sl-shared-assets 3.0.0rc2__py3-none-any.whl → 3.0.0rc4__py3-none-any.whl

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/__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/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/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/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/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/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/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.
 

{sl_shared_assets-3.0.0rc2.dist-info → sl_shared_assets-3.0.0rc4.dist-info}/METADATA

@@ -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.dist-info → sl_shared_assets-3.0.0rc4.dist-info}/RECORD

@@ -1,12 +1,12 @@
-sl_shared_assets/__init__.py,sha256=meu22eFCi7n8KeUPxY_dtLbzlWA4Dxvj8yk7m60UFcI,2243
-sl_shared_assets/__init__.pyi,sha256=jUguKA473IsMR8sYqOOiA0_UORJXNGhcYB2nPGd0NtE,2465
+sl_shared_assets/__init__.py,sha256=0v_te6XWwWEsxfq5RWfLecsNoTx1XVJj0D5OWu1OJtk,2289
+sl_shared_assets/__init__.pyi,sha256=wE_YjwirUFaRql_RVCdbNbvR3tDlyuyq0JF2nQLUO1U,2531
 sl_shared_assets/cli.py,sha256=R_h_Dlla48mG1LpFDDE9flZ_NyDC9UguRUAYZL6gA9s,18383
 sl_shared_assets/cli.pyi,sha256=8ZJK56_jh2QlF3XCN6c7fI6Z022XtehB0eCrQDJbAsU,5515
 sl_shared_assets/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sl_shared_assets/data_classes/__init__.py,sha256=ixn972b-3URCinVLRPjMfDXpO2w24_NkEUUjdqByFrA,1890
-sl_shared_assets/data_classes/__init__.pyi,sha256=bDBLkyhlosB4t09GxHBNKH0kaVBhHSY_j-i3MD2iKVo,2088
-sl_shared_assets/data_classes/configuration_data.py,sha256=h6o7Uaz2HZjV-9-wc5iz5xfkhVpPWPrncU8VU7_AeB8,30587
-sl_shared_assets/data_classes/configuration_data.pyi,sha256=fb12sdDuYJtfEurzbg6WcCU0NIm1mudsgsGdUVFTajQ,10305
+sl_shared_assets/data_classes/__init__.py,sha256=1NusIC_gUoQDFuHtvnpPj4RJQ2pCzZhjfVzgFThG8Ws,1936
+sl_shared_assets/data_classes/__init__.pyi,sha256=gdCYkXzyoZRURR5e5C0kd_frFURHEu_UI_d0QJ0RRwA,2154
+sl_shared_assets/data_classes/configuration_data.py,sha256=a8MDzSJ0T3P3MGz0JyfpJ4bmlIuzXTYUVb-EG4UhyWQ,32683
+sl_shared_assets/data_classes/configuration_data.pyi,sha256=anjl32Z-OgVgy96T7s7y1XN5HM_FfnztOvUFWTUjQfw,10462
 sl_shared_assets/data_classes/runtime_data.py,sha256=V98VSUHBFiqRngHAYtH6r6X_zDht65wi9TpdbbYAhS8,16656
 sl_shared_assets/data_classes/runtime_data.pyi,sha256=zATWUIP0whD0iRpxkvt78cLL_Ajr-d_9C6goHdTLnSw,6927
 sl_shared_assets/data_classes/session_data.py,sha256=0dNv_49WJeUf5IYgbGMWnMwX3aAYPIv7u8OJM5itIJA,50673
@@ -17,8 +17,8 @@ sl_shared_assets/server/__init__.py,sha256=w7y73RXXjBrWQsjU5g1QNCv_gsXDYnHos3NpO
 sl_shared_assets/server/__init__.pyi,sha256=Zc12G90fZdgEMwaVZbFzrRVV1wH_LEj3sxaV3lhk1Cw,316
 sl_shared_assets/server/job.py,sha256=DnEVIswZXm9queBgy6MlpIrCosXvQ_tweOeko7LN9yc,19431
 sl_shared_assets/server/job.pyi,sha256=uYfOuKgPL1hSHQvy5nmXzFkVjS316F3IZTdT-PmluZU,11663
-sl_shared_assets/server/server.py,sha256=fR7SvJDpurYBUTKkt_cImAD0x64thXPTKHmDb6YPYaU,29925
-sl_shared_assets/server/server.pyi,sha256=P3E_jSMlSnQ8O0UwA4fO6p4RSyu8maDEGlIJ_ptGpG4,14267
+sl_shared_assets/server/server.py,sha256=MGk1v49aEFeIChMDsiR7CXjVkWwDpD9kA1TK0fwuTXw,32926
+sl_shared_assets/server/server.pyi,sha256=5Yxq4txhjtd9w-6U9fPehzMeIZL5GcprVCHd9mPP6FI,15113
 sl_shared_assets/tools/__init__.py,sha256=NktXk62E_HHOrO_93z_MVmSd6-Oir3mE4xE9Yr8Qa7U,682
 sl_shared_assets/tools/__init__.pyi,sha256=0UXorfCXXmHQOP5z7hODpsqEX0DAkOta5VZqN6FSS-w,623
 sl_shared_assets/tools/ascension_tools.py,sha256=kIqYGX9F8lRao_LaVOacIiT8J9SypTvarb9mgaI9ZPs,15387
@@ -29,8 +29,8 @@ sl_shared_assets/tools/project_management_tools.py,sha256=Z_U0R26w9Le1O-u66gyF5C
 sl_shared_assets/tools/project_management_tools.pyi,sha256=4kok98nOZ4KnT-Sg-ZCZYg-WIM5qZqiyK8g1XiiDjHM,10375
 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-3.0.0rc2.dist-info/METADATA,sha256=mCoBnEMzF796sZr6H6yqwY0N-T46sSWNoJXg29x0FZ4,49309
-sl_shared_assets-3.0.0rc2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-sl_shared_assets-3.0.0rc2.dist-info/entry_points.txt,sha256=UmO1rl7ly9N7HWPwWyP9E0b5KBUStpBo4TRoqNtizDY,430
-sl_shared_assets-3.0.0rc2.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-sl_shared_assets-3.0.0rc2.dist-info/RECORD,,
+sl_shared_assets-3.0.0rc4.dist-info/METADATA,sha256=35CAPKPkE-DLPvdQ5WuGnsn77wggdxEZDRQGV1e45Ls,49309
+sl_shared_assets-3.0.0rc4.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+sl_shared_assets-3.0.0rc4.dist-info/entry_points.txt,sha256=UmO1rl7ly9N7HWPwWyP9E0b5KBUStpBo4TRoqNtizDY,430
+sl_shared_assets-3.0.0rc4.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+sl_shared_assets-3.0.0rc4.dist-info/RECORD,,