Add methods to find objects of a given neurodata type / pynwb class

[rly]

Motivation

A common feature request is to find objects of a given neurodata type or pynwb class.

For example:

• get all objects with the neurodata type "EcephysSpecimen" from the namespace "ndx-aibs-ecephys"
• get all objects with the neurodata type "Subject" from the namespace "core" including subclasses/subtypes such as "EcephysSpecimen" from the namespace "ndx-aibs-ecephys"
• get all objects that are instances of a PyNWB class such as pynwb.file.Subject

Fix #560

TODO

• Make tests

Checklist

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[codecov]

Codecov Report

Attention: 5 lines in your changes are missing coverage. Please review.

Comparison is base (7c6868b) 91.99% compared to head (46e8878) 91.82%.

Files	Patch %	Lines
src/pynwb/file.py	28.57%	5 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev    #1737      +/-   ##
==========================================
- Coverage   91.99%   91.82%   -0.17%     
==========================================
  Files          27       27              
  Lines        2623     2630       +7     
  Branches      685      688       +3     
==========================================
+ Hits         2413     2415       +2     
- Misses        138      143       +5     
  Partials       72       72              

Flag	Coverage Δ
integration	70.98% <28.57%> (-0.12%)	⬇️
unit	83.53% <28.57%> (-0.15%)	⬇️

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[oruebel]

Could you clarify what use-case this function addresses that NWBFile.find_all_of_class does not?

[rly]

I added a comment in the docstring. It says: This method is useful for getting neurodata type objects from cached extensions where you do not have easy access to a python class to pass to NWBFile.find_all_of_class.

[oruebel]

Makes sense. But it seems a bit strange that this functionality is in two different places. Also, with this we would need to duplicate this also for Zarr. Instead, I'm wondering whether find_all_of_class can be modified to do both, something like:

@docval({'name': 'neurodata_types', 'type': (type, str), 'doc': 'The PyNWB container class to search for instances of or the string with the name of the neurodata_type'},)
def find_all(self, neurodata_type):
     if isinstance(neurodata_type, str):
         pynwb_cls = self.io.manager.type_map.get_dt_container_cls(neurodata_type, namespace)
     else:
        pynwb_cls = neurodata_type
     ret = [obj for obj in self.objects.values() if isinstance(obj, pynwb_class)]
     return ret

[rly]

Yeah, that works too. I'll update it

[CodyCBakerPhD]

Idea LGTM, just needs a quick test or two

[bendichter]

This is a nice idea. I have two suggestions:

1. I'm not crazy about the name. I would prefer something a bit more explicit, like find_all_of_type
2. I would rather this live in Container or maybe NWBContainer. That way it could be used on any container, not just NWBFile.

And yes, I of course agree with @CodyCBakerPhD that this will need tests

[oruebel]

I'm wondering whether it would be simpler from a user perspective to have this part of the existing all_children method. I.e., we could add the query parameters for the types (with default value of None) to all_children. If the query parameters are set to None then all_children behaves as is and returns all the children and if the parameters are set then it would use the new logic to filter for types.

pynwb/src/pynwb/file.py

Line 530 in 46e8878

def all_children(self):