npm - edfcore - Versions diffs - 0.2.17 → 0.2.18 - Mend

edfcore 0.2.17 → 0.2.18

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Files changed (13) hide show

package/CHANGELOG.md CHANGED Viewed

@@ -6,6 +6,26 @@ alone does not tell you whether you were affected.
 edfcore is pre-1.0. Patch releases have carried behaviour changes where the old behaviour was a
 defect; those are called out below.
+## 0.2.18
+- **Fixed** `readTriggers` timing every event on the nominal grid — `sampleIndex * recordDuration /
+  samplesPerRecord` — instead of from its record's true onset. On an EDF+D file every event after a
+  gap was early by the whole gap: a stimulus the amplifier latched at 10 s was reported at 2 s, and
+  the same call was self-inconsistent, answering a request for `[10, 12)` with events labelled 2 s
+  and 3 s. `readWindow` on the identical records returned the correct onsets, so one file had two
+  timebases depending on which function you asked. This is the 0.1.4 defect in the one function
+  that never got the fix.
+- **Fixed** `readTriggers` returning events from outside the requested window, and — the worse
+  half — manufacturing an onset that is not in the file. The scan is record-aligned, and its
+  running trigger state reset at the record boundary rather than carrying across it, so a window
+  starting at 1.5 s reported a *transition* to a code that had been held since 1.0 s. In a file
+  whose only real transition was at 0.75 s, a window containing no transition at all returned a
+  stimulus onset. The error is up to one record duration, which is 30 s in many clinical files.
+- **Changed**, as a consequence: a windowed `readTriggers` now reports the code **in force** at the
+  window's left edge plus every transition inside it, and nothing outside it. That generalises the
+  rule a whole-file read already followed at `t = 0`, so an aligned and an unaligned window behave
+  alike. All eight existing BioSemi tests pass unmodified.
 ## 0.2.17
 - **Changed** the README's compatibility section to say what the browser claim now rests on. The

package/dist/biosemi.d.ts CHANGED Viewed

@@ -40,6 +40,24 @@ export declare function decodeStatusWord(sample: number): EdfStatusWord;
  * Code 0 is "no trigger asserted", so a return to 0 is reported as an event with `trigger: 0`
  * and is easy to filter out. It is reported rather than dropped because the release time is what
  * gives a trigger its duration.
+ *
+ * TIMES ARE ELAPSED RECORDING TIME, on the one axis the package uses: `t = 0` is the start of
+ * record 0, the same axis `selection.startSeconds`, `chunk.startSeconds` and `segment.startSeconds`
+ * live on. A sample's time is its own record's TRUE onset plus its offset within that record —
+ * never the record index times the record duration. The two agree on a contiguous file and diverge
+ * by the whole gap on an EDF+D one, where the nominal form reported a stimulus at 2 s that the
+ * hardware latched at 10 s (fixed in 0.2.18).
+ *
+ * THE WINDOW IS HONOURED. The scan is record-aligned, because records are the unit of I/O, but a
+ * sample outside `[startSeconds, startSeconds + durationSeconds)` is never reported — it only
+ * updates the running trigger state. Reporting the whole record would place events outside the
+ * window a caller asked for, and, worse, would let the first sample of a record report a
+ * "transition" to a code that was already held long before it.
+ *
+ * At the left edge this reports the code IN FORCE, not only transitions strictly inside: the first
+ * in-window sample always produces an event. That is the same rule a whole-file read already
+ * follows — `t = 0` yields an event for whatever the first sample holds, transition or not — so an
+ * aligned and an unaligned window behave alike. Filter on `trigger` if you only want assertions.
  */
 export declare function readTriggers(recording: EdfRecording, selection: TriggerSelection, options?: ReadOptions): Promise<readonly EdfTriggerEvent[]>;
 //# sourceMappingURL=biosemi.d.ts.map

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"biosemi.d.ts","sourceRoot":"","sources":["../src/biosemi.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAOH,OAAO,KAAK,EACV,SAAS,EACT,YAAY,EAEZ,SAAS,EACT,aAAa,EACb,eAAe,EACf,WAAW,EAEX,gBAAgB,EACjB,MAAM,YAAY,CAAC;AAWpB;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,MAAM,EAAE,SAAS,GAAG,SAAS,GAAG,SAAS,CAOxE;AAED;;;;;;GAMG;AACH,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,MAAM,GAAG,aAAa,CAS9D;AAqBD;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA4BG;AACH,wBAAsB,YAAY,CAChC,SAAS,EAAE,YAAY,EACvB,SAAS,EAAE,gBAAgB,EAC3B,OAAO,CAAC,EAAE,WAAW,GACpB,OAAO,CAAC,SAAS,eAAe,EAAE,CAAC,CAyFrC"}

package/dist/biosemi.js CHANGED Viewed

@@ -17,7 +17,7 @@
 import { decodeDigitalCounted } from './decode/digital.js';
 import { readRecordBytes } from './io/read.js';
 import { scanChunkRecords } from './record-index.js';
-import { ticksToSeconds } from './tal/ticks.js';
+import { secondsToTicks, ticksToSeconds } from './tal/ticks.js';
 import { resolveTimeWindow } from './time/window.js';
 /** BioSemi's own label for the channel. Matched case-insensitively after trimming. */
 const STATUS_LABEL = 'status';
@@ -59,6 +59,23 @@ export function decodeStatusWord(sample) {
         batteryLow: (raw & BATTERY_LOW_BIT) !== 0,
     };
 }
+/**
+ * The segment a record belongs to, or `undefined` when the index has not been scanned.
+ *
+ * `undefined` is not a failure: a probed index has no segments, and `resolveTimeWindow` has
+ * already refused one on any file whose span exceeds its coverage — so a caller who gets here
+ * without segments has a contiguous file, where the nominal grid IS the true one.
+ */
+function segmentContaining(segments, recordIndex) {
+    if (segments === undefined)
+        return undefined;
+    for (const segment of segments) {
+        const first = segment.records.start;
+        if (recordIndex >= first && recordIndex < first + segment.records.count)
+            return segment;
+    }
+    return undefined;
+}
 /**
  * Every change of the trigger word in a window, as timed events.
  *
@@ -69,6 +86,24 @@ export function decodeStatusWord(sample) {
  * Code 0 is "no trigger asserted", so a return to 0 is reported as an event with `trigger: 0`
  * and is easy to filter out. It is reported rather than dropped because the release time is what
  * gives a trigger its duration.
+ *
+ * TIMES ARE ELAPSED RECORDING TIME, on the one axis the package uses: `t = 0` is the start of
+ * record 0, the same axis `selection.startSeconds`, `chunk.startSeconds` and `segment.startSeconds`
+ * live on. A sample's time is its own record's TRUE onset plus its offset within that record —
+ * never the record index times the record duration. The two agree on a contiguous file and diverge
+ * by the whole gap on an EDF+D one, where the nominal form reported a stimulus at 2 s that the
+ * hardware latched at 10 s (fixed in 0.2.18).
+ *
+ * THE WINDOW IS HONOURED. The scan is record-aligned, because records are the unit of I/O, but a
+ * sample outside `[startSeconds, startSeconds + durationSeconds)` is never reported — it only
+ * updates the running trigger state. Reporting the whole record would place events outside the
+ * window a caller asked for, and, worse, would let the first sample of a record report a
+ * "transition" to a code that was already held long before it.
+ *
+ * At the left edge this reports the code IN FORCE, not only transitions strictly inside: the first
+ * in-window sample always produces an event. That is the same rule a whole-file read already
+ * follows — `t = 0` yields an event for whatever the first sample holds, transition or not — so an
+ * aligned and an unaligned window behave alike. Filter on `trigger` if you only want assertions.
  */
 export async function readTriggers(recording, selection, options) {
     const { source, header, timeline } = recording;
@@ -79,11 +114,21 @@ export async function readTriggers(recording, selection, options) {
             'annotations with readAnnotations().');
     }
     const ranges = resolveTimeWindow(timeline, recording.index, selection.startSeconds, selection.durationSeconds);
+    const windowStartTicks = secondsToTicks(selection.startSeconds);
+    const windowEndTicks = windowStartTicks + secondsToTicks(selection.durationSeconds);
+    const durationTicks = header.recordDurationTicks;
+    const samplesPerRecord = status.samplesPerRecord;
     const events = [];
-    // Carried across runs so a trigger held over a gap is not reported twice. `undefined` means
-    // nothing has been seen yet, which is what makes the very first sample an event.
+    // The last code SEEN, in the window or before it. Carried across runs so a trigger held over a
+    // gap is not reported twice, and updated for out-of-window samples too — that is what stops a
+    // code asserted before the window from being re-reported as a fresh onset inside it.
     let previous;
+    // Whether anything has been reported yet. The first in-window sample is always an event: it
+    // carries the code in force at the window's left edge, which a transitions-only rule would lose.
+    let reported = false;
     for (const records of ranges) {
+        // A range from `resolveTimeWindow` never spans a gap, so one segment covers all of it.
+        const segment = segmentContaining(recording.index.segments, records.start);
         const chunkRecords = scanChunkRecords(header, options?.maxMaterializeBytes);
         let scanned = 0;
         let scratch;
@@ -95,24 +140,35 @@ export async function readTriggers(recording, selection, options) {
             const bytes = await readRecordBytes(source, header, slice, options);
             const decoded = decodeDigitalCounted(header, bytes, slice, status.index, scratch, options);
             scratch = decoded.digital;
-            const sampleCount = status.samplesPerRecord * slice.count;
-            const firstSampleIndex = slice.start * status.samplesPerRecord;
-            for (let i = 0; i < sampleCount; i += 1) {
-                const word = decodeStatusWord(decoded.digital[i]);
-                if (previous !== undefined && word.trigger === previous)
-                    continue;
-                previous = word.trigger;
-                const sampleIndex = firstSampleIndex + i;
-                const ticks = header.recordDurationTicks > 0n && status.samplesPerRecord > 0
-                    ? (BigInt(sampleIndex) * header.recordDurationTicks) / BigInt(status.samplesPerRecord)
-                    : 0n;
-                events.push({
-                    sampleIndex,
-                    seconds: ticksToSeconds(ticks),
-                    ticks,
-                    trigger: word.trigger,
-                    status: word,
-                });
+            for (let r = 0; r < slice.count; r += 1) {
+                const recordIndex = slice.start + r;
+                // The record's own start on the recording's axis. From the segment when one has been
+                // scanned; from the nominal grid otherwise, which is exact for a contiguous file — and
+                // `resolveTimeWindow` has already refused a probed index on a file that is not.
+                const recordStartTicks = segment === undefined
+                    ? BigInt(recordIndex) * durationTicks
+                    : segment.startTicks + BigInt(recordIndex - segment.records.start) * durationTicks;
+                for (let s = 0; s < samplesPerRecord; s += 1) {
+                    const word = decodeStatusWord(decoded.digital[r * samplesPerRecord + s]);
+                    const changed = previous === undefined || word.trigger !== previous;
+                    previous = word.trigger;
+                    // A zero record duration puts every sample of the record at its start instant.
+                    const ticks = durationTicks > 0n && samplesPerRecord > 0
+                        ? recordStartTicks + (BigInt(s) * durationTicks) / BigInt(samplesPerRecord)
+                        : recordStartTicks;
+                    if (ticks < windowStartTicks || ticks >= windowEndTicks)
+                        continue;
+                    if (reported && !changed)
+                        continue;
+                    reported = true;
+                    events.push({
+                        sampleIndex: recordIndex * samplesPerRecord + s,
+                        seconds: ticksToSeconds(ticks),
+                        ticks,
+                        trigger: word.trigger,
+                        status: word,
+                    });
+                }
             }
             scanned += slice.count;
         }

package/dist/biosemi.js.map CHANGED Viewed

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

@@ -109,5 +109,5 @@ export declare const SIGNAL_FIELD_BLOCK_OFFSETS: {
     readonly reserved: 224;
 };
 /** Published package version. Kept in sync with package.json by a test. */
-export declare const VERSION = "0.2.17";
+export declare const VERSION = "0.2.18";
 //# sourceMappingURL=constants.d.ts.map

package/dist/constants.js CHANGED Viewed

@@ -79,5 +79,5 @@ export const SIGNAL_FIELD_BLOCK_OFFSETS = {
     reserved: 224,
 };
 /** Published package version. Kept in sync with package.json by a test. */
-export const VERSION = '0.2.17';
+export const VERSION = '0.2.18';
 //# sourceMappingURL=constants.js.map

package/dist/types.d.ts CHANGED Viewed

@@ -391,7 +391,16 @@ export interface EdfStatusWord {
     readonly cmsInRange: boolean;
     readonly batteryLow: boolean;
 }
-/** A change of the trigger word, timed on the Status channel's own sample grid. */
+/**
+ * A change of the trigger word, located on the Status channel's own sample grid and timed on the
+ * recording's axis.
+ *
+ * Those are two different things and the distinction is load-bearing. `sampleIndex` counts samples
+ * of the Status channel from the start of the file. `seconds`/`ticks` are elapsed recording time —
+ * `t = 0` is the start of record 0 — derived from the containing record's TRUE onset, so on an
+ * EDF+D file the gaps are in them. Deriving the time from `sampleIndex` instead would place every
+ * post-gap event early by the whole gap.
+ */
 export interface EdfTriggerEvent {
     readonly sampleIndex: number;
     readonly seconds: number;

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

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

@@ -1,6 +1,6 @@
 {
   "name": "edfcore",
-  "version": "0.2.17",
+  "version": "0.2.18",
   "description": "Modern, typed, zero-dependency reader for EDF, EDF+, BDF and BDF+ biosignal files. Works in browsers and Node with true random access.",
   "keywords": [
     "edf",

package/src/biosemi.ts CHANGED Viewed

@@ -18,11 +18,12 @@
 import { decodeDigitalCounted } from './decode/digital.js';
 import { readRecordBytes } from './io/read.js';
 import { scanChunkRecords } from './record-index.js';
-import { ticksToSeconds } from './tal/ticks.js';
+import { secondsToTicks, ticksToSeconds } from './tal/ticks.js';
 import { resolveTimeWindow } from './time/window.js';
 import type {
   EdfHeader,
   EdfRecording,
+  EdfSegment,
   EdfSignal,
   EdfStatusWord,
   EdfTriggerEvent,
@@ -73,6 +74,25 @@ export function decodeStatusWord(sample: number): EdfStatusWord {
   };
 }
+/**
+ * The segment a record belongs to, or `undefined` when the index has not been scanned.
+ *
+ * `undefined` is not a failure: a probed index has no segments, and `resolveTimeWindow` has
+ * already refused one on any file whose span exceeds its coverage — so a caller who gets here
+ * without segments has a contiguous file, where the nominal grid IS the true one.
+ */
+function segmentContaining(
+  segments: readonly EdfSegment[] | undefined,
+  recordIndex: number,
+): EdfSegment | undefined {
+  if (segments === undefined) return undefined;
+  for (const segment of segments) {
+    const first = segment.records.start;
+    if (recordIndex >= first && recordIndex < first + segment.records.count) return segment;
+  }
+  return undefined;
+}
 /**
  * Every change of the trigger word in a window, as timed events.
  *
@@ -83,6 +103,24 @@ export function decodeStatusWord(sample: number): EdfStatusWord {
  * Code 0 is "no trigger asserted", so a return to 0 is reported as an event with `trigger: 0`
  * and is easy to filter out. It is reported rather than dropped because the release time is what
  * gives a trigger its duration.
+ *
+ * TIMES ARE ELAPSED RECORDING TIME, on the one axis the package uses: `t = 0` is the start of
+ * record 0, the same axis `selection.startSeconds`, `chunk.startSeconds` and `segment.startSeconds`
+ * live on. A sample's time is its own record's TRUE onset plus its offset within that record —
+ * never the record index times the record duration. The two agree on a contiguous file and diverge
+ * by the whole gap on an EDF+D one, where the nominal form reported a stimulus at 2 s that the
+ * hardware latched at 10 s (fixed in 0.2.18).
+ *
+ * THE WINDOW IS HONOURED. The scan is record-aligned, because records are the unit of I/O, but a
+ * sample outside `[startSeconds, startSeconds + durationSeconds)` is never reported — it only
+ * updates the running trigger state. Reporting the whole record would place events outside the
+ * window a caller asked for, and, worse, would let the first sample of a record report a
+ * "transition" to a code that was already held long before it.
+ *
+ * At the left edge this reports the code IN FORCE, not only transitions strictly inside: the first
+ * in-window sample always produces an event. That is the same rule a whole-file read already
+ * follows — `t = 0` yields an event for whatever the first sample holds, transition or not — so an
+ * aligned and an unaligned window behave alike. Filter on `trigger` if you only want assertions.
  */
 export async function readTriggers(
   recording: EdfRecording,
@@ -107,12 +145,23 @@ export async function readTriggers(
     selection.durationSeconds,
   );
+  const windowStartTicks = secondsToTicks(selection.startSeconds);
+  const windowEndTicks = windowStartTicks + secondsToTicks(selection.durationSeconds);
+  const durationTicks = header.recordDurationTicks;
+  const samplesPerRecord = status.samplesPerRecord;
   const events: EdfTriggerEvent[] = [];
-  // Carried across runs so a trigger held over a gap is not reported twice. `undefined` means
-  // nothing has been seen yet, which is what makes the very first sample an event.
+  // The last code SEEN, in the window or before it. Carried across runs so a trigger held over a
+  // gap is not reported twice, and updated for out-of-window samples too — that is what stops a
+  // code asserted before the window from being re-reported as a fresh onset inside it.
   let previous: number | undefined;
+  // Whether anything has been reported yet. The first in-window sample is always an event: it
+  // carries the code in force at the window's left edge, which a transitions-only rule would lose.
+  let reported = false;
   for (const records of ranges) {
+    // A range from `resolveTimeWindow` never spans a gap, so one segment covers all of it.
+    const segment = segmentContaining(recording.index.segments, records.start);
     const chunkRecords = scanChunkRecords(header, options?.maxMaterializeBytes);
     let scanned = 0;
     let scratch: Int32Array | undefined;
@@ -126,26 +175,39 @@ export async function readTriggers(
       const decoded = decodeDigitalCounted(header, bytes, slice, status.index, scratch, options);
       scratch = decoded.digital;
-      const sampleCount = status.samplesPerRecord * slice.count;
-      const firstSampleIndex = slice.start * status.samplesPerRecord;
-      for (let i = 0; i < sampleCount; i += 1) {
-        const word = decodeStatusWord(decoded.digital[i] as number);
-        if (previous !== undefined && word.trigger === previous) continue;
-        previous = word.trigger;
-        const sampleIndex = firstSampleIndex + i;
-        const ticks =
-          header.recordDurationTicks > 0n && status.samplesPerRecord > 0
-            ? (BigInt(sampleIndex) * header.recordDurationTicks) / BigInt(status.samplesPerRecord)
-            : 0n;
-        events.push({
-          sampleIndex,
-          seconds: ticksToSeconds(ticks),
-          ticks,
-          trigger: word.trigger,
-          status: word,
-        });
+      for (let r = 0; r < slice.count; r += 1) {
+        const recordIndex = slice.start + r;
+        // The record's own start on the recording's axis. From the segment when one has been
+        // scanned; from the nominal grid otherwise, which is exact for a contiguous file — and
+        // `resolveTimeWindow` has already refused a probed index on a file that is not.
+        const recordStartTicks =
+          segment === undefined
+            ? BigInt(recordIndex) * durationTicks
+            : segment.startTicks + BigInt(recordIndex - segment.records.start) * durationTicks;
+        for (let s = 0; s < samplesPerRecord; s += 1) {
+          const word = decodeStatusWord(decoded.digital[r * samplesPerRecord + s] as number);
+          const changed = previous === undefined || word.trigger !== previous;
+          previous = word.trigger;
+          // A zero record duration puts every sample of the record at its start instant.
+          const ticks =
+            durationTicks > 0n && samplesPerRecord > 0
+              ? recordStartTicks + (BigInt(s) * durationTicks) / BigInt(samplesPerRecord)
+              : recordStartTicks;
+          if (ticks < windowStartTicks || ticks >= windowEndTicks) continue;
+          if (reported && !changed) continue;
+          reported = true;
+          events.push({
+            sampleIndex: recordIndex * samplesPerRecord + s,
+            seconds: ticksToSeconds(ticks),
+            ticks,
+            trigger: word.trigger,
+            status: word,
+          });
+        }
       }
       scanned += slice.count;

package/src/constants.ts CHANGED Viewed

@@ -93,4 +93,4 @@ export const SIGNAL_FIELD_BLOCK_OFFSETS = {
 } as const;
 /** Published package version. Kept in sync with package.json by a test. */
-export const VERSION = '0.2.17';
+export const VERSION = '0.2.18';

package/src/types.ts CHANGED Viewed

@@ -461,7 +461,16 @@ export interface EdfStatusWord {
   readonly batteryLow: boolean;
 }
-/** A change of the trigger word, timed on the Status channel's own sample grid. */
+/**
+ * A change of the trigger word, located on the Status channel's own sample grid and timed on the
+ * recording's axis.
+ *
+ * Those are two different things and the distinction is load-bearing. `sampleIndex` counts samples
+ * of the Status channel from the start of the file. `seconds`/`ticks` are elapsed recording time —
+ * `t = 0` is the start of record 0 — derived from the containing record's TRUE onset, so on an
+ * EDF+D file the gaps are in them. Deriving the time from `sampleIndex` instead would place every
+ * post-gap event early by the whole gap.
+ */
 export interface EdfTriggerEvent {
   readonly sampleIndex: number;
   readonly seconds: number;