np-workflows 1.6.89__py3-none-any.whl → 1.6.91__py3-none-any.whl

np_workflows/experiments/openscope_psycode/main_psycode_pilot.py

@@ -1,41 +1,22 @@
-import configparser
 import contextlib
-import copy
-import dataclasses
-import datetime
 import enum
-import functools
-import pathlib
-import platform
-import shutil
-import threading
 import time
-import zlib
-from typing import ClassVar, Literal, NamedTuple, NoReturn, Optional, TypedDict
 
-import IPython
-import IPython.display
-import ipywidgets as ipw
-import np_config
 import np_logging
-import np_services
 import np_session
-import np_workflows
-import PIL.Image
-import pydantic
-from pyparsing import Any
 from np_services import (
-    Service,
     Finalizable,
-    ScriptCamstim, SessionCamstim, 
-    SessionCamstim,
+    MouseDirector,
+    NewScaleCoordinateRecorder,
     OpenEphys,
+    Service,
+    SessionCamstim,
     Sync,
     VideoMVR,
-    NewScaleCoordinateRecorder,
-    MouseDirector,
 )
 
+import np_workflows
+
 logger = np_logging.getLogger(__name__)
 
 
@@ -49,16 +30,16 @@ class PsyCodeSession(enum.Enum):
 
 class PsyCodeMixin:
     """Provides project-specific methods and attributes, mainly related to camstim scripts."""
-    
+
     workflow: PsyCodeSession
     """Enum for particular workflow/session, e.g. PRETEST, HAB_60, HAB_90,
     EPHYS."""
-    
+
     session: np_session.PipelineSession
     mouse: np_session.Mouse
     user: np_session.User
     platform_json: np_session.PlatformJson
-    
+
     @property
     def recorders(self) -> tuple[Service, ...]:
         """Services to be started before stimuli run, and stopped after. Session-dependent."""
@@ -70,11 +51,11 @@ class PsyCodeMixin:
 
     @property
     def stims(self) -> tuple[Service, ...]:
-        return (SessionCamstim, )
-    
+        return (SessionCamstim,)
+
     def initialize_and_test_services(self) -> None:
         """Configure, initialize (ie. reset), then test all services."""
-        
+
         MouseDirector.user = self.user.id
         MouseDirector.mouse = self.mouse.id
 
@@ -92,79 +73,97 @@ class PsyCodeMixin:
 
     def update_state(self) -> None:
         "Store useful but non-essential info."
-        self.mouse.state['last_session'] = self.session.id
-        self.mouse.state['last_PsyCode_session'] = str(self.workflow)
+        self.mouse.state["last_session"] = self.session.id
+        self.mouse.state["last_PsyCode_session"] = str(self.workflow)
         if self.mouse == 366122:
             return
         match self.workflow:
             case PsyCodeSession.PRETEST:
                 return
             case PsyCodeSession.HAB:
-                self.session.project.state['latest_hab'] = self.session.id
+                self.session.project.state["latest_hab"] = self.session.id
             case PsyCodeSession.EPHYS:
-                self.session.project.state['latest_ephys'] = self.session.id
-                self.session.project.state['sessions'] = self.session.project.state.get('sessions', []) + [self.session.id]
-                
+                self.session.project.state["latest_ephys"] = self.session.id
+                self.session.project.state["sessions"] = self.session.project.state.get(
+                    "sessions", []
+                ) + [self.session.id]
+
     def run_stim(self) -> None:
 
         self.update_state()
-        
+
         if not SessionCamstim.is_ready_to_start():
             raise RuntimeError("SessionCamstim is not ready to start.")
-        
-        np_logging.web(f'PsyCode_{self.workflow.name.lower()}').info(f"Started session {self.mouse.mtrain.stage['name']}")
+
+        np_logging.web(f"PsyCode_{self.workflow.name.lower()}").info(
+            f"Started session {self.mouse.mtrain.stage['name']}"
+        )
         SessionCamstim.start()
-        
+
         with contextlib.suppress(Exception):
             while not SessionCamstim.is_ready_to_start():
                 time.sleep(2.5)
-            
+
         if isinstance(SessionCamstim, Finalizable):
             SessionCamstim.finalize()
 
         with contextlib.suppress(Exception):
-            np_logging.web(f'PsyCode_{self.workflow.name.lower()}').info(f"Finished session {self.mouse.mtrain.stage['name']}")
-    
-    
-    def copy_data_files(self) -> None: 
+            np_logging.web(f"PsyCode_{self.workflow.name.lower()}").info(
+                f"Finished session {self.mouse.mtrain.stage['name']}"
+            )
+
+    def copy_data_files(self) -> None:
         super().copy_data_files()
-        
+
         # When all processing completes, camstim Agent class passes data and uuid to
         # /camstim/lims BehaviorSession class, and write_behavior_data() writes a
         # final .pkl with default name YYYYMMDDSSSS_mouseID_foragingID.pkl
         # - if we have a foraging ID, we can search for that
-        if None == (stim_pkl := next(self.session.npexp_path.glob(f'{self.session.date:%y%m%d}*_{self.session.mouse}_*.pkl'), None)):
-            logger.warning('Did not find stim file on npexp matching the format `YYYYMMDDSSSS_mouseID_foragingID.pkl`')
+        if None == (
+            stim_pkl := next(
+                self.session.npexp_path.glob(
+                    f"{self.session.date:%y%m%d}*_{self.session.mouse}_*.pkl"
+                ),
+                None,
+            )
+        ):
+            logger.warning(
+                "Did not find stim file on npexp matching the format `YYYYMMDDSSSS_mouseID_foragingID.pkl`"
+            )
             return
         assert stim_pkl
         if not self.session.platform_json.foraging_id:
-            self.session.platform_json.foraging_id = stim_pkl.stem.split('_')[-1]
-        new_stem = f'{self.session.folder}.stim'
-        logger.debug(f'Renaming stim file copied to npexp: {stim_pkl} -> {new_stem}')
+            self.session.platform_json.foraging_id = stim_pkl.stem.split("_")[-1]
+        new_stem = f"{self.session.folder}.stim"
+        logger.debug(f"Renaming stim file copied to npexp: {stim_pkl} -> {new_stem}")
         stim_pkl = stim_pkl.rename(stim_pkl.with_stem(new_stem))
-        
+
         # remove other stim pkl, which is nearly identical, if it was also copied
-        for pkl in self.session.npexp_path.glob('*.pkl'):
+        for pkl in self.session.npexp_path.glob("*.pkl"):
             if (
                 self.session.folder not in pkl.stem
-                and 
-                abs(pkl.stat().st_size - stim_pkl.stat().st_size) < 1e6
+                and abs(pkl.stat().st_size - stim_pkl.stat().st_size) < 1e6
             ):
-                logger.debug(f'Deleting extra stim pkl copied to npexp: {pkl.stem}')
+                logger.debug(f"Deleting extra stim pkl copied to npexp: {pkl.stem}")
                 pkl.unlink()
-        
-        
-def validate_selected_workflow(session: PsyCodeSession, mouse: np_session.Mouse) -> None:
-    for workflow in ('hab', 'ephys'):
+
+
+def validate_selected_workflow(
+    session: PsyCodeSession, mouse: np_session.Mouse
+) -> None:
+    for workflow in ("hab", "ephys"):
         if (
             workflow in session.value.lower()
-            and workflow not in mouse.mtrain.stage['name'].lower()
+            and workflow not in mouse.mtrain.stage["name"].lower()
         ) or (
-            session.value.lower() == 'ephys' and 'hab' in mouse.mtrain.stage['name'].lower()
+            session.value.lower() == "ephys"
+            and "hab" in mouse.mtrain.stage["name"].lower()
         ):
-            raise ValueError(f"Workflow selected ({session.value}) does not match MTrain stage ({mouse.mtrain.stage['name']}): please check cells above.")
+            raise ValueError(
+                f"Workflow selected ({session.value}) does not match MTrain stage ({mouse.mtrain.stage['name']}): please check cells above."
+            )
+
 
-    
 class Hab(PsyCodeMixin, np_workflows.PipelineHab):
     def __init__(self, *args, **kwargs):
         self.services = (
@@ -209,9 +208,10 @@ def new_experiment(
         case _:
             raise ValueError(f"Invalid workflow type: {workflow}")
     experiment.workflow = workflow
-    
+
     with contextlib.suppress(Exception):
-        np_logging.web(f'PsyCode_{experiment.workflow.name.lower()}').info(f"{experiment} created")
-            
-    return experiment
+        np_logging.web(f"PsyCode_{experiment.workflow.name.lower()}").info(
+            f"{experiment} created"
+        )
 
+    return experiment

np_workflows/experiments/openscope_psycode/psycode_workflow_widget.py

@@ -1,17 +1,6 @@
-import configparser
-import contextlib
-import copy
-import enum
-import functools
-from typing import ClassVar, Literal, NamedTuple, NoReturn, Optional, TypedDict
-
 import IPython.display
 import ipywidgets as ipw
-import np_config
-import np_logging
 import np_session
-import np_workflows
-from pyparsing import Any
 
 from np_workflows.experiments.openscope_psycode.main_psycode_pilot import PsyCodeSession
 
@@ -20,8 +9,11 @@ global_state = {}
 
 # for widget, before creating a experiment --------------------------------------------- #
 
+
 class SelectedSession:
-    def __init__(self, session: str | PsyCodeSession, mouse: str | int | np_session.Mouse):
+    def __init__(
+        self, session: str | PsyCodeSession, mouse: str | int | np_session.Mouse
+    ):
         if isinstance(session, str):
             session = PsyCodeSession(session)
         self.session = session
@@ -48,17 +40,19 @@ def PsyCode_workflow_widget(
         options=tuple(_.value for _ in PsyCodeSession),
         description="Session",
     )
-    
+
     def update_selection():
         selection.__init__(str(session_dropdown.value), str(mouse))
-        
-    if (previously_selected_value := global_state.get('selected_session')):
+
+    if previously_selected_value := global_state.get("selected_session"):
         session_dropdown.value = previously_selected_value
         update_selection()
-        
+
     console = ipw.Output()
     with console:
-        if last_session := np_session.Mouse(selection.mouse).state.get('last_PsyCode_session'):
+        if last_session := np_session.Mouse(selection.mouse).state.get(
+            "last_PsyCode_session"
+        ):
             print(f"{mouse} last session: {last_session}")
         print(f"Selected: {selection.session}")
 
@@ -74,9 +68,9 @@ def PsyCode_workflow_widget(
         update_selection()
         with console:
             print(f"Selected: {selection.session}")
-        global_state['selected_session'] = selection.session.value
-        
-    session_dropdown.observe(update, names='value')
+        global_state["selected_session"] = selection.session.value
+
+    session_dropdown.observe(update, names="value")
 
     IPython.display.display(ipw.VBox([session_dropdown, console]))
 

np_workflows/experiments/openscope_v2/__init__.py

@@ -1,2 +1,2 @@
-from .main_V2_pilot import new_experiment, Hab, Ephys, validate_selected_workflow
+from .main_V2_pilot import Ephys, Hab, new_experiment, validate_selected_workflow
 from .V2_workflow_widget import V2_workflow_widget

np_workflows/experiments/openscope_v2/main_v2_pilot.py

@@ -1,41 +1,22 @@
-import configparser
 import contextlib
-import copy
-import dataclasses
-import datetime
 import enum
-import functools
-import pathlib
-import platform
-import shutil
-import threading
 import time
-import zlib
-from typing import ClassVar, Literal, NamedTuple, NoReturn, Optional, TypedDict
 
-import IPython
-import IPython.display
-import ipywidgets as ipw
-import np_config
 import np_logging
-import np_services
 import np_session
-import np_workflows
-import PIL.Image
-import pydantic
-from pyparsing import Any
 from np_services import (
-    Service,
     Finalizable,
-    ScriptCamstim, SessionCamstim, 
-    SessionCamstim,
+    MouseDirector,
+    NewScaleCoordinateRecorder,
     OpenEphys,
+    Service,
+    SessionCamstim,
     Sync,
     VideoMVR,
-    NewScaleCoordinateRecorder,
-    MouseDirector,
 )
 
+import np_workflows
+
 logger = np_logging.getLogger(__name__)
 
 
@@ -49,16 +30,16 @@ class V2Session(enum.Enum):
 
 class V2Mixin:
     """Provides project-specific methods and attributes, mainly related to camstim scripts."""
-    
+
     workflow: V2Session
     """Enum for particular workflow/session, e.g. PRETEST, HAB_60, HAB_90,
     EPHYS."""
-    
+
     session: np_session.PipelineSession
     mouse: np_session.Mouse
     user: np_session.User
     platform_json: np_session.PlatformJson
-    
+
     @property
     def recorders(self) -> tuple[Service, ...]:
         """Services to be started before stimuli run, and stopped after. Session-dependent."""
@@ -70,11 +51,11 @@ class V2Mixin:
 
     @property
     def stims(self) -> tuple[Service, ...]:
-        return (SessionCamstim, )
-    
+        return (SessionCamstim,)
+
     def initialize_and_test_services(self) -> None:
         """Configure, initialize (ie. reset), then test all services."""
-        
+
         MouseDirector.user = self.user.id
         MouseDirector.mouse = self.mouse.id
 
@@ -92,79 +73,95 @@ class V2Mixin:
 
     def update_state(self) -> None:
         "Store useful but non-essential info."
-        self.mouse.state['last_session'] = self.session.id
-        self.mouse.state['last_V2_session'] = str(self.workflow)
+        self.mouse.state["last_session"] = self.session.id
+        self.mouse.state["last_V2_session"] = str(self.workflow)
         if self.mouse == 366122:
             return
         match self.workflow:
             case V2Session.PRETEST:
                 return
             case V2Session.HAB:
-                self.session.project.state['latest_hab'] = self.session.id
+                self.session.project.state["latest_hab"] = self.session.id
             case V2Session.EPHYS:
-                self.session.project.state['latest_ephys'] = self.session.id
-                self.session.project.state['sessions'] = self.session.project.state.get('sessions', []) + [self.session.id]
-                
+                self.session.project.state["latest_ephys"] = self.session.id
+                self.session.project.state["sessions"] = self.session.project.state.get(
+                    "sessions", []
+                ) + [self.session.id]
+
     def run_stim(self) -> None:
 
         self.update_state()
-        
+
         if not SessionCamstim.is_ready_to_start():
             raise RuntimeError("SessionCamstim is not ready to start.")
-        
-        np_logging.web(f'V2_{self.workflow.name.lower()}').info(f"Started session {self.mouse.mtrain.stage['name']}")
+
+        np_logging.web(f"V2_{self.workflow.name.lower()}").info(
+            f"Started session {self.mouse.mtrain.stage['name']}"
+        )
         SessionCamstim.start()
-        
+
         with contextlib.suppress(Exception):
             while not SessionCamstim.is_ready_to_start():
                 time.sleep(2.5)
-            
+
         if isinstance(SessionCamstim, Finalizable):
             SessionCamstim.finalize()
 
         with contextlib.suppress(Exception):
-            np_logging.web(f'V2_{self.workflow.name.lower()}').info(f"Finished session {self.mouse.mtrain.stage['name']}")
-    
-    
-    def copy_data_files(self) -> None: 
+            np_logging.web(f"V2_{self.workflow.name.lower()}").info(
+                f"Finished session {self.mouse.mtrain.stage['name']}"
+            )
+
+    def copy_data_files(self) -> None:
         super().copy_data_files()
-        
+
         # When all processing completes, camstim Agent class passes data and uuid to
         # /camstim/lims BehaviorSession class, and write_behavior_data() writes a
         # final .pkl with default name YYYYMMDDSSSS_mouseID_foragingID.pkl
         # - if we have a foraging ID, we can search for that
-        if None == (stim_pkl := next(self.session.npexp_path.glob(f'{self.session.date:%y%m%d}*_{self.session.mouse}_*.pkl'), None)):
-            logger.warning('Did not find stim file on npexp matching the format `YYYYMMDDSSSS_mouseID_foragingID.pkl`')
+        if None == (
+            stim_pkl := next(
+                self.session.npexp_path.glob(
+                    f"{self.session.date:%y%m%d}*_{self.session.mouse}_*.pkl"
+                ),
+                None,
+            )
+        ):
+            logger.warning(
+                "Did not find stim file on npexp matching the format `YYYYMMDDSSSS_mouseID_foragingID.pkl`"
+            )
             return
         assert stim_pkl
         if not self.session.platform_json.foraging_id:
-            self.session.platform_json.foraging_id = stim_pkl.stem.split('_')[-1]
-        new_stem = f'{self.session.folder}.stim'
-        logger.debug(f'Renaming stim file copied to npexp: {stim_pkl} -> {new_stem}')
+            self.session.platform_json.foraging_id = stim_pkl.stem.split("_")[-1]
+        new_stem = f"{self.session.folder}.stim"
+        logger.debug(f"Renaming stim file copied to npexp: {stim_pkl} -> {new_stem}")
         stim_pkl = stim_pkl.rename(stim_pkl.with_stem(new_stem))
-        
+
         # remove other stim pkl, which is nearly identical, if it was also copied
-        for pkl in self.session.npexp_path.glob('*.pkl'):
+        for pkl in self.session.npexp_path.glob("*.pkl"):
             if (
                 self.session.folder not in pkl.stem
-                and 
-                abs(pkl.stat().st_size - stim_pkl.stat().st_size) < 1e6
+                and abs(pkl.stat().st_size - stim_pkl.stat().st_size) < 1e6
             ):
-                logger.debug(f'Deleting extra stim pkl copied to npexp: {pkl.stem}')
+                logger.debug(f"Deleting extra stim pkl copied to npexp: {pkl.stem}")
                 pkl.unlink()
-        
-        
+
+
 def validate_selected_workflow(session: V2Session, mouse: np_session.Mouse) -> None:
-    for workflow in ('hab', 'ephys'):
+    for workflow in ("hab", "ephys"):
         if (
             workflow in session.value.lower()
-            and workflow not in mouse.mtrain.stage['name'].lower()
+            and workflow not in mouse.mtrain.stage["name"].lower()
         ) or (
-            session.value.lower() == 'ephys' and 'hab' in mouse.mtrain.stage['name'].lower()
+            session.value.lower() == "ephys"
+            and "hab" in mouse.mtrain.stage["name"].lower()
         ):
-            raise ValueError(f"Workflow selected ({session.value}) does not match MTrain stage ({mouse.mtrain.stage['name']}): please check cells above.")
+            raise ValueError(
+                f"Workflow selected ({session.value}) does not match MTrain stage ({mouse.mtrain.stage['name']}): please check cells above."
+            )
+
 
-    
 class Hab(V2Mixin, np_workflows.PipelineHab):
     def __init__(self, *args, **kwargs):
         self.services = (
@@ -209,9 +206,10 @@ def new_experiment(
         case _:
             raise ValueError(f"Invalid workflow type: {workflow}")
     experiment.workflow = workflow
-    
+
     with contextlib.suppress(Exception):
-        np_logging.web(f'V2_{experiment.workflow.name.lower()}').info(f"{experiment} created")
-            
-    return experiment
+        np_logging.web(f"V2_{experiment.workflow.name.lower()}").info(
+            f"{experiment} created"
+        )
 
+    return experiment

np_workflows/experiments/openscope_v2/v2_workflow_widget.py

@@ -1,17 +1,6 @@
-import configparser
-import contextlib
-import copy
-import enum
-import functools
-from typing import ClassVar, Literal, NamedTuple, NoReturn, Optional, TypedDict
-
 import IPython.display
 import ipywidgets as ipw
-import np_config
-import np_logging
 import np_session
-import np_workflows
-from pyparsing import Any
 
 from np_workflows.experiments.openscope_V2.main_V2_pilot import V2Session
 
@@ -20,6 +9,7 @@ global_state = {}
 
 # for widget, before creating a experiment --------------------------------------------- #
 
+
 class SelectedSession:
     def __init__(self, session: str | V2Session, mouse: str | int | np_session.Mouse):
         if isinstance(session, str):
@@ -48,17 +38,19 @@ def V2_workflow_widget(
         options=tuple(_.value for _ in V2Session),
         description="Session",
     )
-    
+
     def update_selection():
         selection.__init__(str(session_dropdown.value), str(mouse))
-        
-    if (previously_selected_value := global_state.get('selected_session')):
+
+    if previously_selected_value := global_state.get("selected_session"):
         session_dropdown.value = previously_selected_value
         update_selection()
-        
+
     console = ipw.Output()
     with console:
-        if last_session := np_session.Mouse(selection.mouse).state.get('last_V2_session'):
+        if last_session := np_session.Mouse(selection.mouse).state.get(
+            "last_V2_session"
+        ):
             print(f"{mouse} last session: {last_session}")
         print(f"Selected: {selection.session}")
 
@@ -74,9 +66,9 @@ def V2_workflow_widget(
         update_selection()
         with console:
             print(f"Selected: {selection.session}")
-        global_state['selected_session'] = selection.session.value
-        
-    session_dropdown.observe(update, names='value')
+        global_state["selected_session"] = selection.session.value
+
+    session_dropdown.observe(update, names="value")
 
     IPython.display.display(ipw.VBox([session_dropdown, console]))
 

np_workflows/experiments/openscope_vippo/__init__.py

@@ -1,2 +1,2 @@
-from .main_vippo_pilot import new_experiment, Hab, Ephys, validate_selected_workflow
+from .main_vippo_pilot import Ephys, Hab, new_experiment, validate_selected_workflow
 from .vippo_workflow_widget import vippo_workflow_widget