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Merging autotracker #156

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Merging autotracker #156

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edyoshikun
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@edyoshikun edyoshikun commented Aug 9, 2024

This PR adds autotracker (smart microscopy) tool into shirmPy.

For this PR, I hope to accomplish the following:

Part 1:

  • Checkout the old code and test the different algorithms
  • Ensure the tracking algorithms work for our imaging modalities
  • Write a tests for the tracking algorithms.

Part 2:

  • Integrate the autotracker as part of microscope_settings in the config. This gives the flexibility to be used for lf or ls.
  • Add separate autotracking settings that configure the method, roi, tracking frequency
  • Add a function that relies on the current Mantis_acqusition.go_to_position()
  • Test the autotracker with the Demo mode.

Part 3:

  • Test this with a test target or live sample

@edyoshikun
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edyoshikun commented Aug 16, 2024

@ieivanov so far this works using the demo.cfg in automaton. I am providing some fake calculated shifts and added a sleep()to resemble the actual tracking methods calculating the shifts.

When you review this, I would like feedback on:

  • Do you foresee any issues with the current implementation? Does the current object autotracker_hook_fn() take the proper parameters? Pay attention to how I am modifying the position_settings.xyx_positions().
  • Currently using the demo mode the auotracker() only does XY shifts given that Z is not part of the demo mode. When I read the 'Z' from the stage positions, this returns 'None'. Is that a bug or a feature?
  • When I test this on mantis using the mantis config, I think the ZYX shifts should be fed to the ASI ZYX stage and not the LF remote refocus piezo. Do you agree?

As a side note, I am thinking a bit ahead and making sure this can be used only with one arm either lf or ls.

@edyoshikun edyoshikun marked this pull request as ready for review September 18, 2024 23:14
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