Matsulab UI - #551
Closed
mattakamatsu wants to merge 4 commits into
Closed
Matsulab UI#551mattakamatsu wants to merge 4 commits into
mattakamatsu wants to merge 4 commits into
Conversation
Dark graphite chrome with phalloidin-orange accent; viewport-first layout with collapsible rail sections, floating camera cluster, and a transport bar whose scrubber paints streaming-cache coverage. Also fixes stock harness bugs: scrubber wired to gotoTime (was bound to a nonexistent handler), duration readout no longer NaN (totalSteps was never set), and loading a file now clears the client-simulator badge. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Library: SimulariumController.playbackSpeed (frames advanced per render tick) read by the viewport animate loop through a fractional-step accumulator, so 0.25x-4x playback works for both slow motion and fast-forward. Bench app: speed select in the transport bar plus keyboard control - space play/pause, arrows step one frame (shift = 10), home/end jump, [ ] cycle speed presets. Key handling falls back to event.code for environments that deliver empty key values, and the controller is exposed on window for console debugging. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
simulariumio's built-in SmoldynConverter reads `listmols` output only, which renders point molecules as spheres (viz_type 1000). Filaments are polylines and need viz_type 1001 agents whose vertices live in the flat `subpoints` array, so Smoldyn `printFilaments` output has had no path into the viewer until now. `tools/smoldyn_filaments_to_simularium.py` does that conversion. It infers dimensionality from the coordinate count (2D runs are embedded at z=0), resolves parent links so branch generations can be coloured, and optionally colours by capped vs growing barbed end instead. It also handles a scaling trap that is easy to hit and hard to diagnose: TrajectoryConverter does not centre or scale data on its own — each simulator's converter is expected to call the helpers itself. Sub-micron coordinates left at world scale sit at ~0.5 units while the viewer camera is at z=120, so the scene renders empty with no error. The script calls center_fiber_positions() and center_and_scale_agent_data(), and scales box_size to match. tools/README.md documents the whole path for someone new: clone this branch, build a Python venv, convert an output file, run the viewer with `npm run dev`, and drag the .simularium onto the page. simulariumio is stock upstream, so no lab fork is needed for the Python side. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Converting the actin compression baseline (43 MB, 351 frames, growing from 3 to 3,606 filaments) did not finish in 8 minutes. Cost scales with agent-frames -- frames x filaments per frame -- and grows faster than linearly, so in a branching run where filament count rises exponentially the last few frames dominate the whole conversion. Adds --stride N (keep every Nth frame) and --max-time T (drop frames after T), applied before anything else touches the data. The script now prints its frame and agent-frame counts and warns above 50,000 agent-frames, so the failure mode is visible up front rather than as an apparent hang. Measured on that baseline: --stride 10 gives 36 frames / 19,340 agent-frames in 4 seconds (2.4 MB output), --stride 5 gives 13 seconds, and no stride does not complete. README documents the tradeoff with those numbers and recommends starting at --stride 10. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
mattakamatsu
requested review from
ShrimpCryptid and
meganrm
and removed request for
a team
September 16, 2026 01:10
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Time Estimate or Size
How long do you expect it to take a reviewer to review this PR?
Alternately, is this PR xsmall, small, medium, large, or xlarge?
Problem
What is the problem this work solves, including
Link to story or ticket
Solution
What I/we did to solve this problem
with @pairperson1
Type of change
Please delete options that are not relevant.
Change summary:
Steps to Verify:
Screenshots (optional):
Show-n-tell images/animations here
Keyfiles (delete if not relevant):
Thanks for contributing!