holographic stimulation

[bendichter]

I'd like to add holographic optogenetic stimulation. They key difference with this method is that stimulation can be applied to a very small spatial area, and is often used to stimulate a specific neuron (ophys ROI). I want to associate stimulus sites with an ROI in the PlaneSegmentation table. I think the most straightforward way to add this would be to add a column to the PlaneSegmentation table that is a vector of links to OptogeneticStimulusSite objects (similar to how we link to ElectrodeGroup objects in the electrodes table). I have put together the following script to test this, but it does not currently work.

from pynwb.ogen import OptogeneticStimulusSite
from pynwb.device import Device
from pynwb.ophys import PlaneSegmentation, ImagingPlane, OpticalChannel
import numpy as np
from pynwb import NWBHDF5IO, NWBFile
from datetime import datetime

nwbfile = NWBFile("aa", "aa", datetime.now())
device = nwbfile.create_device("my_device")

optical_channel = OpticalChannel(
    name="optical_channel",
    description="description",
    emission_lambda=500.,
)

imaging_plane = nwbfile.create_imaging_plane(
    name="name",
    optical_channel=optical_channel,
    description="description",
    device=device,
    excitation_lambda=500.,
    indicator="GFP",
    location="M1"
)


ogen_stim_site = nwbfile.create_ogen_site(
    "my_stim_site",
    device=device,
    description="my desc",
    excitation_lambda=500.,
    location="M1",
)

plane_seg = PlaneSegmentation(description="desc", imaging_plane=imaging_plane)

plane_seg.add_column("ogen_stim_site", "link to optogenetic stimulation site")
plane_seg.add_row(ogen_stim_site=ogen_stim_site)


ophys = nwbfile.create_processing_module("ophys", "ophys")
ophys.add(plane_seg)

with NWBHDF5IO("test_ogen.nwb", "w") as io:
    io.write(plane_seg)

---------------------------------------------------------------------------
ReferenceTargetNotBuiltError              Traceback (most recent call last)
/var/folders/cg/mhhypnc14wn9kz5ydllymyc00000gp/T/ipykernel_20605/2585812746.py in <module>
     44 
     45 with NWBHDF5IO("test_ogen.nwb", "w") as io:
---> 46     io.write(plane_seg)

~/dev/hdmf/src/hdmf/utils.py in func_call(*args, **kwargs)
    591             def func_call(*args, **kwargs):
    592                 pargs = _check_args(args, kwargs)
--> 593                 return func(args[0], **pargs)
    594         else:
    595             def func_call(*args, **kwargs):

~/dev/hdmf/src/hdmf/backends/hdf5/h5tools.py in write(self, **kwargs)
    356 
    357         cache_spec = popargs('cache_spec', kwargs)
--> 358         call_docval_func(super().write, kwargs)
    359         if cache_spec:
    360             self.__cache_spec()

~/dev/hdmf/src/hdmf/utils.py in call_docval_func(func, kwargs)
    432 def call_docval_func(func, kwargs):
    433     fargs, fkwargs = fmt_docval_args(func, kwargs)
--> 434     return func(*fargs, **fkwargs)
    435 
    436 

~/dev/hdmf/src/hdmf/utils.py in func_call(*args, **kwargs)
    591             def func_call(*args, **kwargs):
    592                 pargs = _check_args(args, kwargs)
--> 593                 return func(args[0], **pargs)
    594         else:
    595             def func_call(*args, **kwargs):

~/dev/hdmf/src/hdmf/backends/io.py in write(self, **kwargs)
     48         """Write a container to the IO source."""
     49         container = popargs('container', kwargs)
---> 50         f_builder = self.__manager.build(container, source=self.__source, root=True)
     51         self.write_builder(f_builder, **kwargs)
     52 

~/dev/hdmf/src/hdmf/utils.py in func_call(*args, **kwargs)
    591             def func_call(*args, **kwargs):
    592                 pargs = _check_args(args, kwargs)
--> 593                 return func(args[0], **pargs)
    594         else:
    595             def func_call(*args, **kwargs):

~/dev/hdmf/src/hdmf/build/manager.py in build(self, **kwargs)
    186                                  container.__class__.__name__, container.name))
    187         if root:  # create reference builders only after building all other builders
--> 188             self.__add_refs()
    189             self.__active_builders.clear()  # reset active builders now that build process has completed
    190         return result

~/dev/hdmf/src/hdmf/build/manager.py in __add_refs(self)
    231             self.logger.debug("Adding ReferenceBuilder with call id %d from queue (length %d)"
    232                               % (id(call), len(self.__ref_queue)))
--> 233             call()
    234 
    235     def queue_ref(self, func):

~/dev/hdmf/src/hdmf/build/objectmapper.py in _filler()
    841                     bldr_data.append(None)
    842                 else:
--> 843                     target_builder = self.__get_target_builder(d, build_manager, builder)
    844                     bldr_data.append(ReferenceBuilder(target_builder))
    845             builder.data = bldr_data

~/dev/hdmf/src/hdmf/build/objectmapper.py in __get_target_builder(self, container, build_manager, builder)
    885         target_builder = build_manager.get_builder(container)
    886         if target_builder is None:
--> 887             raise ReferenceTargetNotBuiltError(builder, container)
    888         return target_builder
    889 

ReferenceTargetNotBuiltError: ogen_stim_site (name/ogen_stim_site): Could not find already-built Builder for OptogeneticStimulusSite 'my_stim_site' in BuildManager

@rly do you think this is a good approach? Do you know how we might fix this so that it works?

[rly]

I think that approach is fine. If this is a common new type of data, it might be nice to create an extension so that the format becomes more standardized.

    io.write(plane_seg)

should be

    io.write(nwbfile)

to make it work.

[bendichter]

oops haha

[bendichter]

thanks!