def _run(params): # pragma: no cover
controller = TemplateController(**params)
gui = controller.create_gui()
gui.show()
run_app()
gui.close()
del gui
def _run(data_path, **kwargs): # pragma: no cover
controller = NeoController(data_path, **kwargs)
gui = controller.create_gui()
gui.show()
run_app()
gui.close()
del gui
def _run(params):
controller = TemplateController(**params)
gui = controller.create_gui()
gui.show()
run_app()
gui.close()
del gui
def _run(params): # pragma: no cover
controller = TemplateController(**params)
gui = controller.create_gui()
gui.show()
#pdb.set_trace()
gd=controller.model.metadata['group']
gtable = controller.supervisor.cluster_view
outfile = open('tempData.txt','w')
#pdb.set_trace()
header = gtable._get_row(list(gd.keys())[0])
headermsg = ''
for gid,gel in header.items():
headermsg=headermsg +gid +','
outfile.write(headermsg.strip(', ')+'\n')
for icluster in gd.keys():
grow = gtable._get_row(icluster)
msg=''
#pdb.set_trace()
for gid,gel in grow.items():
msg=msg + str(gel) +', '
outfile.write(msg.strip(', ')+'\n')
outfile.close()
run_app()
gui.close()
del gui
def kwik_gui(path, channel_group=None, clustering=None, **kwargs): # pragma: no cover
"""Launch the Kwik GUI."""
assert path
create_app()
controller = KwikController(
path, channel_group=channel_group, clustering=clustering, **kwargs)
gui = controller.create_gui()
gui.show()
run_app()
gui.close()
def _run(path, channel_group, clustering):
controller = KwikController(path,
channel_group=channel_group,
clustering=clustering,
)
gui = controller.create_gui()
gui.show()
run_app()
gui.close()
del gui
def _run(path, channel_group, clustering):
controller = KwikController(
path,
channel_group=channel_group,
clustering=clustering,
)
gui = controller.create_gui()
gui.show()
run_app()
gui.close()
del gui
def kilosort(dat_path, **kwargs):
"""Launch the trace GUI on a raw data file."""
create_app()
with capture_exceptions():
kwargs['n_channels_dat'] = kwargs.pop('n_channels')
kwargs['order'] = 'F' if kwargs.pop('fortran', None) else None
creator = KilosortGUICreator(dat_path, **kwargs)
gui = creator.create_gui()
gui.show()
run_app()
gui.close()
def template_gui(params_path, **kwargs): # pragma: no cover
"""Launch the Template GUI."""
# Create a `phy.log` log file with DEBUG level.
_add_log_file(Path(params_path).parent / 'phy.log')
create_app()
controller = TemplateController(**get_template_params(params_path),
**kwargs)
gui = controller.create_gui()
gui.show()
run_app()
gui.close()
controller.model.close()
def cluster_manual(path, channel_group=None, clustering=None):
"""Launch the Kwik GUI on a Kwik file."""
# Create the Qt application.
create_app()
controller = KwikController(path,
channel_group=channel_group,
clustering=clustering,
)
gui = controller.create_gui()
gui.show()
run_app()
gui.close()
del gui
def template_gui(params_path, **kwargs): # pragma: no cover
"""Launch the Template GUI."""
# Create a `phy.log` log file with DEBUG level.
p = Path(params_path)
dir_path = p.parent
_add_log_file(dir_path / 'phy.log')
create_app()
controller = TemplateController(model=load_model(params_path),
dir_path=dir_path,
**kwargs)
gui = controller.create_gui()
gui.show()
run_app()
gui.close()
controller.model.close()
def template_gui(params_path, **kwargs): # pragma: no cover
"""Launch the Template GUI."""
# Create a `phy.log` log file with DEBUG level.
p = Path(params_path)
dir_path = p.parent
_add_log_file(dir_path / 'phy.log')
model = load_model(params_path)
# Automatically export spike waveforms when using compressed raw ephys.
if model.spike_waveforms is None and isinstance(model.traces, MtscompEphysReader):
# TODO: customizable values below.
model.save_spikes_subset_waveforms(
max_n_spikes_per_template=500, max_n_channels=16)
create_app()
controller = TemplateController(model=model, dir_path=dir_path, **kwargs)
gui = controller.create_gui()
gui.show()
run_app()
gui.close()
controller.model.close()
def trace_gui(dat_path, **kwargs): # pragma: no cover
"""Launch the Trace GUI.
Parameters
----------
dat_path : str or Path
Path to the raw data file
sample_rate : float
The data sampling rate, in Hz.
n_channels_dat : int
The number of columns in the raw data file.
dtype : str
The NumPy data type of the raw binary file.
"""
gui = create_trace_gui(dat_path, **kwargs)
gui.show()
run_app()
gui.close()
def main(argv=None):
if argv is None:
argv = sys.argv[1:]
gheader = Fore.GREEN + get_header()
header = gheader + Fore.RESET
parser = argparse.ArgumentParser(description=header,
formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('datafile', help='data file')
parser.add_argument('-e', '--extension', help='extension to consider for visualization',
default='')
if len(argv) == 0:
parser.print_help()
sys.exit()
args = parser.parse_args(argv)
filename = os.path.abspath(args.datafile)
extension = args.extension
params = circus.shared.utils.io.load_parameters(filename)
mytest = StrictVersion(phycontrib.__version__) >= StrictVersion("1.0.12")
if not mytest:
print_and_log(['You need to update phy-contrib to the latest git version'], 'error', params)
sys.exit(0)
sampling_rate = float(params.getint('data', 'sampling_rate'))
data_dtype = params.get('data', 'data_dtype')
file_out_suff = params.get('data', 'file_out_suff')
data_offset = params.getint('data', 'data_offset')
probe = read_probe(params)
if extension != '':
extension = '-' + extension
output_path = params.get('data', 'file_out_suff') + extension + '.GUI'
if not os.path.exists(output_path):
print_and_log(['Data should be first exported with the converting method!'], 'error', params)
else:
print_and_log(["Launching the phy GUI..."], 'info', params)
gui_params = {}
gui_params['dat_path'] = params.get('data', 'data_file')
gui_params['n_channels_dat'] = params.getint('data', 'N_total')
gui_params['n_features_per_channel'] = 5
gui_params['dtype'] = params.get('data', 'data_dtype')
gui_params['offset'] = params.getint('data', 'data_offset')
gui_params['sample_rate'] = params.getint('data', 'sampling_rate')
gui_params['hp_filtered'] = True
os.chdir(output_path)
create_app()
controller = TemplateController(**gui_params)
gui = controller.create_gui()
gui.show()
run_app()
gui.close()
del gui
def main(argv=None):
if argv is None:
argv = sys.argv[1:]
header = get_colored_header()
header += '''Utility to launch the phy GUI and visualize the results.
[data must be first converted with the converting mode]
'''
parser = argparse.ArgumentParser(
description=header, formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('datafile', help='data file')
parser.add_argument('-e',
'--extension',
help='extension to consider for visualization',
default='')
if len(argv) == 0:
parser.print_help()
sys.exit()
args = parser.parse_args(argv)
filename = os.path.abspath(args.datafile)
extension = args.extension
params = CircusParser(filename)
if os.path.exists(params.logfile):
os.remove(params.logfile)
logger = init_logging(params.logfile)
logger = logging.getLogger(__name__)
if extension != '':
extension = '-' + extension
try:
import traitlets
except ImportError:
print_and_log(
['The package traitlets required by phy is not installed'],
'error', logger)
sys.exit(1)
try:
import click
except ImportError:
print_and_log(['The package click required by phy is not installed'],
'error', logger)
sys.exit(1)
try:
import joblib
except ImportError:
print_and_log(['The package joblib required by phy is not installed'],
'error', logger)
sys.exit(1)
if HAVE_PHYCONTRIB:
mytest = StrictVersion(
phycontrib.__version__) >= StrictVersion("1.0.12")
if not mytest:
print_and_log(
['You need to update phy-contrib to the latest git version'],
'error', logger)
sys.exit(1)
print_and_log([
'phy-contrib is deprecated, you should upgrade to phy 2.0 and phylib'
], 'info', logger)
if HAVE_PHYLIB:
try:
import colorcet
except ImportError:
print_and_log(
['The package colorcet required by phy is not installed'],
'error', logger)
sys.exit(1)
try:
import qtconsole
except ImportError:
print_and_log(
['The package qtconsole required by phy is not installed'],
'error', logger)
sys.exit(1)
if not test_patch_for_similarities(params, extension):
print_and_log(
['You should re-export the data because of a fix in 0.6'], 'error',
logger)
continue_anyway = query_yes_no(
Fore.WHITE + "Continue anyway (results may not be fully correct)?",
default=None)
if not continue_anyway:
sys.exit(1)
data_file = params.get_data_file()
data_dtype = data_file.data_dtype
if data_file.params.has_key('data_offset'):
data_offset = data_file.data_offset
else:
data_offset = 0
file_format = data_file.description
file_out_suff = params.get('data', 'file_out_suff')
if file_format not in supported_by_phy:
print_and_log([
"File format %s is not supported by phy. TraceView disabled" %
file_format
], 'info', logger)
if numpy.iterable(data_file.gain):
print_and_log(
['Multiple gains are not supported, using a default value of 1'],
'info', logger)
gain = 1
else:
if data_file.gain != 1:
print_and_log([
"Gain of %g is not supported by phy. Expecting a scaling mismatch"
% data_file.gain
], 'info', logger)
gain = data_file.gain
probe = params.probe
output_path = params.get('data', 'file_out_suff') + extension + '.GUI'
if not os.path.exists(output_path):
print_and_log(
['Data should be first exported with the converting method!'],
'error', logger)
else:
print_and_log(["Launching the phy GUI..."], 'info', logger)
gui_params = {}
if file_format in supported_by_phy:
if not params.getboolean('data', 'overwrite'):
gui_params['dat_path'] = r"%s" % params.get(
'data', 'data_file_no_overwrite')
else:
if params.get('data', 'stream_mode') == 'multi-files':
data_file = params.get_data_file(source=True,
has_been_created=False)
gui_params['dat_path'] = [
r"%s" % f for f in data_file.get_file_names()
]
else:
gui_params['dat_path'] = r"%s" % params.get(
'data', 'data_file')
else:
gui_params['dat_path'] = 'giverandomname.dat'
gui_params['n_channels_dat'] = params.nb_channels
gui_params['n_features_per_channel'] = 5
gui_params['dtype'] = data_dtype
gui_params['offset'] = data_offset
gui_params['sample_rate'] = params.rate
gui_params['dir_path'] = output_path
gui_params['hp_filtered'] = True
os.chdir(output_path)
create_app()
controller = TemplateController(**gui_params)
gui = controller.create_gui()
gui.show()
run_app()
gui.close()
del gui
def main(argv=None):
if argv is None:
argv = sys.argv[1:]
header = get_colored_header()
parser = argparse.ArgumentParser(
description=header, formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('datafile', help='data file')
parser.add_argument('-e',
'--extension',
help='extension to consider for visualization',
default='')
if len(argv) == 0:
parser.print_help()
sys.exit()
args = parser.parse_args(argv)
filename = os.path.abspath(args.datafile)
extension = args.extension
params = CircusParser(filename)
if os.path.exists(params.logfile):
os.remove(params.logfile)
logger = init_logging(params.logfile)
logger = logging.getLogger(__name__)
mytest = StrictVersion(phycontrib.__version__) >= StrictVersion("1.0.12")
if not mytest:
print_and_log(
['You need to update phy-contrib to the latest git version'],
'error', logger)
sys.exit(1)
data_file = params.get_data_file()
data_dtype = data_file.data_dtype
if hasattr(data_file, 'data_offset'):
data_offset = data_file.data_offset
else:
data_offset = 0
file_format = data_file.description
file_out_suff = params.get('data', 'file_out_suff')
if file_format not in supported_by_phy:
print_and_log([
"File format %s is not supported by phy. TraceView disabled" %
file_format
], 'info', logger)
if numpy.iterable(data_file.gain):
print_and_log(
['Multiple gains are not supported, using a default value of 1'],
'info', logger)
gain = 1
else:
if data_file.gain != 1:
print_and_log([
"Gain of %g is not supported by phy. Expecting a scaling mismatch"
% gain
], 'info', logger)
gain = data_file.gain
probe = params.probe
if extension != '':
extension = '-' + extension
output_path = params.get('data', 'file_out_suff') + extension + '.GUI'
if not os.path.exists(output_path):
print_and_log(
['Data should be first exported with the converting method!'],
'error', logger)
else:
print_and_log(["Launching the phy GUI..."], 'info', logger)
gui_params = {}
if file_format in supported_by_phy:
gui_params['dat_path'] = params.get('data', 'data_file')
else:
gui_params['dat_path'] = ''
gui_params['n_channels_dat'] = params.nb_channels
gui_params['n_features_per_channel'] = 5
gui_params['dtype'] = data_dtype
gui_params['offset'] = data_offset
gui_params['sample_rate'] = params.rate
gui_params['hp_filtered'] = True
os.chdir(output_path)
create_app()
controller = TemplateController(**gui_params)
gui = controller.create_gui()
gui.show()
run_app()
gui.close()
del gui
def main(argv=None):
if argv is None:
argv = sys.argv[1:]
header = get_colored_header()
parser = argparse.ArgumentParser(
description=header, formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('datafile', help='data file')
parser.add_argument('-e',
'--extension',
help='extension to consider for visualization',
default='')
if len(argv) == 0:
parser.print_help()
sys.exit()
args = parser.parse_args(argv)
filename = os.path.abspath(args.datafile)
extension = args.extension
params = CircusParser(filename)
if os.path.exists(params.logfile):
os.remove(params.logfile)
logger = init_logging(params.logfile)
logger = logging.getLogger(__name__)
mytest = StrictVersion(phycontrib.__version__) >= StrictVersion("1.0.12")
if not mytest:
print_and_log(
['You need to update phy-contrib to the latest git version'],
'error', logger)
sys.exit(1)
if not test_patch_for_similarities(params, extension):
print_and_log(
['You should re-export the data because of a fix in 0.6'], 'error',
logger)
continue_anyway = query_yes_no(
Fore.WHITE + "Continue anyway (results may not be fully correct)?",
default=None)
if not continue_anyway:
sys.exit(1)
data_file = params.get_data_file()
data_dtype = data_file.data_dtype
if data_file.params.has_key('data_offset'):
data_offset = data_file.data_offset
else:
data_offset = 0
file_format = data_file.description
file_out_suff = params.get('data', 'file_out_suff')
if file_format not in supported_by_phy:
print_and_log([
"File format %s is not supported by phy. TraceView disabled" %
file_format
], 'info', logger)
if numpy.iterable(data_file.gain):
print_and_log(
['Multiple gains are not supported, using a default value of 1'],
'info', logger)
gain = 1
else:
if data_file.gain != 1:
print_and_log([
"Gain of %g is not supported by phy. Expecting a scaling mismatch"
% data_file.gain
], 'info', logger)
gain = data_file.gain
probe = params.probe
if extension != '':
extension = '-' + extension
output_path = params.get('data', 'file_out_suff') + extension + '.GUI'
if not os.path.exists(output_path):
print_and_log(
['Data should be first exported with the converting method!'],
'error', logger)
else:
print_and_log(["Launching the phy GUI..."], 'info', logger)
gui_params = {}
if file_format in supported_by_phy:
if not params.getboolean('data', 'overwrite'):
gui_params['dat_path'] = params.get('data',
'data_file_no_overwrite')
else:
if params.get('data', 'stream_mode') == 'multi-files':
data_file = params.get_data_file(source=True,
has_been_created=False)
gui_params['dat_path'] = ' '.join(
data_file.get_file_names())
else:
gui_params['dat_path'] = params.get('data', 'data_file')
else:
gui_params['dat_path'] = 'giverandomname.dat'
gui_params['n_channels_dat'] = params.nb_channels
gui_params['n_features_per_channel'] = 5
gui_params['dtype'] = data_dtype
gui_params['offset'] = data_offset
gui_params['sample_rate'] = params.rate
gui_params['dir_path'] = output_path
gui_params['hp_filtered'] = True
f = open(os.path.join(output_path, 'params.py'), 'w')
for key, value in gui_params.items():
if key in ['dir_path', 'dat_path', 'dtype']:
f.write('%s = "%s"\n' % (key, value))
else:
f.write("%s = %s\n" % (key, value))
f.close()
os.chdir(output_path)
create_app()
controller = TemplateController(**gui_params)
gui = controller.create_gui()
gui.show()
run_app()
gui.close()
del gui
lf = Binload(nCh=nCh, fs=fs)
lf.load(filename,'i'+str(numbyte), seekpos=0)
t, data = lf.tonumpyarray()
wave_view = view_multiwave(data[time_slice*span:(time_slice+1)*span,:], fs=25000)
wave_view.gap_value = 0.9
wave_view.attach(gui)
############################################################################################
from phy.gui import Actions
actions = Actions(gui)
@actions.add(shortcut=',')
def page_up():
global time_slice
time_slice -= 1
if time_slice >= 0:
wave_view.set_data(data[time_slice*span:(time_slice+1)*span,:], time_slice)
else:
time_slice = 0
@actions.add(shortcut='.')
def page_down():
global time_slice
time_slice += 1
wave_view.set_data(data[time_slice*span:(time_slice+1)*span,:], time_slice)
gui.show()
run_app()
