pynwb [WIP] Add changes to facilitate lookup of SpikeEventSeries from Units table

[WIP] Add changes to facilitate lookup of SpikeEventSeries from Units table

Open bendichter opened this issue 5 years ago • 5 comments

add link from SpikeEventSeries to UnitSeries
add DEPRECATED to doc for ClusterWaveforms
add link from ElectrodeGroup to SpikeEventSeries
add UnitSeries object to misc, which includes optional link to Units table
Remove DecompositionSeries from LFP (It never worked anyway)
Allow for 3D data in ElectricalSeries to handle SpikeEventSeries
add get_spike_waveforms as method of Units table

Motivation

Now we can pull waveforms for specific spike events in the units table.

How to test the behavior?

import numpy as np

import pynwb
from datetime import datetime
from dateutil import tz

from pynwb.ecephys import SpikeEventSeries
from pynwb.misc import UnitSeries

dataset_zero_time = datetime(2006, 1, 2, 12, 0, 0, tzinfo=tz.gettz('US/Pacific'))
file_create_date = datetime.now(tz.tzlocal())
data_dir = 'path/to/nwb/files'
nwb_filename = 'test.nwb'
nwb = pynwb.NWBFile(session_description='no session description',
                    identifier='no identifier',
                    session_start_time=dataset_zero_time)

ecephys_mod = nwb.create_processing_module('ecephys', 'stores ecephys data')

unit_series = UnitSeries('UnitSeries0', data=np.array([0, 0, 1, 0, 1], dtype=int),
                         timestamps=np.linspace(10, 50, 5))

implant = nwb.create_device('implant')
shank0 = nwb.create_electrode_group('shank0', 'shank 0 (0-indexed)', location='unknown', device=implant)

for i in range(5):
    nwb.add_electrode(np.nan, np.nan, np.nan, np.nan, 'unknown', 'unknown', shank0)

electrode_table_region = nwb.create_electrode_table_region(np.arange(5), 'shank0 electrodes')

spike_event_series0 = SpikeEventSeries('SpikeEventSeries0', np.arange(5*5*30).reshape(5, 5, 30),
                                       np.linspace(10, 50, 5), unit_series=unit_series,
                                       electrodes=electrode_table_region)

ecephys_mod.add_data_interface(spike_event_series0)
shank0.spike_event_series = spike_event_series0


nwb.add_unit(spike_times=[1., 2., 3.], electrode_group=shank0)
nwb.add_unit(spike_times=[1.5, 2.5], electrode_group=shank0)

###

def get_spike_waveforms(units, row, spike_number=None):
    ses = units['electrode_group'].data[row].spike_event_series
    if spike_number is None:
        return ses.data[ses.unit_series.data == row, ...]
    else:
        inds = np.where(ses.unit_series.data == row)[0]
        return ses.data[inds[spike_number], ...]

Checklist

[x] Have you checked our Contributing document?
[x] Have you ensured the PR description clearly describes problem and the solution?
[x] Is your contribution compliant with our coding style ? This can be checked running flake8 from the source directory.
[x] Have you checked to ensure that there aren't other open Pull Requests for the same change?
[x] Have you included the relevant issue number using #XXX notation where XXX is the issue number ?

Feb 17 '19 02:02 bendichter

fix https://github.com/NeurodataWithoutBorders/nwb-schema/issues/248

Feb 17 '19 04:02 bendichter

@ajtritt can you help? I am getting this error and I don't know what's going wrong

import numpy as np

import pynwb
from datetime import datetime
from dateutil import tz

from pynwb.ecephys import SpikeEventSeries
from pynwb.misc import UnitSeries

dataset_zero_time = datetime(2006, 1, 2, 12, 0, 0, tzinfo=tz.gettz('US/Pacific'))
file_create_date = datetime.now(tz.tzlocal())
data_dir = 'path/to/nwb/files'
nwb_filename = 'test.nwb'
nwb = pynwb.NWBFile(session_description='no session description',
                    identifier='no identifier',
                    session_start_time=dataset_zero_time)


unit_series = UnitSeries('UnitSeries0', data=np.array([0, 0, 1, 0, 1], dtype=int),
                         timestamps=np.linspace(10, 50, 5))

implant = nwb.create_device('implant')
shank0 = nwb.create_electrode_group('shank0', 'shank 0 (0-indexed)', location='unknown', device=implant)

for i in range(5):
    nwb.add_electrode(np.nan, np.nan, np.nan, np.nan, 'unknown', 'unknown', shank0)

electrode_table_region = nwb.create_electrode_table_region(np.arange(5), 'shank0 electrodes')

spike_event_series0 = SpikeEventSeries('SpikeEventSeries0', np.arange(5*5*30).reshape(5, 5, 30),
                                       np.linspace(10, 50, 5), unit_series=unit_series,
                                       electrodes=electrode_table_region)
ecephys_mod = nwb.create_processing_module('ecephys', 'stores ecephys data')

ecephys_mod.add_data_interface(spike_event_series0)
shank0.spike_event_series = spike_event_series0


nwb.add_unit(spike_times=[1., 2., 3.], electrode_group=shank0)
nwb.add_unit(spike_times=[1.5, 2.5], electrode_group=shank0)


with pynwb.NWBHDF5IO('test_ses.nwb', 'w') as io:
    io.write(nwb)

Traceback (most recent call last):
  File "/Users/bendichter/dev/pynwb/test_spike_event_times.py", line 44, in <module>
    io.write(nwb)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/backends/hdf5/h5tools.py", line 195, in write
    call_docval_func(super(HDF5IO, self).write, kwargs)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 274, in call_docval_func
    return func(*fargs, **fkwargs)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/backends/io.py", line 39, in write
    f_builder = self.__manager.build(container, source=self.__source)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 159, in build
    result = self.__type_map.build(container, self, source=source)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 1536, in build
    builder = attr_map.build(container, manager, builder=builder, source=getargs('source', kwargs))
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 751, in build
    self.__add_groups(builder, self.__spec.groups, container, manager, source)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 956, in __add_groups
    self.__add_groups(sub_builder, spec.groups, container, build_manager, source)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 972, in __add_groups
    self.__add_containers(builder, spec, attr_value, build_manager, source, container)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 1015, in __add_containers
    self.__add_containers(builder, spec, container, build_manager, source, parent_container)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 982, in __add_containers
    rendered_obj = build_manager.build(value, source=source)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 159, in build
    result = self.__type_map.build(container, self, source=source)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 1536, in build
    builder = attr_map.build(container, manager, builder=builder, source=getargs('source', kwargs))
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 751, in build
    self.__add_groups(builder, self.__spec.groups, container, manager, source)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 972, in __add_groups
    self.__add_containers(builder, spec, attr_value, build_manager, source, container)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 1015, in __add_containers
    self.__add_containers(builder, spec, container, build_manager, source, parent_container)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 982, in __add_containers
    rendered_obj = build_manager.build(value, source=source)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 159, in build
    result = self.__type_map.build(container, self, source=source)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 1536, in build
    builder = attr_map.build(container, manager, builder=builder, source=getargs('source', kwargs))
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 750, in build
    self.__add_datasets(builder, self.__spec.datasets, container, manager, source)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 931, in __add_datasets
    self.__add_containers(builder, spec, attr_value, build_manager, source, container)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 982, in __add_containers
    rendered_obj = build_manager.build(value, source=source)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 159, in build
    result = self.__type_map.build(container, self, source=source)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 1536, in build
    builder = attr_map.build(container, manager, builder=builder, source=getargs('source', kwargs))
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 794, in build
    self.__add_attributes(builder, self.__spec.attributes, container, manager, source)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 866, in __add_attributes
    target_builder = build_manager.build(attr_value, source=source)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 159, in build
    result = self.__type_map.build(container, self, source=source)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 1536, in build
    builder = attr_map.build(container, manager, builder=builder, source=getargs('source', kwargs))
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 750, in build
    self.__add_datasets(builder, self.__spec.datasets, container, manager, source)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 931, in __add_datasets
    self.__add_containers(builder, spec, attr_value, build_manager, source, container)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 1015, in __add_containers
    self.__add_containers(builder, spec, container, build_manager, source, parent_container)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 982, in __add_containers
    rendered_obj = build_manager.build(value, source=source)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 159, in build
    result = self.__type_map.build(container, self, source=source)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 1536, in build
    builder = attr_map.build(container, manager, builder=builder, source=getargs('source', kwargs))
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 784, in build
    bldr_data.append(ReferenceBuilder(manager.build(d)))
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 159, in build
    result = self.__type_map.build(container, self, source=source)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 1536, in build
    builder = attr_map.build(container, manager, builder=builder, source=getargs('source', kwargs))
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 752, in build
    self.__add_links(builder, self.__spec.links, container, manager, source)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 891, in __add_links
    self.__add_containers(builder, spec, attr_value, build_manager, source, container)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 982, in __add_containers
    rendered_obj = build_manager.build(value, source=source)
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/utils.py", line 381, in func_call
    return func(self, **parsed['args'])
  File "/Users/bendichter/dev/pynwb/src/pynwb/form/build/map.py", line 158, in build
    raise ValueError("Can't change container_source once set")
ValueError: Can't change container_source once set

Feb 17 '19 04:02 bendichter

I'm breaking this into smaller commits

Feb 18 '19 21:02 bendichter

is it really still WiP @bendichter or might want to be closed (or converted to draft at least)?

Feb 24 '23 19:02 yarikoptic

The approach we were moving towards (and I believe is even currently possible though not ideal) is to add the waveforms for each spike of a unit as a doubly indexed (index=2 syntax) column to the Units table, which facilitates that lookup

Feb 24 '23 22:02 CodyCBakerPhD

pynwb pynwb copied to clipboard

[WIP] Add changes to facilitate lookup of SpikeEventSeries from Units table

Motivation

How to test the behavior?

Checklist

pynwb
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