def _run(self, recording: se.RecordingExtractor, output_folder: Path):
dataset_dir = output_folder / 'ironclust_dataset'
source_dir = Path(__file__).parent
samplerate = recording.get_sampling_frequency()
num_channels = recording.get_num_channels()
num_timepoints = recording.get_num_frames()
duration_minutes = num_timepoints / samplerate / 60
if self.verbose:
print(
'Num. channels = {}, Num. timepoints = {}, duration = {} minutes'
.format(num_channels, num_timepoints, duration_minutes))
if self.verbose:
print('Creating argfile.txt...')
txt = ''
for key0, val0 in self.params.items():
txt += '{}={}\n'.format(key0, val0)
txt += 'samplerate={}\n'.format(samplerate)
with (dataset_dir / 'argfile.txt').open('w') as f:
f.write(txt)
tmpdir = output_folder / 'tmp'
os.makedirs(str(tmpdir), exist_ok=True)
if self.verbose:
print(
'Running ironclust in {tmpdir}...'.format(tmpdir=str(tmpdir)))
shell_cmd = '''
#!/bin/bash
cd {tmpdir}
exec /run_irc {dataset_dir} {tmpdir} {dataset_dir}/argfile.txt
'''.format(tmpdir=str(tmpdir), dataset_dir=str(dataset_dir))
shell_script = ShellScript(shell_cmd, redirect_output_to_stdout=True)
shell_script.start()
retcode = shell_script.wait()
if retcode != 0:
raise Exception('ironclust returned a non-zero exit code')
result_fname = str(tmpdir / 'firings.mda')
if not os.path.exists(result_fname):
raise Exception('Result file does not exist: ' + result_fname)
samplerate_fname = str(tmpdir / 'samplerate.txt')
with open(samplerate_fname, 'w') as f:
f.write('{}'.format(samplerate))
def _run(self, recording, output_folder):
source_dir = Path(Path(__file__).parent)
p = self.params
recording_folder=str((output_folder / 'recording').absolute())
samplerate = recording.get_sampling_frequency()
txt = ''
for key0, val0 in p.items():
txt += '{}={}\n'.format(key0, val0)
txt += 'samplerate={}\n'.format(samplerate)
params_file = output_folder / 'argfile.txt'
with params_file.open('w') as f:
f.write(txt)
if os.getenv('JRCLUST_BINARY_PATH', None):
shell_cmd = f'''
#!/bin/bash
exec $JRCLUST_BINARY_PATH {str(recording_folder)} {str(output_folder)} {str(params_file)}
'''
else:
# copy m files
shutil.copy(str(source_dir / 'matlab' / 'jrclust_binary.m'), str(output_folder))
shutil.copy(str(source_dir / 'matlab' / 'writemda.m'), str(output_folder))
matlab_script = f'''
addpath(genpath('{self.jrclust_path}'));
jrclust_binary('{str(recording_folder)}', '{str(output_folder)}', '{str(params_file)}')
'''
ShellScript(matlab_script).write(str(output_folder / 'jrclust_script.m'))
if "win" in sys.platform:
shell_cmd = f'''
cd {str(output_folder)}
matlab -nosplash -nodisplay -wait -r jrclust_script
'''
else:
shell_cmd = f'''
#!/bin/bash
cd "{str(output_folder)}"
matlab -nosplash -nodisplay -r jrclust_script
'''
shell_cmd = ShellScript(shell_cmd, redirect_output_to_stdout=True)
shell_cmd.start()
retcode = shell_cmd.wait()
if retcode != 0:
raise Exception('jrclust returned a non-zero exit code')
def _run(self, recording, output_folder):
source_dir = Path(Path(__file__).parent)
p = self.params
dat_file = str((output_folder / 'recording' / 'raw.mda').absolute())
if os.getenv('WAVECLUS_BINARY_PATH', None):
shell_cmd = f'''
#!/bin/bash
exec $WAVECLUS_BINARY_PATH {str(output_folder)} {dat_file} {str(output_folder)}/firings.mda {recording.get_sampling_frequency()}
'''
else:
# copy m files
shutil.copy(str(source_dir / 'matlab' / 'waveclus_binary.m'),
str(output_folder))
shutil.copy(str(source_dir / 'matlab' / 'readmda.m'),
str(output_folder))
shutil.copy(str(source_dir / 'matlab' / 'writemda.m'),
str(output_folder))
shutil.copy(str(source_dir / 'matlab' / 'set_parameters_spf.m'),
str(output_folder))
matlab_script = f'''
addpath(genpath('{self.waveclus_path}'));
waveclus_binary('{str(output_folder)}', '{dat_file}', '{str(output_folder)}/firings.mda', {recording.get_sampling_frequency()})
'''
ShellScript(matlab_script).write(
str(output_folder / 'waveclus_script.m'))
if "win" in sys.platform:
shell_cmd = f'''
cd {str(output_folder)}
matlab -nosplash -nodisplay -wait -r waveclus_script
'''
else:
shell_cmd = f'''
#!/bin/bash
cd "{str(output_folder)}"
matlab -nosplash -nodisplay -r waveclus_script
'''
shell_cmd = ShellScript(shell_cmd, redirect_output_to_stdout=True)
shell_cmd.start()
retcode = shell_cmd.wait()
if retcode != 0:
raise Exception('waveclus returned a non-zero exit code')
def _run(self, recording: se.RecordingExtractor, output_folder: Path):
dataset_dir = output_folder / 'ironclust_dataset'
source_dir = Path(__file__).parent
samplerate = recording.get_sampling_frequency()
num_channels = recording.get_num_channels()
num_timepoints = recording.get_num_frames()
duration_minutes = num_timepoints / samplerate / 60
if self.verbose:
print(
'Num. channels = {}, Num. timepoints = {}, duration = {} minutes'
.format(num_channels, num_timepoints, duration_minutes))
if self.verbose:
print('Creating argfile.txt...')
txt = ''
for key0, val0 in self.params.items():
txt += '{}={}\n'.format(key0, val0)
txt += 'samplerate={}\n'.format(samplerate)
with (dataset_dir / 'argfile.txt').open('w') as f:
f.write(txt)
tmpdir = output_folder / 'tmp'
os.makedirs(str(tmpdir), exist_ok=True)
if self.verbose:
print(
'Running ironclust in {tmpdir}...'.format(tmpdir=str(tmpdir)))
if os.getenv('IRONCLUST_BINARY_PATH', None):
shell_cmd = f'''
#!/bin/bash
cd {tmpdir}
exec $IRONCLUST_BINARY_PATH {dataset_dir} {tmpdir} {dataset_dir}/argfile.txt
'''
else:
matlab_script = f'''
try
addpath(genpath('{self.ironclust_path}'));
irc2('{dataset_dir}', '{str(tmpdir)}', '{dataset_dir}/argfile.txt')
catch
fprintf('----------------------------------------');
fprintf(lasterr());
quit(1);
end
quit(0);
'''
ShellScript(matlab_script).write(
str(output_folder / 'ironclust_script.m'))
if "win" in sys.platform:
shell_cmd = f'''
cd {str(output_folder)}
matlab -nosplash -wait -batch ironclust_script
'''
else:
shell_cmd = f'''
#!/bin/bash
cd "{str(output_folder)}"
matlab -nosplash -nodisplay -r ironclust_script
'''
shell_script = ShellScript(shell_cmd, redirect_output_to_stdout=True)
shell_script.start()
retcode = shell_script.wait()
if retcode != 0:
raise Exception('ironclust returned a non-zero exit code')
result_fname = str(tmpdir / 'firings.mda')
if not os.path.exists(result_fname):
raise Exception('Result file does not exist: ' + result_fname)
samplerate_fname = str(tmpdir / 'samplerate.txt')
with open(samplerate_fname, 'w') as f:
f.write('{}'.format(samplerate))
def _run(self, recording, output_folder):
source_dir = Path(Path(__file__).parent)
p = self.params
dat_file = str((output_folder / 'recording.dat').absolute())
if p['car']:
use_car = 1
else:
use_car = 0
# prepare electrode positions
if self.grouping_property == 'group' and 'group' in recording.get_shared_channel_property_names(
):
groups = recording.get_channel_groups()
else:
groups = [1] * recording.get_num_channels()
if 'location' in recording.get_shared_channel_property_names():
positions = np.array(recording.get_channel_locations())
if positions.shape[1] != 2:
raise RuntimeError(
"3D 'location' are not supported. Set 2D locations instead"
)
else:
print(
"'location' information is not found. Using linear configuration"
)
positions = np.array(
[[0, i_ch] for i_ch in range(recording.get_num_channels())])
xcoords = [positions[i, 0] for i in range(positions.shape[0])]
ycoords = [positions[i, 1] for i in range(positions.shape[0])]
kcoords = groups
params0 = dict(nchan=recording.get_num_channels(),
sample_rate=recording.get_sampling_frequency(),
freq_min=p["freq_min"],
projection_threshold=p["projection_threshold"],
minFR=p["minFR"],
sigmaMask=p["sigmaMask"],
preclust_threshold=p["preclust_threshold"],
kilo_thresh=p["detect_threshold"],
use_car=use_car,
nPCs=p["nPCs"],
xcoords=xcoords,
ycoords=ycoords,
kcoords=kcoords)
params_path = str(output_folder / 'params.json')
with open(params_path, 'w') as f:
json.dump(params0, f)
if os.getenv('KILOSORT2_BINARY_PATH', None):
shell_cmd = f'''
#!/bin/bash
exec $KILOSORT2_BINARY_PATH {dat_file} {str(output_folder)} {params_path}
'''
else:
# copy m files
shutil.copy(str(source_dir / 'matlab' / 'kilosort2_master.m'),
str(output_folder))
shutil.copy(str(source_dir / 'matlab' / 'kilosort2_config.m'),
str(output_folder))
shutil.copy(str(source_dir / 'matlab' / 'kilosort2_channelmap.m'),
str(output_folder))
shutil.copy(str(source_dir / 'matlab' / 'writeNPY.m'),
str(output_folder))
shutil.copy(str(source_dir / 'matlab' / 'constructNPYheader.m'),
str(output_folder))
matlab_script = f'''
try
addpath(genpath('{self.kilosort2_path}'));
kilosort2_master('{dat_file}', '{str(output_folder)}', '{params_path}')
catch
fprintf('----------------------------------------');
fprintf(lasterr());
quit(1);
end
quit(0);
'''
ShellScript(matlab_script).write(
str(output_folder / 'kilosort2_script.m'))
if "win" in sys.platform:
shell_cmd = f'''
cd {str(output_folder)}
matlab -nosplash -nodisplay -wait -r kilosort2_script
'''
else:
shell_cmd = f'''
#!/bin/bash
cd "{str(output_folder)}"
matlab -nosplash -nodisplay -r kilosort2_script
'''
shell_cmd = ShellScript(shell_cmd, redirect_output_to_stdout=True)
shell_cmd.start()
retcode = shell_cmd.wait()
if retcode != 0:
raise Exception('kilosort2 returned a non-zero exit code')