def __init__(self, recording_file, *, experiment_id=0, recording_id=0):
assert HAVE_OE, "To use the OpenEphys extractor, install pyopenephys: \n\n pip install pyopenephys\n\n"
SortingExtractor.__init__(self)
self._recording_file = recording_file
self._recording = pyopenephys.File(
recording_file).experiments[experiment_id].recordings[recording_id]
self._spiketrains = self._recording.spiketrains
self._unit_ids = list(
[np.unique(st.clusters)[0] for st in self._spiketrains])
def __init__(self, folder_path, *, experiment_id=0, recording_id=0, dtype='float'):
assert HAVE_OE, "To use the OpenEphys extractor, install pyopenephys: \n\n pip install pyopenephys\n\n"
assert dtype == 'int16' or 'float' in dtype, "'dtype' can be int16 (memory map) or 'float' (load into memory)"
RecordingExtractor.__init__(self)
self._recording_file = folder_path
self._recording = pyopenephys.File(folder_path).experiments[experiment_id].recordings[recording_id]
self._dtype = dtype
self._kwargs = {'folder_path': str(Path(folder_path).absolute()), 'experiment_id': experiment_id,
'recording_id': recording_id, 'dtype': dtype}
def __init__(self, folder_path, experiment_id=0, recording_id=0, dtype='float'):
assert HAVE_OE, self.installation_mesg
assert dtype == 'int16' or 'float' in dtype, "'dtype' can be int16 (memory map) or 'float' (load into memory)"
RecordingExtractor.__init__(self)
self._recording_file = folder_path
self._fileobj = pyopenephys.File(folder_path)
self._recording = self._fileobj.experiments[experiment_id].recordings[recording_id]
self._analogsignals = self._recording.analog_signals[0]
self._dtype = dtype
self._kwargs = {'folder_path': str(Path(folder_path).absolute()), 'experiment_id': experiment_id,
'recording_id': recording_id, 'dtype': dtype}
def __init__(self, folder_path, *, experiment_id=0, recording_id=0):
assert HAVE_OE, self.installation_mesg
SortingExtractor.__init__(self)
self._recording_file = folder_path
self._recording = pyopenephys.File(folder_path).experiments[experiment_id].recordings[recording_id]
self._spiketrains = self._recording.spiketrains
self._unit_ids = list([np.unique(st.clusters)[0] for st in self._spiketrains])
self._sampling_frequency = float(self._recording.sample_rate.rescale('Hz').magnitude)
self._kwargs = {'folder_path': str(Path(folder_path).absolute()), 'experiment_id': experiment_id,
'recording_id': recording_id}
def __init__(self, file_path, *, experiment_id=0, recording_id=0):
assert HAVE_OE, "To use the OpenEphys extractor, install pyopenephys: \n\n pip install pyopenephys\n\n"
SortingExtractor.__init__(self)
self._recording_file = file_path
self._recording = pyopenephys.File(
file_path).experiments[experiment_id].recordings[recording_id]
self._spiketrains = self._recording.spiketrains
self._unit_ids = list(
[np.unique(st.clusters)[0] for st in self._spiketrains])
self._sampling_frequency = float(
self._recording.sample_rate.rescale('Hz').magnitude)
def __init__(self, experiment_dir):
self.sess_dir = pathlib.Path(experiment_dir)
openephys_file = pyopenephys.File(self.sess_dir.parent) # this is on the Record Node level
# extract the "recordings" for this session
self.experiment = next(experiment for experiment in openephys_file.experiments
if pathlib.Path(experiment.absolute_foldername) == self.sess_dir)
self.recording_time = self.experiment.datetime
# extract probe data
self.probes = self.load_probe_data()
def __init__(self,
recording_file,
*,
experiment_id=0,
recording_id=0,
dtype='float'):
assert HAVE_OE, "To use the OpenEphys extractor, install pyopenephys: \n\n pip install pyopenephys\n\n"
assert dtype == 'int16' or 'float' in dtype, "'dtype' can be int16 (memory map) or 'float' (load into memory)"
RecordingExtractor.__init__(self)
self._recording_file = recording_file
self._recording = pyopenephys.File(
recording_file).experiments[experiment_id].recordings[recording_id]
self._dtype = dtype
def __init__(self, folder_path, experiment_id=0, recording_id=0):
assert self.installed, self.installation_mesg
RecordingExtractor.__init__(self)
self._recording_file = folder_path
self._fileobj = pyopenephys.File(folder_path)
self._recording = self._fileobj.experiments[experiment_id].recordings[
recording_id]
self._set_analogsignal(self._recording.analog_signals[0])
self._kwargs = {
'folder_path': str(Path(folder_path).absolute()),
'experiment_id': experiment_id,
'recording_id': recording_id
}
def __init__(self, recording_file, *, experiment_id=0, recording_id=0):
try:
import pyopenephys
except ModuleNotFoundError:
raise ModuleNotFoundError(
"To use the OpenEphys extractor, install pyopenephys: \n\n"
"pip install pyopenephys\n\n")
SortingExtractor.__init__(self)
self._recording_file = recording_file
self._recording = pyopenephys.File(
recording_file).experiments[experiment_id].recordings[recording_id]
self._spiketrains = self._recording.spiketrains
self._unit_ids = list(
[np.unique(st.clusters)[0] for st in self._spiketrains])
def __init__(self,
recording_file,
*,
probefile=None,
experiment_id=0,
recording_id=0):
try:
import pyopenephys
except ModuleNotFoundError:
raise ModuleNotFoundError(
"To use the OpenEphys extractor, install pyopenephys: \n\n"
"pip install pyopenephys\n\n")
RecordingExtractor.__init__(self)
self._recording_file = recording_file
self._recording = pyopenephys.File(
recording_file,
probefile).experiments[experiment_id].recordings[recording_id]
def __init__(self,
recording_file,
*,
experiment_id=0,
recording_id=0,
dtype='float'):
try:
import pyopenephys
except ModuleNotFoundError:
raise ModuleNotFoundError(
"To use the OpenEphys extractor, install pyopenephys: \n\n"
"pip install pyopenephys\n\n")
assert dtype == 'int16' or 'float' in dtype, "'dtype' can be int16 (memory map) or 'float' (load into memory)"
RecordingExtractor.__init__(self)
self._recording_file = recording_file
self._recording = pyopenephys.File(
recording_file).experiments[experiment_id].recordings[recording_id]
self._dtype = dtype
def test_open_file(self, download, dataset_path, foldername):
if download:
print(f"Testing GIN {dataset_path}")
self.dataset.get(dataset_path)
else:
print(f"Testing local {foldername}")
if foldername.is_dir():
file = pyopenephys.File(foldername)
print("Instantiated File object")
experiments = file.experiments
print(f"\nN experiments: {len(experiments)}")
for e, exp in enumerate(experiments):
print(f"\nExperiment {e}")
recordings = exp.recordings
print(f"N recordings: {len(recordings)}")
for r, rec in enumerate(recordings):
print(
f"\nRecording {r} - duration {rec.duration} - acquisition {rec.experiment.acquisition_system}"
)
analog = rec.analog_signals
gains = [an.gains for an in analog]
signal_shapes = [an.signal.shape for an in analog]
for g, shape in zip(gains, signal_shapes):
assert len(g) == shape[0]
print(
f"N analog signals: {len(analog)} - shapes: {signal_shapes}"
)
events = rec.events
print(f"N event signals: {len(events)}")
spiketrains = rec.spiketrains
print(f"N spiketrains: {len(spiketrains)}")
# test clipping
print(f"Test clipping")
duration = rec.duration
clip_times = 0.2
rec.clip_recording(clip_times)
clip_times = [0.3, 0.8]
rec.clip_recording(clip_times)
else:
print(f"{foldername} not found!")
import pyopenephys
import matplotlib.pylab as plt
import os
import quantities as pq
from exana import tracking as tr
import neo
oe_folder_uni = os.path.join(os.getcwd(), 'OE_Data/closed_loop/closed_loop_uniform_2018-02-09_23-05-54')
# oe_folder_gauss = os.path.join(os.getcwd(), 'OE_Data/closed_loop/closed_loop_gaussi_2018-02-09_22-30-33')
oe_folder_gauss = os.path.join(os.getcwd(), 'OE_Data/closed_loop/tests/closed_loop_gauss_2018-02-10_20-56-42')
source='fpga'
file_uni = pyopenephys.File(oe_folder_uni)
exp1 = file_uni.experiments[0]
rec1 = exp1.recordings[0]
tracking_uni = rec1.tracking
events_uni = rec1.events
for ev in events_uni:
if ev.processor == 'Rhythm_FPGA':
ev_fpga_uni = ev.times[::2]
else:
ev_stim_uni = ev.times
if source=='fpga':
sptr_uni = neo.SpikeTrain(ev_fpga_uni, t_stop=ev_fpga_uni[-1])
else:
sptr_uni = neo.SpikeTrain(ev_stim_uni, t_stop=ev_stim_uni[-1])
'''
Below is the code I have written in order to read data in Binary format
'''
from open_ephys.analysis import Session
from Binary import DatLoad
import pyopenephys
directory = '2021-05-21_16-08-55' # for example
session = Session(directory)
file = pyopenephys.File(
"2021-05-21_16-08-55/Record Node 111/experiment2/recording1/continuous/File_Reader-110.0"
)
print("hello world")
import matplotlib.pylab as plt
import os
import quantities as pq
import seaborn as sns
from plotting_convention import *
fs = 30
fs_tick = 22
fs_leg = 18
oe_folder = os.path.join(
os.getcwd(),
'OE_Data/multiple_sources/multiple_sources_2018-01-12_16-48-23')
data_folder = os.path.join(os.getcwd(), 'Python_Data')
file = pyopenephys.File(oe_folder)
exp1 = file.experiments[0]
rec1 = exp1.recordings[0]
tracking = rec1.tracking
frequencies = np.linspace(30, 300, len(tracking))
nsamples = [len(tr.times) for tr in tracking]
tracking = list(np.array(tracking)[np.argsort(nsamples)])
data_py = np.load(os.path.join(data_folder, 'multiple_sources_data_array.npy'))
ts_py = np.load(os.path.join(data_folder,
'multiple_sources_timestamps.npy')) * pq.s
ts_oe = [tr.times for tr in tracking]
# ts_py = [t - t[0] for t in ts_py]
