seqeyes-python 0.2.11__tar.gz → 0.2.12__tar.gz

{seqeyes_python-0.2.11 → seqeyes_python-0.2.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: seqeyes-python
-Version: 0.2.11
+Version: 0.2.12
 Summary: Interactive Pulseq MRI sequence viewer for Jupyter — lightweight, beautiful, replaces seq.plot() in pypulseq.
 Project-URL: Homepage, https://github.com/bughht/seqeyes_plugin
 Project-URL: Repository, https://github.com/bughht/seqeyes_plugin

{seqeyes_python-0.2.11 → seqeyes_python-0.2.12}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "seqeyes-python"
-version = "0.2.11"
+version = "0.2.12"
 description = "Interactive Pulseq MRI sequence viewer for Jupyter — lightweight, beautiful, replaces seq.plot() in pypulseq."
 readme = "README.md"
 license = {text = "MIT"}

{seqeyes_python-0.2.11 → seqeyes_python-0.2.12}/src/seqeyes/__init__.py

@@ -29,4 +29,4 @@ from seqeyes._plot import set, reset
 from seqeyes._renderer import SeqEyesViewer
 
 __all__ = ["set", "reset", "SeqEyesViewer"]
-__version__ = "0.2.11"
+__version__ = "0.2.12"

{seqeyes_python-0.2.11 → seqeyes_python-0.2.12}/src/seqeyes/resources/pulseq-bundle.js

@@ -31,6 +31,7 @@ var Pulseq = (() => {
     calculatePns: () => calculatePns,
     calculatePnsCoarse: () => calculatePnsCoarse,
     decodeAllBlocks: () => decodeAllBlocks,
+    derivedDetailViewLimitSec: () => derivedDetailViewLimitSec,
     detectSequenceTiming: () => detectSequenceTiming,
     estimateDerivedCost: () => estimateDerivedCost,
     estimateKspaceCost: () => estimateKspaceCost,
@@ -53,7 +54,7 @@ var Pulseq = (() => {
   });
 
   // package.json
-  var version = "0.2.11";
+  var version = "0.2.12";
 
   // src/pulseq/decompressor.ts
   function decompressShape(compressed, numSamples) {
@@ -1403,21 +1404,112 @@ var Pulseq = (() => {
     return parseSequenceText(text);
   }
 
-  // src/pulseq/decoder.ts
+  // src/pulseq/rfClassification.ts
   var GAMMA_HZ_T = 42576e3;
   var DEFAULT_B0_T = 3;
+  var sequenceUseCache = /* @__PURE__ */ new WeakMap();
+  function classifyRfUse(rf, seq) {
+    if (seq.versionCombined >= VER_V15 && rf.use && rf.use.toLowerCase() !== "u") {
+      return rf.use.toLowerCase();
+    }
+    const flipAngleDeg = estimateRfFlipAngleDeg(rf, seq);
+    if (isLegacyFatSaturation(rf, seq)) return "s";
+    return flipAngleDeg >= 120 ? "r" : "e";
+  }
+  function classifyRfUses(seq) {
+    const cachedUses = sequenceUseCache.get(seq);
+    if (cachedUses) return cachedUses;
+    const libraryUses = /* @__PURE__ */ new Map();
+    const uses = seq.blocks.map((block) => {
+      if (block.rfId <= 0) return "";
+      const cached = libraryUses.get(block.rfId);
+      if (cached !== void 0) return cached;
+      const rf = seq.rfs.get(block.rfId);
+      const use = rf ? classifyRfUse(rf, seq) : "";
+      libraryUses.set(block.rfId, use);
+      return use;
+    });
+    if (seq.versionCombined >= VER_V15 || uses.includes("e")) {
+      sequenceUseCache.set(seq, uses);
+      return uses;
+    }
+    const saturationBlocks = uses.map((use, index) => use === "s" ? index : -1).filter((index) => index >= 0);
+    if (saturationBlocks.length < 2) {
+      sequenceUseCache.set(seq, uses);
+      return uses;
+    }
+    for (let anchor = 0; anchor < saturationBlocks.length; anchor++) {
+      const start = saturationBlocks[anchor] + 1;
+      const end = saturationBlocks[anchor + 1] ?? uses.length;
+      for (let index = start; index < end; index++) {
+        if (!uses[index] || uses[index] === "s") continue;
+        uses[index] = "e";
+        break;
+      }
+    }
+    sequenceUseCache.set(seq, uses);
+    return uses;
+  }
+  function estimateRfFlipAngleDeg(rf, seq) {
+    const magShape = seq.shapes.get(rf.magShapeId);
+    if (magShape && magShape.numSamples > 0) {
+      const raster = seq.rasterTimes.rfRaster;
+      const timeShape = rf.timeShapeId > 0 ? seq.shapes.get(rf.timeShapeId)?.samples : void 0;
+      let area = 0;
+      let previousTime = timeShape ? timeShape[0] * raster : 0.5 * raster;
+      let previousAmplitude = Math.abs(rf.amplitude * magShape.samples[0]);
+      for (let index = 1; index < magShape.numSamples; index++) {
+        const time = timeShape ? timeShape[index] * raster : (index + 0.5) * raster;
+        const amplitude = Math.abs(rf.amplitude * magShape.samples[index]);
+        const duration = time - previousTime;
+        if (duration > 0) area += 0.5 * (previousAmplitude + amplitude) * duration;
+        previousTime = time;
+        previousAmplitude = amplitude;
+      }
+      return 360 * area;
+    }
+    const absoluteAmplitude = Math.abs(rf.amplitude);
+    if (absoluteAmplitude > 3e3) return 180;
+    if (absoluteAmplitude > 1500) return 120;
+    return 90;
+  }
+  function isLegacyFatSaturation(rf, seq) {
+    const b0Tesla = getB0(seq);
+    const frequencyPpm = rf.freqPPM !== 0 ? rf.freqPPM : b0Tesla > 0 ? 1e6 * rf.freqOffset / (GAMMA_HZ_T * b0Tesla) : 0;
+    const durationSec = estimateRfDuration(rf, seq);
+    return durationSec > 6e-3 && frequencyPpm >= -4.5 && frequencyPpm <= -3;
+  }
+  function estimateRfDuration(rf, seq) {
+    const magShape = seq.shapes.get(rf.magShapeId);
+    if (!magShape || magShape.numSamples <= 0) return 0;
+    const raster = seq.rasterTimes.rfRaster;
+    const timeShape = rf.timeShapeId > 0 ? seq.shapes.get(rf.timeShapeId)?.samples : void 0;
+    if (timeShape && timeShape.length > 0) {
+      return timeShape[timeShape.length - 1] * raster + raster;
+    }
+    return magShape.numSamples * raster;
+  }
   function getB0(seq) {
+    const raw = seq.definitions.get("B0") ?? seq.definitions.get("b0") ?? seq.definitions.get("b_0");
+    if (raw && raw.length > 0) return +raw[0];
+    return DEFAULT_B0_T;
+  }
+
+  // src/pulseq/decoder.ts
+  var GAMMA_HZ_T2 = 42576e3;
+  var DEFAULT_B0_T2 = 3;
+  function getB02(seq) {
     const raw = seq.definitions.get("B0");
     if (raw && Array.isArray(raw) && raw.length > 0) return +raw[0];
     const raw2 = seq.definitions.get("b0") ?? seq.definitions.get("b_0");
     if (raw2 && Array.isArray(raw2) && raw2.length > 0) return +raw2[0];
-    return DEFAULT_B0_T;
+    return DEFAULT_B0_T2;
   }
   function effFreqOff(freqOffset, freqPPM, b0) {
-    return freqOffset + freqPPM * 1e-6 * GAMMA_HZ_T * b0;
+    return freqOffset + freqPPM * 1e-6 * GAMMA_HZ_T2 * b0;
   }
   function effPhaseOff(phaseOffset, phasePPM, b0) {
-    return phaseOffset + phasePPM * 1e-6 * GAMMA_HZ_T * b0;
+    return phaseOffset + phasePPM * 1e-6 * GAMMA_HZ_T2 * b0;
   }
   function decodeAllBlocks(seq) {
     return decodeBlockRange(seq, 0, seq.blocks.length);
@@ -1434,13 +1526,14 @@ var Pulseq = (() => {
       cumulative += blockDurationSeconds(seq, seq.blocks[i]);
     }
     const decoded = [];
+    const classifiedRfUses = classifyRfUses(seq);
     for (let i = s; i < e; i++) {
       const block = seq.blocks[i];
       const dur = blockDurationSeconds(seq, block);
       const db = { index: block.num, duration: dur, startTime: cumulative };
       if (block.rfId > 0) {
         const rf = seq.rfs.get(block.rfId);
-        if (rf) db.rf = decodeRF(seq, rf, cumulative, dur);
+        if (rf) db.rf = decodeRF(seq, rf, cumulative, dur, classifiedRfUses[i]);
       }
       db.gx = decodeGradient(seq, block.gxId, cumulative, dur, "gx");
       db.gy = decodeGradient(seq, block.gyId, cumulative, dur, "gy");
@@ -1469,11 +1562,11 @@ var Pulseq = (() => {
     if (seq.versionCombined < VER_PRE_14) return block.dur * 1e-6;
     return block.dur * seq.rasterTimes.blockDurationRaster;
   }
-  function decodeRF(seq, rf, blockStart, _blockDur) {
+  function decodeRF(seq, rf, blockStart, _blockDur, classifiedUse) {
     const raster = seq.rasterTimes.rfRaster;
     const rfDelay = rf.delay * 1e-6;
     const rfStart = blockStart + rfDelay;
-    const b0 = getB0(seq);
+    const b0 = getB02(seq);
     const freqFull = effFreqOff(rf.freqOffset, rf.freqPPM, b0);
     const phaseFull = effPhaseOff(rf.phaseOffset, rf.phasePPM, b0);
     const magShape = seq.shapes.get(rf.magShapeId);
@@ -1494,15 +1587,7 @@ var Pulseq = (() => {
     }
     const duration = n > 0 ? t[n - 1] - rfStart + raster : 0;
     const centerTime = rf.center >= 0 ? blockStart + rfDelay + rf.center * 1e-6 : estimateRfPeakTime(t, amp, rfStart, duration);
-    let use = rf.use || "";
-    if (!use || use === "u") {
-      let faDeg = 0;
-      for (let i = 1; i < n; i++) {
-        const dt = t[i] - t[i - 1];
-        faDeg += 360 * (amp[i] + amp[i - 1]) * 0.5 * dt;
-      }
-      use = faDeg >= 120 ? "r" : "e";
-    }
+    const use = classifiedUse || "u";
     return {
       blockIndex: rf.id,
       startTime: rfStart,
@@ -1658,7 +1743,7 @@ var Pulseq = (() => {
     return value * amplitude;
   }
   function decodeADC(adc, blockStart, seq) {
-    const b0 = getB0(seq);
+    const b0 = getB02(seq);
     const freqFull = effFreqOff(adc.freqOffset, adc.freqPPM, b0);
     const phaseFull = effPhaseOff(adc.phaseOffset, adc.phasePPM, b0);
     return {
@@ -2510,7 +2595,7 @@ var Pulseq = (() => {
       }
     }
     warnings.push(
-      `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.`
+      `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.`
     );
     return {
       valid: true,
@@ -2611,7 +2696,7 @@ var Pulseq = (() => {
     const events = [];
     for (const block of blocks) {
       if (!block.rf) continue;
-      const use = classifyRfUse(block.rf.use);
+      const use = classifyRfUse2(block.rf.use);
       if (!use) continue;
       const rec = { tSec: block.rf.centerTime, use };
       events.push(rec);
@@ -2626,7 +2711,7 @@ var Pulseq = (() => {
     events.sort((a, b) => a.tSec - b.tSec);
     return events;
   }
-  function classifyRfUse(raw) {
+  function classifyRfUse2(raw) {
     const c = (raw || "u").toLowerCase();
     if (c === "e" || c === "r" || c === "s" || c === "i" || c === "p") return c;
     return "u";
@@ -2986,7 +3071,7 @@ var Pulseq = (() => {
       }
     }
     const warnings = [
-      `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.`
+      `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.`
     ];
     return {
       valid: true,
@@ -3259,6 +3344,12 @@ var Pulseq = (() => {
     kspaceGridCandidates: 18e6,
     derivedRasterSamples: 2e6
   });
+  function derivedDetailViewLimitSec(gradientRaster, trTimeSec, maxRasterSamples = INTERACTIVE_COMPUTE_LIMITS.derivedRasterSamples) {
+    if (!(gradientRaster > 0) || !(maxRasterSamples > 0)) return 0;
+    const sampleLimitedDuration = maxRasterSamples * gradientRaster / 2;
+    if (!(trTimeSec > 0)) return sampleLimitedDuration;
+    return Math.min(sampleLimitedDuration, trTimeSec * 100.5);
+  }
   function estimateKspaceCost(blocks, gradientRaster, totalDuration) {
     let adcSamples = 0;
     let gradientSupportPoints = 0;
@@ -3328,11 +3419,9 @@ var Pulseq = (() => {
   }
 
   // src/pulseq/trdetect.ts
-  var GAMMA_HZ_T2 = 42576e3;
-  var DEFAULT_B0_T2 = 3;
   function detectSequenceTiming(seq) {
-    const b0 = getB02(seq);
     const supportsRfUse = seq.versionCombined >= 1005e3;
+    const classifiedRfUses = classifyRfUses(seq);
     let teTimeSec = 0;
     let hasExplicitTE = false;
     const teDef = seq.definitions.get("EchoTime") ?? seq.definitions.get("TE");
@@ -3362,7 +3451,7 @@ var Pulseq = (() => {
         rfUsePerBlock.push(0);
         continue;
       }
-      const useChar = classifyRfUse2(rf, seq, supportsRfUse, b0);
+      const useChar = classifiedRfUses[i] || "u";
       const useCode = useChar.charCodeAt(0);
       rfUsePerBlock.push(useCode);
       if (useChar === "e") {
@@ -3415,11 +3504,6 @@ var Pulseq = (() => {
       rfUsePerBlock
     };
   }
-  function getB02(seq) {
-    const raw = seq.definitions.get("B0") ?? seq.definitions.get("b0") ?? seq.definitions.get("b_0");
-    if (raw && Array.isArray(raw) && raw.length > 0) return +raw[0];
-    return DEFAULT_B0_T2;
-  }
   function computeCumulativeTimes(seq) {
     const times = [];
     let cum = 0;
@@ -3433,40 +3517,6 @@ var Pulseq = (() => {
     if (seq.versionCombined < VER_PRE_14) return block.dur * 1e-6;
     return block.dur * seq.rasterTimes.blockDurationRaster;
   }
-  function classifyRfUse2(rf, seq, supportsMetadata, b0Tesla) {
-    if (supportsMetadata && rf.use && rf.use !== "u" && rf.use !== "U") {
-      return rf.use.toLowerCase();
-    }
-    const faDeg = estimateFlipAngleDeg(rf, seq);
-    if (faDeg < 90.01) return "e";
-    const freqPPM = rf.freqPPM !== 0 ? rf.freqPPM : b0Tesla > 0 ? 1e6 * rf.freqOffset / (GAMMA_HZ_T2 * b0Tesla) : 0;
-    const durEst = estimateRfDuration(rf, seq);
-    if (durEst > 6e-3 && freqPPM >= -4.5 && freqPPM <= -3) return "s";
-    return "r";
-  }
-  function estimateFlipAngleDeg(rf, seq) {
-    const magShape = seq.shapes.get(rf.magShapeId);
-    if (magShape && magShape.numSamples > 0) {
-      const raster = seq.rasterTimes.rfRaster;
-      const timeShape = rf.timeShapeId > 0 ? seq.shapes.get(rf.timeShapeId)?.samples : void 0;
-      let area = 0;
-      let prevT = timeShape ? timeShape[0] * raster : 0.5 * raster;
-      let prevAmp = Math.abs(rf.amplitude * magShape.samples[0]);
-      for (let i = 1; i < magShape.numSamples; i++) {
-        const t = timeShape ? timeShape[i] * raster : (i + 0.5) * raster;
-        const amp = Math.abs(rf.amplitude * magShape.samples[i]);
-        const dt = t - prevT;
-        if (dt > 0) area += 0.5 * (prevAmp + amp) * dt;
-        prevT = t;
-        prevAmp = amp;
-      }
-      return 360 * area;
-    }
-    const absAmp = Math.abs(rf.amplitude);
-    if (absAmp > 3e3) return 180;
-    if (absAmp > 1500) return 120;
-    return 90;
-  }
   function estimateRfCenter(rf, _seq) {
     const magShape = _seq.shapes.get(rf.magShapeId);
     if (!magShape || magShape.numSamples <= 0) return 0;
@@ -3483,16 +3533,6 @@ var Pulseq = (() => {
     const timeShape = rf.timeShapeId > 0 ? _seq.shapes.get(rf.timeShapeId)?.samples : void 0;
     return timeShape ? (timeShape[peakIdx] ?? 0) * raster : (peakIdx + 0.5) * raster;
   }
-  function estimateRfDuration(rf, seq) {
-    const magShape = seq.shapes.get(rf.magShapeId);
-    if (!magShape || magShape.numSamples <= 0) return 0;
-    const raster = seq.rasterTimes.rfRaster;
-    const timeShape = rf.timeShapeId > 0 ? seq.shapes.get(rf.timeShapeId)?.samples : void 0;
-    if (timeShape && timeShape.length > 0) {
-      return timeShape[timeShape.length - 1] * raster + raster;
-    }
-    return magShape.numSamples * raster;
-  }
   function estimateTRFromExcitations(excTimesSec) {
     if (excTimesSec.length < 2) return 0;
     const intervals = [];

{seqeyes_python-0.2.11 → seqeyes_python-0.2.12}/src/seqeyes/resources/webview-bundle.js

@@ -97,7 +97,7 @@ function scheduleViewerDraw(includeMinimap){
 }
 
 /* Timing metadata (TR/TE info for minimap tooltip) */
-var seqTiming=null;  // {trTimeSec,trCount,hasExplicitTR,teTimeSec,hasExplicitTE,rfUseGuessed}
+var seqTiming=null;  // {trTimeSec,trCount,hasExplicitTR,teTimeSec,hasExplicitTE,rfUseGuessed,derivedDetailMaxViewSec}
 
 /* Block positions for minimap: [{i,s,d}, ...] */
 var blockPos=[];
@@ -304,7 +304,7 @@ window.addEventListener('message',function(e){
       }else chVis[m1RequestedChannel]=true;
       computeGlobalMax();buildLegend();draw();
       if(m.m1.warnings&&m.m1.warnings.length)console.warn('[SeqEyes M1]',m.m1.warnings.join('\n'));
-      setViewerNotice('m1Coarse',m.m1.coarse?'Large sequence: showing bounded full-sequence M1. Zoom to 100 TRs or fewer for automatic detail.':null);
+      setViewerNotice('m1Coarse',m.m1.coarse?'Large sequence: showing bounded full-sequence M1. Zoom in for automatic detail.':null);
     }else{
       setViewerNotice('m1','M1 calculation failed: '+((m.m1&&m.m1.error)||'unknown error')+' Zoom in to inspect waveform detail.');
     }
@@ -324,7 +324,7 @@ window.addEventListener('message',function(e){
       pnsWindowData=null;pnsWindowPending=null;chVis[7]=true;
       computeGlobalMax();buildLegend();draw();
       setViewerNotice('pnsThreshold',m.pns.ok?null:'PNS warning: predicted level reaches or exceeds 100%.');
-      setViewerNotice('pnsCoarse',m.pns.coarse?'Large sequence: showing bounded full-sequence PNS. Zoom to 100 TRs or fewer for automatic detail.':null);
+      setViewerNotice('pnsCoarse',m.pns.coarse?'Large sequence: showing bounded full-sequence PNS. Zoom in for automatic detail.':null);
     }else{
       setViewerNotice('pns','PNS calculation failed: '+((m.pns&&m.pns.error)||'unknown error')+' Zoom in to inspect waveform detail.');
     }
@@ -396,10 +396,14 @@ function createM1SeriesPayload(m1){
   };
 }
 
+function shouldRequestFineDerivedWindow(vs,ve){
+  var dur=ve-vs,maxView=seqTiming&&Number(seqTiming.derivedDetailMaxViewSec);
+  return !!(dur>0&&isFinite(maxView)&&maxView>0&&dur<=maxView+1e-12);
+}
+
 function shouldRequestFineM1Window(vs,ve){
   if(!vscApi||!m1Data||!m1Data.coarse||!(chVis[8]||chVis[9]||chVis[10]))return false;
-  var dur=ve-vs;
-  return !!(seqTiming&&seqTiming.trTimeSec>0&&dur<=seqTiming.trTimeSec*100.5);
+  return shouldRequestFineDerivedWindow(vs,ve);
 }
 
 function derivedWindowCovers(data,vs,ve){
@@ -421,14 +425,13 @@ function m1SeriesForView(vs,ve){
     requestM1Window(vs,ve);
     if(derivedWindowCovers(m1WindowData,vs,ve)){setViewerNotice('m1Detail',null);setViewerNotice('m1Coarse','Large sequence: full sequence uses bounded M1; the current view is detailed.');return m1WindowData;}
   }
-  if(m1Data.coarse)setViewerNotice('m1Coarse','Large sequence: showing bounded full-sequence M1. Zoom to 100 TRs or fewer for automatic detail.');
+  if(m1Data.coarse)setViewerNotice('m1Coarse','Large sequence: showing bounded full-sequence M1. Zoom in for automatic detail.');
   return m1Data;
 }
 
 function shouldRequestFinePnsWindow(vs,ve){
   if(!vscApi||!pnsData||!pnsData.coarse||!chVis[7])return false;
-  var dur=ve-vs;
-  return !!(seqTiming&&seqTiming.trTimeSec>0&&dur<=seqTiming.trTimeSec*100.5);
+  return shouldRequestFineDerivedWindow(vs,ve);
 }
 
 function pnsWindowCovers(data,vs,ve){
@@ -450,7 +453,7 @@ function pnsSeriesForView(vs,ve){
     requestPnsWindow(vs,ve);
     if(pnsWindowCovers(pnsWindowData,vs,ve)){setViewerNotice('pnsCoarse','Large sequence: full sequence uses bounded PNS; the current view is detailed.');return pnsWindowData;}
   }
-  if(pnsData.coarse)setViewerNotice('pnsCoarse','Large sequence: showing bounded full-sequence PNS. Zoom to 100 TRs or fewer for automatic detail.');
+  if(pnsData.coarse)setViewerNotice('pnsCoarse','Large sequence: showing bounded full-sequence PNS. Zoom in for automatic detail.');
   return pnsData;
 }