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more pep8
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@zm711
zm711 committed Dec 1, 2023
1 parent 92cb150 commit 779325e
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Showing 2 changed files with 31 additions and 26 deletions.
2 changes: 1 addition & 1 deletion neo/io/intanbinaryio.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,4 +8,4 @@ class IntanBinaryIO(IntanBinaryRawIO, BaseFromRaw):

def __init__(self, dirname):
IntanBinaryRawIO.__init__(self, dirname=dirname)
BaseFromRaw.__init__(self, dirname)
BaseFromRaw.__init__(self, dirname)
55 changes: 30 additions & 25 deletions neo/rawio/intanbinaryrawio.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@

from .intanrawio import (read_variable_header, rhd_global_header_base, rhd_global_header_part1,
rhd_global_header_v11, rhd_global_header_v13, rhd_global_header_v20,
rhd_global_header_final, rhd_signal_group_header,
rhd_global_header_final, rhd_signal_group_header,
rhd_signal_channel_header, stream_type_to_name)


Expand Down Expand Up @@ -52,7 +52,7 @@ def _parse_header(self):
dir_path = Path(self.dirname)
assert dir_path.is_dir(), ('IntanBinaryRawIO requires the root '
'directory containing info.rhd')

header_file = dir_path / 'info.rhd'

for file in possible_raw_files:
Expand All @@ -74,7 +74,7 @@ def _parse_header(self):
data_dtype,
self._block_size) = read_rhd(header_file)

self._raw_data ={}
self._raw_data = {}
for stream_index, sub_datatype in data_dtype.items():
if stream_mode:
self._raw_data[stream_index] = np.memmap(raw_file_dict[stream_index],
Expand All @@ -83,11 +83,9 @@ def _parse_header(self):
else:
self._raw_data[stream_index] = []
for channel_index, datatype in enumerate(sub_datatype):
self._raw_data[stream_index].append(
np.memmap(raw_file_dict[stream_index][channel_index],
dtype=[datatype],
mode='r')
)
self._raw_data[stream_index].append(np.memmap(raw_file_dict[stream_index][channel_index],
dtype=[datatype],
mode='r'))

# check timestamp continuity
if stream_mode:
Expand Down Expand Up @@ -121,9 +119,13 @@ def _parse_header(self):
self._max_sampling_rate = np.max(signal_channels['sampling_rate'])

if stream_mode:
self._max_sigs_length = max([raw_data.size * self._block_size for raw_data in self._raw_data.values()])
self._max_sigs_length = max(
[raw_data.size * self._block_size for raw_data in self._raw_data.values()]
)
else:
self._max_sigs_length = max([len(raw_data)* raw_data[0].size * self._block_size for raw_data in self._raw_data.values()])
self._max_sigs_length = max(
[len(raw_data) * raw_data[0].size * self._block_size for raw_data in self._raw_data.values()]
)

# No events
event_channels = []
Expand All @@ -144,7 +146,6 @@ def _parse_header(self):

self._generate_minimal_annotations()


def _segment_t_start(self, block_index, seg_index):
return 0.

Expand Down Expand Up @@ -181,7 +182,7 @@ def _get_analogsignal_chunk(self, block_index, seg_index, i_start, i_stop,
if channel_indexes is None:
channel_indexes = slice(None)
channel_names = signal_channels['name'][channel_indexes]

if self.stream_mode:
shape = self._raw_data[stream_index][channel_names[0]].shape
else:
Expand Down Expand Up @@ -216,23 +217,28 @@ def _get_analogsignal_chunk(self, block_index, seg_index, i_start, i_stop,
# RHD Zone for Binary Files

# For One File Per Signal
possible_raw_files = ['amplifier.dat',
'auxiliary.dat',
possible_raw_files = ['amplifier.dat',
'auxiliary.dat',
'supply.dat',
'analogin.dat',
'digitalin.dat',
'digitalout.dat',]
'analogin.dat',
'digitalin.dat',
'digitalout.dat']

# For One File Per Channel
possible_raw_file_prefixes = ['amp', 'aux', 'vdd', 'board-ANALOG', 'board-DIGITAL-IN', 'board-DIGITAL-OUT']
possible_raw_file_prefixes = ['amp',
'aux',
'vdd',
'board-ANALOG',
'board-DIGITAL-IN',
'board-DIGITAL-OUT']


def create_raw_file_stream(dirname):
"""Function for One File Per Signal Type"""
raw_file_dict = {}
for raw_index, raw_file in enumerate(possible_raw_files):
if Path(dirname / raw_file).is_file():
raw_file_dict[raw_index] = Path(dirname /raw_file)
raw_file_dict[raw_index] = Path(dirname / raw_file)
raw_file_dict[6] = Path(dirname / 'time.dat')

return raw_file_dict
Expand All @@ -244,12 +250,12 @@ def create_raw_file_channel(dirname):
files = [file for file in file_names if file.is_file()]
raw_file_dict = {}
for raw_index, prefix in enumerate(possible_raw_file_prefixes):
raw_file_dict[raw_index]= [file for file in files if prefix in file.name]
raw_file_dict[raw_index] = [file for file in files if prefix in file.name]
raw_file_dict[6] = [Path(dirname / 'time.dat')]

return raw_file_dict


def read_rhd(filename):
with open(filename, mode='rb') as f:

Expand Down Expand Up @@ -280,7 +286,7 @@ def read_rhd(filename):

# read channel group and channel header
channels_by_type = {k: [] for k in [0, 1, 2, 3, 4, 5]}
data_dtype = {k: [] for k in range(7)} # 5 channels + 6 is for time stamps
data_dtype = {k: [] for k in range(7)} # 5 channels + 6 is for time stamps
for g in range(global_info['nb_signal_group']):
group_info = read_variable_header(f, rhd_signal_group_header)

Expand All @@ -290,7 +296,6 @@ def read_rhd(filename):
if bool(chan_info['channel_enabled']):
channels_by_type[chan_info['signal_type']].append(chan_info)


sr = global_info['sampling_rate']

# construct the data block dtype and reorder channels
Expand All @@ -300,12 +305,12 @@ def read_rhd(filename):
BLOCK_SIZE = 60 # 256 channels

ordered_channels = []

# 6: Timestamp stored in time.dat
if version >= V('1.2'):
data_dtype[6] = [('timestamp', 'int32', BLOCK_SIZE)]
else:
data_dtype[6] = [('timestamp','uint32', BLOCK_SIZE)]
data_dtype[6] = [('timestamp', 'uint32', BLOCK_SIZE)]

# 0: RHD2000 amplifier channel stored in amplifier.dat/amp-*
for chan_info in channels_by_type[0]:
Expand Down

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