def create_subject(project_name,
subject_name: str = "_iblrig_test_mouse",
force=False):
project_name = alyx2local_names.get(project_name, project_name)
project_path = IBLRIG_PARAMS_FOLDER / project_name
p = Project()
print(f"Loading [{project_path}]")
p.load(project_path)
subject = p.find_subject(subject_name)
if force or subject is None:
subject = p.create_subject()
subject.name = subject_name
p.save(project_path)
print(f" Created subject: [{subject_name}]")
# Create default subjects for project {project_name} if they don't exist
if p.find_subject("_iblrig_test_mouse") is None:
create_subject(project_name,
subject_name="_iblrig_test_mouse",
force=True)
if p.find_subject("_iblrig_calibration") is None:
create_subject(project_name,
subject_name="_iblrig_calibration",
force=True)
return subject
def _init_com(self) -> dict:
logger.debug("Initializing COM ports")
p = Project()
p.load(str(Path(self.IBLRIG_PARAMS_FOLDER) / 'IBL'))
out = None
if Path(self.BPOD_COMPORTS_FILE).exists():
logger.debug(
f"Found COM port definition file: {self.BPOD_COMPORTS_FILE}")
# If file exists open file
with open(self.BPOD_COMPORTS_FILE, 'r') as f:
out = json.load(f)
# Use the GUI defined COM port for BPOD
out['BPOD'] = p.boards[0].serial_port
logger.debug(f".bpod_comports.json exists with content: {out}")
else:
logger.debug(f"NOT FOUND: COM ports definition file")
# If no file exists create empty file
comports = {
'BPOD': None,
'ROTARY_ENCODER': None,
'FRAME2TTL': None
}
comports['BPOD'] = p.boards[0].serial_port
out = comports
logger.debug(f"Calling create with comports: {comports}")
self.create_bpod_comport_file(self.BPOD_COMPORTS_FILE, comports)
return out
def get_board_comport():
iblproject_path = Path(path_helper.get_iblrig_params_folder()) / 'IBL'
p = Project()
p.load(str(iblproject_path))
params_file = Path(
path_helper.get_iblrig_params_folder()) / '.iblrig_params.json'
if not params_file.exists():
return p.boards[0].serial_port
pars = load_params_file()
if p.boards[0].serial_port != pars['COM_BPOD']:
pars['COM_BPOD'] = p.boards[0].serial_port
update_params_file(data=pars)
return pars['COM_BPOD']
def get_board_name():
iblproject_path = Path(path_helper.get_iblrig_params_folder()) / 'IBL'
p = Project()
p.load(str(iblproject_path))
params_file = Path(
path_helper.get_iblrig_params_folder()) / '.iblrig_params.json'
if not params_file.exists():
return p.boards[0].name
pars = load_params_file()
if p.boards[0].name != pars['NAME']:
pars['NAME'] = p.boards[0].name
update_params_file(data=pars)
return pars['NAME']
def __init__(self):
"""
"""
GenericProject.__init__(self)
self._name = ControlText('Project name')
self.formset = ['_name', ' ']
self._name.changed_event = self._name_changed_evt
Project.__init__(self)
def pybpod_project_exists(project_name):
project_name = alyx2local_names.get(project_name, project_name)
project_path = IBLRIG_PARAMS_FOLDER / project_name
p = Project()
project_exists = None
try:
print(f"Checking existence of project [{project_name}] locally")
p.load(project_path)
project_exists = True
except: # noqa
print(f"Project not found: [{project_path}]")
project_exists = False
return project_exists
def create_subject(iblproject_path, subject_name: str):
p = Project()
p.load(iblproject_path)
if p.find_subject(subject_name) is None:
subject = p.create_subject()
subject.name = subject_name
p.save(iblproject_path)
print(f"Created subject: {subject_name}")
else:
subject = p.find_subject(subject_name)
print(f"Skipping creation: Subject <{subject.name}> already exists")
def create_ibl_users(iblproject_path):
p = Project()
p.load(iblproject_path)
if p.find_user('_iblrig_test_user') is None:
user = p.create_user()
user.name = '_iblrig_test_user'
p.save(iblproject_path)
print(f"Created: IBL default user <{user.name}>")
else:
user = p.find_user('_iblrig_test_user')
print(f"Skipping creation: User <{user.name}> already exists")
def create_task(iblproject_path, task_name: str):
p = Project()
p.load(iblproject_path)
task = p.find_task(task_name)
# if task is None:
task = p.create_task()
task.name = task_name
p.save(iblproject_path)
print(f"Created task: {task_name}")
def config_task(iblproject_path, task_name: str):
p = Project()
p.load(iblproject_path)
task = p.find_task(task_name)
print(f" Configuring task <{task.name}>")
task._commands = []
if task.name == '_iblrig_calibration_screen':
task = create_task_bonsai_stop_command(task, port=7110)
task = create_task_cleanup_command(task)
if task.name == '_iblrig_calibration_water':
task = create_task_cleanup_command(task)
if task.name == '_iblrig_misc_flush_water':
task = create_task_cleanup_command(task)
# For all of tasks stop the stim 7110, stop the recording 7111 and cleanup
if '_iblrig_tasks' in task.name:
task = create_task_bonsai_stop_command(task, port=7110)
task = create_task_bonsai_stop_command(task, port=7111)
task = create_task_cleanup_command(task)
task = create_task_bpod_lights_command(task, onoff=1, when='POST')
if task.name == '_iblrig_tasks_habituationChoiceWorld':
task = create_task_create_command(task, patch=True)
if task.name == '_iblrig_tasks_trainingChoiceWorld':
task = create_task_create_command(task, patch=True)
if task.name == '_iblrig_tasks_biasedChoiceWorld':
task = create_task_create_command(task, patch=False)
if task.name == '_iblrig_tasks_ephysChoiceWorld':
task = create_task_create_command(task, patch=False)
p.save(iblproject_path)
print(" Task configured")
def create_task(iblproject_path, task_name: str):
p = Project()
p.load(iblproject_path)
task = p.find_task(task_name)
if task is None:
task = p.create_task()
task.name = task_name
p.save(iblproject_path)
print(f"Created task: {task_name}")
else:
print(f"Skipping creation: Task {task.name} already exists")
def create_subject(iblproject_path, subject_name: str):
p = Project()
p.load(iblproject_path)
# if p.find_subject(subject_name) is None:
subject = p.create_subject()
subject.name = subject_name
p.save(iblproject_path)
print(f" Created subject: {subject_name}")
def create_project(project_name, force=False):
project_name = alyx2local_names.get(project_name, project_name)
project_path = IBLRIG_PARAMS_FOLDER / project_name
p = Project()
if force or not pybpod_project_exists(project_name):
p.name = project_name
p.save(project_path)
print(f" Project created: [{project_name}]")
else:
print(
f" Skipping creation: project [{project_name}] found in: [{project_path}]"
)
p = Project()
p.load(project_path)
return p
def config_task(iblproject_path, task_name: str): # XXX: THIS!
p = Project()
p.load(iblproject_path)
task = p.find_task(task_name)
print(f" Configuring task <{task.name}>")
task._commands = []
if task.name == "_iblrig_calibration_screen":
task = create_task_bonsai_stop_command(task, port=7110)
task = create_task_cleanup_command(task)
if task.name == "_iblrig_calibration_water":
task = create_task_cleanup_command(task)
if task.name == "_iblrig_calibration_input_listner":
task = create_task_cleanup_command(task)
if task.name == "_iblrig_calibration_frame2TTL":
task = create_task_cleanup_command(task)
if task.name == "_iblrig_misc_flush_water":
task = create_task_cleanup_command(task)
if task.name == "_iblrig_misc_bpod_ttl_test":
task = create_task_bonsai_stop_command(task, port=7110)
task = create_task_cleanup_command(task)
if task.name == "_iblrig_misc_frame2TTL_freq_test":
task = create_task_cleanup_command(task)
# For all bpod tasks turn off bpod lights, stop the stim 7110, stop the camera 7111 and cleanup
btasks = [
"_iblrig_tasks_habituationChoiceWorld",
"_iblrig_tasks_trainingChoiceWorld",
"_iblrig_tasks_biasedChoiceWorld",
"_iblrig_tasks_ephysChoiceWorld",
]
if task.name in btasks:
task = create_task_bonsai_stop_command(task, port=7110) # visual stimulus
task = create_task_bonsai_stop_command(task, port=7111) # camera recording
task = create_task_cleanup_command(task)
task = create_task_bpod_lights_command(task, 1, when="POST")
if task.name == "_iblrig_tasks_habituationChoiceWorld":
task = create_task_create_command(task, poop=True)
if task.name == "_iblrig_tasks_trainingChoiceWorld":
task = create_task_create_command(task, poop=True)
if task.name == "_iblrig_tasks_biasedChoiceWorld":
task = create_task_create_command(task, poop=False)
if task.name == "_iblrig_tasks_ephysChoiceWorld":
task = create_task_create_command(task, poop=False)
if task.name == "_iblrig_tasks_ephys_certification":
task = create_task_cleanup_command(task)
task = create_task_bpod_lights_command(task, 0, when="PRE")
task = create_task_bpod_lights_command(task, 1, when="POST")
if task.name == "_iblrig_tasks_passiveChoiceWorld":
task = create_task_cleanup_command(task)
task = create_task_poop_command(task, when="POST")
task = create_task_bonsai_stop_command(task, port=7110) # stim
task = create_task_bonsai_stop_command(task, port=7112) # record_mic
task = create_task_bpod_lights_command(task, 0, when="PRE")
task = create_task_bpod_lights_command(task, 1, when="POST")
task = create_task_move_passive_command(task, when="POST")
p.save(iblproject_path)
print(" Task configured")
def create_experiment(iblproject_path, exp_name: str):
p = Project()
p.load(iblproject_path)
exp = [e for e in p.experiments if e.name == exp_name]
# if not exp:
exp = p.create_experiment()
exp.name = exp_name
p.save(iblproject_path)
print(f"Created experiment: {exp.name}")
def create_ibl_project(iblproject_path):
p = Project()
try:
p.load(iblproject_path)
print(f"Skipping creation: IBL project found <{iblproject_path}>")
except: # noqa
p.name = 'IBL'
p.save(iblproject_path)
print("Created: IBL project")
def config_task(iblproject_path, task_name: str): # XXX: THIS!
p = Project()
p.load(iblproject_path)
task = p.find_task(task_name)
print(f" Configuring task <{task.name}>")
task._commands = []
if task.name == '_iblrig_calibration_screen':
task = create_task_bonsai_stop_command(task, port=7110)
task = create_task_cleanup_command(task)
if task.name == '_iblrig_calibration_water':
task = create_task_cleanup_command(task)
if task.name == '_iblrig_calibration_input_listner':
task = create_task_cleanup_command(task)
if task.name == '_iblrig_calibration_frame2TTL':
task = create_task_cleanup_command(task)
if task.name == '_iblrig_misc_flush_water':
task = create_task_cleanup_command(task)
if task.name == '_iblrig_misc_bpod_ttl_test':
task = create_task_bonsai_stop_command(task, port=7110)
task = create_task_cleanup_command(task)
if task.name == '_iblrig_misc_frame2TTL_freq_test':
task = create_task_cleanup_command(task)
# For all bpod tasks turn off bpod lights, stop the stim 7110, stop the camera 7111 and cleanup
btasks = [
'_iblrig_tasks_habituationChoiceWorld',
'_iblrig_tasks_trainingChoiceWorld',
'_iblrig_tasks_biasedChoiceWorld',
'_iblrig_tasks_ephysChoiceWorld',
]
if task.name in btasks:
task = create_task_bonsai_stop_command(task, port=7110)
task = create_task_bonsai_stop_command(task, port=7111)
task = create_task_cleanup_command(task)
task = create_task_bpod_lights_command(task, onoff=1, when='POST')
if task.name == '_iblrig_tasks_habituationChoiceWorld':
task = create_task_create_command(task, poop=True)
if task.name == '_iblrig_tasks_trainingChoiceWorld':
task = create_task_create_command(task, poop=True)
if task.name == '_iblrig_tasks_biasedChoiceWorld':
task = create_task_create_command(task, poop=False)
if task.name == '_iblrig_tasks_ephysChoiceWorld':
task = create_task_create_command(task, poop=False)
if task.name == '_iblrig_tasks_ephys_certification':
task = create_task_cleanup_command(task)
task = create_task_bpod_lights_command(task, onoff=0, when='PRE')
task = create_task_bpod_lights_command(task, onoff=1, when='POST')
if task.name == '_iblrig_tasks_passiveChoiceWorld':
task = create_task_cleanup_command(task)
task = create_task_poop_command(task, when='POST')
task = create_task_bpod_lights_command(task, onoff=0, when='PRE')
task = create_task_bpod_lights_command(task, onoff=1, when='POST')
task = create_task_move_passive_command(task, when='POST')
p.save(iblproject_path)
print(" Task configured")
def create_ibl_project(iblproject_path):
p = Project()
print("Creating IBL project")
try:
p.load(iblproject_path)
print(f" Skipping creation: IBL project found in: {iblproject_path}")
except: # noqa
p.name = "IBL"
p.save(iblproject_path)
print(" Created: IBL project")
def create_experiment_setups(iblproject_path, exp_name: str):
p = Project()
p.load(iblproject_path)
exp = [e for e in p.experiments if e.name == exp_name]
if not exp:
print(f'Experiment {exp} not found')
raise KeyError
else:
exp = exp[0]
if exp.name == '_iblrig_calibration':
screen = create_setup(exp, 'screen', p.boards[0].name,
exp.name) # noqa
water = create_setup(exp, 'water', p.boards[0].name, exp.name) # noqa
if exp.name == '_iblrig_misc':
flush_water = create_setup( # noqa
exp, 'flush_water', p.boards[0].name, '_iblrig_test_mouse')
if exp.name == '_iblrig_tasks':
biasedChoiceWorld = create_setup( # noqa
exp, 'biasedChoiceWorld', p.boards[0].name, None)
habituationChoiceWorld = create_setup( # noqa
exp, 'habituationChoiceWorld', p.boards[0].name, None)
trainingChoiceWorld = create_setup( # noqa
exp, 'trainingChoiceWorld', p.boards[0].name, None)
ephysChoiceWorld = create_setup( # noqa
exp, 'ephysChoiceWorld', p.boards[0].name, None)
p.save(iblproject_path)
def create_experiment_setups(iblproject_path, exp_name: str): # XXX:THIS!
p = Project()
p.load(iblproject_path)
exp = [e for e in p.experiments if e.name == exp_name]
calib_subj = [s for s in p.subjects if s.name == "_iblrig_calibration"][0]
test_subj = [s for s in p.subjects if s.name == "_iblrig_test_mouse"][0]
if not exp:
raise KeyError(f"Experiment {exp} not found")
else:
exp = exp[0]
if exp.name == "_iblrig_calibration":
screen = create_setup(exp, "screen", p.boards[0].name, calib_subj) # noqa
water = create_setup(exp, "water", p.boards[0].name, calib_subj) # noqa
input_listner = create_setup( # noqa
exp, "input_listner", p.boards[0].name, calib_subj
)
frame2TTL = create_setup(exp, "frame2TTL", p.boards[0].name, calib_subj) # noqa
if exp.name == "_iblrig_misc":
flush_water = create_setup( # noqa
exp, "flush_water", p.boards[0].name, test_subj
)
bpod_ttl_test = create_setup( # noqa
exp, "bpod_ttl_test", p.boards[0].name, test_subj
)
frame2TTL_freq_test = create_setup( # noqa
exp, "frame2TTL_freq_test", p.boards[0].name, test_subj
)
if exp.name == "_iblrig_tasks":
biasedChoiceWorld = create_setup( # noqa
exp, "biasedChoiceWorld", p.boards[0].name, None
)
habituationChoiceWorld = create_setup( # noqa
exp, "habituationChoiceWorld", p.boards[0].name, None
)
trainingChoiceWorld = create_setup( # noqa
exp, "trainingChoiceWorld", p.boards[0].name, None
)
ephys_certification = create_setup( # noqa
exp, "ephys_certification", p.boards[0].name, None
)
ephysChoiceWorld = create_setup( # noqa
exp,
"ephysChoiceWorld_testing",
p.boards[0].name,
test_subj,
task="_iblrig_tasks_ephysChoiceWorld",
)
passiveChoiceWorld = create_setup( # noqa
exp,
"passiveChoiceWorld_testing",
p.boards[0].name,
test_subj,
task="_iblrig_tasks_passiveChoiceWorld",
)
p.save(iblproject_path)
def create_ibl_board(iblproject_path):
p = Project()
p.load(iblproject_path)
if not p.boards:
BOARD_NAME = 'SELECT_BOARD_NAME_(e.g.[_iblrig_mainenlab_behavior_0])'
b = p.create_board()
b.name = BOARD_NAME
p.save(iblproject_path)
print("Created: IBL default board (please remember to rename it)")
else:
print(f"Skipping creation: Board found with name <{p.boards[0].name}>")
def create_experiment(iblproject_path, exp_name: str):
p = Project()
p.load(iblproject_path)
exp = [e for e in p.experiments if e.name == exp_name]
if not exp:
exp = p.create_experiment()
exp.name = exp_name
p.save(iblproject_path)
print(f"Created experiment: {exp.name}")
else:
exp = exp[0]
print(f"Skipping creation: Experiment {exp.name} already exists")
def create_user(project_name, username="******", force=False):
project_name = alyx2local_names.get(project_name, project_name)
project_path = IBLRIG_PARAMS_FOLDER / project_name
p = Project()
print(f"Loading [{project_path}]")
if not pybpod_project_exists(project_name):
return
p.load(project_path)
if force or p.find_user(username) is None:
user = p.create_user()
user.name = username
p.save(project_path)
print(f" Created user: [{user.name}] in project [{project_name}]")
else:
user = p.find_user(username)
print(
f" Skipping creation: User [{user.name}] already exists in project [{project_name}]"
)
if p.find_user("_iblrig_test_user") is None:
create_user(project_name, username="******", force=True)
return user
def create_experiment_setups(iblproject_path, exp_name: str): # XXX:THIS!
p = Project()
p.load(iblproject_path)
exp = [e for e in p.experiments if e.name == exp_name]
calib_subj = [s for s in p.subjects if s.name == '_iblrig_calibration'][0]
test_subj = [s for s in p.subjects if s.name == '_iblrig_test_mouse'][0]
if not exp:
raise KeyError(f'Experiment {exp} not found')
else:
exp = exp[0]
if exp.name == '_iblrig_calibration':
screen = create_setup(exp, 'screen', p.boards[0].name,
calib_subj) # noqa
water = create_setup(exp, 'water', p.boards[0].name,
calib_subj) # noqa
input_listner = create_setup(exp, 'input_listner', p.boards[0].name,
calib_subj) # noqa
frame2TTL = create_setup(exp, 'frame2TTL', p.boards[0].name,
calib_subj) # noqa
if exp.name == '_iblrig_misc':
flush_water = create_setup( # noqa
exp, 'flush_water', p.boards[0].name, test_subj)
bpod_ttl_test = create_setup( # noqa
exp, 'bpod_ttl_test', p.boards[0].name, test_subj)
frame2TTL_freq_test = create_setup( # noqa
exp, 'frame2TTL_freq_test', p.boards[0].name, test_subj)
if exp.name == '_iblrig_tasks':
biasedChoiceWorld = create_setup( # noqa
exp, 'biasedChoiceWorld', p.boards[0].name, None)
habituationChoiceWorld = create_setup( # noqa
exp, 'habituationChoiceWorld', p.boards[0].name, None)
trainingChoiceWorld = create_setup( # noqa
exp, 'trainingChoiceWorld', p.boards[0].name, None)
ephys_certification = create_setup( # noqa
exp, 'ephys_certification', p.boards[0].name, None)
ephysChoiceWorld = create_setup( # noqa
exp,
'ephysChoiceWorld_testing',
p.boards[0].name,
test_subj,
task='_iblrig_tasks_ephysChoiceWorld')
passiveChoiceWorld = create_setup( # noqa
exp,
'passiveChoiceWorld_testing',
p.boards[0].name,
test_subj,
task='_iblrig_tasks_passiveChoiceWorld')
p.save(iblproject_path)
def setups_to_remove(iblproject_path):
p = Project()
p.load(iblproject_path)
exp = [e for e in p.experiments if e.name == "_iblrig_calibration"]
if not exp:
raise KeyError(f"Experiment {exp} not found")
else:
exp = exp[0]
setup = [s for s in exp.setups if s.name == "screen"]
if not setup:
print(f"Setup {setup} not found")
else:
setup = setup[0]
print()
exp -= setup
p.save(iblproject_path)
def save(self, project_path=None):
if project_path:
Project.save(self, project_path)
elif self.path:
Project.save(self, self.path)
else:
folder = QFileDialog.getExistingDirectory(
self, "Select a directory to save the project: {0}".format(
self.name))
if folder:
folder = os.path.join(folder, self.name)
try:
Project.save(self, str(folder))
except FileExistsError as err:
logger.warning(str(err))
QMessageBox.warning(
self, 'Project exists',
'Project with same name already exists. Please select another path.'
)
def get_pybpod_board_comport():
iblproject_path = Path(ph.get_iblrig_params_folder()) / "IBL"
p = Project()
p.load(str(iblproject_path))
return p.boards[0].serial_port
def create_board_from_main_project_to(project_name, force=False):
project_name = alyx2local_names.get(project_name, project_name)
if project_name == "IBL":
print("Can't create board of main project")
return
project_path = IBLRIG_PARAMS_FOLDER / project_name
iblproj = Project()
iblproj.load(IBLRIG_PARAMS_FOLDER / "IBL")
print("Looking for boards in default project")
if not iblproj.boards or len(iblproj.boards) > 1:
print(
f"0 or 2+ boards found in main project: {[x.name for x in iblproj.boards]}"
)
return
bname = iblproj.boards[0].name
print("Board found: [{}]".format(bname))
p = Project()
if not pybpod_project_exists(project_name):
return
print(f"Loading [{project_path}]")
p.load(project_path)
if force or not p.boards:
board = p.create_board()
board.name = iblproj.boards[0].name
p.save(project_path)
print(f" Created board: [{board.name}] in project [{project_name}]")
elif len(p.boards) > 1:
print(
f" Skipping creation: project [{project_name}] already has [{len(p.boards)}] boards"
)
elif len(p.boards) == 1:
bname = p.boards[0].name
print(
f" Skipping creation: Board [{bname}] already exists in project [{project_name}]"
)
return
def __init__(self, root_path, project_path):
self.root_path = root_path
self.project_path = project_path
self.project = Project()
self.hostname = os.environ['COMPUTERNAME']
from pybpodgui_api.models.project import Project
# create the project
proj = Project()
proj.load('my-project-folder')
exp = proj.experiments[0]
stp = exp.setups[0]
for session in stp.sessions:
for msg in session.messages_history:
if msg.check_type('INFO'):
pass
# Do somehting
elif msg.check_type('stderr'):
pass
# Do something