def __init__(self, file_path: PathType, smrx_ch_inds: list):
assert HAVE_SONPY, self.installation_mesg
file_path = Path(file_path)
assert file_path.is_file() and file_path.suffix == '.smrx', 'file_path must lead to a .smrx file!'
super().__init__()
# Open smrx file
self._recording_file_path = file_path
self._recording_file = sp.SonFile(sName=str(file_path), bReadOnly=True)
if self._recording_file.GetOpenError() != 0:
raise ValueError(f'Error opening file:', sp.GetErrorString(self._recording_file.GetOpenError()))
# Map Recording channel_id to smrx index / test for invalid indexes /
# get channel info / set channel gains
self._channelid_to_smrxind = dict()
self._channel_smrxinfo = dict()
for i, ind in enumerate(smrx_ch_inds):
if self._recording_file.ChannelType(ind) == sp.DataType.Off:
raise ValueError(f'Channel {ind} is type Off and cannot be used')
self._channelid_to_smrxind[i] = ind
self._channel_smrxinfo[i] = get_channel_info(
f=self._recording_file,
smrx_ch_ind=ind
)
# Set channel gains: http://ced.co.uk/img/Spike10.pdf
# from 16-bit encoded int / to ADC +-5V input / to measured Volts
gains = self._channel_smrxinfo[i]['scale'] / 6553.6
self.set_channel_gains(
channel_ids=[i],
gains=gains
)
self._kwargs = {'file_path': str(Path(file_path).absolute()),
'smrx_ch_inds': smrx_ch_inds}
def __init__(self, file_path: PathType, smrx_channel_ids: list):
assert self.installed, self.installation_mesg
file_path = Path(file_path)
assert file_path.is_file(
) and file_path.suffix == '.smrx', 'file_path must lead to a .smrx file!'
assert len(smrx_channel_ids
) > 0, "'smrx_channel_ids' cannot be an empty list!"
super().__init__()
# Open smrx file
self._recording_file_path = file_path
self._recording_file = sp.SonFile(sName=str(file_path), bReadOnly=True)
if self._recording_file.GetOpenError() != 0:
raise ValueError(
f'Error opening file:',
sp.GetErrorString(self._recording_file.GetOpenError()))
# Map Recording channel_id to smrx index / test for invalid indexes /
# get channel info / set channel gains
self._channelid_to_smrxind = dict()
self._channel_smrxinfo = dict()
self._channel_names = []
gains = []
for i, ind in enumerate(smrx_channel_ids):
if self._recording_file.ChannelType(ind) == sp.DataType.Off:
raise ValueError(
f'Channel {ind} is type Off and cannot be used')
self._channelid_to_smrxind[i] = ind
self._channel_smrxinfo[i] = get_channel_info(
f=self._recording_file, smrx_ch_ind=ind)
# Set channel gains: http://ced.co.uk/img/Spike10.pdf
# from 16-bit encoded int / to ADC +-5V input / to measured Volts
gain = self._channel_smrxinfo[i]['scale'] / 6553.6
gain *= 1000 # mV --> uV
gains.append(gain)
self._channel_names.append(self._channel_smrxinfo[i]['title'])
# Set gains
self.set_channel_gains(gains=gains)
self.has_unscaled = True
rate0 = self._channel_smrxinfo[0]['rate']
for chan, info in self._channel_smrxinfo.items():
assert info['rate'] == rate0, "Inconsistency between 'sampling_frequency' of different channels. The " \
"extractor only supports channels with the same 'rate'"
# Set self._times
times = (self._channel_smrxinfo[0]['frame_offset'] + np.arange(
self.get_num_frames())) / self.get_sampling_frequency()
self.set_times(times=times)
self._kwargs = {
'file_path': str(Path(file_path).absolute()),
'smrx_channel_ids': smrx_channel_ids
}
def get_all_channels_info(file_path):
"""
Extract info from all channels in the smrx file. Returns a dictionary with
valid smrx channel indexes as keys and the respective channel information as
value.
Parameters:
-----------
f: str
Path to .smrx file
"""
f = sp.SonFile(sName=str(file_path), bReadOnly=True)
n_channels = f.MaxChannels()
return {
i: get_channel_info(f, i)
for i in range(n_channels) if f.ChannelType(i) != sp.DataType.Off
}