def _combine_metrics(metrics1, metrics2, metrics_out):
code = '''
#!/bin/bash
ml-exec-process ms3.combine_cluster_metrics -i metrics_list:{} metrics_list:{} -o metrics_out:{}
'''.format(metrics1, metrics2, metrics_out)
print(code)
script = ShellScript(code)
script.start()
retcode = script.wait()
if retcode != 0:
raise Exception('problem running ms3.combine_metrics')
def _isolation_metrics(timeseries, firings, metrics_out, pair_metrics_out):
code = '''
#!/bin/bash
ml-exec-process ms3.isolation_metrics -i timeseries:{} firings:{} -o metrics_out:{} pair_metrics_out:{} -p compute_bursting_parents:true
'''.format(timeseries, firings, metrics_out, pair_metrics_out)
print(code)
script = ShellScript(code)
script.start()
retcode = script.wait()
if retcode != 0:
raise Exception('problem running ms3.isolation_metrics')
def _cluster_metrics(timeseries, firings, metrics_out):
code = '''
#!/bin/bash
ml-exec-process ms3.cluster_metrics -i timeseries:{} firings:{} -o cluster_metrics_out:{} -p samplerate:30000
'''.format(timeseries, firings, metrics_out)
print(code)
script = ShellScript(code)
script.start()
retcode = script.wait()
if retcode != 0:
raise Exception('problem running ms3.cluster_metrics')
def _mask_out_artifacts(timeseries_in, timeseries_out):
code = '''
#!/bin/bash
ml-exec-process ms3.mask_out_artifacts -i timeseries:{} -o timeseries_out:{} -p threshold:6 interval_size:2000
'''.format(timeseries_in, timeseries_out)
print(code)
script = ShellScript(code)
script.start()
retcode = script.wait()
if retcode != 0:
raise Exception('problem running ms3.mask_out_artifacts')
def _whiten(timeseries_in, timeseries_out):
code = '''
#!/bin/bash
ml-exec-process ms3.whiten -i timeseries:{} -o timeseries_out:{}
'''.format(timeseries_in, timeseries_out)
print(code)
script = ShellScript(code)
script.start()
retcode = script.wait()
if retcode != 0:
raise Exception('problem running ms3.whiten')
def _bandpass_filter(timeseries_in, timeseries_out):
code = '''
#!/bin/bash
ml-exec-process ms3.bandpass_filter -i timeseries:{} -o timeseries_out:{} -p samplerate:30000 freq_min:300 freq_max:6000
'''.format(timeseries_in, timeseries_out)
print(code)
script = ShellScript(code)
script.start()
retcode = script.wait()
if retcode != 0:
raise Exception('problem running ms3.bandpass_filter')
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}
/run_irc {dataset_dir} {tmpdir} {dataset_dir}/argfile.txt
'''.format(tmpdir=str(tmpdir), dataset_dir=str(dataset_dir))
shell_script = ShellScript(shell_cmd)
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))