edf2csv 0.1.0

package/dist/edf/header.js

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+/**
+ * EDF / EDF+ header parsing.
+ *
+ * Layout (all fields are ASCII, left-justified, space-padded):
+ *
+ *   fixed header, 256 bytes
+ *     0    8   version ('0', or 255 + 'BIOSEMI' for BDF)
+ *     8   80   patient identification
+ *    88   80   recording identification
+ *   168    8   start date  dd.mm.yy
+ *   176    8   start time  hh.mm.ss
+ *   184    8   number of bytes in the header record
+ *   192   44   reserved  ('EDF+C' / 'EDF+D' live here)
+ *   236    8   number of data records (-1 if unknown)
+ *   244    8   duration of a data record, in seconds (may be fractional)
+ *   252    4   number of signals (ns)
+ *
+ *   signal header, ns * 256 bytes, stored FIELD-major rather than signal-major:
+ *   all ns labels, then all ns transducer types, and so on.
+ *     ns * 16   label
+ *     ns * 80   transducer type
+ *     ns *  8   physical dimension
+ *     ns *  8   physical minimum
+ *     ns *  8   physical maximum
+ *     ns *  8   digital minimum
+ *     ns *  8   digital maximum
+ *     ns * 80   prefiltering
+ *     ns *  8   number of samples in each data record
+ *     ns * 32   reserved
+ */
+import { EdfError } from './errors.js';
+/** Label the EDF+ spec reserves for the annotations channel. */
+export const ANNOTATIONS_LABEL = 'EDF Annotations';
+/** BDF+ uses its own spelling for the same channel. */
+export const BDF_ANNOTATIONS_LABEL = 'BDF Annotations';
+export const FIXED_HEADER_BYTES = 256;
+export const SIGNAL_HEADER_BYTES = 256;
+const dec = (buf, start, len) => buf.subarray(start, start + len).toString('latin1');
+/** EDF fields are space-padded; trailing NULs also occur in files written by sloppy tools. */
+const trimField = (s) => s.replace(/[\0\s]+$/u, '').replace(/^\s+/u, '');
+function parseNumberField(raw, field, { integer = false, sawComma } = {}) {
+    let text = trimField(raw);
+    // Some writers emit a comma decimal separator despite the spec requiring '.'.
+    if (text.includes(',') && !text.includes('.')) {
+        text = text.replace(',', '.');
+        if (sawComma)
+            sawComma.value = true;
+    }
+    if (text === '') {
+        throw new EdfError('BAD_HEADER_FIELD', `Header field "${field}" is empty.`);
+    }
+    const n = Number(text);
+    if (!Number.isFinite(n)) {
+        throw new EdfError('BAD_HEADER_FIELD', `Header field "${field}" is not a number (found ${JSON.stringify(text)}).`, 'The file may be truncated, byte-shifted, or not an EDF file at all.');
+    }
+    if (integer && !Number.isInteger(n)) {
+        throw new EdfError('BAD_HEADER_FIELD', `Header field "${field}" must be a whole number (found ${JSON.stringify(text)}).`);
+    }
+    return n;
+}
+/**
+ * EDF stores a two-digit year. The spec pins the century: 85-99 mean 1985-1999
+ * and 00-84 mean 2000-2084. Files outside 1985-2084 cannot express their date.
+ */
+function resolveStartDateTime(dateRaw, timeRaw) {
+    const d = /^(\d{2})[.\-/](\d{2})[.\-/](\d{2})$/u.exec(trimField(dateRaw));
+    const t = /^(\d{2})[.:\-](\d{2})[.:\-](\d{2})$/u.exec(trimField(timeRaw));
+    if (!d || !t)
+        return null;
+    const dd = Number(d[1]);
+    const mm = Number(d[2]);
+    const yy = Number(d[3]);
+    const hh = Number(t[1]);
+    const mi = Number(t[2]);
+    const ss = Number(t[3]);
+    if (mm < 1 || mm > 12 || dd < 1 || dd > 31 || hh > 23 || mi > 59 || ss > 60)
+        return null;
+    const year = yy >= 85 ? 1900 + yy : 2000 + yy;
+    const date = new Date(Date.UTC(year, mm - 1, dd, hh, mi, Math.min(ss, 59)));
+    // Reject dates that rolled over, e.g. 31.02.
+    if (date.getUTCMonth() !== mm - 1 || date.getUTCDate() !== dd)
+        return null;
+    return date;
+}
+/**
+ * Parse the fixed 256-byte header plus the per-signal header block.
+ *
+ * @param buf   At least FIXED_HEADER_BYTES + ns * SIGNAL_HEADER_BYTES bytes.
+ * @param fileSize Total size of the file on disk, used to derive the real record count.
+ */
+export function parseHeader(buf, fileSize) {
+    const diagnostics = [];
+    const sawComma = { value: false };
+    if (buf.length < FIXED_HEADER_BYTES) {
+        throw new EdfError('FILE_TOO_SMALL', `File is ${fileSize} bytes; an EDF header alone needs at least ${FIXED_HEADER_BYTES}.`);
+    }
+    // BDF (BioSemi) marks itself with byte 255 followed by 'BIOSEMI', and stores
+    // 3-byte samples instead of 2. Everything else about the layout is identical.
+    const isBdf = buf[0] === 0xff && dec(buf, 1, 7) === 'BIOSEMI';
+    const version = isBdf ? 'BIOSEMI' : trimField(dec(buf, 0, 8));
+    const patientId = trimField(dec(buf, 8, 80));
+    const recordingId = trimField(dec(buf, 88, 80));
+    const startDateRaw = trimField(dec(buf, 168, 8));
+    const startTimeRaw = trimField(dec(buf, 176, 8));
+    const headerBytes = parseNumberField(dec(buf, 184, 8), 'number of header bytes', {
+        integer: true,
+        sawComma,
+    });
+    const reserved = trimField(dec(buf, 192, 44));
+    const declaredRecordCount = parseNumberField(dec(buf, 236, 8), 'number of data records', {
+        integer: true,
+        sawComma,
+    });
+    const recordDuration = parseNumberField(dec(buf, 244, 8), 'duration of a data record', {
+        sawComma,
+    });
+    const signalCount = parseNumberField(dec(buf, 252, 4), 'number of signals', {
+        integer: true,
+        sawComma,
+    });
+    if (signalCount <= 0) {
+        throw new EdfError('INVALID_SIGNAL_COUNT', `Header declares ${signalCount} signals; expected at least 1.`);
+    }
+    if (!(recordDuration > 0)) {
+        throw new EdfError('INVALID_RECORD_DURATION', `Header declares a data record duration of ${recordDuration}s; expected a positive number.`);
+    }
+    const expectedHeaderBytes = FIXED_HEADER_BYTES + signalCount * SIGNAL_HEADER_BYTES;
+    if (buf.length < expectedHeaderBytes) {
+        throw new EdfError('FILE_TOO_SMALL', `File declares ${signalCount} signals, which needs a ${expectedHeaderBytes}-byte header, ` +
+            `but the file is only ${fileSize} bytes.`);
+    }
+    if (headerBytes !== expectedHeaderBytes) {
+        diagnostics.push({
+            code: 'HEADER_BYTES_MISMATCH',
+            severity: 'warning',
+            message: `Header says it is ${headerBytes} bytes, but ${signalCount} signals require ` +
+                `${expectedHeaderBytes} bytes. Using the value computed from the signal count.`,
+        });
+    }
+    // Signal headers are field-major: all labels, then all transducers, and so on.
+    const base = FIXED_HEADER_BYTES;
+    const readField = (offsetUnits, width, i) => dec(buf, base + offsetUnits * signalCount + i * width, width);
+    // EDF+ writes 'EDF+C'/'EDF+D' here; BDF+ writes 'BDF+C'/'BDF+D'. The two mean the
+    // same thing, so both are normalised to a single continuity marker.
+    const continuityTag = /^(?:EDF|BDF)\+([CD])/u.exec(reserved);
+    const continuity = continuityTag === null ? null : continuityTag[1] === 'D' ? 'EDF+D' : 'EDF+C';
+    const signals = [];
+    let byteOffsetInRecord = 0;
+    const bytesPerSample = isBdf ? 3 : 2;
+    const seenLabels = new Map();
+    for (let i = 0; i < signalCount; i++) {
+        const label = trimField(readField(0, 16, i));
+        const transducer = trimField(readField(16, 80, i));
+        const physicalDimension = trimField(readField(96, 8, i));
+        const physicalMin = parseNumberField(readField(104, 8, i), `physical minimum (signal ${i})`, {
+            sawComma,
+        });
+        const physicalMax = parseNumberField(readField(112, 8, i), `physical maximum (signal ${i})`, {
+            sawComma,
+        });
+        const digitalMin = parseNumberField(readField(120, 8, i), `digital minimum (signal ${i})`, {
+            integer: true,
+            sawComma,
+        });
+        const digitalMax = parseNumberField(readField(128, 8, i), `digital maximum (signal ${i})`, {
+            integer: true,
+            sawComma,
+        });
+        const prefiltering = trimField(readField(136, 80, i));
+        const samplesPerRecord = parseNumberField(readField(216, 8, i), `samples per record (signal ${i})`, { integer: true, sawComma });
+        const sigReserved = trimField(readField(224, 32, i));
+        if (samplesPerRecord < 0) {
+            throw new EdfError('BAD_HEADER_FIELD', `Signal ${i} ("${label}") declares ${samplesPerRecord} samples per record.`);
+        }
+        const isAnnotations = label === ANNOTATIONS_LABEL || label === BDF_ANNOTATIONS_LABEL;
+        signals.push({
+            index: i,
+            label,
+            transducer,
+            physicalDimension,
+            physicalMin,
+            physicalMax,
+            digitalMin,
+            digitalMax,
+            prefiltering,
+            samplesPerRecord,
+            reserved: sigReserved,
+            isAnnotations,
+            samplingRate: samplesPerRecord / recordDuration,
+            byteOffsetInRecord,
+        });
+        byteOffsetInRecord += samplesPerRecord * bytesPerSample;
+        if (!isAnnotations) {
+            if (label === '') {
+                diagnostics.push({
+                    code: 'EMPTY_LABEL',
+                    severity: 'warning',
+                    message: `Signal ${i} has no label. It will appear as "signal_${i}".`,
+                });
+            }
+            else {
+                // Collected rather than reported here: a label repeated five times should
+                // produce one warning naming all five, not four near-identical pairs.
+                const seen = seenLabels.get(label);
+                if (seen)
+                    seen.push(i);
+                else
+                    seenLabels.set(label, [i]);
+            }
+            if (samplesPerRecord === 0) {
+                diagnostics.push({
+                    code: 'NO_SAMPLES',
+                    severity: 'warning',
+                    message: `Signal ${i} ("${label}") carries no samples at all (0 per data record).`,
+                    hint: 'It is described in channels.csv but left out of the converted data.',
+                });
+            }
+            if (digitalMax === digitalMin) {
+                diagnostics.push({
+                    code: 'DEGENERATE_DIGITAL_RANGE',
+                    severity: 'warning',
+                    message: `Signal ${i} ("${label}") has digital minimum equal to digital maximum ` +
+                        `(${digitalMin}), so its values cannot be scaled.`,
+                    hint: 'Its samples are written as the physical minimum. Treat this channel with suspicion.',
+                });
+            }
+            else if (physicalMax === physicalMin) {
+                diagnostics.push({
+                    code: 'DEGENERATE_PHYSICAL_RANGE',
+                    severity: 'warning',
+                    message: `Signal ${i} ("${label}") has physical minimum equal to physical maximum ` +
+                        `(${physicalMin}), so every sample converts to the same value.`,
+                });
+            }
+            else if (physicalMax < physicalMin) {
+                diagnostics.push({
+                    code: 'INVERTED_PHYSICAL_RANGE',
+                    severity: 'warning',
+                    message: `Signal ${i} ("${label}") declares physical minimum ${physicalMin} above physical ` +
+                        `maximum ${physicalMax}, which inverts its polarity.`,
+                    hint: 'The values are converted exactly as the header specifies, inversion included.',
+                });
+            }
+        }
+    }
+    for (const [label, indices] of seenLabels) {
+        if (indices.length < 2)
+            continue;
+        diagnostics.push({
+            code: 'DUPLICATE_LABEL',
+            severity: 'warning',
+            message: `${indices.length} signals share the label "${label}" (positions ${indices.join(', ')}).`,
+            hint: 'Their columns are suffixed with the signal number so they stay distinguishable.',
+        });
+    }
+    const recordBytes = byteOffsetInRecord;
+    if (recordBytes <= 0) {
+        throw new EdfError('NO_SAMPLES', 'No signal in this file carries any samples (every channel declares 0 samples per record).');
+    }
+    if (sawComma.value) {
+        diagnostics.push({
+            code: 'COMMA_DECIMAL',
+            severity: 'warning',
+            message: 'Some header numbers use a comma decimal separator, which the EDF spec does not allow.',
+            hint: 'They were read as decimal points. Check the values in the channel table.',
+        });
+    }
+    const dataBytes = fileSize - expectedHeaderBytes;
+    if (dataBytes < 0) {
+        throw new EdfError('FILE_TOO_SMALL', `File is smaller than its own header.`);
+    }
+    const recordCount = Math.floor(dataBytes / recordBytes);
+    const trailingBytes = dataBytes - recordCount * recordBytes;
+    if (recordCount === 0) {
+        throw new EdfError('NO_DATA_RECORDS', 'The file contains a header but no complete data record.', 'The recording was probably interrupted before any data was written.');
+    }
+    if (declaredRecordCount === -1) {
+        diagnostics.push({
+            code: 'RECORD_COUNT_UNKNOWN',
+            severity: 'warning',
+            message: `The header does not say how many data records the file has (-1), which the spec allows ` +
+                `for recordings still in progress. Using the ${recordCount} records the file actually contains.`,
+        });
+    }
+    else if (declaredRecordCount !== recordCount) {
+        diagnostics.push({
+            code: 'RECORD_COUNT_MISMATCH',
+            severity: 'warning',
+            message: `The header declares ${declaredRecordCount} data records but the file contains ` +
+                `${recordCount}. Converting the ${recordCount} records that are present.`,
+            hint: declaredRecordCount > recordCount
+                ? 'The recording looks truncated. It may have been cut short or copied incompletely.'
+                : 'The file is longer than its header claims.',
+        });
+    }
+    if (trailingBytes > 0) {
+        diagnostics.push({
+            code: 'TRAILING_BYTES',
+            severity: 'warning',
+            message: `${trailingBytes} bytes after the last complete data record were ignored.`,
+        });
+    }
+    const isEdfPlus = continuity !== null;
+    if (continuity === 'EDF+D') {
+        diagnostics.push({
+            code: 'DISCONTINUOUS',
+            severity: 'warning',
+            message: `This is a discontinuous (${isBdf ? 'BDF+D' : 'EDF+D'}) recording: its data records are ` +
+                `not contiguous in time.`,
+            hint: 'Each row carries its true recording time, so gaps stay visible instead of being closed.',
+        });
+    }
+    const dataSignals = signals.filter((s) => !s.isAnnotations);
+    if (dataSignals.length === 0) {
+        diagnostics.push({
+            code: 'NO_SIGNAL_CHANNELS',
+            severity: 'warning',
+            message: 'This file has no signal channels; it contains only EDF+ annotations.',
+        });
+    }
+    const rates = new Set(dataSignals.map((s) => s.samplingRate));
+    if (rates.size > 1) {
+        diagnostics.push({
+            code: 'MIXED_SAMPLING_RATES',
+            severity: 'warning',
+            message: `Channels use ${rates.size} different sampling rates ` +
+                `(${[...rates].sort((a, b) => b - a).map((r) => `${formatRate(r)} Hz`).join(', ')}).`,
+            hint: 'They are written to one file per rate so no channel is resampled.',
+        });
+    }
+    return {
+        header: {
+            version,
+            patientId,
+            recordingId,
+            startDateRaw,
+            startTimeRaw,
+            startDateTime: resolveStartDateTime(startDateRaw, startTimeRaw),
+            headerBytes: expectedHeaderBytes,
+            reserved,
+            isEdfPlus,
+            isBdf,
+            continuity,
+            declaredRecordCount,
+            recordDuration,
+            signalCount,
+            signals,
+            bytesPerSample,
+            recordBytes,
+        },
+        recordCount,
+        trailingBytes,
+        diagnostics,
+    };
+}
+/**
+ * The recording start as a zone-less wall clock, "YYYY-MM-DDTHH:MM:SS".
+ *
+ * EDF stores the start time as local wall-clock digits with no timezone anywhere in
+ * the format. `startDateTime` is built with Date.UTC purely so those digits survive a
+ * round trip unshifted, which makes it a carrier for the wall clock rather than a
+ * real instant. Serialising it with `toISOString()` would append a Z and assert UTC,
+ * and any reader converting to local time would then shift the recording by their own
+ * offset: 13:43:04 in the file becomes 08:43:04 in New York. The Z is omitted because
+ * the file genuinely does not say which zone it meant.
+ */
+export function formatWallClock(date) {
+    if (!date)
+        return null;
+    return date.toISOString().slice(0, 19);
+}
+/** "EDF", "EDF+ (EDF+D)", "BDF", "BDF+ (EDF+C)". */
+export function describeFormat(header) {
+    const base = header.isBdf ? 'BDF' : 'EDF';
+    if (!header.isEdfPlus)
+        return base;
+    return `${base}+ (${header.continuity === 'EDF+D' ? 'discontinuous' : 'continuous'})`;
+}
+/** Render a sampling rate without trailing noise: 256, 0.5, 12.5. */
+export function formatRate(hz) {
+    return Number.isInteger(hz) ? String(hz) : String(Number(hz.toFixed(6)));
+}
+//# sourceMappingURL=header.js.map

package/dist/edf/header.js.map

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package/dist/edf/reader.d.ts

@@ -0,0 +1,75 @@
+/**
+ * Chunked reader for EDF / EDF+ files.
+ *
+ * Data records are read in batches sized by a byte budget rather than all at once,
+ * so peak memory stays flat regardless of how long the recording is. A 4 GB file
+ * and a 4 MB file use the same working set.
+ */
+import type { Diagnostic } from './errors.js';
+import type { EdfHeader, EdfSignal } from './header.js';
+import type { Annotation } from './annotations.js';
+/** Default read budget per batch. Large enough to amortise syscalls, small enough to stay cheap. */
+export declare const DEFAULT_CHUNK_BYTES: number;
+export interface RecordBatch {
+    /** Index of the first record in this batch, relative to the whole file. */
+    firstRecordIndex: number;
+    recordCount: number;
+    /**
+     * Raw record bytes, `recordCount * header.recordBytes` long.
+     *
+     * The buffer is reused between iterations. Copy anything you need to keep past
+     * the current loop turn.
+     */
+    data: Buffer;
+}
+export interface ReadRecordsOptions {
+    /** First record to read, inclusive. Defaults to 0. */
+    startRecord?: number;
+    /** Last record to read, exclusive. Defaults to the file's record count. */
+    endRecord?: number;
+    chunkBytes?: number;
+}
+export declare class EdfFile {
+    #private;
+    readonly path: string;
+    readonly fileSize: number;
+    readonly header: EdfHeader;
+    /** Records actually present in the file, which may differ from the header's claim. */
+    readonly recordCount: number;
+    readonly trailingBytes: number;
+    readonly diagnostics: Diagnostic[];
+    private constructor();
+    static open(path: string): Promise<EdfFile>;
+    /** Signal channels, excluding the EDF+ annotations channel. */
+    get dataSignals(): EdfSignal[];
+    get annotationSignals(): EdfSignal[];
+    /** Total recording duration in seconds, based on records actually present. */
+    get durationSeconds(): number;
+    /** Read a half-open range of records in batches. */
+    readRecords(options?: ReadRecordsOptions): AsyncGenerator<RecordBatch>;
+    /** Read one sample as its raw digital value. */
+    sampleAt(batch: RecordBatch, recordOffset: number, signal: EdfSignal, sampleIndex: number): number;
+    /** Byte offset of a signal's samples within a batch. */
+    offsetOf(batch: RecordBatch, recordOffset: number, signal: EdfSignal): number;
+    /** The annotation channel's raw bytes for one record in a batch. */
+    annotationBytes(batch: RecordBatch, recordOffset: number, signal: EdfSignal): Buffer;
+    /**
+     * Read every EDF+ annotation in the file, plus the start time each record declares.
+     *
+     * Only the annotation channel is read, seeking straight to it inside each record
+     * rather than pulling whole records through memory. On a multi-gigabyte recording
+     * that is the difference between a few kilobytes of I/O and all of it.
+     *
+     * The whole file is always scanned, never just the records inside a requested
+     * window: writers are not obliged to store an annotation in the record its onset
+     * falls in, and some put every annotation in the first record. Reading only the
+     * window's records would drop those entirely.
+     */
+    readAnnotations(): Promise<{
+        annotations: Annotation[];
+        recordStarts: (number | null)[];
+        malformed: number;
+    }>;
+    close(): Promise<void>;
+}
+//# sourceMappingURL=reader.d.ts.map

package/dist/edf/reader.d.ts.map

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