sl-shared-assets 3.0.0rc2__tar.gz → 3.0.0rc4__tar.gz

{sl_shared_assets-3.0.0rc2 → sl_shared_assets-3.0.0rc4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sl-shared-assets
-Version: 3.0.0rc2
+Version: 3.0.0rc4
 Summary: Provides data acquisition and processing assets shared between Sun (NeuroAI) lab libraries.
 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-3.0.0rc2 → sl_shared_assets-3.0.0rc4}/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 = "3.0.0rc2"
+version = "3.0.0rc4"
 description = "Provides data acquisition and processing assets shared between Sun (NeuroAI) lab libraries."
 readme = "README.md"
 license = { file = "LICENSE" }

{sl_shared_assets-3.0.0rc2 → sl_shared_assets-3.0.0rc4}/src/sl_shared_assets/__init__.py

@@ -28,6 +28,7 @@ from .data_classes import (
     ZaberPositions,
     ExperimentState,
     MesoscopeCameras,
+    TrialCueSequence,
     ProcessingTracker,
     MesoscopePositions,
     ProjectConfiguration,
@@ -81,6 +82,7 @@ __all__ = [
     "MesoscopeAdditionalFirmware",
     "get_system_configuration_data",
     "set_system_configuration_file",
+    "TrialCueSequence",
     # Tools package
     "resolve_p53_marker",
     "transfer_directory",

{sl_shared_assets-3.0.0rc2 → sl_shared_assets-3.0.0rc4}/src/sl_shared_assets/__init__.pyi

@@ -24,6 +24,7 @@ from .data_classes import (
     ZaberPositions as ZaberPositions,
     ExperimentState as ExperimentState,
     MesoscopeCameras as MesoscopeCameras,
+    TrialCueSequence as TrialCueSequence,
     ProcessingTracker as ProcessingTracker,
     MesoscopePositions as MesoscopePositions,
     ProjectConfiguration as ProjectConfiguration,
@@ -71,6 +72,7 @@ __all__ = [
     "MesoscopeAdditionalFirmware",
     "get_system_configuration_data",
     "set_system_configuration_file",
+    "TrialCueSequence",
     "resolve_p53_marker",
     "transfer_directory",
     "calculate_directory_checksum",

{sl_shared_assets-3.0.0rc2 → sl_shared_assets-3.0.0rc4}/src/sl_shared_assets/data_classes/__init__.py

@@ -24,6 +24,7 @@ from .configuration_data import (
     MesoscopePaths,
     ExperimentState,
     MesoscopeCameras,
+    TrialCueSequence,
     MesoscopeMicroControllers,
     MesoscopeAdditionalFirmware,
     MesoscopeSystemConfiguration,
@@ -60,4 +61,5 @@ __all__ = [
     "MesoscopeMicroControllers",
     "MesoscopeAdditionalFirmware",
     "ProcessingTracker",
+    "TrialCueSequence",
 ]

{sl_shared_assets-3.0.0rc2 → sl_shared_assets-3.0.0rc4}/src/sl_shared_assets/data_classes/__init__.pyi

@@ -26,6 +26,7 @@ from .configuration_data import (
     MesoscopePaths as MesoscopePaths,
     ExperimentState as ExperimentState,
     MesoscopeCameras as MesoscopeCameras,
+    TrialCueSequence as TrialCueSequence,
     MesoscopeMicroControllers as MesoscopeMicroControllers,
     MesoscopeAdditionalFirmware as MesoscopeAdditionalFirmware,
     MesoscopeSystemConfiguration as MesoscopeSystemConfiguration,
@@ -62,4 +63,5 @@ __all__ = [
     "MesoscopeMicroControllers",
     "MesoscopeAdditionalFirmware",
     "ProcessingTracker",
+    "TrialCueSequence",
 ]

{sl_shared_assets-3.0.0rc2 → sl_shared_assets-3.0.0rc4}/src/sl_shared_assets/data_classes/configuration_data.py

@@ -39,6 +39,20 @@ class ExperimentState:
     system currently support two system state codes: REST (1) and RUN (2)."""
     state_duration_s: float
     """The time, in seconds, to maintain the current combination of the experiment and system states."""
+    initial_guided_trials: int
+    """Specifies the number of trials (laps) at the onset of the experiment state, for which lick guidance will be 
+    automatically enabled. Specifically, if the experiment state supports running linearized Virtual Reality track, the 
+    system will enable lick guidance for this many trials at the beginning of the experiment state and automatically 
+    disable it for the following trials."""
+    failed_trial_threshold: int
+    """Specifies the number of failed (non-rewarded) non-guided trials (laps), after which the system will re-enable 
+    guidance for the 'recovery_guided_trials' number of following trials. For this to take effect, the trials must be 
+    failed this many times in a row."""
+    recovery_guided_trials: int
+    """Specifies the number of trials (laps) for which the system will re-enable lick guidance, when the animal 
+    repeatedly fails 'failed_trial_threshold' number of trials. This field works similar to the 'initial_guided_trials' 
+    field, but is triggered by repeated performance failures, rather than experiment state onset. After the animal 
+    runs this many guided trials, the system will automatically disable guidance for the following trials."""
 
 
 @dataclass()
@@ -54,6 +68,10 @@ class TrialCueSequence:
 
     cue_sequence: tuple[int, ...]
     """Specifies the sequence of wall cues experienced by the animal while running this trial."""
+    trial_length_unity_unit: float
+    """The length of the trial cue sequence, in Unity units."""
+    trial_length_cm: float
+    """The length of the trial cue sequence in centimeters."""
 
 
 # noinspection PyArgumentList
@@ -82,15 +100,40 @@ class MesoscopeExperimentConfiguration(YamlConfig):
     to travel to fully traverse the wall cue region from start to end."""
     experiment_states: dict[str, ExperimentState] = field(
         default_factory=lambda: {
-            "baseline": ExperimentState(experiment_state_code=1, system_state_code=1, state_duration_s=30),
-            "experiment": ExperimentState(experiment_state_code=2, system_state_code=2, state_duration_s=120),
-            "cooldown": ExperimentState(experiment_state_code=3, system_state_code=1, state_duration_s=15),
+            "baseline": ExperimentState(
+                experiment_state_code=1,
+                system_state_code=1,
+                state_duration_s=30,
+                initial_guided_trials=0,
+                failed_trial_threshold=0,
+                recovery_guided_trials=0,
+            ),
+            "experiment": ExperimentState(
+                experiment_state_code=2,
+                system_state_code=2,
+                state_duration_s=120,
+                initial_guided_trials=3,
+                failed_trial_threshold=6,
+                recovery_guided_trials=3,
+            ),
+            "cooldown": ExperimentState(
+                experiment_state_code=3,
+                system_state_code=1,
+                state_duration_s=15,
+                initial_guided_trials=1000000,
+                failed_trial_threshold=0,
+                recovery_guided_trials=0,
+            ),
         }
     )
     """A dictionary that uses human-readable state-names as keys and ExperimentState instances as values. Each 
     ExperimentState instance represents a phase of the experiment."""
     trial_structures: dict[str, TrialCueSequence] = field(
-        default_factory=lambda: {"circular_4cue": TrialCueSequence(cue_sequence=(0, 1, 0, 2, 0, 3, 0, 4))}
+        default_factory=lambda: {
+            "circular 4 cue": TrialCueSequence(
+                cue_sequence=(0, 1, 0, 2, 0, 3, 0, 4), trial_length_unity_unit=24.0, trial_length_cm=240.0
+            )
+        }
     )
     """A dictionary that maps human-readable trial structure names as keys and TrialCueSequence instances as values. 
     Each TrialCueSequence instance represents a specific VR wall cue sequence used by a given trial structure."""

{sl_shared_assets-3.0.0rc2 → sl_shared_assets-3.0.0rc4}/src/sl_shared_assets/data_classes/configuration_data.pyi

@@ -23,6 +23,9 @@ class ExperimentState:
     experiment_state_code: int
     system_state_code: int
     state_duration_s: float
+    initial_guided_trials: int
+    failed_trial_threshold: int
+    recovery_guided_trials: int
 
 @dataclass()
 class TrialCueSequence:
@@ -36,6 +39,8 @@ class TrialCueSequence:
     """
 
     cue_sequence: tuple[int, ...]
+    trial_length_unity_unit: float
+    trial_length_cm: float
 
 @dataclass()
 class MesoscopeExperimentConfiguration(YamlConfig):

{sl_shared_assets-3.0.0rc2 → sl_shared_assets-3.0.0rc4}/src/sl_shared_assets/server/server.py

@@ -4,6 +4,7 @@ the running job status. All lab processing and analysis pipelines use this inter
 resources.
 """
 
+import stat
 from random import randint
 from pathlib import Path
 import tempfile
@@ -486,6 +487,71 @@ class Server:
         finally:
             sftp.close()
 
+    def pull_directory(self, local_directory_path: Path, remote_directory_path: Path) -> None:
+        """Recursively downloads the entire target directory from the remote server to the local machine.
+
+        Args:
+            local_directory_path: The path to the local directory where the remote directory will be copied.
+            remote_directory_path: The path to the directory on the remote server to be downloaded.
+        """
+        sftp = self._client.open_sftp()
+
+        try:
+            # Creates the local directory if it doesn't exist
+            local_directory_path.mkdir(parents=True, exist_ok=True)
+
+            # Gets the list of items in the remote directory
+            remote_items = sftp.listdir_attr(str(remote_directory_path))
+
+            for item in remote_items:
+                remote_item_path = remote_directory_path.joinpath(item.filename)
+                local_item_path = local_directory_path.joinpath(item.filename)
+
+                # Checks if item is a directory
+                if stat.S_ISDIR(item.st_mode):  # type: ignore
+                    # Recursively pulls the subdirectory
+                    self.pull_directory(local_item_path, remote_item_path)
+                else:
+                    # Pulls the individual file using existing method
+                    sftp.get(localpath=str(local_item_path), remotepath=str(remote_item_path))
+
+        finally:
+            sftp.close()
+
+    def push_directory(self, local_directory_path: Path, remote_directory_path: Path) -> None:
+        """Recursively uploads the entire target directory from the local machine to the remote server.
+
+        Args:
+            local_directory_path: The path to the local directory to be uploaded.
+            remote_directory_path: The path on the remote server where the directory will be copied.
+        """
+        if not local_directory_path.exists() or not local_directory_path.is_dir():
+            message = (
+                f"Unable to upload the target local directory {local_directory_path} to the server, as it does not "
+                f"exist."
+            )
+            console.error(message=message, error=FileNotFoundError)
+
+        sftp = self._client.open_sftp()
+
+        try:
+            # Creates the remote directory using existing method
+            self.create_directory(remote_directory_path, parents=True)
+
+            # Iterates through all items in the local directory
+            for local_item_path in local_directory_path.iterdir():
+                remote_item_path = remote_directory_path.joinpath(local_item_path.name)
+
+                if local_item_path.is_dir():
+                    # Recursively pushes subdirectory
+                    self.push_directory(local_item_path, remote_item_path)
+                else:
+                    # Pushes the individual file using existing method
+                    sftp.put(localpath=str(local_item_path), remotepath=str(remote_item_path))
+
+        finally:
+            sftp.close()
+
     def remove(self, remote_path: Path, is_dir: bool) -> None:
         """Removes the specified file or directory from the remote server.
 

{sl_shared_assets-3.0.0rc2 → sl_shared_assets-3.0.0rc4}/src/sl_shared_assets/server/server.pyi

@@ -216,6 +216,20 @@ class Server:
             local_file_path: The path to the file that needs to be copied to the remote server.
             remote_file_path: The path to the file on the remote server (where to copy the file).
         """
+    def pull_directory(self, local_directory_path: Path, remote_directory_path: Path) -> None:
+        """Recursively downloads the entire target directory from the remote server to the local machine.
+
+        Args:
+            local_directory_path: The path to the local directory where the remote directory will be copied.
+            remote_directory_path: The path to the directory on the remote server to be downloaded.
+        """
+    def push_directory(self, local_directory_path: Path, remote_directory_path: Path) -> None:
+        """Recursively uploads the entire target directory from the local machine to the remote server.
+
+        Args:
+            local_directory_path: The path to the local directory to be uploaded.
+            remote_directory_path: The path on the remote server where the directory will be copied.
+        """
     def remove(self, remote_path: Path, is_dir: bool) -> None:
         """Removes the specified file or directory from the remote server.