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Fix tests to use new metadata format #22

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merged 2 commits into from
Dec 20, 2024
Merged

Fix tests to use new metadata format #22

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73fed42
Fix tests to use new metadata format
rly Dec 20, 2024
5c53378
Fix dict init
rly Dec 20, 2024
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16 changes: 0 additions & 16 deletions tests/metadata.yaml
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22 changes: 12 additions & 10 deletions tests/test_convert_raw_ephys.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,11 @@ def test_add_electrode_data():
"""
# Create a test metadata dictionary
metadata = {}
metadata["impedance_file_path"] = "tests/test_data/processed_ephys/impedance.csv"
metadata["channel_geometry_file_path"] = "tests/test_data/processed_ephys/geom.csv"
metadata["electrodes_location"] = "Nucleus Accumbens core"
metadata["device"] = {
metadata["ephys"] = {}
metadata["ephys"]["impedance_file_path"] = "tests/test_data/processed_ephys/impedance.csv"
metadata["ephys"]["channel_geometry_file_path"] = "tests/test_data/processed_ephys/geom.csv"
metadata["ephys"]["electrodes_location"] = "Nucleus Accumbens core"
metadata["ephys"]["device"] = {
"name": "Probe",
"description": "Berke Lab Probe",
"manufacturer": "My Manufacturer",
Expand Down Expand Up @@ -51,7 +52,7 @@ def test_add_electrode_data():
eg = nwbfile.electrode_groups["ElectrodeGroup"]
assert eg is not None
assert eg.description == "All electrodes"
assert eg.location == metadata["electrodes_location"]
assert eg.location == metadata["ephys"]["electrodes_location"]
assert eg.device is device

# Test that the nwbfile has the expected electrodes after filtering
Expand Down Expand Up @@ -111,11 +112,12 @@ def test_add_raw_ephys():
)

metadata = {}
metadata["openephys_folder_path"] = "tests/test_data/raw_ephys/2022-07-25_15-30-00"
metadata["impedance_file_path"] = "tests/test_data/processed_ephys/impedance.csv"
metadata["channel_geometry_file_path"] = "tests/test_data/processed_ephys/geom.csv"
metadata["electrodes_location"] = "Nucleus Accumbens core"
metadata["device"] = {
metadata["ephys"] = {}
metadata["ephys"]["openephys_folder_path"] = "tests/test_data/raw_ephys/2022-07-25_15-30-00"
metadata["ephys"]["impedance_file_path"] = "tests/test_data/processed_ephys/impedance.csv"
metadata["ephys"]["channel_geometry_file_path"] = "tests/test_data/processed_ephys/geom.csv"
metadata["ephys"]["electrodes_location"] = "Nucleus Accumbens core"
metadata["ephys"]["device"] = {
"name": "Probe",
"description": "Berke Lab Probe",
"manufacturer": "My Manufacturer",
Expand Down
5 changes: 3 additions & 2 deletions tests/test_convert_spikes.py
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Expand Up @@ -13,8 +13,9 @@ def test_add_spikes():
`python tests/test_data/create_spike_test_data.py`.
"""
metadata = {}
metadata["mountain_sort_output_file_path"] = "tests/test_data/processed_ephys/firings.mda"
metadata["sampling_frequency"] = 30_000
metadata["ephys"] = {}
metadata["ephys"]["mountain_sort_output_file_path"] = "tests/test_data/processed_ephys/firings.mda"
metadata["ephys"]["sampling_frequency"] = 30_000

nwbfile = NWBFile(
session_description="Mock session",
Expand Down
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