Merge branch 'iblrigv8dev' into valve_calibration_pt2

CHANGELOG.md

@@ -7,6 +7,11 @@ Changelog
 * automated validation of rig components
 * adaptive reward parameter for trainingPhaseChoiceWorld
 * add validate_video entry-point
+* switch from flake8 to ruff for linting & code-checks
+* automatically set correct trigger-mode when setting up the cameras
+* support rotary encoder on arbitrary module port
+* add ambient sensor reading back to trial log
+* allow negative stimulus gain (reverse wheel contingency)
 
 8.18.0
 ------

iblrig/base_choice_world.py

@@ -159,8 +159,6 @@ def _run(self):
         This is the method that runs the task with the actual state machine
         :return:
         """
-        # make the bpod send spacer signals to the main sync clock for protocol discovery
-        self.send_spacers()
         time_last_trial_end = time.time()
         for i in range(self.task_params.NTRIALS):  # Main loop
             # t_overhead = time.time()
@@ -186,6 +184,7 @@ def _run(self):
             self.bpod.run_state_machine(sma)  # Locks until state machine 'exit' is reached
             time_last_trial_end = time.time()
             self.trial_completed(self.bpod.session.current_trial.export())
+            self.ambient_sensor_table.loc[i] = self.bpod.get_ambient_sensor_reading()
             self.show_trial_log()
 
             # handle pause and stop events
@@ -427,22 +426,24 @@ def next_trial(self):
         pass
 
     @property
-    def reward_amount(self):
+    def default_reward_amount(self):
         return self.task_params.REWARD_AMOUNT_UL
 
-    def draw_next_trial_info(self, pleft=0.5, contrast=None, position=None):
         """Draw next trial variables.
 
-        This is called by the `next_trial` method before updating the Bpod state machine. This also
         calls :meth:`send_trial_info_to_bonsai`.
+        This is called by the `next_trial` method before updating the Bpod state machine. This also
         """
+
+    def draw_next_trial_info(self, pleft=0.5, contrast=None, position=None, reward_amount=None):
         if contrast is None:
             contrast = misc.draw_contrast(self.task_params.CONTRAST_SET, self.task_params.CONTRAST_SET_PROBABILITY_TYPE)
         assert len(self.task_params.STIM_POSITIONS) == 2, 'Only two positions are supported'
         position = position or int(np.random.choice(self.task_params.STIM_POSITIONS, p=[pleft, 1 - pleft]))
         quiescent_period = self.task_params.QUIESCENT_PERIOD + misc.truncated_exponential(
             scale=0.35, min_value=0.2, max_value=0.5
         )
+        reward_amount = self.default_reward_amount if reward_amount is None else reward_amount
         self.trials_table.at[self.trial_num, 'quiescent_period'] = quiescent_period
         self.trials_table.at[self.trial_num, 'contrast'] = contrast
         self.trials_table.at[self.trial_num, 'stim_phase'] = random.uniform(0, 2 * math.pi)
@@ -452,7 +453,7 @@ def draw_next_trial_info(self, pleft=0.5, contrast=None, position=None):
         self.trials_table.at[self.trial_num, 'stim_freq'] = self.task_params.STIM_FREQ
         self.trials_table.at[self.trial_num, 'trial_num'] = self.trial_num
         self.trials_table.at[self.trial_num, 'position'] = position
-        self.trials_table.at[self.trial_num, 'reward_amount'] = self.reward_amount
+        self.trials_table.at[self.trial_num, 'reward_amount'] = reward_amount
         self.trials_table.at[self.trial_num, 'stim_probability_left'] = pleft
         self.send_trial_info_to_bonsai()
 
@@ -527,13 +528,17 @@ def quiescent_period(self):
     def position(self):
         return self.trials_table.at[self.trial_num, 'position']
 
+    @property
+    def reverse_wheel(self):
+        return self.task_params.STIM_GAIN < 0
+
     @property
     def event_error(self):
-        return self.device_rotary_encoder.THRESHOLD_EVENTS[self.position]
+        return self.device_rotary_encoder.THRESHOLD_EVENTS[-self.position if self.reverse_wheel else self.position]
 
     @property
     def event_reward(self):
-        return self.device_rotary_encoder.THRESHOLD_EVENTS[-self.position]
+        return self.device_rotary_encoder.THRESHOLD_EVENTS[self.position if self.reverse_wheel else -self.position]
 
 
 class HabituationChoiceWorldSession(ChoiceWorldSession):
@@ -628,7 +633,9 @@ def _run(self):
         # starts online plotting
         if self.interactive:
             subprocess.Popen(
-                ['viewsession', str(self.paths['DATA_FILE_PATH'])], stdout=subprocess.DEVNULL, stderr=subprocess.STDOUT
+                ['view_session', str(self.paths['DATA_FILE_PATH']), str(self.paths['SETTINGS_FILE_PATH'])],
+                stdout=subprocess.DEVNULL,
+                stderr=subprocess.STDOUT,
             )
         super()._run()
 
@@ -783,7 +790,7 @@ def __init__(self, training_phase=-1, adaptive_reward=-1.0, adaptive_gain=None,
         self.trials_table['debias_trial'] = np.zeros(NTRIALS_INIT, dtype=bool)
 
     @property
-    def reward_amount(self):
+    def default_reward_amount(self):
         return self.session_info.get('ADAPTIVE_REWARD_AMOUNT_UL', self.task_params.REWARD_AMOUNT_UL)
 
     def get_subject_training_info(self):

iblrig/base_tasks.py

@@ -34,7 +34,7 @@
 import pybpodapi
 from ibllib.oneibl.registration import IBLRegistrationClient
 from iblrig import sound
-from iblrig.constants import BASE_PATH, BONSAI_EXE
+from iblrig.constants import BASE_PATH, BONSAI_EXE, PYSPIN_AVAILABLE
 from iblrig.frame2ttl import Frame2TTL
 from iblrig.hardware import SOFTCODE, Bpod, MyRotaryEncoder, sound_device_factory
 from iblrig.hifi import HiFi
@@ -191,6 +191,8 @@ def _init_paths(self, append: bool = False):
             >>> C:\iblrigv8_data\mainenlab\Subjects\SWC_043\2019-01-01\001\raw_task_data_00  # noqa
         DATA_FILE_PATH: contains the bpod trials
             >>> C:\iblrigv8_data\mainenlab\Subjects\SWC_043\2019-01-01\001\raw_task_data_00\_iblrig_taskData.raw.jsonable  # noqa
+        SETTINGS_FILE_PATH: contains the task settings
+            >>>C:\iblrigv8_data\mainenlab\Subjects\SWC_043\2019-01-01\001\raw_task_data_00\_iblrig_taskSettings.raw.json  # noqa
         """
         rig_computer_paths = iblrig.path_helper.get_local_and_remote_paths(
             local_path=self.iblrig_settings['iblrig_local_data_path'],
@@ -230,6 +232,7 @@ def _init_paths(self, append: bool = False):
         self.session_info.SESSION_NUMBER = int(paths.SESSION_FOLDER.name)
         paths.SESSION_RAW_DATA_FOLDER = paths.SESSION_FOLDER.joinpath(paths.TASK_COLLECTION)
         paths.DATA_FILE_PATH = paths.SESSION_RAW_DATA_FOLDER.joinpath('_iblrig_taskData.raw.jsonable')
+        paths.SETTINGS_FILE_PATH = paths.SESSION_RAW_DATA_FOLDER.joinpath('_iblrig_taskSettings.raw.json')
         return paths
 
     def _setup_loggers(self, level='INFO', level_bpod='WARNING', file=None):
@@ -336,18 +339,19 @@ def _make_task_parameters_dict(self):
         output_dict.update(patch_dict)
         return output_dict
 
-    def save_task_parameters_to_json_file(self, destination_folder=None) -> Path:
+    def save_task_parameters_to_json_file(self, destination_folder: Path | None = None) -> Path:
         """
-        Given a session object, collects the various settings and parameters of the session and outputs them to a JSON file
+        Collects the various settings and parameters of the session and outputs them to a JSON file
 
         Returns
         -------
         Path to the resultant JSON file
         """
         output_dict = self._make_task_parameters_dict()
-        destination_folder = destination_folder or self.paths.SESSION_RAW_DATA_FOLDER
-        # Output dict to json file
-        json_file = destination_folder.joinpath('_iblrig_taskSettings.raw.json')
+        if destination_folder:
+            json_file = destination_folder.joinpath('_iblrig_taskSettings.raw.json')
+        else:
+            json_file = self.paths['SETTINGS_FILE_PATH']
         json_file.parent.mkdir(parents=True, exist_ok=True)
         with open(json_file, 'w') as outfile:
             json.dump(output_dict, outfile, indent=4, sort_keys=True, default=str)  # converts datetime objects to string
@@ -368,7 +372,10 @@ def one(self):
             )
             try:
                 self._one = ONE(
-                    base_url=str(self.iblrig_settings['ALYX_URL']), username=self.iblrig_settings['ALYX_USER'], mode='remote'
+                    base_url=str(self.iblrig_settings['ALYX_URL']),
+                    username=self.iblrig_settings['ALYX_USER'],
+                    mode='remote',
+                    cache_rest=None,
                 )
                 log.info('instantiated ' + info_str)
             except Exception:
@@ -453,7 +460,7 @@ def mock(self):
     def create_session(self):
         # create the session path and save json parameters in the task collection folder
         # this will also create the protocol folder
-        self.save_task_parameters_to_json_file()
+        self.paths['TASK_PARAMETERS_FILE'] = self.save_task_parameters_to_json_file()
         # enable file logging
         logfile = self.paths.SESSION_RAW_DATA_FOLDER.joinpath('_ibl_log.info-acquisition.log')
         self._setup_loggers(level=self._logger.level, file=logfile)
@@ -651,10 +658,13 @@ def start_mixin_bonsai_cameras(self):
         configuration = self.hardware_settings.device_cameras[self.config]
         if (workflow_file := self._camera_mixin_bonsai_get_workflow_file(configuration, 'setup')) is None:
             return
-        # TODO: Disable Trigger in Bonsai workflow - PySpin won't help here
-        # if PYSPIN_AVAILABLE:
-        #     from iblrig.video_pyspin import enable_camera_trigger
-        #     enable_camera_trigger(True)
+
+        # enable trigger of cameras (so Bonsai can disable it again ... sigh)
+        if PYSPIN_AVAILABLE:
+            from iblrig.video_pyspin import enable_camera_trigger
+
+            enable_camera_trigger(True)
+
         call_bonsai(workflow_file, wait=True)  # TODO Parameterize using configuration cameras
         log.info('Bonsai cameras setup module loaded: OK')
 
@@ -793,7 +803,8 @@ def start_mixin_bpod(self):
         self.bpod.set_status_led(False)
         assert self.bpod.is_connected
         log.info('Bpod hardware module loaded: OK')
-        # self.send_spacers()
+        # make the bpod send spacer signals to the main sync clock for protocol discovery
+        self.send_spacers()
 
     def send_spacers(self):
         log.info('Starting task by sending a spacer signal on BNC1')
@@ -971,16 +982,15 @@ def start_mixin_sound(self):
         match self.hardware_settings.device_sound['OUTPUT']:
             case 'harp':
                 assert self.bpod.sound_card is not None, 'No harp sound-card connected to Bpod'
-                module_port = f'Serial{self.bpod.sound_card.serial_port}'
                 sound.configure_sound_card(
                     sounds=[self.sound.GO_TONE, self.sound.WHITE_NOISE],
                     indexes=[self.task_params.GO_TONE_IDX, self.task_params.WHITE_NOISE_IDX],
                     sample_rate=self.sound['samplerate'],
                 )
                 self.bpod.define_harp_sounds_actions(
+                    module=self.bpod.sound_card,
                     go_tone_index=self.task_params.GO_TONE_IDX,
                     noise_index=self.task_params.WHITE_NOISE_IDX,
-                    sound_port=module_port,
                 )
             case 'hifi':
                 module = self.bpod.get_module('^HiFi')
@@ -991,12 +1001,10 @@ def start_mixin_sound(self):
                 hifi.load(index=self.task_params.WHITE_NOISE_IDX, data=self.sound.WHITE_NOISE)
                 hifi.push()
                 hifi.close()
-                module_port = f'Serial{module.serial_port}'
                 self.bpod.define_harp_sounds_actions(
+                    module=module,
                     go_tone_index=self.task_params.GO_TONE_IDX,
                     noise_index=self.task_params.WHITE_NOISE_IDX,
-                    sound_port=module_port,
-                    module=module,
                 )
             case _:
                 self.bpod.define_xonar_sounds_actions()

iblrig/commands.py

@@ -338,17 +338,19 @@ def remove_local_sessions(weeks=2, local_path=None, remote_path=None, dry=False,
     return removed
 
 
-def viewsession():
+def view_session():
     """
     Entry point for command line: usage as below
-    >>> viewsession /full/path/to/jsonable/_iblrig_taskData.raw.jsonable
+    >>> view_session /full/path/to/jsonable/_iblrig_taskData.raw.jsonable
     :return: None
     """
     parser = argparse.ArgumentParser()
     parser.add_argument('file_jsonable', help='full file path to jsonable file')
+    parser.add_argument('file_settings', help='full file path to settings file', nargs='?', default=None)
     args = parser.parse_args()
-    self = OnlinePlots()
-    self.run(Path(args.file_jsonable))
+
+    online_plots = OnlinePlots(task_file=args.file_jsonable, settings_file=args.file_settings)
+    online_plots.run(task_file=args.file_jsonable)
 
 
 def flush():

iblrig/gui/wizard.py

@@ -15,6 +15,7 @@
 from dataclasses import dataclass
 from pathlib import Path
 
+import numpy as np
 import pyqtgraph as pg
 from pydantic import ValidationError
 from PyQt5 import QtCore, QtGui, QtWidgets
@@ -45,7 +46,7 @@
 from iblrig.path_helper import load_pydantic_yaml
 from iblrig.pydantic_definitions import HardwareSettings, RigSettings
 from iblrig.tools import alyx_reachable, get_anydesk_id, internet_available
-from iblrig.version_management import check_for_updates, get_changelog, is_dirty
+from iblrig.version_management import check_for_updates, get_changelog
 from iblutil.util import setup_logger
 from one.webclient import AlyxClient
 from pybpodapi.exceptions.bpod_error import BpodErrorException
@@ -825,6 +826,9 @@ def controls_for_extra_parameters(self):
                     )
                     widget.valueChanged.emit(widget.value())
 
+                case 'reward_set_ul':
+                    label = 'Reward Set, μl'
+
                 case 'adaptive_gain':
                     label = 'Stimulus Gain'
                     minimum = 0
@@ -844,6 +848,7 @@ def controls_for_extra_parameters(self):
 
                 case 'stim_gain':
                     label = 'Stimulus Gain'
+                    widget.setMinimum(-np.inf)
 
             widget.wheelEvent = lambda event: None
             layout.addRow(self.tr(label), widget)