edf2csv 0.4.1 → 0.4.3

package/CHANGELOG.md

@@ -3,6 +3,86 @@
 Notable changes to edf2csv. Versions follow [semantic versioning](https://semver.org); while the
 major version is 0, a minor bump may contain breaking changes.
 
+## 0.4.3
+
+### Added: a folder as input
+
+```bash
+edf2csv /data/study --out ./converted --jobs auto
+```
+
+Every `.edf` and `.bdf` inside is converted, at any depth. Recordings arrive organised into
+folders and a shell has no tidy way to reach them, which is why the recipes here carried a
+`find` incantation to do it. Passing the folder is the obvious thing to try, and until now it
+failed with "is a directory, not an EDF file".
+
+**The layout is kept.** A recording at `study/night-1/rec.edf` comes out at
+`converted/night-1/rec`. That is not only tidiness: one folder per night with the file always
+called `rec.edf` is a normal way to lay out a study, and flattening those onto their file names
+would have every one of them claim `converted/rec` — which 0.4.0 correctly refuses, so the
+whole run would have stopped before writing anything.
+
+Anything in the folder that is not a recording is skipped, and a folder holding none says so
+rather than converting nothing in silence:
+
+```
+No EDF or BDF recordings found in "/data/empty".
+```
+
+A path that is not a directory is passed through untouched, so a file named on the command line
+that does not exist still reports itself instead of quietly vanishing from the list.
+
+Folders and files can be mixed in one command, and everything else — `--jobs`, `--out`,
+`--channels`, the time window — applies to the lot.
+
+## 0.4.2
+
+### Added: `--jobs`, converting several recordings at once
+
+0.4.0 made a batch possible; this makes it use the machine. Eight recordings of 19 MB, each
+converting to 168 MB of CSV, on eight cores:
+
+| | wall clock |
+| --- | --- |
+| `--jobs 1` | 9.7 s |
+| `--jobs 2` | 5.6 s |
+| `--jobs 4` | 3.3 s |
+| `--jobs auto` | 3.8 s |
+
+```bash
+edf2csv /data/recordings/*.edf --out /data/csv --jobs auto
+```
+
+`auto` is one job per core less one, so a long batch leaves the machine usable. It is not
+always the fastest setting: past a point the conversions compete for the disk rather than the
+CPU, which is why it lands slightly behind `4` above.
+
+**Each conversion runs in its own process.** The first attempt used concurrent promises inside
+one process and gained 6%, which is the overlap in the file reads and nothing else — converting
+is almost entirely arithmetic and string building, 1.17 s of CPU for 1.24 s of wall clock, and
+Node runs that on one thread. Since each conversion is already a whole command, each one gets a
+whole process, which is what `xargs -P` would do by hand.
+
+The output is byte-identical to a serial run, and the tests check that across four recordings
+rather than asserting it.
+
+A recording's output is held until it finishes and then released in one piece, so two ending
+together cannot interleave one's summary with the other's warnings. They therefore appear in
+the order they finish rather than the order given, each announced by the `[n/m]` line naming
+it. `--json` is still one object per line: a child sees a single recording and prints the
+indented document a single conversion prints, so the batch puts it back on one line.
+
+A failure still names its recording. The child converted one file and prefixed nothing the way
+a batch does, so the parent puts the name in — the `[n/m]` header is not necessarily alongside
+in a log.
+
+`--stdout` ignores `--jobs`, since that path takes one recording anyway.
+
+### Fixed: an unusable `--jobs` was accepted in silence under `--info`
+
+Validation lived in the conversion path, so `--info --jobs 0` ignored the flag and printed the
+report. A flag that cannot be honoured is a usage error whatever mode it was given in.
+
 ## 0.4.1
 
 ### Faster: large conversions run in about two thirds of the time

package/README.md

@@ -60,6 +60,7 @@ npx edf2csv recording.edf --start 30m --duration 5m
       --decimals <n>     Force a number of decimal places
       --checksum         Put a SHA-256 of the input in metadata.json
       --gzip             Compress every CSV, writing .csv.gz files
+  -j, --jobs <n>         Convert this many recordings at once, or "auto"
   -f, --force            Overwrite the output folder
   -q, --quiet            Less output
       --json             Machine-readable JSON on stdout (works with --info too)

package/dist/cli.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"cli.d.ts","sourceRoot":"","sources":["../src/cli.ts"],"names":[],"mappings":";AACA;;;;;;;GAOG;AAWH,OAAO,EAA4B,gBAAgB,EAAE,MAAM,kBAAkB,CAAC;AAwF9E,wBAAsB,IAAI,CAAC,IAAI,EAAE,SAAS,MAAM,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC,CAsMnE;AAsQD,OAAO,EAAE,gBAAgB,EAAE,CAAC"}
+{"version":3,"file":"cli.d.ts","sourceRoot":"","sources":["../src/cli.ts"],"names":[],"mappings":";AACA;;;;;;;GAOG;AAcH,OAAO,EAA4B,gBAAgB,EAAE,MAAM,kBAAkB,CAAC;AA+F9E,wBAAsB,IAAI,CAAC,IAAI,EAAE,SAAS,MAAM,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC,CAgRnE;AAiaD,OAAO,EAAE,gBAAgB,EAAE,CAAC"}

package/dist/cli.js

@@ -10,6 +10,9 @@
 import { parseArgs } from 'node:util';
 import { pathToFileURL, fileURLToPath } from 'node:url';
 import { realpathSync } from 'node:fs';
+import { readdir, stat } from 'node:fs/promises';
+import { cpus } from 'node:os';
+import { fork } from 'node:child_process';
 import path from 'node:path';
 import process from 'node:process';
 import { EdfError } from './edf/errors.js';
@@ -20,12 +23,13 @@ import { ChannelSelectionError } from './convert/channels.js';
 import { TimeRangeError, parseTimeSpec } from './convert/time-range.js';
 import { deriveRecordStarts } from './convert/timing.js';
 import { formatDiagnostics, formatInfo, infoJson, formatSummary, printable, printableLines, summaryJson } from './cli/report.js';
+import { listed } from './format/list.js';
 import { VERSION } from './version.js';
 const USAGE = `edf2csv ${VERSION}
 Convert EDF, EDF+ and BDF recordings to CSV
 
 Usage
-  edf2csv <recording.edf> [more.edf ...] [options]
+  edf2csv <recording.edf | folder> [more ...] [options]
 
 Options
   -i, --info             Show the recording's structure and estimated output size,
@@ -40,6 +44,7 @@ Options
       --decimals <n>     Fix the decimal places instead of deriving them per channel
       --checksum         Record a SHA-256 of the input in metadata.json
       --gzip             Compress every CSV, writing .csv.gz files
+  -j, --jobs <n>         Convert this many recordings at once, or "auto" (default: 1)
   -f, --force            Overwrite the output directory if it exists
   -q, --quiet            Suppress the summary; warnings and errors still print
       --json             Print machine-readable JSON to stdout (works with --info too)
@@ -50,10 +55,13 @@ Options
   -V, --version          Show the version
 
 Several recordings
+  A folder is expanded to every .edf and .bdf inside it, at any depth, and the
+  layout is kept: recordings in sub-folders come out in sub-folders.
   Pass more than one and each is converted in turn. Without --out each lands
   beside itself as usual; with --out that directory becomes the parent and each
   recording gets its own inside it. A file that cannot be read is reported and
-  the rest still convert, with a non-zero exit at the end.
+  the rest still convert, with a non-zero exit at the end. --jobs converts
+  several at once, which is worth it for a folder of them.
 
 Output
   A directory containing signals.csv, channels.csv, metadata.json, and
@@ -69,6 +77,8 @@ Examples
   edf2csv recording.edf --start 30m --duration 5m
   edf2csv recording.edf --annotations-only
   edf2csv /data/*.edf --out ./converted
+  edf2csv /data/*.edf --out ./converted --jobs auto
+  edf2csv /data/study --out ./converted --jobs auto
 `;
 /** A problem with how the command was invoked, as opposed to a problem with the file. */
 class OptionError extends Error {
@@ -119,6 +129,7 @@ export async function main(argv) {
                 decimals: { type: 'string' },
                 checksum: { type: 'boolean' },
                 gzip: { type: 'boolean' },
+                jobs: { type: 'string', short: 'j' },
                 force: { type: 'boolean', short: 'f' },
                 quiet: { type: 'boolean', short: 'q' },
                 json: { type: 'boolean' },
@@ -147,7 +158,18 @@ export async function main(argv) {
         process.stderr.write(`No input file given.\n\n${USAGE}`);
         return EXIT_USAGE;
     }
-    const inputs = positionals;
+    let expanded;
+    try {
+        expanded = await expandInputs(positionals);
+    }
+    catch (error) {
+        return reportError(error);
+    }
+    if (expanded.length === 0) {
+        process.stderr.write(`No EDF or BDF recordings found in ${listed(positionals.map((p) => `"${p}"`))}.\n`);
+        return EXIT_USAGE;
+    }
+    const inputs = expanded.map((entry) => entry.path);
     const batch = inputs.length > 1;
     const quiet = values['quiet'] === true;
     const asJson = values['json'] === true;
@@ -184,7 +206,7 @@ export async function main(argv) {
     const jsonIndent = batch ? null : 2;
     try {
         const outOption = typeof values['out'] === 'string' ? values['out'] : undefined;
-        const destinations = destinationsFor(inputs, outOption);
+        const destinations = destinationsFor(expanded, outOption);
         assertDistinct(inputs, destinations);
         const shared = {
             channels: splitChannels(values['channels']),
@@ -197,6 +219,10 @@ export async function main(argv) {
             annotationsOnly: values['annotations-only'] === true,
             gzip: values['gzip'] === true,
         };
+        // Validated before the --info branch, not inside the conversion path: a flag that
+        // cannot be honoured is a usage error whatever mode it was given in, and accepting
+        // "--jobs 0" in silence under --info is the kind of quiet that this tool avoids.
+        const jobs = toStdout ? 1 : parseJobs(values['jobs'], inputs.length);
         if (values['info'] === true) {
             const failures = [];
             let warnings = 0;
@@ -215,16 +241,20 @@ export async function main(argv) {
                 return worstOf(failures);
             return strict && warnings > 0 ? EXIT_ERROR : EXIT_OK;
         }
-        const showProgress = !quiet && !asJson && !toStdout && process.stderr.isTTY === true;
+        // The meter redraws one line in place, which two conversions cannot share. Running them
+        // at once replaces it with the completion count each file prints as it lands.
+        const showProgress = !quiet && !asJson && !toStdout && jobs === 1 && process.stderr.isTTY === true;
         const failures = [];
         let warnings = 0;
         let converted = 0;
-        for (const [index, input] of inputs.entries()) {
+        /** Convert input `index`, sending its output wherever the caller wants it. */
+        const runOne = async (index, emit) => {
+            const input = inputs[index];
             const destination = destinations[index];
             // Which recording this is, before anything it prints. Without it a batch produces a
             // stack of summaries and errors with nothing saying which file each belongs to.
             if (batch && !quiet && !asJson) {
-                process.stderr.write(`[${index + 1}/${inputs.length}] ${printable(input)}\n`);
+                emit('err', `[${index + 1}/${inputs.length}] ${printable(input)}\n`);
             }
             try {
                 warnings += await convertOne(input, destination, {
@@ -239,21 +269,69 @@ export async function main(argv) {
                     asJson,
                     showProgress,
                     jsonIndent,
-                });
+                }, emit);
                 converted++;
             }
             catch (error) {
-                failures.push(reportError(error, batch ? input : undefined));
                 /*
                   A batch keeps going. One unreadable recording among five hundred is a reason to
                   report that file, not to abandon the ones already converted and refuse the rest.
                   The exit code still reports the run as failed, and the closing line says how many
                   of them made it, so nothing about the failure is quiet.
                 */
-                if (!batch)
+                failures.push(reportError(error, batch ? input : undefined, emit));
+            }
+        };
+        if (jobs === 1) {
+            for (let index = 0; index < inputs.length; index++) {
+                await runOne(index, writeThrough);
+                // A single recording keeps the exit code it has always had rather than the batch's.
+                if (!batch && failures.length > 0)
                     return failures[0];
             }
         }
+        else {
+            /*
+              Real processes, not concurrent promises.
+      
+              Converting is almost entirely arithmetic and string building — 1.17 s of CPU for
+              1.24 s of wall clock on a 168 MB conversion — and Node runs that on one thread. An
+              in-process pool was tried first and gained 6% on eight recordings, which is the
+              overlap in the file reads and nothing else. Each conversion is already a whole
+              command, so each one gets its own process, which is what `xargs -P` would do by hand.
+      
+              Workers take the next recording as they free up rather than splitting the list into
+              equal shares. Recordings in a folder differ wildly in length, and a fixed split
+              leaves every worker but one idle behind the longest file.
+      
+              Each child's output is held until it exits, so two finishing together cannot
+              interleave one's summary with the other's warnings.
+            */
+            let next = 0;
+            const worker = async () => {
+                for (let index = next++; index < inputs.length; index = next++) {
+                    const input = inputs[index];
+                    const sink = buffered();
+                    if (!quiet && !asJson) {
+                        sink.emit('err', `[${index + 1}/${inputs.length}] ${printable(input)}\n`);
+                    }
+                    const child = await convertInChild(input, destinations[index], values);
+                    if (child.code === 0)
+                        converted++;
+                    else
+                        failures.push(child.code);
+                    // The child saw one recording, so it printed the indented document a single
+                    // conversion prints. A batch is one object per line.
+                    sink.emit('out', asJson ? compactJson(child.out) : child.out);
+                    // The child converted a single recording, so it named no file in its errors the
+                    // way a batch does. Naming it here keeps the two paths identical to a reader and
+                    // to anything grepping a log, where the [n/m] header may not be alongside.
+                    sink.emit('err', named(child.err, input));
+                    sink.flush();
+                }
+            };
+            await Promise.all(Array.from({ length: jobs }, () => worker()));
+        }
         if (batch && !quiet && !asJson) {
             process.stderr.write(`\nConverted ${converted} of ${inputs.length} recordings` +
                 `${failures.length > 0 ? `; ${failures.length} failed` : ''}.\n`);
@@ -324,7 +402,7 @@ async function showInfo(input, shared, asJson, jsonIndent) {
     }
 }
 /** Convert one recording, and return how many diagnostics it raised. */
-async function convertOne(input, destination, options) {
+async function convertOne(input, destination, options, emit = writeThrough) {
     const { quiet, asJson, showProgress, toStdout } = options;
     let lastTick = 0;
     /*
@@ -362,22 +440,22 @@ async function convertOne(input, destination, options) {
         if (showProgress)
             process.stderr.write('\r\u001b[K');
         if (result.diagnostics.length > 0 && !asJson) {
-            process.stderr.write(`${formatDiagnostics(result.diagnostics)}\n\n`);
+            emit('err', `${formatDiagnostics(result.diagnostics)}\n\n`);
         }
         if (asJson) {
             // One object per line, so a batch is JSON Lines — `jq` reads a record at a time
             // rather than waiting for the whole run to finish.
-            process.stdout.write(`${summaryJson(result, options.jsonIndent)}\n`);
+            emit('out', `${summaryJson(result, options.jsonIndent)}\n`);
         }
         else if (!quiet) {
             // With --stdout there is no directory to summarise, and the row count is the only
             // thing worth saying — on stderr, so the CSV on stdout stays clean.
             if (toStdout) {
                 const rows = result.files[0]?.rows ?? 0;
-                process.stderr.write(`Wrote ${rows.toLocaleString('en-US')} rows to stdout.\n`);
+                emit('err', `Wrote ${rows.toLocaleString('en-US')} rows to stdout.\n`);
             }
             else {
-                process.stderr.write(`${formatSummary(result)}\n`);
+                emit('err', `${formatSummary(result)}\n`);
             }
         }
         return result.diagnostics.length;
@@ -387,6 +465,37 @@ async function convertOne(input, destination, options) {
         process.off('SIGTERM', onInterrupt);
     }
 }
+/**
+ * Recordings to convert, with directories expanded to what is inside them.
+ *
+ * A directory yields every `.edf` and `.bdf` beneath it, at any depth. Recordings arrive
+ * organised into folders, and a shell has no tidy way to reach them — which is why the
+ * recipes here carried a `find` incantation to do it. Passing the folder is the obvious
+ * thing to try, and it used to fail with "is a directory, not an EDF file".
+ */
+async function expandInputs(positionals) {
+    const found = [];
+    for (const given of positionals) {
+        const info = await stat(given).catch(() => null);
+        if (info === null || !info.isDirectory()) {
+            // Anything that is not a directory is passed through untouched, so a file that does
+            // not exist still reports itself rather than vanishing from the list.
+            found.push({ path: given, name: path.basename(given) });
+            continue;
+        }
+        for (const entry of await readdir(given, { recursive: true, withFileTypes: true })) {
+            if (!entry.isFile() || !/\.(edf|bdf)$/iu.test(entry.name))
+                continue;
+            // parentPath is the directory the entry was found in, which for a recursive read is
+            // below the one that was asked for.
+            const full = path.join(entry.parentPath ?? given, entry.name);
+            found.push({ path: full, name: path.relative(given, full) });
+        }
+    }
+    // A directory hands them back in whatever order the filesystem stored them.
+    found.sort((a, b) => (a.path < b.path ? -1 : a.path > b.path ? 1 : 0));
+    return found;
+}
 /**
  * Where each recording's output goes.
  *
@@ -400,16 +509,16 @@ async function convertOne(input, destination, options) {
  */
 function destinationsFor(inputs, out) {
     if (out === undefined)
-        return inputs.map((input) => defaultOutputDir(input));
+        return inputs.map((input) => defaultOutputDir(input.path));
     if (inputs.length === 1)
         return [out];
-    return inputs.map((input) => path.join(out, stemOf(input)));
+    return inputs.map((input) => path.join(out, stemOf(input.name)));
 }
-/** File name without its extension, keeping a leading dot: `.hidden.edf` -> `.hidden`. */
-function stemOf(file) {
-    const base = path.basename(file);
-    const dot = base.lastIndexOf('.');
-    return dot > 0 ? base.slice(0, dot) : base;
+/** A name without its extension, keeping a leading dot: `.hidden.edf` -> `.hidden`. */
+function stemOf(name) {
+    const dot = name.lastIndexOf('.');
+    const slash = Math.max(name.lastIndexOf('/'), name.lastIndexOf('\\'));
+    return dot > slash + 1 ? name.slice(0, dot) : name;
 }
 /**
  * Refuse a batch in which two recordings would land in the same directory.
@@ -444,29 +553,123 @@ function assertDistinct(inputs, destinations) {
 function worstOf(codes) {
     return codes.includes(EXIT_ERROR) ? EXIT_ERROR : EXIT_USAGE;
 }
+/**
+ * Convert one recording in a separate process, and collect everything it printed.
+ *
+ * The arguments are rebuilt from the parsed options rather than sliced out of argv, so the
+ * child receives exactly the flags this run was given and nothing that only makes sense to
+ * the parent: not the other recordings, not --jobs, and not --info or --stdout, neither of
+ * which reaches this path.
+ */
+async function convertInChild(input, destination, values) {
+    const args = [input, '--out', destination];
+    for (const flag of ['annotations-only', 'checksum', 'gzip', 'force', 'quiet', 'json', 'strict']) {
+        if (values[flag] === true)
+            args.push(`--${flag}`);
+    }
+    for (const flag of ['start', 'duration', 'end', 'decimals']) {
+        if (typeof values[flag] === 'string')
+            args.push(`--${flag}`, values[flag]);
+    }
+    // --channels is repeatable, and each term is passed as given so that a label containing a
+    // comma survives: joining them back into one list would split it in the child.
+    const channels = values['channels'];
+    if (channels !== undefined) {
+        for (const term of Array.isArray(channels) ? channels : [String(channels)]) {
+            args.push('--channels', term);
+        }
+    }
+    return new Promise((resolve) => {
+        const child = fork(fileURLToPath(import.meta.url), args, {
+            stdio: ['ignore', 'pipe', 'pipe', 'ipc'],
+        });
+        let out = '';
+        let err = '';
+        child.stdout?.setEncoding('utf8').on('data', (chunk) => {
+            out += chunk;
+        });
+        child.stderr?.setEncoding('utf8').on('data', (chunk) => {
+            err += chunk;
+        });
+        child.on('error', (error) => {
+            resolve({ code: EXIT_ERROR, out, err: `${err}error: ${input}: ${error.message}\n` });
+        });
+        child.on('close', (code) => resolve({ code: code ?? EXIT_ERROR, out, err }));
+    });
+}
+/** Put the recording's name into the error lines a child produced. */
+function named(text, input) {
+    return text.replace(/^error: /gmu, `error: ${printable(input)}: `);
+}
+/** Re-render a child's pretty-printed summary onto one line, leaving anything else alone. */
+function compactJson(text) {
+    const trimmed = text.trim();
+    if (trimmed === '')
+        return '';
+    try {
+        return `${JSON.stringify(JSON.parse(trimmed))}\n`;
+    }
+    catch {
+        // Not the document expected; passing it through unchanged beats losing it.
+        return text;
+    }
+}
+const writeThrough = (stream, text) => {
+    (stream === 'out' ? process.stdout : process.stderr).write(text);
+};
+/** Collects output so it can be released in one piece when a conversion finishes. */
+function buffered() {
+    const parts = [];
+    return {
+        emit: (stream, text) => parts.push([stream, text]),
+        flush: () => {
+            for (const [stream, text] of parts)
+                writeThrough(stream, text);
+        },
+    };
+}
 /**
  * Report an error the way this command always has, and give the exit code it implies.
  *
  * `input` names the recording while a batch is running: several failures otherwise arrive
  * as a stack of messages with nothing saying which file each belongs to.
  */
-function reportError(error, input) {
+function reportError(error, input, emit = writeThrough) {
     const where = input === undefined ? '' : `${printable(input)}: `;
     if (error instanceof EdfError || error instanceof ConversionError) {
-        process.stderr.write(`error: ${where}${printableLines(error.message, '       ')}\n`);
+        emit('err', `error: ${where}${printableLines(error.message, '       ')}\n`);
         if (error.hint)
-            process.stderr.write(`       ${error.hint}\n`);
+            emit('err', `       ${error.hint}\n`);
         return EXIT_ERROR;
     }
     if (error instanceof ChannelSelectionError ||
         error instanceof TimeRangeError ||
         error instanceof OptionError) {
-        process.stderr.write(`error: ${where}${printableLines(error.message, '       ')}\n`);
+        emit('err', `error: ${where}${printableLines(error.message, '       ')}\n`);
         return EXIT_USAGE;
     }
-    process.stderr.write(`error: ${where}${message(error, '       ')}\n`);
+    emit('err', `error: ${where}${message(error, '       ')}\n`);
     return EXIT_ERROR;
 }
+/**
+ * How many conversions to run at once.
+ *
+ * `auto` is one per core, less one, so a long batch does not take the machine over. A batch
+ * is the only place this means anything: a single recording is a single conversion however
+ * many jobs are asked for.
+ */
+function parseJobs(raw, inputs) {
+    if (raw === undefined)
+        return 1;
+    const text = String(raw).trim();
+    if (text === 'auto')
+        return Math.max(1, Math.min(inputs, cpus().length - 1));
+    const value = Number(text);
+    if (!Number.isInteger(value) || value < 1) {
+        throw new OptionError(`--jobs must be a whole number of 1 or more, or "auto", got "${text}".`);
+    }
+    return Math.min(value, Math.max(1, inputs));
+}
 function splitChannels(raw) {
     if (raw === undefined)
         return undefined;

package/dist/cli.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "edf2csv",
-  "version": "0.4.1",
+  "version": "0.4.3",
   "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.",
   "keywords": [
     "edf",