npm - edf2csv - Versions diffs - 0.4.12 → 0.4.14 - Mend

edf2csv 0.4.12 → 0.4.14

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.

Files changed (9) hide show

package/CHANGELOG.md CHANGED Viewed

@@ -3,6 +3,82 @@
 Notable changes to edf2csv. Versions follow [semantic versioning](https://semver.org); while the
 major version is 0, a minor bump may contain breaking changes.
+## 0.4.14
+### Fixed: two recordings whose output directories nest produced a different result each run
+0.4.0 refuses a batch in which two recordings would land in the same directory. It compared
+destinations for equality, which misses the case where one contains the other:
+```
+study/
+  rec.edf         ->  out/rec
+  rec/inner.edf   ->  out/rec/inner
+```
+A recording named `rec.edf` sitting beside a folder named `rec` is enough, and that is a normal
+thing to find in a study folder. The two paths are not equal, so both went through.
+What happened next depended on which conversion got there first. Each claims its own directory
+with a single non-recursive mkdir — the atomic claim that stops two conversions sharing one
+`signals.csv` — but creates its parents recursively. So whichever started second either found
+the directory the other had already made as a parent, and failed:
+```
+error: study/rec.edf: "out/rec" already exists.
+Converted 1 of 2 recordings; 1 failed.
+```
+or did not, and both succeeded. Under `--jobs 2`, **five runs in twenty failed and fifteen
+succeeded** — the same command over the same files. Serially it always worked, because the
+expanded list is sorted and `rec.edf` happens to sort before `rec/inner.edf`.
+A destination inside another destination is now refused up front, with nothing written:
+```
+error: "study/rec/inner.edf" would be converted into "out/rec/inner", which is inside
+       "out/rec" — where "study/rec.edf" is converted.
+       One recording's output cannot sit inside another's. Convert them separately, or
+       rename one of them.
+```
+Only nesting is refused; recordings that merely share a parent are the ordinary case and are
+unaffected.
+Found by a fuzzer that builds random folder trees and requires a batch to produce the same
+files serially and in parallel — the two disagreed, which is what a race looks like from
+outside.
+## 0.4.13
+### Fixed: `--info` disagreed with the conversion on a recording that starts mid-second
+0.4.9 made a continuous recording take its origin from the first record's timekeeping TAL,
+which is where EDF+ says it is. `--info` went on placing a requested window against zero, so
+the two stopped agreeing about the same file:
+```
+edf2csv fractional-start.edf --info --start 1     Would write 8 rows
+edf2csv fractional-start.edf --out ./converted --start 1
+                                                  signals.csv   10  rows
+```
+The estimate exists so that someone can decide whether a conversion is worth starting, and it
+was off by a fifth on a file whose discontinuous twin — byte-identical apart from the reserved
+field — agreed with itself the whole time. Which is what made it findable: the two are supposed
+to give the same answer, and 0.4.9 tested exactly that for a whole-file conversion, but not for
+a windowed one.
+`--info` reads annotations only for discontinuous files, on purpose: an earlier version was
+fixed for scanning every record of a continuous one just to report a header summary, at 0.29 s
+on a 12 MB file. So this does not undo that. A continuous recording needs one number, and the
+reader now offers one read to get it — its first record's timekeeping TAL, rather than every
+record's. `--info` on an 18 MB, 30,000-record EDF+C still returns in 0.05 s.
+The test now compares the estimate against the rows actually written for both twins across five
+windows, rather than asserting a number either one happens to produce.
 ## 0.4.12
 ### Fixed: `--info` could print a duration that cannot exist

package/dist/cli.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"cli.d.ts","sourceRoot":"","sources":["../src/cli.ts"],"names":[],"mappings":";AACA;;;;;;;GAOG;AAeH,OAAO,EAA4B,gBAAgB,EAAE,MAAM,kBAAkB,CAAC;AAiH9E,wBAAsB,IAAI,CAAC,IAAI,EAAE,SAAS,MAAM,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC,CAmTnE;AAohBD,OAAO,EAAE,gBAAgB,EAAE,CAAC"}

package/dist/cli.js CHANGED Viewed

@@ -421,10 +421,24 @@ async function showInfo(input, shared, asJson, jsonIndent) {
           A discontinuous file still needs the scan: without it the reported span and row
           estimate are wrong, which is a bug that has already been fixed once here.
         */
-        const needsRecordStarts = file.header.continuity === 'EDF+D' && file.annotationSignals.length > 0;
-        const annotationData = needsRecordStarts
+        const hasAnnotations = file.annotationSignals.length > 0;
+        const needsEveryRecordStart = file.header.continuity === 'EDF+D' && hasAnnotations;
+        /*
+          A continuous recording needs its origin too, which is one read rather than one per
+          record: 0.4.9 made its first record's timekeeping TAL the point the samples are timed
+          from, and this report went on placing a requested window against zero. `--info --start 1`
+          predicted 8 rows where the conversion wrote 10, on a file whose discontinuous twin —
+          identical but for the reserved field — agreed with itself.
+        */
+        const annotationData = needsEveryRecordStart
             ? await file.readAnnotations()
-            : { annotations: [], recordStarts: [], malformed: 0 };
+            : {
+                annotations: [],
+                recordStarts: file.header.continuity === 'EDF+C' && hasAnnotations
+                    ? [await file.readFirstRecordStart()]
+                    : [],
+                malformed: 0,
+            };
         const timing = deriveRecordStarts(file, annotationData);
         const plan = buildPlan({
             signals: file.header.signals,
@@ -650,6 +664,34 @@ function assertDistinct(inputs, destinations) {
         }
         claimed.set(key, inputs[index]);
     }
+    /*
+      And refuse one destination sitting inside another.
+      A recording named `rec.edf` beside a folder named `rec` is enough: their outputs are
+      `<out>/rec` and `<out>/rec/inner`, which are not equal, so the check above let both
+      through. What happened next depended on which conversion got there first. Each creates
+      its own directory with a single non-recursive mkdir but its parents recursively, so
+      whichever started second either claimed a directory the other had already made as a
+      parent — failing with "already exists" — or did not. Five runs in twenty failed that way
+      under --jobs 2, converting one recording of two; the same command succeeded the other
+      fifteen times.
+      Sorting first puts an ancestor next to its descendant: anything sorting between them
+      shares the same prefix, and would be caught as its own adjacent pair.
+    */
+    const ordered = destinations
+        .map((destination, index) => ({ resolved: path.resolve(destination), destination, index }))
+        .sort((a, b) => (a.resolved < b.resolved ? -1 : a.resolved > b.resolved ? 1 : 0));
+    for (let i = 1; i < ordered.length; i++) {
+        const outer = ordered[i - 1];
+        const inner = ordered[i];
+        if (!inner.resolved.startsWith(outer.resolved + path.sep))
+            continue;
+        throw new OptionError(`"${inputs[inner.index]}" would be converted into "${inner.destination}", which is ` +
+            `inside "${outer.destination}" — where "${inputs[outer.index]}" is converted.\n` +
+            `One recording's output cannot sit inside another's. Convert them separately, or ` +
+            `rename one of them.`);
+    }
 }
 /**
  * The exit code for a run in which several files failed for different reasons.

package/dist/cli.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/edf/reader.d.ts CHANGED Viewed

@@ -65,6 +65,18 @@ export declare class EdfFile {
      * falls in, and some put every annotation in the first record. Reading only the
      * window's records would drop those entirely.
      */
+    /**
+     * Where the first data record starts, from its own timekeeping TAL.
+     *
+     * One record's worth of annotation bytes rather than the whole channel. A continuous
+     * recording's origin is the fraction of a second by which its first record follows the
+     * header's start time, and `--info` needs that to place a requested window — but it does
+     * not need the events, and finding one number by reading every record costs a seek per
+     * record across the whole file, which is the scan `--info` was deliberately spared.
+     *
+     * Returns null when there is nothing to read it from, in which case the origin is zero.
+     */
+    readFirstRecordStart(): Promise<number | null>;
     readAnnotations(): Promise<{
         annotations: Annotation[];
         recordStarts: (number | null)[];

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

	@@ -1 +1 @@
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package/dist/edf/reader.js CHANGED Viewed

@@ -171,6 +171,32 @@ export class EdfFile {
      * falls in, and some put every annotation in the first record. Reading only the
      * window's records would drop those entirely.
      */
+    /**
+     * Where the first data record starts, from its own timekeeping TAL.
+     *
+     * One record's worth of annotation bytes rather than the whole channel. A continuous
+     * recording's origin is the fraction of a second by which its first record follows the
+     * header's start time, and `--info` needs that to place a requested window — but it does
+     * not need the events, and finding one number by reading every record costs a seek per
+     * record across the whole file, which is the scan `--info` was deliberately spared.
+     *
+     * Returns null when there is nothing to read it from, in which case the origin is zero.
+     */
+    async readFirstRecordStart() {
+        this.#assertOpen();
+        const channel = this.annotationSignals[0];
+        if (!channel || this.recordCount === 0)
+            return null;
+        const { headerBytes, bytesPerSample } = this.header;
+        const buffer = Buffer.alloc(channel.samplesPerRecord * bytesPerSample);
+        if (buffer.length === 0)
+            return null;
+        const offset = headerBytes + channel.byteOffsetInRecord;
+        const bytesRead = await readFully(this.#handle, buffer, 0, buffer.length, offset);
+        if (bytesRead < buffer.length)
+            return null;
+        return decodeRecordAnnotations(buffer, 0).recordStart;
+    }
     async readAnnotations() {
         this.#assertOpen();
         const annotations = [];

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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "edf2csv",
-  "version": "0.4.12",
+  "version": "0.4.14",
   "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",