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Fix #225 Add NWBZarrIO.read_nwb convenience function
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Original file line number | Diff line number | Diff line change |
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import unittest | ||
from hdmf_zarr import NWBZarrIO | ||
import os | ||
import shutil | ||
import datetime | ||
from dateutil.tz import tzlocal | ||
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try: | ||
from pynwb import NWBFile | ||
PYNWB_AVAILABLE = True | ||
except ImportError: | ||
PYNWB_AVAILABLE = False | ||
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@unittest.skipIf(not PYNWB_AVAILABLE, "PyNWB not installed") | ||
class TestNWBZarrIO(unittest.TestCase): | ||
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def setUp(self): | ||
self.filepath = "test_io.zarr" | ||
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def tearDown(self): | ||
if os.path.exists(self.filepath): | ||
shutil.rmtree(self.filepath) | ||
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def write_test_file(self): | ||
# Create the NWBFile | ||
nwbfile = NWBFile( | ||
session_description="my first synthetic recording", | ||
identifier="EXAMPLE_ID", | ||
session_start_time=datetime.now(tzlocal()), | ||
experimenter="Dr. Bilbo Baggins", | ||
lab="Bag End Laboratory", | ||
institution="University of Middle Earth at the Shire", | ||
experiment_description="I went on an adventure with thirteen dwarves " | ||
"to reclaim vast treasures.", | ||
session_id="LONELYMTN", | ||
) | ||
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# Create a device | ||
device = nwbfile.create_device( | ||
name="array", description="the best array", manufacturer="Probe Company 9000" | ||
) | ||
with NWBZarrIO(path=self.filepath, mode="w") as io: | ||
io.write(nwbfile) | ||
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||
@unittest.skip | ||
def test_read_nwb(self): | ||
""" | ||
Test reading a local file with NWBZarrIO.read_nwb. | ||
NOTE: See TestFSSpecStreaming.test_fsspec_streaming_via_read_nwb for corresponding tests | ||
for reading a remote file with NWBZarrIO.read_nwb | ||
""" | ||
self.write_test_file() | ||
nwbfile = NWBZarrIO.read_nwb(path=self.filepath, mode="r") | ||
self.assertEqual(len(nwbfile.devices), 1) | ||
self.assertEqual(nwbfile.experimenter, "Dr. Bilbo Baggins") |