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Extend HolographicSeries from Timeseries #5

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alessandratrapani
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@alessandratrapani alessandratrapani commented Nov 3, 2023

Fix #4

  • extend HolographicSeries from TimeSeries
  • extend HolographicStimulusPattern from LabMetadata
  • implement SpiralScanning table
  • implement TemporalFocusing table
  • unit test
  • example files that use this structure from both the mouse V1 and Pinto lab

@alessandratrapani alessandratrapani self-assigned this Nov 3, 2023
@alessandratrapani alessandratrapani changed the base branch from main to create_specification November 3, 2023 13:31
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@alessandratrapani alessandratrapani marked this pull request as ready for review November 8, 2023 10:30
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Tests and extension overall look very good! k

After thinking about it some more, if we put the rois in the holographicseries then we should be able to make multiple references to a subset of the rois in the plane segmentation table with only a single plane segmentation object, right? Earlier I was worried that we would need to create many plane segmentation objects, but since rois is a dynamic table region, that shouldn't be the case. If we keep rois in the holographic stimulus site, that we would run into the issue that the data array is much bigger than it needs to be if you only stimulates a subset of rois. Sorry for flip-flopping on this issue, I just wanted to consider it and make sure we get it right.

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@CodyCBakerPhD CodyCBakerPhD marked this pull request as draft December 7, 2023 16:22
@CodyCBakerPhD CodyCBakerPhD changed the base branch from create_specification to no_pattern_table December 7, 2023 16:23
@CodyCBakerPhD CodyCBakerPhD changed the base branch from no_pattern_table to create_specification December 7, 2023 16:23
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Cannot extend OptogeneticSeries to have 2D data
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