Ambient data

iblrig/base_choice_world.py

@@ -137,8 +137,10 @@ def __init__(self, *args, delay_mins: float = 0, **kwargs):
                 'Temperature_C': np.zeros(NTRIALS_INIT) * np.nan,
                 'AirPressure_mb': np.zeros(NTRIALS_INIT) * np.nan,
                 'RelativeHumidity': np.zeros(NTRIALS_INIT) * np.nan,
-            }
+            },
+            dtype=np.float16,
         )
+        self.ambient_sensor_table.rename_axis('Trial', inplace=True)
 
     @staticmethod
     def extra_parser():
@@ -218,7 +220,6 @@ def _run(self):
 
             # save trial and update log
             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 stop event
@@ -526,6 +527,15 @@ def trial_completed(self, bpod_data: dict[str, Any]) -> None:
         self.session_info.NTRIALS += 1
         # SAVE TRIAL DATA
         self.save_trial_data_to_json(bpod_data)
+
+        # save ambient data
+        if self.hardware_settings.device_bpod.USE_AMBIENT_MODULE:
+            sensor_reading = self.bpod.get_ambient_sensor_reading()
+            self.ambient_sensor_table.iloc[self.trial_num] = sensor_reading
+            self.bpod.write_ambient_data(
+                filepath=self.paths['AMBIENT_FILE_PATH'], trial_number=self.trial_num, sensor_reading=sensor_reading
+            )
+
         # this is a flag for the online plots. If online plots were in pyqt5, there is a file watcher functionality
         Path(self.paths['DATA_FILE_PATH']).parent.joinpath('new_trial.flag').touch()
         self.paths.SESSION_FOLDER.joinpath('transfer_me.flag').touch()

iblrig/base_tasks.py

@@ -269,6 +269,8 @@ def _init_paths(self, append: bool = False) -> Bunch:
                 `C:\iblrigv8_data\mainenlab\Subjects\SWC_043\2019-01-01\001\raw_task_data_00`
             *   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`
+            *   AMBIENT_FILE_PATH: contains the ambient sensor data
+                `C:\iblrigv8_data\mainenlab\Subjects\SWC_043\2019-01-01\001\raw_task_data_00\_iblrig_ambientSensorData.raw.bin`
             *   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`
         """
@@ -310,6 +312,7 @@ def _init_paths(self, append: bool = False) -> Bunch:
         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.AMBIENT_FILE_PATH = paths.SESSION_RAW_DATA_FOLDER.joinpath('_iblrig_ambientSensorData.raw.bin')
         paths.SETTINGS_FILE_PATH = paths.SESSION_RAW_DATA_FOLDER.joinpath('_iblrig_taskSettings.raw.json')
         return paths
 

iblrig/hardware.py

@@ -14,6 +14,7 @@
 from typing import Annotated, Literal
 
 import numpy as np
+import pandas as pd
 import serial
 import sounddevice as sd
 from annotated_types import Ge, Le
@@ -30,6 +31,10 @@
 from pybpodapi.state_machine import StateMachine
 
 SOFTCODE = IntEnum('SOFTCODE', ['STOP_SOUND', 'PLAY_TONE', 'PLAY_NOISE', 'TRIGGER_CAMERA'])
+DTYPE_AMBIENT_SENSOR_RAW = np.dtype(
+    [('Temperature_C', np.float16), ('AirPressure_mb', np.float16), ('RelativeHumidity', np.float16)]
+)
+DTYPE_AMBIENT_SENSOR_BIN = np.dtype([('Trial', np.uint16)] + DTYPE_AMBIENT_SENSOR_RAW.descr)
 
 # some annotated types
 Uint8 = Annotated[int, Ge(0), Le(255)]
@@ -206,23 +211,69 @@ def define_rotary_encoder_actions(self, module: BpodModule | None = None) -> Non
             }
         )
 
-    def get_ambient_sensor_reading(self):
+    def get_ambient_sensor_reading(self) -> np.ndarray:
+        """
+        Retrieve ambient sensor readings.
+
+        If the ambient sensor module is not available, returns an array filled with NaN values.
+        Otherwise, retrieves the temperature, air pressure, and relative humidity readings.
+
+        Returns
+        -------
+        np.ndarray
+            A NumPy array containing the sensor readings in the following order:
+
+            - [0] : Temperature in degrees Celsius
+            - [1] : Air pressure in millibars
+            - [2] : Relative humidity in percentage
+        """
         if self.ambient_module is None:
-            return {
-                'Temperature_C': np.nan,
-                'AirPressure_mb': np.nan,
-                'RelativeHumidity': np.nan,
-            }
-        self.ambient_module.start_module_relay()
-        self.bpod_modules.module_write(self.ambient_module, 'R')
-        reply = self.bpod_modules.module_read(self.ambient_module, 12)
-        self.ambient_module.stop_module_relay()
-
-        return {
-            'Temperature_C': np.frombuffer(bytes(reply[:4]), np.float32)[0],
-            'AirPressure_mb': np.frombuffer(bytes(reply[4:8]), np.float32)[0] / 100,
-            'RelativeHumidity': np.frombuffer(bytes(reply[8:]), np.float32)[0],
-        }
+            data = np.full(3, np.nan, np.float16)
+        else:
+            self.ambient_module.start_module_relay()
+            self.bpod_modules.module_write(self.ambient_module, 'R')
+            reply = self.bpod_modules.module_read(self.ambient_module, 12)
+            self.ambient_module.stop_module_relay()
+            data = np.frombuffer(bytes(reply), dtype=np.float16).copy()
+            data[1] /= 100
+        return data
+
+    @staticmethod
+    def write_ambient_data(filepath: Path | str, trial_number: int, sensor_reading: np.ndarray):
+        """
+        Write ambient sensor data to a binary file.
+
+        Parameters
+        ----------
+        filepath : Path or str
+            The path to the file where the data will be written.
+        trial_number : int
+            The trial number associated with the sensor readings.
+        sensor_reading : np.ndarray
+            A 1D array containing three sensor readings: temperature, air pressure, and relative humidity.
+        """
+        with Path(filepath).open('ab') as f:
+            ambient_data = np.array([(trial_number, *sensor_reading)], dtype=DTYPE_AMBIENT_SENSOR_BIN)
+            ambient_data.tofile(f)
+
+    @staticmethod
+    def read_ambient_data(filepath: Path | str) -> pd.DataFrame:
+        """
+        Read ambient sensor data from a binary file into a DataFrame.
+
+        Parameters
+        ----------
+        filepath : Path or str
+            The path to the file from which the data will be read.
+
+        Returns
+        -------
+        pd.DataFrame
+            A DataFrame containing the ambient sensor data, with columns corresponding to the fields
+            defined in `DTYPE_AMBIENT_SENSOR_BIN`.
+        """
+        data = np.fromfile(filepath, dtype=DTYPE_AMBIENT_SENSOR_BIN)
+        return pd.DataFrame(data)
 
     def flush(self):
         """Flushes valve 1."""