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pypl2lib.py
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pypl2lib.py
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# pypl2lib.py - Classes and functions for accessing functions
# in PL2FileReader.dll
#
# (c) 2016 Plexon, Inc., Dallas, Texas
# www.plexon.com
#
# This software is provided as-is, without any warranty.
# You are free to modify or share this file, provided that the above
# copyright notice is kept intact.
from sys import platform
import pathlib
import warnings
if any(platform.startswith(name) for name in ('linux', 'darwin', 'freebsd')):
from zugbruecke import CtypesSession
ctypes = CtypesSession(log_level=100)
elif platform.startswith('win'):
import ctypes
else:
raise SystemError('unsupported platform')
import numpy as np
class tm(ctypes.Structure):
_fields_ = [("tm_sec", ctypes.c_int),
("tm_min", ctypes.c_int),
("tm_hour", ctypes.c_int),
("tm_mday", ctypes.c_int),
("tm_mon", ctypes.c_int),
("tm_year", ctypes.c_int),
("tm_wday", ctypes.c_int),
("tm_yday", ctypes.c_int),
("tm_isdst", ctypes.c_int)]
class PL2FileInfo(ctypes.Structure):
_fields_ = [("m_CreatorComment", ctypes.c_char * 256),
("m_CreatorSoftwareName", ctypes.c_char * 64),
("m_CreatorSoftwareVersion", ctypes.c_char * 16),
("m_CreatorDateTime", tm),
("m_CreatorDateTimeMilliseconds", ctypes.c_int),
("m_TimestampFrequency", ctypes.c_double),
("m_NumberOfChannelHeaders", ctypes.c_uint),
("m_TotalNumberOfSpikeChannels", ctypes.c_uint),
("m_NumberOfRecordedSpikeChannels", ctypes.c_uint),
("m_TotalNumberOfAnalogChannels", ctypes.c_uint),
("m_NumberOFRecordedAnalogChannels", ctypes.c_uint),
("m_NumberOfDigitalChannels", ctypes.c_uint),
("m_MinimumTrodality", ctypes.c_uint),
("m_MaximumTrodality", ctypes.c_uint),
("m_NumberOfNonOmniPlexSources", ctypes.c_uint),
("m_Unused", ctypes.c_int),
("m_ReprocessorComment", ctypes.c_char * 256),
("m_ReprocessorSoftwareName", ctypes.c_char * 64),
("m_ReprocessorSoftwareVersion", ctypes.c_char * 16),
("m_ReprocessorDateTime", tm),
("m_ReprocessorDateTimeMilliseconds", ctypes.c_int),
("m_StartRecordingTime", ctypes.c_ulonglong),
("m_DurationOfRecording", ctypes.c_ulonglong)]
class PL2AnalogChannelInfo(ctypes.Structure):
_fields_ = [("m_Name", ctypes.c_char * 64),
("m_Source", ctypes.c_uint),
("m_Channel", ctypes.c_uint),
("m_ChannelEnabled", ctypes.c_uint),
("m_ChannelRecordingEnabled", ctypes.c_uint),
("m_Units", ctypes.c_char * 16),
("m_SamplesPerSecond", ctypes.c_double),
("m_CoeffToConvertToUnits", ctypes.c_double),
("m_SourceTrodality", ctypes.c_uint),
("m_OneBasedTrode", ctypes.c_ushort),
("m_OneBasedChannelInTrode", ctypes.c_ushort),
("m_NumberOfValues", ctypes.c_ulonglong),
("m_MaximumNumberOfFragments", ctypes.c_ulonglong)]
class PL2SpikeChannelInfo(ctypes.Structure):
_fields_ = [("m_Name", ctypes.c_char * 64),
("m_Source", ctypes.c_uint),
("m_Channel", ctypes.c_uint),
("m_ChannelEnabled", ctypes.c_uint),
("m_ChannelRecordingEnabled", ctypes.c_uint),
("m_Units", ctypes.c_char * 16),
("m_SamplesPerSecond", ctypes.c_double),
("m_CoeffToConvertToUnits", ctypes.c_double),
("m_SamplesPerSpike", ctypes.c_uint),
("m_Threshold", ctypes.c_int),
("m_PreThresholdSamples", ctypes.c_uint),
("m_SortEnabled", ctypes.c_uint),
("m_SortMethod", ctypes.c_uint),
("m_NumberOfUnits", ctypes.c_uint),
("m_SortRangeStart", ctypes.c_uint),
("m_SortRangeEnd", ctypes.c_uint),
("m_UnitCounts", ctypes.c_ulonglong * 256),
("m_SourceTrodality", ctypes.c_uint),
("m_OneBasedTrode", ctypes.c_ushort),
("m_OneBasedChannelInTrode", ctypes.c_ushort),
("m_NumberOfSpikes", ctypes.c_ulonglong)]
class PL2DigitalChannelInfo(ctypes.Structure):
_fields_ = [("m_Name", ctypes.c_char * 64),
("m_Source", ctypes.c_uint),
("m_Channel", ctypes.c_uint),
("m_ChannelEnabled", ctypes.c_uint),
("m_ChannelRecordingEnabled", ctypes.c_uint),
("m_NumberOfEvents", ctypes.c_ulonglong)]
def to_array(c_array):
return np.ctypeslib.as_array(c_array)
def to_array_nonzero(c_array):
a = np.ctypeslib.as_array(c_array)
return a[np.where(a)]
class PyPL2FileReader:
def __init__(self, pl2_dll_file_path=None):
"""
PyPL2FileReader class implements functions in the C++ PL2 File Reader
API provided by Plexon, Inc.
Args:
pl2_dll_file_path - path where PL2FileReader.dll is location.
The default value assumes the .dll files are located in the
'bin' directory, which is a subdirectory of this package.
Any file path passed is converted to an absolute path and checked
to see if the .dll exists there.
Returns:
None
"""
self._file_handle = ctypes.c_int(0)
self.pl2_file_info = None
if pl2_dll_file_path is None:
if platform == 'win64':
pl2_dll_file_path = pathlib.Path(__file__).parent / 'bin' / 'PL2FileReader64.dll'
else:
# use default '32bit' dll version
pl2_dll_file_path = pathlib.Path(__file__).parent / 'bin' / 'PL2FileReader.dll'
self.pl2_dll_file_path = pathlib.Path(pl2_dll_file_path).absolute()
try:
self.pl2_dll = ctypes.CDLL(str(self.pl2_dll_file_path))
except IOError:
raise IOError(f"Error: Can't load PL2FileReader.dll at: {self.pl2_dll_file_path}"
"PL2FileReader.dll is bundled with the C++ PL2 Offline Files SDK"
"located on the Plexon Inc website: www.plexon.com"
"Contact Plexon Support for more information: [email protected]")
def pl2_open_file(self, pl2_file):
"""
Opens and returns a handle to a PL2 file.
Args:
pl2_file - full path of the file
Returns:
None
"""
if isinstance(pl2_file, pathlib.Path):
pl2_file = str(pl2_file)
self.pl2_dll.PL2_OpenFile.argtypes = (
ctypes.POINTER(ctypes.c_char),
ctypes.POINTER(ctypes.c_int),
)
self.pl2_dll.PL2_OpenFile.memsync = [
{
'p': [0], # ctypes.POINTER argument
'n': True, # null-terminated string flag
}
]
self.pl2_dll.PL2_OpenFile(
pl2_file.encode('ascii'),
ctypes.byref(self._file_handle),
)
# load file info
self.pl2_get_file_info()
# check if spiking data can be loaded using zugbruecke
self._check_spike_channel_data_consistency()
def pl2_close_file(self):
"""
Closes handle to PL2 file.
Returns:
None
"""
self.pl2_dll.PL2_CloseFile.argtypes = (
ctypes.POINTER(ctypes.c_int),
)
self.pl2_dll.PL2_CloseFile(ctypes.c_int(1))
def pl2_close_all_files(self):
"""
Closes all files that have been opened by the .dll
Args:
None
Returns:
None
"""
self.pl2_dll.PL2_CloseAllFiles.argtypes = ()
self.pl2_dll.PL2_CloseAllFiles()
def pl2_get_last_error(self):
"""
Retrieve description of the last error
Returns:
str - error message
"""
self.pl2_dll.PL2_GetLastError.argtypes = (
ctypes.POINTER(ctypes.c_char),
ctypes.c_int,
)
self.pl2_dll.PL2_GetLastError.memsync = [
{
'p': [0],
'l': [1],
't': ctypes.c_char
}
]
buffer = (ctypes.c_char * 256)()
self.pl2_dll.PL2_GetLastError(buffer, ctypes.c_int(256))
return str(buffer.value)
def _check_spike_channel_data_consistency(self):
"""
Check if all spiking channels use the same number of samples per
waveform. Only in this case can zugbruecke reliably load spiking data
"""
if not self.pl2_file_info.m_TotalNumberOfSpikeChannels:
return
# extract samples per spike of first channel
channel_info = self.pl2_get_spike_channel_info(0)
n_samples_per_spike = channel_info.m_SamplesPerSpike
# compare with all other channels
for i in range(1, self.pl2_file_info.m_TotalNumberOfSpikeChannels):
channel_info = self.pl2_get_spike_channel_info(i)
if channel_info.m_SamplesPerSpike != n_samples_per_spike:
warnings.warn('The spike channels contain different number of samples per spike. '
'Spiking data can probably not be loaded using zugbruecke. '
'Use a windows operating system or remove the offending channels '
'from the file.')
return
def pl2_get_file_info(self):
"""
Retrieve information about pl2 file.
Returns:
pl2_file_info - PL2FileInfo class instance
"""
self.pl2_file_info = PL2FileInfo()
self.pl2_dll.PL2_GetFileInfo.argtypes = (
ctypes.c_int,
ctypes.POINTER(PL2FileInfo),
)
result = self.pl2_dll.PL2_GetFileInfo(self._file_handle, ctypes.byref(self.pl2_file_info))
# If res is 0, print error message
if result == 0:
self._print_error()
return None
return self.pl2_file_info
def pl2_get_analog_channel_info(self, zero_based_channel_index):
"""
Retrieve information about an analog channel
Args:
zero_based_channel_index - zero-based analog channel index
Returns:
pl2_analog_channel_info - PL2AnalogChannelInfo class instance
"""
self.pl2_dll.PL2_GetAnalogChannelInfo.argtypes = (
ctypes.c_int,
ctypes.c_int,
ctypes.POINTER(PL2AnalogChannelInfo),
)
pl2_analog_channel_info = PL2AnalogChannelInfo()
result = self.pl2_dll.PL2_GetAnalogChannelInfo(self._file_handle,
ctypes.c_int(zero_based_channel_index),
ctypes.byref(pl2_analog_channel_info))
if not result:
self._print_error()
return None
return pl2_analog_channel_info
def pl2_get_analog_channel_info_by_name(self, channel_name):
"""
Retrieve information about an analog channel
Args:
channel_name - analog channel name
Returns:
pl2_analog_channel_info - PL2AnalogChannelInfo class instance
"""
self.pl2_dll.PL2_GetAnalogChannelInfoByName.argtypes = (
ctypes.c_int,
ctypes.POINTER(ctypes.c_char),
ctypes.POINTER(PL2AnalogChannelInfo),
)
self.pl2_dll.PL2_GetAnalogChannelInfoByName.memsync = [
{
'p': [1],
'n': True, # null-terminated string flag
}
]
if hasattr(channel_name, 'encode'):
channel_name = channel_name.encode('ascii')
pl2_analog_channel_info = PL2AnalogChannelInfo()
result = self.pl2_dll.PL2_GetAnalogChannelInfoByName(self._file_handle,
channel_name,
ctypes.byref(pl2_analog_channel_info))
if not result:
self._print_error()
return None
return pl2_analog_channel_info
def pl2_get_analog_channel_info_by_source(self, source_id, one_based_channel_index_in_source):
"""
Retrieve information about an analog channel
Args:
source_id - numeric source ID
one_based_channel_index_in_source - one-based channel index within the source
Returns:
pl2_analog_channel_info - PL2AnalogChannelInfo class instance
"""
self.pl2_dll.PL2_GetAnalogChannelInfoBySource.argtypes = (
ctypes.c_int,
ctypes.c_int,
ctypes.c_int,
ctypes.POINTER(PL2AnalogChannelInfo),
)
pl2_analog_channel_info = PL2AnalogChannelInfo()
result = self.pl2_dll.PL2_GetAnalogChannelInfoBySource(
self._file_handle,
ctypes.c_int(source_id),
ctypes.c_int(one_based_channel_index_in_source),
ctypes.byref(pl2_analog_channel_info))
if not result:
self._print_error()
return None
return pl2_analog_channel_info
def pl2_get_analog_channel_data(self, zero_based_channel_index):
"""
Retrieve analog channel data
Args:
zero_based_channel_index - zero based channel index
Returns:
fragment_timestamps - array the size of PL2AnalogChannelInfo.m_MaximumNumberOfFragments
fragment_counts - array the size of PL2AnalogChannelInfo.m_MaximumNumberOfFragments
values - array the size of PL2AnalogChannelInfo.m_NumberOfValues
"""
achannel_info = self.pl2_get_analog_channel_info(zero_based_channel_index)
num_fragments_returned = ctypes.c_ulonglong(achannel_info.m_MaximumNumberOfFragments)
num_data_points_returned = ctypes.c_ulonglong(achannel_info.m_NumberOfValues)
fragment_timestamps = (ctypes.c_longlong * achannel_info.m_MaximumNumberOfFragments)()
fragment_counts = (ctypes.c_ulonglong * achannel_info.m_MaximumNumberOfFragments)()
values = (ctypes.c_short * achannel_info.m_NumberOfValues)()
self.pl2_dll.PL2_GetAnalogChannelData.argtypes = (
ctypes.c_int,
ctypes.c_int,
ctypes.POINTER(ctypes.c_ulonglong),
ctypes.POINTER(ctypes.c_ulonglong),
ctypes.POINTER(ctypes.c_longlong),
ctypes.POINTER(ctypes.c_ulonglong),
ctypes.POINTER(ctypes.c_short),
)
self.pl2_dll.PL2_GetAnalogChannelData.memsync = [
{
'p': [4],
'l': [2],
't': ctypes.c_longlong
},
{
'p': [5],
'l': [2],
't': ctypes.c_ulonglong
},
{
'p': [6],
'l': [3],
't': ctypes.c_short
}
]
result = self.pl2_dll.PL2_GetAnalogChannelData(self._file_handle,
ctypes.c_int(zero_based_channel_index),
num_fragments_returned,
num_data_points_returned,
fragment_timestamps,
fragment_counts,
values)
if not result:
self._print_error()
return None
return to_array(fragment_timestamps), to_array(fragment_counts), to_array(values)
def pl2_get_analog_channel_data_subset(self):
pass
def pl2_get_analog_channel_data_by_name(self, channel_name):
"""
Retrieve analog channel data
Args:
channel_name - analog channel name
Returns:
fragment_timestamps - array the size of PL2AnalogChannelInfo.m_MaximumNumberOfFragments
fragment_counts - array the size of PL2AnalogChannelInfo.m_MaximumNumberOfFragments
values - array the size of PL2AnalogChannelInfo.m_NumberOfValues
"""
if hasattr(channel_name, 'encode'):
channel_name = channel_name.encode('ascii')
achannel_info = self.pl2_get_analog_channel_info_by_name(channel_name)
num_fragments_returned = ctypes.c_ulonglong(achannel_info.m_MaximumNumberOfFragments)
num_data_points_returned = ctypes.c_ulonglong(achannel_info.m_NumberOfValues)
fragment_timestamps = (ctypes.c_longlong * achannel_info.m_MaximumNumberOfFragments)()
fragment_counts = (ctypes.c_ulonglong * achannel_info.m_MaximumNumberOfFragments)()
values = (ctypes.c_short * achannel_info.m_NumberOfValues)()
self.pl2_dll.PL2_GetAnalogChannelDataByName.argtypes = (
ctypes.c_int,
ctypes.POINTER(ctypes.c_char),
ctypes.POINTER(ctypes.c_ulonglong),
ctypes.POINTER(ctypes.c_ulonglong),
ctypes.POINTER(ctypes.c_longlong),
ctypes.POINTER(ctypes.c_ulonglong),
ctypes.POINTER(ctypes.c_short),
)
self.pl2_dll.PL2_GetAnalogChannelDataByName.memsync = [
{
'p': [1],
'n': True, # null-terminated string flag
},
{
'p': [4],
'l': [2],
't': ctypes.c_longlong
},
{
'p': [5],
'l': [2],
't': ctypes.c_ulonglong
},
{
'p': [6],
'l': [3],
't': ctypes.c_short
}
]
result = self.pl2_dll.PL2_GetAnalogChannelDataByName(
self._file_handle,
channel_name,
num_fragments_returned,
num_data_points_returned,
fragment_timestamps,
fragment_counts,
values)
if not result:
self._print_error()
return None
return to_array(fragment_timestamps), to_array(fragment_counts), to_array(values)
def pl2_get_analog_channel_data_by_source(self, source_id, one_based_channel_index_in_source):
"""
Retrieve analog channel data
Args:
source_id - numeric source ID
one_based_channel_index_in_source - one-based channel index within the source
Returns:
fragment_timestamps - array the size of PL2AnalogChannelInfo.m_MaximumNumberOfFragments
fragment_counts - array the size of PL2AnalogChannelInfo.m_MaximumNumberOfFragments
values - array the size of PL2AnalogChannelInfo.m_NumberOfValues
"""
achannel_info = self.pl2_get_analog_channel_info_by_source(source_id, one_based_channel_index_in_source)
num_fragments_returned = ctypes.c_ulonglong(achannel_info.m_MaximumNumberOfFragments)
num_data_points_returned = ctypes.c_ulonglong(achannel_info.m_NumberOfValues)
fragment_timestamps = (ctypes.c_longlong * achannel_info.m_MaximumNumberOfFragments)()
fragment_counts = (ctypes.c_ulonglong * achannel_info.m_MaximumNumberOfFragments)()
values = (ctypes.c_short * achannel_info.m_NumberOfValues)()
self.pl2_dll.PL2_GetAnalogChannelDataBySource.argtypes = (
ctypes.c_int,
ctypes.c_int,
ctypes.c_int,
ctypes.POINTER(ctypes.c_ulonglong),
ctypes.POINTER(ctypes.c_ulonglong),
ctypes.POINTER(ctypes.c_longlong),
ctypes.POINTER(ctypes.c_ulonglong),
ctypes.POINTER(ctypes.c_short),
)
self.pl2_dll.PL2_GetAnalogChannelDataBySource.memsync = [
{
'p': [5],
'l': [3],
't': ctypes.c_longlong
},
{
'p': [6],
'l': [3],
't': ctypes.c_ulonglong
},
{
'p': [7],
'l': [4],
't': ctypes.c_short
}
]
result = self.pl2_dll.PL2_GetAnalogChannelDataBySource(self._file_handle,
ctypes.c_int(source_id),
ctypes.c_int(one_based_channel_index_in_source),
num_fragments_returned,
num_data_points_returned,
fragment_timestamps,
fragment_counts,
values)
if not result:
self._print_error()
return None
return to_array(fragment_timestamps), to_array(fragment_counts), to_array(values)
def pl2_get_spike_channel_info(self, zero_based_channel_index):
"""
Retrieve information about a spike channel
Args:
zero_based_channel_index - zero-based spike channel index
Returns:
pl2_spike_channel_info - PL2SpikeChannelInfo class instance
"""
pl2_spike_channel_info = PL2SpikeChannelInfo()
self.pl2_dll.PL2_GetSpikeChannelInfo.argtypes = (
ctypes.c_int,
ctypes.c_int,
ctypes.POINTER(PL2SpikeChannelInfo),
)
result = self.pl2_dll.PL2_GetSpikeChannelInfo(self._file_handle,
ctypes.c_int(zero_based_channel_index),
ctypes.byref(pl2_spike_channel_info))
if not result:
self._print_error()
return None
return pl2_spike_channel_info
def pl2_get_spike_channel_info_by_name(self, channel_name):
"""
Retrieve information about a spike channel
Args:
channel_name - spike channel name
Returns:
pl2_spike_channel_info - PL2SpikeChannelInfo class instance
"""
self.pl2_dll.PL2_GetSpikeChannelInfoByName.argtypes = (
ctypes.c_int,
ctypes.c_char * len(channel_name),
ctypes.POINTER(PL2SpikeChannelInfo),
)
if hasattr(channel_name, 'encode'):
channel_name = channel_name.encode('ascii')
self.pl2_dll.PL2_GetSpikeChannelInfoByName.memsync = [
{
'p': [1],
'n': True, # null-terminated string flag
}
]
pl2_spike_channel_info = PL2SpikeChannelInfo()
result = self.pl2_dll.PL2_GetSpikeChannelInfoByName(self._file_handle,
channel_name,
ctypes.byref(pl2_spike_channel_info))
if not result:
self._print_error()
return None
return pl2_spike_channel_info
def pl2_get_spike_channel_info_by_source(self, source_id, one_based_channel_index_in_source):
"""
Retrieve information about a spike channel
Args:
source_id - numeric source ID
one_based_channel_index_in_source - one-based channel index within the source
Returns:
pl2_spike_channel_info - PL2SpikeChannelInfo class instance
"""
pl2_spike_channel_info = PL2SpikeChannelInfo()
self.pl2_dll.PL2_GetSpikeChannelInfoBySource.argtypes = (
ctypes.c_int,
ctypes.c_int,
ctypes.c_int,
ctypes.POINTER(PL2SpikeChannelInfo),
)
result = self.pl2_dll.PL2_GetSpikeChannelInfoBySource(
self._file_handle,
ctypes.c_int(source_id),
ctypes.c_int(one_based_channel_index_in_source),
ctypes.byref(pl2_spike_channel_info))
if not result:
self._print_error()
return None
return pl2_spike_channel_info
def pl2_get_spike_channel_data(self, zero_based_channel_index):
"""
Retrieve spike channel data
Args:
zero_based_channel_index - zero based channel index
Returns:
spike_timestamps - array the size of PL2SpikeChannelInfo.m_NumberOfSpikes
units - array the size of PL2SpikeChannelInfo.m_NumberOfSpikes
values - array the size of (PL2SpikeChannelInfo.m_NumberOfSpikes * PL2SpikeChannelInfo.m_SamplesPerSpike)
"""
# extracting m_SamplesPerSpike to prepare data reading
# This solution only works if all channels have the same number of samples per spike
# as ctypes / zugbruecke is caching the memsync attribute once defined once
schannel_info = self.pl2_get_spike_channel_info(zero_based_channel_index)
samples_per_spike = schannel_info.m_SamplesPerSpike
self.pl2_dll.PL2_GetSpikeChannelData.argtypes = (
ctypes.c_int,
ctypes.c_int,
ctypes.POINTER(ctypes.c_ulonglong),
ctypes.POINTER(ctypes.c_ulonglong),
ctypes.POINTER(ctypes.c_ushort),
ctypes.POINTER(ctypes.c_short)
)
self.pl2_dll.PL2_GetSpikeChannelData.memsync = [
{
'p': [3],
'l': [2],
't': ctypes.c_longlong
},
{
'p': [4],
'l': [2],
't': ctypes.c_ushort
},
{
'p': [5],
'l': ([2],),
'func': f'lambda x: x.value * {samples_per_spike}',
't': ctypes.c_short
}
]
# These will be filled in by the dll method.
num_spikes_returned = ctypes.c_ulonglong(schannel_info.m_NumberOfSpikes)
spike_timestamps = (ctypes.c_ulonglong * schannel_info.m_NumberOfSpikes)()
units = (ctypes.c_ushort * schannel_info.m_NumberOfSpikes)()
values = (ctypes.c_short * (
schannel_info.m_NumberOfSpikes * schannel_info.m_SamplesPerSpike))()
result = self.pl2_dll.PL2_GetSpikeChannelData(self._file_handle,
ctypes.c_int(zero_based_channel_index),
num_spikes_returned,
spike_timestamps,
units,
values)
if not result:
self._print_error()
return None
spike_array_shape = (schannel_info.m_NumberOfSpikes, schannel_info.m_SamplesPerSpike)
return to_array(spike_timestamps), to_array(units), to_array(values).reshape(spike_array_shape)
def pl2_get_spike_channel_data_by_name(self, channel_name):
"""
Retrieve spike channel data
Args:
channel_name = channel name
Returns:
spike_timestamps - array the size of PL2SpikeChannelInfo.m_NumberOfSpikes
units - array the size of PL2SpikeChannelInfo.m_NumberOfSpikes
values - array the size of (PL2SpikeChannelInfo.m_NumberOfSpikes * PL2SpikeChannelInfo.m_SamplesPerSpike)
"""
if hasattr(channel_name, 'encode'):
channel_name = channel_name.encode('ascii')
self.pl2_dll.PL2_GetSpikeChannelDataByName.argtypes = (
ctypes.c_int,
ctypes.c_char,
ctypes.POINTER(ctypes.c_ulonglong),
ctypes.POINTER(ctypes.c_ulonglong),
ctypes.POINTER(ctypes.c_ushort),
ctypes.POINTER(ctypes.c_short)
)
# extracting m_SamplesPerSpike to prepare data reading
# This solution only works if all channels have the same number of samples per spike
# as ctypes / zugbruecke is caching the memsync attribute once defined once
schannel_info = self.pl2_get_spike_channel_info_by_name(channel_name)
samples_per_spike = schannel_info.m_SamplesPerSpike
self.pl2_dll.PL2_GetSpikeChannelDataByName.memsync = [
{
'p': [1],
'n': True, # null-terminated string flag
},
{
'p': [3],
'l': [2],
't': ctypes.c_longlong
},
{
'p': [4],
'l': [2],
't': ctypes.c_ushort
},
{
'p': [5],
'l': ([2],),
'func': f'lambda x: x.value * {samples_per_spike}',
't': ctypes.c_short
}
]
# These will be filled in by the dll method.
num_spikes_returned = ctypes.c_ulonglong(schannel_info.m_NumberOfSpikes)
spike_timestamps = (ctypes.c_ulonglong * schannel_info.m_NumberOfSpikes)()
units = (ctypes.c_ushort * schannel_info.m_NumberOfSpikes)()
values = (ctypes.c_short * (
schannel_info.m_NumberOfSpikes * schannel_info.m_SamplesPerSpike))()
result = self.pl2_dll.PL2_GetSpikeChannelDataByName(self._file_handle,
channel_name,
num_spikes_returned,
spike_timestamps,
units,
values)
if not result:
self._print_error()
return None
spike_array_shape = (schannel_info.m_NumberOfSpikes, schannel_info.m_SamplesPerSpike)
return to_array(spike_timestamps), to_array(units), to_array(values).reshape(
spike_array_shape)
def pl2_get_spike_channel_data_by_source(self, source_id, one_based_channel_index_in_source):
"""
Retrieve spike channel data
Args:
source_id - numeric source ID
one_based_channel_index_in_source - one-based channel index within the source
Returns:
spike_timestamps - array the size of PL2SpikeChannelInfo.m_NumberOfSpikes
units - array the size of PL2SpikeChannelInfo.m_NumberOfSpikes
values - array the size of (PL2SpikeChannelInfo.m_NumberOfSpikes * PL2SpikeChannelInfo.m_SamplesPerSpike)
"""
self.pl2_dll.PL2_GetSpikeChannelDataBySource.argtypes = (
ctypes.c_int,
ctypes.c_int,
ctypes.c_int,
ctypes.POINTER(ctypes.c_ulonglong),
ctypes.POINTER(ctypes.c_ulonglong),
ctypes.POINTER(ctypes.c_ushort),
ctypes.POINTER(ctypes.c_short),
)
# extracting m_SamplesPerSpike to prepare data reading
# This solution only works if all channels have the same number of samples per spike
# as ctypes / zugbruecke is caching the memsync attribute once defined once
schannel_info = self.pl2_get_spike_channel_info_by_source(source_id, one_based_channel_index_in_source)
samples_per_spike = schannel_info.m_SamplesPerSpike
self.pl2_dll.PL2_GetSpikeChannelDataBySource.memsync = [
{
'p': [4],
'l': [3],
't': ctypes.c_longlong
},
{
'p': [5],
'l': [3],
't': ctypes.c_ushort
},
{
'p': [6],
'l': ([3],),
'func': f'lambda x: x.value * {samples_per_spike}',
't': ctypes.c_short
}
]
# These will be filled in by the dll method.
num_spikes_returned = ctypes.c_ulonglong(schannel_info.m_NumberOfSpikes)
spike_timestamps = (ctypes.c_ulonglong * schannel_info.m_NumberOfSpikes)()
units = (ctypes.c_ushort * schannel_info.m_NumberOfSpikes)()
values = (ctypes.c_short * (
schannel_info.m_NumberOfSpikes * schannel_info.m_SamplesPerSpike))()
result = self.pl2_dll.PL2_GetSpikeChannelDataBySource(self._file_handle,
ctypes.c_int(source_id),
ctypes.c_int(one_based_channel_index_in_source),
num_spikes_returned,
spike_timestamps,
units,
values)
if not result:
self._print_error()
return None
spike_array_shape = (schannel_info.m_NumberOfSpikes, schannel_info.m_SamplesPerSpike)
return to_array(spike_timestamps), to_array(units), to_array(values).reshape(
spike_array_shape)
def pl2_get_digital_channel_info(self, zero_based_channel_index):
"""
Retrieve information about a digital event channel
Args:
zero_based_channel_index - zero-based digital event channel index
Returns:
pl2_digital_channel_info - PL2DigitalChannelInfo class instance
"""
self.pl2_dll.PL2_GetDigitalChannelInfo.argtypes = (
ctypes.c_int,
ctypes.c_int,
ctypes.POINTER(PL2DigitalChannelInfo),
)
pl2_digital_channel_info = PL2DigitalChannelInfo()
result = self.pl2_dll.PL2_GetDigitalChannelInfo(
self._file_handle,
ctypes.c_int(zero_based_channel_index),
ctypes.byref(pl2_digital_channel_info)
)
if not result:
self._print_error()
return None
return pl2_digital_channel_info
def pl2_get_digital_channel_info_by_name(self, channel_name):
"""
Retrieve information about a digital event channel
Args:
channel_name - digital event channel name
Returns:
pl2_digital_channel_info - PL2DigitalChannelInfo class instance
"""
if hasattr(channel_name, 'encode'):
channel_name = channel_name.encode('ascii')
self.pl2_dll.PL2_GetDigitalChannelInfoByName.argtypes = (
ctypes.c_int,
ctypes.POINTER(ctypes.c_char),
ctypes.POINTER(PL2DigitalChannelInfo),
)
self.pl2_dll.PL2_GetDigitalChannelInfoByName.memsync = [
{
'p': [1], # ctypes.POINTER argument
'n': True, # null-terminated string flag
}
]
pl2_digital_channel_info = PL2DigitalChannelInfo()
result = self.pl2_dll.PL2_GetDigitalChannelInfoByName(
self._file_handle,
channel_name,
ctypes.byref(pl2_digital_channel_info)
)
if not result:
self._print_error()
return None
return pl2_digital_channel_info
def pl2_get_digital_channel_info_by_source(self, source_id, one_based_channel_index_in_source):
"""
Retrieve information about a digital event channel
Args:
source_id - numeric source ID
one_based_channel_index_in_source - one-based channel index within the source
Returns:
pl2_digital_channel_info - PL2DigitalChannelInfo class instance
"""
self.pl2_dll.PL2_GetDigitalChannelInfoBySource.argtypes = (
ctypes.c_int,
ctypes.c_int,
ctypes.c_int,
ctypes.POINTER(PL2DigitalChannelInfo),