edf2csv 0.4.78 → 0.5.0
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 +48 -0
- package/README.md +3 -0
- package/dist/cli/report.d.ts.map +1 -1
- package/dist/cli/report.js +5 -2
- package/dist/cli/report.js.map +1 -1
- package/dist/cli.d.ts.map +1 -1
- package/dist/cli.js +17 -1
- package/dist/cli.js.map +1 -1
- package/dist/convert/plan.d.ts +20 -0
- package/dist/convert/plan.d.ts.map +1 -1
- package/dist/convert/plan.js +47 -9
- package/dist/convert/plan.js.map +1 -1
- package/dist/convert/run.d.ts.map +1 -1
- package/dist/convert/run.js +109 -10
- package/dist/convert/run.js.map +1 -1
- package/package.json +1 -1
package/CHANGELOG.md
CHANGED
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@@ -3,6 +3,54 @@
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3
3
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Notable changes to edf2csv. Versions follow [semantic versioning](https://semver.org); while the
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major version is 0, a minor bump may contain breaking changes.
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## 0.5.0
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7
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+
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8
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### Added: `--layout long`, so a mixed-rate recording can be one table
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+
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Until now a recording whose channels run at different rates came out as several files, one
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per rate, and that was the honest answer to a real problem: a 100 Hz channel and a 1 Hz
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channel share no rows, so a single wide table holding both means either ninety-nine empty
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cells in every hundred or inventing the samples to fill them. This tool exists not to invent
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them.
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+
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The long layout is the other honest answer. One file, three columns — `time_s`, `channel`,
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`value` — and one row per sample. Each sample carries its own time, so nothing has to line
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up, every rate goes in one table, and not a value is invented:
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```
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time_s,channel,value
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0.000,EEG Fpz-Cz,0.061
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0.000,EEG Pz-Oz,0.061
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0.000,Resp oro-nasal,0.000244
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0.000,Temp rectal,37.00073
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0.010,EEG Fpz-Cz,1.648
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```
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+
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Rows come out sorted by `time_s`. That is not free — the groups are merged rather than
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written one after another, since every sample of a record falls inside that record's span,
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so taking the earliest next sample across the groups leaves the whole file in order. Sorting
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three million rows afterwards would be the reader's problem, and a large one.
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It is also the one layout `--stdout` can stream for a mixed-rate recording, because there is
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only ever one table. `--stdout` on such a file used to have nothing to offer but
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`--channels`; its error now says so.
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Some details that follow from one table:
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- `time_s` shares a precision across rates — the finest any of them needs — because one
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column cannot mean three things. A file mixing 256 Hz and 1 Hz writes both at eight places.
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- One writer, not one per rate group. Separate buffers over one stream would reach the file
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in whatever order they happened to fill, which is not the order the rows were produced in.
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- `--info` reports the long figures when `--layout long` is given, so the estimate always
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describes the command you typed. The estimate sweep now crosses every fixture with the
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long layout too: 308 predictions, rows exact and bytes never under.
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- The cost is size. A long row repeats the time and the channel name on every sample, so the
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same recording runs two to three times larger. `--gzip` recovers most of it, since a
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repeated channel name is what compression is best at. An eight-hour recording converts
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under a 64 MB heap cap either way.
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+
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`--layout wide` is the default and unchanged.
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+
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## 0.4.78
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### Fixed: `sleep-study.edf` was four different recordings across the site
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package/README.md
CHANGED
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@@ -59,6 +59,9 @@ npx edf2csv recording.edf --start 30m --duration 5m
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--annotations-only Just the EDF+ events
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--decimals <n> Force a number of decimal places
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--checksum Put a SHA-256 of the input in metadata.json
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--layout <kind> wide (default): one column per channel, one file per
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sampling rate. long: one file of time_s,channel,value,
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every rate together, one row per sample
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--gzip Compress every CSV, writing .csv.gz files
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--bom Start each CSV with a UTF-8 byte order mark, so Excel
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reads accented text and units like µV correctly
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package/dist/cli/report.d.ts.map
CHANGED
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@@ -1 +1 @@
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1
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{"version":3,"file":"report.d.ts","sourceRoot":"","sources":["../../src/cli/report.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,kBAAkB,CAAC;AACnD,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,kBAAkB,CAAC;AAGhD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,oBAAoB,CAAC;AAEzD,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,mBAAmB,CAAC;AAuBvD;;;;;;;;;;;;;GAaG;AACH,wBAAgB,SAAS,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAK9C;AAED;;;;;;;;;;;;;GAaG;AACH,wBAAgB,cAAc,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,SAAK,GAAG,MAAM,CAKhE;AAED,0FAA0F;AAC1F,wBAAgB,UAAU,CAAC,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,cAAc,GAAG,MAAM,CAgHtE;AAED;;;;;;;;;;;;;;;;;;GAkBG;AACH,wBAAgB,QAAQ,CAAC,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,cAAc,EAAE,MAAM,GAAE,MAAM,GAAG,IAAQ,GAAG,MAAM,CAwD/F;AAED,mEAAmE;AACnE,wBAAgB,iBAAiB,CAAC,WAAW,EAAE,SAAS,UAAU,EAAE,GAAG,MAAM,CAS5E;AAED,wBAAgB,aAAa,CAAC,MAAM,EAAE,aAAa,GAAG,MAAM,CAU3D;AAED,wBAAgB,WAAW,CAAC,MAAM,EAAE,aAAa,EAAE,MAAM,GAAE,MAAM,GAAG,IAAQ,GAAG,MAAM,CAcpF"}
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package/dist/cli/report.js
CHANGED
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@@ -123,8 +123,11 @@ export function formatInfo(file, plan) {
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lines.push(table(rows, new Set([0])));
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lines.push('');
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if (plan.groups.length > 1) {
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-
lines.push(
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`
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lines.push(plan.layout === 'long'
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? `Sampling rates differ, and the long layout puts them in one table anyway: each row ` +
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`carries its own time, so nothing has to line up. No channel is resampled.`
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: `Sampling rates differ, so channels are written to ${plan.groups.length} files, one per rate. ` +
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`No channel is resampled.`);
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}
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/*
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The estimate describes the signal tables, and says so when that is not what will be
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package/dist/cli/report.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
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* Human-readable output for the terminal.\n *\n * Everything here is plain text with no colour codes, so piping to a file or a log\n * produces exactly what appeared on screen.\n */\n\nimport type { Diagnostic } from '../edf/errors.js';\nimport type { EdfFile } from '../edf/reader.js';\nimport { describeFormat, formatRates, formatWallClock } from '../edf/header.js';\nimport { formatBytes, formatDuration } from '../format/number.js';\nimport type { ConversionPlan } from '../convert/plan.js';\nimport { withoutFileRateWarning } from '../convert/plan.js';\nimport type { ConvertResult } from '../convert/run.js';\n\nfunction table(rows: readonly (readonly string[])[], alignRight: ReadonlySet<number>): string {\n if (rows.length === 0) return '';\n const width: number[] = [];\n for (const row of rows) {\n row.forEach((cell, i) => {\n width[i] = Math.max(width[i] ?? 0, cell.length);\n });\n }\n return rows\n .map((row) =>\n row\n .map((cell, i) => {\n const w = width[i] ?? 0;\n return alignRight.has(i) ? cell.padStart(w) : cell.padEnd(w);\n })\n .join(' ')\n .trimEnd(),\n )\n .join('\\n');\n}\n\n/**\n * Make header text safe to print to a terminal.\n *\n * EDF identification fields and channel labels are free text copied verbatim out of the\n * file, and `--info` puts them straight on stdout. A header carrying ANSI escapes could\n * therefore drive the reader's terminal — `\\x1b[2J\\x1b[H` clears the screen and homes the\n * cursor, which is enough to hide the rest of the output or repaint it as something else.\n * Nobody writes an EDF header that way on purpose, which is exactly why a file that does\n * should not be trusted with the terminal.\n *\n * Control bytes are shown as their escape instead, so a corrupt field stays diagnosable\n * rather than being silently swallowed. This affects display only: `channels.csv` and\n * `metadata.json` still copy the field verbatim, and CSV quoting already makes that safe.\n */\nexport function printable(text: string): string {\n // eslint-disable-next-line no-control-regex\n return text.replace(/[\\u0000-\\u001f\\u007f-\\u009f]/gu, (c) =>\n `\\\\x${c.codePointAt(0)!.toString(16).padStart(2, '0')}`,\n );\n}\n\n/**\n * The same protection for text that is meant to span lines.\n *\n * `printable` escapes newlines along with everything else, which is right for a channel\n * label — one has no business containing a line break, and it would break the `--info`\n * table's alignment. It is wrong for a whole message: several are written on two lines,\n * and Node's own option errors run to three. Escaping those turned the break into text:\n *\n * error: No channel named \"ECQ\". Did you mean \"ECG\"?\\x0aRun with --info to list ...\n *\n * Each line is escaped on its own, so nothing here gains the ability to drive a terminal.\n * A carriage return is still escaped, so no line can be repainted after it is printed —\n * which is the property that mattered. A newline can only add a line, never overwrite one.\n */\nexport function printableLines(text: string, indent = ''): string {\n return text\n .split('\\n')\n .map((line, index) => (index === 0 ? '' : indent) + printable(line))\n .join('\\n');\n}\n\n/** The `--info` view: what is in this recording, and what would converting it produce. */\nexport function formatInfo(file: EdfFile, plan: ConversionPlan): string {\n const { header } = file;\n const lines: string[] = [];\n\n lines.push(`File ${file.path}`);\n lines.push(`Format ${describeFormat(header)}`);\n lines.push(\n `Recorded ${\n formatWallClock(header.startDateTime)?.replace('T', ' ') ??\n `${printable(header.startDateRaw)} ${printable(header.startTimeRaw)} (unparseable)`\n }`,\n );\n lines.push(\n `Duration ${formatDuration(file.durationSeconds)} (${file.recordCount} records of ${header.recordDuration}s)`,\n );\n const elapsedSpan = plan.range.recordingEndSeconds - plan.range.recordingStartSeconds;\n if (Math.abs(elapsedSpan - file.durationSeconds) > 1e-9) {\n lines.push(`Time span ${formatDuration(elapsedSpan)} (includes discontinuities)`);\n }\n lines.push(`Size ${formatBytes(file.fileSize)}`);\n if (header.patientId) lines.push(`Patient ${printable(header.patientId)}`);\n if (header.recordingId) lines.push(`Recording ${printable(header.recordingId)}`);\n\n const signals = file.dataSignals;\n lines.push('');\n // The signal count was pluralised but the annotation-channel count was not, so a file\n // carrying two of them read \"2 annotation channel\". EDF+ permits more than one.\n const annotationCount = file.annotationSignals.length;\n const annotationPart =\n annotationCount > 0\n ? ` + ${annotationCount} annotation channel${annotationCount === 1 ? '' : 's'}`\n : '';\n lines.push(\n `Channels ${signals.length} signal${signals.length === 1 ? '' : 's'}${annotationPart}`,\n );\n lines.push('');\n\n const rows: string[][] = [['#', 'COLUMN', 'LABEL', 'UNIT', 'RATE', 'RANGE', 'OUTPUT']];\n const fileFor = new Map<number, string>();\n for (const group of plan.groups) {\n for (const channel of group.channels) fileFor.set(channel.signal.index, group.fileName);\n }\n // Rendered as a group so that two channels recorded at different rates never show the\n // same figure in the RATE column, which is the one thing this table is asked to settle.\n const rateText = formatRates(signals.map((signal) => signal.samplingRate));\n for (const [row, signal] of signals.entries()) {\n rows.push([\n String(signal.index),\n printable(plan.columnNames.get(signal.index) ?? ''),\n printable(signal.label),\n printable(signal.physicalDimension),\n `${rateText[row]} Hz`,\n `${signal.physicalMin} to ${signal.physicalMax}`,\n /*\n A channel with no samples was reported as \"(not selected)\", which is a different\n thing and not true when it was named on --channels. `edf2csv rec.edf --info\n --channels unused` said the channel the command asked for had not been chosen, when\n what is actually the case is that the file gives it nothing to convert. The\n NO_SAMPLES warning below the table says so; the table contradicted it.\n */\n fileFor.get(signal.index) ??\n (signal.samplesPerRecord === 0 ? '(no samples)' : '(not selected)'),\n ]);\n }\n lines.push(table(rows, new Set([0])));\n\n lines.push('');\n if (plan.groups.length > 1) {\n lines.push(\n `Sampling rates differ, so channels are written to ${plan.groups.length} files, one per rate. ` +\n `No channel is resampled.`,\n );\n }\n /*\n The estimate describes the signal tables, and says so when that is not what will be\n written.\n\n Under --annotations-only there are no signal tables, and the line read \"Would write 0\n rows, roughly 0 B.\" for a conversion that goes on to write annotations.csv with three\n events in it. --info exists to say what a conversion will do; asserting it will write\n nothing, when it will write a file, is the one thing it must not do.\n\n How many events there are cannot be answered from the header — the annotation channel has\n to be read record by record, which is the scan --info is for avoiding. So it says which\n file, and that the count is not knowable this cheaply, rather than inventing a zero.\n */\n if (!plan.writeSignals) {\n // Named as they will be written. --info is read to find out what a run leaves behind,\n // and a script that opens the name it was given must find a file there.\n const suffix = plan.gzip ? '.csv.gz' : '.csv';\n lines.push(\n file.annotationSignals.length > 0\n ? `Would write annotations${suffix} and channels${suffix}, and no signal data. How ` +\n 'many events there are cannot be told from the header.'\n : `Would write channels${suffix} and no signal data — and no annotations${suffix} ` +\n 'either, since this recording has no annotation channel.',\n );\n return lines.join('\\n');\n }\n\n // The estimate counts the characters of the CSV, which is what --gzip then compresses.\n // Reporting it as the size on disk would overstate a compressed conversion several-fold.\n const compressing = plan.gzip;\n lines.push(\n `Would write ${plan.estimate.rows.toLocaleString('en-US')} rows, roughly ` +\n `${formatBytes(plan.estimate.bytes)}${compressing ? ' before compression' : ''}.`,\n );\n\n return lines.join('\\n');\n}\n\n/**\n * The `--info` view as JSON, for surveying files from a script.\n *\n * `indent` is 2 for a single recording, matching what this has always printed, and null for\n * a batch — several pretty-printed documents run together are readable by a streaming parser\n * but not by anything that expects one record per line, and a batch is exactly where\n * line-oriented reading is wanted. null rather than undefined because a default parameter\n * takes effect when undefined is passed, which quietly restored the indentation this was\n * meant to drop; JSON.stringify itself wants undefined, so it is translated at the call.\n *\n * `--info` answers \"what is in this recording and what would converting it cost\", which\n * is exactly the question you want to ask across a directory of hundreds of recordings —\n * and the text table is the wrong shape for that. `--json` previously applied only to\n * conversions, so scripts had to parse the aligned columns or convert files just to learn\n * what was in them.\n *\n * Field names match `metadata.json` where the two describe the same thing, so a survey and\n * a conversion can be read by the same code.\n */\nexport function infoJson(file: EdfFile, plan: ConversionPlan, indent: number | null = 2): string {\n const { header } = file;\n const fileFor = new Map<number, string>();\n for (const group of plan.groups) {\n for (const channel of group.channels) fileFor.set(channel.signal.index, group.fileName);\n }\n\n return JSON.stringify(\n {\n path: file.path,\n bytes: file.fileSize,\n format: describeFormat(header),\n start_datetime_local: formatWallClock(header.startDateTime),\n start_date_raw: header.startDateRaw,\n start_time_raw: header.startTimeRaw,\n patient_id: header.patientId,\n recording_id: header.recordingId,\n data_records: file.recordCount,\n data_records_declared: header.declaredRecordCount,\n record_duration_seconds: header.recordDuration,\n duration_seconds: file.durationSeconds,\n // For a discontinuous file this exceeds duration_seconds by the length of the gaps.\n time_span_seconds: plan.range.recordingEndSeconds - plan.range.recordingStartSeconds,\n annotation_channels: file.annotationSignals.length,\n channels: file.dataSignals.map((signal) => ({\n signal_index: signal.index,\n column: plan.columnNames.get(signal.index) ?? '',\n label: signal.label,\n unit: signal.physicalDimension,\n sampling_rate_hz: signal.samplingRate,\n samples_per_record: signal.samplesPerRecord,\n physical_min: signal.physicalMin,\n physical_max: signal.physicalMax,\n digital_min: signal.digitalMin,\n digital_max: signal.digitalMax,\n transducer: signal.transducer,\n prefiltering: signal.prefiltering,\n output_file: fileFor.get(signal.index) ?? null,\n })),\n estimate: {\n rows: plan.estimate.rows,\n // Character count of the CSV. With --gzip the file on disk is smaller than this.\n bytes: plan.estimate.bytes,\n exceeds_spreadsheet_limit: plan.estimate.exceedsSpreadsheetLimit,\n },\n // The plan's mixed-rate warning replaces the header parser's, as it does everywhere\n // else. This was the one consumer left out of that when 0.3.2 made the warning follow\n // --channels, so `--info --json` carried it twice: once counting the rates being\n // converted and once counting every rate in the file, with the same code and severity.\n warnings: plan.diagnostics\n .concat(withoutFileRateWarning(file.diagnostics))\n .map((d) => ({ code: d.code, severity: d.severity, message: d.message })),\n },\n null,\n indent ?? undefined,\n );\n}\n\n/** One line per diagnostic, prefixed so warnings are greppable. */\nexport function formatDiagnostics(diagnostics: readonly Diagnostic[]): string {\n return diagnostics\n .map((d) => {\n // Diagnostics quote channel labels, which come from the file, so they need the\n // same treatment as the --info table.\n const head = `${d.severity === 'warning' ? 'warning' : 'note'}: ${printable(d.message)}`;\n return d.hint ? `${head}\\n ${printable(d.hint)}` : head;\n })\n .join('\\n');\n}\n\nexport function formatSummary(result: ConvertResult): string {\n const lines: string[] = [];\n const rows: string[][] = [];\n for (const file of result.files) {\n rows.push([` ${file.name}`, file.rows.toLocaleString('en-US'), file.name.endsWith('.csv') ? 'rows' : '']);\n }\n lines.push(`Wrote ${result.outputDir}`);\n lines.push(table(rows, new Set([1])));\n lines.push(`Done in ${(result.elapsedMs / 1000).toFixed(1)}s.`);\n return lines.join('\\n');\n}\n\nexport function summaryJson(result: ConvertResult, indent: number | null = 2): string {\n return JSON.stringify(\n {\n output_dir: result.outputDir,\n files: result.files,\n annotations: result.annotationCount,\n duration_seconds: result.file.durationSeconds,\n records: result.file.recordCount,\n elapsed_ms: result.elapsedMs,\n warnings: result.diagnostics.map((d) => ({ code: d.code, severity: d.severity, message: d.message })),\n },\n null,\n indent ?? undefined,\n );\n}\n"]}
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+
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* Human-readable output for the terminal.\n *\n * Everything here is plain text with no colour codes, so piping to a file or a log\n * produces exactly what appeared on screen.\n */\n\nimport type { Diagnostic } from '../edf/errors.js';\nimport type { EdfFile } from '../edf/reader.js';\nimport { describeFormat, formatRates, formatWallClock } from '../edf/header.js';\nimport { formatBytes, formatDuration } from '../format/number.js';\nimport type { ConversionPlan } from '../convert/plan.js';\nimport { withoutFileRateWarning } from '../convert/plan.js';\nimport type { ConvertResult } from '../convert/run.js';\n\nfunction table(rows: readonly (readonly string[])[], alignRight: ReadonlySet<number>): string {\n if (rows.length === 0) return '';\n const width: number[] = [];\n for (const row of rows) {\n row.forEach((cell, i) => {\n width[i] = Math.max(width[i] ?? 0, cell.length);\n });\n }\n return rows\n .map((row) =>\n row\n .map((cell, i) => {\n const w = width[i] ?? 0;\n return alignRight.has(i) ? cell.padStart(w) : cell.padEnd(w);\n })\n .join(' ')\n .trimEnd(),\n )\n .join('\\n');\n}\n\n/**\n * Make header text safe to print to a terminal.\n *\n * EDF identification fields and channel labels are free text copied verbatim out of the\n * file, and `--info` puts them straight on stdout. A header carrying ANSI escapes could\n * therefore drive the reader's terminal — `\\x1b[2J\\x1b[H` clears the screen and homes the\n * cursor, which is enough to hide the rest of the output or repaint it as something else.\n * Nobody writes an EDF header that way on purpose, which is exactly why a file that does\n * should not be trusted with the terminal.\n *\n * Control bytes are shown as their escape instead, so a corrupt field stays diagnosable\n * rather than being silently swallowed. This affects display only: `channels.csv` and\n * `metadata.json` still copy the field verbatim, and CSV quoting already makes that safe.\n */\nexport function printable(text: string): string {\n // eslint-disable-next-line no-control-regex\n return text.replace(/[\\u0000-\\u001f\\u007f-\\u009f]/gu, (c) =>\n `\\\\x${c.codePointAt(0)!.toString(16).padStart(2, '0')}`,\n );\n}\n\n/**\n * The same protection for text that is meant to span lines.\n *\n * `printable` escapes newlines along with everything else, which is right for a channel\n * label — one has no business containing a line break, and it would break the `--info`\n * table's alignment. It is wrong for a whole message: several are written on two lines,\n * and Node's own option errors run to three. Escaping those turned the break into text:\n *\n * error: No channel named \"ECQ\". Did you mean \"ECG\"?\\x0aRun with --info to list ...\n *\n * Each line is escaped on its own, so nothing here gains the ability to drive a terminal.\n * A carriage return is still escaped, so no line can be repainted after it is printed —\n * which is the property that mattered. A newline can only add a line, never overwrite one.\n */\nexport function printableLines(text: string, indent = ''): string {\n return text\n .split('\\n')\n .map((line, index) => (index === 0 ? '' : indent) + printable(line))\n .join('\\n');\n}\n\n/** The `--info` view: what is in this recording, and what would converting it produce. */\nexport function formatInfo(file: EdfFile, plan: ConversionPlan): string {\n const { header } = file;\n const lines: string[] = [];\n\n lines.push(`File ${file.path}`);\n lines.push(`Format ${describeFormat(header)}`);\n lines.push(\n `Recorded ${\n formatWallClock(header.startDateTime)?.replace('T', ' ') ??\n `${printable(header.startDateRaw)} ${printable(header.startTimeRaw)} (unparseable)`\n }`,\n );\n lines.push(\n `Duration ${formatDuration(file.durationSeconds)} (${file.recordCount} records of ${header.recordDuration}s)`,\n );\n const elapsedSpan = plan.range.recordingEndSeconds - plan.range.recordingStartSeconds;\n if (Math.abs(elapsedSpan - file.durationSeconds) > 1e-9) {\n lines.push(`Time span ${formatDuration(elapsedSpan)} (includes discontinuities)`);\n }\n lines.push(`Size ${formatBytes(file.fileSize)}`);\n if (header.patientId) lines.push(`Patient ${printable(header.patientId)}`);\n if (header.recordingId) lines.push(`Recording ${printable(header.recordingId)}`);\n\n const signals = file.dataSignals;\n lines.push('');\n // The signal count was pluralised but the annotation-channel count was not, so a file\n // carrying two of them read \"2 annotation channel\". EDF+ permits more than one.\n const annotationCount = file.annotationSignals.length;\n const annotationPart =\n annotationCount > 0\n ? ` + ${annotationCount} annotation channel${annotationCount === 1 ? '' : 's'}`\n : '';\n lines.push(\n `Channels ${signals.length} signal${signals.length === 1 ? '' : 's'}${annotationPart}`,\n );\n lines.push('');\n\n const rows: string[][] = [['#', 'COLUMN', 'LABEL', 'UNIT', 'RATE', 'RANGE', 'OUTPUT']];\n const fileFor = new Map<number, string>();\n for (const group of plan.groups) {\n for (const channel of group.channels) fileFor.set(channel.signal.index, group.fileName);\n }\n // Rendered as a group so that two channels recorded at different rates never show the\n // same figure in the RATE column, which is the one thing this table is asked to settle.\n const rateText = formatRates(signals.map((signal) => signal.samplingRate));\n for (const [row, signal] of signals.entries()) {\n rows.push([\n String(signal.index),\n printable(plan.columnNames.get(signal.index) ?? ''),\n printable(signal.label),\n printable(signal.physicalDimension),\n `${rateText[row]} Hz`,\n `${signal.physicalMin} to ${signal.physicalMax}`,\n /*\n A channel with no samples was reported as \"(not selected)\", which is a different\n thing and not true when it was named on --channels. `edf2csv rec.edf --info\n --channels unused` said the channel the command asked for had not been chosen, when\n what is actually the case is that the file gives it nothing to convert. The\n NO_SAMPLES warning below the table says so; the table contradicted it.\n */\n fileFor.get(signal.index) ??\n (signal.samplesPerRecord === 0 ? '(no samples)' : '(not selected)'),\n ]);\n }\n lines.push(table(rows, new Set([0])));\n\n lines.push('');\n if (plan.groups.length > 1) {\n lines.push(\n plan.layout === 'long'\n ? `Sampling rates differ, and the long layout puts them in one table anyway: each row ` +\n `carries its own time, so nothing has to line up. No channel is resampled.`\n : `Sampling rates differ, so channels are written to ${plan.groups.length} files, one per rate. ` +\n `No channel is resampled.`,\n );\n }\n /*\n The estimate describes the signal tables, and says so when that is not what will be\n written.\n\n Under --annotations-only there are no signal tables, and the line read \"Would write 0\n rows, roughly 0 B.\" for a conversion that goes on to write annotations.csv with three\n events in it. --info exists to say what a conversion will do; asserting it will write\n nothing, when it will write a file, is the one thing it must not do.\n\n How many events there are cannot be answered from the header — the annotation channel has\n to be read record by record, which is the scan --info is for avoiding. So it says which\n file, and that the count is not knowable this cheaply, rather than inventing a zero.\n */\n if (!plan.writeSignals) {\n // Named as they will be written. --info is read to find out what a run leaves behind,\n // and a script that opens the name it was given must find a file there.\n const suffix = plan.gzip ? '.csv.gz' : '.csv';\n lines.push(\n file.annotationSignals.length > 0\n ? `Would write annotations${suffix} and channels${suffix}, and no signal data. How ` +\n 'many events there are cannot be told from the header.'\n : `Would write channels${suffix} and no signal data — and no annotations${suffix} ` +\n 'either, since this recording has no annotation channel.',\n );\n return lines.join('\\n');\n }\n\n // The estimate counts the characters of the CSV, which is what --gzip then compresses.\n // Reporting it as the size on disk would overstate a compressed conversion several-fold.\n const compressing = plan.gzip;\n lines.push(\n `Would write ${plan.estimate.rows.toLocaleString('en-US')} rows, roughly ` +\n `${formatBytes(plan.estimate.bytes)}${compressing ? ' before compression' : ''}.`,\n );\n\n return lines.join('\\n');\n}\n\n/**\n * The `--info` view as JSON, for surveying files from a script.\n *\n * `indent` is 2 for a single recording, matching what this has always printed, and null for\n * a batch — several pretty-printed documents run together are readable by a streaming parser\n * but not by anything that expects one record per line, and a batch is exactly where\n * line-oriented reading is wanted. null rather than undefined because a default parameter\n * takes effect when undefined is passed, which quietly restored the indentation this was\n * meant to drop; JSON.stringify itself wants undefined, so it is translated at the call.\n *\n * `--info` answers \"what is in this recording and what would converting it cost\", which\n * is exactly the question you want to ask across a directory of hundreds of recordings —\n * and the text table is the wrong shape for that. `--json` previously applied only to\n * conversions, so scripts had to parse the aligned columns or convert files just to learn\n * what was in them.\n *\n * Field names match `metadata.json` where the two describe the same thing, so a survey and\n * a conversion can be read by the same code.\n */\nexport function infoJson(file: EdfFile, plan: ConversionPlan, indent: number | null = 2): string {\n const { header } = file;\n const fileFor = new Map<number, string>();\n for (const group of plan.groups) {\n for (const channel of group.channels) fileFor.set(channel.signal.index, group.fileName);\n }\n\n return JSON.stringify(\n {\n path: file.path,\n bytes: file.fileSize,\n format: describeFormat(header),\n start_datetime_local: formatWallClock(header.startDateTime),\n start_date_raw: header.startDateRaw,\n start_time_raw: header.startTimeRaw,\n patient_id: header.patientId,\n recording_id: header.recordingId,\n data_records: file.recordCount,\n data_records_declared: header.declaredRecordCount,\n record_duration_seconds: header.recordDuration,\n duration_seconds: file.durationSeconds,\n // For a discontinuous file this exceeds duration_seconds by the length of the gaps.\n time_span_seconds: plan.range.recordingEndSeconds - plan.range.recordingStartSeconds,\n annotation_channels: file.annotationSignals.length,\n channels: file.dataSignals.map((signal) => ({\n signal_index: signal.index,\n column: plan.columnNames.get(signal.index) ?? '',\n label: signal.label,\n unit: signal.physicalDimension,\n sampling_rate_hz: signal.samplingRate,\n samples_per_record: signal.samplesPerRecord,\n physical_min: signal.physicalMin,\n physical_max: signal.physicalMax,\n digital_min: signal.digitalMin,\n digital_max: signal.digitalMax,\n transducer: signal.transducer,\n prefiltering: signal.prefiltering,\n output_file: fileFor.get(signal.index) ?? null,\n })),\n estimate: {\n rows: plan.estimate.rows,\n // Character count of the CSV. With --gzip the file on disk is smaller than this.\n bytes: plan.estimate.bytes,\n exceeds_spreadsheet_limit: plan.estimate.exceedsSpreadsheetLimit,\n },\n // The plan's mixed-rate warning replaces the header parser's, as it does everywhere\n // else. This was the one consumer left out of that when 0.3.2 made the warning follow\n // --channels, so `--info --json` carried it twice: once counting the rates being\n // converted and once counting every rate in the file, with the same code and severity.\n warnings: plan.diagnostics\n .concat(withoutFileRateWarning(file.diagnostics))\n .map((d) => ({ code: d.code, severity: d.severity, message: d.message })),\n },\n null,\n indent ?? undefined,\n );\n}\n\n/** One line per diagnostic, prefixed so warnings are greppable. */\nexport function formatDiagnostics(diagnostics: readonly Diagnostic[]): string {\n return diagnostics\n .map((d) => {\n // Diagnostics quote channel labels, which come from the file, so they need the\n // same treatment as the --info table.\n const head = `${d.severity === 'warning' ? 'warning' : 'note'}: ${printable(d.message)}`;\n return d.hint ? `${head}\\n ${printable(d.hint)}` : head;\n })\n .join('\\n');\n}\n\nexport function formatSummary(result: ConvertResult): string {\n const lines: string[] = [];\n const rows: string[][] = [];\n for (const file of result.files) {\n rows.push([` ${file.name}`, file.rows.toLocaleString('en-US'), file.name.endsWith('.csv') ? 'rows' : '']);\n }\n lines.push(`Wrote ${result.outputDir}`);\n lines.push(table(rows, new Set([1])));\n lines.push(`Done in ${(result.elapsedMs / 1000).toFixed(1)}s.`);\n return lines.join('\\n');\n}\n\nexport function summaryJson(result: ConvertResult, indent: number | null = 2): string {\n return JSON.stringify(\n {\n output_dir: result.outputDir,\n files: result.files,\n annotations: result.annotationCount,\n duration_seconds: result.file.durationSeconds,\n records: result.file.recordCount,\n elapsed_ms: result.elapsedMs,\n warnings: result.diagnostics.map((d) => ({ code: d.code, severity: d.severity, message: d.message })),\n },\n null,\n indent ?? undefined,\n );\n}\n"]}
|
package/dist/cli.d.ts.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"cli.d.ts","sourceRoot":"","sources":["../src/cli.ts"],"names":[],"mappings":";AACA;;;;;;;GAOG;AAeH,OAAO,EAA+C,gBAAgB,EAAE,MAAM,kBAAkB,CAAC;
|
|
1
|
+
{"version":3,"file":"cli.d.ts","sourceRoot":"","sources":["../src/cli.ts"],"names":[],"mappings":";AACA;;;;;;;GAOG;AAeH,OAAO,EAA+C,gBAAgB,EAAE,MAAM,kBAAkB,CAAC;AA6HjG,wBAAsB,IAAI,CAAC,IAAI,EAAE,SAAS,MAAM,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC,CA0WnE;AA2xBD,OAAO,EAAE,gBAAgB,EAAE,CAAC"}
|
package/dist/cli.js
CHANGED
|
@@ -45,6 +45,9 @@ Options
|
|
|
45
45
|
--annotations-only Write only the EDF+ annotations, no signal data
|
|
46
46
|
--decimals <n> Fix the decimal places instead of deriving them per channel
|
|
47
47
|
--checksum Record a SHA-256 of the input in metadata.json
|
|
48
|
+
--layout <kind> wide (default): one column per channel, one file per
|
|
49
|
+
sampling rate. long: one file of time_s,channel,value,
|
|
50
|
+
every rate together, one row per sample
|
|
48
51
|
--gzip Compress every CSV, writing .csv.gz files
|
|
49
52
|
--bom Start each CSV with a UTF-8 byte order mark, so Excel
|
|
50
53
|
reads accented text and units like µV correctly
|
|
@@ -74,6 +77,9 @@ Output
|
|
|
74
77
|
With --gzip each CSV becomes a .csv.gz; metadata.json stays plain text so the
|
|
75
78
|
directory can still be read at a glance. With --bom each CSV starts with a
|
|
76
79
|
UTF-8 byte order mark and metadata.json does not, since JSON.parse rejects one.
|
|
80
|
+
With --layout long every channel goes into one signals.csv as time_s, channel
|
|
81
|
+
and value, in time order, whatever rates the recording mixes — which is also
|
|
82
|
+
the one arrangement --stdout can stream for a mixed-rate file.
|
|
77
83
|
|
|
78
84
|
Examples
|
|
79
85
|
edf2csv recording.edf
|
|
@@ -152,6 +158,7 @@ export async function main(argv) {
|
|
|
152
158
|
'annotations-only': { type: 'boolean' },
|
|
153
159
|
decimals: { type: 'string' },
|
|
154
160
|
checksum: { type: 'boolean' },
|
|
161
|
+
layout: { type: 'string' },
|
|
155
162
|
gzip: { type: 'boolean' },
|
|
156
163
|
bom: { type: 'boolean' },
|
|
157
164
|
jobs: { type: 'string', short: 'j' },
|
|
@@ -264,6 +271,7 @@ export async function main(argv) {
|
|
|
264
271
|
annotationsOnly: values['annotations-only'] === true,
|
|
265
272
|
gzip: values['gzip'] === true,
|
|
266
273
|
bom: values['bom'] === true,
|
|
274
|
+
layout: optionalLayout(values['layout']),
|
|
267
275
|
};
|
|
268
276
|
// Validated before the --info branch, not inside the conversion path: a flag that
|
|
269
277
|
// cannot be honoured is a usage error whatever mode it was given in, and accepting
|
|
@@ -974,7 +982,7 @@ async function convertInChild(input, destination, values, running) {
|
|
|
974
982
|
if (values[flag] === true)
|
|
975
983
|
args.push(`--${flag}`);
|
|
976
984
|
}
|
|
977
|
-
for (const flag of ['start', 'duration', 'end', 'decimals']) {
|
|
985
|
+
for (const flag of ['start', 'duration', 'end', 'decimals', 'layout']) {
|
|
978
986
|
if (typeof values[flag] === 'string')
|
|
979
987
|
args.push(`--${flag}=${values[flag]}`);
|
|
980
988
|
}
|
|
@@ -1132,6 +1140,14 @@ function optionalTime(raw, option) {
|
|
|
1132
1140
|
return undefined;
|
|
1133
1141
|
return parseTimeSpec(String(raw), option);
|
|
1134
1142
|
}
|
|
1143
|
+
/** `--layout`, which is one of two words and not a guess at what was meant. */
|
|
1144
|
+
function optionalLayout(raw) {
|
|
1145
|
+
if (raw === undefined)
|
|
1146
|
+
return undefined;
|
|
1147
|
+
if (raw === 'wide' || raw === 'long')
|
|
1148
|
+
return raw;
|
|
1149
|
+
throw new OptionError(`--layout must be "wide" or "long", got "${String(raw)}".`);
|
|
1150
|
+
}
|
|
1135
1151
|
function optionalDecimals(raw) {
|
|
1136
1152
|
if (raw === undefined)
|
|
1137
1153
|
return undefined;
|