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Json converter failed for bonds as fibers and Binary output cannot be played on the website #200

@sangmk

Description

@sangmk

System and Software

  • simulariumio Version: Forked from github repo, main branch, commit Mem3DG converter #195
  • Python Version: 3.11.7
  • Operating System: MacOS

Description

I have a NERDSS simulation converted to simularium file for web visualization.

  1. The binary conversion which worked previously cannot be played on the website now. When I hit the triangle start button, all buttons shows loading status and the video is never played. However, each single frame can be viewed normally.
  2. I also tried converting to Json. The website plays the video. However, all bonds (set as fibers) have wrong positions.
    I checked the function Writer._get_frame_buffer() and it seems binary writer and Json writer should give the same result.

Expected Behavior

What did you expect to happen instead?

  1. Binary file should be played normally.
  2. Json files should be viewed normally.

Reproduction

A minimal example that exhibits the behavior.

Files needed to reproduce is attached in this zip file. Please follow the instructions:

  1. Edit the import part of simularium_converter.py, to make sure it finds the simulariumio package. Or, you may remove all the sys.path setup and use installed simulariumio.
  2. Run the simularium_converter.py file.
  3. Converted files can be uploaded to https://simularium.allencell.org/viewer for visulization. The Json file is het3mer.json.simularium and the binary file is het3mer.simularium

nerdss_simularium_conversion.zip

Environment

Any additional information about your environment
I use the base env of conda 24.11.3.

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