def __init__(self, task_settings, user_settings):
# =====================================================================
# IMPORT task_settings, user_settings, and SessionPathCreator params
# =====================================================================
ts = {
i: task_settings.__dict__[i]
for i in [x for x in dir(task_settings) if '__' not in x]
}
self.__dict__.update(ts)
us = {
i: user_settings.__dict__[i]
for i in [x for x in dir(user_settings) if '__' not in x]
}
self.__dict__.update(us)
self = iotasks.deserialize_pybpod_user_settings(self)
spc = SessionPathCreator(self.IBLRIG_FOLDER,
self.IBLRIG_DATA_FOLDER,
self.PYBPOD_SUBJECTS[0],
protocol=self.PYBPOD_PROTOCOL,
board=self.PYBPOD_BOARD,
make=True)
self.__dict__.update(spc.__dict__)
# =====================================================================
# OSC CLIENT
# =====================================================================
self.OSC_CLIENT_PORT = 7110
self.OSC_CLIENT_IP = '127.0.0.1'
self.OSC_CLIENT = udp_client.SimpleUDPClient(self.OSC_CLIENT_IP,
self.OSC_CLIENT_PORT)
# =====================================================================
# frame2TTL
# =====================================================================
self.F2TTL_GET_AND_SET_THRESHOLDS = frame2TTL.get_and_set_thresholds(
self)
# =====================================================================
# PROBES + WEIGHT
# =====================================================================
self.FORM_DATA = user_input.session_form(mouse_name=self.SUBJECT_NAME)
self = user_input.parse_form_data(self)
# =====================================================================
# RUN VISUAL STIM
# =====================================================================
self.VISUAL_STIMULUS_TYPE = 'ephys_certification'
# bonsai.start_visual_stim(self)
# =====================================================================
# SAVE SETTINGS FILE AND TASK CODE
# =====================================================================
iotasks.save_session_settings(self)
def __init__(self, task_settings, user_settings, debug=False, fmake=True):
self.DEBUG = debug
make = True
self.IBLRIG_FOLDER = 'C:\\iblrig'
self.IBLRIG_DATA_FOLDER = None # ..\\iblrig_data if None
# =====================================================================
# IMPORT task_settings, user_settings, and SessionPathCreator params
# =====================================================================
ts = {i: task_settings.__dict__[i]
for i in [x for x in dir(task_settings) if '__' not in x]}
self.__dict__.update(ts)
us = {i: user_settings.__dict__[i]
for i in [x for x in dir(user_settings) if '__' not in x]}
self.__dict__.update(us)
self = iotasks.deserialize_pybpod_user_settings(self)
spc = SessionPathCreator(self.PYBPOD_SUBJECTS[0],
protocol=self.PYBPOD_PROTOCOL,
make=make)
self.__dict__.update(spc.__dict__)
# =====================================================================
# SETTINGS
# =====================================================================
self.RECORD_SOUND = True
self.RECORD_AMBIENT_SENSOR_DATA = True
self.RECORD_VIDEO = True
self.OPEN_CAMERA_VIEW = True # Always True if RECORD_VIDEO is True
self.NTRIALS = 2000 # Number of trials for the current session
self.USE_AUTOMATIC_STOPPING_CRITERIONS = True # Weather to check for the Automatic stopping criterions or not # noqa
self.REPEAT_ON_ERROR = False # not used
self.INTERACTIVE_DELAY = 0.0
self.RESPONSE_WINDOW = 60
self.ITI_CORRECT = 1
self.ITI_ERROR = 2
self.CONTRAST_SET = [1., 0.25, 0.125, 0.0625, 0.] # Full contrast set
self.CONTRAST_SET_PROBABILITY_TYPE = 'biased'
self.STIM_FREQ = 0.10 # Probably constant - NOT IN USE
self.STIM_ANGLE = 0. # Vertical orientation of Gabor patch
self.STIM_SIGMA = 7. # (azimuth_degree) Size of Gabor patch
self.STIM_GAIN = 4. # (azimuth_degree/mm) Gain of the RE
# =====================================================================
# SUBJECT
# =====================================================================
# self.SUBJECT_WEIGHT = self.ask_subject_weight()
self.POOP_COUNT = False
self.SUBJECT_DISENGAGED_TRIGGERED = False
self.SUBJECT_DISENGAGED_TRIALNUM = None
# =====================================================================
# OSC CLIENT
# =====================================================================
self.OSC_CLIENT_PORT = 7110
self.OSC_CLIENT_IP = '127.0.0.1'
self.OSC_CLIENT = udp_client.SimpleUDPClient(self.OSC_CLIENT_IP,
self.OSC_CLIENT_PORT)
# =====================================================================
# PREVIOUS DATA FILES
# =====================================================================
self.LAST_TRIAL_DATA = iotasks.load_data(self.PREVIOUS_SESSION_PATH)
self.LAST_SETTINGS_DATA = iotasks.load_settings(
self.PREVIOUS_SESSION_PATH)
bonsai.start_mic_recording(self)
self.IS_MOCK = user_input.ask_is_mock() # Change to False if mock has its own task
# Get preloaded session num (the num in the filename!)
if self.IS_MOCK:
self.SESSION_ORDER = None
self.SESSION_IDX = None
self.PRELOADED_SESSION_NUM = 'mock'
else:
(
self.SESSION_ORDER,
self.SESSION_IDX
) = iotasks.load_session_order_idx(self.LAST_SETTINGS_DATA)
self.SESSION_IDX = user_input.ask_confirm_session_idx(self.SESSION_IDX)
self.PRELOADED_SESSION_NUM = self.SESSION_ORDER[self.SESSION_IDX]
# Load session from file
(
self.POSITIONS,
self.CONTRASTS,
self.QUIESCENT_PERIOD,
self.STIM_PHASE,
self.LEN_BLOCKS,
) = iotasks.load_ephys_session_pcqs(self.PRELOADED_SESSION_NUM)
# =====================================================================
# ADAPTIVE STUFF
# =====================================================================
self.AUTOMATIC_CALIBRATION = True
self.CALIBRATION_VALUE = 0.067
self.REWARD_AMOUNT = 1.5
self.REWARD_TYPE = 'Water 10% Sucrose'
self.CALIB_FUNC = None
if self.AUTOMATIC_CALIBRATION:
self.CALIB_FUNC = adaptive.init_calib_func()
self.CALIB_FUNC_RANGE = adaptive.init_calib_func_range()
self.REWARD_VALVE_TIME = adaptive.init_reward_valve_time(self)
# =====================================================================
# ROTARY ENCODER
# =====================================================================
self.STIM_POSITIONS = [-35, 35] # All possible positions (deg)
self.QUIESCENCE_THRESHOLDS = [-2, 2] # degree
self.ALL_THRESHOLDS = (self.STIM_POSITIONS +
self.QUIESCENCE_THRESHOLDS)
self.ROTARY_ENCODER = MyRotaryEncoder(self.ALL_THRESHOLDS,
self.STIM_GAIN,
self.PARAMS['COM_ROTARY_ENCODER'])
# =====================================================================
# frame2TTL
# =====================================================================
self.F2TTL_GET_AND_SET_THRESHOLDS = frame2TTL.get_and_set_thresholds()
# =====================================================================
# SOUNDS
# =====================================================================
self.SOFT_SOUND = None
self.SOUND_SAMPLE_FREQ = sound.sound_sample_freq(self.SOFT_SOUND)
self.SOUND_BOARD_BPOD_PORT = 'Serial3'
self.WHITE_NOISE_DURATION = float(0.5)
self.WHITE_NOISE_AMPLITUDE = float(0.05)
self.GO_TONE_DURATION = float(0.1)
self.GO_TONE_FREQUENCY = int(5000)
self.GO_TONE_AMPLITUDE = float(0.0151) # 0.0151 for 70.0 dB SPL CCU
self.SD = sound.configure_sounddevice(
output=self.SOFT_SOUND, samplerate=self.SOUND_SAMPLE_FREQ)
# Create sounds and output actions of state machine
self.GO_TONE = sound.make_sound(
rate=self.SOUND_SAMPLE_FREQ, frequency=self.GO_TONE_FREQUENCY,
duration=self.GO_TONE_DURATION, amplitude=self.GO_TONE_AMPLITUDE,
fade=0.01, chans='stereo')
self.WHITE_NOISE = sound.make_sound(
rate=self.SOUND_SAMPLE_FREQ, frequency=-1,
duration=self.WHITE_NOISE_DURATION,
amplitude=self.WHITE_NOISE_AMPLITUDE, fade=0.01, chans='stereo')
self.GO_TONE_IDX = 2
self.WHITE_NOISE_IDX = 3
sound.configure_sound_card(
sounds=[self.GO_TONE, self.WHITE_NOISE],
indexes=[self.GO_TONE_IDX, self.WHITE_NOISE_IDX],
sample_rate=self.SOUND_SAMPLE_FREQ)
self.OUT_TONE = ('SoftCode', 1) if self.SOFT_SOUND else ('Serial3', 6)
self.OUT_NOISE = ('SoftCode', 2) if self.SOFT_SOUND else ('Serial3', 7)
self.OUT_STOP_SOUND = (
'SoftCode', 0) if self.SOFT_SOUND else ('Serial3', ord('X'))
# =====================================================================
# PROBES + WEIGHT
# =====================================================================
form_data = -1
while form_data == -1:
form_data = user_input.session_form(mouse_name=self.SUBJECT_NAME)
self.SUBJECT_WEIGHT = user_input.get_form_subject_weight(form_data)
self.PROBE_DATA = user_input.get_form_probe_data(form_data)
# =====================================================================
# VISUAL STIM
# =====================================================================
self.SYNC_SQUARE_X = 1.33
self.SYNC_SQUARE_Y = -1.03
self.USE_VISUAL_STIMULUS = True # Run the visual stim in bonsai
self.BONSAI_EDITOR = False # Open the Bonsai editor of visual stim
bonsai.start_visual_stim(self)
# =====================================================================
# SAVE SETTINGS FILE AND TASK CODE
# =====================================================================
if not self.DEBUG:
iotasks.save_session_settings(self)
iotasks.copy_task_code(self)
iotasks.save_task_code(self)
self.bpod_lights(0)
self.display_logs()
def __init__(self, task_settings, user_settings):
# =====================================================================
# IMPORT task_settings, user_settings, and SessionPathCreator params
# =====================================================================
ts = {
i: task_settings.__dict__[i]
for i in [x for x in dir(task_settings) if '__' not in x]
}
self.__dict__.update(ts)
us = {
i: user_settings.__dict__[i]
for i in [x for x in dir(user_settings) if '__' not in x]
}
self.__dict__.update(us)
self = iotasks.deserialize_pybpod_user_settings(self)
spc = SessionPathCreator(self.PYBPOD_SUBJECTS[0],
protocol=self.PYBPOD_PROTOCOL,
make=True)
self.__dict__.update(spc.__dict__)
# =====================================================================
# OSC CLIENT
# =====================================================================
self.OSC_CLIENT_PORT = 7110
self.OSC_CLIENT_IP = '127.0.0.1'
self.OSC_CLIENT = udp_client.SimpleUDPClient(self.OSC_CLIENT_IP,
self.OSC_CLIENT_PORT)
# =====================================================================
# frame2TTL
# =====================================================================
self.F2TTL_GET_AND_SET_THRESHOLDS = frame2TTL.get_and_set_thresholds()
# =====================================================================
# PROBES + WEIGHT
# =====================================================================
self.FORM_DATA = user_input.session_form(mouse_name=self.SUBJECT_NAME)
self.PROBE_DATA = user_input.get_form_probe_data(self.FORM_DATA)
self.SUBJECT_WEIGHT = user_input.get_form_subject_weight(
self.FORM_DATA)
# =====================================================================
# VISUAL STIM
# =====================================================================
self.VISUAL_STIMULUS_FILE = None
self.SCREEN_DIMENSIONS = {'width': 20, 'height': 15} # cm
self.SCREEN_EXTRINSICS = {
'rotation': (0, 0, 0),
'translation': (0, 0, -8)
}
self.SCREEN_VISUAL_SPAN_X = np.rad2deg(
math.atan(self.SCREEN_DIMENSIONS['width'] / 2 /
abs(self.SCREEN_EXTRINSICS['translation'][2]))) * 2
self.SCREEN_VISUAL_SPAN_Y = np.rad2deg(
math.atan(self.SCREEN_DIMENSIONS['height'] / 2 /
abs(self.SCREEN_EXTRINSICS['translation'][2]))) * 2
self.VISUAL_STIMULI = {
0: 'SPACER',
1: 'receptive_field_mapping',
2: 'orientation-direction_selectivity',
3: 'contrast_reversal',
4: 'task_stimuli',
5: 'spontaneous_activity',
}
self.STIM_ORDER = [0, 5, 0, 2, 0, 1, 0, 3, 0, 4, 0, 5, 0, 2, 0]
self.VISUAL_STIM_0 = {
'ttl_num':
16,
'ttl_frame_nums': [
1, 2, 4, 8, 16, 32, 64, 128, 192, 224, 240, 248, 252, 254, 255,
256
],
'delay_around':
4 # seconds
}
self.VISUAL_STIM_1 = {
'ttl_num': None,
'stim_shape': 'square',
'stim_npatches': 15 * 15,
'patch_dva': 8,
'dva_mat': make_square_dvamat(size=15, dva=8),
'stim_data_file_name': '_iblrig_RFMapStim.raw.bin',
'stim_file_shape': [15, 15, 'nframes'],
'stim_on_time': 0.2, # seconds
'polarity_start': -1,
'polarity_end': +1
}
self.VISUAL_STIM_2 = {
'ttl_num': 320,
'stim_directions_rad': {
1: 3 * np.pi / 2,
2: 5 * np.pi / 4,
3: 1 * np.pi / 1,
4: 3 * np.pi / 4,
5: 1 * np.pi / 2,
6: 1 * np.pi / 4,
7: 0 * np.pi / 2,
8: 7 * np.pi / 4,
},
'stim_sequence': [1, 2, 3, 4, 5, 6, 7, 8] * 20,
'stim_tf': 2, # Hz
'stim_cpd': 0.05, # spatial freq, cycles per degree
'stim_on_time': 2, # seconds
'stim_off_time': 1, # seconds
'polarity_start': +1,
'polarity_end': -1,
}
self.VISUAL_STIM_3 = {
'ttl_num': 180,
'stim_shape': 'square',
'stim_npatches': 15 * 15,
'patch_dva': 25,
'dva_mat': make_square_dvamat(size=15, dva=25),
'stim_patch_contrasts': {
1: checkerboard((15, 15)) * 255,
2: np.abs(checkerboard((15, 15)) - 1) * 255
},
'stim_sequence': [1, 2] * 90,
'stim_on_time': 1, # seconds
'stim_off_time': 0, # seconds
'polarity_start': +1,
'polarity_end': -1,
}
self.VISUAL_STIM_4 = {
'ttl_num': 400,
'stim_spatial_freq': 0.1, # cyc/º
'sigma': 7**2, # dva
'elevation': 0,
'orientation': 0,
'phase': 0,
'stim_on_time': 2, # seconds
'stim_off_time': 1, # seconds
'stim_azimuth_set': [-35, 35],
'stim_contrast_set': [1.0, 0.5, 0.25, 0.125, 0.0625],
'stim_file':
'iblrig/visual_stim/ephys_certification/04_ContrastSelectivityTaskStim/stims.csv',
'stim_file_columns': ('azimuth', 'contrast'),
'polarity_start': +1,
'polarity_end': -1,
}
# =====================================================================
# SAVE SETTINGS FILE AND TASK CODE
# =====================================================================
iotasks.copy_task_code(self)
iotasks.save_task_code(self)
iotasks.save_session_settings(self)
def __init__(self, task_settings, user_settings):
# =====================================================================
# IMPORT task_settings, user_settings, and SessionPathCreator params
# =====================================================================
ts = {
i: task_settings.__dict__[i]
for i in [x for x in dir(task_settings) if "__" not in x]
}
self.__dict__.update(ts)
us = {
i: user_settings.__dict__[i]
for i in [x for x in dir(user_settings) if "__" not in x]
}
self.__dict__.update(us)
self = iotasks.deserialize_pybpod_user_settings(self)
spc = SessionPathCreator(
self.PYBPOD_SUBJECTS[0], protocol=self.PYBPOD_PROTOCOL, make=True
)
self.__dict__.update(spc.__dict__)
# =====================================================================
# OSC CLIENT
# =====================================================================
self.OSC_CLIENT_PORT = 7110
self.OSC_CLIENT_IP = "127.0.0.1"
self.OSC_CLIENT = udp_client.SimpleUDPClient(
self.OSC_CLIENT_IP, self.OSC_CLIENT_PORT
)
# =====================================================================
# frame2TTL
# =====================================================================
self.F2TTL_GET_AND_SET_THRESHOLDS = frame2TTL.get_and_set_thresholds()
# =====================================================================
# PROBES + WEIGHT
# =====================================================================
self.FORM_DATA = user_input.session_form(mouse_name=self.SUBJECT_NAME)
self.PROBE_DATA = user_input.get_form_probe_data(self.FORM_DATA)
self.SUBJECT_WEIGHT = user_input.get_form_subject_weight(self.FORM_DATA)
# =====================================================================
# VISUAL STIM
# =====================================================================
self.VISUAL_STIMULUS_FILE = None
self.SCREEN_DIMENSIONS = {"width": 20, "height": 15} # cm
self.SCREEN_EXTRINSICS = {"rotation": (0, 0, 0), "translation": (0, 0, -8)}
self.SCREEN_VISUAL_SPAN_X = (
np.rad2deg(
math.atan(
self.SCREEN_DIMENSIONS["width"]
/ 2
/ abs(self.SCREEN_EXTRINSICS["translation"][2])
)
)
* 2
)
self.SCREEN_VISUAL_SPAN_Y = (
np.rad2deg(
math.atan(
self.SCREEN_DIMENSIONS["height"]
/ 2
/ abs(self.SCREEN_EXTRINSICS["translation"][2])
)
)
* 2
)
self.VISUAL_STIMULI = {
0: "SPACER",
1: "receptive_field_mapping",
2: "orientation-direction_selectivity",
3: "contrast_reversal",
4: "task_stimuli",
5: "spontaneous_activity",
}
self.STIM_ORDER = [0, 5, 0, 2, 0, 1, 0, 3, 0, 4, 0, 5, 0, 2, 0]
self.VISUAL_STIM_0 = {
"ttl_num": 16,
"ttl_frame_nums": [
1,
2,
4,
8,
16,
32,
64,
128,
192,
224,
240,
248,
252,
254,
255,
256,
],
"delay_around": 4, # seconds
}
self.VISUAL_STIM_1 = {
"ttl_num": None,
"stim_shape": "square",
"stim_npatches": 15 * 15,
"patch_dva": 8,
"dva_mat": make_square_dvamat(size=15, dva=8),
"stim_data_file_name": "_iblrig_RFMapStim.raw.bin",
"stim_file_shape": [15, 15, "nframes"],
"stim_on_time": 0.2, # seconds
"polarity_start": -1,
"polarity_end": +1,
}
self.VISUAL_STIM_2 = {
"ttl_num": 320,
"stim_directions_rad": {
1: 3 * np.pi / 2,
2: 5 * np.pi / 4,
3: 1 * np.pi / 1,
4: 3 * np.pi / 4,
5: 1 * np.pi / 2,
6: 1 * np.pi / 4,
7: 0 * np.pi / 2,
8: 7 * np.pi / 4,
},
"stim_sequence": [1, 2, 3, 4, 5, 6, 7, 8] * 20,
"stim_tf": 2, # Hz
"stim_cpd": 0.05, # spatial freq, cycles per degree
"stim_on_time": 2, # seconds
"stim_off_time": 1, # seconds
"polarity_start": +1,
"polarity_end": -1,
}
self.VISUAL_STIM_3 = {
"ttl_num": 180,
"stim_shape": "square",
"stim_npatches": 15 * 15,
"patch_dva": 25,
"dva_mat": make_square_dvamat(size=15, dva=25),
"stim_patch_contrasts": {
1: checkerboard((15, 15)) * 255,
2: np.abs(checkerboard((15, 15)) - 1) * 255,
},
"stim_sequence": [1, 2] * 90,
"stim_on_time": 1, # seconds
"stim_off_time": 0, # seconds
"polarity_start": +1,
"polarity_end": -1,
}
self.VISUAL_STIM_4 = {
"ttl_num": 400,
"stim_spatial_freq": 0.1, # cyc/º
"sigma": 7 ** 2, # dva
"elevation": 0,
"orientation": 0,
"phase": 0,
"stim_on_time": 2, # seconds
"stim_off_time": 1, # seconds
"stim_azimuth_set": [-35, 35],
"stim_contrast_set": [1.0, 0.5, 0.25, 0.125, 0.0625],
"stim_file":
"iblrig/visual_stim/ephys_certification/04_ContrastSelectivityTaskStim/stims.csv",
"stim_file_columns": ("azimuth", "contrast"),
"polarity_start": +1,
"polarity_end": -1,
}
# =====================================================================
# SAVE SETTINGS FILE AND TASK CODE
# =====================================================================
iotasks.copy_task_code(self)
iotasks.save_task_code(self)
iotasks.save_session_settings(self)