np-workflows 1.6.87__py3-none-any.whl → 1.6.91__py3-none-any.whl

np_workflows/experiments/openscope_vippo/main_vippo_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 VippoSession(enum.Enum):
 
 class VippoMixin:
     """Provides project-specific methods and attributes, mainly related to camstim scripts."""
-    
+
     workflow: VippoSession
     """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 VippoMixin:
 
     @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 VippoMixin:
 
     def update_state(self) -> None:
         "Store useful but non-essential info."
-        self.mouse.state['last_session'] = self.session.id
-        self.mouse.state['last_vippo_session'] = str(self.workflow)
+        self.mouse.state["last_session"] = self.session.id
+        self.mouse.state["last_vippo_session"] = str(self.workflow)
         if self.mouse == 366122:
             return
         match self.workflow:
             case VippoSession.PRETEST:
                 return
             case VippoSession.HAB:
-                self.session.project.state['latest_hab'] = self.session.id
+                self.session.project.state["latest_hab"] = self.session.id
             case VippoSession.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'vippo_{self.workflow.name.lower()}').info(f"Started session {self.mouse.mtrain.stage['name']}")
+
+        np_logging.web(f"vippo_{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'vippo_{self.workflow.name.lower()}').info(f"Finished session {self.mouse.mtrain.stage['name']}")
-    
-    
-    def copy_data_files(self) -> None: 
+            np_logging.web(f"vippo_{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: VippoSession, 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(VippoMixin, 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'vippo_{experiment.workflow.name.lower()}').info(f"{experiment} created")
-            
-    return experiment
+        np_logging.web(f"vippo_{experiment.workflow.name.lower()}").info(
+            f"{experiment} created"
+        )
 
+    return experiment

np_workflows/experiments/openscope_vippo/vippo_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_vippo.main_vippo_pilot import VippoSession
 
@@ -20,8 +9,11 @@ global_state = {}
 
 # for widget, before creating a experiment --------------------------------------------- #
 
+
 class SelectedSession:
-    def __init__(self, session: str | VippoSession, mouse: str | int | np_session.Mouse):
+    def __init__(
+        self, session: str | VippoSession, mouse: str | int | np_session.Mouse
+    ):
         if isinstance(session, str):
             session = VippoSession(session)
         self.session = session
@@ -48,17 +40,19 @@ def vippo_workflow_widget(
         options=tuple(_.value for _ in VippoSession),
         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_vippo_session'):
+        if last_session := np_session.Mouse(selection.mouse).state.get(
+            "last_vippo_session"
+        ):
             print(f"{mouse} last session: {last_session}")
         print(f"Selected: {selection.session}")
 
@@ -74,9 +68,9 @@ def vippo_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/task_trained_network/__init__.py

@@ -1,2 +1,2 @@
-from .main_ttn_pilot import new_experiment, Hab, Ephys
+from .main_ttn_pilot import Ephys, Hab, new_experiment
 from .ttn_session_widget import stim_session_select_widget

np_workflows/experiments/task_trained_network/camstim_scripts/make_tt_stims.py

@@ -1,23 +1,33 @@
 import pathlib
 
-out_path = pathlib.Path(__file__).parent / 'stims'
-movie_path = 'C:\\ProgramData\\StimulusFiles\\dev\\'
+out_path = pathlib.Path(__file__).parent / "stims"
+movie_path = "C:\\ProgramData\\StimulusFiles\\dev\\"
 
 paths = {
-    'old_stim.stim': movie_path+'old_movie\\ds_unwarped_15_test_movie_one.npy',
-    'shuffle_reversed.stim': movie_path+'new_movies\\ds_unwarped_15_reverse.npy',
-    'shuffle_reversed_1st.stim': movie_path+'new_movies\\ds_unwarped_15_reverse_first_half.npy',
-    'shuffle_reversed_2nd.stim': movie_path+'new_movies\\ds_unwarped_15_reverse_second_half.npy',
+    "old_stim.stim": movie_path + "old_movie\\ds_unwarped_15_test_movie_one.npy",
+    "shuffle_reversed.stim": movie_path + "new_movies\\ds_unwarped_15_reverse.npy",
+    "shuffle_reversed_1st.stim": movie_path
+    + "new_movies\\ds_unwarped_15_reverse_first_half.npy",
+    "shuffle_reversed_2nd.stim": movie_path
+    + "new_movies\\ds_unwarped_15_reverse_second_half.npy",
 }
-paths.update({'densely_annotated_%02d.stim'%i: movie_path+'tt_stim_dense\\ds_unwarped_15_clip_%02d.npy'%i for i in range(19)})
+paths.update(
+    {
+        "densely_annotated_%02d.stim" % i: movie_path
+        + "tt_stim_dense\\ds_unwarped_15_clip_%02d.npy" % i
+        for i in range(19)
+    }
+)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     out_path.mkdir(exist_ok=True, parents=True)
     for file, path in paths.items():
-        with open(out_path / file, 'w') as f:
-            f.write('import os, shutil\n')
-            f.write('import numpy as np\n')
-            f.write('from camstim.misc import ImageStimNumpyuByte, checkDirs\n')
-            f.write('moviesource = '+"r'"+path+"'"+'\n')
-            f.write('stimulus = MovieStim(movie_path=moviesource,window=window,frame_length=2.0/60.0,size=(1920, 1200),start_time=0.0,stop_time=None,flip_v=True,runs=10,)')
+        with open(out_path / file, "w") as f:
+            f.write("import os, shutil\n")
+            f.write("import numpy as np\n")
+            f.write("from camstim.misc import ImageStimNumpyuByte, checkDirs\n")
+            f.write("moviesource = " + "r'" + path + "'" + "\n")
+            f.write(
+                "stimulus = MovieStim(movie_path=moviesource,window=window,frame_length=2.0/60.0,size=(1920, 1200),start_time=0.0,stop_time=None,flip_v=True,runs=10,)"
+            )

np_workflows/experiments/task_trained_network/camstim_scripts/oct22_tt_stim_script.py

@@ -1,68 +1,81 @@
 """
 Oct'22 task-trained ephys stimuli
 """
-#from psychopy import visual
-from camstim import Stimulus, SweepStim
-from camstim import Foraging
-from camstim import Window, Warp
-import numpy as np
+
+# from psychopy import visual
+from camstim import Foraging, Stimulus, SweepStim, Warp, Window
 
 # Create display window
-window = Window(fullscr=True,
-                monitor='GammaCorrect30', #MUST CONFIRM
-                screen=0,
-                warp=Warp.Disabled
-                )
+window = Window(
+    fullscr=True, monitor="GammaCorrect30", screen=0, warp=Warp.Disabled  # MUST CONFIRM
+)
 
-movie_path = 'C:\\Users\\svc_flex4\\tt_testing\\'
+movie_path = "C:\\Users\\svc_flex4\\tt_testing\\"
 
 session = 1
 segment_secs = (
-    [('old_stim.stim', 40)]*25 +
-    [('shuffle_reversed.stim', 40), ('shuffle_reversed_1st.stim', 40), ('shuffle_reversed_2nd.stim', 40),]*8 +
-    [('densely_annotated_%02d.stim'%i, 60) for i in range(19)] * 2 +
-    [('old_stim.stim', 40)]*25 +
-    [('shuffle_reversed.stim', 40), ('shuffle_reversed_1st.stim', 40), ('shuffle_reversed_2nd.stim', 40),]*8
+    [("old_stim.stim", 40)] * 25
+    + [
+        ("shuffle_reversed.stim", 40),
+        ("shuffle_reversed_1st.stim", 40),
+        ("shuffle_reversed_2nd.stim", 40),
+    ]
+    * 8
+    + [("densely_annotated_%02d.stim" % i, 60) for i in range(19)] * 2
+    + [("old_stim.stim", 40)] * 25
+    + [
+        ("shuffle_reversed.stim", 40),
+        ("shuffle_reversed_1st.stim", 40),
+        ("shuffle_reversed_2nd.stim", 40),
+    ]
+    * 8
 )  # 6200 seconds = 103 minutes, 20 secs
-       
+
 num_segments = len(segment_secs)
 
-#build the stimulus array
+# build the stimulus array
 frames_per_sec = 30.0
 stim = []
 total_movie_sec = 0
 
 for file, length in segment_secs:
-    segment = Stimulus.from_file(movie_path+file, window)
-    segment_ds = [(total_movie_sec,total_movie_sec+length)]
+    segment = Stimulus.from_file(movie_path + file, window)
+    segment_ds = [(total_movie_sec, total_movie_sec + length)]
     segment.set_display_sequence(segment_ds)
-    
+
     total_movie_sec += length
-    
+
     stim.append(segment)
-    
-params = {'syncsqr': True,
-          'syncsqrloc': (875,550),
-          'syncsqrsize': (150,150),
-          'syncpulse': True,
-          'syncpulseport': 1,
-          'syncpulselines': [5, 6],  # frame, start/stop
-          'trigger_delay_sec': 5.0}
+
+params = {
+    "syncsqr": True,
+    "syncsqrloc": (875, 550),
+    "syncsqrsize": (150, 150),
+    "syncpulse": True,
+    "syncpulseport": 1,
+    "syncpulselines": [5, 6],  # frame, start/stop
+    "trigger_delay_sec": 5.0,
+}
 
 # create SweepStim instance
-ss = SweepStim(window,
-               stimuli=stim,
-               pre_blank_sec=2,
-               post_blank_sec=2,
-               params=params,
-               )
+ss = SweepStim(
+    window,
+    stimuli=stim,
+    pre_blank_sec=2,
+    post_blank_sec=2,
+    params=params,
+)
 
 # add in foraging so we can track wheel, potentially give rewards, etc
-f = Foraging(window=window,
-             auto_update=False,
-             params=params,
-             nidaq_tasks={'digital_input': ss.di,
-                          'digital_output': ss.do,})  #share di and do with SS
+f = Foraging(
+    window=window,
+    auto_update=False,
+    params=params,
+    nidaq_tasks={
+        "digital_input": ss.di,
+        "digital_output": ss.do,
+    },
+)  # share di and do with SS
 ss.add_item(f, "foraging")
 
 # run it

np_workflows/experiments/task_trained_network/camstim_scripts/ttn_main_script.py

@@ -4,18 +4,9 @@ Oct'22 task-trained ephys stimuli
 
 import argparse
 import json
-import logging
-import os
-import time
-
-import numpy as np
-from psychopy import visual
-from camstim import Foraging
-from camstim import Stimulus_v2
-from camstim import SweepStim_v2, MovieStim
-from camstim import Warp, Window
-from camstim.misc import wecanpicklethat
 
+from camstim import Foraging, MovieStim, Stimulus_v2, SweepStim_v2, Warp, Window
+from camstim.misc import wecanpicklethat
 
 # get params ------------------------------------------------------------------
 # stored in json file -
@@ -30,7 +21,7 @@ parser.add_argument(
 )
 args, _ = parser.parse_known_args()
 
-with open(args.params_path, "r") as f:
+with open(args.params_path) as f:
     json_params = json.load(f)
 
 # Create display window
@@ -45,6 +36,7 @@ window = Window(
 # monkey-patch MovieStim to serialize without large redundant arrays
 # ----------------------------------------------------------------------------
 
+
 def package(self):
     """
     Package for serializing - minus large arrays of frame timing/order.
@@ -53,12 +45,13 @@ def package(self):
         self.sweep_table = None
         self.sweep_params = self.sweep_params.keys()
     self_dict = self.__dict__
-    del self_dict['sweep_frames']
-    del self_dict['sweep_order']
-    del self_dict['frame_list']
-    self_dict['stim'] = str(self_dict['stim'])
+    del self_dict["sweep_frames"]
+    del self_dict["sweep_order"]
+    del self_dict["frame_list"]
+    self_dict["stim"] = str(self_dict["stim"])
     return wecanpicklethat(self_dict)
 
+
 MovieStim.package = package
 
 # setup main stim
@@ -80,7 +73,8 @@ segment_stim_secs = (
         ("shuffle_reversed.stim", reversed_sec),
         ("shuffle_reversed_1st.stim", reversed_sec),
         ("shuffle_reversed_2nd.stim", reversed_sec),
-    ] * reversed_repeats
+    ]
+    * reversed_repeats
     + [("densely_annotated_%02d.stim" % i, annotated_sec) for i in range(19)]
     * annotated_repeats
     + [("old_stim.stim", old_sec)] * old_repeats
@@ -88,15 +82,18 @@ segment_stim_secs = (
         ("shuffle_reversed.stim", reversed_sec),
         ("shuffle_reversed_1st.stim", reversed_sec),
         ("shuffle_reversed_2nd.stim", reversed_sec),
-    ] * reversed_repeats
+    ]
+    * reversed_repeats
 )
 
 # setup stim list and timing
-cumulative_duration_sec = (
-    main_sequence_start_sec
-) = 0  # if stims are daisy-chained within one script, this should be the end of the prev stim
+cumulative_duration_sec = main_sequence_start_sec = (
+    0  # if stims are daisy-chained within one script, this should be the end of the prev stim
+)
 for stim_file, duration_sec in segment_stim_secs:
-    segment = Stimulus_v2.from_file(stim_file, window) # stim file actually instantiates MovieStim
+    segment = Stimulus_v2.from_file(
+        stim_file, window
+    )  # stim file actually instantiates MovieStim
     segment_ds = [(cumulative_duration_sec, cumulative_duration_sec + duration_sec)]
     segment.set_display_sequence(segment_ds)
 

np_workflows/experiments/task_trained_network/camstim_scripts/ttn_mapping_script.py

@@ -5,16 +5,8 @@ Oct'22 task-trained ephys stimuli
 import argparse
 import json
 import logging
-import os
-import time
-
-import numpy as np
-from psychopy import visual
-from camstim import Foraging
-from camstim import Stimulus_v2
-from camstim import SweepStim_v2
-from camstim import Warp, Window
 
+from camstim import Foraging, Stimulus_v2, SweepStim_v2, Warp, Window
 
 # get params ------------------------------------------------------------------
 # stored in json file -
@@ -29,7 +21,7 @@ parser.add_argument(
 )
 args, _ = parser.parse_known_args()
 
-with open(args.params_path, "r") as f:
+with open(args.params_path) as f:
     json_params = json.load(f)
 
 # Create display window
@@ -41,6 +33,7 @@ window = Window(
     warp=Warp.Spherical,
 )
 
+
 # patch the Stimulus_v2 class to allow for serializing without large arrays
 # ----------------------------------------------------------------------------
 class Stimulus_v2_MinusFrameArrays(Stimulus_v2):
@@ -56,11 +49,12 @@ class Stimulus_v2_MinusFrameArrays(Stimulus_v2):
             self.sweep_table = None
             self.sweep_params = self.sweep_params.keys()
         self_dict = self.__dict__
-        del self_dict['sweep_frames']
-        del self_dict['sweep_order']
-        self_dict['stim'] = str(self_dict['stim'])
+        del self_dict["sweep_frames"]
+        del self_dict["sweep_order"]
+        self_dict["stim"] = str(self_dict["stim"])
         return wecanpicklethat(self_dict)
-    
+
+
 # ----------------------------------------------------------------------------
 # setup mapping stim
 """from mapping_script_v2.py"""