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Implement the by_side grouping with probes #4272

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f258e2e
Implement the by_side grouping with probes
samuelgarcia Dec 17, 2025
d5f15d2
better handling of grouping when set_probe()
samuelgarcia Dec 19, 2025
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58 changes: 35 additions & 23 deletions src/spikeinterface/core/baserecordingsnippets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -61,17 +61,17 @@ def is_filtered(self):
# the is_filtered is handle with annotation
return self._annotations.get("is_filtered", False)

def set_probe(self, probe, group_mode="by_probe", in_place=False):
def set_probe(self, probe, group_mode="auto", in_place=False):
"""
Attach a list of Probe object to a recording.

Parameters
----------
probe_or_probegroup: Probe, list of Probe, or ProbeGroup
The probe(s) to be attached to the recording
group_mode: "by_probe" | "by_shank", default: "by_probe
"by_probe" or "by_shank". Adds grouping property to the recording based on the probes ("by_probe")
or shanks ("by_shanks")
group_mode: "auto" | "by_probe" | "by_shank" | "by_side", default: "auto"
How to add the "group" property.
"auto" is the best splitting possible that can be all at once when multiple, probe with multiple shanks and 2 sides.
in_place: bool
False by default.
Useful internally when extractor do self.set_probegroup(probe)
Expand All @@ -86,10 +86,10 @@ def set_probe(self, probe, group_mode="by_probe", in_place=False):
probegroup.add_probe(probe)
return self._set_probes(probegroup, group_mode=group_mode, in_place=in_place)

def set_probegroup(self, probegroup, group_mode="by_probe", in_place=False):
def set_probegroup(self, probegroup, group_mode="auto", in_place=False):
return self._set_probes(probegroup, group_mode=group_mode, in_place=in_place)

def _set_probes(self, probe_or_probegroup, group_mode="by_probe", in_place=False):
def _set_probes(self, probe_or_probegroup, group_mode="auto", in_place=False):
"""
Attach a list of Probe objects to a recording.
For this Probe.device_channel_indices is used to link contacts to recording channels.
Expand All @@ -103,9 +103,9 @@ def _set_probes(self, probe_or_probegroup, group_mode="by_probe", in_place=False
----------
probe_or_probegroup: Probe, list of Probe, or ProbeGroup
The probe(s) to be attached to the recording
group_mode: "by_probe" | "by_shank", default: "by_probe"
"by_probe" or "by_shank". Adds grouping property to the recording based on the probes ("by_probe")
or shanks ("by_shank")
group_mode: "auto" | "by_probe" | "by_shank" | "by_side", default: "auto"
How to add the "group" property.
"auto" is the best splitting possible that can be all at once when multiple, probe with multiple shanks and 2 sides.
in_place: bool
False by default.
Useful internally when extractor do self.set_probegroup(probe)
Expand All @@ -115,7 +115,7 @@ def _set_probes(self, probe_or_probegroup, group_mode="by_probe", in_place=False
sub_recording: BaseRecording
A view of the recording (ChannelSlice or clone or itself)
"""
assert group_mode in ("by_probe", "by_shank"), "'group_mode' can be 'by_probe' or 'by_shank'"
assert group_mode in ("auto", "by_probe", "by_shank", "by_side"), "'group_mode' can be 'auto' 'by_probe' 'by_shank' or 'by_side'"

# handle several input possibilities
if isinstance(probe_or_probegroup, Probe):
Expand Down Expand Up @@ -199,20 +199,32 @@ def _set_probes(self, probe_or_probegroup, group_mode="by_probe", in_place=False
sub_recording.set_property("location", locations, ids=None)

# handle groups
groups = np.zeros(probe_as_numpy_array.size, dtype="int64")
if group_mode == "by_probe":
for group, probe_index in enumerate(np.unique(probe_as_numpy_array["probe_index"])):
mask = probe_as_numpy_array["probe_index"] == probe_index
groups[mask] = group
all_has_shank_id = all(probe.shank_ids is not None for probe in probegroup.probes)
all_has_contact_side = all(probe.contact_sides is not None for probe in probegroup.probes)
if group_mode == "auto":
group_keys = ["probe_index"]
if all_has_shank_id:
group_keys += ["shank_ids"]
if all_has_contact_side:
group_keys += ["contact_sides"]
elif group_mode == "by_probe":
group_keys = ["probe_index"]
elif group_mode == "by_shank":
assert all(
probe.shank_ids is not None for probe in probegroup.probes
), "shank_ids is None in probe, you cannot group by shank"
for group, a in enumerate(np.unique(probe_as_numpy_array[["probe_index", "shank_ids"]])):
mask = (probe_as_numpy_array["probe_index"] == a["probe_index"]) & (
probe_as_numpy_array["shank_ids"] == a["shank_ids"]
)
groups[mask] = group
assert all_has_shank_id, "shank_ids is None in probe, you cannot group by shank"
group_keys = ["probe_index", "shank_ids"]
elif group_mode == "by_side":
assert all_has_contact_side, "contact_sides is None in probe, you cannot group by side"
if all_has_shank_id:
group_keys = ["probe_index", "shank_ids", "contact_sides"]
else:
group_keys = ["probe_index", "contact_sides"]
groups = np.zeros(probe_as_numpy_array.size, dtype="int64")
unique_keys = np.unique(probe_as_numpy_array[group_keys])
for group, a in enumerate(unique_keys):
mask = np.ones(probe_as_numpy_array.size, dtype=bool)
for k in group_keys:
mask &= (probe_as_numpy_array[k] == a[k])
groups[mask] = group
sub_recording.set_property("group", groups, ids=None)

# add probe annotations to recording
Expand Down
12 changes: 8 additions & 4 deletions src/spikeinterface/core/tests/test_baserecording.py
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Original file line number Diff line number Diff line change
Expand Up @@ -179,11 +179,15 @@ def test_BaseRecording(create_cache_folder):

# set/get Probe only 2 channels
probe = Probe(ndim=2)
positions = [[0.0, 0.0], [0.0, 15.0], [0, 30.0]]
probe.set_contacts(positions=positions, shapes="circle", shape_params={"radius": 5})
probe.set_device_channel_indices([2, -1, 0])
positions = [[0.0, 0.0], [0.0, 15.0], [0, 30.0],
[100.0, 0.0], [100.0, 15.0], [100.0, 30.0],
]
probe.set_contacts(positions=positions, shapes="circle", shape_params={"radius": 5}, shank_ids=["a"]*3 + ["b"]*3)
probe.set_device_channel_indices([2, -1, 0, -1, -1, -1 ], )
probe.create_auto_shape()

print("ici", probe.shank_ids)

rec_p = rec.set_probe(probe, group_mode="by_shank")
rec_p = rec.set_probe(probe, group_mode="by_probe")
positions2 = rec_p.get_channel_locations()
Expand Down Expand Up @@ -216,7 +220,7 @@ def test_BaseRecording(create_cache_folder):
# set unconnected probe
probe = Probe(ndim=2)
positions = [[0.0, 0.0], [0.0, 15.0], [0, 30.0]]
probe.set_contacts(positions=positions, shapes="circle", shape_params={"radius": 5})
probe.set_contacts(positions=positions, shapes="circle", shape_params={"radius": 5}, shank_ids=["a", "a", "a"])
probe.set_device_channel_indices([-1, -1, -1])
probe.create_auto_shape()

Expand Down