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swmr implementation#28

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Harrison-Oatman merged 1 commit intomainfrom
13-hdf5-swmr
Feb 1, 2026
Merged

swmr implementation#28
Harrison-Oatman merged 1 commit intomainfrom
13-hdf5-swmr

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Implemented swmr mode for data saving. Major changes

  • hdf5 mode is now the only mode for saving data. This is basically how it already was, because tifs are not well supported here.
  • hdf5 files are opened at the beginning of the experiment, and kept open until the experiment closes / fails
  • hdf5 files are saved by MicroscopeOutbox in swmr mode, which allows other processes to open the files during the experiment
  • convert_hdf5s.py opens files to read in swmr mode, which should not interrupt the ongoing experiment.
  • AquisitionEvent class no longer keeps a "super_axes" parameter, which had been kept around in case we wanted to organize hdf5 files into different folders. I don't see a good use case for it, and it makes the implementation of microscopeoutbox more confusing, so I've removed it.

@Harrison-Oatman Harrison-Oatman linked an issue Feb 1, 2026 that may be closed by this pull request
@Harrison-Oatman Harrison-Oatman merged commit afe8f2f into main Feb 1, 2026
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Rework: hdf5 single writer multiple reader

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