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https://github.com/p2p-ld/nwb-linkml.git
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114 lines
3 KiB
Python
114 lines
3 KiB
Python
from typing import Tuple
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import numpy as np
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import pytest
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# FIXME: Make this just be the output of the provider by patching into import machinery
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from nwb_linkml.models.pydantic.core.v2_7_0.namespace import (
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Device,
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DynamicTableRegion,
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ElectricalSeries,
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ElectrodeGroup,
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ExtracellularEphysElectrodes,
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)
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@pytest.fixture()
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def electrical_series() -> Tuple["ElectricalSeries", "ExtracellularEphysElectrodes"]:
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"""
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Demo electrical series with adjoining electrodes
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"""
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n_electrodes = 5
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n_times = 100
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data = np.arange(0, n_electrodes * n_times).reshape(n_times, n_electrodes).astype(float)
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timestamps = np.linspace(0, 1, n_times)
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device = Device(name="my electrode")
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# electrode group is the physical description of the electrodes
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electrode_group = ElectrodeGroup(
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name="GroupA",
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device=device,
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description="an electrode group",
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location="you know where it is",
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)
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# make electrodes tables
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electrodes = ExtracellularEphysElectrodes(
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description="idk these are also electrodes",
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id=np.arange(0, n_electrodes),
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x=np.arange(0, n_electrodes).astype(float),
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y=np.arange(n_electrodes, n_electrodes * 2).astype(float),
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group=[electrode_group] * n_electrodes,
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group_name=[electrode_group.name] * n_electrodes,
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location=[str(i) for i in range(n_electrodes)],
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extra_column=["sup"] * n_electrodes,
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)
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electrical_series = ElectricalSeries(
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name="my recording!",
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electrodes=DynamicTableRegion(
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table=electrodes, value=np.arange(0, n_electrodes), name="electrodes", description="hey"
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),
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timestamps=timestamps,
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data=data,
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)
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return electrical_series, electrodes
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def test_dynamictable_indexing(electrical_series):
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"""
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Can index values from a dynamictable
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"""
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series, electrodes = electrical_series
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colnames = [
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"id",
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"x",
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"y",
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"group",
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"group_name",
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"location",
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"extra_column",
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]
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dtypes = [
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np.dtype("int64"),
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np.dtype("float64"),
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np.dtype("float64"),
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] + ([np.dtype("O")] * 4)
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row = electrodes[0]
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# successfully get a single row :)
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assert row.shape == (1, 7)
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assert row.dtypes.values.tolist() == dtypes
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assert row.columns.tolist() == colnames
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# slice a range of rows
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rows = electrodes[0:3]
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assert rows.shape == (3, 7)
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assert rows.dtypes.values.tolist() == dtypes
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assert rows.columns.tolist() == colnames
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# get a single column
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col = electrodes["y"]
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assert all(col == [5, 6, 7, 8, 9])
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# get a single cell
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val = electrodes[0, "y"]
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assert val == 5
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val = electrodes[0, 2]
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assert val == 5
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# get a slice of rows and columns
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subsection = electrodes[0:3, 0:3]
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assert subsection.shape == (3, 3)
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assert subsection.columns.tolist() == colnames[0:3]
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assert subsection.dtypes.values.tolist() == dtypes[0:3]
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def test_dynamictable_append_column():
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pass
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def test_dynamictable_append_row():
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pass
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