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from probeinterface import Probe
from probeinterface.generator import generate_dummy_probe
from pathlib import Path
import numpy as np
import pytest
def _dummy_position():
n = 24
positions = np.zeros((n, 2))
for i in range(n):
x = i // 8
y = i % 8
positions[i] = x, y
positions *= 20
positions[8:16, 1] -= 10
return positions
def test_probe():
positions = _dummy_position()
probe = Probe(ndim=2, si_units="um")
probe.set_contacts(positions=positions, shapes="circle", shape_params={"radius": 5})
probe.set_contacts(positions=positions, shapes="square", shape_params={"width": 5})
probe.set_contacts(positions=positions, shapes="rect", shape_params={"width": 8, "height": 5})
assert probe.get_contact_count() == 24
# shape of the probe
vertices = [(-20, -30), (20, -110), (60, -30), (60, 190), (-20, 190)]
probe.set_planar_contour(vertices)
# auto shape (test no error)
probe.create_auto_shape(probe_type="rect")
probe.create_auto_shape(probe_type="circular")
probe.create_auto_shape()
# annotation
probe.annotate(manufacturer="me")
assert "manufacturer" in probe.annotations
probe.annotate_contacts(impedance=np.random.rand(24) * 1000)
assert "impedance" in probe.contact_annotations
# device channel
chans = np.arange(0, 24, dtype="int")
np.random.shuffle(chans)
probe.set_device_channel_indices(chans)
# contact_ids int or str
elec_ids = np.arange(24)
probe.set_contact_ids(elec_ids)
elec_ids = [f"elec #{e}" for e in range(24)]
probe.set_contact_ids(elec_ids)
# copy
probe2 = probe.copy()
# move rotate
probe.move([20, 50])
probe.rotate(theta=40, center=[0, 0], axis=None)
# make annimage
values = np.random.randn(24)
image, xlims, ylims = probe.to_image(values, method="cubic")
image2, xlims, ylims = probe.to_image(values, method="cubic", num_pixel=16)
# ~ from probeinterface.plotting import plot_probe_group, plot_probe
# ~ import matplotlib.pyplot as plt
# ~ fig, ax = plt.subplots()
# ~ plot_probe(probe, ax=ax)
# ~ ax.imshow(image, extent=xlims+ylims, origin='lower')
# ~ ax.imshow(image2, extent=xlims+ylims, origin='lower')
# ~ plt.show()
# 3d
probe_3d = probe.to_3d()
probe_3d.rotate(theta=60, center=[0, 0, 0], axis=[0, 1, 0])
# 3d-2d
probe_3d = probe.to_3d()
probe_2d = probe_3d.to_2d(axes="xz")
assert np.allclose(probe_2d.contact_positions, probe_3d.contact_positions[:, [0, 2]])
# ~ from probeinterface.plotting import plot_probe_group, plot_probe
# ~ import matplotlib.pyplot as plt
# ~ plot_probe(probe_3d)
# ~ plt.show()
# get shanks
for shank in probe.get_shanks():
pass
# print(shank)
# print(shank.contact_positions)
# get dict and df
d = probe.to_dict()
other = Probe.from_dict(d)
# export to/from numpy
arr = probe.to_numpy(complete=False)
other = Probe.from_numpy(arr)
arr = probe.to_numpy(complete=True)
other2 = Probe.from_numpy(arr)
arr = probe_3d.to_numpy(complete=True)
other_3d = Probe.from_numpy(arr)
# export to/from DataFrame
df = probe.to_dataframe(complete=True)
other = Probe.from_dataframe(df)
df = probe.to_dataframe(complete=False)
other2 = Probe.from_dataframe(df)
df = probe_3d.to_dataframe(complete=True)
# print(df.index)
other_3d = Probe.from_dataframe(df)
assert other_3d.ndim == 3
# slice handling
selection = np.arange(0, 18, 2)
# print(selection.dtype.kind)
sliced_probe = probe.get_slice(selection)
assert sliced_probe.get_contact_count() == 9
assert sliced_probe.contact_annotations["impedance"].shape == (9,)
# ~ from probeinterface.plotting import plot_probe_group, plot_probe
# ~ import matplotlib.pyplot as plt
# ~ plot_probe(probe)
# ~ plot_probe(sliced_probe)
selection = np.ones(24, dtype="bool")
selection[::2] = False
sliced_probe = probe.get_slice(selection)
assert sliced_probe.get_contact_count() == 12
assert sliced_probe.contact_annotations["impedance"].shape == (12,)
# ~ plot_probe(probe)
# ~ plot_probe(sliced_probe)
# ~ plt.show()
def test_set_contacts_auto_generates_contact_ids():
"""When contact_ids is not supplied, Probe auto-generates ['0', ..., str(n-1)]."""
probe = Probe(ndim=2, si_units="um")
positions = np.array([[0, 0], [10, 0], [20, 0], [30, 0]])
probe.set_contacts(positions=positions, shapes="circle", shape_params={"radius": 5})
assert probe.contact_ids is not None
np.testing.assert_array_equal(probe.contact_ids, np.array(["0", "1", "2", "3"]))
def test_set_contacts_respects_explicit_contact_ids():
"""An explicit contact_ids argument is preserved verbatim."""
probe = Probe(ndim=2, si_units="um")
positions = np.array([[0, 0], [10, 0], [20, 0]])
probe.set_contacts(
positions=positions,
shapes="circle",
shape_params={"radius": 5},
contact_ids=["a", "b", "c"],
)
np.testing.assert_array_equal(probe.contact_ids, np.array(["a", "b", "c"]))
def test_set_contact_ids_all_empty_strings_regenerates():
"""Backward compat: older serialized probes used empty strings for 'unset'."""
probe = Probe(ndim=2, si_units="um")
positions = np.array([[0, 0], [10, 0], [20, 0]])
probe.set_contacts(positions=positions, shapes="circle", shape_params={"radius": 5})
probe.set_contact_ids(["", "", ""])
np.testing.assert_array_equal(probe.contact_ids, np.array(["0", "1", "2"]))
def test_set_device_channel_indices_rejects_wrong_size():
"""Setting device_channel_indices with wrong count raises ValueError."""
probe = Probe(ndim=2, si_units="um")
probe.set_contacts(
positions=np.array([[0, 0], [10, 0], [20, 0]]),
shapes="circle",
shape_params={"radius": 5},
)
with pytest.raises(ValueError, match="do not have"):
probe.set_device_channel_indices([0, 1])
def test_probe_equality_dunder():
probe1 = generate_dummy_probe()
probe2 = generate_dummy_probe()
assert probe1 == probe1
assert probe2 == probe2
assert probe1 == probe2
# Modify probe2
probe2.move([1, 1])
assert probe1 != probe2
def test_set_shanks():
probe = Probe(ndim=2, si_units="um")
probe.set_contacts(positions=np.arange(20).reshape(10, 2), shapes="circle", shape_params={"radius": 5})
# for simplicity each contact is on separate shank
shank_ids = np.arange(10)
probe.set_shank_ids(shank_ids)
assert all(probe.shank_ids == shank_ids.astype(str))
def test_save_to_zarr(tmp_path):
# Generate a dummy probe instance
probe = generate_dummy_probe()
# Define file path in the temporary directory
folder_path = Path(tmp_path) / "probe.zarr"
# Save the probe object to Zarr format
probe.to_zarr(folder_path=folder_path)
# Reload the probe object from the saved Zarr file
reloaded_probe = Probe.from_zarr(folder_path=folder_path)
# Assert that the reloaded probe is equal to the original
assert probe == reloaded_probe, "Reloaded Probe object does not match the original"
@pytest.mark.parametrize("zarr_format", [2, 3])
def test_zarr_group_formats(tmp_path, zarr_format):
# A probe saved in a zarr format 2 group, as zarr-python 2 wrote it, is still readable
import zarr
probe = generate_dummy_probe()
folder_path = Path(tmp_path) / "probe.zarr"
group = zarr.open_group(folder_path, mode="w", zarr_format=zarr_format)
probe.add_probe_to_zarr_group(group)
reloaded_probe = Probe.from_zarr(folder_path=folder_path)
assert probe == reloaded_probe
def test_position_uniqueness():
"""Test that the error message matches the full expected string for three duplicates using pytest's match regex."""
import re
positions_with_dups = np.array([[0, 0], [10, 10], [0, 0], [20, 20], [0, 0], [10, 10]])
probe = Probe(ndim=2, si_units="um")
expected_error = (
"Contact positions must be unique within a probe. "
"Found 2 duplicate(s): Position (0, 0) appears at indices [0, 2, 4]; Position (10, 10) appears at indices [1, 5]"
)
with pytest.raises(ValueError, match=re.escape(expected_error)):
probe.set_contacts(positions=positions_with_dups, shapes="circle", shape_params={"radius": 5})
def test_double_side_probe():
probe = Probe()
probe.set_contacts(
positions=np.array(
[
[0, 0],
[0, 10],
[0, 20],
[0, 0],
[0, 10],
[0, 20],
]
),
shapes="circle",
contact_sides=["front", "front", "front", "back", "back", "back"],
)
print(probe)
assert "contact_sides" in probe.to_dict()
probe2 = Probe.from_dict(probe.to_dict())
assert probe2 == probe
probe3 = Probe.from_numpy(probe.to_numpy())
assert probe3 == probe
probe4 = Probe.from_dataframe(probe.to_dataframe())
assert probe4 == probe
def _annotated_probe():
probe = generate_dummy_probe()
n = probe.get_contact_count()
probe.set_contact_ids([f"c{i}" for i in range(n)])
probe.set_shank_ids(np.array(["s0"] * (n // 2) + ["s1"] * (n - n // 2)))
probe.set_device_channel_indices(np.arange(n)[::-1])
probe.annotate(name="dummy", manufacturer="acme", model_name="x1", serial_number="sn-42")
probe.annotate_contacts(impedance=np.linspace(1.0, 2.0, n))
return probe
def test_copy_preserves_identity():
probe = _annotated_probe()
probe2 = probe.copy()
assert probe2 is not probe
np.testing.assert_array_equal(probe2.contact_ids, probe.contact_ids)
np.testing.assert_array_equal(probe2.shank_ids, probe.shank_ids)
assert probe2.annotations == probe.annotations
assert probe2.contact_annotations.keys() == probe.contact_annotations.keys()
for key in probe.contact_annotations:
np.testing.assert_array_equal(probe2.contact_annotations[key], probe.contact_annotations[key])
def test_copy_drops_device_channel_indices():
probe = _annotated_probe()
probe2 = probe.copy()
assert probe2.device_channel_indices is None
def test_copy_is_independent():
probe = _annotated_probe()
probe2 = probe.copy()
probe2.annotations["manufacturer"] = "mutated"
probe2.contact_annotations["impedance"][0] = 999.0
probe2.move([999, 999])
probe2._contact_ids[0] = "zzz"
assert probe.annotations["manufacturer"] == "acme"
assert probe.contact_annotations["impedance"][0] != 999.0
assert probe.contact_ids[0] == "c0"
def test_to_dict_array_as_list_does_not_modify_probe():
probe = _annotated_probe()
d = probe.to_dict(array_as_list=True)
assert isinstance(d["contact_annotations"]["impedance"], list)
assert isinstance(probe.contact_annotations["impedance"], np.ndarray)
# slicing relies on contact annotations staying numpy arrays
sliced = probe.get_slice(np.arange(2))
np.testing.assert_array_equal(sliced.contact_annotations["impedance"], probe.contact_annotations["impedance"][:2])
def _probe_3d_for_rotation():
probe = Probe(ndim=2)
positions = np.array([[0.0, 0.0], [10.0, 0.0], [0.0, 20.0], [10.0, 20.0]])
probe.set_contacts(positions=positions, shapes="circle", shape_params={"radius": 5})
return probe.to_3d(axes="xy")
@pytest.mark.parametrize(
"plane, vector",
[("xy", [0, 0, 1]), ("yz", [1, 0, 0]), ("xz", [0, 1, 0])],
)
def test_rotate_3d_accepts_plane_name(plane, vector):
"""A plane name must rotate about the axis normal to that plane (issue #273)."""
from_plane = _probe_3d_for_rotation()
from_vector = _probe_3d_for_rotation()
from_plane.rotate(theta=37, center=[0, 0, 0], axis=plane)
from_vector.rotate(theta=37, center=[0, 0, 0], axis=vector)
assert np.allclose(from_plane.contact_positions, from_vector.contact_positions)
assert np.allclose(from_plane.contact_plane_axes, from_vector.contact_plane_axes)
def test_rotate_3d_plane_name_keeps_normal_coordinate_fixed():
"""Rotating in the xy plane leaves z untouched."""
probe_3d = _probe_3d_for_rotation()
original_z = probe_3d.contact_positions[:, 2].copy()
probe_3d.rotate(theta=90, center=[0, 0, 0], axis="xy")
assert np.allclose(probe_3d.contact_positions[:, 2], original_z)
def test_rotate_3d_rejects_unknown_axis():
probe_3d = _probe_3d_for_rotation()
with pytest.raises(ValueError, match="axis must be one of"):
probe_3d.rotate(theta=90, center=[0, 0, 0], axis="zz")
with pytest.raises(ValueError, match="axis must be a 3-element vector"):
probe_3d.rotate(theta=90, center=[0, 0, 0], axis=[0, 1])
if __name__ == "__main__":
import tempfile
tmp_path = Path(tempfile.mkdtemp())
test_probe()
test_save_to_zarr(tmp_path)
test_double_side_probe()