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NeurodataWithoutBorders / lindi

Linked Data Interface (LINDI) - cloud-friendly access to NWB data
BSD 3-Clause "New" or "Revised" License
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region references #29

Closed magland closed 5 months ago

magland commented 5 months ago

@oruebel @rly

Do you have a dandi example that uses region references? And a way to check that they are being loaded properly in pynwb?

Thx.

rly commented 5 months ago

Region references are not fully supported in the NWB software, so we can ignore those.

oruebel commented 5 months ago

Region references in the HDF5 sense (I.e. referencing an arbitrary subblock of a dataset) are currently not being used in NWB. When we need to reference subsets, we define our own types. In particular DynamucTableRegion is a type that we use where the dataset stores the indices (rows in a table) we want to select and an attribute with an object reference defines the target (here a DynamicTable, so the selection applies to the whole table not just a dataset). Another example is TimeSeriesReference to select a range in time from a TimeSeries. NWB does this in part because the selections we need apply to higher-level data types (not just individual datasets) and because region references are not easy to introspect (eg. to get the indices rather than the data) and it's easy to use them in an inefficient way. Long story short, for the purposes of NWB it's ok to leave RegionReferences out of scope

magland commented 5 months ago

Got it, thanks.