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h-mayorquinh-mayorquin
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Merge branch 'master' into fix_edf_handle
2 parents 1e3c6bc + de6b3b5 commit ade13db

23 files changed

+81
-33
lines changed

‎neo/io/igorproio.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -142,7 +142,7 @@ def _wave_to_analogsignal(self, content, dirpath):
142142
_time_unit_structure = header["dimUnits"].ravel()
143143
# For the files we've seen so far, the first element of _time_unit_structure contains the units.
144144
# If someone has a file for which this assumption does not hold an Exception will be raised.
145-
if not all([element == b'' for element in _time_unit_structure[1:]]):
145+
if not all([element == b"" for element in _time_unit_structure[1:]]):
146146
raise Exception(
147147
"Neo cannot yet handle the units in this file. "
148148
"Please create a new issue in the Neo issue tracker at "

‎neo/rawio/axographrawio.py

Lines changed: 11 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -814,7 +814,17 @@ def _scan_axograph_file(self):
814814
# channel_info will be cast to _signal_channel_dtype
815815
buffer_id = ""
816816
stream_id = "0"
817-
channel_info = (name, str(i), 1 / sampling_period, f.byte_order + dtype, units, gain, offset, stream_id, buffer_id)
817+
channel_info = (
818+
name,
819+
str(i),
820+
1 / sampling_period,
821+
f.byte_order + dtype,
822+
units,
823+
gain,
824+
offset,
825+
stream_id,
826+
buffer_id,
827+
)
818828

819829
self.logger.debug("channel_info: {channel_info}")
820830
self.logger.debug("")

‎neo/rawio/axonrawio.py

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -229,7 +229,9 @@ def _parse_header(self):
229229
gain, offset = 1.0, 0.0
230230
stream_id = "0"
231231
buffer_id = "0"
232-
signal_channels.append((name, str(chan_id), self._sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id))
232+
signal_channels.append(
233+
(name, str(chan_id), self._sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id)
234+
)
233235

234236
signal_channels = np.array(signal_channels, dtype=_signal_channel_dtype)
235237

‎neo/rawio/baserawio.py

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -94,7 +94,10 @@
9494
_signal_stream_dtype = [
9595
("name", "U64"), # not necessarily unique
9696
("id", "U64"), # must be unique
97-
("buffer_id", "U64"), # should be "" (empty string) when the stream is not nested under a buffer or the buffer is undefined for some reason.
97+
(
98+
"buffer_id",
99+
"U64",
100+
), # should be "" (empty string) when the stream is not nested under a buffer or the buffer is undefined for some reason.
98101
]
99102

100103
_signal_channel_dtype = [

‎neo/rawio/brainvisionrawio.py

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -118,7 +118,9 @@ def _parse_header(self):
118118
offset = 0
119119
stream_id = "0"
120120
buffer_id = "0"
121-
sig_channels.append((name, chan_id, self._sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id))
121+
sig_channels.append(
122+
(name, chan_id, self._sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id)
123+
)
122124
sig_channels = np.array(sig_channels, dtype=_signal_channel_dtype)
123125

124126
# No spikes

‎neo/rawio/elanrawio.py

Lines changed: 11 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -158,7 +158,6 @@ def _parse_header(self):
158158
# unique buffer and stream
159159
signal_buffers = np.array([("Signals", "0")], dtype=_signal_buffer_dtype)
160160
signal_streams = np.array([("Signals", "0", "0")], dtype=_signal_stream_dtype)
161-
162161

163162
sig_channels = []
164163
for c, chan_info in enumerate(channel_infos[:-2]):
@@ -172,7 +171,17 @@ def _parse_header(self):
172171
stream_id = "0"
173172
buffer_id = "0"
174173
sig_channels.append(
175-
(chan_name, chan_id, self._sampling_rate, sig_dtype, chan_info["units"], gain, offset, stream_id, buffer_id)
174+
(
175+
chan_name,
176+
chan_id,
177+
self._sampling_rate,
178+
sig_dtype,
179+
chan_info["units"],
180+
gain,
181+
offset,
182+
stream_id,
183+
buffer_id,
184+
)
176185
)
177186

178187
sig_channels = np.array(sig_channels, dtype=_signal_channel_dtype)

‎neo/rawio/intanrawio.py

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -242,7 +242,6 @@ def _parse_header(self):
242242

243243
stream_ids = np.unique(signal_channels["stream_id"])
244244
signal_streams = np.zeros(stream_ids.size, dtype=_signal_stream_dtype)
245-
246245

247246
# we need to sort the data because the string of stream_index 10 is mis-sorted.
248247
buffer_ids = []

‎neo/rawio/maxwellrawio.py

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -111,13 +111,12 @@ def _parse_header(self):
111111
raise NotImplementedError(f"This version {version} is not supported")
112112

113113
signal_streams = np.array(signal_streams, dtype=_signal_stream_dtype)
114-
114+
115115
# one stream per buffer
116116
signal_buffers = np.zeros(signal_streams.size, dtype=_signal_buffer_dtype)
117117
signal_buffers["id"] = signal_streams["id"]
118118
signal_buffers["name"] = signal_streams["name"]
119119

120-
121120
# create signal channels
122121
max_sig_length = 0
123122
self._signals = {}
@@ -160,7 +159,6 @@ def _parse_header(self):
160159
warnings.warn(f"No 'routed' group found for well {stream_id}")
161160
well_indices_to_remove.append(stream_index)
162161
continue
163-
164162

165163
channel_ids = np.array(mapping["channel"])
166164
electrode_ids = np.array(mapping["electrode"])
@@ -173,7 +171,9 @@ def _parse_header(self):
173171
ch_name = f"ch{chan_id} elec{elec_id}"
174172
offset_uV = 0
175173
buffer_id = stream_id
176-
sig_channels.append((ch_name, str(chan_id), sr, "uint16", "uV", gain_uV, offset_uV, stream_id, buffer_id))
174+
sig_channels.append(
175+
(ch_name, str(chan_id), sr, "uint16", "uV", gain_uV, offset_uV, stream_id, buffer_id)
176+
)
177177

178178
self._signals[stream_id] = sigs
179179
max_sig_length = max(max_sig_length, sigs.shape[1])

‎neo/rawio/micromedrawio.py

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -130,7 +130,9 @@ def _parse_header(self):
130130
chan_id = str(c)
131131
stream_id = "0"
132132
buffer_id = "0"
133-
signal_channels.append((chan_name, chan_id, sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id))
133+
signal_channels.append(
134+
(chan_name, chan_id, sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id)
135+
)
134136

135137
signal_channels = np.array(signal_channels, dtype=_signal_channel_dtype)
136138

‎neo/rawio/neuralynxrawio/neuralynxrawio.py

Lines changed: 11 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -279,7 +279,17 @@ def _parse_header(self):
279279
gain *= -1
280280
offset = 0.0
281281
signal_channels.append(
282-
(chan_name, str(chan_id), info["sampling_rate"], "int16", units, gain, offset, stream_id, buffer_id)
282+
(
283+
chan_name,
284+
str(chan_id),
285+
info["sampling_rate"],
286+
"int16",
287+
units,
288+
gain,
289+
offset,
290+
stream_id,
291+
buffer_id,
292+
)
283293
)
284294
self.ncs_filenames[chan_uid] = filename
285295
keys = [

‎neo/rawio/neuronexusrawio.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -191,7 +191,7 @@ def _parse_header(self):
191191
1, # no gain
192192
0, # no offset
193193
stream_id,
194-
buffer_id
194+
buffer_id,
195195
)
196196
)
197197

@@ -203,7 +203,7 @@ def _parse_header(self):
203203
stream_ids = np.unique(signal_channels["stream_id"])
204204
signal_streams = np.zeros(stream_ids.size, dtype=_signal_stream_dtype)
205205
signal_streams["id"] = [str(stream_id) for stream_id in stream_ids]
206-
# One unique buffer
206+
# One unique buffer
207207
signal_streams["buffer_id"] = buffer_id
208208

209209
for stream_index, stream_id in enumerate(stream_ids):

‎neo/rawio/neuroscoperawio.py

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -121,7 +121,9 @@ def _parse_header(self):
121121
offset = 0.0
122122
stream_id = "0"
123123
buffer_id = "0"
124-
sig_channels.append((name, chan_id, self._sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id))
124+
sig_channels.append(
125+
(name, chan_id, self._sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id)
126+
)
125127
sig_channels = np.array(sig_channels, dtype=_signal_channel_dtype)
126128

127129
# No events

‎neo/rawio/openephysrawio.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -230,7 +230,7 @@ def _parse_header(self):
230230
signal_streams = []
231231
signal_streams = np.array(signal_streams, dtype=_signal_stream_dtype)
232232
# no buffer handling in this format because one channel per file
233-
signal_buffers = np.array( [], dtype=_signal_buffer_dtype)
233+
signal_buffers = np.array([], dtype=_signal_buffer_dtype)
234234

235235
# scan for spikes files
236236
spike_channels = []

‎neo/rawio/plexonrawio.py

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -272,11 +272,12 @@ def _parse_header(self):
272272
)
273273
offset = 0.0
274274

275-
276275
channel_prefix = re.match(regex_prefix_pattern, name).group(0)
277276
stream_id = channel_prefix
278277
buffer_id = ""
279-
signal_channels.append((name, str(chan_id), sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id))
278+
signal_channels.append(
279+
(name, str(chan_id), sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id)
280+
)
280281

281282
signal_channels = np.array(signal_channels, dtype=_signal_channel_dtype)
282283

‎neo/rawio/rawbinarysignalrawio.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -105,7 +105,7 @@ def _parse_header(self):
105105
self.signal_gain,
106106
self.signal_offset,
107107
stream_id,
108-
buffer_id
108+
buffer_id,
109109
)
110110
)
111111

‎neo/rawio/spike2rawio.py

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -256,7 +256,9 @@ def _parse_header(self):
256256
sig_dtype = "float32"
257257
stream_id = "0" # set it after the loop
258258
buffer_id = ""
259-
signal_channels.append((name, str(chan_id), sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id))
259+
signal_channels.append(
260+
(name, str(chan_id), sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id)
261+
)
260262

261263
elif chan_info["kind"] in [2, 3, 4, 5, 8]:
262264
# Event

‎neo/rawio/spikegadgetsrawio.py

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -271,7 +271,6 @@ def _parse_header(self):
271271
self._mask_channels_bytes[stream_id] = mask
272272
self._mask_streams[stream_id] = np.any(mask, axis=0)
273273

274-
275274
signal_streams = np.array(signal_streams, dtype=_signal_stream_dtype)
276275
signal_channels = np.array(signal_channels, dtype=_signal_channel_dtype)
277276
# no buffer concept here data are too fragmented

‎neo/rawio/tdtrawio.py

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -311,7 +311,9 @@ def _parse_header(self):
311311
gain = 1.0
312312
offset = 0.0
313313
buffer_id = ""
314-
signal_channels.append((chan_name, str(chan_id), sampling_rate, dtype, units, gain, offset, stream_id, buffer_id))
314+
signal_channels.append(
315+
(chan_name, str(chan_id), sampling_rate, dtype, units, gain, offset, stream_id, buffer_id)
316+
)
315317

316318
if missing_sev_channels:
317319
warnings.warn(f"Could not identify sev files for channels {missing_sev_channels}.")

‎neo/rawio/winedrrawio.py

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -94,7 +94,9 @@ def _parse_header(self):
9494
offset = -YZ * gain
9595
stream_id = "0"
9696
buffer_id = "0"
97-
signal_channels.append((name, str(chan_id), self._sampling_rate, "int16", units, gain, offset, stream_id, buffer_id))
97+
signal_channels.append(
98+
(name, str(chan_id), self._sampling_rate, "int16", units, gain, offset, stream_id, buffer_id)
99+
)
98100

99101
signal_channels = np.array(signal_channels, dtype=_signal_channel_dtype)
100102

@@ -104,7 +106,7 @@ def _parse_header(self):
104106
for i in range(unique_characteristics.size):
105107
mask = unique_characteristics[i] == characteristics
106108
signal_channels["stream_id"][mask] = str(i)
107-
# unique buffer for all streams
109+
# unique buffer for all streams
108110
buffer_id = "0"
109111
signal_streams.append((f"stream {i}", str(i), buffer_id))
110112
signal_streams = np.array(signal_streams, dtype=_signal_stream_dtype)

‎neo/rawio/winwcprawio.py

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -119,7 +119,9 @@ def _parse_header(self):
119119
offset = 0.0
120120
stream_id = "0"
121121
buffer_id = "0"
122-
signal_channels.append((name, chan_id, self._sampling_rate, "int16", units, gain, offset, stream_id, buffer_id))
122+
signal_channels.append(
123+
(name, chan_id, self._sampling_rate, "int16", units, gain, offset, stream_id, buffer_id)
124+
)
123125

124126
signal_channels = np.array(signal_channels, dtype=_signal_channel_dtype)
125127

@@ -129,7 +131,7 @@ def _parse_header(self):
129131
for i in range(unique_characteristics.size):
130132
mask = unique_characteristics[i] == characteristics
131133
signal_channels["stream_id"][mask] = str(i)
132-
# unique buffer for all streams
134+
# unique buffer for all streams
133135
buffer_id = "0"
134136
signal_streams.append((f"stream {i}", str(i), buffer_id))
135137
signal_streams = np.array(signal_streams, dtype=_signal_stream_dtype)

‎neo/test/rawiotest/rawio_compliance.py

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -78,6 +78,7 @@ def header_is_total(reader):
7878
for k, _ in _event_channel_dtype:
7979
assert k in dt.fields, f"{k} not in event_channels.dtype"
8080

81+
8182
def check_signal_stream_buffer_hierachy(reader):
8283
# rules:
8384
# * a channel always belong to a stream
@@ -95,7 +96,7 @@ def check_signal_stream_buffer_hierachy(reader):
9596
assert channel["stream_id"] in h["signal_streams"]["id"]
9697
if channel["buffer_id"] != "":
9798
assert channel["buffer_id"] in h["signal_buffers"]["id"]
98-
99+
99100
stream_ids = h["signal_streams"]["id"]
100101
if stream_ids.size > 0:
101102
assert stream_ids.size == np.unique(stream_ids).size

‎neo/test/rawiotest/test_neuronexusrawio.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -15,4 +15,4 @@ class TestNeuroNexusRawIO(
1515

1616

1717
if __name__ == "__main__":
18-
unittest.main()
18+
unittest.main()

‎pyproject.toml

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -45,7 +45,7 @@ iocache = [
4545
]
4646

4747
test = [
48-
"dhn_med_py>=1.0.0",
48+
"dhn_med_py<2.0", # ci failing with 2.0 test future version when stable
4949
"pytest",
5050
"pytest-cov",
5151
# datalad # this dependency is covered by conda (environment_testing.yml)
@@ -100,13 +100,13 @@ ced = ["sonpy"]
100100
nwb = ["pynwb"]
101101
maxwell = ["h5py"]
102102
biocam = ["h5py"]
103-
med = ["dhn_med_py>=1.0.0"]
103+
med = ["dhn_med_py<2.0"] # ci failing with 2.0 test future version when stable
104104
plexon2 = ["zugbruecke>=0.2; sys_platform!='win32'", "wenv; sys_platform!='win32'"]
105105

106106
all = [
107107
"coverage",
108108
"coveralls",
109-
"dhn_med_py>=1.0.0",
109+
"dhn_med_py<2.0", # ci failing with 2.0 test future version when stable
110110
"h5py",
111111
"igor2",
112112
"ipython",

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