seqeyes-python 0.2.11__tar.gz → 0.2.13__tar.gz

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 (20) hide show
  1. {seqeyes_python-0.2.11 → seqeyes_python-0.2.13}/PKG-INFO +2 -2
  2. {seqeyes_python-0.2.11 → seqeyes_python-0.2.13}/pyproject.toml +1 -1
  3. {seqeyes_python-0.2.11 → seqeyes_python-0.2.13}/src/seqeyes/__init__.py +1 -1
  4. {seqeyes_python-0.2.11 → seqeyes_python-0.2.13}/src/seqeyes/resources/pulseq-bundle.js +125 -76
  5. {seqeyes_python-0.2.11 → seqeyes_python-0.2.13}/src/seqeyes/resources/webview-bundle.js +95 -10
  6. {seqeyes_python-0.2.11 → seqeyes_python-0.2.13}/.gitignore +0 -0
  7. {seqeyes_python-0.2.11 → seqeyes_python-0.2.13}/README.md +0 -0
  8. {seqeyes_python-0.2.11 → seqeyes_python-0.2.13}/examples/demo.ipynb +0 -0
  9. {seqeyes_python-0.2.11 → seqeyes_python-0.2.13}/examples/demo.py +0 -0
  10. {seqeyes_python-0.2.11 → seqeyes_python-0.2.13}/src/seqeyes/_plot.py +0 -0
  11. {seqeyes_python-0.2.11 → seqeyes_python-0.2.13}/src/seqeyes/_renderer.py +0 -0
  12. {seqeyes_python-0.2.11 → seqeyes_python-0.2.13}/src/seqeyes/resources/viewer.html +0 -0
  13. {seqeyes_python-0.2.11 → seqeyes_python-0.2.13}/tests/conftest.py +0 -0
  14. {seqeyes_python-0.2.11 → seqeyes_python-0.2.13}/tests/debug_full.html +0 -0
  15. {seqeyes_python-0.2.11 → seqeyes_python-0.2.13}/tests/debug_minimal.html +0 -0
  16. {seqeyes_python-0.2.11 → seqeyes_python-0.2.13}/tests/debug_viewer.html +0 -0
  17. {seqeyes_python-0.2.11 → seqeyes_python-0.2.13}/tests/debug_viewer.py +0 -0
  18. {seqeyes_python-0.2.11 → seqeyes_python-0.2.13}/tests/integration_test.py +0 -0
  19. {seqeyes_python-0.2.11 → seqeyes_python-0.2.13}/tests/test_plot.py +0 -0
  20. {seqeyes_python-0.2.11 → seqeyes_python-0.2.13}/tests/test_renderer.py +0 -0
@@ -1,6 +1,6 @@
1
- Metadata-Version: 2.4
1
+ Metadata-Version: 2.5
2
2
  Name: seqeyes-python
3
- Version: 0.2.11
3
+ Version: 0.2.13
4
4
  Summary: Interactive Pulseq MRI sequence viewer for Jupyter — lightweight, beautiful, replaces seq.plot() in pypulseq.
5
5
  Project-URL: Homepage, https://github.com/bughht/seqeyes_plugin
6
6
  Project-URL: Repository, https://github.com/bughht/seqeyes_plugin
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
4
4
 
5
5
  [project]
6
6
  name = "seqeyes-python"
7
- version = "0.2.11"
7
+ version = "0.2.13"
8
8
  description = "Interactive Pulseq MRI sequence viewer for Jupyter — lightweight, beautiful, replaces seq.plot() in pypulseq."
9
9
  readme = "README.md"
10
10
  license = {text = "MIT"}
@@ -29,4 +29,4 @@ from seqeyes._plot import set, reset
29
29
  from seqeyes._renderer import SeqEyesViewer
30
30
 
31
31
  __all__ = ["set", "reset", "SeqEyesViewer"]
32
- __version__ = "0.2.11"
32
+ __version__ = "0.2.13"
@@ -31,6 +31,7 @@ var Pulseq = (() => {
31
31
  calculatePns: () => calculatePns,
32
32
  calculatePnsCoarse: () => calculatePnsCoarse,
33
33
  decodeAllBlocks: () => decodeAllBlocks,
34
+ derivedDetailViewLimitSec: () => derivedDetailViewLimitSec,
34
35
  detectSequenceTiming: () => detectSequenceTiming,
35
36
  estimateDerivedCost: () => estimateDerivedCost,
36
37
  estimateKspaceCost: () => estimateKspaceCost,
@@ -53,7 +54,7 @@ var Pulseq = (() => {
53
54
  });
54
55
 
55
56
  // package.json
56
- var version = "0.2.11";
57
+ var version = "0.2.13";
57
58
 
58
59
  // src/pulseq/decompressor.ts
59
60
  function decompressShape(compressed, numSamples) {
@@ -1403,21 +1404,112 @@ var Pulseq = (() => {
1403
1404
  return parseSequenceText(text);
1404
1405
  }
1405
1406
 
1406
- // src/pulseq/decoder.ts
1407
+ // src/pulseq/rfClassification.ts
1407
1408
  var GAMMA_HZ_T = 42576e3;
1408
1409
  var DEFAULT_B0_T = 3;
1410
+ var sequenceUseCache = /* @__PURE__ */ new WeakMap();
1411
+ function classifyRfUse(rf, seq) {
1412
+ if (seq.versionCombined >= VER_V15 && rf.use && rf.use.toLowerCase() !== "u") {
1413
+ return rf.use.toLowerCase();
1414
+ }
1415
+ const flipAngleDeg = estimateRfFlipAngleDeg(rf, seq);
1416
+ if (isLegacyFatSaturation(rf, seq)) return "s";
1417
+ return flipAngleDeg >= 120 ? "r" : "e";
1418
+ }
1419
+ function classifyRfUses(seq) {
1420
+ const cachedUses = sequenceUseCache.get(seq);
1421
+ if (cachedUses) return cachedUses;
1422
+ const libraryUses = /* @__PURE__ */ new Map();
1423
+ const uses = seq.blocks.map((block) => {
1424
+ if (block.rfId <= 0) return "";
1425
+ const cached = libraryUses.get(block.rfId);
1426
+ if (cached !== void 0) return cached;
1427
+ const rf = seq.rfs.get(block.rfId);
1428
+ const use = rf ? classifyRfUse(rf, seq) : "";
1429
+ libraryUses.set(block.rfId, use);
1430
+ return use;
1431
+ });
1432
+ if (seq.versionCombined >= VER_V15 || uses.includes("e")) {
1433
+ sequenceUseCache.set(seq, uses);
1434
+ return uses;
1435
+ }
1436
+ const saturationBlocks = uses.map((use, index) => use === "s" ? index : -1).filter((index) => index >= 0);
1437
+ if (saturationBlocks.length < 2) {
1438
+ sequenceUseCache.set(seq, uses);
1439
+ return uses;
1440
+ }
1441
+ for (let anchor = 0; anchor < saturationBlocks.length; anchor++) {
1442
+ const start = saturationBlocks[anchor] + 1;
1443
+ const end = saturationBlocks[anchor + 1] ?? uses.length;
1444
+ for (let index = start; index < end; index++) {
1445
+ if (!uses[index] || uses[index] === "s") continue;
1446
+ uses[index] = "e";
1447
+ break;
1448
+ }
1449
+ }
1450
+ sequenceUseCache.set(seq, uses);
1451
+ return uses;
1452
+ }
1453
+ function estimateRfFlipAngleDeg(rf, seq) {
1454
+ const magShape = seq.shapes.get(rf.magShapeId);
1455
+ if (magShape && magShape.numSamples > 0) {
1456
+ const raster = seq.rasterTimes.rfRaster;
1457
+ const timeShape = rf.timeShapeId > 0 ? seq.shapes.get(rf.timeShapeId)?.samples : void 0;
1458
+ let area = 0;
1459
+ let previousTime = timeShape ? timeShape[0] * raster : 0.5 * raster;
1460
+ let previousAmplitude = Math.abs(rf.amplitude * magShape.samples[0]);
1461
+ for (let index = 1; index < magShape.numSamples; index++) {
1462
+ const time = timeShape ? timeShape[index] * raster : (index + 0.5) * raster;
1463
+ const amplitude = Math.abs(rf.amplitude * magShape.samples[index]);
1464
+ const duration = time - previousTime;
1465
+ if (duration > 0) area += 0.5 * (previousAmplitude + amplitude) * duration;
1466
+ previousTime = time;
1467
+ previousAmplitude = amplitude;
1468
+ }
1469
+ return 360 * area;
1470
+ }
1471
+ const absoluteAmplitude = Math.abs(rf.amplitude);
1472
+ if (absoluteAmplitude > 3e3) return 180;
1473
+ if (absoluteAmplitude > 1500) return 120;
1474
+ return 90;
1475
+ }
1476
+ function isLegacyFatSaturation(rf, seq) {
1477
+ const b0Tesla = getB0(seq);
1478
+ const frequencyPpm = rf.freqPPM !== 0 ? rf.freqPPM : b0Tesla > 0 ? 1e6 * rf.freqOffset / (GAMMA_HZ_T * b0Tesla) : 0;
1479
+ const durationSec = estimateRfDuration(rf, seq);
1480
+ return durationSec > 6e-3 && frequencyPpm >= -4.5 && frequencyPpm <= -3;
1481
+ }
1482
+ function estimateRfDuration(rf, seq) {
1483
+ const magShape = seq.shapes.get(rf.magShapeId);
1484
+ if (!magShape || magShape.numSamples <= 0) return 0;
1485
+ const raster = seq.rasterTimes.rfRaster;
1486
+ const timeShape = rf.timeShapeId > 0 ? seq.shapes.get(rf.timeShapeId)?.samples : void 0;
1487
+ if (timeShape && timeShape.length > 0) {
1488
+ return timeShape[timeShape.length - 1] * raster + raster;
1489
+ }
1490
+ return magShape.numSamples * raster;
1491
+ }
1409
1492
  function getB0(seq) {
1493
+ const raw = seq.definitions.get("B0") ?? seq.definitions.get("b0") ?? seq.definitions.get("b_0");
1494
+ if (raw && raw.length > 0) return +raw[0];
1495
+ return DEFAULT_B0_T;
1496
+ }
1497
+
1498
+ // src/pulseq/decoder.ts
1499
+ var GAMMA_HZ_T2 = 42576e3;
1500
+ var DEFAULT_B0_T2 = 3;
1501
+ function getB02(seq) {
1410
1502
  const raw = seq.definitions.get("B0");
1411
1503
  if (raw && Array.isArray(raw) && raw.length > 0) return +raw[0];
1412
1504
  const raw2 = seq.definitions.get("b0") ?? seq.definitions.get("b_0");
1413
1505
  if (raw2 && Array.isArray(raw2) && raw2.length > 0) return +raw2[0];
1414
- return DEFAULT_B0_T;
1506
+ return DEFAULT_B0_T2;
1415
1507
  }
1416
1508
  function effFreqOff(freqOffset, freqPPM, b0) {
1417
- return freqOffset + freqPPM * 1e-6 * GAMMA_HZ_T * b0;
1509
+ return freqOffset + freqPPM * 1e-6 * GAMMA_HZ_T2 * b0;
1418
1510
  }
1419
1511
  function effPhaseOff(phaseOffset, phasePPM, b0) {
1420
- return phaseOffset + phasePPM * 1e-6 * GAMMA_HZ_T * b0;
1512
+ return phaseOffset + phasePPM * 1e-6 * GAMMA_HZ_T2 * b0;
1421
1513
  }
1422
1514
  function decodeAllBlocks(seq) {
1423
1515
  return decodeBlockRange(seq, 0, seq.blocks.length);
@@ -1434,13 +1526,14 @@ var Pulseq = (() => {
1434
1526
  cumulative += blockDurationSeconds(seq, seq.blocks[i]);
1435
1527
  }
1436
1528
  const decoded = [];
1529
+ const classifiedRfUses = classifyRfUses(seq);
1437
1530
  for (let i = s; i < e; i++) {
1438
1531
  const block = seq.blocks[i];
1439
1532
  const dur = blockDurationSeconds(seq, block);
1440
1533
  const db = { index: block.num, duration: dur, startTime: cumulative };
1441
1534
  if (block.rfId > 0) {
1442
1535
  const rf = seq.rfs.get(block.rfId);
1443
- if (rf) db.rf = decodeRF(seq, rf, cumulative, dur);
1536
+ if (rf) db.rf = decodeRF(seq, rf, cumulative, dur, classifiedRfUses[i]);
1444
1537
  }
1445
1538
  db.gx = decodeGradient(seq, block.gxId, cumulative, dur, "gx");
1446
1539
  db.gy = decodeGradient(seq, block.gyId, cumulative, dur, "gy");
@@ -1469,11 +1562,11 @@ var Pulseq = (() => {
1469
1562
  if (seq.versionCombined < VER_PRE_14) return block.dur * 1e-6;
1470
1563
  return block.dur * seq.rasterTimes.blockDurationRaster;
1471
1564
  }
1472
- function decodeRF(seq, rf, blockStart, _blockDur) {
1565
+ function decodeRF(seq, rf, blockStart, _blockDur, classifiedUse) {
1473
1566
  const raster = seq.rasterTimes.rfRaster;
1474
1567
  const rfDelay = rf.delay * 1e-6;
1475
1568
  const rfStart = blockStart + rfDelay;
1476
- const b0 = getB0(seq);
1569
+ const b0 = getB02(seq);
1477
1570
  const freqFull = effFreqOff(rf.freqOffset, rf.freqPPM, b0);
1478
1571
  const phaseFull = effPhaseOff(rf.phaseOffset, rf.phasePPM, b0);
1479
1572
  const magShape = seq.shapes.get(rf.magShapeId);
@@ -1494,15 +1587,7 @@ var Pulseq = (() => {
1494
1587
  }
1495
1588
  const duration = n > 0 ? t[n - 1] - rfStart + raster : 0;
1496
1589
  const centerTime = rf.center >= 0 ? blockStart + rfDelay + rf.center * 1e-6 : estimateRfPeakTime(t, amp, rfStart, duration);
1497
- let use = rf.use || "";
1498
- if (!use || use === "u") {
1499
- let faDeg = 0;
1500
- for (let i = 1; i < n; i++) {
1501
- const dt = t[i] - t[i - 1];
1502
- faDeg += 360 * (amp[i] + amp[i - 1]) * 0.5 * dt;
1503
- }
1504
- use = faDeg >= 120 ? "r" : "e";
1505
- }
1590
+ const use = classifiedUse || "u";
1506
1591
  return {
1507
1592
  blockIndex: rf.id,
1508
1593
  startTime: rfStart,
@@ -1658,7 +1743,7 @@ var Pulseq = (() => {
1658
1743
  return value * amplitude;
1659
1744
  }
1660
1745
  function decodeADC(adc, blockStart, seq) {
1661
- const b0 = getB0(seq);
1746
+ const b0 = getB02(seq);
1662
1747
  const freqFull = effFreqOff(adc.freqOffset, adc.freqPPM, b0);
1663
1748
  const phaseFull = effPhaseOff(adc.phaseOffset, adc.phasePPM, b0);
1664
1749
  return {
@@ -2510,7 +2595,7 @@ var Pulseq = (() => {
2510
2595
  }
2511
2596
  }
2512
2597
  warnings.push(
2513
- `Showing a bounded full-sequence M1 envelope (at most ${maxBuckets.toLocaleString()} buckets per axis). Zoom to 100 TRs or fewer for an automatic detailed calculation.`
2598
+ `Showing a bounded full-sequence M1 envelope (at most ${maxBuckets.toLocaleString()} buckets per axis). Zoom in for an automatic detailed calculation; viewport sample limits also apply.`
2514
2599
  );
2515
2600
  return {
2516
2601
  valid: true,
@@ -2611,7 +2696,7 @@ var Pulseq = (() => {
2611
2696
  const events = [];
2612
2697
  for (const block of blocks) {
2613
2698
  if (!block.rf) continue;
2614
- const use = classifyRfUse(block.rf.use);
2699
+ const use = classifyRfUse2(block.rf.use);
2615
2700
  if (!use) continue;
2616
2701
  const rec = { tSec: block.rf.centerTime, use };
2617
2702
  events.push(rec);
@@ -2626,7 +2711,7 @@ var Pulseq = (() => {
2626
2711
  events.sort((a, b) => a.tSec - b.tSec);
2627
2712
  return events;
2628
2713
  }
2629
- function classifyRfUse(raw) {
2714
+ function classifyRfUse2(raw) {
2630
2715
  const c = (raw || "u").toLowerCase();
2631
2716
  if (c === "e" || c === "r" || c === "s" || c === "i" || c === "p") return c;
2632
2717
  return "u";
@@ -2986,7 +3071,7 @@ var Pulseq = (() => {
2986
3071
  }
2987
3072
  }
2988
3073
  const warnings = [
2989
- `Showing a bounded full-sequence PNS envelope (at most ${maxBuckets.toLocaleString()} buckets per curve). Zoom to 100 TRs or fewer for an automatic detailed calculation.`
3074
+ `Showing a bounded full-sequence PNS envelope (at most ${maxBuckets.toLocaleString()} buckets per curve). Zoom in for an automatic detailed calculation; viewport sample limits also apply.`
2990
3075
  ];
2991
3076
  return {
2992
3077
  valid: true,
@@ -3257,8 +3342,23 @@ var Pulseq = (() => {
3257
3342
  kspaceRasterSamples: 12e6,
3258
3343
  kspaceAdcSamples: 8e6,
3259
3344
  kspaceGridCandidates: 18e6,
3260
- derivedRasterSamples: 2e6
3345
+ derivedRasterSamples: 2e6,
3346
+ /**
3347
+ * Ceiling on the display samples one sequence load may carry to the VS Code
3348
+ * webview, counted as (time, amplitude) pairs across every RF and gradient
3349
+ * waveform. At 12 bytes per pair this bounds the shared binary buffers at
3350
+ * roughly 137 MiB in the extension host and again in the renderer.
3351
+ * Per-waveform detail is reduced uniformly once a sequence would exceed it,
3352
+ * because the alternative is an allocation neither process can satisfy.
3353
+ */
3354
+ displayTransportSamples: 12e6
3261
3355
  });
3356
+ function derivedDetailViewLimitSec(gradientRaster, trTimeSec, maxRasterSamples = INTERACTIVE_COMPUTE_LIMITS.derivedRasterSamples) {
3357
+ if (!(gradientRaster > 0) || !(maxRasterSamples > 0)) return 0;
3358
+ const sampleLimitedDuration = maxRasterSamples * gradientRaster / 2;
3359
+ if (!(trTimeSec > 0)) return sampleLimitedDuration;
3360
+ return Math.min(sampleLimitedDuration, trTimeSec * 100.5);
3361
+ }
3262
3362
  function estimateKspaceCost(blocks, gradientRaster, totalDuration) {
3263
3363
  let adcSamples = 0;
3264
3364
  let gradientSupportPoints = 0;
@@ -3328,11 +3428,9 @@ var Pulseq = (() => {
3328
3428
  }
3329
3429
 
3330
3430
  // src/pulseq/trdetect.ts
3331
- var GAMMA_HZ_T2 = 42576e3;
3332
- var DEFAULT_B0_T2 = 3;
3333
3431
  function detectSequenceTiming(seq) {
3334
- const b0 = getB02(seq);
3335
3432
  const supportsRfUse = seq.versionCombined >= 1005e3;
3433
+ const classifiedRfUses = classifyRfUses(seq);
3336
3434
  let teTimeSec = 0;
3337
3435
  let hasExplicitTE = false;
3338
3436
  const teDef = seq.definitions.get("EchoTime") ?? seq.definitions.get("TE");
@@ -3362,7 +3460,7 @@ var Pulseq = (() => {
3362
3460
  rfUsePerBlock.push(0);
3363
3461
  continue;
3364
3462
  }
3365
- const useChar = classifyRfUse2(rf, seq, supportsRfUse, b0);
3463
+ const useChar = classifiedRfUses[i] || "u";
3366
3464
  const useCode = useChar.charCodeAt(0);
3367
3465
  rfUsePerBlock.push(useCode);
3368
3466
  if (useChar === "e") {
@@ -3415,11 +3513,6 @@ var Pulseq = (() => {
3415
3513
  rfUsePerBlock
3416
3514
  };
3417
3515
  }
3418
- function getB02(seq) {
3419
- const raw = seq.definitions.get("B0") ?? seq.definitions.get("b0") ?? seq.definitions.get("b_0");
3420
- if (raw && Array.isArray(raw) && raw.length > 0) return +raw[0];
3421
- return DEFAULT_B0_T2;
3422
- }
3423
3516
  function computeCumulativeTimes(seq) {
3424
3517
  const times = [];
3425
3518
  let cum = 0;
@@ -3433,40 +3526,6 @@ var Pulseq = (() => {
3433
3526
  if (seq.versionCombined < VER_PRE_14) return block.dur * 1e-6;
3434
3527
  return block.dur * seq.rasterTimes.blockDurationRaster;
3435
3528
  }
3436
- function classifyRfUse2(rf, seq, supportsMetadata, b0Tesla) {
3437
- if (supportsMetadata && rf.use && rf.use !== "u" && rf.use !== "U") {
3438
- return rf.use.toLowerCase();
3439
- }
3440
- const faDeg = estimateFlipAngleDeg(rf, seq);
3441
- if (faDeg < 90.01) return "e";
3442
- const freqPPM = rf.freqPPM !== 0 ? rf.freqPPM : b0Tesla > 0 ? 1e6 * rf.freqOffset / (GAMMA_HZ_T2 * b0Tesla) : 0;
3443
- const durEst = estimateRfDuration(rf, seq);
3444
- if (durEst > 6e-3 && freqPPM >= -4.5 && freqPPM <= -3) return "s";
3445
- return "r";
3446
- }
3447
- function estimateFlipAngleDeg(rf, seq) {
3448
- const magShape = seq.shapes.get(rf.magShapeId);
3449
- if (magShape && magShape.numSamples > 0) {
3450
- const raster = seq.rasterTimes.rfRaster;
3451
- const timeShape = rf.timeShapeId > 0 ? seq.shapes.get(rf.timeShapeId)?.samples : void 0;
3452
- let area = 0;
3453
- let prevT = timeShape ? timeShape[0] * raster : 0.5 * raster;
3454
- let prevAmp = Math.abs(rf.amplitude * magShape.samples[0]);
3455
- for (let i = 1; i < magShape.numSamples; i++) {
3456
- const t = timeShape ? timeShape[i] * raster : (i + 0.5) * raster;
3457
- const amp = Math.abs(rf.amplitude * magShape.samples[i]);
3458
- const dt = t - prevT;
3459
- if (dt > 0) area += 0.5 * (prevAmp + amp) * dt;
3460
- prevT = t;
3461
- prevAmp = amp;
3462
- }
3463
- return 360 * area;
3464
- }
3465
- const absAmp = Math.abs(rf.amplitude);
3466
- if (absAmp > 3e3) return 180;
3467
- if (absAmp > 1500) return 120;
3468
- return 90;
3469
- }
3470
3529
  function estimateRfCenter(rf, _seq) {
3471
3530
  const magShape = _seq.shapes.get(rf.magShapeId);
3472
3531
  if (!magShape || magShape.numSamples <= 0) return 0;
@@ -3483,16 +3542,6 @@ var Pulseq = (() => {
3483
3542
  const timeShape = rf.timeShapeId > 0 ? _seq.shapes.get(rf.timeShapeId)?.samples : void 0;
3484
3543
  return timeShape ? (timeShape[peakIdx] ?? 0) * raster : (peakIdx + 0.5) * raster;
3485
3544
  }
3486
- function estimateRfDuration(rf, seq) {
3487
- const magShape = seq.shapes.get(rf.magShapeId);
3488
- if (!magShape || magShape.numSamples <= 0) return 0;
3489
- const raster = seq.rasterTimes.rfRaster;
3490
- const timeShape = rf.timeShapeId > 0 ? seq.shapes.get(rf.timeShapeId)?.samples : void 0;
3491
- if (timeShape && timeShape.length > 0) {
3492
- return timeShape[timeShape.length - 1] * raster + raster;
3493
- }
3494
- return magShape.numSamples * raster;
3495
- }
3496
3545
  function estimateTRFromExcitations(excTimesSec) {
3497
3546
  if (excTimesSec.length < 2) return 0;
3498
3547
  const intervals = [];
@@ -1,5 +1,69 @@
1
1
  /* SeqEyes WebView Bundle — auto-generated, do not edit */
2
2
  "use strict";
3
+ /* ══ block-transport.js ══ */
4
+ /* ══════════════════════════════════════════════════════════════════════════
5
+ block-transport.js — rehydrate the packed block payload from the extension.
6
+
7
+ The standalone web app builds BL in this same heap, so its waveform arrays
8
+ cost one copy and nothing more. The VS Code extension has to cross a process
9
+ boundary, and VS Code serialises webview messages with JSON.stringify: every
10
+ sample becomes ~19 characters of text, the extension host and the renderer
11
+ each hold that string alongside the object graph, and V8 refuses to build a
12
+ string longer than 512 MiB at all. Dense arbitrary waveforms reach ~18 KB of
13
+ JSON per block, so a few tens of thousands of them cannot be delivered as
14
+ JSON at any amount of memory.
15
+
16
+ src/editor/blockTransport.ts therefore sends the samples as two shared binary
17
+ buffers — Float64 times, Float32 amplitudes — plus an envelope carrying each
18
+ waveform's offset and count. Restoring the arrays as typed-array views over
19
+ those buffers reproduces the exact block shape the renderer reads, without
20
+ copying a single sample: the renderer only ever indexes these arrays and asks
21
+ for their length, which a typed array answers identically.
22
+ ══════════════════════════════════════════════════════════════════════════ */
23
+
24
+ /** Interpret a transferred buffer as `Ctor`, or null if it did not arrive. */
25
+ function asTypedView(buffer,Ctor){
26
+ if(buffer instanceof Ctor)return buffer;
27
+ if(buffer instanceof ArrayBuffer)return new Ctor(buffer);
28
+ // Some hosts hand the transfer back as a byte view rather than the buffer.
29
+ if(buffer&&buffer.buffer instanceof ArrayBuffer&&typeof buffer.byteLength==='number')
30
+ return new Ctor(buffer.buffer,buffer.byteOffset||0,Math.floor(buffer.byteLength/Ctor.BYTES_PER_ELEMENT));
31
+ return null;
32
+ }
33
+
34
+ /**
35
+ * Attach typed-array views to the envelope in place and return it as BL.
36
+ * Throws rather than returning partial blocks: a viewer that silently draws
37
+ * half a sequence is worse than one that says why it cannot.
38
+ */
39
+ function unpackSequenceBlocks(envelope,timeBuffer,valueBuffer,sampleCount){
40
+ if(!envelope||!envelope.length)return [];
41
+ var times=asTypedView(timeBuffer,Float64Array),values=asTypedView(valueBuffer,Float32Array);
42
+ if(!times||!values)throw new Error('the waveform sample buffers did not arrive as binary data');
43
+ var available=Math.min(times.length,values.length);
44
+ if(sampleCount>available)
45
+ throw new Error('the waveform sample buffers are short by '+(sampleCount-available)+' samples');
46
+ for(var i=0;i<envelope.length;i++){
47
+ var b=envelope[i];
48
+ if(b.rf){
49
+ b.rf.t=times.subarray(b.rf.o,b.rf.o+b.rf.n);
50
+ b.rf.m=values.subarray(b.rf.o,b.rf.o+b.rf.n);
51
+ b.rf.pt=times.subarray(b.rf.qo,b.rf.qo+b.rf.qn);
52
+ b.rf.p=values.subarray(b.rf.qo,b.rf.qo+b.rf.qn);
53
+ }
54
+ if(b.gx)attachGradientSamples(b.gx,times,values);
55
+ if(b.gy)attachGradientSamples(b.gy,times,values);
56
+ if(b.gz)attachGradientSamples(b.gz,times,values);
57
+ }
58
+ return envelope;
59
+ }
60
+
61
+ function attachGradientSamples(gradient,times,values){
62
+ gradient.t=times.subarray(gradient.o,gradient.o+gradient.n);
63
+ gradient.w=values.subarray(gradient.o,gradient.o+gradient.n);
64
+ }
65
+
66
+
3
67
  /* ══ state.js ══ */
4
68
  /* ═══════════════════════════════════════════════════════════════════════
5
69
  Application state & configuration
@@ -97,7 +161,7 @@ function scheduleViewerDraw(includeMinimap){
97
161
  }
98
162
 
99
163
  /* Timing metadata (TR/TE info for minimap tooltip) */
100
- var seqTiming=null; // {trTimeSec,trCount,hasExplicitTR,teTimeSec,hasExplicitTE,rfUseGuessed}
164
+ var seqTiming=null; // {trTimeSec,trCount,hasExplicitTR,teTimeSec,hasExplicitTE,rfUseGuessed,derivedDetailMaxViewSec}
101
165
 
102
166
  /* Block positions for minimap: [{i,s,d}, ...] */
103
167
  var blockPos=[];
@@ -248,6 +312,16 @@ function applySerializedKspace(payload){
248
312
  }
249
313
  }
250
314
 
315
+ /* Report a load that did not arrive. Clearing the previous sequence matters as
316
+ much as the message: the progress overlay reaches "Ready" either way, so
317
+ leaving stale blocks on screen would read as a successful load. */
318
+ function showSequenceLoadFailure(message){
319
+ BL=[];waveformOverview=null;blockPos=[];mmCache=null;
320
+ setViewerNotice('sequence',message);
321
+ setExportButtonEnabled(false);
322
+ draw();drawMinimap();
323
+ }
324
+
251
325
  /* ── Data reception ───────────────────────────────────────────────────── */
252
326
  window.addEventListener('message',function(e){
253
327
  var m=e.data;
@@ -270,7 +344,13 @@ window.addEventListener('message',function(e){
270
344
  return;
271
345
  }
272
346
  if(m.type==='sequenceData'){
273
- BL=m.blocks||[];TD=m.totalDuration||0;GR=m.gradRaster||1e-5;
347
+ try{
348
+ BL=unpackSequenceBlocks(m.blocks,m.sampleTimes,m.sampleValues,m.sampleCount||0);
349
+ }catch(err){
350
+ showSequenceLoadFailure('Failed to load the sequence waveforms: '+(err&&err.message||err)+'.');
351
+ return;
352
+ }
353
+ TD=m.totalDuration||0;GR=m.gradRaster||1e-5;
274
354
  setViewerNotice('sequence',m.notices&&m.notices.length?m.notices.join(' '):null);
275
355
  setViewerNotice('kspaceOverrideFailure',null);setKspaceSafetyWarning(m.kspaceSafety||null);
276
356
  setViewerNotice('m1',null);setViewerNotice('pns',null);setViewerNotice('pnsThreshold',null);
@@ -288,6 +368,8 @@ window.addEventListener('message',function(e){
288
368
  if(seqTiming&&seqTiming.trTimeSec>0){fitToFirstTR();}else{fit();}
289
369
  draw();drawKs();drawMinimap();
290
370
  setExportButtonEnabled(true);
371
+ }else if(m.type==='loadError'){
372
+ showSequenceLoadFailure(m.message||'The sequence could not be loaded.');
291
373
  }else if(m.type==='kspaceData'){
292
374
  applySerializedKspace(m.kspace);finishDangerousKspaceCalculation(null);drawKs();
293
375
  if(typeof kOpen!=='undefined'&&!kOpen)document.getElementById('kbtn').click();
@@ -304,7 +386,7 @@ window.addEventListener('message',function(e){
304
386
  }else chVis[m1RequestedChannel]=true;
305
387
  computeGlobalMax();buildLegend();draw();
306
388
  if(m.m1.warnings&&m.m1.warnings.length)console.warn('[SeqEyes M1]',m.m1.warnings.join('\n'));
307
- setViewerNotice('m1Coarse',m.m1.coarse?'Large sequence: showing bounded full-sequence M1. Zoom to 100 TRs or fewer for automatic detail.':null);
389
+ setViewerNotice('m1Coarse',m.m1.coarse?'Large sequence: showing bounded full-sequence M1. Zoom in for automatic detail.':null);
308
390
  }else{
309
391
  setViewerNotice('m1','M1 calculation failed: '+((m.m1&&m.m1.error)||'unknown error')+' Zoom in to inspect waveform detail.');
310
392
  }
@@ -324,7 +406,7 @@ window.addEventListener('message',function(e){
324
406
  pnsWindowData=null;pnsWindowPending=null;chVis[7]=true;
325
407
  computeGlobalMax();buildLegend();draw();
326
408
  setViewerNotice('pnsThreshold',m.pns.ok?null:'PNS warning: predicted level reaches or exceeds 100%.');
327
- setViewerNotice('pnsCoarse',m.pns.coarse?'Large sequence: showing bounded full-sequence PNS. Zoom to 100 TRs or fewer for automatic detail.':null);
409
+ setViewerNotice('pnsCoarse',m.pns.coarse?'Large sequence: showing bounded full-sequence PNS. Zoom in for automatic detail.':null);
328
410
  }else{
329
411
  setViewerNotice('pns','PNS calculation failed: '+((m.pns&&m.pns.error)||'unknown error')+' Zoom in to inspect waveform detail.');
330
412
  }
@@ -396,10 +478,14 @@ function createM1SeriesPayload(m1){
396
478
  };
397
479
  }
398
480
 
481
+ function shouldRequestFineDerivedWindow(vs,ve){
482
+ var dur=ve-vs,maxView=seqTiming&&Number(seqTiming.derivedDetailMaxViewSec);
483
+ return !!(dur>0&&isFinite(maxView)&&maxView>0&&dur<=maxView+1e-12);
484
+ }
485
+
399
486
  function shouldRequestFineM1Window(vs,ve){
400
487
  if(!vscApi||!m1Data||!m1Data.coarse||!(chVis[8]||chVis[9]||chVis[10]))return false;
401
- var dur=ve-vs;
402
- return !!(seqTiming&&seqTiming.trTimeSec>0&&dur<=seqTiming.trTimeSec*100.5);
488
+ return shouldRequestFineDerivedWindow(vs,ve);
403
489
  }
404
490
 
405
491
  function derivedWindowCovers(data,vs,ve){
@@ -421,14 +507,13 @@ function m1SeriesForView(vs,ve){
421
507
  requestM1Window(vs,ve);
422
508
  if(derivedWindowCovers(m1WindowData,vs,ve)){setViewerNotice('m1Detail',null);setViewerNotice('m1Coarse','Large sequence: full sequence uses bounded M1; the current view is detailed.');return m1WindowData;}
423
509
  }
424
- if(m1Data.coarse)setViewerNotice('m1Coarse','Large sequence: showing bounded full-sequence M1. Zoom to 100 TRs or fewer for automatic detail.');
510
+ if(m1Data.coarse)setViewerNotice('m1Coarse','Large sequence: showing bounded full-sequence M1. Zoom in for automatic detail.');
425
511
  return m1Data;
426
512
  }
427
513
 
428
514
  function shouldRequestFinePnsWindow(vs,ve){
429
515
  if(!vscApi||!pnsData||!pnsData.coarse||!chVis[7])return false;
430
- var dur=ve-vs;
431
- return !!(seqTiming&&seqTiming.trTimeSec>0&&dur<=seqTiming.trTimeSec*100.5);
516
+ return shouldRequestFineDerivedWindow(vs,ve);
432
517
  }
433
518
 
434
519
  function pnsWindowCovers(data,vs,ve){
@@ -450,7 +535,7 @@ function pnsSeriesForView(vs,ve){
450
535
  requestPnsWindow(vs,ve);
451
536
  if(pnsWindowCovers(pnsWindowData,vs,ve)){setViewerNotice('pnsCoarse','Large sequence: full sequence uses bounded PNS; the current view is detailed.');return pnsWindowData;}
452
537
  }
453
- if(pnsData.coarse)setViewerNotice('pnsCoarse','Large sequence: showing bounded full-sequence PNS. Zoom to 100 TRs or fewer for automatic detail.');
538
+ if(pnsData.coarse)setViewerNotice('pnsCoarse','Large sequence: showing bounded full-sequence PNS. Zoom in for automatic detail.');
454
539
  return pnsData;
455
540
  }
456
541