edf2csv 0.1.0

package/dist/convert/channels.d.ts

@@ -0,0 +1,40 @@
+/**
+ * Channel naming and selection.
+ *
+ * Two real-world facts drive this module. EDF labels are free text that routinely
+ * contain spaces and punctuation ("EEG Fpz-Cz"), and they are not guaranteed to be
+ * unique — CHB-MIT recordings ship two channels both labelled "T8-P8", and some
+ * carry a channel labelled "-". Labels are therefore preserved verbatim in output,
+ * and only disambiguated when the file itself is ambiguous.
+ */
+import type { EdfSignal } from '../edf/header.js';
+export declare class ChannelSelectionError extends Error {
+    constructor(message: string);
+}
+/**
+ * Column name for a signal.
+ *
+ * Names are derived from the whole file, not from the current selection, so a given
+ * channel always produces the same column regardless of which channels were asked
+ * for. Duplicated labels get a `_ch<index>` suffix pointing at their position in
+ * the file, which is the only thing that reliably tells them apart.
+ */
+export declare function buildColumnNames(signals: readonly EdfSignal[]): Map<number, string>;
+export interface ChannelSelection {
+    signals: EdfSignal[];
+    /** Labels that matched more than one channel, so the user knows why they got extras. */
+    ambiguous: {
+        term: string;
+        matched: EdfSignal[];
+    }[];
+}
+/**
+ * Resolve a `--channels` specification against the file's signals.
+ *
+ * Matching is case-insensitive on the exact label, with `#<index>` available to
+ * address a specific channel when labels collide. A term that matches nothing is an
+ * error rather than a silent omission: quietly dropping a requested channel would
+ * hand the user a CSV that is missing data they explicitly asked for.
+ */
+export declare function selectChannels(signals: readonly EdfSignal[], terms: readonly string[]): ChannelSelection;
+//# sourceMappingURL=channels.d.ts.map

package/dist/convert/channels.d.ts.map

@@ -0,0 +1 @@
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package/dist/convert/channels.js

@@ -0,0 +1,134 @@
+/**
+ * Channel naming and selection.
+ *
+ * Two real-world facts drive this module. EDF labels are free text that routinely
+ * contain spaces and punctuation ("EEG Fpz-Cz"), and they are not guaranteed to be
+ * unique — CHB-MIT recordings ship two channels both labelled "T8-P8", and some
+ * carry a channel labelled "-". Labels are therefore preserved verbatim in output,
+ * and only disambiguated when the file itself is ambiguous.
+ */
+export class ChannelSelectionError extends Error {
+    constructor(message) {
+        super(message);
+        this.name = 'ChannelSelectionError';
+    }
+}
+/**
+ * Column name for a signal.
+ *
+ * Names are derived from the whole file, not from the current selection, so a given
+ * channel always produces the same column regardless of which channels were asked
+ * for. Duplicated labels get a `_ch<index>` suffix pointing at their position in
+ * the file, which is the only thing that reliably tells them apart.
+ */
+export function buildColumnNames(signals) {
+    const counts = new Map();
+    for (const signal of signals) {
+        if (signal.isAnnotations)
+            continue;
+        const base = baseName(signal);
+        counts.set(base, (counts.get(base) ?? 0) + 1);
+    }
+    const names = new Map();
+    for (const signal of signals) {
+        if (signal.isAnnotations)
+            continue;
+        const base = baseName(signal);
+        const duplicated = (counts.get(base) ?? 0) > 1;
+        names.set(signal.index, duplicated ? `${base}_ch${signal.index}` : base);
+    }
+    return names;
+}
+function baseName(signal) {
+    return signal.label === '' ? `signal_${signal.index}` : signal.label;
+}
+/**
+ * Resolve a `--channels` specification against the file's signals.
+ *
+ * Matching is case-insensitive on the exact label, with `#<index>` available to
+ * address a specific channel when labels collide. A term that matches nothing is an
+ * error rather than a silent omission: quietly dropping a requested channel would
+ * hand the user a CSV that is missing data they explicitly asked for.
+ */
+export function selectChannels(signals, terms) {
+    const candidates = signals.filter((s) => !s.isAnnotations);
+    const byLabel = new Map();
+    for (const signal of candidates) {
+        const key = signal.label.toLowerCase();
+        const bucket = byLabel.get(key);
+        if (bucket)
+            bucket.push(signal);
+        else
+            byLabel.set(key, [signal]);
+    }
+    const chosen = new Map();
+    const ambiguous = [];
+    for (const rawTerm of terms) {
+        const term = rawTerm.trim();
+        if (term === '')
+            continue;
+        // '#N' addresses a channel by position, but a label may literally be "#5".
+        // A real label always wins, so no channel becomes unreachable.
+        const literal = byLabel.get(term.toLowerCase());
+        if (term.startsWith('#') && (!literal || literal.length === 0)) {
+            const index = Number(term.slice(1));
+            const signal = candidates.find((s) => s.index === index);
+            if (!signal) {
+                throw new ChannelSelectionError(`No channel at position ${term}. This file has signal channels at ` +
+                    `#${candidates.map((s) => s.index).join(', #')}.`);
+            }
+            chosen.set(signal.index, signal);
+            continue;
+        }
+        const matched = byLabel.get(term.toLowerCase());
+        if (!matched || matched.length === 0) {
+            throw new ChannelSelectionError(`No channel named "${term}".${suggest(term, candidates)}\n` +
+                `Run with --info to list the channels in this file.`);
+        }
+        if (matched.length > 1)
+            ambiguous.push({ term, matched: [...matched] });
+        for (const signal of matched)
+            chosen.set(signal.index, signal);
+    }
+    const selected = [...chosen.values()].sort((a, b) => a.index - b.index);
+    if (selected.length === 0) {
+        throw new ChannelSelectionError('No channels were selected.');
+    }
+    return { signals: selected, ambiguous };
+}
+function suggest(term, candidates) {
+    // Duplicated labels would otherwise be suggested twice, which reads like two
+    // different options while naming the same thing.
+    const unique = [...new Set(candidates.map((s) => s.label))];
+    const scored = unique
+        .map((label) => ({ label, distance: editDistance(term.toLowerCase(), label.toLowerCase()) }))
+        .filter((c) => c.label !== '' && c.distance <= Math.max(2, Math.floor(term.length / 3)))
+        .sort((a, b) => a.distance - b.distance)
+        .slice(0, 3);
+    if (scored.length === 0)
+        return '';
+    return ` Did you mean ${scored.map((c) => `"${c.label}"`).join(', ')}?`;
+}
+/** Levenshtein distance, two-row variant. */
+function editDistance(a, b) {
+    if (a === b)
+        return 0;
+    if (a.length === 0)
+        return b.length;
+    if (b.length === 0)
+        return a.length;
+    let previous = Array.from({ length: b.length + 1 }, (_, i) => i);
+    let current = new Array(b.length + 1).fill(0);
+    for (let i = 1; i <= a.length; i++) {
+        current[0] = i;
+        for (let j = 1; j <= b.length; j++) {
+            const cost = a.charCodeAt(i - 1) === b.charCodeAt(j - 1) ? 0 : 1;
+            current[j] = Math.min((current[j - 1] ?? 0) + 1, (previous[j] ?? 0) + 1, (previous[j - 1] ?? 0) + cost);
+        }
+        const swap = previous;
+        previous = current;
+        current = swap;
+    }
+    return previous[b.length] ?? 0;
+}
+//# sourceMappingURL=channels.js.map

package/dist/convert/channels.js.map

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package/dist/convert/plan.d.ts

@@ -0,0 +1,70 @@
+/**
+ * Turning a request into a concrete conversion plan.
+ *
+ * The plan is where the tool's central promise is enforced: channels recorded at
+ * different sampling rates are never merged into one table. A single wide CSV can
+ * only hold mixed rates by inventing samples for the slow channels — MNE, for
+ * instance, expands three genuine 1 Hz temperature readings into 768 interpolated
+ * values without warning. Instead each distinct rate gets its own file, so every
+ * number in every output file is a number that was actually recorded.
+ */
+import type { Diagnostic } from '../edf/errors.js';
+import type { EdfSignal } from '../edf/header.js';
+import type { ResolvedRange } from './time-range.js';
+export interface PlannedChannel {
+    signal: EdfSignal;
+    column: string;
+    decimals: number;
+}
+export interface RateGroup {
+    /** Sampling rate in Hz shared by every channel in this group. */
+    rate: number;
+    samplesPerRecord: number;
+    fileName: string;
+    timeDecimals: number;
+    channels: PlannedChannel[];
+}
+export interface PlanInput {
+    signals: readonly EdfSignal[];
+    recordDuration: number;
+    recordCount: number;
+    hasAnnotationChannel: boolean;
+    /**
+     * True start time of each data record, supplied for discontinuous files. The
+     * requested time window is resolved against these rather than against
+     * `recordCount * recordDuration`, which for a file with gaps is the amount of
+     * data rather than the span of time it covers.
+     */
+    recordStarts?: Float64Array | null | undefined;
+}
+export interface PlanOptions {
+    channels?: readonly string[] | undefined;
+    start?: number | undefined;
+    duration?: number | undefined;
+    end?: number | undefined;
+    annotationsOnly?: boolean | undefined;
+    /** Force a fixed number of decimals instead of deriving it per channel. */
+    decimals?: number | undefined;
+}
+export interface ConversionPlan {
+    groups: RateGroup[];
+    range: ResolvedRange;
+    columnNames: Map<number, string>;
+    writeSignals: boolean;
+    diagnostics: Diagnostic[];
+    estimate: OutputEstimate;
+}
+export interface OutputEstimate {
+    /** Total data rows across every signal file. */
+    rows: number;
+    /** Approximate size of the signal CSVs on disk. */
+    bytes: number;
+    /** True when any single file would exceed Excel's row limit. */
+    exceedsSpreadsheetLimit: boolean;
+}
+/** Excel and most spreadsheet tools stop at 1,048,576 rows including the header. */
+export declare const SPREADSHEET_ROW_LIMIT = 1048576;
+export declare function buildPlan(input: PlanInput, options?: PlanOptions): ConversionPlan;
+/** `256hz`, `12_5hz` — safe in a filename on every platform. */
+export declare function rateSlug(rate: number): string;
+//# sourceMappingURL=plan.d.ts.map

package/dist/convert/plan.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"plan.d.ts","sourceRoot":"","sources":["../../src/convert/plan.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,kBAAkB,CAAC;AACnD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AAMlD,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAErD,MAAM,WAAW,cAAc;IAC7B,MAAM,EAAE,SAAS,CAAC;IAClB,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,EAAE,MAAM,CAAC;CAClB;AAED,MAAM,WAAW,SAAS;IACxB,iEAAiE;IACjE,IAAI,EAAE,MAAM,CAAC;IACb,gBAAgB,EAAE,MAAM,CAAC;IACzB,QAAQ,EAAE,MAAM,CAAC;IACjB,YAAY,EAAE,MAAM,CAAC;IACrB,QAAQ,EAAE,cAAc,EAAE,CAAC;CAC5B;AAED,MAAM,WAAW,SAAS;IACxB,OAAO,EAAE,SAAS,SAAS,EAAE,CAAC;IAC9B,cAAc,EAAE,MAAM,CAAC;IACvB,WAAW,EAAE,MAAM,CAAC;IACpB,oBAAoB,EAAE,OAAO,CAAC;IAC9B;;;;;OAKG;IACH,YAAY,CAAC,EAAE,YAAY,GAAG,IAAI,GAAG,SAAS,CAAC;CAChD;AAED,MAAM,WAAW,WAAW;IAC1B,QAAQ,CAAC,EAAE,SAAS,MAAM,EAAE,GAAG,SAAS,CAAC;IACzC,KAAK,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC3B,QAAQ,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC9B,GAAG,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IACzB,eAAe,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IACtC,2EAA2E;IAC3E,QAAQ,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;CAC/B;AAED,MAAM,WAAW,cAAc;IAC7B,MAAM,EAAE,SAAS,EAAE,CAAC;IACpB,KAAK,EAAE,aAAa,CAAC;IACrB,WAAW,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACjC,YAAY,EAAE,OAAO,CAAC;IACtB,WAAW,EAAE,UAAU,EAAE,CAAC;IAC1B,QAAQ,EAAE,cAAc,CAAC;CAC1B;AAED,MAAM,WAAW,cAAc;IAC7B,gDAAgD;IAChD,IAAI,EAAE,MAAM,CAAC;IACb,mDAAmD;IACnD,KAAK,EAAE,MAAM,CAAC;IACd,gEAAgE;IAChE,uBAAuB,EAAE,OAAO,CAAC;CAClC;AAED,oFAAoF;AACpF,eAAO,MAAM,qBAAqB,UAAY,CAAC;AAE/C,wBAAgB,SAAS,CAAC,KAAK,EAAE,SAAS,EAAE,OAAO,GAAE,WAAgB,GAAG,cAAc,CAmDrF;AA4CD,gEAAgE;AAChE,wBAAgB,QAAQ,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAE7C"}

package/dist/convert/plan.js

@@ -0,0 +1,127 @@
+/**
+ * Turning a request into a concrete conversion plan.
+ *
+ * The plan is where the tool's central promise is enforced: channels recorded at
+ * different sampling rates are never merged into one table. A single wide CSV can
+ * only hold mixed rates by inventing samples for the slow channels — MNE, for
+ * instance, expands three genuine 1 Hz temperature readings into 768 interpolated
+ * values without warning. Instead each distinct rate gets its own file, so every
+ * number in every output file is a number that was actually recorded.
+ */
+import { formatRate } from '../edf/header.js';
+import { decimalsForSignal } from '../edf/scale.js';
+import { timeDecimals } from '../format/number.js';
+import { buildColumnNames, selectChannels } from './channels.js';
+import { countSamplesInRange, resolveRange } from './time-range.js';
+/** Excel and most spreadsheet tools stop at 1,048,576 rows including the header. */
+export const SPREADSHEET_ROW_LIMIT = 1_048_576;
+export function buildPlan(input, options = {}) {
+    const diagnostics = [];
+    const columnNames = buildColumnNames(input.signals);
+    const range = resolveRange({
+        start: options.start,
+        duration: options.duration,
+        end: options.end,
+        recordDuration: input.recordDuration,
+        recordCount: input.recordCount,
+        recordStarts: input.recordStarts,
+    });
+    const writeSignals = options.annotationsOnly !== true;
+    let chosen = input.signals.filter((s) => !s.isAnnotations);
+    if (writeSignals && options.channels && options.channels.length > 0) {
+        const selection = selectChannels(input.signals, options.channels);
+        chosen = selection.signals;
+        for (const { term, matched } of selection.ambiguous) {
+            diagnostics.push({
+                code: 'DUPLICATE_LABEL',
+                severity: 'warning',
+                message: `"${term}" matches ${matched.length} channels (positions ` +
+                    `${matched.map((s) => `#${s.index}`).join(', ')}); all of them were selected.`,
+                hint: `Use --channels "#${matched[0]?.index ?? 0}" to pick just one.`,
+            });
+        }
+    }
+    const groups = writeSignals ? groupByRate(chosen, columnNames, options.decimals) : [];
+    const estimate = estimateOutput(groups, range, input.recordDuration, input.recordStarts);
+    if (estimate.exceedsSpreadsheetLimit) {
+        diagnostics.push({
+            code: 'LARGE_OUTPUT',
+            severity: 'warning',
+            message: `At least one output file will have more than ${SPREADSHEET_ROW_LIMIT.toLocaleString('en-US')} ` +
+                `rows, which is more than Excel or Numbers can open.`,
+            hint: 'Use --start and --duration to convert a section, or read the file with pandas or R.',
+        });
+    }
+    return { groups, range, columnNames, writeSignals, diagnostics, estimate };
+}
+/**
+ * Partition channels by sampling rate, largest first.
+ *
+ * The common case — every channel at one rate — collapses to a single group and a
+ * single `signals.csv`, so the honest behaviour costs nothing when there is nothing
+ * to be honest about.
+ */
+function groupByRate(signals, columnNames, forcedDecimals) {
+    const byRate = new Map();
+    for (const signal of signals) {
+        // A channel with no samples has no sampling rate to group by, and would
+        // otherwise produce an empty "0hz" file. The header parser already warned.
+        if (signal.samplesPerRecord === 0)
+            continue;
+        const bucket = byRate.get(signal.samplingRate);
+        if (bucket)
+            bucket.push(signal);
+        else
+            byRate.set(signal.samplingRate, [signal]);
+    }
+    const rates = [...byRate.keys()].sort((a, b) => b - a);
+    const single = rates.length === 1;
+    return rates.map((rate) => {
+        const members = byRate.get(rate) ?? [];
+        const first = members[0];
+        return {
+            rate,
+            samplesPerRecord: first ? first.samplesPerRecord : 0,
+            fileName: single ? 'signals.csv' : `signals_${rateSlug(rate)}.csv`,
+            timeDecimals: timeDecimals(rate),
+            channels: members.map((signal) => ({
+                signal,
+                column: columnNames.get(signal.index) ?? `signal_${signal.index}`,
+                decimals: forcedDecimals ?? decimalsForSignal(signal),
+            })),
+        };
+    });
+}
+/** `256hz`, `12_5hz` — safe in a filename on every platform. */
+export function rateSlug(rate) {
+    return `${formatRate(rate).replace('.', '_')}hz`;
+}
+function estimateOutput(groups, range, recordDuration, recordStarts) {
+    let rows = 0;
+    let bytes = 0;
+    let exceeds = false;
+    for (const group of groups) {
+        let groupRows = 0;
+        for (let record = range.startRecord; record < range.endRecord; record++) {
+            const recordStart = recordStarts
+                ? (recordStarts[record] ?? record * recordDuration)
+                : record * recordDuration;
+            groupRows += countSamplesInRange({
+                recordStart,
+                rate: group.rate,
+                samplesPerRecord: group.samplesPerRecord,
+                startSeconds: range.startSeconds,
+                endSeconds: range.endSeconds,
+            });
+        }
+        rows += groupRows;
+        if (groupRows + 1 > SPREADSHEET_ROW_LIMIT)
+            exceeds = true;
+        // A cell is roughly the sign, a few integer digits, the point and its decimals.
+        const timeWidth = group.timeDecimals + 6;
+        const cellWidth = group.channels.reduce((sum, c) => sum + c.decimals + 6, 0);
+        bytes += groupRows * (timeWidth + cellWidth + 1);
+    }
+    return { rows, bytes, exceedsSpreadsheetLimit: exceeds };
+}
+//# sourceMappingURL=plan.js.map

package/dist/convert/plan.js.map

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package/dist/convert/run.d.ts

@@ -0,0 +1,48 @@
+/**
+ * Executing a conversion.
+ *
+ * Everything is written in a single pass over the data records. All rate groups are
+ * open at once and fed from the same batch of bytes, so a file is read once no
+ * matter how many output tables it produces, and memory stays flat.
+ */
+import { EdfFile } from '../edf/reader.js';
+import type { Diagnostic } from '../edf/errors.js';
+import type { ConversionPlan, PlanOptions } from './plan.js';
+import { VERSION as TOOL_VERSION } from '../version.js';
+export { TOOL_VERSION };
+export type ConversionErrorCode = 'OUTPUT_EXISTS' | 'OUTPUT_UNWRITABLE' | 'INPUT_OUTPUT_COLLISION' | 'WRITE_FAILED';
+export declare class ConversionError extends Error {
+    readonly code: ConversionErrorCode;
+    readonly hint: string | undefined;
+    constructor(code: ConversionErrorCode, message: string, hint?: string);
+}
+export interface ConvertOptions extends PlanOptions {
+    /** Destination directory. Defaults to the input file's name without its extension. */
+    outputDir?: string | undefined;
+    /** Overwrite an existing output directory. */
+    force?: boolean | undefined;
+    /** Record a SHA-256 of the input in metadata.json. Costs one extra read of the file. */
+    checksum?: boolean | undefined;
+    onProgress?: ((progress: ConversionProgress) => void) | undefined;
+}
+export interface ConversionProgress {
+    recordsDone: number;
+    recordsTotal: number;
+    bytesWritten: number;
+}
+export interface WrittenFile {
+    name: string;
+    rows: number;
+}
+export interface ConvertResult {
+    outputDir: string;
+    files: WrittenFile[];
+    annotationCount: number;
+    diagnostics: Diagnostic[];
+    plan: ConversionPlan;
+    file: EdfFile;
+    elapsedMs: number;
+}
+export declare function convert(inputPath: string, options?: ConvertOptions): Promise<ConvertResult>;
+export declare function defaultOutputDir(inputPath: string): string;
+//# sourceMappingURL=run.d.ts.map

package/dist/convert/run.d.ts.map

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