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Unify NP reading with probe part number #232

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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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189 changes: 115 additions & 74 deletions src/probeinterface/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -711,8 +711,8 @@ def write_csv(file, probe):
npx_probe = {
# Neuropixels 1.0
# This probably should be None or something else because NOT ONLY the neuropixels 1.0 have that imDatPrb_type
0: {
"probe_name": "Neuropixels 1.0",
"0": {
"model_name": "Neuropixels 1.0",
"x_pitch": 32,
"y_pitch": 20,
"contact_width": 12,
Expand All @@ -729,10 +729,11 @@ def write_csv(file, probe):
"lf_gains",
"ap_hp_filters",
),
"x_shift": -11,
},
# Neuropixels 2.0 - Single Shank - Prototype
21: {
"probe_name": "Neuropixels 2.0 - Single Shank - Prototype",
"21": {
"model_name": "Neuropixels 2.0 - Single Shank - Prototype",
"x_pitch": 32,
"y_pitch": 15,
"contact_width": 12,
Expand All @@ -742,10 +743,11 @@ def write_csv(file, probe):
"ncol": 2,
"polygon": polygon_description["default"],
"fields_in_imro_table": ("channel_ids", "banks", "references", "elec_ids"),
"x_shift": -8,
},
# Neuropixels 2.0 - Four Shank - Prototype
24: {
"probe_name": "Neuropixels 2.0 - Four Shank - Prototype",
"24": {
"model_name": "Neuropixels 2.0 - Four Shank - Prototype",
"x_pitch": 32,
"y_pitch": 15,
"contact_width": 12,
Expand All @@ -761,10 +763,11 @@ def write_csv(file, probe):
"references",
"elec_ids",
),
"x_shift": -8,
},
# Neuropixels 2.0 - Single Shank - Commercial without metal cap
2003: {
"probe_name": "Neuropixels 2.0 - Single Shank",
"2003": {
"model_name": "Neuropixels 2.0 - Single Shank",
"x_pitch": 32,
"y_pitch": 15,
"contact_width": 12,
Expand All @@ -774,10 +777,11 @@ def write_csv(file, probe):
"ncol": 2,
"polygon": polygon_description["default"],
"fields_in_imro_table": ("channel_ids", "banks", "references", "elec_ids"),
"x_shift": -8,
},
# Neuropixels 2.0 - Single Shank - Commercial with metal cap
2004: {
"probe_name": "Neuropixels 2.0 - Single Shank",
"2004": {
"model_name": "Neuropixels 2.0 - Single Shank",
"x_pitch": 32,
"y_pitch": 15,
"contact_width": 12,
Expand All @@ -787,10 +791,11 @@ def write_csv(file, probe):
"ncol": 2,
"polygon": polygon_description["default"],
"fields_in_imro_table": ("channel_ids", "banks", "references", "elec_ids"),
"x_shift": -8,
},
# Neuropixels 2.0 - Four Shank - Commercial without metal cap
2013: {
"probe_name": "Neuropixels 2.0 - Four Shank",
"2013": {
"model_name": "Neuropixels 2.0 - Four Shank",
"x_pitch": 32,
"y_pitch": 15,
"contact_width": 12,
Expand All @@ -806,10 +811,11 @@ def write_csv(file, probe):
"references",
"elec_ids",
),
"x_shift": -8,
},
# Neuropixels 2.0 - Four Shank - Commercial with metal cap
2014: {
"probe_name": "Neuropixels 2.0 - Four Shank",
"2014": {
"model_name": "Neuropixels 2.0 - Four Shank",
"x_pitch": 32,
"y_pitch": 15,
"contact_width": 12,
Expand All @@ -825,10 +831,11 @@ def write_csv(file, probe):
"references",
"elec_ids",
),
"x_shift": -8,
},
# Experimental probes previous to 1.0
"Phase3a": {
"probe_name": "Phase3a",
"model_name": "Phase3a",
"x_pitch": 32,
"y_pitch": 20,
"contact_width": 12,
Expand All @@ -844,10 +851,11 @@ def write_csv(file, probe):
"ap_gains",
"lf_gains",
),
"x_shift": -11,
},
# Neuropixels 1.0-NHP Short (10mm)
1015: {
"probe_name": "Neuropixels 1.0-NHP - short",
"1015": {
"model_name": "Neuropixels 1.0-NHP - short",
"x_pitch": 32,
"y_pitch": 20,
"contact_width": 12,
Expand All @@ -864,10 +872,11 @@ def write_csv(file, probe):
"lf_gains",
"ap_hp_filters",
),
"x_shift": -11,
},
# Neuropixels 1.0-NHP Medium (25mm)
1022: {
"probe_name": "Neuropixels 1.0-NHP - medium",
"1022": {
"model_name": "Neuropixels 1.0-NHP - medium",
"x_pitch": 103,
"y_pitch": 20,
"contact_width": 12,
Expand All @@ -884,10 +893,11 @@ def write_csv(file, probe):
"lf_gains",
"ap_hp_filters",
),
"x_shift": -11,
},
# Neuropixels 1.0-NHP 45mm SOI90 - NHP long 90um wide, staggered contacts
1030: {
"probe_name": "Neuropixels 1.0-NHP - long SOI90 staggered",
"1030": {
"model_name": "Neuropixels 1.0-NHP - long SOI90 staggered",
"x_pitch": 56,
"y_pitch": 20,
"stagger": 12,
Expand All @@ -904,10 +914,11 @@ def write_csv(file, probe):
"lf_gains",
"ap_hp_filters",
),
"x_shift": -11,
},
# Neuropixels 1.0-NHP 45mm SOI125 - NHP long 125um wide, staggered contacts
1031: {
"probe_name": "Neuropixels 1.0-NHP - long SOI125 staggered",
"1031": {
"model_name": "Neuropixels 1.0-NHP - long SOI125 staggered",
"x_pitch": 91,
"y_pitch": 20,
"contact_width": 12,
Expand All @@ -924,10 +935,11 @@ def write_csv(file, probe):
"lf_gains",
"ap_hp_filters",
),
"x_shift": -11,
},
# 1.0-NHP 45mm SOI115 / 125 linear - NHP long 125um wide, linear contacts
1032: {
"probe_name": "Neuropixels 1.0-NHP - long SOI125 linear",
"1032": {
"model_name": "Neuropixels 1.0-NHP - long SOI125 linear",
"x_pitch": 103,
"y_pitch": 20,
"contact_width": 12,
Expand All @@ -944,10 +956,11 @@ def write_csv(file, probe):
"lf_gains",
"ap_hp_filters",
),
"x_shift": -11,
},
# Ultra probe
1100: {
"probe_name": "Ultra probe",
"1100": {
"model_name": "Neuropixels Ultra",
"x_pitch": 6,
"y_pitch": 6,
"contact_width": 5,
Expand All @@ -964,21 +977,59 @@ def write_csv(file, probe):
"lf_gains",
"ap_hp_filters",
),
"x_shift": -8,
},
# NP-Opto
"1300": {
"model_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",
),
"x_shift": -11,
},
}


# TODO: unify implementation with https://github.com/jenniferColonell/SGLXMetaToCoords/blob/main/SGLXMetaToCoords.py

# Map imDatPrb_pn (probe number) to imDatPrb_type (probe type) when the latter is missing
probe_number_to_probe_type = {
"PRB_1_4_0480_1": 0,
"PRB_1_4_0480_1_C": 0,
"NP1010": 0,
"NP1015": 1015,
"NP1022": 1022,
"NP1030": 1030,
"NP1031": 1031,
"NP1032": 1032,
None: 0,
probe_part_number_to_probe_type = {
# NP1.0
"PRB_1_4_0480_1": "0",
"PRB_1_4_0480_1_C": "0",
"NP1010": "0",
None: "0", # for old version without a probe number we assume 1.0
# NHP probes
"NP1015": "1015",
"NP1022": "1022",
"NP1030": "1030",
"NP1031": "1031",
"NP1032": "1032",
# NP2.0
"NP2000": "21",
"NP2010": "24",
"NP2013": "2013",
"NP2014": "2014",
"NP2003": "2003",
"NP2004": "2004",
"PRB2_1_2_0640_0": "21",
# Other probes
"NP1100": "1100", # Ultra probe - 1 bank
"NP1110": "1100", # Ultra probe - 16 banks
"NP1300": "1300", # Opto probe
}


Expand Down Expand Up @@ -1026,22 +1077,25 @@ def _read_imro_string(imro_str: str, imDatPrb_pn: Optional[str] = None) -> Probe

"""
imro_table_header_str, *imro_table_values_list, _ = imro_str.strip().split(")")

imro_table_header = tuple(map(int, imro_table_header_str[1:].split(",")))
if len(imro_table_header) == 3:
# In older versions of neuropixel arrays (phase 3A), imro tables were structured differently.
probe_serial_number, probe_option, num_contact = imro_table_header
imDatPrb_type = "Phase3a"
elif len(imro_table_header) == 2:
imDatPrb_type, num_contact = imro_table_header
else:
raise ValueError(f"read_imro error, the header has a strange length: {imro_table_header}")

if imDatPrb_type in [0, None]:
imDatPrb_type = probe_number_to_probe_type[imDatPrb_pn]
if imDatPrb_pn is None:
if len(imro_table_header) == 3:
# In older versions of neuropixel arrays (phase 3A), imro tables were structured differently.
probe_serial_number, probe_option, num_contact = imro_table_header
imDatPrb_type = "Phase3a"
elif len(imro_table_header) == 2:
imDatPrb_type, num_contact = imro_table_header
else:
raise ValueError(f"read_imro error, the header has a strange length: {imro_table_header}")
imDatPrb_type = str(imDatPrb_type)
else:
if imDatPrb_pn not in probe_part_number_to_probe_type:
raise NotImplementedError(f"Probe part number {imDatPrb_pn} is not supported yet")
imDatPrb_type = probe_part_number_to_probe_type[imDatPrb_pn]

probe_description = npx_probe[imDatPrb_type]
probe_name = probe_description["probe_name"]
model_name = probe_description["model_name"]

fields = probe_description["fields_in_imro_table"]
contact_info = {k: [] for k in fields}
Expand Down Expand Up @@ -1079,7 +1133,7 @@ def _read_imro_string(imro_str: str, imDatPrb_pn: Optional[str] = None) -> Probe
positions = np.stack((x_pos, y_pos), axis=1)

# construct Probe object
probe = Probe(ndim=2, si_units="um", model_name=probe_name, manufacturer="IMEC")
probe = Probe(ndim=2, si_units="um", model_name=model_name, manufacturer="IMEC")
probe.set_contacts(
positions=positions,
shapes="square",
Expand Down Expand Up @@ -1134,21 +1188,21 @@ def write_imro(file: str | Path, probe: Probe):
annotations = probe.contact_annotations
ret = [f"({probe_type},{len(data)})"]

if probe_type == 0:
if probe_type == "0":
for ch in range(len(data)):
ret.append(
f"({ch} 0 {annotations['references'][ch]} {annotations['ap_gains'][ch]} "
f"{annotations['lf_gains'][ch]} {annotations['ap_hp_filters'][ch]})"
)

elif probe_type == 21:
elif probe_type in ("21", "2003", "2004"):
for ch in range(len(data)):
ret.append(
f"({data['device_channel_indices'][ch]} {annotations['banks'][ch]} "
f"{annotations['references'][ch]} {data['contact_ids'][ch][1:]})"
)

elif probe_type == 24:
elif probe_type in ("24", "2013", "2014"):
for ch in range(len(data)):
ret.append(
f"({data['device_channel_indices'][ch]} {data['shank_ids'][ch]} {annotations['banks'][ch]} "
Expand Down Expand Up @@ -1435,33 +1489,19 @@ def read_openephys(
ypos = np.array([float(electrode_ypos.attrib[ch]) for ch in channel_names])
positions = np.array([xpos, ypos]).T

contact_ids = []
pname = np_probe.attrib["probe_name"]
if "2.0" in pname:
x_shift = -8
if "Multishank" in pname:
ptype = 24
else:
ptype = 21
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
else: # Probe type unknown
ptype = None
x_shift = 0
probe_part_number = np_probe.get("probe_part_number", None)
if probe_part_number not in probe_part_number_to_probe_type:
raise NotImplementedError(f"Probe part number {probe_part_number} is not supported yet")
ptype = probe_part_number_to_probe_type[probe_part_number]
x_shift = npx_probe[ptype]["x_shift"] if ptype is not None else 0

if fix_x_position_for_oe_5 and oe_version < parse("0.6.0") and shank_ids is not None:
positions[:, 1] = positions[:, 1] - npx_probe[ptype]["shank_pitch"] * shank_ids

# x offset
positions[:, 0] += x_shift

contact_ids = []
for i, pos in enumerate(positions):
if ptype is None:
contact_ids = None
Expand All @@ -1479,8 +1519,9 @@ def read_openephys(
else:
contact_ids.append(f"e{contact_id}")

model_name = npx_probe[ptype]["model_name"] if ptype is not None else "Unknown"
np_probe_dict = {
"model_name": pname,
"model_name": model_name,
"shank_ids": shank_ids,
"contact_ids": contact_ids,
"positions": positions,
Expand Down
2 changes: 1 addition & 1 deletion src/probeinterface/probe.py
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Original file line number Diff line number Diff line change
Expand Up @@ -409,7 +409,7 @@ def set_contact_ids(self, contact_ids: np.array | list):

"""
contact_ids = np.asarray(contact_ids)
if np.all(contact_ids == ""):
if np.all([c == "" for c in contact_ids]):
self._contact_ids = None
return

Expand Down
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