sl-shared-assets 1.0.0rc24__tar.gz → 1.0.0rc26__tar.gz

{sl_shared_assets-1.0.0rc24 → sl_shared_assets-1.0.0rc26}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sl-shared-assets
-Version: 1.0.0rc24
+Version: 1.0.0rc26
 Summary: Stores assets shared between multiple Sun (NeuroAI) lab data pipelines.
 Project-URL: Homepage, https://github.com/Sun-Lab-NBB/sl-shared-assets
 Project-URL: Documentation, https://sl-shared-assets-api-docs.netlify.app/

{sl_shared_assets-1.0.0rc24 → sl_shared_assets-1.0.0rc26}/pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "hatchling.build"
 # Project metdata section. Provides the genral ID information about the project.
 [project]
 name = "sl-shared-assets"
-version = "1.0.0rc24"
+version = "1.0.0rc26"
 description = "Stores assets shared between multiple Sun (NeuroAI) lab data pipelines."
 readme = "README.md"
 license = { file = "LICENSE" }

sl_shared_assets-1.0.0rc26/src/sl_shared_assets/data_classes/configuration_data.pyi

@@ -0,0 +1,199 @@
+from pathlib import Path
+from dataclasses import field, dataclass
+
+from _typeshed import Incomplete
+from ataraxis_data_structures import YamlConfig
+
+@dataclass()
+class ExperimentState:
+    """Encapsulates the information used to set and maintain the desired experiment and system state.
+
+    Broadly, each experiment runtime can be conceptualized as a two state-system. The first state is that of the
+    experimental task, which reflects the behavior goal, the rules for achieving the goal, and the reward for
+    achieving the goal. The second state is that of the data acquisition and experiment control system, which is a
+    snapshot of all hardware module states that make up the system that acquires the data and controls the task
+    environment. Overall, experiment state is about 'what the animal is doing', while the system state is about
+    'what the hardware is doing'.
+
+    Note:
+        This class is acquisition-system-agnostic. It can be used to define the ExperimentConfiguration class for any
+        valid data acquisition system.
+    """
+
+    experiment_state_code: int
+    system_state_code: int
+    state_duration_s: float
+
+@dataclass()
+class MesoscopeExperimentConfiguration(YamlConfig):
+    """Stores the configuration of a single experiment runtime that uses the Mesoscope_VR data acquisition system.
+
+    Primarily, this includes the sequence of experiment and system states that defines the flow of the experiment
+    runtime. During runtime, the main runtime control function traverses the sequence of states stored in this class
+    instance start-to-end in the exact order specified by the user. Together with custom Unity projects that define
+    the task logic (how the system responds to animal interactions with the VR system) this class allows flexibly
+    implementing a wide range of experiments using the Mesoscope-VR system.
+
+    Each project should define one or more experiment configurations and save them as .yaml files inside the project
+    'configuration' folder. The name for each configuration file is defined by the user and is used to identify and load
+    the experiment configuration when 'sl-experiment' CLI command exposed by the sl-experiment library is executed.
+
+    Notes:
+        This class is designed exclusively for the Mesoscope-VR system. Any other system needs to define a separate
+        ExperimentConfiguration class to specify its experiment runtimes and additional data.
+    """
+
+    cue_map: dict[int, float] = field(default_factory=Incomplete)
+    experiment_states: dict[str, ExperimentState] = field(default_factory=Incomplete)
+
+@dataclass()
+class MesoscopePaths:
+    """Stores the filesystem configuration parameters for the Mesoscope-VR data acquisition system."""
+
+    server_credentials_path: Path = ...
+    google_credentials_path: Path = ...
+    root_directory: Path = ...
+    server_storage_directory: Path = ...
+    server_working_directory: Path = ...
+    nas_directory: Path = ...
+    mesoscope_directory: Path = ...
+    harvesters_cti_path: Path = ...
+    server_processed_data_root: Path = ...
+    server_raw_data_root: Path = ...
+
+@dataclass()
+class MesoscopeCameras:
+    """Stores the configuration parameters for the cameras used by the Mesoscope-VR system to record behavior videos."""
+
+    face_camera_index: int = ...
+    left_camera_index: int = ...
+    right_camera_index: int = ...
+    face_camera_quantization_parameter: int = ...
+    body_camera_quantization_parameter: int = ...
+    display_face_camera_frames: bool = ...
+    display_body_camera_frames: bool = ...
+
+@dataclass()
+class MesoscopeMicroControllers:
+    """Stores the configuration parameters for the microcontrollers used by the Mesoscope-VR system."""
+
+    actor_port: str = ...
+    sensor_port: str = ...
+    encoder_port: str = ...
+    debug: bool = ...
+    mesoscope_ttl_pulse_duration_ms: int = ...
+    minimum_break_strength_g_cm: float = ...
+    maximum_break_strength_g_cm: float = ...
+    wheel_diameter_cm: float = ...
+    lick_threshold_adc: int = ...
+    lick_signal_threshold_adc: int = ...
+    lick_delta_threshold_adc: int = ...
+    lick_averaging_pool_size: int = ...
+    torque_baseline_voltage_adc: int = ...
+    torque_maximum_voltage_adc: int = ...
+    torque_sensor_capacity_g_cm: float = ...
+    torque_report_cw: bool = ...
+    torque_report_ccw: bool = ...
+    torque_signal_threshold_adc: int = ...
+    torque_delta_threshold_adc: int = ...
+    torque_averaging_pool_size: int = ...
+    wheel_encoder_ppr = ...
+    wheel_encoder_report_cw: bool = ...
+    wheel_encoder_report_ccw: bool = ...
+    wheel_encoder_delta_threshold_pulse: int = ...
+    wheel_encoder_polling_delay_us = ...
+    cm_per_unity_unit = ...
+    screen_trigger_pulse_duration_ms: int = ...
+    auditory_tone_duration_ms: int = ...
+    valve_calibration_pulse_count: int = ...
+    sensor_polling_delay_ms: int = ...
+    valve_calibration_data: dict[int | float, int | float] | tuple[tuple[int | float, int | float], ...] = ...
+
+@dataclass()
+class MesoscopeAdditionalFirmware:
+    """Stores the configuration parameters for all firmware and hardware components not assembled in the Sun lab."""
+
+    headbar_port: str = ...
+    lickport_port: str = ...
+    wheel_port: str = ...
+    unity_ip: str = ...
+    unity_port: int = ...
+
+@dataclass()
+class MesoscopeSystemConfiguration(YamlConfig):
+    """Stores the hardware and filesystem configuration parameters for the Mesoscope-VR data acquisition system used in
+    the Sun lab.
+
+    This class is specifically designed to encapsulate the configuration parameters for the Mesoscope-VR system. It
+    expects the system to be configured according to the specifications available from the sl_experiment repository
+    (https://github.com/Sun-Lab-NBB/sl-experiment) and should be used exclusively by the VRPC machine
+    (main Mesoscope-VR PC).
+
+    Notes:
+        Each SystemConfiguration class is uniquely tied to a specific hardware configuration used in the lab. This
+        class will only work with the Mesoscope-VR system. Any other data acquisition and runtime management system in
+        the lab should define its own SystemConfiguration class to specify its own hardware and filesystem configuration
+        parameters.
+    """
+
+    name: str = ...
+    paths: MesoscopePaths = field(default_factory=MesoscopePaths)
+    cameras: MesoscopeCameras = field(default_factory=MesoscopeCameras)
+    microcontrollers: MesoscopeMicroControllers = field(default_factory=MesoscopeMicroControllers)
+    additional_firmware: MesoscopeAdditionalFirmware = field(default_factory=MesoscopeAdditionalFirmware)
+    def __post_init__(self) -> None:
+        """Ensures that variables converted to different types for storage purposes are always set to expected types
+        upon class instantiation."""
+    def save(self, path: Path) -> None:
+        """Saves class instance data to disk as a 'mesoscope_system_configuration.yaml' file.
+
+        This method converts certain class variables to yaml-safe types (for example, Path objects -> strings) and
+        saves class data to disk as a .yaml file. The method is intended to be used solely by the
+        set_system_configuration_file() function and should not be called from any other context.
+
+        Args:
+            path: The path to the .yaml file to save the data to.
+        """
+
+_supported_configuration_files: Incomplete
+
+def set_system_configuration_file(path: Path) -> None:
+    """Sets the system configuration .yaml file specified by the input path as the default system configuration file for
+    the managed machine (PC).
+
+    This function is used to initially configure or override the existing configuration of any data acquisition system
+    used in the lab. The path to the configuration file is stored inside the user's data directory, so that all
+    Sun lab libraries can automatically access that information during every runtime. Since the storage directory is
+    typically hidden and varies between OSes and machines, this function provides a convenient way for setting that
+    path without manually editing the storage cache.
+
+    Notes:
+        If the input path does not point to an existing file, but the file name and extension are correct, the function
+        will automatically generate a default SystemConfiguration class instance and save it under the specified path.
+
+        A data acquisition system can include multiple machines (PCs). However, the configuration file is typically
+        only present on the 'main' machine that manages all runtimes.
+
+    Args:
+        path: The path to the new system configuration file to be used by the local data acquisition system (PC).
+
+    Raises:
+        ValueError: If the input path is not a valid system configuration file or does not use a supported data
+            acquisition system name.
+    """
+
+def get_system_configuration_data() -> MesoscopeSystemConfiguration:
+    """Resolves the path to the local system configuration file and loads the system configuration data.
+
+    This service function is used by all Sun lab data acquisition runtimes to load the system configuration data from
+    the shared configuration file. It supports resolving and returning the data for all data acquisition systems used
+    in the lab.
+
+    Returns:
+        The initialized SystemConfiguration class instance for the local acquisition system that stores the loaded
+        configuration parameters.
+
+    Raises:
+        FileNotFoundError: If the local machine does not have the Sun lab data directory, or the system configuration
+            file does not exist.
+    """

{sl_shared_assets-1.0.0rc24 → sl_shared_assets-1.0.0rc26}/src/sl_shared_assets/data_classes/session_data.py

@@ -381,6 +381,14 @@ class SessionData(YamlConfig):
     """Stores the paths to all subfolders and files found under the /project/animal/session/processed_data directory of 
     any PC used to work with Sun lab data."""
 
+    def __post_init__(self) -> None:
+        """Ensures raw_data and processed_data are always instances of RawData and ProcessedData."""
+        if not isinstance(self.raw_data, RawData):
+            self.raw_data = RawData()
+
+        if not isinstance(self.processed_data, ProcessedData):
+            self.processed_data = ProcessedData()
+
     @classmethod
     def create(
         cls,

{sl_shared_assets-1.0.0rc24 → sl_shared_assets-1.0.0rc26}/src/sl_shared_assets/data_classes/session_data.pyi

@@ -172,6 +172,8 @@ class SessionData(YamlConfig):
     experiment_name: str | None
     raw_data: RawData = field(default_factory=Incomplete)
     processed_data: ProcessedData = field(default_factory=Incomplete)
+    def __post_init__(self) -> None:
+        """Ensures raw_data and processed_data are always instances of RawData and ProcessedData."""
     @classmethod
     def create(
         cls,

{sl_shared_assets-1.0.0rc24 → sl_shared_assets-1.0.0rc26}/src/sl_shared_assets/server/server.py

@@ -162,7 +162,7 @@ class Server:
         # If batch_job is not in the output received from SLURM in response to issuing the submission command, raises an
         # error.
         if "Submitted batch job" not in job_output:
-            message = f"Failed to submit the {job.job_name} job to the BioHPC cluster."
+            message = f"Failed to submit the '{job.job_name}' job to the BioHPC cluster."
             console.error(message, RuntimeError)
 
             # Fallback to appease mypy, should not be reachable