once the bytes turn out to need it, so
+ * a page that never opens an SPC never downloads its parser.
+ */
+import { describeSource } from "../../error/core/index.js";
+import { detectIrFormat } from "./detectIrFormat.js";
+/**
+ * Read every infrared spectrum a file holds.
+ * @param data - The file, as bytes, or the pasted text.
+ * @param options - The file's name.
+ * @returns The spectra, and the format they were read from.
+ * @throws {Error} When nothing in the file names a format this can read, or when
+ * the reader for that format gave up on it.
+ */
+export async function loadIrSpectra(data, options = {}) {
+    const { fileName } = options;
+    const format = detectIrFormat(data, fileName);
+    if (format === 'jcamp') {
+        const { fromJcamp } = await import("./fromJcamp.js");
+        return { spectra: fromJcamp(data, options), format };
+    }
+    if (format === 'spc') {
+        if (typeof data === 'string') {
+            throw new Error(`${describeSource(fileName)} looks like an SPC file but arrived as text — SPC is binary, and reading it as text loses bytes it cannot get back.`);
+        }
+        const { fromSpc } = await import("./fromSpc.js");
+        return { spectra: fromSpc(data, options), format };
+    }
+    if (format === 'text') {
+        // Deliberately refused rather than half-read. `ir-spectrum` adds the
+        // absorbance and transmittance pair to everything `fromJcamp` and `fromSPC`
+        // produce, but not to `fromText`, so a two-column file arrives carrying only
+        // the axis it was written in. Deriving the other one here would put a second
+        // implementation of that conversion in this package, which is exactly what
+        // depending on `ir-spectrum` is meant to avoid.
+        throw new Error(`${describeSource(fileName)} is two columns of numbers, which this viewer cannot read yet: ir-spectrum derives the absorbance and transmittance pair for JCAMP-DX and SPC but not for plain text, and this package deliberately does not do that conversion itself. Export the spectrum as JCAMP-DX (.jdx) instead.`);
+    }
+    throw new Error(`${describeSource(fileName)} is not a spectrum this viewer can read — JCAMP-DX (.jdx, .dx) and Thermo Galactic SPC (.spc) are understood.`);
+}
+//# sourceMappingURL=loadIrSpectra.js.map

package/lib/ir/core/loadIrSpectra.js.map

@@ -0,0 +1 @@
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package/lib/ir/core/nearestBand.d.ts

@@ -0,0 +1,35 @@
+/**
+ * Which band the pointer is asking about.
+ *
+ * Found in pixels rather than in wavenumbers, because what a user means by
+ * "that band" is what is under the pointer on screen: at a full-scan zoom two
+ * bands thirty wavenumbers apart are three pixels apart and either will do,
+ * while at a deep zoom the same thirty wavenumbers is half the plot and only one
+ * of them is being pointed at.
+ */
+import type { ChartScale } from '../../chart/core/chartScale.ts';
+import type { IrBand } from './irBand.ts';
+/**
+ * How close the pointer has to be to a band, in pixels.
+ *
+ * Eight is about a fingertip's worth of aim on a trackpad. Wider and the readout
+ * claims a band while the pointer is plainly on the baseline beside it; narrower
+ * and a band has to be hit exactly, which on a dense fingerprint region is not
+ * a gesture anyone can make.
+ */
+export declare const BAND_HIT_RADIUS = 8;
+/**
+ * The band nearest a place on the axis, when one is within reach.
+ *
+ * A plain scan rather than a binary search: a spectrum is picked down to a few
+ * dozen bands, so the whole list is shorter than the setup a search would need,
+ * and it stays correct if the bands ever arrive in another order.
+ * @param bands - The bands of every spectrum currently drawn.
+ * @param xScale - The wavenumber axis as it is currently zoomed, which may run
+ * either way round.
+ * @param pixelX - Where the pointer is, in user units of the SVG.
+ * @param radius - How close it has to be. Defaults to `BAND_HIT_RADIUS`.
+ * @returns The band, or `null` when none is within reach.
+ */
+export declare function nearestBandAt(bands: readonly IrBand[], xScale: ChartScale, pixelX: number, radius?: number): IrBand | null;
+//# sourceMappingURL=nearestBand.d.ts.map

package/lib/ir/core/nearestBand.d.ts.map

@@ -0,0 +1 @@
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package/lib/ir/core/nearestBand.js

@@ -0,0 +1,47 @@
+/**
+ * Which band the pointer is asking about.
+ *
+ * Found in pixels rather than in wavenumbers, because what a user means by
+ * "that band" is what is under the pointer on screen: at a full-scan zoom two
+ * bands thirty wavenumbers apart are three pixels apart and either will do,
+ * while at a deep zoom the same thirty wavenumbers is half the plot and only one
+ * of them is being pointed at.
+ */
+import { chartPixel } from "../../chart/core/chartScale.js";
+/**
+ * How close the pointer has to be to a band, in pixels.
+ *
+ * Eight is about a fingertip's worth of aim on a trackpad. Wider and the readout
+ * claims a band while the pointer is plainly on the baseline beside it; narrower
+ * and a band has to be hit exactly, which on a dense fingerprint region is not
+ * a gesture anyone can make.
+ */
+export const BAND_HIT_RADIUS = 8;
+/**
+ * The band nearest a place on the axis, when one is within reach.
+ *
+ * A plain scan rather than a binary search: a spectrum is picked down to a few
+ * dozen bands, so the whole list is shorter than the setup a search would need,
+ * and it stays correct if the bands ever arrive in another order.
+ * @param bands - The bands of every spectrum currently drawn.
+ * @param xScale - The wavenumber axis as it is currently zoomed, which may run
+ * either way round.
+ * @param pixelX - Where the pointer is, in user units of the SVG.
+ * @param radius - How close it has to be. Defaults to `BAND_HIT_RADIUS`.
+ * @returns The band, or `null` when none is within reach.
+ */
+export function nearestBandAt(bands, xScale, pixelX, radius = BAND_HIT_RADIUS) {
+    let found = null;
+    let bestDistance = radius;
+    for (const band of bands) {
+        const distance = Math.abs(chartPixel(xScale, band.wavenumber) - pixelX);
+        // Strictly nearer, so the first of two bands at one wavenumber wins and the
+        // answer does not flicker between them as the pointer rests still.
+        if (distance < bestDistance) {
+            bestDistance = distance;
+            found = band;
+        }
+    }
+    return found;
+}
+//# sourceMappingURL=nearestBand.js.map

package/lib/ir/core/nearestBand.js.map

@@ -0,0 +1 @@
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package/lib/ir/core/pickBands.d.ts

@@ -0,0 +1,70 @@
+/**
+ * Finding the bands in a spectrum, which `ir-spectrum` does.
+ *
+ * Everything here is the two things that call needs and does not have: a
+ * `MeasurementXY` built out of the arrays the viewer holds, and the decision to
+ * pick on **absorbance** rather than on transmittance. That second one is the
+ * only judgement in the file and it is not a preference — peak picking finds
+ * maxima, and a band is a maximum in absorbance but a *minimum* in transmittance,
+ * so picking on transmittance would return the flat baseline between the bands
+ * and miss every band there is.
+ */
+import type { IrBand } from './irBand.ts';
+import type { IrSpectrum } from './irSpectrum.ts';
+/** How the bands are picked. */
+export interface PickBandsOptions {
+    /**
+     * Lowest wavenumber to pick in, in cm⁻¹.
+     * @default the start of the spectrum
+     */
+    from?: number;
+    /**
+     * Highest wavenumber to pick in, in cm⁻¹.
+     * @default the end of the spectrum
+     */
+    to?: number;
+    /**
+     * How tall a band must be against the tallest one to count, as a fraction.
+     *
+     * Two percent by default, which on a real ATR spectrum is a little above the
+     * noise and a long way below any band worth naming. Lowered, the fingerprint
+     * region fills with shoulders that have no assignment; raised past about a
+     * tenth, weak but diagnostic bands — a nitrile, an alkyne — stop being found.
+     * @default 0.02
+     */
+    minRelativeHeight?: number;
+    /**
+     * Narrowest band to keep, in cm⁻¹.
+     *
+     * A spike one point wide is a detector glitch rather than a vibration: real
+     * infrared bands are several wavenumbers across even at their sharpest.
+     * @default 4
+     */
+    minPeakWidth?: number;
+    /**
+     * At most how many bands to keep, the strongest first.
+     * @default every band found
+     */
+    limit?: number;
+}
+/**
+ * Pick the bands of one spectrum.
+ *
+ * The bands come back in ascending wavenumber, which is the order a spectrum is
+ * read in rather than the order they were found — `limit` cuts by height, and
+ * then what survives is put back in axis order, so a table of them reads like
+ * the chart.
+ *
+ * **A band centre is a sampled point, not an interpolated one.** `ir-spectrum`
+ * reports each picked band at the wavenumber of the sample it peaked on, so on a
+ * bench instrument's 4 cm⁻¹ grid a carbonyl centred at 1710 is reported at 1708
+ * or 1712. That is within the tolerance the assignment table is matched with, and
+ * refining it here would mean re-deriving a peak position this package has
+ * deliberately delegated — but it is why a band should never be quoted as though
+ * it were measured to the wavenumber.
+ * @param spectrum - The spectrum to pick from.
+ * @param options - Where to pick, and what to keep.
+ * @returns The bands, ascending by wavenumber.
+ */
+export declare function pickBands(spectrum: IrSpectrum, options?: PickBandsOptions): IrBand[];
+//# sourceMappingURL=pickBands.d.ts.map

package/lib/ir/core/pickBands.d.ts.map

@@ -0,0 +1 @@
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package/lib/ir/core/pickBands.js

@@ -0,0 +1,125 @@
+/**
+ * Finding the bands in a spectrum, which `ir-spectrum` does.
+ *
+ * Everything here is the two things that call needs and does not have: a
+ * `MeasurementXY` built out of the arrays the viewer holds, and the decision to
+ * pick on **absorbance** rather than on transmittance. That second one is the
+ * only judgement in the file and it is not a preference — peak picking finds
+ * maxima, and a band is a maximum in absorbance but a *minimum* in transmittance,
+ * so picking on transmittance would return the flat baseline between the bands
+ * and miss every band there is.
+ */
+import { autoPeakPicking } from 'ir-spectrum';
+import { xMaxValue, xMinValue } from 'ml-spectra-processing';
+/**
+ * Pick the bands of one spectrum.
+ *
+ * The bands come back in ascending wavenumber, which is the order a spectrum is
+ * read in rather than the order they were found — `limit` cuts by height, and
+ * then what survives is put back in axis order, so a table of them reads like
+ * the chart.
+ *
+ * **A band centre is a sampled point, not an interpolated one.** `ir-spectrum`
+ * reports each picked band at the wavenumber of the sample it peaked on, so on a
+ * bench instrument's 4 cm⁻¹ grid a carbonyl centred at 1710 is reported at 1708
+ * or 1712. That is within the tolerance the assignment table is matched with, and
+ * refining it here would mean re-deriving a peak position this package has
+ * deliberately delegated — but it is why a band should never be quoted as though
+ * it were measured to the wavenumber.
+ * @param spectrum - The spectrum to pick from.
+ * @param options - Where to pick, and what to keep.
+ * @returns The bands, ascending by wavenumber.
+ */
+export function pickBands(spectrum, options = {}) {
+    const { from, to, minRelativeHeight = 0.02, minPeakWidth = 4, limit, } = options;
+    if (spectrum.wavenumber.length < 2)
+        return [];
+    const picked = autoPeakPicking(measurementOf(spectrum), {
+        // Absorbance, because a band is a maximum there and a minimum in the other.
+        yVariable: 'a',
+        minMaxRatio: minRelativeHeight,
+        minPeakWidth,
+        ...(from === undefined ? {} : { from }),
+        ...(to === undefined ? {} : { to }),
+    });
+    const bands = [];
+    for (const peak of picked) {
+        if (!Number.isFinite(peak.wavenumber))
+            continue;
+        bands.push({
+            spectrumId: spectrum.id,
+            wavenumber: peak.wavenumber,
+            absorbance: peak.absorbance,
+            // `ConvertedPeak.transmittance` is a fraction where the spectrum's own
+            // transmittance is a percentage; brought onto the one scale here so that
+            // nothing downstream has to remember which of the two it is holding.
+            transmittance: peak.transmittance * 100,
+            strength: peak.kind,
+        });
+    }
+    const kept = limit === undefined || bands.length <= limit
+        ? bands
+        : bands.toSorted(byDescendingAbsorbance).slice(0, limit);
+    return kept.toSorted(byAscendingWavenumber);
+}
+/**
+ * The spectrum as `ir-spectrum` wants it.
+ *
+ * The `t` variable is given its extremes, because that is what the strength
+ * letter is worked out from: without them the conversion assumes a spectrum
+ * running the full 0 to 100 percent, and every band of a shallow ATR trace that
+ * never leaves the eighties comes back weak.
+ * @param spectrum - The spectrum the viewer holds.
+ * @returns A measurement carrying all three variables.
+ */
+function measurementOf(spectrum) {
+    const transmittance = {
+        label: 'Transmittance (%)',
+        units: '%',
+        symbol: 't',
+        data: spectrum.transmittance,
+        min: xMinValue(spectrum.transmittance),
+        max: xMaxValue(spectrum.transmittance),
+    };
+    return {
+        variables: {
+            x: {
+                label: 'Wavenumber',
+                units: '1/cm',
+                symbol: 'x',
+                data: spectrum.wavenumber,
+            },
+            // `y` is required of every measurement, and stands for whichever axis was
+            // recorded. Nothing here reads it — the picking is told to use `a` and the
+            // strength letter is read off `t` — so it carries the transmittance rather
+            // than a third copy of anything.
+            y: transmittance,
+            a: {
+                label: 'Absorbance',
+                units: '',
+                symbol: 'a',
+                data: spectrum.absorbance,
+            },
+            t: transmittance,
+        },
+    };
+}
+/**
+ * Order two bands by height, tallest first.
+ * @param first - One band.
+ * @param second - The other.
+ * @returns The comparison.
+ */
+function byDescendingAbsorbance(first, second) {
+    return second.absorbance - first.absorbance;
+}
+/**
+ * Order two bands along the axis, lowest wavenumber first.
+ * @param first - One band.
+ * @param second - The other.
+ * @returns The comparison.
+ */
+function byAscendingWavenumber(first, second) {
+    return first.wavenumber - second.wavenumber;
+}
+//# sourceMappingURL=pickBands.js.map

package/lib/ir/core/pickBands.js.map

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package/lib/ir/core/spectrumJcamp.d.ts

@@ -0,0 +1,58 @@
+/**
+ * Writing spectra back out as JCAMP-DX, so what was loaded can be taken away.
+ *
+ * JCAMP is the format to write rather than two columns of text because it says
+ * what its second column means: an infrared spectrum is read either as
+ * absorbance or as percent transmittance, the two are the same measurement
+ * turned inside out, and a bare column of numbers leaves whoever opens it next
+ * to guess which. `##YUNITS=` states it, and `ir-spectrum` reads it back and
+ * derives the other axis from it, so a spectrum written here returns carrying
+ * both.
+ *
+ * The points are written as an `##PEAK TABLE=` of explicit `x y` pairs rather
+ * than as a compressed `##XYDATA=` record. An XYDATA record states a first
+ * wavenumber and an increment and lets the reader rebuild the axis, which is
+ * exact only for an evenly sampled trace — and an interferogram transformed onto
+ * a wavenumber grid is evenly sampled only until somebody trims or splices it.
+ * Explicit pairs round trip whatever the spacing.
+ */
+import type { IrMode, IrSpectrum } from './irSpectrum.ts';
+/** The extension a written spectrum is saved under. */
+export declare const JCAMP_EXTENSION = ".jdx";
+/** What a JCAMP-DX file is served as. */
+export declare const JCAMP_MIME_TYPE = "chemical/x-jcamp-dx";
+/** How the technique is named when the file that was read named nothing. */
+export declare const DEFAULT_DATA_TYPE = "INFRARED SPECTRUM";
+/**
+ * Write one spectrum as a JCAMP-DX block.
+ *
+ * The axis written is the one the instrument recorded wherever the file said
+ * which that was, and only otherwise the one being read. Writing what is on
+ * screen instead would export a spectrum that had been through a logarithm it
+ * was never measured with — and, where a band bottoms out at zero transmittance,
+ * an absorbance of infinity that no reader can take back.
+ * @param spectrum - The spectrum.
+ * @param mode - The axis being read, used when the file named none.
+ * @returns The block, `##TITLE=` through `##END=`.
+ */
+export declare function irSpectrumToJcamp(spectrum: IrSpectrum, mode: IrMode): string;
+/**
+ * Write every spectrum of a list as one JCAMP-DX file.
+ *
+ * One file rather than one download per spectrum: a browser asked for six files
+ * in a row blocks all but the first, and a sample and its background are wanted
+ * back as the pair they were compared as. The blocks go inside a `LINK` block,
+ * which is what JCAMP has for a container and what the instruments that write a
+ * pair already use, so dropping the file back on the chart brings the whole list
+ * back.
+ *
+ * A list of one is written as that block alone: wrapping a single spectrum in a
+ * container gains nothing, and the file is then exactly what asking for that one
+ * spectrum would have written.
+ * @param spectra - The spectra, in the order the list holds them.
+ * @param mode - The axis being read, used for a spectrum whose file named none.
+ * @param title - What to call the file's own outer block.
+ * @returns The file.
+ */
+export declare function irSpectraToJcamp(spectra: readonly IrSpectrum[], mode: IrMode, title?: string): string;
+//# sourceMappingURL=spectrumJcamp.d.ts.map

package/lib/ir/core/spectrumJcamp.d.ts.map

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package/lib/ir/core/spectrumJcamp.js

@@ -0,0 +1,156 @@
+/**
+ * Writing spectra back out as JCAMP-DX, so what was loaded can be taken away.
+ *
+ * JCAMP is the format to write rather than two columns of text because it says
+ * what its second column means: an infrared spectrum is read either as
+ * absorbance or as percent transmittance, the two are the same measurement
+ * turned inside out, and a bare column of numbers leaves whoever opens it next
+ * to guess which. `##YUNITS=` states it, and `ir-spectrum` reads it back and
+ * derives the other axis from it, so a spectrum written here returns carrying
+ * both.
+ *
+ * The points are written as an `##PEAK TABLE=` of explicit `x y` pairs rather
+ * than as a compressed `##XYDATA=` record. An XYDATA record states a first
+ * wavenumber and an increment and lets the reader rebuild the axis, which is
+ * exact only for an evenly sampled trace — and an interferogram transformed onto
+ * a wavenumber grid is evenly sampled only until somebody trims or splices it.
+ * Explicit pairs round trip whatever the spacing.
+ */
+import { fromJSON } from 'convert-to-jcamp';
+/** The extension a written spectrum is saved under. */
+export const JCAMP_EXTENSION = '.jdx';
+/** What a JCAMP-DX file is served as. */
+export const JCAMP_MIME_TYPE = 'chemical/x-jcamp-dx';
+/** How the technique is named when the file that was read named nothing. */
+export const DEFAULT_DATA_TYPE = 'INFRARED SPECTRUM';
+/**
+ * Write one spectrum as a JCAMP-DX block.
+ *
+ * The axis written is the one the instrument recorded wherever the file said
+ * which that was, and only otherwise the one being read. Writing what is on
+ * screen instead would export a spectrum that had been through a logarithm it
+ * was never measured with — and, where a band bottoms out at zero transmittance,
+ * an absorbance of infinity that no reader can take back.
+ * @param spectrum - The spectrum.
+ * @param mode - The axis being read, used when the file named none.
+ * @returns The block, `##TITLE=` through `##END=`.
+ */
+export function irSpectrumToJcamp(spectrum, mode) {
+    const written = spectrum.origin.recorded ?? mode;
+    const values = written === 'absorbance' ? spectrum.absorbance : spectrum.transmittance;
+    return fromJSON({ x: spectrum.wavenumber, y: values }, { info: infoRecords(spectrum, written), meta: metaRecords(spectrum) });
+}
+/**
+ * Write every spectrum of a list as one JCAMP-DX file.
+ *
+ * One file rather than one download per spectrum: a browser asked for six files
+ * in a row blocks all but the first, and a sample and its background are wanted
+ * back as the pair they were compared as. The blocks go inside a `LINK` block,
+ * which is what JCAMP has for a container and what the instruments that write a
+ * pair already use, so dropping the file back on the chart brings the whole list
+ * back.
+ *
+ * A list of one is written as that block alone: wrapping a single spectrum in a
+ * container gains nothing, and the file is then exactly what asking for that one
+ * spectrum would have written.
+ * @param spectra - The spectra, in the order the list holds them.
+ * @param mode - The axis being read, used for a spectrum whose file named none.
+ * @param title - What to call the file's own outer block.
+ * @returns The file.
+ */
+export function irSpectraToJcamp(spectra, mode, title = `${spectra.length} infrared spectra`) {
+    const only = spectra.length === 1 ? spectra[0] : undefined;
+    if (only !== undefined)
+        return irSpectrumToJcamp(only, mode);
+    const blocks = [];
+    for (const spectrum of spectra) {
+        blocks.push(irSpectrumToJcamp(spectrum, mode));
+    }
+    return `##TITLE=${recordValue(title)}
+##JCAMP-DX=4.24
+##DATA TYPE=LINK
+##BLOCKS=${blocks.length}
+${blocks.join('\n')}
+##END=
+`;
+}
+/**
+ * The standard records of a block: what it is called, and what its axes are.
+ * @param spectrum - The spectrum.
+ * @param written - The axis being written.
+ * @returns The records, as `convert-to-jcamp` takes them.
+ */
+function infoRecords(spectrum, written) {
+    return {
+        title: recordValue(spectrum.name),
+        // The technique as the file stated it, so a Raman spectrum that was opened
+        // here is not written back out claiming to be infrared.
+        dataType: technique(spectrum) ?? DEFAULT_DATA_TYPE,
+        xUnits: '1/CM',
+        // Spelled the way `ir-spectrum` reads it: it takes the axis to be
+        // transmittance when the label says `trans`, and to be a percentage rather
+        // than a fraction when it carries a `%`.
+        yUnits: written === 'absorbance' ? 'ABSORBANCE' : 'Transmittance (%)',
+    };
+}
+/**
+ * The `$`-prefixed records of a block: the acquisition, as the file stated it.
+ *
+ * The table's labels are the record names themselves — the reader lists whatever
+ * `##$` records a block carried, under their own names — so writing it back is a
+ * matter of putting the `$` in front again. `Technique` is the one row that is
+ * not a record of that bag: it is the block's `##DATA TYPE=`, and it goes back
+ * there rather than becoming a user-defined record of its own.
+ * @param spectrum - The spectrum.
+ * @returns The records, keyed without their `##$`.
+ */
+function metaRecords(spectrum) {
+    const records = {};
+    const fields = spectrum.meta?.fields ?? [];
+    for (const field of fields) {
+        if (field.label === TECHNIQUE)
+            continue;
+        records[recordKey(field.label)] = recordValue(field.value);
+    }
+    return records;
+}
+/** The row of the table that holds the block's own data type. */
+const TECHNIQUE = 'Technique';
+/**
+ * What the file said the spectrum was, if it said.
+ * @param spectrum - The spectrum.
+ * @returns The technique, or `undefined` when the file stated none.
+ */
+function technique(spectrum) {
+    for (const field of spectrum.meta?.fields ?? []) {
+        if (field.label === TECHNIQUE)
+            return recordValue(field.value);
+    }
+    return undefined;
+}
+/**
+ * A label put where a JCAMP record's name goes.
+ *
+ * A record name runs to the `=` and holds no whitespace, so a label that picked
+ * up a space on its way through some other tool would otherwise write a record
+ * whose name is its first word and whose value starts with the rest of it.
+ * @param label - The row's label.
+ * @returns It as a record name.
+ */
+function recordKey(label) {
+    return label.replaceAll(/[\s=]+/g, '_');
+}
+/**
+ * A value put where a JCAMP record's value goes.
+ *
+ * A record is one line and `$$` opens a comment that runs to the end of it, so a
+ * value with a newline in it would otherwise either break the file in two or
+ * lose its tail. Both failures are silent on the way back in, which is why this
+ * is done to every value rather than to the ones known to be long.
+ * @param value - The value as it is held.
+ * @returns The value as one line, with no comment marker in it.
+ */
+function recordValue(value) {
+    return value.replaceAll(/\s+/g, ' ').replaceAll('$$', '$').trim();
+}
+//# sourceMappingURL=spectrumJcamp.js.map

package/lib/ir/core/spectrumJcamp.js.map

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