edf2csv 0.4.7 → 0.4.8
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 +86 -0
- package/dist/cli/report.d.ts.map +1 -1
- package/dist/cli/report.js +6 -1
- package/dist/cli/report.js.map +1 -1
- package/dist/cli.d.ts.map +1 -1
- package/dist/cli.js +6 -1
- package/dist/cli.js.map +1 -1
- package/dist/convert/run.js +25 -7
- package/dist/convert/run.js.map +1 -1
- package/dist/format/csv.d.ts.map +1 -1
- package/dist/format/csv.js +15 -0
- package/dist/format/csv.js.map +1 -1
- package/package.json +1 -1
package/CHANGELOG.md
CHANGED
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@@ -3,6 +3,92 @@
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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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## 0.4.8
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8
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### Fixed: `--duration` dropped every annotation on a recording that starts after zero
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9
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10
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The signal window and the annotation window read the same absent `--start` two different
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ways. `resolveRange` defaults it to the earliest record, taken from the EDF+D timekeeping
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TALs; the annotation filter defaulted it to 0. On a recording whose first record sits at 30 s,
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`--duration 5` converted samples from [30, 35) while filtering annotations against
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`(-inf, 5)` — windows that do not overlap at all:
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```
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edf2csv late-start.edf --duration 5 --out ./converted
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```
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```
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signals.csv 30.000, 30.250, 30.500, … every sample in the window
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annotations.csv onset_s,duration_s,… nothing but the header
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```
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Silent: the run exits 0 and writes a well-formed file, so nothing about the output says the
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events were lost. `--duration` is now measured from wherever the conversion actually starts.
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`--end` was never affected, since it names an absolute offset.
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### Fixed: `--stdout --gzip | head` reported a write failure
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30
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0.2.30 made `edf2csv big.edf --stdout | head` exit 0. 0.3.1 said compression would behave
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identically. It did not:
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```
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35
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$ edf2csv recording.edf --stdout --gzip | head -c 100
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36
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error: Writing to stdout failed: Cannot call end after a stream was destroyed
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exit 1
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```
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The EPIPE forwarded from stdout destroys the compressor, and the writer's guard against
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closing stdout compares against `process.stdout` — which under `--gzip` is not the stream it
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holds. Calling `end()` on the destroyed compressor fails with `ERR_STREAM_DESTROYED`, which is
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not `EPIPE`, so it escaped the hang-up path and came back as a conversion failure. All three
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symptoms 0.2.30 removed — exit 1 for a routine shell idiom, a claim about files that were
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never written, advice about disk space — had reappeared on the one path 0.3.1 promised would
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match. The writer now stops at a hang-up whatever stream it is holding.
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### Fixed: `--gzip` could overwrite the recording it was reading
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50
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The guard that stops an output from resolving to the input builds its list from the plan's
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file names, which carry `.csv.gz`, and then spelled out the two sidecars uncompressed. A
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compressed run therefore checked two names it would never write and missed the two it would.
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A recording sitting at `<outdir>/channels.csv.gz` was overwritten by its own conversion, with
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`--force`, and the run reported success. The same file named `signals.csv.gz` was refused,
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which is what gives the oversight away.
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### Fixed: `--info --json` carried the mixed-rate warning twice
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0.3.2 made that warning describe the conversion rather than the file, and reached every
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consumer but one. `--info --json` emitted both copies — same code, same severity, one counting
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the rates being converted and one counting every rate in the file. Anything matching on `code`
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saw it twice.
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### Fixed: interrupting `--stdout` named a directory that was never created
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```
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interrupted (SIGINT): the conversion stopped part way through.
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Files already written to "recording_csv" are incomplete and should not be used.
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```
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`--stdout` writes no directory. It now says what is actually true — that the CSV on stdout
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stops mid-recording — which is the same "files that were never written" complaint 0.2.30
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fixed in this path's error message.
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### Documentation that had gone false
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- The correctness page said a non-finite gain writes the physical minimum. It has written
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empty cells and raised `UNUSABLE_PHYSICAL_RANGE` since 0.2.15; the page was not updated
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with the rest, and contradicted the warnings reference. The row covered two conditions
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and is now two rows, since only the `gain === 0` half was ever true.
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- Its test transcript still showed 88 tests in 19 suites. It is 148 in 32, and the per-file
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counts were stale too.
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- The sampling-rates page said the mixed-rate warning ignores `--channels`. 0.3.2 made it
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follow the selection.
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- The warnings reference said `DISCONTINUOUS` can only be raised by a conversion. `--info`
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raises it, because it has to read the record times to report the span correctly.
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All five code defects were found by an adversarial sweep of the subsystems: 51 agents raising
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findings and then trying to refute each other's, of which 18 survived and 24 did not. The rest
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are recorded and not yet addressed.
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## 0.4.7
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### Added: `npm run fuzz`, which damages real recordings and checks nothing crashes
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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;
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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,CA0EtE;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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@@ -6,6 +6,7 @@
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*/
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import { describeFormat, formatRates, formatWallClock } from '../edf/header.js';
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import { formatBytes, formatDuration } from '../format/number.js';
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import { withoutFileRateWarning } from '../convert/plan.js';
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function table(rows, alignRight) {
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if (rows.length === 0)
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return '';
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@@ -187,8 +188,12 @@ export function infoJson(file, plan, indent = 2) {
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bytes: plan.estimate.bytes,
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exceeds_spreadsheet_limit: plan.estimate.exceedsSpreadsheetLimit,
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},
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// The plan's mixed-rate warning replaces the header parser's, as it does everywhere
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// else. This was the one consumer left out of that when 0.3.2 made the warning follow
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// --channels, so `--info --json` carried it twice: once counting the rates being
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// converted and once counting every rate in the file, with the same code and severity.
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warnings: plan.diagnostics
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.concat(file.diagnostics)
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.concat(withoutFileRateWarning(file.diagnostics))
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.map((d) => ({ code: d.code, severity: d.severity, message: d.message })),
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}, null, indent ?? undefined);
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}
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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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-
{"version":3,"file":"report.js","sourceRoot":"","sources":["../../src/cli/report.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAIH,OAAO,EAAE,cAAc,EAAE,WAAW,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAC;AAChF,OAAO,EAAE,WAAW,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAC;
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+
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|
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,EAA4B,gBAAgB,EAAE,MAAM,kBAAkB,CAAC;AA+F9E,wBAAsB,IAAI,CAAC,IAAI,EAAE,SAAS,MAAM,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC,CAmTnE;
|
|
1
|
+
{"version":3,"file":"cli.d.ts","sourceRoot":"","sources":["../src/cli.ts"],"names":[],"mappings":";AACA;;;;;;;GAOG;AAeH,OAAO,EAA4B,gBAAgB,EAAE,MAAM,kBAAkB,CAAC;AA+F9E,wBAAsB,IAAI,CAAC,IAAI,EAAE,SAAS,MAAM,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC,CAmTnE;AAueD,OAAO,EAAE,gBAAgB,EAAE,CAAC"}
|
package/dist/cli.js
CHANGED
|
@@ -442,8 +442,13 @@ async function convertOne(input, destination, options, emit = writeThrough) {
|
|
|
442
442
|
const onInterrupt = (signal) => {
|
|
443
443
|
if (showProgress)
|
|
444
444
|
process.stderr.write('\r\u001b[K');
|
|
445
|
+
// --stdout writes no directory, so there is none to warn about. Naming one anyway
|
|
446
|
+
// pointed at a path that was never created — the same "files that were never written"
|
|
447
|
+
// that 0.2.30 removed from this path's error message.
|
|
445
448
|
process.stderr.write(`\ninterrupted (${signal}): the conversion stopped part way through.\n` +
|
|
446
|
-
|
|
449
|
+
(toStdout
|
|
450
|
+
? ` The CSV on stdout stops mid-recording and should not be used.\n`
|
|
451
|
+
: ` Files already written to "${destination}" are incomplete and should not be used.\n`));
|
|
447
452
|
// 128 + signal number, the conventional exit status for dying to a signal.
|
|
448
453
|
process.exit(signal === 'SIGINT' ? 130 : 143);
|
|
449
454
|
};
|
package/dist/cli.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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|
package/dist/convert/run.js
CHANGED
|
@@ -78,7 +78,7 @@ export async function convert(inputPath, options = {}) {
|
|
|
78
78
|
};
|
|
79
79
|
}
|
|
80
80
|
const outputDir = options.outputDir ?? defaultOutputDir(inputPath);
|
|
81
|
-
await assertInputDoesNotOverlapOutputs(inputPath, outputDir, file, plan);
|
|
81
|
+
await assertInputDoesNotOverlapOutputs(inputPath, outputDir, file, plan, options);
|
|
82
82
|
await prepareOutputDir(outputDir, options.force === true);
|
|
83
83
|
const written = [];
|
|
84
84
|
if (plan.writeSignals && plan.groups.length > 0) {
|
|
@@ -95,7 +95,7 @@ export async function convert(inputPath, options = {}) {
|
|
|
95
95
|
}
|
|
96
96
|
let annotationsWritten = 0;
|
|
97
97
|
if (file.annotationSignals.length > 0) {
|
|
98
|
-
const result = await writeAnnotationsCsv(outputDir, annotationData.annotations, requestedAnnotationWindow(options), options.gzip === true);
|
|
98
|
+
const result = await writeAnnotationsCsv(outputDir, annotationData.annotations, requestedAnnotationWindow(options, plan.range.recordingStartSeconds), options.gzip === true);
|
|
99
99
|
written.push(result);
|
|
100
100
|
annotationsWritten = result.rows;
|
|
101
101
|
}
|
|
@@ -166,11 +166,21 @@ export function defaultOutputDir(inputPath) {
|
|
|
166
166
|
return path.join(path.dirname(inputPath), `${base}_csv`);
|
|
167
167
|
}
|
|
168
168
|
/** Never let an output target resolve to the recording being read, even with --force. */
|
|
169
|
-
async function assertInputDoesNotOverlapOutputs(inputPath, outputDir, file, plan) {
|
|
169
|
+
async function assertInputDoesNotOverlapOutputs(inputPath, outputDir, file, plan, options) {
|
|
170
|
+
/*
|
|
171
|
+
The names this run will actually write, compressed ones included.
|
|
172
|
+
|
|
173
|
+
The rate files come from the plan and already carry `.csv.gz` under --gzip; the sidecars
|
|
174
|
+
were spelled out here and did not. So a compressed run checked two names it would never
|
|
175
|
+
write and missed the two it would: a recording sitting at <outdir>/channels.csv.gz was
|
|
176
|
+
overwritten by its own conversion, with --force, reported as a success. The same file
|
|
177
|
+
named signals.csv.gz was refused, which is what gives the oversight away.
|
|
178
|
+
*/
|
|
179
|
+
const suffix = options.gzip === true ? '.csv.gz' : '.csv';
|
|
170
180
|
const names = new Set(plan.groups.map((group) => group.fileName));
|
|
171
181
|
if (file.annotationSignals.length > 0)
|
|
172
|
-
names.add(
|
|
173
|
-
names.add(
|
|
182
|
+
names.add(`annotations${suffix}`);
|
|
183
|
+
names.add(`channels${suffix}`);
|
|
174
184
|
names.add('metadata.json');
|
|
175
185
|
const inputResolved = path.resolve(inputPath);
|
|
176
186
|
const inputInfo = await stat(inputPath);
|
|
@@ -458,13 +468,21 @@ async function writeChannelsCsv(outputDir, file, plan, gzip) {
|
|
|
458
468
|
|
|
459
469
|
An end the caller did not give is unbounded, not "the end of the data": EDF+ lets an
|
|
460
470
|
annotation sit past the last sample, which is exactly where an end-of-recording marker is.
|
|
471
|
+
|
|
472
|
+
`--duration` is measured from wherever the conversion actually starts. Anchoring it at 0
|
|
473
|
+
instead read the same absent `--start` two ways in two adjacent lines, and on a recording
|
|
474
|
+
that does not begin at zero the two windows did not even overlap: an EDF+D file whose first
|
|
475
|
+
record sits at 30 s converted its samples from [30, 35) while filtering annotations against
|
|
476
|
+
(-inf, 5), so every event inside the converted window was dropped and `annotations.csv` came
|
|
477
|
+
back empty. `resolveRange` has always defaulted the same missing start to the earliest
|
|
478
|
+
record, which is where this now takes it from.
|
|
461
479
|
*/
|
|
462
|
-
function requestedAnnotationWindow(options) {
|
|
480
|
+
function requestedAnnotationWindow(options, recordingStart) {
|
|
463
481
|
const from = options.start ?? -Infinity;
|
|
464
482
|
const to = options.end !== undefined
|
|
465
483
|
? options.end
|
|
466
484
|
: options.duration !== undefined
|
|
467
|
-
? (options.start ??
|
|
485
|
+
? (options.start ?? recordingStart) + options.duration
|
|
468
486
|
: Infinity;
|
|
469
487
|
return { from, to };
|
|
470
488
|
}
|
package/dist/convert/run.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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|
package/dist/format/csv.d.ts.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"csv.d.ts","sourceRoot":"","sources":["../../src/format/csv.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAC;AAQ5C,6EAA6E;AAC7E,wBAAgB,cAAc,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAIpD;AAED,wBAAgB,MAAM,CAAC,KAAK,EAAE,SAAS,MAAM,EAAE,GAAG,MAAM,CAEvD;AAED;;;;;GAKG;AACH,qBAAa,kBAAkB;;gBAWjB,MAAM,EAAE,QAAQ,EAAE,SAAS,GAAE,MAAgC;IAwBzE,iFAAiF;IACjF,IAAI,MAAM,IAAI,OAAO,CAEpB;IAED,8EAA8E;IAC9E,IAAI,YAAY,IAAI,MAAM,CAEzB;IAED,IAAI,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI;IAKxB,QAAQ,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI;IAK5B,qEAAqE;IAC/D,UAAU,IAAI,OAAO,CAAC,IAAI,CAAC;IAI3B,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;IAoE5B,gDAAgD;IAC1C,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;
|
|
1
|
+
{"version":3,"file":"csv.d.ts","sourceRoot":"","sources":["../../src/format/csv.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAC;AAQ5C,6EAA6E;AAC7E,wBAAgB,cAAc,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAIpD;AAED,wBAAgB,MAAM,CAAC,KAAK,EAAE,SAAS,MAAM,EAAE,GAAG,MAAM,CAEvD;AAED;;;;;GAKG;AACH,qBAAa,kBAAkB;;gBAWjB,MAAM,EAAE,QAAQ,EAAE,SAAS,GAAE,MAAgC;IAwBzE,iFAAiF;IACjF,IAAI,MAAM,IAAI,OAAO,CAEpB;IAED,8EAA8E;IAC9E,IAAI,YAAY,IAAI,MAAM,CAEzB;IAED,IAAI,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI;IAKxB,QAAQ,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI;IAK5B,qEAAqE;IAC/D,UAAU,IAAI,OAAO,CAAC,IAAI,CAAC;IAI3B,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;IAoE5B,gDAAgD;IAC1C,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;IA6B1B,oEAAoE;IACpE,OAAO,IAAI,IAAI;CAOhB"}
|
package/dist/format/csv.js
CHANGED
|
@@ -154,6 +154,21 @@ export class BufferedLineWriter {
|
|
|
154
154
|
return;
|
|
155
155
|
this.#ended = true;
|
|
156
156
|
await this.flush();
|
|
157
|
+
/*
|
|
158
|
+
The reader is gone, so there is nothing to close and possibly nothing left to close it
|
|
159
|
+
on. Under --gzip this stream is the compressor, and the EPIPE forwarded from stdout
|
|
160
|
+
destroyed it — end() on a destroyed stream fails with ERR_STREAM_DESTROYED, which is
|
|
161
|
+
not EPIPE, so it escaped the hang-up guard and came back as a write failure:
|
|
162
|
+
|
|
163
|
+
edf2csv big.edf --stdout --gzip | head
|
|
164
|
+
error: Writing to stdout failed: Cannot call end after a stream was destroyed
|
|
165
|
+
|
|
166
|
+
Exactly the three symptoms 0.2.30 removed from the uncompressed path — exit 1 for a
|
|
167
|
+
routine shell idiom, a claim about files that were never written, and advice about disk
|
|
168
|
+
space — reappearing on the one path 0.3.1 said would behave identically.
|
|
169
|
+
*/
|
|
170
|
+
if (this.#hungUp)
|
|
171
|
+
return;
|
|
157
172
|
// stdout must not be closed; ending it would break piping for the rest of the process.
|
|
158
173
|
if (this.#stream === process.stdout || this.#stream === process.stderr)
|
|
159
174
|
return;
|
package/dist/format/csv.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
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|
package/package.json
CHANGED