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Unify NP reading with probe part number #232

Merged
merged 12 commits into from
Nov 2, 2023
Merged

Unify NP reading with probe part number #232

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0aa2810
Explicitly add NP-Opto and new NP2 OE test
alejoe91 Nov 2, 2023
d971925
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 2, 2023
5b623b8
Use probe_part_number to reduce NP type ambiguity
alejoe91 Nov 2, 2023
4ac26c7
Solve conflicts and warning
alejoe91 Nov 2, 2023
510fcc4
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 2, 2023
cb20be8
Small fix
alejoe91 Nov 2, 2023
d9c5da9
Merge branch 'np-opto-ptype' of github.com:SpikeInterface/probeinterf…
alejoe91 Nov 2, 2023
2aaf634
Raise error if probe part number not supported
alejoe91 Nov 2, 2023
61f7c28
Fix NP-ultra probe part numbers (NP1100 and NP1110)
alejoe91 Nov 2, 2023
2dcb7a5
Add bank info to UHD
alejoe91 Nov 2, 2023
ce44730
Wrong code
alejoe91 Nov 2, 2023
aecd15c
oups
alejoe91 Nov 2, 2023
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34 changes: 30 additions & 4 deletions src/probeinterface/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -965,6 +965,26 @@ def write_csv(file, probe):
"ap_hp_filters",
),
},
# NP-Opto
"opto": {
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"probe_name": "Neuropixels Opto",
"x_pitch": 48,
"y_pitch": 20,
"contact_width": 12,
"stagger": 0.0,
"shank_pitch": 0,
"shank_number": 1,
"ncol": 2,
"polygon": polygon_description["default"],
"fields_in_imro_table": (
"channel_ids",
"banks",
"references",
"ap_gains",
"lf_gains",
"ap_hp_filters",
),
},
}


Expand Down Expand Up @@ -1437,6 +1457,7 @@ def read_openephys(

contact_ids = []
pname = np_probe.attrib["probe_name"]
headstage_part_number = np_probe.attrib.get("headstage_part_number", "")
if "2.0" in pname:
x_shift = -8
if "Multishank" in pname:
Expand All @@ -1446,12 +1467,16 @@ def read_openephys(
elif "NHP" in pname:
ptype = 0
x_shift = -11
elif "1.0" in pname:
ptype = 0
x_shift = -11
elif "Ultra" in pname:
ptype = 1100
x_shift = -8
elif "1.0" in pname and "OPTO" in headstage_part_number:
# take care of OE NPIX v<0.4.1, where Opto probes were named 1.0
ptype = "opto"
x_shift = -11
elif "1.0" in pname:
ptype = 0
x_shift = -11
else: # Probe type unknown
ptype = None
x_shift = 0
Expand Down Expand Up @@ -1479,8 +1504,9 @@ def read_openephys(
else:
contact_ids.append(f"e{contact_id}")

model_name = npx_probe[ptype]["probe_name"] if ptype is not None else pname
np_probe_dict = {
"model_name": pname,
"model_name": model_name,
"shank_ids": shank_ids,
"contact_ids": contact_ids,
"positions": positions,
Expand Down
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