edf2csv 0.4.65 → 0.4.67
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CHANGELOG.md +29 -0
- package/dist/cli/report.js.map +1 -1
- package/dist/cli.js.map +1 -1
- package/dist/convert/channels.js.map +1 -1
- package/dist/convert/options.js.map +1 -1
- package/dist/convert/plan.js.map +1 -1
- package/dist/convert/run.js.map +1 -1
- package/dist/convert/time-range.js.map +1 -1
- package/dist/convert/timing.js.map +1 -1
- package/dist/edf/annotations.js.map +1 -1
- package/dist/edf/bytes.js.map +1 -1
- package/dist/edf/errors.js.map +1 -1
- package/dist/edf/header.js.map +1 -1
- package/dist/edf/reader.js.map +1 -1
- package/dist/edf/scale.js.map +1 -1
- package/dist/format/csv.js.map +1 -1
- package/dist/format/list.js.map +1 -1
- package/dist/format/number.js.map +1 -1
- package/dist/index.js.map +1 -1
- package/dist/version.js.map +1 -1
- package/package.json +1 -1
package/dist/edf/reader.js.map
CHANGED
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1
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1
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+
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Re-opening the path to hash it afterwards described whatever was at\n * that name by then: a recording still being written grew from 2,000 records to 3,000\n * mid-conversion and metadata.json recorded `data_records: 2000` beside the checksum and\n * byte count of the 3,000-record file, which is provenance for bytes nobody converted.\n * Replacing the file at that path did the same thing more completely.\n */\n async sha256(): Promise<string> {\n this.#assertOpen();\n const hash = createHash('sha256');\n const buffer = Buffer.alloc(Math.min(this.fileSize, 4 * 1024 * 1024) || 1);\n for (let at = 0; at < this.fileSize; ) {\n const want = Math.min(buffer.length, this.fileSize - at);\n const { bytesRead } = await this.#handle.read(buffer, 0, want, at);\n if (bytesRead <= 0) {\n throw new EdfError(\n 'UNREADABLE',\n `Expected ${this.fileSize} bytes to checksum but the file ended at ${at}; ` +\n `it appears to have changed size while it was being read.`,\n 'Make sure the recording is not still being written to, then try again.',\n );\n }\n hash.update(buffer.subarray(0, bytesRead));\n at += bytesRead;\n }\n return hash.digest('hex');\n }\n\n /**\n * Whether the file has changed since it was opened, by size or by modification time.\n *\n * Checked through the descriptor, so it answers for the bytes that were read rather than\n * for whatever now answers to the same name. A recording still being written is the\n * ordinary cause, and the conversion is still correct for the data it saw — it is the\n * claim that the output describes the file as it now stands that stops being true.\n */\n async changedSinceOpen(): Promise<boolean> {\n /*\n A closed file remembers its last answer rather than inventing a new one.\n\n Returning false once closed asserted \"it did not change\", which is not something a\n closed descriptor can know — and `convert()` closes the file before it returns, so\n `result.file.changedSinceOpen()` denied the very change the INPUT_CHANGED diagnostic\n in the same result object had just reported. One object, two answers.\n\n `convert()` always asks before closing, so the cached answer is the true one. 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A ConvertResult carries the answer already, since ' +\n 'convert() checks it on the way out.',\n );\n }\n const now = await this.#handle.stat().catch(() => null);\n if (now === null) return this.#changed ?? false;\n this.#changed = now.size !== this.fileSize || now.mtimeMs !== this.modifiedAtOpenMs;\n return this.#changed;\n }\n\n static async open(path: string): Promise<EdfFile> {\n const info = await stat(path).catch((cause: unknown) => {\n throw new EdfError('UNREADABLE', `Cannot read \"${path}\": ${describe(cause)}`);\n });\n if (info.isDirectory()) {\n throw new EdfError('UNREADABLE', `\"${path}\" is a directory, not an EDF file.`);\n }\n if (!info.isFile()) {\n throw new EdfError('UNREADABLE', `\"${path}\" is not a regular file.`);\n }\n\n const handle = await open(path, 'r');\n try {\n const fixed = Buffer.alloc(Math.min(FIXED_HEADER_BYTES, info.size));\n if (fixed.length > 0) {\n const bytesRead = await readFully(handle, fixed, 0, fixed.length, 0);\n if (bytesRead < fixed.length) throw changedWhileReading(0, fixed.length, bytesRead);\n }\n\n // The signal count decides how much more header there is to read. 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Clamping\n silently would be no better, since a caller asking for record 1.5 has a bug the\n library should name rather than paper over.\n */\n for (const [name, value] of [\n ['startRecord', options.startRecord],\n ['endRecord', options.endRecord],\n ] as const) {\n if (value !== undefined && !Number.isInteger(value)) {\n throw new EdfError(\n 'BAD_HEADER_FIELD',\n `readRecords: ${name} must be a whole record index, got ${value}.`,\n 'Record boundaries are the unit the file can be read in; a fractional index would decode samples from the middle of a record.',\n );\n }\n }\n\n const start = Math.max(0, options.startRecord ?? 0);\n const end = Math.min(this.recordCount, options.endRecord ?? this.recordCount);\n if (start >= end) return;\n\n const { recordBytes } = this.header;\n const budget = options.chunkBytes ?? 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Nothing was wrong with the data; the\n memory just had nothing to do with it.\n\n Bounded by what is actually going to be read, so a batch of five hundred short\n recordings costs five hundred short buffers rather than five hundred 8 MB ones.\n */\n const perChunk = Math.max(1, Math.min(Math.floor(budget / recordBytes), end - start));\n const buffer = Buffer.alloc(perChunk * recordBytes);\n\n for (let record = start; record < end; record += perChunk) {\n const count = Math.min(perChunk, end - record);\n const bytes = count * recordBytes;\n const position = this.header.headerBytes + record * recordBytes;\n\n const bytesRead = await readFully(this.#handle, buffer, 0, bytes, position);\n if (bytesRead < bytes) {\n // The file is shorter than its own size said. Quietly stopping here would\n // hand back a conversion missing its tail with nothing to show for it.\n throw new EdfError(\n 'UNREADABLE',\n `Expected ${bytes} bytes of data at record ${record} but only ${bytesRead} were ` +\n `available; the file appears to have changed size while it was being read.`,\n 'Make sure the recording is not still being written to, then try again.',\n );\n }\n\n yield { firstRecordIndex: record, recordCount: count, data: buffer.subarray(0, bytes) };\n }\n }\n\n /** Read one sample as its raw digital value. */\n sampleAt(batch: RecordBatch, recordOffset: number, signal: EdfSignal, sampleIndex: number): number {\n const position =\n recordOffset * this.header.recordBytes +\n signal.byteOffsetInRecord +\n sampleIndex * this.header.bytesPerSample;\n\n if (this.header.bytesPerSample === 3) {\n // BDF stores 24-bit little-endian two's complement. Loading the three bytes\n // into the top of a 32-bit word and shifting back down sign-extends them.\n const data = batch.data;\n return (\n ((data[position] as number) << 8) |\n ((data[position + 1] as number) << 16) |\n ((data[position + 2] as number) << 24)\n ) >> 8;\n }\n return readInt16LE(batch.data, position);\n }\n\n /** Byte offset of a signal's samples within a batch. */\n offsetOf(batch: RecordBatch, recordOffset: number, signal: EdfSignal): number {\n return recordOffset * this.header.recordBytes + signal.byteOffsetInRecord;\n }\n\n /** The annotation channel's raw bytes for one record in a batch. */\n annotationBytes(batch: RecordBatch, recordOffset: number, signal: EdfSignal): Uint8Array {\n const start = this.offsetOf(batch, recordOffset, signal);\n return batch.data.subarray(start, start + signal.samplesPerRecord * this.header.bytesPerSample);\n }\n\n /**\n * Read every EDF+ annotation in the file, plus the start time each record declares.\n *\n * Only the annotation channel is read, seeking straight to it inside each record\n * rather than pulling whole records through memory. On a multi-gigabyte recording\n * that is the difference between a few kilobytes of I/O and all of it.\n *\n * The whole file is always scanned, never just the records inside a requested\n * window: writers are not obliged to store an annotation in the record its onset\n * falls in, and some put every annotation in the first record. Reading only the\n * window's records would drop those entirely.\n */\n /**\n * Where this continuous recording begins, from the first record that says.\n *\n * A few records' worth of annotation bytes rather than the whole channel. A continuous\n * recording's origin is the fraction of a second by which its first record follows the\n * header's start time, and `--info` needs that to place a requested window — but it does\n * not need the events, and finding one number by reading every record costs a seek per\n * record across the whole file, which is the scan `--info` was deliberately spared.\n *\n * It reads on past record 0 because a conversion does. This used to stop there, so the\n * moment one timekeeping TAL was unreadable the two disagreed: the conversion took the\n * origin from record 1 and timed the file from 0.5s, while `--info` found nothing at\n * record 0 and reported a recording starting at zero — the same file described two ways by\n * one tool. Records are contiguous, so record `i` beginning at `t` puts the origin at\n * `t - i * duration`, and any one of them settles it.\n *\n * The bound is what keeps this cheap: a file whose first `RECORDS_SEARCHED_FOR_ORIGIN`\n * timekeeping entries are all unreadable reports an origin of zero here, and converting it\n * raises ANNOTATION_DECODE_FAILED for every one of them.\n *\n * Returns null when there is nothing to read it from, in which case the origin is zero.\n */\n async readOrigin(): Promise<number | null> {\n this.#assertOpen();\n\n const channel = this.annotationSignals[0];\n if (!channel || this.recordCount === 0) return null;\n\n const { headerBytes, bytesPerSample, recordBytes, recordDuration } = this.header;\n const buffer = Buffer.alloc(channel.samplesPerRecord * bytesPerSample);\n if (buffer.length === 0) return null;\n\n const searched = Math.min(this.recordCount, RECORDS_SEARCHED_FOR_ORIGIN);\n for (let record = 0; record < searched; record++) {\n const offset = headerBytes + record * recordBytes + channel.byteOffsetInRecord;\n const bytesRead = await readFully(this.#handle, buffer, 0, buffer.length, offset);\n if (bytesRead < buffer.length) return null;\n\n const start = decodeRecordAnnotations(buffer, record).recordStart;\n if (start !== null) return start - record * recordDuration;\n }\n return null;\n }\n\n async readAnnotations(): Promise<{\n annotations: Annotation[];\n recordStarts: (number | null)[];\n malformed: number;\n /** Unreadable TALs in first position, which carry timing rather than an event. */\n malformedTimekeeping: number;\n }> {\n this.#assertOpen();\n\n const annotations: Annotation[] = [];\n const recordStarts: (number | null)[] = new Array<number | null>(this.recordCount).fill(null);\n let malformed = 0;\n let malformedTimekeeping = 0;\n\n const channels = this.annotationSignals;\n if (channels.length === 0) {\n return { annotations, recordStarts, malformed, malformedTimekeeping };\n }\n\n const { headerBytes, recordBytes, bytesPerSample } = this.header;\n const buffers = channels.map((c) => Buffer.alloc(c.samplesPerRecord * bytesPerSample));\n\n for (let record = 0; record < this.recordCount; record++) {\n for (const [position, channel] of channels.entries()) {\n const buffer = buffers[position];\n if (!buffer || buffer.length === 0) continue;\n\n const offset = headerBytes + record * recordBytes + channel.byteOffsetInRecord;\n const bytesRead = await readFully(this.#handle, buffer, 0, buffer.length, offset);\n if (bytesRead < buffer.length) {\n throw changedWhileReading(record, buffer.length, bytesRead, 'annotation data');\n }\n\n const decoded = decodeRecordAnnotations(buffer, record);\n // Only the first annotation channel carries the record's timekeeping TAL.\n if (position === 0) recordStarts[record] = decoded.recordStart;\n for (const annotation of decoded.annotations) annotations.push(annotation);\n malformed += decoded.malformed;\n malformedTimekeeping += decoded.malformedTimekeeping;\n }\n }\n\n annotations.sort((a, b) => a.onset - b.onset || a.recordIndex - b.recordIndex);\n return { annotations, recordStarts, malformed, malformedTimekeeping };\n }\n\n async close(): Promise<void> {\n if (this.#closed) return;\n this.#closed = true;\n await this.#handle.close();\n }\n\n #assertOpen(): void {\n if (this.#closed) throw new EdfError('UNREADABLE', 'This EDF file has already been closed.');\n }\n}\n\nfunction describe(cause: unknown): string {\n if (cause instanceof Error) {\n const code = (cause as NodeJS.ErrnoException).code;\n if (code === 'ENOENT') return 'no such file';\n if (code === 'EACCES') return 'permission denied';\n return cause.message;\n }\n return String(cause);\n}\n\n/**\n * The most `fs.read` will accept as a length.\n *\n * Node asserts on a length that does not fit in a signed 32-bit integer, and it asserts in\n * C++: `Assertion failed: args[3]->IsInt32()`, forty frames of native stack, SIGABRT. Not an\n * exception — nothing in JavaScript sees it, so no catch block and no `uncaughtException`\n * handler runs, and a library consumer's whole process goes down with it.\n *\n * A round gigabyte rather than the exact limit, so the loop below does whole even reads.\n */\nconst MAX_READ_BYTES = 1024 * 1024 * 1024;\n\n/** Fill a requested region unless EOF is reached; regular-file reads may legally be short. */\nasync function readFully(\n handle: FileHandle,\n buffer: Buffer,\n offset: number,\n length: number,\n position: number,\n): Promise<number> {\n let total = 0;\n while (total < length) {\n /*\n Capped, because one data record can be larger than a single read may be.\n\n A record is read in one call when it exceeds the chunk budget — there is nothing\n smaller to divide it by, since a record is the unit the format is addressed in. EDF's\n samples-per-record field is 8 characters, so eleven channels at 99,999,999 samples make\n a record of 2.2 GB, and a long record duration at ordinary rates gets there too. That\n went to `fs.read` as a single length over 2^31-1 and took the process out with a native\n assertion rather than an error.\n\n Looping was already how a short read is handled, so the cap costs one more iteration\n per gigabyte and nothing else.\n */\n const want = Math.min(length - total, MAX_READ_BYTES);\n const { bytesRead } = await handle.read(buffer, offset + total, want, position + total);\n if (bytesRead === 0) break;\n total += bytesRead;\n }\n return total;\n}\n\nfunction changedWhileReading(\n record: number,\n expected: number,\n actual: number,\n subject = 'data',\n): EdfError {\n return new EdfError(\n 'UNREADABLE',\n `Expected ${expected} bytes of ${subject} at record ${record} but only ${actual} were ` +\n `available; the file appears to have changed size while it was being read.`,\n 'Make sure the recording is not still being written to, then try again.',\n );\n}\n"]}
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Written the first way, a channel spanning\n * +/-800 uV computes a value near 800 and then subtracts 800, and the cancellation\n * throws away low-order bits: digital 0 yields 0.19536019536019467 when the exact\n * value is 0.19536019536019536. EDFlib's form keeps the intermediate small\n * (offset + digital = 0.5 here) and returns the correctly rounded result.\n *\n * Both properties matter. The values are as accurate as a double can express, and\n * they are bit-identical to pyEDFlib and EDFbrowser, which share EDFlib's arithmetic,\n * so the test suite can assert exact equality against a reference implementation\n * rather than settling for a tolerance.\n */\n\nimport type { EdfSignal } from './header.js';\n\nexport type Scaler = (digital: number) => number;\n\nexport function makeScaler(signal: EdfSignal): Scaler {\n const { digitalMin, digitalMax, physicalMin, physicalMax } = signal;\n\n // A zero digital span leaves the mapping undefined — the header contradicts itself,\n // so there is no physical value for any sample on this channel.\n //\n // NaN rather than a stand-in number. Writing the physical minimum produces a column\n // of plausible readings (\"-100.000\" repeated) that is indistinguishable from a real\n // flat recording once the CSV is opened somewhere else, which is exactly the kind of\n // invented data this tool exists to avoid. NaN carries through to an empty CSV cell\n // and reads back as NaN in pandas, matching how a missing annotation duration is\n // already written. DEGENERATE_DIGITAL_RANGE is raised alongside it.\n if (digitalMax === digitalMin) return () => NaN;\n\n const gain = (physicalMax - physicalMin) / (digitalMax - digitalMin);\n\n // A flat physical range makes every sample the same value, and would divide by\n // zero in the offset below. That mapping is defined, so its constant is written.\n if (gain === 0) return () => physicalMin;\n\n // A non-finite gain is a different thing: the physical span overflowed a double, so\n // there is no mapping at all. Returning physicalMin filled the column with one enormous\n // constant — every distinct sample rendered as the same 300-digit number — and raised\n // nothing. 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For every realistic calibration that is\n // both safe and more accurate, but an absurd header (a huge physical range over a\n // near-zero gain) could overflow it, so fall back to the specification's own\n // arrangement rather than emitting Infinity.\n const offset = physicalMax / gain - digitalMax;\n if (!Number.isFinite(offset)) {\n return (digital: number): number => (digital - digitalMin) * gain + physicalMin;\n }\n\n return (digital: number): number => gain * (offset + digital);\n}\n\n/**\n * Smallest physical step this channel can express — one digital unit.\n * Used to choose a decimal precision that preserves every distinct sample value.\n */\nexport function quantizationStep(signal: EdfSignal): number {\n const digitalSpan = signal.digitalMax - signal.digitalMin;\n if (digitalSpan === 0) return 0;\n return Math.abs((signal.physicalMax - signal.physicalMin) / digitalSpan);\n}\n\n/**\n * Decimal places needed so that two adjacent digital codes never round to the same\n * string. Two places past the quantization step keep rounding error far below the\n * resolution the hardware actually recorded, without padding the file with digits\n * that carry no information.\n *\n * The ceiling is 20 rather than a tidier number because a channel calibrated in\n * volts rather than microvolts has a step near 1e-7, and one in tesla smaller\n * still. A lower cap would round genuinely different samples to the same text. It\n * costs nothing for ordinary channels, whose step lands them at three or four.\n */\nexport function decimalsForSignal(signal: EdfSignal, max = 20): number {\n const step = quantizationStep(signal);\n if (!(step > 0) || !Number.isFinite(step)) return 3;\n const needed = Math.ceil(-Math.log10(step)) + 2;\n return Math.min(max, Math.max(0, needed));\n}\n"]}
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package/dist/format/csv.js.map
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Capturing the error here lets the next\n // flush surface it as a normal failure with a usable message.\n this.#stream.on('error', (error: NodeJS.ErrnoException) => {\n /*\n EPIPE is the reader hanging up, not a write failure.\n\n `edf2csv recording.edf --stdout | head -1` closes the pipe while the conversion is\n still writing, and treating that as an error produced exit 1 and a message about\n files that do not exist and disk space that is not the problem. A file stream\n cannot raise EPIPE, so this only ever means \"the consumer stopped reading\", which\n is what a shell pipeline does routinely and on purpose.\n */\n if (error.code === 'EPIPE') {\n this.#hungUp = true;\n return;\n }\n this.#failure ??= error;\n });\n }\n\n /** True once the reader closed the pipe. Nothing more can reach the consumer. */\n get hungUp(): boolean {\n return this.#hungUp;\n }\n\n /** Characters written to the stream so far, before any encoding expansion. */\n get charsWritten(): number {\n return this.#bytesWritten;\n }\n\n /**\n * Bytes handed to the stream, counting a multi-byte character once per byte.\n *\n * `charsWritten` drives the progress meter, where the difference does not matter. This is\n * for checking that what was handed over actually arrived, which is a byte question: a\n * channel labelled in Cyrillic makes the two differ by hundreds of bytes on the header\n * line alone.\n */\n get bytesOut(): number {\n return this.#bytesOut;\n }\n\n push(text: string): void {\n this.#parts.push(text);\n this.#pending += text.length;\n }\n\n pushLine(text: string): void {\n this.push(text);\n this.push('\\n');\n }\n\n /**\n * Whether enough has accumulated to be worth writing out.\n *\n * A synchronous question, so a row loop can ask it every row without paying for a\n * microtask on the twenty million that answer no.\n */\n get full(): boolean {\n return this.#pending >= this.#threshold;\n }\n\n /** Flush if enough has accumulated. 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Returning without clearing it let\n push() keep appending for the rest of the conversion with nothing ever draining it,\n so `--stdout | head -1` on a 165 MB conversion grew to a 1.3 GB working set and died\n with a heap out-of-memory under a 256 MB limit — worse than the error this replaced.\n Bounded memory is the invariant this class exists to hold, and a hung-up reader is no\n reason to abandon it.\n\n Deliberately not `#ended`, which end() sets before its own final flush.\n */\n if (this.#hungUp) {\n this.#parts = [];\n this.#pending = 0;\n return;\n }\n if (this.#parts.length === 0) return;\n\n const chunk = this.#parts.join('');\n this.#parts = [];\n this.#pending = 0;\n this.#bytesWritten += chunk.length;\n this.#bytesOut += Buffer.byteLength(chunk);\n\n if (!this.#stream.write(chunk)) {\n // The consumer is behind; wait rather than letting Node buffer without bound.\n // Waiting only on 'drain' would hang forever if the stream fails instead.\n await this.#drain();\n }\n }\n\n /** Resolve on 'drain', reject if the stream fails first. */\n async #drain(): Promise<void> {\n if (this.#failure) throw this.#failure;\n await new Promise<void>((resolve, reject) => {\n const cleanup = (): void => {\n this.#stream.off('drain', onDrain);\n this.#stream.off('error', onError);\n this.#stream.off('close', onClose);\n };\n const onDrain = (): void => {\n cleanup();\n resolve();\n };\n const onError = (error: NodeJS.ErrnoException): void => {\n cleanup();\n // A pipe closing while we wait for drain is the same benign hang-up as one\n // closing during a write, and has to be handled here too: this listener is\n // registered for the duration of the wait and sees the error first.\n if (error.code === 'EPIPE') {\n this.#hungUp = true;\n resolve();\n return;\n }\n reject(error);\n };\n const onClose = (): void => {\n cleanup();\n reject(this.#failure ?? new Error('The output stream closed before the data was written.'));\n };\n this.#stream.once('drain', onDrain);\n this.#stream.once('error', onError);\n this.#stream.once('close', onClose);\n });\n }\n\n /** Flush anything left and close the stream. */\n async end(): Promise<void> {\n if (this.#ended) return;\n this.#ended = true;\n await this.flush();\n /*\n The reader is gone, so there is nothing to close and possibly nothing left to close it\n on. 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package/dist/format/list.js.map
CHANGED
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@@ -1 +1 @@
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1
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{"version":3,"file":"list.js","sourceRoot":"","sources":["../../src/format/list.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAEH,kEAAkE;AAClE,MAAM,aAAa,GAAG,CAAC,CAAC;AAExB;;;;;;;;GAQG;AACH,MAAM,UAAU,MAAM,CAAC,KAAwB,EAAE,KAAK,GAAG,aAAa;IACpE,IAAI,KAAK,CAAC,MAAM,IAAI,KAAK;QAAE,OAAO,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IACnD,MAAM,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IAC/C,OAAO,GAAG,KAAK,QAAQ,KAAK,CAAC,MAAM,GAAG,KAAK,OAAO,CAAC;AACrD,CAAC","sourcesContent":["/**\n * Rendering a set of things inside a sentence, without letting the file decide how long\n * the sentence gets.\n *\n * Several messages enumerate something the recording controls: its sampling rates, its\n * channel positions. On an ordinary file that is a handful of items and listing them all is\n * exactly right — the rates are what `--channels` has to choose between, so naming them is\n * the whole use of the message. On a file with two hundred channels the same code produced a\n * single 1,600-character line:\n *\n * warning: Channels use 200 different sampling rates (200 Hz, 199 Hz, 198 Hz, ... 1 Hz).\n *\n * which wraps across a whole terminal and buries the sentence that mattered. Nothing was\n * wrong with the conversion; the message was simply unreadable at a size the header is free\n * to ask for.\n */\n\n/** How many items a message shows before summarising the rest. */\nconst DEFAULT_LIMIT = 8;\n\n/**\n * Join items for a sentence, keeping at most `limit` of them.\n *\n * Beyond the limit the remainder is counted rather than named. The count is the honest part:\n * it says the list was cut without pretending the tail does not exist.\n *\n * listed(['1 Hz', '2 Hz']) -> '1 Hz, 2 Hz'\n * listed(rates200) -> '200 Hz, 199 Hz, ... 193 Hz and 192 more'\n */\nexport function listed(items: readonly string[], limit = DEFAULT_LIMIT): string {\n if (items.length <= limit) return items.join(', ');\n const shown = items.slice(0, limit).join(', ');\n return `${shown} and ${items.length - limit} more`;\n}\n"]}
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@@ -1 +1 @@
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Two things keep it cheap:\n *\n * - Every sample in a channel comes from a bounded set of integers (digitalMin to\n * digitalMax, typically 4096 distinct values for a 12-bit ADC). The formatted\n * text for a digital code never changes, so it is computed once and reused.\n * - The cache fills lazily. Real recordings visit only a fraction of the range,\n * and a channel with an implausibly wide range falls back to direct formatting\n * rather than reserving memory it will never use.\n */\n\nimport type { EdfSignal } from '../edf/header.js';\nimport { makeScaler } from '../edf/scale.js';\n\n/** Widest digital range worth caching: 16 bits of pointers is 512 KB per channel. */\nconst MAX_CACHED_SPAN = 1 << 16;\n\n/**\n * Format with a fixed number of decimals, normalising negative zero.\n *\n * Without this, a sample that scales to a very small negative value prints as\n * \"-0.000\", which looks like a distinct measurement but is not.\n */\nexport function fixed(value: number, decimals: number): string {\n // An undefined value becomes an empty cell rather than the text \"NaN\" or \"Infinity\".\n // A channel whose header leaves the digital-to-physical mapping undefined scales to\n // NaN, and an empty field is the CSV convention for \"no value here\" — the same one\n // annotations.csv uses for an absent duration. Readers parse it back as NaN / NA\n // rather than as a measurement.\n if (!Number.isFinite(value)) return '';\n\n // toFixed switches to exponent notation at 1e21, which would put \"1e+21\" in a column\n // whose every other cell is plain fixed-decimal — and a reader parsing the column as\n // decimal text has no reason to expect it. Reachable because EDF's 8-character physical\n // range fields accept exponent form, so a header may legitimately say \"1e30\".\n //\n // Above 2^53 a double carries no fractional part anyway, so the integer expansion is\n // exact rather than an approximation of one.\n if (Math.abs(value) >= 1e21) {\n const whole = BigInt(Math.trunc(value)).toString();\n return decimals > 0 ? `${whole}.${'0'.repeat(decimals)}` : whole;\n }\n\n const text = value.toFixed(decimals);\n if (text.charCodeAt(0) !== 45 /* - */) return text;\n // Cheap check for \"-0\", \"-0.0\", \"-0.000\"...\n for (let i = 1; i < text.length; i++) {\n const c = text.charCodeAt(i);\n if (c === 46 /* . */ || c === 48 /* 0 */) continue;\n return text;\n }\n return text.slice(1);\n}\n\n/** Maps a raw digital sample to its formatted physical value. */\nexport type SampleFormatter = (digital: number) => string;\n\nexport function makeSampleFormatter(signal: EdfSignal, decimals: number): SampleFormatter {\n const scale = makeScaler(signal);\n const low = Math.min(signal.digitalMin, signal.digitalMax);\n const high = Math.max(signal.digitalMin, signal.digitalMax);\n const span = high - low + 1;\n\n if (!Number.isFinite(span) || span <= 0 || span > MAX_CACHED_SPAN) {\n return (digital: number): string => fixed(scale(digital), decimals);\n }\n\n /*\n The cache covers the channel's declared digital range, not the whole int16 domain.\n\n Allocating 65536 slots regardless of span cost 512 KB of pointers per channel, which a\n dense montage cannot afford: a 400-channel recording needed over 200 MB of cache alone\n and died with a V8 out-of-memory fatal error before writing a row. Sizing to the\n declared span makes the ordinary 12-bit channel 32 KB instead — the same 400 channels\n now fit in about 13 MB.\n\n Samples outside the declared range still occur in non-conforming files. They simply\n miss the cache and are formatted directly, which produces identical text.\n */\n const cache = new Array<string | undefined>(span);\n return (digital: number): string => {\n const slot = digital - low;\n if (slot >= 0 && slot < span) {\n const hit = cache[slot];\n if (hit !== undefined) return hit;\n const text = fixed(scale(digital), decimals);\n cache[slot] = text;\n return text;\n }\n return fixed(scale(digital), decimals);\n };\n}\n\n/**\n * Decimals for the time column.\n *\n * The interval between samples is 1/rate, which has a terminating decimal expansion of d\n * places exactly when 10^d divides evenly by the rate. Writing that many places makes sample\n * times exact rather than rounded, so `time_s * rate` comes back as a whole number instead\n * of 8191.999999.\n *\n * The search used to stop at nine places, and the comment here claimed \"every rate in common\n * use clears this — 256 Hz needs 8 places, 512 Hz needs 9\". The next two powers of two do\n * not: 1/1024 needs ten places and 1/2048 needs eleven, and those are the rates a BioSemi\n * ActiveTwo records at by default. Both fell through to the rounding fallback, so the two\n * most common high-rate EEG recordings got exactly the behaviour this function exists to\n * avoid — 0.0009766 for an interval of 0.0009765625.\n *\n * A rate of 2^a * 5^b terminates in max(a, b) places, so fifteen covers every power of two up\n * to 32768 Hz, far past anything that records biosignals. Rates with a repeating expansion\n * (3 Hz, say) still fall back to enough places to keep consecutive samples distinct, and that\n * fallback keeps its own cap.\n *\n * Fifteen and not more, because the test below has to stay exact: 10^16 is past 2^53, where a\n * double can no longer hold every integer, and `Number.isInteger(10 ** 17 / 3)` is true — so a\n * larger bound reports a terminating expansion for rates that have none, and 3 Hz would ask\n * for seventeen decimals of a number that repeats forever.\n *\n * The fallback is bounded by the same fifteen. It used to stop at nine, which defeated the\n * one thing it exists to do: at 3e10 Hz — non-terminating, so no exact expansion to find —\n * the interval is 3.3e-11 and nine places rounded every sample in a record to the same\n * timestamp. A column that cannot tell two samples apart is not keeping them distinct, which\n * is what this branch is for.\n */\nconst MAX_TIME_DECIMALS = 15;\n\nexport function timeDecimals(samplingRate: number): number {\n if (!(samplingRate > 0) || !Number.isFinite(samplingRate)) return 3;\n for (let d = 0; d <= MAX_TIME_DECIMALS; d++) {\n if (Number.isInteger(10 ** d / samplingRate)) return Math.max(3, d);\n }\n return Math.min(MAX_TIME_DECIMALS, Math.max(3, Math.ceil(Math.log10(samplingRate)) + 3));\n}\n\n/** Human-readable byte size for warnings and summaries. */\nexport function formatBytes(bytes: number): string {\n const units = ['B', 'KB', 'MB', 'GB', 'TB'];\n let value = bytes;\n let unit = 0;\n while (value >= 1024 && unit < units.length - 1) {\n value /= 1024;\n unit++;\n }\n const rounded = value >= 100 || unit === 0 ? Math.round(value) : Number(value.toFixed(1));\n return `${rounded} ${units[unit]}`;\n}\n\n/** Human-readable duration: 1h 05m 12s. */\nexport function formatDuration(seconds: number): string {\n // A duration that is not a number cannot be broken into hours and minutes, and saying so\n // beats the alternative: the fallback below rendered these as \"NaNs\" and \"Infinitys\".\n if (!Number.isFinite(seconds)) return 'unknown';\n\n /*\n Past 2^53 the decomposition stops being arithmetic and starts being noise.\n\n `total - h * 3600 - m * 60` cannot be exact once `total` exceeds what a double can hold\n as a whole number, and the error lands in the seconds field, where it shows up as a\n value that cannot exist. A header declaring a record duration of 1e300 printed:\n\n Duration 8.333333333333333e+296h 48m -2880s\n\n Forty-eight minutes and minus forty-eight seconds, under an hours field in exponent\n notation. The seconds are the honest form for a figure this size — nobody reads\n 285 million years as hours — and the record count and duration are printed beside it\n anyway, so a corrupt header stays just as visible.\n */\n if (seconds < 0 || seconds >= Number.MAX_SAFE_INTEGER) return `${seconds}s`;\n\n // Round to the precision that will actually be printed BEFORE splitting into units.\n // Splitting first left the remainder to be rounded on its own, so 3599.9996 s decomposed\n // as 59 minutes and 59.9996 seconds and then printed as \"59m 60s\" — a duration that\n // cannot exist. Rounding first carries the extra second into the minute where it belongs.\n const total = Math.round(seconds * 1000) / 1000;\n const h = Math.floor(total / 3600);\n const m = Math.floor((total % 3600) / 60);\n const s = Math.round((total - h * 3600 - m * 60) * 1000) / 1000;\n const sText = Number.isInteger(s) ? String(s) : s.toFixed(3).replace(/\\.?0+$/u, '');\n if (h > 0) return `${h}h ${String(m).padStart(2, '0')}m ${sText}s`;\n if (m > 0) return `${m}m ${sText}s`;\n return `${sText}s`;\n}\n\n/** A record can declare a great many samples; two arrays this size is the cost of caching. */\nconst MAX_CACHED_OFFSETS = 1 << 20;\n\n/**\n * How many cached offsets a conversion has left to spend.\n *\n * The cap used to be per rate group, and a file may hold as many rate groups as it has\n * channels. Twelve channels at twelve rates just under the cap — a 25 MB file — took\n * 1.66 GB and 36 seconds, where a 92 MB file at one rate takes 283 MB and finishes in a\n * fraction of that; twenty-four of them never finished at all. A per-group limit is not a\n * limit, since nothing bounds the number of groups.\n *\n * One budget for the whole conversion makes the single-group case identical to what it was\n * and the many-group case bounded. Groups ask in order of rate, fastest first, so the cache\n * goes to the tables with the most rows to write and the ones that miss out are the ones\n * that would have gained least.\n */\nexport interface OffsetBudget {\n remaining: number;\n}\n\nexport function newOffsetBudget(): OffsetBudget {\n return { remaining: MAX_CACHED_OFFSETS };\n}\n\n/**\n * Formats the time column, reusing the part of it that repeats.\n *\n * Every value cell is already cached — a channel has at most `digitalMax - digitalMin + 1`\n * distinct readings, so the same handful of strings serve millions of rows. The time column\n * had no such luck: it rises monotonically, so no two rows share a string and `toFixed` ran\n * once per row. On a ten-million-row conversion that was a third of the total time, more\n * than reading the file and writing the CSV put together.\n *\n * What repeats is the offset within a record. Sample `s` sits at `s / rate` from the start of\n * whichever record holds it, and there are only `samplesPerRecord` such offsets in the whole\n * recording. Splitting each into whole seconds and printed fraction turns the per-row work\n * into one integer addition and a concatenation:\n *\n * record starting at 42s, sample 7 of a 100 Hz record\n * -> 42 + 0 whole seconds, fraction \".070\" -> \"42.070\"\n *\n * The decomposition is only valid when the record starts on a whole, non-negative second,\n * which is what lets the fraction come entirely from the offset. A record starting at 0.5 s would mix the\n * two, so those fall back to formatting the sum directly. Continuous recordings start every\n * record at `index * recordDuration`, so this holds for all of them whose record duration is\n * a whole number of seconds, and for discontinuous files it holds per record depending on\n * where that record actually starts.\n */\nexport function makeTimeFormatter(\n samplesPerRecord: number,\n rate: number,\n decimals: number,\n budget: OffsetBudget = newOffsetBudget(),\n): (recordStart: number, sample: number) => string {\n const direct = (recordStart: number, sample: number): string =>\n fixed(recordStart + sample / rate, decimals);\n\n if (\n !(rate > 0) ||\n !Number.isFinite(rate) ||\n samplesPerRecord <= 0 ||\n samplesPerRecord > budget.remaining\n ) {\n return direct;\n }\n budget.remaining -= samplesPerRecord;\n\n // Whole seconds and printed fraction of each offset, taken from the formatted offset\n // itself so that an offset which rounds up to the next second (0.9996 at three places)\n // carries that second rather than losing it.\n const wholeOffset = new Float64Array(samplesPerRecord);\n const fractionText: string[] = new Array<string>(samplesPerRecord);\n for (let sample = 0; sample < samplesPerRecord; sample++) {\n const text = fixed(sample / rate, decimals);\n const dot = text.indexOf('.');\n wholeOffset[sample] = dot === -1 ? Number(text) : Number(text.slice(0, dot));\n fractionText[sample] = dot === -1 ? '' : text.slice(dot);\n }\n\n return (recordStart: number, sample: number): string => {\n /*\n Non-negative only. Appending a fraction to a negative whole part moves the time the\n wrong way: a record at -5 s and an offset of half a second is -4.5, but \"-5\" and\n \".500\" concatenate to -5.500. Recording times start at zero, so this is unreachable\n from a well-formed file — an EDF+ timekeeping TAL is free to carry a negative onset\n though, and that is enough reason for the fast path to decline it.\n */\n if (\n sample < 0 ||\n sample >= samplesPerRecord ||\n !Number.isInteger(recordStart) ||\n recordStart < 0\n ) {\n return direct(recordStart, sample);\n }\n const whole = recordStart + (wholeOffset[sample] as number);\n /*\n The same 1e21 cliff `fixed` guards against, arriving through the back door.\n\n `${whole}` is the implicit Number-to-String conversion, which switches to exponent\n notation at 1e21 exactly as `toFixed` does — and then the cached fraction is glued onto\n the end of it, so the cell reads \"1e+21.000\". That is not a number in any notation:\n pandas and R both parse it as NaN, and a column of ordinary decimals ends in a run of\n them. A header may legitimately say `1e21` in its 8-character record-duration field, so\n three records are enough to reach it.\n\n The slow path already expands these with BigInt. One comparison per row keeps that\n correct without giving up the cache for the other twenty million.\n */\n if (whole >= 1e21) return direct(recordStart, sample);\n return `${whole}${fractionText[sample] as string}`;\n };\n}\n"]}
|
package/dist/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,OAAO,EAAE,mBAAmB,EAAE,MAAM,iBAAiB,CAAC;AAG/D,OAAO,EAAE,WAAW,EAAE,UAAU,EAAE,WAAW,EAAE,cAAc,EAAE,eAAe,EAAE,iBAAiB,EAAE,qBAAqB,EAAE,MAAM,iBAAiB,CAAC;AAGlJ,OAAO,EAAE,uBAAuB,EAAE,MAAM,sBAAsB,CAAC;AAG/D,OAAO,EAAE,UAAU,EAAE,gBAAgB,EAAE,iBAAiB,EAAE,MAAM,gBAAgB,CAAC;AAGjF,OAAO,EAAE,QAAQ,EAAE,MAAM,iBAAiB,CAAC;AAG3C,OAAO,EAAE,OAAO,EAAE,gBAAgB,EAAE,eAAe,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAC;AAG5F,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,qBAAqB,EAAE,MAAM,mBAAmB,CAAC;AAG/E,OAAO,EAAE,cAAc,EAAE,gBAAgB,EAAE,qBAAqB,EAAE,MAAM,uBAAuB,CAAC;AAChG,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAC;AACnD,OAAO,EAAE,aAAa,EAAE,YAAY,EAAE,cAAc,EAAE,MAAM,yBAAyB,CAAC"}
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,OAAO,EAAE,mBAAmB,EAAE,MAAM,iBAAiB,CAAC;AAG/D,OAAO,EAAE,WAAW,EAAE,UAAU,EAAE,WAAW,EAAE,cAAc,EAAE,eAAe,EAAE,iBAAiB,EAAE,qBAAqB,EAAE,MAAM,iBAAiB,CAAC;AAGlJ,OAAO,EAAE,uBAAuB,EAAE,MAAM,sBAAsB,CAAC;AAG/D,OAAO,EAAE,UAAU,EAAE,gBAAgB,EAAE,iBAAiB,EAAE,MAAM,gBAAgB,CAAC;AAGjF,OAAO,EAAE,QAAQ,EAAE,MAAM,iBAAiB,CAAC;AAG3C,OAAO,EAAE,OAAO,EAAE,gBAAgB,EAAE,eAAe,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAC;AAG5F,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,qBAAqB,EAAE,MAAM,mBAAmB,CAAC;AAG/E,OAAO,EAAE,cAAc,EAAE,gBAAgB,EAAE,qBAAqB,EAAE,MAAM,uBAAuB,CAAC;AAChG,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAC;AACnD,OAAO,EAAE,aAAa,EAAE,YAAY,EAAE,cAAc,EAAE,MAAM,yBAAyB,CAAC","sourcesContent":["/**\n * Programmatic API.\n *\n * edf2csv is primarily a command-line tool, but the parser underneath is useful on\n * its own — reading an EDF header, listing channels, or streaming raw samples\n * without going through CSV at all.\n */\n\nexport { EdfFile, DEFAULT_CHUNK_BYTES } from './edf/reader.js';\nexport type { RecordBatch, ReadRecordsOptions } from './edf/reader.js';\n\nexport { parseHeader, formatRate, formatRates, describeFormat, formatWallClock, ANNOTATIONS_LABEL, BDF_ANNOTATIONS_LABEL } from './edf/header.js';\nexport type { EdfHeader, EdfHeaderInfo, EdfSignal } from './edf/header.js';\n\nexport { decodeRecordAnnotations } from './edf/annotations.js';\nexport type { Annotation, DecodedRecordAnnotations } from './edf/annotations.js';\n\nexport { makeScaler, quantizationStep, decimalsForSignal } from './edf/scale.js';\nexport type { Scaler } from './edf/scale.js';\n\nexport { EdfError } from './edf/errors.js';\nexport type { Diagnostic, DiagnosticCode, EdfErrorCode } from './edf/errors.js';\n\nexport { convert, defaultOutputDir, ConversionError, TOOL_VERSION } from './convert/run.js';\nexport type { ConvertOptions, ConvertResult, ConversionProgress, WrittenFile } from './convert/run.js';\n\nexport { buildPlan, rateSlug, SPREADSHEET_ROW_LIMIT } from './convert/plan.js';\nexport type { ConversionPlan, PlanOptions, PlanInput, RateGroup, PlannedChannel } from './convert/plan.js';\n\nexport { selectChannels, buildColumnNames, ChannelSelectionError } from './convert/channels.js';\nexport { OptionError } from './convert/options.js';\nexport { parseTimeSpec, resolveRange, TimeRangeError } from './convert/time-range.js';\nexport type { ResolvedRange } from './convert/time-range.js';\n"]}
|
package/dist/version.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"version.js","sourceRoot":"","sources":["../src/version.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,SAAS,CAAC;AAMvC,MAAM,QAAQ,GAAG,IAAI,CAAC,KAAK,CACzB,YAAY,CAAC,IAAI,GAAG,CAAC,iBAAiB,EAAE,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,MAAM,CAAC,CAC/C,CAAC;AAErB,IAAI,OAAO,QAAQ,CAAC,OAAO,KAAK,QAAQ,IAAI,QAAQ,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;IAC1E,MAAM,IAAI,KAAK,CAAC,gDAAgD,CAAC,CAAC;AACpE,CAAC;AAED,oFAAoF;AACpF,MAAM,CAAC,MAAM,OAAO,GAAG,QAAQ,CAAC,OAAO,CAAC"}
|
|
1
|
+
{"version":3,"file":"version.js","sourceRoot":"","sources":["../src/version.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,SAAS,CAAC;AAMvC,MAAM,QAAQ,GAAG,IAAI,CAAC,KAAK,CACzB,YAAY,CAAC,IAAI,GAAG,CAAC,iBAAiB,EAAE,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,MAAM,CAAC,CAC/C,CAAC;AAErB,IAAI,OAAO,QAAQ,CAAC,OAAO,KAAK,QAAQ,IAAI,QAAQ,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;IAC1E,MAAM,IAAI,KAAK,CAAC,gDAAgD,CAAC,CAAC;AACpE,CAAC;AAED,oFAAoF;AACpF,MAAM,CAAC,MAAM,OAAO,GAAG,QAAQ,CAAC,OAAO,CAAC","sourcesContent":["import { readFileSync } from 'node:fs';\n\ninterface PackageMetadata {\n version?: unknown;\n}\n\nconst metadata = JSON.parse(\n readFileSync(new URL('../package.json', import.meta.url), 'utf8'),\n) as PackageMetadata;\n\nif (typeof metadata.version !== 'string' || metadata.version.length === 0) {\n throw new Error('package.json does not contain a valid version.');\n}\n\n/** The package version reported by the CLI and written into conversion metadata. */\nexport const VERSION = metadata.version;\n"]}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "edf2csv",
|
|
3
|
-
"version": "0.4.
|
|
3
|
+
"version": "0.4.67",
|
|
4
4
|
"description": "Convert EDF, EDF+ and BDF biosignal recordings (European Data Format) to CSV from the command line. Local, streaming, and never resamples or alters units.",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"edf",
|