sl-shared-assets 1.0.0rc22__py3-none-any.whl → 1.0.0rc24__py3-none-any.whl

sl_shared_assets/cli.py

@@ -25,7 +25,32 @@ from .data_classes import (
     required=True,
     help="The absolute path to the session whose raw data needs to be verified for potential corruption.",
 )
-def verify_session_integrity(session_path: str) -> None:
+@click.option(
+    "-c",
+    "--create_processed_directories",
+    is_flag=True,
+    show_default=True,
+    default=False,
+    help=(
+        "Determines whether to created the processed data hierarchy. This flag should be disabled for most runtimes. "
+        "Primarily, it is used by lab acquisition system code to generate processed data directories on the remote "
+        "compute servers as part of the data preprocessing pipeline."
+    ),
+)
+@click.option(
+    "-pdr",
+    "--processed_data_root",
+    type=click.Path(exists=True, file_okay=False, dir_okay=True, path_type=Path),
+    required=False,
+    help=(
+        "The absolute path to the directory where processed data from all projects is stored on the machine that runs "
+        "this command. This argument is used when calling the CLI on the BioHPC server, which uses different data "
+        "volumes for raw and processed data. Note, the input path must point to the root directory, as it will be "
+        "automatically modified to include the project name, the animal id, and the session ID. This argument is only "
+        "used if 'create_processed_directories' flag is True."
+    ),
+)
+def verify_session_integrity(session_path: str, create_processed_directories: bool, processed_data_root: Path) -> None:
     """Checks the integrity of the target session's raw data (contents of the raw_data directory).
 
     This command assumes that the data has been checksummed during acquisition and contains an ax_checksum.txt file
@@ -33,9 +58,14 @@ def verify_session_integrity(session_path: str) -> None:
     always verified the integrity of the 'raw_data' directory. It does not work with 'processed_data' or any other
     directories. If the session data was corrupted, the command removes the 'telomere.bin' file, marking the session as
     'incomplete' and automatically excluding it from all further automated processing runtimes.
+
+    The command is also used by Sun lab data acquisition systems to generate the processed data hierarchy for each
+    processed session. This use case is fully automated and should not be triggered manually by the user.
     """
     session = Path(session_path)
-    if verify_session_checksum(session):
+    if verify_session_checksum(
+        session, create_processed_data_directory=create_processed_directories, processed_data_root=processed_data_root
+    ):
         console.echo(message=f"Session {session.stem} raw data integrity: verified.", level=LogLevel.SUCCESS)
     else:
         console.echo(message=f"Session {session.stem} raw data integrity: compromised!", level=LogLevel.ERROR)
@@ -288,6 +318,15 @@ def generate_experiment_configuration_file(project: str, experiment: str, state_
     acquisition_system = get_system_configuration_data()
     file_path = acquisition_system.paths.root_directory.joinpath(project, "configuration", f"{experiment}.yaml")
 
+    if not acquisition_system.paths.root_directory.joinpath(project).exists():
+        message = (
+            f"Unable to generate the experiment {experiment} configuration file for the project {project}. "
+            f"The target project does not exist on the local machine (PC). Use the "
+            f"'sl-create-project' CLI command to create the project before creating new experiment configuration(s). "
+        )
+        console.error(message=message, error=ValueError)
+        raise ValueError(message)  # Fall-back to appease mypy, should not be reachable
+
     # Loops over the number of requested states and, for each, generates a precursor experiment state field inside the
     # 'states' dictionary.
     states = {}

sl_shared_assets/cli.pyi

@@ -1,3 +1,5 @@
+from pathlib import Path
+
 from .tools import (
     ascend_tyche_data as ascend_tyche_data,
     verify_session_checksum as verify_session_checksum,
@@ -13,7 +15,7 @@ from .data_classes import (
     set_system_configuration_file as set_system_configuration_file,
 )
 
-def verify_session_integrity(session_path: str) -> None:
+def verify_session_integrity(session_path: str, create_processed_directories: bool, processed_data_root: Path) -> None:
     """Checks the integrity of the target session's raw data (contents of the raw_data directory).
 
     This command assumes that the data has been checksummed during acquisition and contains an ax_checksum.txt file
@@ -21,6 +23,9 @@ def verify_session_integrity(session_path: str) -> None:
     always verified the integrity of the 'raw_data' directory. It does not work with 'processed_data' or any other
     directories. If the session data was corrupted, the command removes the 'telomere.bin' file, marking the session as
     'incomplete' and automatically excluding it from all further automated processing runtimes.
+
+    The command is also used by Sun lab data acquisition systems to generate the processed data hierarchy for each
+    processed session. This use case is fully automated and should not be triggered manually by the user.
     """
 
 def generate_project_manifest_file(

sl_shared_assets/data_classes/configuration_data.py

@@ -111,6 +111,12 @@ class MesoscopePaths:
     sharing protocol, such as SMB."""
     harvesters_cti_path: Path = Path("/opt/mvIMPACT_Acquire/lib/x86_64/mvGenTLProducer.cti")
     """The path to the GeniCam CTI file used to connect to Harvesters-managed cameras."""
+    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()
@@ -125,10 +131,17 @@ class MesoscopeCameras:
     right_camera_index: int = 2
     """The index of the right body camera (from animal's perspective) in the list of all available OpenCV-managed
      cameras."""
-    quantization_parameter: int = 15
-    """The quantization parameter used by all cameras to encode acquired frames as video files. This controls how much
-    data is discarded when encoding each video frame, directly contributing to the encoding speed, resultant video file
-    size and video quality."""
+    face_camera_quantization_parameter: int = 15
+    """The quantization parameter used by the face camera to encode acquired frames as video files. This controls how
+    much data is discarded when encoding each video frame, directly contributing to the encoding speed, resultant video 
+    file size and video quality."""
+    body_camera_quantization_parameter: int = 15
+    """SThe quantization parameter used by the left and right body cameras to encode acquired frames as video files.
+    See 'face_camera_quantization_parameter' field for more information on what this parameter does."""
+    display_face_camera_frames: bool = True
+    """Determines whether to display the frames grabbed from the face camera during runtime."""
+    display_body_camera_frames: bool = True
+    """Determines whether to display the frames grabbed from the left and right body cameras during runtime."""
 
 
 @dataclass()
@@ -141,14 +154,13 @@ class MesoscopeMicroControllers:
     """The USB port used by the Sensor Microcontroller."""
     encoder_port: str = "/dev/ttyACM2"
     """The USB port used by the Encoder Microcontroller."""
-    mesoscope_start_ttl_module_id: int = 1
-    """The unique byte-code ID of the TTL module instance used to send mesoscope frame acquisition start trigger 
-    signals to the ScanImagePC."""
-    mesoscope_stop_ttl_module_id: int = 2
-    """The unique byte-code ID of the TTL module instance used to send mesoscope frame acquisition stop trigger 
-    signals to the ScanImagePC."""
+    debug: bool = False
+    """Determines whether to run the managed acquisition system in the 'debug mode'. This mode should be disabled 
+    during most runtimes. It is used during initial system calibration and testing and prints a lot of generally 
+    redundant information into the terminal."""
     mesoscope_ttl_pulse_duration_ms: int = 10
-    """The duration of the HIGH phase of all outgoing mesoscope TTL pulses, in milliseconds."""
+    """The duration of the HIGH phase of all outgoing TTL pulses that target the Mesoscope (enable or disable mesoscope
+    frame acquisition), in milliseconds."""
     minimum_break_strength_g_cm: float = 43.2047
     """The minimum torque applied by the running wheel break in gram centimeter. This is the torque the break delivers 
     at minimum voltage (break is disabled)."""
@@ -292,6 +304,8 @@ class MesoscopeSystemConfiguration(YamlConfig):
         self.paths.nas_directory = Path(self.paths.nas_directory)
         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):
@@ -299,6 +313,23 @@ class MesoscopeSystemConfiguration(YamlConfig):
                 (k, v) for k, v in self.microcontrollers.valve_calibration_data.items()
             )
 
+        # Verifies the contents of the valve calibration data loaded from the config file.
+        valve_calibration_data = self.microcontrollers.valve_calibration_data
+        if not all(
+            isinstance(item, tuple)
+            and len(item) == 2
+            and isinstance(item[0], (int, float))
+            and isinstance(item[1], (int, float))
+            for item in valve_calibration_data
+        ):
+            message = (
+                f"Unable to initialize the MesoscopeSystemConfiguration class. Expected each item under the "
+                f"'valve_calibration_data' field of the Mesoscope-VR acquisition system configuration .yaml file to be "
+                f"a tuple of two integer or float values, but instead encountered {valve_calibration_data} with at "
+                f"least one incompatible element."
+            )
+            console.error(message=message, error=TypeError)
+
     def save(self, path: Path) -> None:
         """Saves class instance data to disk as a 'mesoscope_system_configuration.yaml' file.
 
@@ -323,6 +354,8 @@ class MesoscopeSystemConfiguration(YamlConfig):
         original.paths.nas_directory = str(original.paths.nas_directory)  # type: ignore
         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/data_classes/session_data.py

@@ -438,6 +438,16 @@ class SessionData(YamlConfig):
         # Constructs the root session directory path
         session_path = acquisition_system.paths.root_directory.joinpath(project_name, animal_id, session_name)
 
+        # Prevents creating new sessions for non-existent projects.
+        if not acquisition_system.paths.root_directory.joinpath(project_name).exists():
+            message = (
+                f"Unable to create the session directory hierarchy for the session {session_name} of the animal "
+                f"'{animal_id}' and project '{project_name}'. The project does not exist on the local machine (PC). "
+                f"Use the 'sl-create-project' CLI command to create the project on the local machine before creating "
+                f"new sessions."
+            )
+            console.error(message=message, error=FileNotFoundError)
+
         # Handles potential session name conflicts
         counter = 0
         while session_path.exists():

sl_shared_assets/tools/project_management_tools.py

@@ -5,6 +5,7 @@ up a given project."""
 from pathlib import Path
 
 import polars as pl
+from ataraxis_base_utilities import console
 
 from ..data_classes import SessionData
 from .packaging_tools import calculate_directory_checksum
@@ -33,9 +34,25 @@ def generate_project_manifest(
             is different from the 'raw_project_directory'. Typically, this would be the case on remote compute server(s)
             and not on local machines.
     """
+
+    if not raw_project_directory.exists():
+        message = (
+            f"Unable to generate the project manifest file for the requested project {raw_project_directory.stem}. The "
+            f"specified project directory does not exist."
+        )
+        console.error(message=message, error=FileNotFoundError)
+
     # Finds all raw data directories
     session_directories = [directory.parent for directory in raw_project_directory.rglob("raw_data")]
 
+    if len(session_directories) == 0:
+        message = (
+            f"Unable to generate the project manifest file for the requested project {raw_project_directory.stem}. The "
+            f"project does not contain any raw session data. To generate the manifest file, the project must contain "
+            f"at least one valid experiment or training session."
+        )
+        console.error(message=message, error=FileNotFoundError)
+
     # Precreates the 'manifest' dictionary structure
     manifest: dict[str, list[str | bool]] = {
         "animal": [],  # Animal IDs.
@@ -120,7 +137,9 @@ def generate_project_manifest(
     )
 
 
-def verify_session_checksum(session_path: Path) -> bool:
+def verify_session_checksum(
+    session_path: Path, create_processed_data_directory: bool = True, processed_data_root: None | Path = None
+) -> bool:
     """Verifies the integrity of the session's raw data by generating the checksum of the raw_data directory and
     comparing it against the checksum stored in the ax_checksum.txt file.
 
@@ -132,16 +151,27 @@ def verify_session_checksum(session_path: Path) -> bool:
         Removing the telomere.bin marker file from session's raw_data folder marks the session as incomplete, excluding
         it from all further automatic processing.
 
+        This function is also used to create the processed data hierarchy on the BioHPC server, when it is called as
+        part of the data preprocessing runtime performed by a data acquisition system.
+
     Args:
         session_path: The path to the session directory to be verified. Note, the input session directory must contain
             the 'raw_data' subdirectory.
+        create_processed_data_directory: Determines whether to create the processed data hierarchy during runtime.
+        processed_data_root: The root directory where to store the processed data hierarchy. This path has to point to
+            the root directory where to store the processed data from all projects, and it will be automatically
+            modified to include the project name, the animal name, and the session ID.
 
     Returns:
         True if the checksum matches, False otherwise.
     """
 
-    # Loads session data layout
-    session_data = SessionData.load(session_path=session_path)
+    # Loads session data layout. If configured to do so, also creates the processed data hierarchy
+    session_data = SessionData.load(
+        session_path=session_path,
+        processed_data_root=processed_data_root,
+        make_processed_data_directory=create_processed_data_directory,
+    )
 
     # Re-calculates the checksum for the raw_data directory
     calculated_checksum = calculate_directory_checksum(

sl_shared_assets/tools/project_management_tools.pyi

@@ -27,7 +27,9 @@ def generate_project_manifest(
             and not on local machines.
     """
 
-def verify_session_checksum(session_path: Path) -> bool:
+def verify_session_checksum(
+    session_path: Path, create_processed_data_directory: bool = True, processed_data_root: None | Path = None
+) -> bool:
     """Verifies the integrity of the session's raw data by generating the checksum of the raw_data directory and
     comparing it against the checksum stored in the ax_checksum.txt file.
 
@@ -39,9 +41,16 @@ def verify_session_checksum(session_path: Path) -> bool:
         Removing the telomere.bin marker file from session's raw_data folder marks the session as incomplete, excluding
         it from all further automatic processing.
 
+        This function is also used to create the processed data hierarchy on the BioHPC server, when it is called as
+        part of the data preprocessing runtime performed by a data acquisition system.
+
     Args:
         session_path: The path to the session directory to be verified. Note, the input session directory must contain
             the 'raw_data' subdirectory.
+        create_processed_data_directory: Determines whether to create the processed data hierarchy during runtime.
+        processed_data_root: The root directory where to store the processed data hierarchy. This path has to point to
+            the root directory where to store the processed data from all projects, and it will be automatically
+            modified to include the project name, the animal name, and the session ID.
 
     Returns:
         True if the checksum matches, False otherwise.

{sl_shared_assets-1.0.0rc22.dist-info → sl_shared_assets-1.0.0rc24.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sl-shared-assets
-Version: 1.0.0rc22
+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-1.0.0rc22.dist-info → sl_shared_assets-1.0.0rc24.dist-info}/RECORD

@@ -1,15 +1,14 @@
 sl_shared_assets/__init__.py,sha256=rscR353jiyUQ-wpguTLOM-A5Lqr1ftQtuTan1D0AtR0,2196
 sl_shared_assets/__init__.pyi,sha256=Ye6eY_y_l9CTqwbCf-OxXOphxXKfn9UJnuw09DdLEtc,2405
-sl_shared_assets/cli.py,sha256=FRc452bUQCDMtMLVxIRr178pbuCVTYWplJAzumy0Ruo,14971
-sl_shared_assets/cli.pyi,sha256=dmkg30arGgA3pLipiuQFb8jq2IPy53srE6CdFAaCdwc,5620
+sl_shared_assets/cli.py,sha256=-w9RAbHEcMspp6UDiXHM0fYSUwPSjJpZZcX3T9hLzUc,17103
+sl_shared_assets/cli.pyi,sha256=DuhJhqAXB7e5uOdzCI2c29FwsVwpQefR2eLUfW0gWyQ,5931
 sl_shared_assets/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sl_shared_assets/data_classes/__init__.py,sha256=b0BwTAJCD1zbwjd2UdpXheq61q1sgBuYhtAL-GHA2h4,1835
 sl_shared_assets/data_classes/__init__.pyi,sha256=e2082sm5pSw3bxNZGqwcRhuKLH8T7hcEo6kWtOZNDBU,1968
-sl_shared_assets/data_classes/configuration_data.py,sha256=NL5dMQkd_wigUiik8Yvzp2FQb_PQF3C0utvUcSo6b08,27903
-sl_shared_assets/data_classes/configuration_data.pyi,sha256=ePWbPROL_bWuFuQKMhBVbZal0taTY7twSibKbrd-_Qw,9439
+sl_shared_assets/data_classes/configuration_data.py,sha256=wuPFz3zx1DN12KimPhH-fU1geU3pFzRuRB53JEJ2T6I,30343
 sl_shared_assets/data_classes/runtime_data.py,sha256=Q7Ykf9hgrw1jYKXa53mn_LW8G2cPmLLuxgGkP6qQcc4,15483
 sl_shared_assets/data_classes/runtime_data.pyi,sha256=PxaCbeF9COR4ri91pdzh7zVrqaz2KEDYB1EoLhZQC_c,6618
-sl_shared_assets/data_classes/session_data.py,sha256=tQMt1i9Bloj5K9kYS1gkCdOtksd_8_nHFMZQHLaKCoE,36754
+sl_shared_assets/data_classes/session_data.py,sha256=Jf-WPX1f7sPxWOrU2oq79YZhwZZlLOSVjN7YntZdO80,37401
 sl_shared_assets/data_classes/session_data.pyi,sha256=a3nPC42mQniUPk2HsAM1_DWUa-BfhzDljQfDQh2rSus,13071
 sl_shared_assets/data_classes/surgery_data.py,sha256=qsMj3NkjhylAT9b_wHBY-1XwTu2xsZcZatdECmkA7Bs,7437
 sl_shared_assets/data_classes/surgery_data.pyi,sha256=rf59lJ3tGSYKHQlEGXg75MnjajBwl0DYhL4TClAO4SM,2605
@@ -25,12 +24,12 @@ sl_shared_assets/tools/ascension_tools.py,sha256=kIqYGX9F8lRao_LaVOacIiT8J9SypTv
 sl_shared_assets/tools/ascension_tools.pyi,sha256=tQCDdWZ20ZjUjpMs8aGIN0yBg5ff3j6spi62b3Han4o,3755
 sl_shared_assets/tools/packaging_tools.py,sha256=oY-EWuTiMfWobYllVZy0piGlVnTHCpPY1GF-WmqQdj4,7269
 sl_shared_assets/tools/packaging_tools.pyi,sha256=vgGbAQCExwg-0A5F72MzEhzHxu97Nqg1yuz-5P89ycU,3118
-sl_shared_assets/tools/project_management_tools.py,sha256=IV4xAfy3_SpV50Xvt7EdVPVLojp9di1rEmO4KoAgFtY,8740
-sl_shared_assets/tools/project_management_tools.pyi,sha256=pQY2--Kn3pKSADsArDRmbwGR7JqHD_2qdB0LJBbW_xo,2735
+sl_shared_assets/tools/project_management_tools.py,sha256=E50xhjJZlq6zQXnj8DHm1KkVcTDK7lr61m1ge-u25TY,10476
+sl_shared_assets/tools/project_management_tools.pyi,sha256=bRwohpGa98LDIy1ntLAPSKEGRB4S7ZmnIfyDy097c94,3467
 sl_shared_assets/tools/transfer_tools.py,sha256=J26kwOp_NpPSY0-xu5FTw9udte-rm_mW1FJyaTNoqQI,6606
 sl_shared_assets/tools/transfer_tools.pyi,sha256=FoH7eYZe7guGHfPr0MK5ggO62uXKwD2aJ7h1Bu7PaEE,3294
-sl_shared_assets-1.0.0rc22.dist-info/METADATA,sha256=ZOXR6uB8yVsMjAntWJBTbyV0qjNsS1Q2mzA04JQ6j9E,48613
-sl_shared_assets-1.0.0rc22.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-sl_shared_assets-1.0.0rc22.dist-info/entry_points.txt,sha256=76c00fRS4IuXBP2xOBdvycT15Zen-lHiDg2FaSt-HB4,547
-sl_shared_assets-1.0.0rc22.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-sl_shared_assets-1.0.0rc22.dist-info/RECORD,,
+sl_shared_assets-1.0.0rc24.dist-info/METADATA,sha256=NwEZ5XdK0iaApWqMvAkrPsEA7kMdEvO6uw2XOpAAf3k,48613
+sl_shared_assets-1.0.0rc24.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+sl_shared_assets-1.0.0rc24.dist-info/entry_points.txt,sha256=76c00fRS4IuXBP2xOBdvycT15Zen-lHiDg2FaSt-HB4,547
+sl_shared_assets-1.0.0rc24.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+sl_shared_assets-1.0.0rc24.dist-info/RECORD,,

sl_shared_assets/data_classes/configuration_data.pyi

@@ -1,195 +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 = ...
-
-@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 = ...
-    quantization_parameter: int = ...
-
-@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 = ...
-    mesoscope_start_ttl_module_id: int = ...
-    mesoscope_stop_ttl_module_id: int = ...
-    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.
-    """