seqeyes-python 0.2.6__py3-none-any.whl → 0.2.7__py3-none-any.whl

seqeyes/__init__.py

@@ -29,4 +29,4 @@ from seqeyes._plot import set, reset
 from seqeyes._renderer import SeqEyesViewer
 
 __all__ = ["set", "reset", "SeqEyesViewer"]
-__version__ = "0.2.6"
+__version__ = "0.2.7"

seqeyes/resources/pulseq-bundle.js

@@ -23,15 +23,23 @@ var Pulseq = (() => {
   // web/pulseq-browser.ts
   var pulseq_browser_exports = {};
   __export(pulseq_browser_exports, {
+    INTERACTIVE_COMPUTE_LIMITS: () => INTERACTIVE_COMPUTE_LIMITS,
     PACKAGE_VERSION: () => PACKAGE_VERSION,
     calculateKspace: () => calculateKspace,
     calculateM1: () => calculateM1,
+    calculateM1Coarse: () => calculateM1Coarse,
     calculatePns: () => calculatePns,
+    calculatePnsCoarse: () => calculatePnsCoarse,
     decodeAllBlocks: () => decodeAllBlocks,
     detectSequenceTiming: () => detectSequenceTiming,
+    estimateDerivedCost: () => estimateDerivedCost,
+    estimateKspaceCost: () => estimateKspaceCost,
+    estimateKspacePeakMemoryBytes: () => estimateKspacePeakMemoryBytes,
     exportKspaceArtifacts: () => exportKspaceArtifacts,
     exportKspaceArtifactsFromBytes: () => exportKspaceArtifactsFromBytes,
     exportKspaceArtifactsFromSequence: () => exportKspaceArtifactsFromSequence,
+    formatMemorySize: () => formatMemorySize,
+    formatSampleCount: () => formatSampleCount,
     formatTrajectoryText: () => formatTrajectoryText,
     getTotalDuration: () => getTotalDuration,
     hasPulseqBinaryMagic: () => hasPulseqBinaryMagic,
@@ -39,11 +47,13 @@ var Pulseq = (() => {
     parseSequenceBinary: () => parseSequenceBinary,
     parseSequenceBytes: () => parseSequenceBytes,
     parseSequenceText: () => parseSequenceText,
-    safePnsModel: () => safePnsModel
+    safePnsModel: () => safePnsModel,
+    selectM1WindowBlocks: () => selectM1WindowBlocks,
+    selectPnsWindowBlocks: () => selectPnsWindowBlocks
   });
 
   // package.json
-  var version = "0.2.6";
+  var version = "0.2.7";
 
   // src/pulseq/decompressor.ts
   function decompressShape(compressed, numSamples) {
@@ -1784,6 +1794,11 @@ var Pulseq = (() => {
     for (const b of blocks) {
       if (b.adc) totalAdcSamples += b.adc.numSamples;
     }
+    if (_options?.maxAdcSamples && totalAdcSamples > _options.maxAdcSamples) return null;
+    if (_options?.maxGridPoints && totalDuration > 0) {
+      const rasterPointCount = Math.max(2, Math.round(totalDuration / GR) + 1);
+      if (rasterPointCount + totalAdcSamples > _options.maxGridPoints) return null;
+    }
     const adcT = new Float64Array(totalAdcSamples);
     let adcIdx = 0;
     for (const b of blocks) {
@@ -2015,8 +2030,140 @@ var Pulseq = (() => {
     return [gx, gy, gz];
   }
 
-  // src/pulseq/m1.ts
+  // src/pulseq/boundedSeries.ts
+  var BoundedSeriesBuilder = class {
+    constructor(startSec, endSec, maxPoints) {
+      __publicField(this, "startSec", startSec);
+      __publicField(this, "endSec", endSec);
+      __publicField(this, "buckets");
+      __publicField(this, "bucketCount");
+      __publicField(this, "span");
+      this.bucketCount = Math.max(1, Math.floor(Math.max(4, maxPoints) / 4));
+      this.buckets = new Array(this.bucketCount);
+      this.span = Math.max(0, endSec - startSec);
+    }
+    add(tSec, value) {
+      if (!Number.isFinite(tSec) || !Number.isFinite(value)) return;
+      const normalized = this.span > 0 ? (tSec - this.startSec) / this.span : 0;
+      const index = Math.max(0, Math.min(
+        this.bucketCount - 1,
+        Math.floor(normalized * this.bucketCount)
+      ));
+      const bucket = this.buckets[index];
+      if (!bucket) {
+        this.buckets[index] = {
+          firstT: tSec,
+          firstV: value,
+          minV: value,
+          maxV: value,
+          lastT: tSec,
+          lastV: value
+        };
+        return;
+      }
+      if (value < bucket.minV) {
+        bucket.minV = value;
+      }
+      if (value > bucket.maxV) {
+        bucket.maxV = value;
+      }
+      bucket.lastT = tSec;
+      bucket.lastV = value;
+    }
+    finish() {
+      const startTime = [];
+      const endTime = [];
+      const min = [];
+      const max = [];
+      const first = [];
+      const last = [];
+      for (const bucket of this.buckets) {
+        if (!bucket) continue;
+        startTime.push(bucket.firstT);
+        endTime.push(bucket.lastT);
+        min.push(bucket.minV);
+        max.push(bucket.maxV);
+        first.push(bucket.firstV);
+        last.push(bucket.lastV);
+      }
+      return {
+        startTime: new Float64Array(startTime),
+        endTime: new Float64Array(endTime),
+        min: new Float64Array(min),
+        max: new Float64Array(max),
+        first: new Float64Array(first),
+        last: new Float64Array(last)
+      };
+    }
+  };
+
+  // src/pulseq/gradientSampler.ts
   var TIME_EPS = 1e-15;
+  function decodedGradientTimeRange(blocks) {
+    let first = Number.POSITIVE_INFINITY;
+    let last = Number.NEGATIVE_INFINITY;
+    for (const block of blocks) {
+      for (const gradient of [block.gx, block.gy, block.gz]) {
+        if (!gradient?.timePoints.length) continue;
+        const gradientFirst = gradient.timePoints[0];
+        const gradientLast = gradient.timePoints[gradient.timePoints.length - 1];
+        if (Number.isFinite(gradientFirst)) first = Math.min(first, gradientFirst);
+        if (Number.isFinite(gradientLast)) last = Math.max(last, gradientLast);
+      }
+    }
+    return Number.isFinite(first) && Number.isFinite(last) && last >= first ? { first, last } : void 0;
+  }
+  function createDecodedGradientSampler(blocks, channel) {
+    const events = [];
+    for (const block of blocks) {
+      const gradient = block[channel];
+      if (!gradient?.timePoints.length || !gradient.waveform.length) continue;
+      const n = Math.min(gradient.timePoints.length, gradient.waveform.length);
+      if (n < 1) continue;
+      events.push({
+        gradient,
+        first: gradient.timePoints[0],
+        last: gradient.timePoints[n - 1]
+      });
+    }
+    events.sort((a, b) => a.first - b.first);
+    let eventIndex = 0;
+    let pointIndex = 0;
+    let previousTime = Number.NEGATIVE_INFINITY;
+    return (timeSec) => {
+      if (timeSec < previousTime - TIME_EPS) {
+        eventIndex = 0;
+        pointIndex = 0;
+      }
+      previousTime = timeSec;
+      while (eventIndex < events.length && events[eventIndex].last < timeSec - TIME_EPS) {
+        eventIndex++;
+        pointIndex = 0;
+      }
+      if (eventIndex >= events.length) return 0;
+      const event = events[eventIndex];
+      if (timeSec < event.first - TIME_EPS || timeSec > event.last + TIME_EPS) return 0;
+      const times = event.gradient.timePoints;
+      const values = event.gradient.waveform;
+      const n = Math.min(times.length, values.length);
+      if (Math.abs(timeSec - event.last) <= TIME_EPS && eventIndex + 1 < events.length) {
+        const next = events[eventIndex + 1];
+        if (Math.abs(next.first - timeSec) <= TIME_EPS && next.gradient.waveform.length) {
+          return 0.5 * (values[n - 1] + next.gradient.waveform[0]);
+        }
+      }
+      while (pointIndex + 1 < n && times[pointIndex + 1] <= timeSec + TIME_EPS) pointIndex++;
+      if (pointIndex >= n - 1 || timeSec <= times[pointIndex] + TIME_EPS) return values[pointIndex];
+      const t0 = times[pointIndex];
+      const t1 = times[pointIndex + 1];
+      if (!(t1 > t0)) return values[pointIndex];
+      const alpha = (timeSec - t0) / (t1 - t0);
+      return values[pointIndex] + alpha * (values[pointIndex + 1] - values[pointIndex]);
+    };
+  }
+
+  // src/pulseq/m1.ts
+  var TIME_EPS2 = 1e-15;
   function calculateM1(blocks, gradientRaster, options = {}) {
     const referenceMode = normalizeReferenceMode(options.referenceMode);
     if (!blocks.length) {
@@ -2039,10 +2186,38 @@ var Pulseq = (() => {
     const excitationTimes = rfEvents.filter((rf) => rf.use === "e").map((rf) => rf.tSec);
     const refocusingTimes = rfEvents.filter((rf) => rf.use === "r").map((rf) => rf.tSec);
     const events = buildWalkerEvents(rfEvents);
+    appendM1AdvisoryWarnings(rfEvents, tMin, warnings);
+    const rasterSec = gradientRaster > 0 ? gradientRaster : 1e-5;
+    if (rasterSec <= 0) {
+      return invalidM1("gradientRaster must be positive.", referenceMode);
+    }
+    const samples = buildSampleTimes(tMin, tMax, rasterSec);
+    const x = walkM1(gx, samples, events, excitationTimes, tMin, referenceMode);
+    const y = walkM1(gy, samples, events, excitationTimes, tMin, referenceMode);
+    const z = walkM1(gz, samples, events, excitationTimes, tMin, referenceMode);
+    if (x.t.length !== y.t.length || x.t.length !== z.t.length) {
+      warnings.push(`Internal warning: per-axis M1 output sizes disagree (${x.t.length}, ${y.t.length}, ${z.t.length}). Plot may be inconsistent.`);
+    }
+    return {
+      valid: true,
+      ok: true,
+      referenceMode,
+      tSec: new Float64Array(x.t),
+      m1x: new Float64Array(x.m1),
+      m1y: new Float64Array(y.m1),
+      m1z: new Float64Array(z.m1),
+      warnings,
+      excitationTimesSec: new Float64Array(excitationTimes),
+      refocusingTimesSec: new Float64Array(refocusingTimes)
+    };
+  }
+  function appendM1AdvisoryWarnings(rfEvents, tMin, warnings) {
     let recentExcCount = 0;
     let lastExcT = -1e9;
+    let excitationCount = 0;
     for (const rf of rfEvents) {
       if (rf.use === "e") {
+        excitationCount++;
         if (rf.tSec - lastExcT < 0.1) recentExcCount++;
         lastExcT = rf.tSec;
       }
@@ -2052,28 +2227,122 @@ var Pulseq = (() => {
         `Sequence shows ${recentExcCount} closely-spaced (<100 ms) excitation events. This pattern is consistent with a steady-state sequence for which the simplified reset/flip bookkeeping does NOT model coherent pathway interference. Treat the M1 curve as advisory only.`
       );
     }
-    if (!excitationTimes.length) {
+    if (!excitationCount) {
       warnings.push(`No excitation RF events found in sequence. M1 will be integrated from t=${tMin.toFixed(6)} s with no signal basis.`);
     }
-    const rasterSec = gradientRaster > 0 ? gradientRaster : 1e-5;
-    if (rasterSec <= 0) {
-      return invalidM1("gradientRaster must be positive.", referenceMode);
-    }
-    const samples = buildSampleTimes(tMin, tMax, rasterSec);
-    const x = walkM1(gx, samples, events, excitationTimes, tMin, referenceMode);
-    const y = walkM1(gy, samples, events, excitationTimes, tMin, referenceMode);
-    const z = walkM1(gz, samples, events, excitationTimes, tMin, referenceMode);
-    if (x.t.length !== y.t.length || x.t.length !== z.t.length) {
-      warnings.push(`Internal warning: per-axis M1 output sizes disagree (${x.t.length}, ${y.t.length}, ${z.t.length}). Plot may be inconsistent.`);
+  }
+  function calculateM1Coarse(blocks, gradientRaster, options = {}) {
+    const referenceMode = normalizeReferenceMode(options.referenceMode);
+    const emptySeries = () => ({
+      startTime: new Float64Array(),
+      endTime: new Float64Array(),
+      min: new Float64Array(),
+      max: new Float64Array(),
+      first: new Float64Array(),
+      last: new Float64Array()
+    });
+    const invalid = (error) => ({
+      valid: false,
+      ok: false,
+      coarse: true,
+      referenceMode,
+      error,
+      startSec: 0,
+      endSec: 0,
+      x: emptySeries(),
+      y: emptySeries(),
+      z: emptySeries(),
+      warnings: [],
+      excitationTimesSec: new Float64Array(),
+      refocusingTimesSec: new Float64Array()
+    });
+    if (!blocks.length) return invalid("Empty or invalid block list.");
+    if (!(gradientRaster > 0)) return invalid("gradientRaster must be positive.");
+    const range = decodedGradientTimeRange(blocks);
+    if (!range) return invalid("No gradient waveform available for M1.");
+    const warnings = [];
+    const rfEvents = collectRfEvents(blocks, warnings);
+    appendM1AdvisoryWarnings(rfEvents, range.first, warnings);
+    const excitationTimes = rfEvents.filter((rf) => rf.use === "e").map((rf) => rf.tSec);
+    const refocusingTimes = rfEvents.filter((rf) => rf.use === "r").map((rf) => rf.tSec);
+    const events = buildWalkerEvents(rfEvents);
+    const startSec = Math.min(range.first, events[0]?.tSec ?? range.first);
+    const endSec = Math.max(range.last, events[events.length - 1]?.tSec ?? range.last);
+    const maxPoints = Math.max(1024, Math.min(12e4, options.maxPoints ?? 3e4));
+    const maxBuckets = Math.floor(maxPoints / 4);
+    const builders = [
+      new BoundedSeriesBuilder(startSec, endSec, maxPoints),
+      new BoundedSeriesBuilder(startSec, endSec, maxPoints),
+      new BoundedSeriesBuilder(startSec, endSec, maxPoints)
+    ];
+    const samplers = [
+      createDecodedGradientSampler(blocks, "gx"),
+      createDecodedGradientSampler(blocks, "gy"),
+      createDecodedGradientSampler(blocks, "gz")
+    ];
+    const unsignedM0 = [0, 0, 0];
+    const unsignedM1 = [0, 0, 0];
+    let sign = 1;
+    let tReset = excitationTimes.length ? excitationTimes[0] : range.first;
+    if (range.first < tReset) tReset = range.first;
+    let currentT = tReset;
+    const reported = (axis, tSec) => referenceMode === "observationTime" ? sign * (unsignedM1[axis] - (tSec - tReset) * unsignedM0[axis]) : sign * unsignedM1[axis];
+    const advanceTo = (targetT) => {
+      if (!(targetT > currentT + TIME_EPS2)) return;
+      for (let axis = 0; axis < 3; axis++) {
+        const ga = samplers[axis](currentT);
+        const gb = samplers[axis](targetT);
+        const integrated = integrateLinearSegment(currentT, targetT, tReset, ga, gb);
+        unsignedM0[axis] += integrated[0];
+        unsignedM1[axis] += integrated[1];
+      }
+      currentT = targetT;
+    };
+    const addReported = (tSec) => {
+      for (let axis = 0; axis < 3; axis++) builders[axis].add(tSec, reported(axis, tSec));
+    };
+    const regularCount = Math.floor((range.last - range.first) / gradientRaster) + 1;
+    const regularLast = range.first + Math.max(0, regularCount - 1) * gradientRaster;
+    const hasFinalSample = regularLast < range.last - TIME_EPS2;
+    const totalSamples = regularCount + (hasFinalSample ? 1 : 0);
+    let eventIndex = 0;
+    let sampleIndex = 0;
+    while (eventIndex < events.length || sampleIndex < totalSamples) {
+      const eventTime = eventIndex < events.length ? events[eventIndex].tSec : Number.POSITIVE_INFINITY;
+      const sampleTime = sampleIndex < totalSamples ? sampleIndex < regularCount ? range.first + sampleIndex * gradientRaster : range.last : Number.POSITIVE_INFINITY;
+      if (eventTime <= sampleTime) {
+        advanceTo(eventTime);
+        if (events[eventIndex].kind === "reset") {
+          sign = 1;
+          tReset = eventTime;
+          currentT = eventTime;
+          unsignedM0.fill(0);
+          unsignedM1.fill(0);
+          for (const builder of builders) builder.add(eventTime, 0);
+        } else {
+          addReported(eventTime);
+          sign = -sign;
+        }
+        eventIndex++;
+      } else {
+        advanceTo(sampleTime);
+        addReported(sampleTime);
+        sampleIndex++;
+      }
     }
+    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.`
+    );
     return {
       valid: true,
       ok: true,
+      coarse: true,
       referenceMode,
-      tSec: new Float64Array(x.t),
-      m1x: new Float64Array(x.m1),
-      m1y: new Float64Array(y.m1),
-      m1z: new Float64Array(z.m1),
+      startSec,
+      endSec,
+      x: builders[0].finish(),
+      y: builders[1].finish(),
+      z: builders[2].finish(),
       warnings,
       excitationTimesSec: new Float64Array(excitationTimes),
       refocusingTimesSec: new Float64Array(refocusingTimes)
@@ -2112,7 +2381,7 @@ var Pulseq = (() => {
   function appendGradientPoint(series, t, value) {
     if (!Number.isFinite(t) || !Number.isFinite(value)) return;
     const last = series.time.length - 1;
-    if (last >= 0 && Math.abs(t - series.time[last]) <= TIME_EPS) {
+    if (last >= 0 && Math.abs(t - series.time[last]) <= TIME_EPS2) {
       series.value[last] = 0.5 * (series.value[last] + value);
     } else if (last < 0 || t > series.time[last]) {
       series.time.push(t);
@@ -2162,7 +2431,7 @@ var Pulseq = (() => {
     const samples = [];
     const nSamples = Math.floor((tMax - tMin) / rasterSec) + 1;
     for (let i = 0; i < nSamples; i++) samples.push(tMin + i * rasterSec);
-    if (!samples.length || samples[samples.length - 1] < tMax - TIME_EPS) samples.push(tMax);
+    if (!samples.length || samples[samples.length - 1] < tMax - TIME_EPS2) samples.push(tMax);
     return samples;
   }
   function walkM1(gradient, samples, events, excitationTimes, tMin, referenceMode) {
@@ -2176,16 +2445,16 @@ var Pulseq = (() => {
     let unsignedM1 = 0;
     let gradientIndex = -1;
     const seekGradient = (t) => {
-      while (gradientIndex + 1 < gradient.time.length && gradient.time[gradientIndex + 1] <= t + TIME_EPS) {
+      while (gradientIndex + 1 < gradient.time.length && gradient.time[gradientIndex + 1] <= t + TIME_EPS2) {
         gradientIndex++;
       }
     };
     const sampleGradient = (t) => {
       const n = gradient.time.length;
-      if (n === 0 || t < gradient.time[0] - TIME_EPS || t > gradient.time[n - 1] + TIME_EPS) return 0;
+      if (n === 0 || t < gradient.time[0] - TIME_EPS2 || t > gradient.time[n - 1] + TIME_EPS2) return 0;
       seekGradient(t);
       if (gradientIndex < 0) return 0;
-      if (gradientIndex >= n - 1 || Math.abs(t - gradient.time[gradientIndex]) <= TIME_EPS) {
+      if (gradientIndex >= n - 1 || Math.abs(t - gradient.time[gradientIndex]) <= TIME_EPS2) {
         return gradient.value[gradientIndex];
       }
       const t0 = gradient.time[gradientIndex];
@@ -2199,8 +2468,8 @@ var Pulseq = (() => {
       return sign * unsignedM1;
     };
     const advanceTo = (targetT) => {
-      if (!(targetT > currentT + TIME_EPS)) return;
-      while (currentT < targetT - TIME_EPS) {
+      if (!(targetT > currentT + TIME_EPS2)) return;
+      while (currentT < targetT - TIME_EPS2) {
         seekGradient(currentT);
         let nextT = gradientIndex + 1 < gradient.time.length ? Math.min(targetT, gradient.time[gradientIndex + 1]) : targetT;
         if (!(nextT > currentT)) nextT = targetT;
@@ -2220,7 +2489,7 @@ var Pulseq = (() => {
       if (nextEvtT <= nextSampT) {
         advanceTo(nextEvtT);
         if (events[ei].kind === "reset") {
-          if (!outT.length || outT[outT.length - 1] < nextEvtT - TIME_EPS) {
+          if (!outT.length || outT[outT.length - 1] < nextEvtT - TIME_EPS2) {
             outT.push(nextEvtT);
             outM1.push(0);
           } else {
@@ -2259,7 +2528,7 @@ var Pulseq = (() => {
 
   // src/pulseq/pns.ts
   var GAMMA_HZ_PER_T = 42576e3;
-  var TIME_EPS2 = 1e-15;
+  var TIME_EPS3 = 1e-15;
   function parsePnsHardwareAsc(text) {
     const asc = parseAscText(text);
     const prefix = resolvePnsPrefix(asc);
@@ -2391,6 +2660,148 @@ var Pulseq = (() => {
     }
     return { valid: true, ok, timeSec, pnsX, pnsY, pnsZ, pnsNorm };
   }
+  function calculatePnsCoarse(blocks, gradientRaster, hardware, options = {}) {
+    const emptySeries = () => ({
+      startTime: new Float64Array(),
+      endTime: new Float64Array(),
+      min: new Float64Array(),
+      max: new Float64Array(),
+      first: new Float64Array(),
+      last: new Float64Array()
+    });
+    const invalid = (error) => ({
+      valid: false,
+      ok: false,
+      coarse: true,
+      error,
+      startSec: 0,
+      endSec: 0,
+      x: emptySeries(),
+      y: emptySeries(),
+      z: emptySeries(),
+      norm: emptySeries(),
+      warnings: []
+    });
+    const gammaHzPerT = options.gammaHzPerT ?? GAMMA_HZ_PER_T;
+    if (!hardware.valid) return invalid("PNS hardware is not initialized.");
+    if (!blocks.length) return invalid("No sequence loaded.");
+    if (!(gradientRaster > 0) || !(gammaHzPerT > 0)) return invalid("Missing GradientRasterTime or gamma.");
+    const range = decodedGradientTimeRange(blocks);
+    if (!range || !(range.last > range.first)) return invalid("No gradient waveform available for PNS.");
+    const dtSec = gradientRaster;
+    let ntMin = Math.floor(range.first / dtSec + Number.EPSILON) + 0.5;
+    const ntMax = Math.ceil(range.last / dtSec - Number.EPSILON) - 0.5;
+    if (ntMin < 0.5) ntMin = 0.5;
+    if (ntMax < ntMin) return invalid("Unable to build regular PNS raster.");
+    const nSamples = Math.floor(ntMax - ntMin + 1);
+    if (nSamples < 2) return invalid("Too few samples for PNS computation.");
+    const longestTauMs = Math.max(
+      hardware.x.tau1Ms,
+      hardware.x.tau2Ms,
+      hardware.x.tau3Ms,
+      hardware.y.tau1Ms,
+      hardware.y.tau2Ms,
+      hardware.y.tau3Ms,
+      hardware.z.tau1Ms,
+      hardware.z.tau2Ms,
+      hardware.z.tau3Ms
+    );
+    const zptSec = longestTauMs * 4 / 1e3;
+    const preCount = Math.max(0, Math.round(zptSec / (4 * dtSec)));
+    const postCount = Math.max(0, Math.round(zptSec / dtSec));
+    const totalSamples = preCount + nSamples + postCount;
+    const hasAnyNonTrap = blocks.some((block) => block.gx?.type === "arb" || block.gy?.type === "arb" || block.gz?.type === "arb");
+    const hasAnyLabelExt = blocks.some((block) => !!(block.labelSets?.length || block.labelIncs?.length));
+    const shift = hasAnyNonTrap || hasAnyLabelExt ? 1 : 0;
+    const stimLength = Math.max(0, totalSamples - 1);
+    const desiredStimIndex = (origIndex) => {
+      const paddedIndex = preCount + origIndex;
+      if (shift > 0 && hasAnyLabelExt && origIndex === nSamples - 1) {
+        return Math.min(paddedIndex, stimLength - 1);
+      }
+      return paddedIndex - shift;
+    };
+    const startSec = ntMin * dtSec;
+    const endSec = (ntMin + nSamples - 1) * dtSec;
+    const maxPoints = Math.max(1024, Math.min(12e4, options.maxPoints ?? 3e4));
+    const maxBuckets = Math.floor(maxPoints / 4);
+    const builders = [
+      new BoundedSeriesBuilder(startSec, endSec, maxPoints),
+      new BoundedSeriesBuilder(startSec, endSec, maxPoints),
+      new BoundedSeriesBuilder(startSec, endSec, maxPoints),
+      new BoundedSeriesBuilder(startSec, endSec, maxPoints)
+    ];
+    const samplers = [
+      createDecodedGradientSampler(blocks, "gx"),
+      createDecodedGradientSampler(blocks, "gy"),
+      createDecodedGradientSampler(blocks, "gz")
+    ];
+    const hardwareAxes = [hardware.x, hardware.y, hardware.z];
+    const filterStates = hardwareAxes.map((axis) => createPnsFilterState(axis, dtSec));
+    const paddedValue = (axis, index) => {
+      if (index < preCount || index >= preCount + nSamples) return 0;
+      const rasterIndex = index - preCount;
+      return samplers[axis]((ntMin + rasterIndex) * dtSec) / gammaHzPerT;
+    };
+    const previous = [paddedValue(0, 0), paddedValue(1, 0), paddedValue(2, 0)];
+    let outputIndex = 0;
+    let ok = true;
+    for (let stimIndex = 0; stimIndex < stimLength; stimIndex++) {
+      const normalized = [0, 0, 0];
+      for (let axis = 0; axis < 3; axis++) {
+        const current = paddedValue(axis, stimIndex + 1);
+        const derivative = (current - previous[axis]) / dtSec;
+        previous[axis] = current;
+        normalized[axis] = updatePnsFilter(filterStates[axis], derivative);
+      }
+      while (outputIndex < nSamples && desiredStimIndex(outputIndex) < stimIndex) outputIndex++;
+      if (outputIndex < nSamples && desiredStimIndex(outputIndex) === stimIndex) {
+        const timeSec = (ntMin + outputIndex) * dtSec;
+        const norm = Math.hypot(normalized[0], normalized[1], normalized[2]);
+        builders[0].add(timeSec, normalized[0]);
+        builders[1].add(timeSec, normalized[1]);
+        builders[2].add(timeSec, normalized[2]);
+        builders[3].add(timeSec, norm);
+        if (norm >= 1) ok = false;
+        outputIndex++;
+      }
+    }
+    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.`
+    ];
+    return {
+      valid: true,
+      ok,
+      coarse: true,
+      startSec,
+      endSec,
+      x: builders[0].finish(),
+      y: builders[1].finish(),
+      z: builders[2].finish(),
+      norm: builders[3].finish(),
+      warnings
+    };
+  }
+  function createPnsFilterState(hardware, dtSec) {
+    const dtMs = dtSec * 1e3;
+    return {
+      alpha1: lowpassAlpha(hardware.tau1Ms, dtMs),
+      alpha2: lowpassAlpha(hardware.tau2Ms, dtMs),
+      alpha3: lowpassAlpha(hardware.tau3Ms, dtMs),
+      lp1: 0,
+      lp2: 0,
+      lp3: 0,
+      hardware
+    };
+  }
+  function updatePnsFilter(state, derivative) {
+    state.lp1 = state.alpha1 * derivative + (1 - state.alpha1) * state.lp1;
+    state.lp2 = state.alpha2 * Math.abs(derivative) + (1 - state.alpha2) * state.lp2;
+    state.lp3 = state.alpha3 * derivative + (1 - state.alpha3) * state.lp3;
+    const hw = state.hardware;
+    const numerator = hw.a1 * Math.abs(state.lp1) + hw.a2 * state.lp2 + hw.a3 * Math.abs(state.lp3);
+    return numerator / (hw.stimLimit > 0 ? hw.stimLimit : 1) * hw.gScale;
+  }
   function safePnsModel(dgdt, dtSec, hw) {
     return runPnsModel(dgdt.length, (index) => dgdt[index], dtSec, hw);
   }
@@ -2529,7 +2940,7 @@ var Pulseq = (() => {
   function appendGradientPoint2(series, t, value) {
     if (!Number.isFinite(t) || !Number.isFinite(value)) return;
     const last = series.time.length - 1;
-    if (last >= 0 && Math.abs(t - series.time[last]) <= TIME_EPS2) {
+    if (last >= 0 && Math.abs(t - series.time[last]) <= TIME_EPS3) {
       series.value[last] = 0.5 * (series.value[last] + value);
     } else if (last < 0 || t > series.time[last]) {
       series.time.push(t);
@@ -2557,9 +2968,9 @@ var Pulseq = (() => {
     return (t) => {
       const n = series.time.length;
       if (n === 0 || t < series.time[0] || t > series.time[n - 1]) return 0;
-      while (index + 1 < n && series.time[index + 1] <= t + TIME_EPS2) index++;
+      while (index + 1 < n && series.time[index + 1] <= t + TIME_EPS3) index++;
       if (index < 0) return 0;
-      if (index >= n - 1 || t <= series.time[index] + TIME_EPS2) return series.value[index];
+      if (index >= n - 1 || t <= series.time[index] + TIME_EPS3) return series.value[index];
       const t0 = series.time[index];
       const t1 = series.time[index + 1];
       if (!(t1 > t0)) return series.value[index];
@@ -2568,6 +2979,135 @@ var Pulseq = (() => {
     };
   }
 
+  // src/pulseq/derivedWindow.ts
+  function selectM1WindowBlocks(blocks, startSec, endSec) {
+    const displayStartSec = finiteMin(startSec, endSec);
+    const displayEndSec = finiteMax(startSec, endSec, displayStartSec);
+    let calculationStartSec = displayStartSec;
+    for (const block of blocks) {
+      const center = block.rf?.centerTime;
+      if (center === void 0 || center > displayStartSec) continue;
+      const use = (block.rf?.use || "").toLowerCase();
+      if (use === "e") calculationStartSec = Math.min(center, block.startTime);
+    }
+    return {
+      blocks: overlappingBlocks(blocks, calculationStartSec, displayEndSec),
+      calculationStartSec,
+      displayStartSec,
+      displayEndSec
+    };
+  }
+  function selectPnsWindowBlocks(blocks, startSec, endSec, hardware) {
+    const displayStartSec = finiteMin(startSec, endSec);
+    const displayEndSec = finiteMax(startSec, endSec, displayStartSec);
+    const longestTauMs = Math.max(
+      hardware.x.tau1Ms,
+      hardware.x.tau2Ms,
+      hardware.x.tau3Ms,
+      hardware.y.tau1Ms,
+      hardware.y.tau2Ms,
+      hardware.y.tau3Ms,
+      hardware.z.tau1Ms,
+      hardware.z.tau2Ms,
+      hardware.z.tau3Ms
+    );
+    const calculationStartSec = Math.max(0, displayStartSec - longestTauMs * 4 / 1e3);
+    return {
+      blocks: overlappingBlocks(blocks, calculationStartSec, displayEndSec),
+      calculationStartSec,
+      displayStartSec,
+      displayEndSec
+    };
+  }
+  function overlappingBlocks(blocks, startSec, endSec) {
+    return blocks.filter((block) => block.startTime + block.duration > startSec && block.startTime <= endSec);
+  }
+  function finiteMin(a, b) {
+    const aa = Number.isFinite(a) ? a : 0;
+    const bb = Number.isFinite(b) ? b : aa;
+    return Math.max(0, Math.min(aa, bb));
+  }
+  function finiteMax(a, b, fallback) {
+    const aa = Number.isFinite(a) ? a : fallback;
+    const bb = Number.isFinite(b) ? b : aa;
+    return Math.max(fallback, Math.max(aa, bb));
+  }
+
+  // src/pulseq/computeBudget.ts
+  var INTERACTIVE_COMPUTE_LIMITS = Object.freeze({
+    kspaceRasterSamples: 12e6,
+    kspaceAdcSamples: 8e6,
+    kspaceGridCandidates: 18e6,
+    derivedRasterSamples: 2e6
+  });
+  function estimateKspaceCost(blocks, gradientRaster, totalDuration) {
+    let adcSamples = 0;
+    let gradientSupportPoints = 0;
+    let rfSupportPoints = 0;
+    for (const block of blocks) {
+      if (block.adc?.numSamples && block.adc.numSamples > 0) {
+        adcSamples += block.adc.numSamples;
+      }
+      for (const gradient of [block.gx, block.gy, block.gz]) {
+        if (gradient && gradient.type !== "none" && gradient.timePoints.length >= 2) {
+          gradientSupportPoints += 2;
+        }
+      }
+      if (block.rf) rfSupportPoints += block.rf.use === "r" ? 2 : 3;
+    }
+    const rasterSamples = gradientRaster > 0 && totalDuration > 0 ? Math.max(2, Math.round(totalDuration / gradientRaster) + 1) : 0;
+    const gridCandidatePoints = rasterSamples + adcSamples + gradientSupportPoints + rfSupportPoints + 2;
+    return { rasterSamples, adcSamples, gridCandidatePoints };
+  }
+  function estimateKspacePeakMemoryBytes(estimate) {
+    const gridBytes = Math.max(0, estimate.gridCandidatePoints) * 96;
+    const adcAndTransferBytes = Math.max(0, estimate.adcSamples) * 104;
+    return Math.ceil(Math.min(Number.MAX_SAFE_INTEGER, (gridBytes + adcAndTransferBytes) * 1.25));
+  }
+  function estimateDerivedCost(blocks, gradientRaster) {
+    let firstGradientTime = Infinity;
+    let lastGradientTime = -Infinity;
+    for (const block of blocks) {
+      for (const gradient of [block.gx, block.gy, block.gz]) {
+        const times = gradient?.timePoints;
+        if (!times?.length) continue;
+        const first = times[0];
+        const last = times[times.length - 1];
+        if (Number.isFinite(first) && first < firstGradientTime) firstGradientTime = first;
+        if (Number.isFinite(last) && last > lastGradientTime) lastGradientTime = last;
+      }
+    }
+    if (!Number.isFinite(firstGradientTime) || !Number.isFinite(lastGradientTime) || lastGradientTime < firstGradientTime || gradientRaster <= 0) {
+      return { rasterSamples: 0, firstGradientTime: null, lastGradientTime: null };
+    }
+    const span = lastGradientTime - firstGradientTime;
+    let rasterSamples = Math.max(1, Math.floor(span / gradientRaster) + 1);
+    const finalRasterTime = firstGradientTime + (rasterSamples - 1) * gradientRaster;
+    if (finalRasterTime < lastGradientTime - 1e-15) rasterSamples++;
+    return { rasterSamples, firstGradientTime, lastGradientTime };
+  }
+  function formatSampleCount(value) {
+    if (value >= 1e6) return `${(value / 1e6).toFixed(1)} million`;
+    if (value >= 1e3) return `${(value / 1e3).toFixed(1)} thousand`;
+    return String(value);
+  }
+  function formatMemorySize(bytes) {
+    const safeBytes = Math.max(0, Number.isFinite(bytes) ? bytes : 0);
+    const kib = 1024;
+    const mib = kib * 1024;
+    const gib = mib * 1024;
+    if (safeBytes >= gib) {
+      const value = safeBytes / gib;
+      return `${value.toFixed(value >= 10 ? 0 : 1)} GiB`;
+    }
+    if (safeBytes >= mib) {
+      const value = safeBytes / mib;
+      return `${value.toFixed(value >= 10 ? 0 : 1)} MiB`;
+    }
+    if (safeBytes >= kib) return `${(safeBytes / kib).toFixed(1)} KiB`;
+    return `${Math.round(safeBytes)} bytes`;
+  }
+
   // src/pulseq/trdetect.ts
   var GAMMA_HZ_T2 = 42576e3;
   var DEFAULT_B0_T2 = 3;

{seqeyes_python-0.2.6.dist-info → seqeyes_python-0.2.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: seqeyes-python
-Version: 0.2.6
+Version: 0.2.7
 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-0.2.7.dist-info/RECORD

@@ -0,0 +1,8 @@
+seqeyes/__init__.py,sha256=CkueqLPBYnhJ9e4fuwd-FMMbeN5c9QGoGq_xArH7Nso,944
+seqeyes/_plot.py,sha256=v5cPAn3mO017lQlNR4bthC0QgIBK1YxjygJTAPFUz1E,8114
+seqeyes/_renderer.py,sha256=vIB0lBeuOyK6p3MyQ0qeBy-JoEUVGISxtfdny7JoqKE,9862
+seqeyes/resources/pulseq-bundle.js,sha256=CEmr0iT7GW_PswlxBJpD21q7e9igqLzotzywjBQbTEY,127007
+seqeyes/resources/viewer.html,sha256=AovT33ptVfkP2iEaIBklRQGZV1tag_OBQardKtxpru8,88066
+seqeyes_python-0.2.7.dist-info/METADATA,sha256=89YG68tvjFmsNplgLUpI6RiSSah4Tui3Nf6uZELYdaw,4502
+seqeyes_python-0.2.7.dist-info/WHEEL,sha256=lCkmxWfQsSc9CfIClYeavTdQeEX2toPqufh9gI35EQA,87
+seqeyes_python-0.2.7.dist-info/RECORD,,

seqeyes_python-0.2.6.dist-info/RECORD

@@ -1,8 +0,0 @@
-seqeyes/__init__.py,sha256=GpvQX637Z8yqYHz6arELQmXasuQm8dC-sJu6M1IP0Fs,944
-seqeyes/_plot.py,sha256=v5cPAn3mO017lQlNR4bthC0QgIBK1YxjygJTAPFUz1E,8114
-seqeyes/_renderer.py,sha256=vIB0lBeuOyK6p3MyQ0qeBy-JoEUVGISxtfdny7JoqKE,9862
-seqeyes/resources/pulseq-bundle.js,sha256=IJpZwkgi3-pftb3qVMuUNK1xMQwkVpbXecuj_jem2JE,104992
-seqeyes/resources/viewer.html,sha256=AovT33ptVfkP2iEaIBklRQGZV1tag_OBQardKtxpru8,88066
-seqeyes_python-0.2.6.dist-info/METADATA,sha256=9jH27I0J6qeaDP9gjHtvDdsjRHDifiwstn4GueZ-4Hw,4502
-seqeyes_python-0.2.6.dist-info/WHEEL,sha256=lCkmxWfQsSc9CfIClYeavTdQeEX2toPqufh9gI35EQA,87
-seqeyes_python-0.2.6.dist-info/RECORD,,