def _load_backup(params_path):
params = _read_python(params_path)
params['dat_path'] = op.join(op.dirname(params_path), params['dat_path'])
dat_path = params['dat_path']
assert dat_path
dir_path = op.dirname(op.realpath(op.expanduser(dat_path)))
dir_path = params.get('dir_path', dir_path)
# Make sure we start from a clean state.
if op.exists(op.join(dir_path, '.phy')):
logger.warn("Please delete the .phy subfolder before loading "
"the backup.")
return
for filename in ('spike_clusters.npy', 'cluster_group.tsv'):
if op.exists(op.join(dir_path, filename)):
logger.warn(
"Please delete the %s file "
"before loading the backup.", filename)
return
# Create the controller.
from phycontrib.template import TemplateController
controller = TemplateController(config_dir=op.dirname(params_path),
**params)
backup_dir = op.join(dir_path, '.phy-backup')
# Get the log path.
log_path = op.join(backup_dir, 'history.tsv')
if not op.exists(log_path):
logger.warn("The file `%s` doesn't exist.", log_path)
return
_replay_actions(log_path, controller)
def export_best_channels(path):
create_app()
chdir(path)
all_clusters = np.load(path + '\\spike_clusters.npy')
cluster_quality = pd.read_csv(path + '\\cluster_groups.csv', sep = "\t")
tc = TemplateController(**_read_python(path + '\\params.py'))
cluster_best_dict = dict()
for cluster in all_clusters:
cluster_best_dict.update({cluster: tc.get_best_channel(cluster)})
cluster_best_df = pd.DataFrame.from_dict(cluster_best_dict, orient='index')
cluster_best_df.reset_index(level=0, inplace=True)
cluster_best_df.columns = ['Cluster_id', 'Best_channel']
cluster_best_df.to_csv(path + '\\best_channels.csv', index=False)
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
# -*- coding: utf-8 -*-
import logging
import numpy as np
from phy import add_default_handler
from phy.utils._misc import _read_python
from phy.gui import create_app, run_app
from phycontrib.template import TemplateController
logger = logging.getLogger(__name__)
add_default_handler('DEBUG')
params = _read_python('params.py')
params['dtype'] = getattr(np, params['dtype'], 'int16')
create_app()
controller = TemplateController(**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:]
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
