npm - edfcore - Versions diffs - 0.2.28 → 0.2.31 - Mend

edfcore 0.2.28 → 0.2.31

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 (14) hide show

package/CHANGELOG.md CHANGED Viewed

@@ -6,6 +6,42 @@ 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.
+## 0.2.31
+- **Fixed** `readEnvelopeAtResolution` not delivering the resolution it was asked for. A chunk
+  covers one record-aligned contiguous run, and a run is not the window, but one bucket count was
+  computed from the window and handed to every chunk. A window of 11 s over an EDF+D file asked at
+  1 s per bucket came back as 0.27 s per bucket in one chunk and 0.09 s in the other — widths that
+  are not commensurable, so a viewer could not place the two on one axis, which is the entire
+  promise of the function. A contiguous window that did not start on a record boundary got 1.33 s
+  per bucket for the same reason. The count is now derived from each run's own span; the ceil rule
+  is unchanged, so the tail of a window is still never dropped.
+### A note on version numbers
+`0.2.29` was never released: a failed release run consumed the number before the tag was cut.
+`0.2.26` has a git tag and a GitHub release but is **not on npm** — GitHub Actions was dropping
+events and failing to acquire runners while these went out, and by the time 0.2.26 was retried npm
+refused to tag it `latest` because 0.2.28 was already above it. Everything 0.2.26 fixed, including
+the patient-identification leak, is present in 0.2.27 and every release after it; that was verified
+against the published 0.2.27 tarball rather than assumed.
+## 0.2.30
+- **Fixed** `validateRecording({ scanSamples: true })` refusing a small file for a scratch buffer
+  it could never fill. The buffer was sized from `chunkRecords` — a chunk size chosen from the
+  record geometry, not from the file's length — so a four-record file was budgeted for a full
+  chunk, and a 552-byte one demanded 8 MB and was refused under any budget below 8 MiB. That is
+  the opposite of the failure the guard exists for. It is now clamped to the records that exist.
+- **Changed**, as a consequence, what 0.1.3's fixture does. That file declares zero records and a
+  `samplesPerRecord` of 99,999,999, and 0.1.3 fixed the resulting 400 MB allocation by REFUSING
+  it. With the clamp the allocation is never demanded, so there is nothing to refuse and the scan
+  simply reports zero records scanned. The invariant is unchanged and stronger — a 512-byte file
+  still never causes a large allocation — but it is now enforced by not allocating rather than by
+  throwing, so the two tests that pinned the budget error now pin success. A new case pins the
+  refusal for a file whose records really do exist and really are too big, so the guard is still
+  covered.
 ## 0.2.28
 - **Fixed** `readAnnotations` answering on the header's axis for any record range that does not

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 = "0.2.28";
+export declare const VERSION = "0.2.31";
 //# 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 = '0.2.28';
+export const VERSION = '0.2.31';
 //# sourceMappingURL=constants.js.map

package/dist/envelope.d.ts CHANGED Viewed

@@ -60,6 +60,15 @@ export declare function envelopeOfSamples(chunkSignal: EdfChunkSignal, buckets:
  * which is what a fixed-scale view wants — 30 s per bucket for a sleep hypnogram, whatever the
  * window length. Deriving one from the other by hand means dividing and rounding, and rounding
  * the wrong way produces a final bucket covering a sliver of time that reads as a dropout.
+ *
+ * The bucket count is computed PER RUN, from that run's own span, not once from the window. A
+ * chunk covers one record-aligned contiguous run, and a run is not the window: an EDF+D window
+ * spanning a gap produces two runs of different lengths, and even a contiguous window that does
+ * not start on a record boundary produces a run wider than it asked for. Handing one bucket count
+ * to every chunk therefore delivered a different resolution in each — a window of 11 s asked at
+ * 1 s per bucket came back as 0.27 s per bucket in one chunk and 0.09 s in the other, which are
+ * not commensurable, so a viewer cannot place the two on one axis. That is the whole promise of
+ * this function, so it is computed where the run's length is known (fixed in 0.2.31).
  */
 export declare function readEnvelopeAtResolution(recording: EdfRecording, selection: {
     readonly signalIndices: readonly number[];

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

	@@ -1 +1 @@
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package/dist/envelope.js CHANGED Viewed

@@ -293,6 +293,15 @@ export function envelopeOfSamples(chunkSignal, buckets) {
  * which is what a fixed-scale view wants — 30 s per bucket for a sleep hypnogram, whatever the
  * window length. Deriving one from the other by hand means dividing and rounding, and rounding
  * the wrong way produces a final bucket covering a sliver of time that reads as a dropout.
+ *
+ * The bucket count is computed PER RUN, from that run's own span, not once from the window. A
+ * chunk covers one record-aligned contiguous run, and a run is not the window: an EDF+D window
+ * spanning a gap produces two runs of different lengths, and even a contiguous window that does
+ * not start on a record boundary produces a run wider than it asked for. Handing one bucket count
+ * to every chunk therefore delivered a different resolution in each — a window of 11 s asked at
+ * 1 s per bucket came back as 0.27 s per bucket in one chunk and 0.09 s in the other, which are
+ * not commensurable, so a viewer cannot place the two on one axis. That is the whole promise of
+ * this function, so it is computed where the run's length is known (fixed in 0.2.31).
  */
 export async function readEnvelopeAtResolution(recording, selection, options) {
     const { secondsPerBucket } = selection;
@@ -300,14 +309,29 @@ export async function readEnvelopeAtResolution(recording, selection, options) {
         throw new RangeError(`readEnvelopeAtResolution(): secondsPerBucket must be a positive finite number, received ` +
             `${secondsPerBucket}.`);
     }
-    // Ceil, not round: a window of 100 s at 30 s per bucket needs four buckets, not three. Three
-    // would silently drop the last 10 s off the end of the picture.
-    const buckets = Math.max(1, Math.ceil(selection.durationSeconds / secondsPerBucket));
-    return readEnvelope(recording, {
-        signalIndices: selection.signalIndices,
-        startSeconds: selection.startSeconds,
-        durationSeconds: selection.durationSeconds,
-        buckets,
-    }, options);
+    // Validated before the window is resolved, exactly as `readEnvelope` does it and for the same
+    // reason: a bad signalIndices must not read back as an empty stretch of recording.
+    resolveEnvelopeSignals(recording.header, selection.signalIndices);
+    // Resolved here, rather than inside `readEnvelope`, so each run's own span is known before its
+    // bucket count is chosen.
+    const ranges = resolveTimeWindow(recording.timeline, recording.index, selection.startSeconds, selection.durationSeconds);
+    const recordSeconds = recording.header.recordDurationSeconds;
+    const chunks = [];
+    for (const records of ranges) {
+        // A run's span is exactly its record count times the record duration: records within one run
+        // are contiguous by construction. A zero record duration is legal EDF and leaves no time axis
+        // at all, so one bucket is the only honest answer for it.
+        const runSeconds = records.count * recordSeconds;
+        // Ceil, not round: 100 s at 30 s per bucket needs four buckets, not three. Three would
+        // silently drop the last 10 s off the end of the picture.
+        const buckets = runSeconds > 0 ? Math.max(1, Math.ceil(runSeconds / secondsPerBucket)) : 1;
+        chunks.push(await reduceRange(recording, records, {
+            signalIndices: selection.signalIndices,
+            startSeconds: selection.startSeconds,
+            durationSeconds: selection.durationSeconds,
+            buckets,
+        }, options));
+    }
+    return Object.freeze(chunks);
 }
 //# sourceMappingURL=envelope.js.map

package/dist/envelope.js.map CHANGED Viewed

	@@ -1 +1 @@
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	@@ -1 +1 @@
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1	+ {"version":3,"file":"validate.d.ts","sourceRoot":"","sources":["../src/validate.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAcH,OAAO,KAAK,EAEV,aAAa,EAEb,SAAS,EAET,YAAY,EAIZ,eAAe,EACf,gBAAgB,EACjB,MAAM,YAAY,CAAC;AAEpB,OAAO,EAAE,sBAAsB,EAAE,MAAM,oBAAoB,CAAC;AAC5D;;;;;;GAMG;AACH,YAAY,EACV,mBAAmB,EACnB,mBAAmB,EACnB,eAAe,EACf,gBAAgB,GACjB,MAAM,YAAY,CAAC;AAiSpB;;;;;GAKG;AACH,wBAAgB,cAAc,CAAC,MAAM,EAAE,SAAS,GAAG,SAAS,aAAa,EAAE,CAe1E;AAsND;;;;;;;;;;;;;;;GAeG;AACH,wBAAsB,iBAAiB,CACrC,SAAS,EAAE,YAAY,EACvB,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,gBAAgB,CAAC,CA+C3B"}

package/dist/validate.js CHANGED Viewed

@@ -395,16 +395,22 @@ async function traverse(recording, options, scanSamples) {
                 maxSamplesPerRecord = Math.max(maxSamplesPerRecord, signal.samplesPerRecord);
             }
         }
-        const scratchBytes = chunkRecords * maxSamplesPerRecord * BYTES_PER_SCRATCH_SAMPLE;
+        // Clamped to the records that EXIST. `chunkRecords` is a chunk size, chosen from the record
+        // geometry and not from the file's length, so on a short file it is larger than the whole
+        // recording — a 4-record file was budgeted and allocated for a full chunk it can never fill,
+        // and a 552-byte file was refused under any budget below 8 MiB. That is the opposite of the
+        // failure this guard exists for: refusing a read that is genuinely small.
+        const scratchRecords = Math.min(chunkRecords, Math.max(0, header.recordCount));
+        const scratchBytes = scratchRecords * maxSamplesPerRecord * BYTES_PER_SCRATCH_SAMPLE;
         const budgetBytes = options?.maxMaterializeBytes ?? DEFAULT_MAX_MATERIALIZE_BYTES;
         if (scratchBytes > budgetBytes) {
-            throw new EdfBudgetError(`Scanning samples needs a ${scratchBytes}-byte scratch buffer for ${chunkRecords} ` +
+            throw new EdfBudgetError(`Scanning samples needs a ${scratchBytes}-byte scratch buffer for ${scratchRecords} ` +
                 `record(s) of up to ${maxSamplesPerRecord} samples, above the ${budgetBytes}-byte ` +
                 'maxMaterializeBytes budget, so the scan was refused before anything was allocated. ' +
                 'Next: raise options.maxMaterializeBytes, or drop scanSamples and validate the ' +
                 'header alone.', { requiredBytes: scratchBytes, budgetBytes });
         }
-        scratch = new Int32Array(chunkRecords * maxSamplesPerRecord);
+        scratch = new Int32Array(scratchRecords * maxSamplesPerRecord);
     }
     let recordsScanned = 0;
     let bytesRead = 0;

package/dist/validate.js.map CHANGED Viewed

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

@@ -1,6 +1,6 @@
 {
   "name": "edfcore",
-  "version": "0.2.28",
+  "version": "0.2.31",
   "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/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 = '0.2.28';
+export const VERSION = '0.2.31';

package/src/envelope.ts CHANGED Viewed

@@ -387,6 +387,15 @@ export function envelopeOfSamples(chunkSignal: EdfChunkSignal, buckets: number):
  * which is what a fixed-scale view wants — 30 s per bucket for a sleep hypnogram, whatever the
  * window length. Deriving one from the other by hand means dividing and rounding, and rounding
  * the wrong way produces a final bucket covering a sliver of time that reads as a dropout.
+ *
+ * The bucket count is computed PER RUN, from that run's own span, not once from the window. A
+ * chunk covers one record-aligned contiguous run, and a run is not the window: an EDF+D window
+ * spanning a gap produces two runs of different lengths, and even a contiguous window that does
+ * not start on a record boundary produces a run wider than it asked for. Handing one bucket count
+ * to every chunk therefore delivered a different resolution in each — a window of 11 s asked at
+ * 1 s per bucket came back as 0.27 s per bucket in one chunk and 0.09 s in the other, which are
+ * not commensurable, so a viewer cannot place the two on one axis. That is the whole promise of
+ * this function, so it is computed where the run's length is known (fixed in 0.2.31).
  */
 export async function readEnvelopeAtResolution(
   recording: EdfRecording,
@@ -405,17 +414,42 @@ export async function readEnvelopeAtResolution(
         `${secondsPerBucket}.`,
     );
   }
-  // Ceil, not round: a window of 100 s at 30 s per bucket needs four buckets, not three. Three
-  // would silently drop the last 10 s off the end of the picture.
-  const buckets = Math.max(1, Math.ceil(selection.durationSeconds / secondsPerBucket));
-  return readEnvelope(
-    recording,
-    {
-      signalIndices: selection.signalIndices,
-      startSeconds: selection.startSeconds,
-      durationSeconds: selection.durationSeconds,
-      buckets,
-    },
-    options,
+  // Validated before the window is resolved, exactly as `readEnvelope` does it and for the same
+  // reason: a bad signalIndices must not read back as an empty stretch of recording.
+  resolveEnvelopeSignals(recording.header, selection.signalIndices);
+  // Resolved here, rather than inside `readEnvelope`, so each run's own span is known before its
+  // bucket count is chosen.
+  const ranges = resolveTimeWindow(
+    recording.timeline,
+    recording.index,
+    selection.startSeconds,
+    selection.durationSeconds,
   );
+  const recordSeconds = recording.header.recordDurationSeconds;
+  const chunks: EdfEnvelopeChunk[] = [];
+  for (const records of ranges) {
+    // A run's span is exactly its record count times the record duration: records within one run
+    // are contiguous by construction. A zero record duration is legal EDF and leaves no time axis
+    // at all, so one bucket is the only honest answer for it.
+    const runSeconds = records.count * recordSeconds;
+    // Ceil, not round: 100 s at 30 s per bucket needs four buckets, not three. Three would
+    // silently drop the last 10 s off the end of the picture.
+    const buckets = runSeconds > 0 ? Math.max(1, Math.ceil(runSeconds / secondsPerBucket)) : 1;
+    chunks.push(
+      await reduceRange(
+        recording,
+        records,
+        {
+          signalIndices: selection.signalIndices,
+          startSeconds: selection.startSeconds,
+          durationSeconds: selection.durationSeconds,
+          buckets,
+        },
+        options,
+      ),
+    );
+  }
+  return Object.freeze(chunks);
 }

package/src/validate.ts CHANGED Viewed

@@ -509,11 +509,17 @@ async function traverse(
         maxSamplesPerRecord = Math.max(maxSamplesPerRecord, signal.samplesPerRecord);
       }
     }
-    const scratchBytes = chunkRecords * maxSamplesPerRecord * BYTES_PER_SCRATCH_SAMPLE;
+    // Clamped to the records that EXIST. `chunkRecords` is a chunk size, chosen from the record
+    // geometry and not from the file's length, so on a short file it is larger than the whole
+    // recording — a 4-record file was budgeted and allocated for a full chunk it can never fill,
+    // and a 552-byte file was refused under any budget below 8 MiB. That is the opposite of the
+    // failure this guard exists for: refusing a read that is genuinely small.
+    const scratchRecords = Math.min(chunkRecords, Math.max(0, header.recordCount));
+    const scratchBytes = scratchRecords * maxSamplesPerRecord * BYTES_PER_SCRATCH_SAMPLE;
     const budgetBytes = options?.maxMaterializeBytes ?? DEFAULT_MAX_MATERIALIZE_BYTES;
     if (scratchBytes > budgetBytes) {
       throw new EdfBudgetError(
-        `Scanning samples needs a ${scratchBytes}-byte scratch buffer for ${chunkRecords} ` +
+        `Scanning samples needs a ${scratchBytes}-byte scratch buffer for ${scratchRecords} ` +
           `record(s) of up to ${maxSamplesPerRecord} samples, above the ${budgetBytes}-byte ` +
           'maxMaterializeBytes budget, so the scan was refused before anything was allocated. ' +
           'Next: raise options.maxMaterializeBytes, or drop scanSamples and validate the ' +
@@ -521,7 +527,7 @@ async function traverse(
         { requiredBytes: scratchBytes, budgetBytes },
       );
     }
-    scratch = new Int32Array(chunkRecords * maxSamplesPerRecord);
+    scratch = new Int32Array(scratchRecords * maxSamplesPerRecord);
   }
   let recordsScanned = 0;