def save_csv(self,
directory=None,
extra_array_names=None,
extra_arrays=None):
if (extra_arrays != None and extra_array_names == None):
raise ValueError(
"Enter a list of array names associated with 'extra_arrays'.")
if (extra_arrays == None and extra_array_names != None):
raise ValueError(
"Names for 'extra_arrays' entered, but no extra arrays.")
##### Make variables #####
subject = str(self.subject)
experiment_name = str(self.experiment_name)
start_date = str(self.start_date)
start_time = str(self.start_time)
end_date = str(self.end_date)
end_time = str(self.end_time)
session = str(self.session)
###########################
self.file_name = "%s_%s_%s_%s.csv" % (start_date, start_time, subject,
experiment_name)
if directory != None:
self.file_name = directory + self.file_name
##### Organise meta data and extend if needed for extra events #####
time_event_column = ["Time", "Event"]
if (self.extra_columns != None):
time_event_column.append(self.extra_columns)
meta_data = [["Start_date", start_date], ["Start_time", start_time],
["End_date", end_date], ["End_time", end_time],
["Subject", subject], ["Session", session],
["Experiment_name", experiment_name], time_event_column]
with open(self.file_name, "w") as file:
writer = writer(file, delimiter=",", lineterminator="\n")
writer.writerows(meta_data)
writer.writerows(self.event_record)
if extra_arrays != None:
for array in range(len(extra_array_names)):
writer.writerows(((extra_array_names[array], ), ))
writer.writerows(zip(extra_arrays[array]))
msg = " subject %s, session %s, saved event record" % (subject,
session)
log_file.update_log(time=clock.get_date_hmdmy(),
entry=msg,
directory=self.directory)
def read_session_info(subject, file_name, directory):
""" Read session information """
with open(file_name, mode="r") as file:
csv_file = reader(file, delimiter=",")
# First row is always a header
# Always has "subject" and "session"
header = csv_file.__next__()
# Try to read subject and session
try:
subject_column = header.index("subject")
except ValueError:
msg = " 'subject' column not found"
print(msg)
log_file.update_log(time=get_date_hmdmy(),
entry=msg,
directory=directory)
return (None)
try:
session_column = header.index("session")
except ValueError:
msg = " 'session' column not found"
print(msg)
log_file.update_log(time=get_date_hmdmy(),
entry=msg,
directory=directory)
return (None)
got_session = False
for row in csv_file:
if row[subject_column] == subject:
session = row[session_column]
msg = " from %s found session %s" % (file_name, session)
log_file.update_log(time=get_date_hmdmy(),
entry=msg,
directory=directory)
got_session = True
if not got_session:
msg = " failed to find session in %s" % (file_name)
log_file.update_log(time=get_date_hmdmy(),
entry=msg,
directory=directory)
return (None)
return (session)
def teardown(self):
msg = "stop pigpio.pi"
log_file.update_log(get_date_hmdmy(), msg, self.directory)
self.pi.stop()
msg = "stop pigpiod"
system("sudo killall pigpiod")
log_file.update_log(get_date_hmdmy(), msg, self.directory)
msg = " stop experiment, subject %s, session %s" % (self.subject,
self.session)
log_file.update_log(get_date_hmdmy(), msg, self.directory)
def __init__(self,
subject,
parameter_file,
session=None,
session_info_file=None,
directory="/home/pi/Experiment",
windows_test=False):
chdir(directory)
self.directory = directory
msg = " start experiment, subject %s, session %s" % (subject, session)
log_file.update_log(get_date_hmdmy(), msg, directory)
if (session_info_file != None):
# Logs are updated inside
session = experiment_reader.read_session_info(
subject, session_info_file, directory)
elif (session != None):
msg = " from args set session %s" % (session)
log_file.update_log(get_date_hmdmy(), msg, directory)
self.session = session
if (not windows_test):
msg = " start pigpiod"
log_file.update_log(get_date_hmdmy(), msg, directory)
system("sudo pigpiod")
sleep(0.1)
msg = " make pigpio.pi"
log_file.update_log(get_date_hmdmy(), msg, directory)
# Make the pigpio.pi object
self.pi = pigpio.pi()
self.subject = subject
# Log files are updated inside read_experiment_params()
self.parameters = experiment_reader.read_experiment_params(
subject, session, parameter_file, directory)
def read_experiment_params(subject, session, file_name, directory):
""" Read a CSV file and return a dictionary of parameters """
session = str(session)
msg = " subject %s, session %s, reading %s" % (subject, session, file_name)
log_file.update_log(time=get_date_hmdmy(), entry=msg, directory=directory)
with open(file_name, mode="r") as file:
csv_file = reader(file, delimiter=",")
# First row is always a header
# Always has "subject" and "session"
header = csv_file.__next__()
try:
subject_column = header.index("subject")
except ValueError:
msg = " 'subject' column not found"
print(msg)
log_file.update_log(time=get_date_hmdmy(),
entry=msg,
directory=directory)
return (None)
try:
session_column = header.index("session")
except ValueError:
msg = " 'session' column not found"
print(msg)
log_file.update_log(time=get_date_hmdmy(),
entry=msg,
directory=directory)
return (None)
# Find columns for parameters
parameter_cols = [
x for x in range(len(header))
if x not in [subject_column, session_column]
]
parameter_dict = {}
got_subject_session = False
for row in csv_file:
if row[subject_column] == subject and row[
session_column] == session:
parameter_dict["subject"] = row[subject_column]
parameter_dict["session"] = int(row[session_column])
for col in parameter_cols:
# Record log files
value = row[col]
parameter_name = header[col]
parameter_dict[parameter_name] = value
msg = " subject %s, session %s, %s := %s" % (
subject, session, parameter_name, value)
log_file.update_log(time=get_date_hmdmy(),
entry=msg,
directory=directory)
got_subject_session = True
if not got_subject_session:
msg = " failed to find subject %s, session %s" % (subject, session)
log_file.update_log(time=get_date_hmdmy(),
entry=msg,
directory=directory)
return (parameter_dict)