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Optimize TRK reader - #173

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hanayik merged 3 commits into
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Sep 7, 2026
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hanayik merged 3 commits into
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@neurolabusc

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Inspired by trx-javascript PR#13. This accelerates the reading of a 137mb TRK file time goes from 63ms to 37ms.

…o copies

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
@neurolabusc
neurolabusc requested a review from cdrake September 3, 2026 16:46
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github-actions Bot commented Sep 3, 2026 •

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Nx Release Preview

If merged, nx release will tag 1 package(s):

Package Bump From To
ipyniivue minor 0.0.0 0.1.0
Changelog preview

ipyniivue

0.1.0 (2026-09-06)

Features

  • niivue: gradient opacity, silhouette, and a shared gradient estimator (b246878)
  • niivue: pick an exploded block and open it in its own pane (d2b61c4)
  • niivue: make the LOD compensation settings introspectable (bb2bc23)
  • niivue: add opt-in per-level opacity compensation for coarse LOD bricks (770556b)
  • niivue: back streamed chunks with an automatic coarse floor (403d7ce)
  • niivue: clipPlaneOverlay to clip overlays with the base volume (02f4281)
  • ipyniivue: NumPy-style docstrings for generated and wrapper methods (1a67982)
  • ipyniivue: surface JS errors and trim acked inbox items (ffa1dc4)
  • ipyniivue: bundle nv-ext-drawing interpolation (98cd55d)
  • ipyniivue: bundle nv-ext-image-processing transforms (1285161)
  • ipyniivue: exercise locationChange JS-to-Python event path (5442d81)
  • ipyniivue: wait_ready() + safer toJsonSafe + delayed attach (cfdfde7)
  • ipyniivue: Pythonic load helpers + canvas-init fix (9025fea)
  • ipyniivue: request/response, self-contained bundle, asset inlining (4110807)
  • ipyniivue: scaffold anywidget Jupyter widget with TS-driven codegen (23b6500)

Fixes

  • niivue: compensate the coarse floor's brightness too (6931055)
  • niivue: oversample the 3D ray march to kill render ringing (6843b5b)
  • ipyniivue: exclude overlay renderer hooks (3e0860d)
  • harden streaming budget and generated bindings (577d052)
  • niivue: audit round - per-series triggers, default trigger exclusion, doc restore (d6725ad)
  • ipyniivue: make _GeneratedNiiVue docstring actually attach (90cfa5b)
  • ipyniivue: use camelCase calMinNeg/calMaxNeg in mesh_layers demo (0ef036b)
  • ipyniivue: align codegen protocol with NiiVue defaults and binary results (6ac4aab)
  • ipyniivue: keep uploaded bytes authoritative in add_*_from_bytes (a98d4c4)
  • ipyniivue: address second-round Copilot PR review feedback (20794bf)
  • ipyniivue: suppress JupyterLab cell context menu on canvas right-click (a58bd8c)
  • ipyniivue: address Copilot PR review feedback (#9)
  • ipyniivue: paragraph-aware NumPy summary + CLAUDE.md refresh (39e42c1)
  • ipyniivue: route buffer ingress through synced inbox (2c51350)
  • stabilize ipyniivue notebook rendering (ba38839)
  • ipyniivue: anywidget initialize+render lifecycle + _msg_outbox workaround (25ab299)
  • ipyniivue: register cmdHandler before mount to fix wait_ready race (d0bbeeb)
  • ipyniivue: bump wait_ready timeout in smoke notebook to 10s (0ee4442)

Performance

  • niivue: cache affine overlay rebakes (2717694)

Thank You

  • Chris Drake
  • Claude Opus 4.7 (1M context)
  • Claude Opus 4.8
  • Claude Opus 5
  • neurolabusc
  • Taylor Hanayik @hanayik

Dry-run preview only. Versions and tags are created when a maintainer runs the Release workflow manually.

@hanayik
hanayik merged commit eaa9f3e into main Sep 7, 2026
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@hanayik
hanayik deleted the trk branch September 7, 2026 08:59
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2 participants