def update_alyx_params(data: dict, force: bool = False) -> dict:
old = load_alyx_params(data["NAME"])
if old is None:
log.info("board params not found, creating...")
new = rig_params.create_new_params_dict()
write_alyx_params(new)
old = load_alyx_params(new["NAME"])
board = rig_params.get_board_name()
if "NAME" in data and data["NAME"] != board:
log.error(f"Board {board} not equal to data['NAME'] {data['NAME']}")
raise (AttributeError)
for k in data:
if k in old.keys():
old[k] = data[k]
else:
if not force:
log.info(f"Unknown key {k}: skipping key...")
continue
elif force:
log.info(
f"Adding new key {k} with value {data[k]} to {board} json field"
)
old[k] = data[k]
write_alyx_params(data=old, force=True)
log.info(f"Changed board params: {data}")
return old
def load_board_params() -> dict:
board = rig_params.get_board_name()
one = get_one()
try:
out = one.alyx.rest('locations', 'read', id=board)['json']
out = json.loads(out)
except Exception as e:
log.error(e)
out = None
return out
def write_board_params(data: dict = None, force: bool = False) -> None:
if data is None:
data = rig_params.EMPTY_BOARD_PARAMS
data['NAME'] = rig_params.get_board_name()
data['COM_BPOD'] = rig_params.get_board_comport()
board = data['NAME']
one = get_one()
p = load_board_params()
if p and not force:
log.info('Board params already present, exiting...')
return p
patch_dict = {"json": json.dumps(data)}
one.alyx.rest('locations', 'partial_update', id=board, data=patch_dict)
return data
def __init__(self, subject_name, protocol=False, make=False):
self.IBLRIG_FOLDER = get_iblrig_folder()
self.IBLRIG_EPHYS_SESSION_FOLDER = get_pregen_session_folder()
self._BOARD = params.get_board_name()
self._PROTOCOL = protocol
self.IBLRIG_COMMIT_HASH = get_commit_hash(self.IBLRIG_FOLDER)
self.IBLRIG_VERSION_TAG = get_version_tag(self.IBLRIG_FOLDER)
self.IBLRIG_PARAMS_FOLDER = get_iblrig_params_folder()
self.IBLRIG_DATA_FOLDER = get_iblrig_data_folder(subjects=False)
self.IBLRIG_DATA_SUBJECTS_FOLDER = get_iblrig_data_folder(subjects=True)
self.PARAMS = params.load_params_file()
# TODO: check if can remove old bpod_comports file
self.IBLRIG_PARAMS_FILE = str(Path(self.IBLRIG_PARAMS_FOLDER) / ".bpod_comports.json")
self.SUBJECT_NAME = subject_name
self.SUBJECT_FOLDER = os.path.join(self.IBLRIG_DATA_SUBJECTS_FOLDER, self.SUBJECT_NAME)
self.BONSAI = get_bonsai_path(use_iblrig_bonsai=True)
self.VISUAL_STIM_FOLDER = str(Path(self.IBLRIG_FOLDER) / "visual_stim")
self.VISUAL_STIMULUS_TYPE = get_visual_stim_type(self._PROTOCOL)
self.VISUAL_STIMULUS_FILE_NAME = get_visual_stim_file_name(self.VISUAL_STIMULUS_TYPE)
self.VISUAL_STIMULUS_FILE = str(
Path(self.VISUAL_STIM_FOLDER)
/ self.VISUAL_STIMULUS_TYPE
/ self.VISUAL_STIMULUS_FILE_NAME
)
self.VIDEO_RECORDING_FOLDER = os.path.join(
self.IBLRIG_FOLDER, "devices", "camera_recordings"
)
self.VIDEO_RECORDING_FILE = os.path.join(
self.VIDEO_RECORDING_FOLDER, "TrainingRig_SaveVideo_TrainingTasks.bonsai"
)
self.MIC_RECORDING_FOLDER = os.path.join(self.IBLRIG_FOLDER, "devices", "microphone")
self.MIC_RECORDING_FILE = os.path.join(self.MIC_RECORDING_FOLDER, "record_mic.bonsai")
self.SESSION_DATETIME = datetime.datetime.now().isoformat()
self.SESSION_DATE = datetime.datetime.now().date().isoformat()
self.SESSION_DATE_FOLDER = os.path.join(self.SUBJECT_FOLDER, self.SESSION_DATE)
self.SESSION_NUMBER = get_session_number(self.SESSION_DATE_FOLDER)
self.SESSION_FOLDER = str(Path(self.SESSION_DATE_FOLDER) / self.SESSION_NUMBER)
self.SESSION_RAW_DATA_FOLDER = os.path.join(self.SESSION_FOLDER, "raw_behavior_data")
self.SESSION_RAW_VIDEO_DATA_FOLDER = os.path.join(self.SESSION_FOLDER, "raw_video_data")
self.SESSION_RAW_EPHYS_DATA_FOLDER = os.path.join(self.SESSION_FOLDER, "raw_ephys_data")
self.SESSION_RAW_IMAGING_DATA_FOLDER = os.path.join(
self.SESSION_FOLDER, "raw_imaging_data"
)
self.SESSION_RAW_PASSIVE_DATA_FOLDER = os.path.join(
self.SESSION_FOLDER, "raw_passive_data"
)
self.SESSION_NAME = "{}".format(os.path.sep).join(
[self.SUBJECT_NAME, self.SESSION_DATE, self.SESSION_NUMBER]
)
self.BASE_FILENAME = "_iblrig_task"
self.SETTINGS_FILE_PATH = os.path.join(
self.SESSION_RAW_DATA_FOLDER, self.BASE_FILENAME + "Settings.raw.json"
)
self.DATA_FILE_PATH = os.path.join(
self.SESSION_RAW_DATA_FOLDER, self.BASE_FILENAME + "Data.raw.jsonable"
)
# Water calinbration files
self.LATEST_WATER_CALIBRATION_FILE = get_water_calibration_func_file(latest=True)
self.LATEST_WATER_CALIB_RANGE_FILE = get_water_calibration_range_file(latest=True)
if self.LATEST_WATER_CALIBRATION_FILE.parent != self.LATEST_WATER_CALIB_RANGE_FILE.parent:
self.LATEST_WATER_CALIBRATION_FILE = str(self.LATEST_WATER_CALIBRATION_FILE)
self.LATEST_WATER_CALIB_RANGE_FILE = None
else:
self.LATEST_WATER_CALIBRATION_FILE = str(self.LATEST_WATER_CALIBRATION_FILE)
self.LATEST_WATER_CALIB_RANGE_FILE = str(self.LATEST_WATER_CALIB_RANGE_FILE)
if str(self.LATEST_WATER_CALIBRATION_FILE) == ".":
self.LATEST_WATER_CALIBRATION_FILE = None
self.LATEST_WATER_CALIB_RANGE_FILE = None
# Previous session files
self.PREVIOUS_DATA_FILE = get_previous_data_file(
self._PROTOCOL, self.SUBJECT_NAME, self.SESSION_FOLDER
)
self.PREVIOUS_SETTINGS_FILE = get_previous_settings_file(
self._PROTOCOL, self.SUBJECT_NAME, self.SESSION_FOLDER
)
self.PREVIOUS_SESSION_PATH = get_previous_session_path(
self._PROTOCOL, self.SUBJECT_NAME, self.SESSION_FOLDER
)
if make:
self.make_missing_folders(make)
self.display_logs()
# Load PARAMS file ports
# If file exists open file if not initialize
log.debug("Loading params file...")
PARAMS = params.load_params()
# Check PARAMS values
checks = []
for k in PARAMS:
if PARAMS[k] is None or PARAMS[k] == "":
checks.append(1)
log.warning(f"{k}: Value not found")
if sum(checks) != 0:
log.error("Missing values in params file")
raise (ValueError)
# Check board name
assert PARAMS["NAME"] == params.get_board_name()
# COM ports check
PARAMS["COM_BPOD"]
PARAMS["COM_ROTARY_ENCODER"]
PARAMS["COM_F2TTL"]
# F2TTL CALIBRATION: check f2ttl values from params, warn if old calibration
PARAMS["F2TTL_DARK_THRESH"]
PARAMS["F2TTL_LIGHT_THRESH"]
PARAMS["F2TTL_CALIBRATION_DATE"]
# WATER CALIBRATION: check water calibration values from params, warn if old calibration
log.debug("Checking water calibration...")
PARAMS["WATER_CALIBRATION_RANGE"]
PARAMS["WATER_CALIBRATION_OPEN_TIMES"]
PARAMS["WATER_CALIBRATION_WEIGHT_PERDROP"]
PARAMS["WATER_CALIBRATION_DATE"]
# F2TTL CALIBRATION: check f2ttl values from params, warn if old calibration
# Load PARAMS file ports
# If file exists open file if not initialize
log.debug("Loading params file...")
PARAMS = params.load_params()
# Check PARAMS values
checks = []
for k in PARAMS:
if PARAMS[k] is None or PARAMS[k] == '':
checks.append(1)
log.warning(f'{k}: Value not found')
if sum(checks) != 0:
log.error('Missing values in params file')
raise (ValueError)
# Check board name
assert (PARAMS['NAME'] == params.get_board_name())
# COM ports check
PARAMS['COM_BPOD']
PARAMS['COM_ROTARY_ENCODER']
PARAMS['COM_F2TTL']
# F2TTL CALIBRATION: check f2ttl values from params, warn if old calibration
PARAMS['F2TTL_DARK_THRESH']
PARAMS['F2TTL_LIGHT_THRESH']
PARAMS['F2TTL_CALIBRATION_DATE']
# WATER CALIBRATION: check water calibration values from params, warn if old calibration
log.debug("Checking water calibration...")
PARAMS['WATER_CALIBRATION_RANGE']
PARAMS['WATER_CALIBRATION_OPEN_TIMES']
PARAMS['WATER_CALIBRATION_WEIGHT_PERDROP']
PARAMS['WATER_CALIBRATION_DATE']
# F2TTL CALIBRATION: check f2ttl values from params, warn if old calibration
def __init__(self, subject_name, protocol=False, make=False):
self.IBLRIG_FOLDER = get_iblrig_folder()
self.IBLRIG_EPHYS_SESSION_FOLDER = str(
Path(self.IBLRIG_FOLDER) / 'tasks' /
'_iblrig_tasks_ephysChoiceWorld' / 'sessions')
self._BOARD = params.get_board_name()
self._PROTOCOL = protocol
self.IBLRIG_COMMIT_HASH = get_commit_hash(self.IBLRIG_FOLDER)
self.IBLRIG_VERSION_TAG = get_version_tag(self.IBLRIG_FOLDER)
self.IBLRIG_PARAMS_FOLDER = get_iblrig_params_folder()
self.IBLRIG_DATA_FOLDER = get_iblrig_data_folder(subjects=False)
self.IBLRIG_DATA_SUBJECTS_FOLDER = get_iblrig_data_folder(subjects=True)
self.PARAMS = params.load_params_file()
self.IBLRIG_PARAMS_FILE = str(
Path(self.IBLRIG_PARAMS_FOLDER) / '.bpod_comports.json')
self.SUBJECT_NAME = subject_name
self.SUBJECT_FOLDER = os.path.join(
self.IBLRIG_DATA_SUBJECTS_FOLDER, self.SUBJECT_NAME)
self.BONSAI = get_bonsai_path(use_iblrig_bonsai=True)
self.VISUAL_STIM_FOLDER = str(Path(self.IBLRIG_FOLDER) / 'visual_stim')
self.VISUAL_STIMULUS_TYPE = get_visual_stim_type(self._PROTOCOL)
self.VISUAL_STIMULUS_FILE = str(
Path(self.VISUAL_STIM_FOLDER) /
self.VISUAL_STIMULUS_TYPE / 'Gabor2D.bonsai')
self.VIDEO_RECORDING_FOLDER = os.path.join(
self.IBLRIG_FOLDER, 'devices', 'camera_recordings')
self.VIDEO_RECORDING_FILE = os.path.join(
self.VIDEO_RECORDING_FOLDER, 'one_camera.bonsai')
self.SESSION_DATETIME = datetime.datetime.now()
self.SESSION_DATE = self.SESSION_DATETIME.date().isoformat()
self.SESSION_DATETIME = self.SESSION_DATETIME.isoformat()
self.SESSION_DATE_FOLDER = os.path.join(
self.SUBJECT_FOLDER, self.SESSION_DATE)
self.SESSION_NUMBER = get_session_number(self.SESSION_DATE_FOLDER)
self.SESSION_FOLDER = str(
Path(self.SESSION_DATE_FOLDER) / self.SESSION_NUMBER)
self.SESSION_RAW_DATA_FOLDER = os.path.join(
self.SESSION_FOLDER, 'raw_behavior_data')
self.SESSION_RAW_VIDEO_DATA_FOLDER = os.path.join(
self.SESSION_FOLDER, 'raw_video_data')
self.SESSION_RAW_EPHYS_DATA_FOLDER = os.path.join(
self.SESSION_FOLDER, 'raw_ephys_data')
self.SESSION_RAW_IMAGING_DATA_FOLDER = os.path.join(
self.SESSION_FOLDER, 'raw_imaging_data')
self.SESSION_NAME = '{}'.format(os.path.sep).join(
[self.SUBJECT_NAME, self.SESSION_DATE, self.SESSION_NUMBER])
self.BASE_FILENAME = '_iblrig_task'
self.SETTINGS_FILE_PATH = os.path.join(self.SESSION_RAW_DATA_FOLDER,
self.BASE_FILENAME +
'Settings.raw.json')
self.DATA_FILE_PATH = os.path.join(self.SESSION_RAW_DATA_FOLDER,
self.BASE_FILENAME +
'Data.raw.jsonable')
# Water calinbration files
self.LATEST_WATER_CALIBRATION_FILE = get_water_calibration_func_file(latest=True)
self.LATEST_WATER_CALIB_RANGE_FILE = get_water_calibration_range_file(latest=True)
if self.LATEST_WATER_CALIBRATION_FILE.parent != self.LATEST_WATER_CALIB_RANGE_FILE.parent:
self.LATEST_WATER_CALIBRATION_FILE = str(self.LATEST_WATER_CALIBRATION_FILE)
self.LATEST_WATER_CALIB_RANGE_FILE = None
else:
self.LATEST_WATER_CALIBRATION_FILE = str(self.LATEST_WATER_CALIBRATION_FILE)
self.LATEST_WATER_CALIB_RANGE_FILE = str(self.LATEST_WATER_CALIB_RANGE_FILE)
if str(self.LATEST_WATER_CALIBRATION_FILE) == '.':
self.LATEST_WATER_CALIBRATION_FILE = None
self.LATEST_WATER_CALIB_RANGE_FILE = None
# Previous session files
self.PREVIOUS_DATA_FILE = get_previous_data_file(self._PROTOCOL,
self.SUBJECT_NAME,
self.SESSION_FOLDER)
self.PREVIOUS_SETTINGS_FILE = get_previous_settings_file(self._PROTOCOL,
self.SUBJECT_NAME,
self.SESSION_FOLDER)
self.PREVIOUS_SESSION_PATH = get_previous_session_path(self._PROTOCOL,
self.SUBJECT_NAME,
self.SESSION_FOLDER)
if make:
self.make_missing_folders(make)
self.display_logs()