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JaerongAJaerongA
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fixed typo & black formatting
1 parent dc9b293 commit f1d6a87

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+91
-36
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+91
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‎element_array_ephys/probe.py‎

Lines changed: 91 additions & 36 deletions
Original file line numberDiff line numberDiff line change
@@ -15,11 +15,18 @@ def activate(schema_name, *, create_schema=True, create_tables=True):
1515
:param create_schema: when True (default), create schema in the database if it does not yet exist.
1616
:param create_tables: when True (default), create tables in the database if they do not yet exist.
1717
"""
18-
schema.activate(schema_name, create_schema=create_schema, create_tables=create_tables)
18+
schema.activate(
19+
schema_name, create_schema=create_schema, create_tables=create_tables
20+
)
1921

2022
# Add neuropixels probes
21-
for probe_type in ('neuropixels 1.0 - 3A', 'neuropixels 1.0 - 3B', 'neuropixels UHD',
22-
'neuropixels 2.0 - SS', 'neuropixels 2.0 - MS'):
23+
for probe_type in (
24+
"neuropixels 1.0 - 3A",
25+
"neuropixels 1.0 - 3B",
26+
"neuropixels UHD",
27+
"neuropixels 2.0 - SS",
28+
"neuropixels 2.0 - MS",
29+
):
2330
ProbeType.create_neuropixels_probe(probe_type)
2431

2532

@@ -43,7 +50,7 @@ class Electrode(dj.Part):
4350
"""
4451

4552
@staticmethod
46-
def create_neuropixels_probe(probe_type='neuropixels 1.0 - 3A'):
53+
def create_neuropixels_probe(probe_type="neuropixels 1.0 - 3A"):
4754
"""
4855
Create `ProbeType` and `Electrode` for neuropixels probes:
4956
+ neuropixels 1.0 - 3A
@@ -58,29 +65,65 @@ def create_neuropixels_probe(probe_type='neuropixels 1.0 - 3A'):
5865
"""
5966

6067
neuropixels_probes_config = {
61-
'neuropixels 1.0 - 3A': dict(site_count=960, col_spacing=32, row_spacing=20,
62-
white_spacing=16, col_count=2,
63-
shank_count=1, shank_spacing=0),
64-
'neuropixels 1.0 - 3B': dict(site_count=960, col_spacing=32, row_spacing=20,
65-
white_spacing=16, col_count=2,
66-
shank_count=1, shank_spacing=0),
67-
'neuropixels UHD': dict(site_count=384, col_spacing=6, row_spacing=6,
68-
white_spacing=0, col_count=8,
69-
shank_count=1, shank_spacing=0),
70-
'neuropixels 2.0 - SS': dict(site_count=1280, col_spacing=32, row_spacing=15,
71-
white_spacing=0, col_count=2,
72-
shank_count=1, shank_spacing=250),
73-
'neuropixels 2.0 - MS': dict(site_count=1280, col_spacing=32, row_spacing=15,
74-
white_spacing=0, col_count=2,
75-
shank_count=4, shank_spacing=250)
68+
"neuropixels 1.0 - 3A": dict(
69+
site_count=960,
70+
col_spacing=32,
71+
row_spacing=20,
72+
white_spacing=16,
73+
col_count=2,
74+
shank_count=1,
75+
shank_spacing=0,
76+
),
77+
"neuropixels 1.0 - 3B": dict(
78+
site_count=960,
79+
col_spacing=32,
80+
row_spacing=20,
81+
white_spacing=16,
82+
col_count=2,
83+
shank_count=1,
84+
shank_spacing=0,
85+
),
86+
"neuropixels UHD": dict(
87+
site_count=384,
88+
col_spacing=6,
89+
row_spacing=6,
90+
white_spacing=0,
91+
col_count=8,
92+
shank_count=1,
93+
shank_spacing=0,
94+
),
95+
"neuropixels 2.0 - SS": dict(
96+
site_count=1280,
97+
col_spacing=32,
98+
row_spacing=15,
99+
white_spacing=0,
100+
col_count=2,
101+
shank_count=1,
102+
shank_spacing=250,
103+
),
104+
"neuropixels 2.0 - MS": dict(
105+
site_count=1280,
106+
col_spacing=32,
107+
row_spacing=15,
108+
white_spacing=0,
109+
col_count=2,
110+
shank_count=4,
111+
shank_spacing=250,
112+
),
76113
}
77114

78-
def build_electrodes(site_count, col_spacing, row_spacing,
79-
white_spacing, col_count,
80-
shank_count, shank_spacing):
115+
def build_electrodes(
116+
site_count,
117+
col_spacing,
118+
row_spacing,
119+
white_spacing,
120+
col_count,
121+
shank_count,
122+
shank_spacing,
123+
):
81124
"""
82125
:param site_count: site count per shank
83-
:param col_spacing: (um) horrizontal spacing between sites
126+
:param col_spacing: (um) horizontal spacing between sites
84127
:param row_spacing: (um) vertical spacing between columns
85128
:param white_spacing: (um) offset spacing
86129
:param col_count: number of column per shank
@@ -89,35 +132,47 @@ def build_electrodes(site_count, col_spacing, row_spacing,
89132
:return:
90133
"""
91134
row_count = int(site_count / col_count)
92-
x_coords = np.tile(np.arange(0, col_spacing * col_count, col_spacing), row_count)
135+
x_coords = np.tile(
136+
np.arange(0, col_spacing * col_count, col_spacing), row_count
137+
)
93138
y_coords = np.repeat(np.arange(row_count) * row_spacing, col_count)
94139

95140
if white_spacing:
96-
x_white_spaces = np.tile([white_spacing, white_spacing, 0, 0], int(row_count / 2))
141+
x_white_spaces = np.tile(
142+
[white_spacing, white_spacing, 0, 0], int(row_count / 2)
143+
)
97144
x_coords = x_coords + x_white_spaces
98145

99146
shank_cols = np.tile(range(col_count), row_count)
100147
shank_rows = np.repeat(range(row_count), col_count)
101148

102149
npx_electrodes = []
103150
for shank_no in range(shank_count):
104-
npx_electrodes.extend([{'electrode': (site_count * shank_no) + e_id,
105-
'shank': shank_no,
106-
'shank_col': c_id,
107-
'shank_row': r_id,
108-
'x_coord': x + (shank_no * shank_spacing),
109-
'y_coord': y}
110-
for e_id, (c_id, r_id, x, y) in enumerate(
111-
zip(shank_cols, shank_rows, x_coords, y_coords))])
151+
npx_electrodes.extend(
152+
[
153+
{
154+
"electrode": (site_count * shank_no) + e_id,
155+
"shank": shank_no,
156+
"shank_col": c_id,
157+
"shank_row": r_id,
158+
"x_coord": x + (shank_no * shank_spacing),
159+
"y_coord": y,
160+
}
161+
for e_id, (c_id, r_id, x, y) in enumerate(
162+
zip(shank_cols, shank_rows, x_coords, y_coords)
163+
)
164+
]
165+
)
112166

113167
return npx_electrodes
114168

115169
electrodes = build_electrodes(**neuropixels_probes_config[probe_type])
116-
probe_type = {'probe_type': probe_type}
170+
probe_type = {"probe_type": probe_type}
117171
with ProbeType.connection.transaction:
118172
ProbeType.insert1(probe_type, skip_duplicates=True)
119-
ProbeType.Electrode.insert([{**probe_type, **e} for e in electrodes],
120-
skip_duplicates=True)
173+
ProbeType.Electrode.insert(
174+
[{**probe_type, **e} for e in electrodes], skip_duplicates=True
175+
)
121176

122177

123178
@schema

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