sl-shared-assets 1.0.0rc23__tar.gz → 1.0.0rc24__tar.gz

{sl_shared_assets-1.0.0rc23 → sl_shared_assets-1.0.0rc24}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sl-shared-assets
-Version: 1.0.0rc23
+Version: 1.0.0rc24
 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-1.0.0rc23 → sl_shared_assets-1.0.0rc24}/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 = "1.0.0rc23"
+version = "1.0.0rc24"
 description = "Stores assets shared between multiple Sun (NeuroAI) lab data pipelines."
 readme = "README.md"
 license = { file = "LICENSE" }

{sl_shared_assets-1.0.0rc23 → sl_shared_assets-1.0.0rc24}/src/sl_shared_assets/data_classes/configuration_data.py

@@ -114,6 +114,9 @@ class MesoscopePaths:
     server_processed_data_root: Path = Path("/workdir/sun_data")
     """The absolute path to the BioHPC server directory used to store the processed data from all Sun lab projects. 
     This path is relative to the server root and is only used when submitting remote jobs to the server."""
+    server_raw_data_root: Path = Path("/storage/sun_data")
+    """The absolute path to the BioHPC server directory used to store the raw data from all Sun lab projects. 
+    This path is relative to the server root and is only used when submitting remote jobs to the server."""
 
 
 @dataclass()
@@ -302,6 +305,7 @@ class MesoscopeSystemConfiguration(YamlConfig):
         self.paths.mesoscope_directory = Path(self.paths.mesoscope_directory)
         self.paths.harvesters_cti_path = Path(self.paths.harvesters_cti_path)
         self.paths.server_processed_data_root = Path(self.paths.server_processed_data_root)
+        self.paths.server_raw_data_root = Path(self.paths.server_raw_data_root)
 
         # Converts valve_calibration data from dictionary to a tuple of tuples format
         if not isinstance(self.microcontrollers.valve_calibration_data, tuple):
@@ -351,6 +355,7 @@ class MesoscopeSystemConfiguration(YamlConfig):
         original.paths.mesoscope_directory = str(original.paths.mesoscope_directory)  # type: ignore
         original.paths.harvesters_cti_path = str(original.paths.harvesters_cti_path)  # type: ignore
         original.paths.server_processed_data_root = str(original.paths.server_processed_data_root)  # type: ignore
+        original.paths.server_raw_data_root = str(original.paths.server_raw_data_root)  # type: ignore
 
         # Converts valve calibration data into dictionary format
         if isinstance(original.microcontrollers.valve_calibration_data, tuple):

sl_shared_assets-1.0.0rc23/src/sl_shared_assets/data_classes/configuration_data.pyi

@@ -1,198 +0,0 @@
-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 = ...
-
-@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.
-    """