Implement a JSON writer replacing NaN with null #199
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Add a replacing NaN with null version of save JSON function. Currently, if there is any `nan` in the input files or during calculations within `simulariumio` using `numpy`, it might break the output JSON since JSON does not support `NaN` as a valid numerical value. This new implemented `save_replacing_nan` saves the `TrajectoryData` to a `JSON` while replacing all `NaN` with `null` (which is supported by `JSON`). This should fix the error you get when uploading the `.simularium` to the simularium website converted from `NERDSS` trajectory with `simulariumio`.
yingyue2030699
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meganrm and
toloudis
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Thank you for this contribution! We'll take a look! |
toloudis
reviewed
Aug 11, 2025
| print(f"saved to {output_path}.simularium") | ||
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| @staticmethod | ||
| def save_replacing_nan( |
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I wonder if we could do this with just an additional function argument to the main save function rather than having an entirely different function?
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Time estimate or Size
xsmall
Problem
Currently, if there is any
nanin the input files or during calculations withinsimulariumiousingnumpy, it might break the output JSON since JSON does not supportNaNas a valid numerical value.Solution
This new implemented
save_replacing_nansaves theTrajectoryDatato aJSONwhile replacing allNaNwithnull(which is supported byJSON). This should fix the error you get when uploading the.simulariumto the simularium website converted fromNERDSStrajectory withsimulariumio.A new pytest for this function is included.
Type of change
Please delete options that are not relevant.
Change summary:
Steps to Verify:
Pytest implemented at
simulariumio/tests/writers/test_json_writer.py. See the file level docstring.Screenshots (optional):
Previous
savefunction that breaks the web interface:New
save_replacing_nanfunction:Yue "Moon" Ying
NERDSS software development
Dr. Margaret Johnson Group, JHU