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

np_workflows/experiments/task_trained_network/ttn_stim_config.py

@@ -3,15 +3,11 @@ import contextlib
 import copy
 import enum
 import functools
-from typing import ClassVar, Literal, NamedTuple, NoReturn, Optional, TypedDict
+from typing import Any, Literal
 
-import IPython.display
-import ipywidgets as ipw
 import np_config
 import np_logging
 import np_session
-import np_workflows
-from typing import Any
 
 logger = np_logging.getLogger(__name__)
 
@@ -29,9 +25,10 @@ class TTNSession(enum.Enum):
 # setup parameters ---------------------------------------------------------------------
 default_ttn_params = {}
 
+
 def camstim_defaults() -> dict:
     """Try to load defaults from camstim config file on the Stim computer.
-    
+
     May encounter permission error if not running as svc_neuropix.
     """
     with contextlib.suppress(OSError):
@@ -56,6 +53,7 @@ def camstim_defaults() -> dict:
     logger.warning("Could not load camstim defaults from config file on Stim computer.")
     return {}
 
+
 ## no longer added to default_ttn_params:
 # default_ttn_params.update(**camstim_defaults())
 
@@ -64,14 +62,13 @@ def camstim_defaults() -> dict:
 default_ttn_params["main"] = {}
 
 default_ttn_params["main"]["sweepstim"] = {
-    "trigger_delay_sec": 5.0,           #! does it matter?
-    'sync_sqr_loc': (870, 525),         # for Window.warp=Warp.Disabled 
-    'sync_sqr_loc_warp': (540, 329),    # for Window.warp=Warp.Spherical
+    "trigger_delay_sec": 5.0,  #! does it matter?
+    "sync_sqr_loc": (870, 525),  # for Window.warp=Warp.Disabled
+    "sync_sqr_loc_warp": (540, 329),  # for Window.warp=Warp.Spherical
 }
 # default_ttn_params["main"]["movie_path"] = "C:/ProgramData/StimulusFiles/dev/"
-default_ttn_params["main"][
-    "monitor"
-] = 'Gamma1.Luminance50'
+default_ttn_params["main"]["monitor"] = "Gamma1.Luminance50"
+
 
 # other parameters that vary depending on session type (pretest, hab, ephys):
 def per_session_main_stim_params(session: TTNSession) -> dict[str, Any]:
@@ -105,7 +102,7 @@ def per_session_main_stim_params(session: TTNSession) -> dict[str, Any]:
     def main_blank_screen(session: TTNSession) -> dict[str, float | int]:
         match session:
             case TTNSession.PRETEST:
-                return {"pre_blank_screen_sec": .5, "post_blank_screen_sec": .5}
+                return {"pre_blank_screen_sec": 0.5, "post_blank_screen_sec": 0.5}
             case _:
                 return {"pre_blank_screen_sec": 2, "post_blank_screen_sec": 2}
 
@@ -122,6 +119,7 @@ default_ttn_params["opto"] = {}
 
 # all parameters depend on session type (pretest, hab, ephys):
 
+
 def per_session_opto_params(
     session: TTNSession, mouse: str | int | np_session.Mouse
 ) -> dict[str, dict[str, str | list[float] | Literal["pretest", "experiment"]]]:
@@ -169,14 +167,20 @@ def per_session_opto_params(
 default_ttn_params["mapping"] = {}
 
 default_ttn_params["mapping"]["monitor"] = "Gamma1.Luminance50"
-default_ttn_params["mapping"]["gabor_path"] = "gabor_20_deg_250ms.stim" 
-default_ttn_params["mapping"]["flash_path"] = "flash_250ms.stim" # relpath in StimulusFiles dir (for _v2 objects)
+default_ttn_params["mapping"]["gabor_path"] = "gabor_20_deg_250ms.stim"
+default_ttn_params["mapping"][
+    "flash_path"
+] = "flash_250ms.stim"  # relpath in StimulusFiles dir (for _v2 objects)
 default_ttn_params["mapping"]["default_gabor_duration_seconds"] = 1200
-default_ttn_params["mapping"]["default_flash_duration_seconds"] = 300 # may be overriden by 'max_total_duration_minutes'
+default_ttn_params["mapping"][
+    "default_flash_duration_seconds"
+] = 300  # may be overriden by 'max_total_duration_minutes'
 
 default_ttn_params["mapping"]["sweepstim"] = {
-    'sync_sqr_loc_warp': (540, 329),     # for Window.warp=Warp.Spherical
-} 
+    "sync_sqr_loc_warp": (540, 329),  # for Window.warp=Warp.Spherical
+}
+
+
 # trigger_delay_sec not specified
 # all stim parameters depend on session type (pretest, hab, ephys):
 def per_session_mapping_params(session: TTNSession) -> dict[str, dict[str, int]]:
@@ -195,7 +199,7 @@ def per_session_mapping_params(session: TTNSession) -> dict[str, dict[str, int]]
     def mapping_blank_screen(session: TTNSession) -> dict[str, float | int]:
         match session:
             case TTNSession.PRETEST:
-                return {"pre_blank_screen_sec": .5, "post_blank_screen_sec": .5}
+                return {"pre_blank_screen_sec": 0.5, "post_blank_screen_sec": 0.5}
             case TTNSession.EPHYS | TTNSession.HAB_120:
                 return {"pre_blank_screen_sec": 2, "post_blank_screen_sec": 2}
             case _:

np_workflows/experiments/templeton/main.py

@@ -1,65 +1,39 @@
 from __future__ import annotations
 
-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, Type, 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 fabric
-import PIL.Image
-import pydantic
-from pyparsing import Any
 from np_services import (
-    Service,
-    Finalizable,
-    ScriptCamstim,
+    MouseDirector,
+    NewScaleCoordinateRecorder,
     OpenEphys,
+    ScriptCamstim,
     Sync,
-    ImageMVR,
     VideoMVR,
-    NewScaleCoordinateRecorder,
-    MouseDirector,
 )
 
 from np_workflows.shared import base_experiments
 
 logger = np_logging.getLogger(__name__)
 
+
 class TempletonPilot(base_experiments.DynamicRoutingExperiment):
     """Provides project-specific methods and attributes, mainly related to camstim scripts."""
-    
+
     default_session_subclass = np_session.TempletonPilotSession
-    
+
     workflow: base_experiments.DynamicRoutingExperiment.Workflow
     """Enum for workflow type, e.g. PRETEST, HAB_AUD, HAB_VIS, EPHYS_ etc."""
 
     @property
     def task_name(self) -> str:
         task_name = super().task_name
-        return f'templeton {task_name}' if 'templeton' not in task_name else task_name
-    
+        return f"templeton {task_name}" if "templeton" not in task_name else task_name
+
     @task_name.setter
     def task_name(self, value: str):
         super().task_name = value
-       
+
+
 def new_experiment(
     mouse: int | str | np_session.Mouse,
     user: str | np_session.User,
@@ -67,17 +41,20 @@ def new_experiment(
 ) -> TempletonPilot:
     """Create a new experiment for the given mouse and user."""
     experiment: Ephys | Hab
-    if any(tag in workflow.name for tag in ('EPHYS', 'PRETEST')):
+    if any(tag in workflow.name for tag in ("EPHYS", "PRETEST")):
         experiment = Ephys(mouse, user)
-    elif 'HAB' in workflow.name:
+    elif "HAB" in workflow.name:
         experiment = Hab(mouse, user)
     else:
-        raise ValueError(f"Unknown {workflow = }. Create an experiment with e.g.\n\n\texperiment = Ephys(mouse, user)\nexperiment.session.npexp_path.mkdir()")
+        raise ValueError(
+            f"Unknown {workflow = }. Create an experiment with e.g.\n\n\texperiment = Ephys(mouse, user)\nexperiment.session.npexp_path.mkdir()"
+        )
     experiment.workflow = workflow
     experiment.log(f"{experiment} created")
-    experiment.session.npexp_path.mkdir(parents=True, exist_ok=True) 
+    experiment.session.npexp_path.mkdir(parents=True, exist_ok=True)
     return experiment
 
+
 class Hab(TempletonPilot):
     def __init__(self, *args, **kwargs):
         self.services = (
@@ -102,4 +79,4 @@ class Ephys(TempletonPilot):
             OpenEphys,
             NewScaleCoordinateRecorder,
         )
-        super().__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)

np_workflows/experiments/templeton/widgets.py

@@ -1,28 +1,22 @@
-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.templeton.main import Ephys, Hab
 from np_workflows.shared.base_experiments import DynamicRoutingExperiment
 
 # for widget, before creating a experiment --------------------------------------------- #
 
 
 class SelectedWorkflow:
-    def __init__(self, workflow: str | DynamicRoutingExperiment.Workflow, mouse: str | int | np_session.Mouse):
+    def __init__(
+        self,
+        workflow: str | DynamicRoutingExperiment.Workflow,
+        mouse: str | int | np_session.Mouse,
+    ):
         if isinstance(workflow, str):
-            workflow = DynamicRoutingExperiment.Workflow[workflow] # uses enum name (not value)
+            workflow = DynamicRoutingExperiment.Workflow[
+                workflow
+            ]  # uses enum name (not value)
         self.workflow = workflow
         self.mouse = str(mouse)
 
@@ -50,11 +44,13 @@ def workflow_select_widget(
     workflow_descriptions = ipw.Select(
         options=tuple(_.value for _ in DynamicRoutingExperiment.Workflow),
         disabled=True,
-        value=None
+        value=None,
     )
     console = ipw.Output()
     with console:
-        if last_workflow := np_session.Mouse(selection.mouse).state.get('last_workflow'):
+        if last_workflow := np_session.Mouse(selection.mouse).state.get(
+            "last_workflow"
+        ):
             print(f"{mouse} last workflow: {last_workflow}")
         print(f"Selected: {selection.workflow.name}")
 
@@ -67,16 +63,23 @@ def workflow_select_widget(
             return
         if change["new"] == change["old"]:
             return
-        selection.__init__(str(workflow_dropdown.value), mouse.id if isinstance(mouse, np_session.Mouse) else str(mouse))
+        selection.__init__(
+            str(workflow_dropdown.value),
+            mouse.id if isinstance(mouse, np_session.Mouse) else str(mouse),
+        )
         with console:
             print(f"Selected: {selection.workflow}")
-    workflow_dropdown.observe(update, names='value')
 
-    IPython.display.display(ipw.VBox([ipw.HBox([workflow_dropdown, workflow_descriptions]), console]))
+    workflow_dropdown.observe(update, names="value")
+
+    IPython.display.display(
+        ipw.VBox([ipw.HBox([workflow_dropdown, workflow_descriptions]), console])
+    )
 
     return selection
-    
-    
 
-def photodoc_widget(session: np_session.Session, reminder: str) -> None: 
-    print(f'Take an image in Vimba Viewer and save as:\n{session.npexp_path.name}_{reminder}.png')
+
+def photodoc_widget(session: np_session.Session, reminder: str) -> None:
+    print(
+        f"Take an image in Vimba Viewer and save as:\n{session.npexp_path.name}_{reminder}.png"
+    )

np_workflows/shared/__init__.py

@@ -1,3 +1,3 @@
 from np_workflows.shared.base_experiments import *
 from np_workflows.shared.npxc import *
-from np_workflows.shared.widgets import *
+from np_workflows.shared.widgets import *