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Improvements to do for NWBIO #1013

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legouee opened this issue Jul 7, 2021 · 1 comment
Open
12 tasks

Improvements to do for NWBIO #1013

legouee opened this issue Jul 7, 2021 · 1 comment
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@legouee
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legouee commented Jul 7, 2021

This issue gives a list of all the improvements to be made for the NWBIO class.

  • Have a mechanism which writes an AnalogSignal in a chunk mode to avoid a full load in memory otherwise it will be impossible to write big files to nwb.
  • Handle the general case where len(module_path) isn't 2 (in def get_class).
  • Move the function def statistics(block) to be a property of Block.
  • Handle the subclass where timeseries_class.__name__ is neither CurrentClamp nor VoltageClamp (in def get_units_conversion).
  • For NWB files created with other applications, we put everything in a single segment in a single block. We have now to investigate whether there is a reliable way to create multiple segments, e.g. using Trial information (in def read_timeseries_group).
  • Allow metadata in NWBFile constructor to be taken from kwargs ; concatenate descriptions of multiple blocks if different ; handle subject ; store additional Neo annotations somewhere in NWB file (in def write_all_blocks).
  • Check for consistency if the name is already there (in def write_electrodes).
  • Try to add array_annotations via “control” attribute (in def write_signal).
  • Handle annotations (using add_unit_column()) ; handle Neo Units ; hanle spike waveforms if any (see SpikeEventSeries in def _write_spiketrain).
  • Once the Group class is available, we could add electrode metadata to a Group containing all signals that share that electrode. This would reduce the amount of redundancy (repeated metadata in every signal in class AnalogSignalProxy).
  • Add timeseries.control or control_description in self.annotations (in def load of class AnalogSignalProxy).
  • Add ImplementError if time_slice in def load in class EventProxy and in class EpochProxy.
@apdavison apdavison mentioned this issue Jul 8, 2021
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@JuliaSprenger
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additional open issues

@JuliaSprenger JuliaSprenger added this to the 0.11.0 milestone Jul 22, 2021
@apdavison apdavison modified the milestones: 0.10.3, 0.11.0 Aug 30, 2022
@apdavison apdavison modified the milestones: 0.11.0, 0.12.0 Sep 29, 2022
@JuliaSprenger JuliaSprenger modified the milestones: 0.12.0, 0.12.1 Apr 2, 2023
@JuliaSprenger JuliaSprenger modified the milestones: 0.12.1, 0.13.0 Jul 19, 2023
@apdavison apdavison modified the milestones: 0.13.0, 0.13.1 Feb 23, 2024
@zm711 zm711 modified the milestones: 0.13.1, 0.14.0 May 3, 2024
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