#write csvs
def write_csv(fh, data, description, units='connection probability %'):
"""Used to generate csv file accompanying figure.
"""
if isinstance(data, Trace):
write_csv(fh, data, description + "distance(um)")
write_csv(fh, data, description + " %s" % units)
else:
cols = ['"' + description + '"'] + list(data)
line = ','.join(map(str, cols))
fh.write(line)
fh.write('\n')
all_expts = ExperimentList(cache=cache_file)
mouse_expts = all_expts.select(calcium='high', age='40-1000', organism='mouse')
human_expts = all_expts.select(organism='human')
pg.mkQApp()
mouse_ee_types = OrderedDict([
(('2/3', 'unknown'), 'L23pyr'),
((None, 'rorb'), 'rorb'),
((None, 'sim1'), 'sim1'),
((None, 'tlx3'), 'tlx3'),
((None, 'ntsr1'), 'ntsr1'),
])
human_types = OrderedDict([
parser.add_argument('--list-stims', action='store_true', default=False, dest='list_stims',
help='print a list of each connection and the stimulus sets acquired')
parser.add_argument('--sweep-threshold', nargs = '*', type=int, action='store', default=[5,10], dest='sweep_threshold',
help='Combined with --list-stims, for each connection type, prints the number of connections '
'for which there are >= sweep_threshold number of sweeps/stimulus set. Two thresholds '
'are set one for induction protocols (default=5) and one for recovery (default=10')
parser.add_argument('files', nargs='*', type=os.path.abspath)
parser.add_argument('--cre-type', nargs=2, type=str)
parser.add_argument('--calcium', type=str,
help='define external calcium concentration as "Low", "High"')
parser.add_argument('--age', type=str, help='Define age as a range from min to max. Ex age=30-40')
parser.add_argument('--temp', type=int)
args = parser.parse_args(sys.argv[1:])
all_expts = ExperimentList(cache=cache_file)
if args.reload:
all_expts.load_from_server()
if args.reload_old:
files = config.summary_files
if len(files) == 0:
print("No old-format summary files given in config.yml:summary_files")
sys.exit(-1)
for f in files:
all_expts.load(f)
for f in args.files:
all_expts.load(f)
import sys
import pyqtgraph as pg
from multipatch_analysis.experiment_list import ExperimentList
from multipatch_analysis.synaptic_dynamics import DynamicsAnalyzer
if __name__ == '__main__':
app = pg.mkQApp()
pg.dbg()
expt_ind = sys.argv[1]
all_expts = ExperimentList(cache='expts_cache.pkl')
expt = all_expts[expt_ind]
pre_cell = int(sys.argv[2])
post_cell = int(sys.argv[3])
method = 'fit' if '--no-deconv' in sys.argv else 'deconv'
analyzer = DynamicsAnalyzer(expt, pre_cell, post_cell, method=method)
if len(analyzer.pulse_responses) == 0:
raise Exception(
"No suitable data found for cell %d -> cell %d in expt %s" %
(pre_cell, post_cell, expt_ind))
# Plot all individual and averaged train responses for all sets of stimulus parameters
train_plots = analyzer.plot_train_responses()
if '--no-fit' in sys.argv:
sys.exit(0) # user requested no fitting; bail out early
if '--no-deconv' in sys.argv:
action='store_true',
default=False,
dest='trains',
help='plot 50Hz train and deconvolution')
parser.add_argument('--link-y-axis',
action='store_true',
default=False,
dest='link-y-axis',
help='link all y-axis down a column')
args = vars(parser.parse_args(sys.argv[1:]))
plot_sweeps = args['sweeps']
plot_trains = args['trains']
link_y_axis = args['link-y-axis']
expt_cache = 'C:/Users/Stephanies/multipatch_analysis/tools/expts_cache.pkl'
all_expts = ExperimentList(cache=expt_cache)
test = PlotGrid()
test.set_shape(len(connection_types.keys()), 1)
test.show()
grid = PlotGrid()
if plot_trains is True:
grid.set_shape(len(connection_types.keys()), 3)
grid[0, 1].setTitle(title='50 Hz Train')
grid[0, 2].setTitle(title='Exponential Deconvolution')
tau = 15e-3
lp = 1000
else:
grid.set_shape(len(connection_types.keys()), 2)
grid.show()
row = 0
parser.add_argument('--list-stims', action='store_true', default=False, dest='list_stims',
help='print a list of each connection and the stimulus sets acquired')
parser.add_argument('--sweep-threshold', nargs = '*', type=int, action='store', default=[5,10], dest='sweep_threshold',
help='Combined with --list-stims, for each connection type, prints the number of connections '
'for which there are >= sweep_threshold number of sweeps/stimulus set. Two thresholds '
'are set one for induction protocols (default=5) and one for recovery (default=10')
parser.add_argument('files', nargs='*', type=os.path.abspath)
parser.add_argument('--cre-type', nargs=2, type=str)
parser.add_argument('--calcium', type=str,
help='define external calcium concentration as "Low", "High"')
parser.add_argument('--age', type=str, help='Define age as a range from min to max. Ex age=30-40')
parser.add_argument('--temp', type=int)
args = parser.parse_args(sys.argv[1:])
all_expts = ExperimentList(cache=cache_file)
if args.reload:
all_expts.load_from_server()
if args.reload_old:
files = config.summary_files
if len(files) == 0:
print("No old-format summary files given in config.yml:summary_files")
sys.exit(-1)
for f in files:
all_expts.load(f)
for f in args.files:
all_expts.load(f)