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Best way to use Stage Position List for multi_d_acquisition_events #778

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jones-lab-tamu opened this issue Jun 17, 2024 · 1 comment
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@jones-lab-tamu
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I am trying to run a multi_d_acquisition_events() acquisition to image a slide, and I have managed to figure out how to generate a coordinate list that is saved in the Stage Position List in micro-manager, but I cannot find any good way to use this with multi_d,
calling get_positions() on positionList returns
<pyjavaz.bridge.[Lorg_micromanager_MultiStagePosition; object at 0x000001CA4B636420>
rather than a list of positions. trying to call get_x() or get_y() at any index on this object or on positionList throws an error.
And finally, trying to save the list as a json file to be parsed using save() creates a file with an empty coordinates list.
Is getting the coordinates into a list for the acquisition necessary, or is there some way to tell the acquisition to use the coordinates already saved in micromanager?
If the list is necessary, how do I actually get a list of coordinates from micromanager to use?

Thanks

@jones-lab-tamu jones-lab-tamu added the question Further information is requested label Jun 17, 2024
@henrypinkard
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You're calling the Java side position list code. To access the positions in there you'll need to convert them to python objects using the Java API somehow

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