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Merged
apdavison merged 2 commits into from
Jun 22, 2022
Merged

Enable NWBIO to write lazy data objects #1130

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462446a
Enable NWBIO to write lazy data objects
JuliaSprenger Jun 21, 2022
5d30cfe
pep8
JuliaSprenger Jun 21, 2022
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22 changes: 17 additions & 5 deletions neo/io/nwbio.py
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Original file line number Diff line number Diff line change
Expand Up @@ -561,6 +561,9 @@ def _write_signal(self, nwbfile, signal, electrodes):
additional_metadata["conversion"] = conversion
else:
units = signal.units
if hasattr(signal, 'proxy_for') and signal.proxy_for in [AnalogSignal,
IrregularlySampledSignal]:
signal = signal.load()
if isinstance(signal, AnalogSignal):
sampling_rate = signal.sampling_rate.rescale("Hz")
tS = timeseries_class(
Expand Down Expand Up @@ -597,20 +600,26 @@ def _write_signal(self, nwbfile, signal, electrodes):
return tS

def _write_spiketrain(self, nwbfile, spiketrain):
segment = spiketrain.segment
if hasattr(spiketrain, 'proxy_for') and spiketrain.proxy_for is SpikeTrain:
spiketrain = spiketrain.load()
nwbfile.add_unit(spike_times=spiketrain.rescale('s').magnitude,
obs_intervals=[[float(spiketrain.t_start.rescale('s')),
float(spiketrain.t_stop.rescale('s'))]],
_name=spiketrain.name,
# _description=spiketrain.description,
segment=spiketrain.segment.name,
block=spiketrain.segment.block.name)
segment=segment.name,
block=segment.block.name)
# todo: handle annotations (using add_unit_column()?)
# todo: handle Neo Units
# todo: handle spike waveforms, if any (see SpikeEventSeries)
return nwbfile.units

def _write_event(self, nwbfile, event):
hierarchy = {'block': event.segment.block.name, 'segment': event.segment.name}
segment = event.segment
if hasattr(event, 'proxy_for') and event.proxy_for == Event:
event = event.load()
hierarchy = {'block': segment.block.name, 'segment': segment.name}
tS_evt = AnnotationSeries(
name=event.name,
data=event.labels,
Expand All @@ -621,13 +630,16 @@ def _write_event(self, nwbfile, event):
return tS_evt

def _write_epoch(self, nwbfile, epoch):
segment = epoch.segment
if hasattr(epoch, 'proxy_for') and epoch.proxy_for == Epoch:
epoch = epoch.load()
for t_start, duration, label in zip(epoch.rescale('s').magnitude,
epoch.durations.rescale('s').magnitude,
epoch.labels):
nwbfile.add_epoch(t_start, t_start + duration, [label], [],
_name=epoch.name,
segment=epoch.segment.name,
block=epoch.segment.block.name)
segment=segment.name,
block=segment.block.name)
return nwbfile.epochs


Expand Down
59 changes: 59 additions & 0 deletions neo/test/iotest/test_nwbio.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,9 @@
from neo.core import AnalogSignal, SpikeTrain, Event, Epoch, IrregularlySampledSignal, Segment, \
Block

from neo.rawio.examplerawio import ExampleRawIO
from neo.io.proxyobjects import (AnalogSignalProxy, SpikeTrainProxy, EventProxy, EpochProxy)

try:
import pynwb
from neo.io.nwbio import NWBIO
Expand Down Expand Up @@ -250,6 +253,62 @@ def test_roundtrip_with_annotations(self):

os.remove(test_file_name)

def test_write_proxy_objects(self):
test_file_name = self.local_test_dir / "test_round_trip_with_annotations.nwb"

# generate dummy IO as basis for ProxyObjects
self.proxy_reader = ExampleRawIO(filename='my_filename.fake')
self.proxy_reader.parse_header()

# generate test structure with proxy objects
original_block = Block(name='myblock', session_start_time=datetime.now().astimezone(),
session_description=str(test_file_name),
identifier=str(test_file_name))
seg = Segment(name='mysegment')
original_block.segments.append(seg)

# create proxy objects
proxy_anasig = AnalogSignalProxy(rawio=self.proxy_reader, stream_index=0,
inner_stream_channels=None, block_index=0, seg_index=0,)
proxy_anasig.segment = seg
seg.analogsignals.append(proxy_anasig)

proxy_sptr = SpikeTrainProxy(rawio=self.proxy_reader, spike_channel_index=0, block_index=0,
seg_index=0)
proxy_sptr.segment = seg
seg.spiketrains.append(proxy_sptr)

proxy_event = EventProxy(rawio=self.proxy_reader, event_channel_index=0, block_index=0,
seg_index=0)
proxy_event.segment = seg
seg.events.append(proxy_event)

proxy_epoch = EpochProxy(rawio=self.proxy_reader, event_channel_index=1, block_index=0,
seg_index=0)
proxy_epoch.segment = seg
seg.epochs.append(proxy_epoch)

original_block.create_relationship()

iow = NWBIO(filename=test_file_name, mode='w')

# writing data via proxyobjects
iow.write_all_blocks([original_block])

# checking written data
ior = NWBIO(filename=test_file_name, mode='r')
retrieved_block = ior.read_all_blocks()[0]

for original_segment, retrieved_segment in zip(original_block.segments,
retrieved_block.segments):
assert_array_equal(original_segment.analogsignals[0].load().magnitude,
retrieved_segment.analogsignals[0].magnitude)
assert_array_equal(original_segment.spiketrains[0].load().magnitude,
retrieved_segment.spiketrains[0].magnitude)
assert_array_equal(original_segment.events[0].load().magnitude,
retrieved_segment.events[0].magnitude)
assert_array_equal(original_segment.epochs[0].load().magnitude,
retrieved_segment.epochs[0].magnitude)

if __name__ == "__main__":
if HAVE_PYNWB:
Expand Down