sl-shared-assets 1.0.0rc15__py3-none-any.whl → 1.0.0rc17__py3-none-any.whl

sl_shared_assets-1.0.0rc17.dist-info/RECORD

@@ -0,0 +1,23 @@
+sl_shared_assets/__init__.py,sha256=VASYVzsHnaFykp1xdEjOgQdnfuqwokaKIp387zXyFqA,2080
+sl_shared_assets/cli.py,sha256=a4Ja2gm4ykOac7QmHen14Jhgu6955IUQDZrysp1RpFM,4207
+sl_shared_assets/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+sl_shared_assets/data_classes/__init__.py,sha256=pq-iyd4eyv1CPVcLcQQJBVAm7XCDWuZqxurrLOMW3e0,1702
+sl_shared_assets/data_classes/configuration_data.py,sha256=zKZ3cE2pZFDRiQ7off8hu2nV9JsBly9Phc5goY4qCH4,4163
+sl_shared_assets/data_classes/runtime_data.py,sha256=jSCvZG01gkcSUexFiKITjTJ8ZoF18qRfxiwhyrWW7-I,13964
+sl_shared_assets/data_classes/session_data.py,sha256=Xn7t6kbhQfif7oneT2SLppBGXCfmDGtYOKj3HM7t64U,79135
+sl_shared_assets/data_classes/surgery_data.py,sha256=Z4QZAZCz0_w7qrGMMzYn-fwwwycw3ki9SPJU0kD5Ap4,7425
+sl_shared_assets/server/__init__.py,sha256=nyX6-9ACcrQeRQOCNvBVrWSTHGjRPANIG_u0aq7HPTg,426
+sl_shared_assets/server/job.py,sha256=M7ZytqhluEV-YQPM9VQV3SqK-F9egQ3UcLc1SLBH4rA,7885
+sl_shared_assets/server/server.py,sha256=NpqWVjvxdtxHZIooBVaKY2jEBDN3dGohBzrFA0TSKIU,9380
+sl_shared_assets/suite2p/__init__.py,sha256=8N2BQNINBkH7JNODmYACHhvUH_uurTuw7w0PW3rVRYM,411
+sl_shared_assets/suite2p/multi_day.py,sha256=2_AHI91wuxwS07GFJn8S1454uLrQGmt0bS_qBoZsHVc,13102
+sl_shared_assets/suite2p/single_day.py,sha256=7dgYN9FnIvxNL0uHo0CtoLng2nRxZJYtV_AfskMt6tE,29961
+sl_shared_assets/tools/__init__.py,sha256=UWrNfseGupOrY4OK2PgDEJ-Q3LbSrPLC2pfaLm8wYBA,468
+sl_shared_assets/tools/ascension_tools.py,sha256=y2w72Czpbw9LwgsbdEx_ckzMKTZ78cgKPTIk6vRYmAk,15877
+sl_shared_assets/tools/packaging_tools.py,sha256=LOKCKvT6UD_cidCONaI4ctWyej5zEwwdhhgwYrj60Kg,6746
+sl_shared_assets/tools/transfer_tools.py,sha256=J26kwOp_NpPSY0-xu5FTw9udte-rm_mW1FJyaTNoqQI,6606
+sl_shared_assets-1.0.0rc17.dist-info/METADATA,sha256=71y5EAy43UddnuutTvU2PGjupezOo8haw-PmMYQ30PM,47807
+sl_shared_assets-1.0.0rc17.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+sl_shared_assets-1.0.0rc17.dist-info/entry_points.txt,sha256=bdnmVAcK3nrKi9QEYeNMrCLFH5LQ4BMBfwbLIgLPtq4,222
+sl_shared_assets-1.0.0rc17.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+sl_shared_assets-1.0.0rc17.dist-info/RECORD,,

sl_shared_assets/__init__.pyi

@@ -1,71 +0,0 @@
-from .tools import (
-    transfer_directory as transfer_directory,
-    calculate_directory_checksum as calculate_directory_checksum,
-)
-from .server import (
-    Server as Server,
-    ServerCredentials as ServerCredentials,
-)
-from .suite2p import (
-    MultiDayS2PConfiguration as MultiDayS2PConfiguration,
-    SingleDayS2PConfiguration as SingleDayS2PConfiguration,
-)
-from .data_classes import (
-    RawData as RawData,
-    DrugData as DrugData,
-    ImplantData as ImplantData,
-    SessionData as SessionData,
-    SubjectData as SubjectData,
-    SurgeryData as SurgeryData,
-    InjectionData as InjectionData,
-    MesoscopeData as MesoscopeData,
-    ProcedureData as ProcedureData,
-    ProcessedData as ProcessedData,
-    DeepLabCutData as DeepLabCutData,
-    ZaberPositions as ZaberPositions,
-    ExperimentState as ExperimentState,
-    VRPCDestinations as VRPCDestinations,
-    ConfigurationData as ConfigurationData,
-    MesoscopePositions as MesoscopePositions,
-    VRPCPersistentData as VRPCPersistentData,
-    ProjectConfiguration as ProjectConfiguration,
-    HardwareConfiguration as HardwareConfiguration,
-    RunTrainingDescriptor as RunTrainingDescriptor,
-    LickTrainingDescriptor as LickTrainingDescriptor,
-    ExperimentConfiguration as ExperimentConfiguration,
-    ScanImagePCPersistentData as ScanImagePCPersistentData,
-    MesoscopeExperimentDescriptor as MesoscopeExperimentDescriptor,
-)
-
-__all__ = [
-    "Server",
-    "ServerCredentials",
-    "SingleDayS2PConfiguration",
-    "MultiDayS2PConfiguration",
-    "DrugData",
-    "ImplantData",
-    "SessionData",
-    "RawData",
-    "ProcessedData",
-    "ConfigurationData",
-    "DeepLabCutData",
-    "VRPCPersistentData",
-    "ScanImagePCPersistentData",
-    "MesoscopeData",
-    "VRPCDestinations",
-    "SubjectData",
-    "SurgeryData",
-    "InjectionData",
-    "ProcedureData",
-    "ZaberPositions",
-    "ExperimentState",
-    "MesoscopePositions",
-    "ProjectConfiguration",
-    "HardwareConfiguration",
-    "RunTrainingDescriptor",
-    "LickTrainingDescriptor",
-    "ExperimentConfiguration",
-    "MesoscopeExperimentDescriptor",
-    "transfer_directory",
-    "calculate_directory_checksum",
-]

sl_shared_assets/cli.pyi

@@ -1,28 +0,0 @@
-from .tools import ascend_tyche_data as ascend_tyche_data
-from .server import generate_server_credentials as generate_server_credentials
-from .data_classes import replace_root_path as replace_root_path
-
-def replace_local_root_directory(path: str) -> None:
-    """Replaces the root directory used to store all lab projects on the local PC with the specified directory.
-
-    To ensure all projects are saved in the same location, this library resolves and saves the absolute path to the
-    project directory the first time ProjectConfiguration class instance is created on a new PC. All future projects
-    automatically reuse the same 'root' directory path. Since this information is stored in a typically hidden user
-    directory, this CLI can be used to replace the local directory path, if necessary.
-    """
-
-def generate_server_credentials_file(output_directory: str, host: str, username: str, password: str) -> None:
-    """Generates a new server_credentials.yaml file under the specified directory, using input information.
-
-    This CLI is used to set up new PCs to work with the lab BioHPC server. While this is primarily intended for the
-    VRPC, any machined that interacts with BioHPC server can use this CLI to build the access credentials file.
-    """
-
-def ascend_tyche_directory(path: str, output_directory: str, server_directory: str) -> None:
-    """Restructures old Tyche project data to use the modern Sun lab data structure.
-
-    This CLI is used to convert ('ascend') the old Tyche project data to the modern Sun lab structure. After
-    ascension, the data can be processed and analyzed using all modern Sun lab (sl-) tools and libraries. Note, this
-    process expects the input data to be preprocessed using an old Sun lab mesoscope data preprocessing pipeline. It
-    will not work for any other project or data.
-    """

sl_shared_assets/data_classes/__init__.pyi

@@ -1,61 +0,0 @@
-from .runtime_data import (
-    ZaberPositions as ZaberPositions,
-    MesoscopePositions as MesoscopePositions,
-    HardwareConfiguration as HardwareConfiguration,
-    RunTrainingDescriptor as RunTrainingDescriptor,
-    LickTrainingDescriptor as LickTrainingDescriptor,
-    MesoscopeExperimentDescriptor as MesoscopeExperimentDescriptor,
-)
-from .session_data import (
-    RawData as RawData,
-    SessionData as SessionData,
-    MesoscopeData as MesoscopeData,
-    ProcessedData as ProcessedData,
-    DeepLabCutData as DeepLabCutData,
-    VRPCDestinations as VRPCDestinations,
-    ConfigurationData as ConfigurationData,
-    VRPCPersistentData as VRPCPersistentData,
-    ProjectConfiguration as ProjectConfiguration,
-    ScanImagePCPersistentData as ScanImagePCPersistentData,
-    replace_root_path as replace_root_path,
-)
-from .surgery_data import (
-    DrugData as DrugData,
-    ImplantData as ImplantData,
-    SubjectData as SubjectData,
-    SurgeryData as SurgeryData,
-    InjectionData as InjectionData,
-    ProcedureData as ProcedureData,
-)
-from .configuration_data import (
-    ExperimentState as ExperimentState,
-    ExperimentConfiguration as ExperimentConfiguration,
-)
-
-__all__ = [
-    "DrugData",
-    "ImplantData",
-    "SessionData",
-    "RawData",
-    "ProcessedData",
-    "ConfigurationData",
-    "DeepLabCutData",
-    "VRPCPersistentData",
-    "ScanImagePCPersistentData",
-    "MesoscopeData",
-    "VRPCDestinations",
-    "SubjectData",
-    "SurgeryData",
-    "InjectionData",
-    "ProcedureData",
-    "ZaberPositions",
-    "ExperimentState",
-    "MesoscopePositions",
-    "ProjectConfiguration",
-    "HardwareConfiguration",
-    "RunTrainingDescriptor",
-    "LickTrainingDescriptor",
-    "ExperimentConfiguration",
-    "MesoscopeExperimentDescriptor",
-    "replace_root_path",
-]

sl_shared_assets/data_classes/configuration_data.pyi

@@ -1,37 +0,0 @@
-from pathlib import Path as 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 Mesoscope-VR system state.
-
-    Primarily, experiment runtime logic (task logic) is resolved by the Unity game engine. However, the Mesoscope-VR
-    system configuration may also need to change throughout the experiment to optimize the runtime by disabling or
-    reconfiguring specific hardware modules. For example, some experiment stages may require the running wheel to be
-    locked to prevent the animal from running, and other may require the VR screens to be turned off.
-    """
-
-    experiment_state_code: int
-    vr_state_code: int
-    state_duration_s: float
-
-@dataclass()
-class ExperimentConfiguration(YamlConfig):
-    """Stores the configuration of a single experiment runtime.
-
-    Primarily, this includes the sequence of experiment and Virtual Reality (Mesoscope-VR) 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.
-
-    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-run-experiment' CLI command exposed by the sl-experiment library is executed.
-    """
-
-    cue_map: dict[int, float] = field(default_factory=Incomplete)
-    experiment_states: dict[str, ExperimentState] = field(default_factory=Incomplete)

sl_shared_assets/data_classes/runtime_data.pyi

@@ -1,145 +0,0 @@
-from dataclasses import dataclass
-
-from ataraxis_data_structures import YamlConfig
-
-@dataclass()
-class HardwareConfiguration(YamlConfig):
-    """This class is used to save the runtime hardware configuration parameters as a .yaml file.
-
-    This information is used to read and decode the data saved to the .npz log files during runtime as part of data
-    processing.
-
-    Notes:
-        All fields in this dataclass initialize to None. During log processing, any log associated with a hardware
-        module that provides the data stored in a field will be processed, unless that field is None. Therefore, setting
-        any field in this dataclass to None also functions as a flag for whether to parse the log associated with the
-        module that provides this field's information.
-
-        This class is automatically configured by MesoscopeExperiment and BehaviorTraining classes from sl-experiment
-        library to facilitate log parsing.
-    """
-
-    cue_map: dict[int, float] | None = ...
-    cm_per_pulse: float | None = ...
-    maximum_break_strength: float | None = ...
-    minimum_break_strength: float | None = ...
-    lick_threshold: int | None = ...
-    valve_scale_coefficient: float | None = ...
-    valve_nonlinearity_exponent: float | None = ...
-    torque_per_adc_unit: float | None = ...
-    screens_initially_on: bool | None = ...
-    recorded_mesoscope_ttl: bool | None = ...
-
-@dataclass()
-class LickTrainingDescriptor(YamlConfig):
-    """This class is used to save the description information specific to lick training sessions as a .yaml file.
-
-    The information stored in this class instance is filled in two steps. The main runtime function fills most fields
-    of the class, before it is saved as a .yaml file. After runtime, the experimenter manually fills leftover fields,
-    such as 'experimenter_notes,' before the class instance is transferred to the long-term storage destination.
-
-    The fully filled instance data is also used during preprocessing to write the water restriction log entry for the
-    trained animal.
-    """
-
-    experimenter: str
-    mouse_weight_g: float
-    dispensed_water_volume_ml: float
-    minimum_reward_delay: int
-    maximum_reward_delay_s: int
-    maximum_water_volume_ml: float
-    maximum_training_time_m: int
-    experimenter_notes: str = ...
-    experimenter_given_water_volume_ml: float = ...
-
-@dataclass()
-class RunTrainingDescriptor(YamlConfig):
-    """This class is used to save the description information specific to run training sessions as a .yaml file.
-
-    The information stored in this class instance is filled in two steps. The main runtime function fills most fields
-    of the class, before it is saved as a .yaml file. After runtime, the experimenter manually fills leftover fields,
-    such as 'experimenter_notes,' before the class instance is transferred to the long-term storage destination.
-
-    The fully filled instance data is also used during preprocessing to write the water restriction log entry for the
-    trained animal.
-    """
-
-    experimenter: str
-    mouse_weight_g: float
-    dispensed_water_volume_ml: float
-    final_run_speed_threshold_cm_s: float
-    final_run_duration_threshold_s: float
-    initial_run_speed_threshold_cm_s: float
-    initial_run_duration_threshold_s: float
-    increase_threshold_ml: float
-    run_speed_increase_step_cm_s: float
-    run_duration_increase_step_s: float
-    maximum_water_volume_ml: float
-    maximum_training_time_m: int
-    experimenter_notes: str = ...
-    experimenter_given_water_volume_ml: float = ...
-
-@dataclass()
-class MesoscopeExperimentDescriptor(YamlConfig):
-    """This class is used to save the description information specific to experiment sessions as a .yaml file.
-
-    The information stored in this class instance is filled in two steps. The main runtime function fills most fields
-    of the class, before it is saved as a .yaml file. After runtime, the experimenter manually fills leftover fields,
-    such as 'experimenter_notes,' before the class instance is transferred to the long-term storage destination.
-
-    The fully filled instance data is also used during preprocessing to write the water restriction log entry for the
-    animal participating in the experiment runtime.
-    """
-
-    experimenter: str
-    mouse_weight_g: float
-    dispensed_water_volume_ml: float
-    experimenter_notes: str = ...
-    experimenter_given_water_volume_ml: float = ...
-
-@dataclass()
-class ZaberPositions(YamlConfig):
-    """This class is used to save Zaber motor positions as a .yaml file to reuse them between sessions.
-
-    The class is specifically designed to store, save, and load the positions of the LickPort and HeadBar motors
-    (axes). It is used to both store Zaber motor positions for each session for future analysis and to restore the same
-    Zaber motor positions across consecutive runtimes for the same project and animal combination.
-
-    Notes:
-        All positions are saved using native motor units. All class fields initialize to default placeholders that are
-        likely NOT safe to apply to the VR system. Do not apply the positions loaded from the file unless you are
-        certain they are safe to use.
-
-        Exercise caution when working with Zaber motors. The motors are powerful enough to damage the surrounding
-        equipment and manipulated objects. Do not modify the data stored inside the .yaml file unless you know what you
-        are doing.
-    """
-
-    headbar_z: int = ...
-    headbar_pitch: int = ...
-    headbar_roll: int = ...
-    lickport_z: int = ...
-    lickport_x: int = ...
-    lickport_y: int = ...
-
-@dataclass()
-class MesoscopePositions(YamlConfig):
-    """This class is used to save the real and virtual Mesoscope objective positions as a .yaml file to reuse it
-    between experiment sessions.
-
-    Primarily, the class is used to help the experimenter to position the Mesoscope at the same position across
-    multiple imaging sessions. It stores both the physical (real) position of the objective along the motorized
-    X, Y, Z, and Roll axes and the virtual (ScanImage software) tip, tilt, and fastZ focus axes.
-
-    Notes:
-        Since the API to read and write these positions automatically is currently not available, this class relies on
-        the experimenter manually entering all positions and setting the mesoscope to these positions when necessary.
-    """
-
-    mesoscope_x_position: float = ...
-    mesoscope_y_position: float = ...
-    mesoscope_roll_position: float = ...
-    mesoscope_z_position: float = ...
-    mesoscope_fast_z_position: float = ...
-    mesoscope_tip_position: float = ...
-    mesoscope_tilt_position: float = ...