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Merge pull request #232 from SpikeInterface/np-opto-ptype
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Unify NP reading with probe part number
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@samuelgarcia
samuelgarcia authored Nov 2, 2023
2 parents c5e74d9 + aecd15c commit aac4339
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Showing 6 changed files with 464 additions and 88 deletions.
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
View file
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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