np-workflows 1.6.89__py3-none-any.whl

np_workflows/shared/camstim_scripts/flash_250ms.stim

@@ -0,0 +1,20 @@
+stimulus = Stimulus(visual.GratingStim(window,
+    pos = (0, 0),
+    units = 'deg',
+    size = (300, 300),
+    mask = "None",
+    texRes = 256,
+    sf = 0,
+),
+    sweep_params = {
+        'Contrast': ([0.8], 0),
+        'Color': ([-1, 1], 1)
+    },
+    sweep_length = 0.25,
+    start_time = 0.0,
+    blank_length = 1.75,
+    blank_sweeps = 0,
+    runs = 75,
+    shuffle = True,
+    save_sweep_table = True,
+)

np_workflows/shared/camstim_scripts/gabor_20_deg_250ms.stim

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+x = np.arange(-40,45,10)
+y = np.arange(-40,45,10)
+position = []
+for i in x:
+    for j in y:
+        position.append([i,j])
+
+
+stimulus = Stimulus(visual.GratingStim(window,
+                    units='deg',
+                    size=20,
+                    mask="circle",
+                    texRes=256,
+                    sf=0.1,
+                    ),
+    sweep_params={
+               'Pos':(position, 0),
+               'Contrast': ([0.8], 4),
+               'TF': ([4.0], 1),
+               'SF': ([0.08], 2),
+               'Ori': ([0,45,90], 3),
+               },
+    sweep_length=0.25,
+    start_time=0.0,
+    blank_length=0.0,
+    blank_sweeps=0,
+    runs=15,
+    shuffle=True,
+    save_sweep_table=True,
+    )

np_workflows/shared/npxc.py

@@ -0,0 +1,187 @@
+import contextlib
+import datetime
+import inspect
+import pathlib
+import shutil
+import sys
+import time
+from typing import Any, Generator, Sequence, Type
+import zlib
+
+import fabric
+import np_config
+import np_logging
+import np_session
+from np_services import Initializable, Testable, TestError, Finalizable, Service
+from np_services import Sync, VideoMVR, ImageMVR, Cam3d, ScriptCamstim, OpenEphys  
+import np_services 
+from np_config import Rig
+
+logger = np_logging.getLogger(__name__)
+
+# Assign default values to global variables so they can be imported elsewhere
+# experiment: Experiment | str = ''
+operator: np_session.User | str = ""
+mouse: np_session.Mouse | str = ""
+is_mouse_in_lims: bool | None = None
+session: np_session.Session | str | int = ""
+
+# experiments: tuple[Type[Experiment], ...] = (
+#     classes.Pretest,
+#     classes.NpUltra,
+#     ) # TODO plug-in experiments
+
+RIG = np_config.Rig()
+CONFIG = RIG.config
+
+lims_user_ids: tuple[str, ...] = tuple(
+    sorted(
+        CONFIG.get('lims_user_ids',
+            [
+            "hannah.belski",
+            "hannah.cabasco",
+            "ryan.gillis",
+            "henry.loeffler",
+            "corbettb",
+            "ben.hardcastle",
+            "samg",
+            "ethan.mcbride",
+            "jackie.kuyat",
+            "andrew.shelton",
+            ]
+        )
+    )
+)
+
+default_mouse_id: int = int(CONFIG.get('default_mouse_id', 366122))
+
+
+def get_operators() -> list[str]:
+    return list(lims_user_ids)
+
+
+def print_countdown_timer(seconds: int | float | datetime.timedelta = 0, **kwargs):
+    """Block execution for a given number of seconds (or any timedelta kwargs), printing a countdown timer to the console."""
+    if isinstance(seconds, datetime.timedelta):
+        wait = seconds
+    else:
+        wait = datetime.timedelta(seconds=seconds, **kwargs)
+    time_0: float = time.time()
+    time_remaining = lambda: datetime.timedelta(
+        seconds=wait.total_seconds() - (time.time() - time_0)
+    )
+    while time_remaining().total_seconds() > 0:
+        print(f"Waiting {wait} \t{time_remaining()}", end="\r", flush=True)
+        time.sleep(0.1)
+
+def photodoc(img_name: str) -> pathlib.Path:
+    """Capture image with `label` appended to filename, and return the filepath.
+            
+    If multiple images are captured, only the last will remain in the Imager.data_files list.
+    """
+    if RIG.idx == 0:
+        from np_services import Cam3d as ImageCamera
+    else:
+        from np_services import ImageMVR as ImageCamera
+    from np_services import NewScaleCoordinateRecorder
+    
+    ImageCamera.label = img_name
+    if isinstance(ImageCamera, Initializable) and not getattr(ImageCamera, 'initialization', None):
+        ImageCamera.initialize()
+        
+    ImageCamera.start()
+    
+    if isinstance(ImageCamera, Finalizable):
+        ImageCamera.finalize()
+        
+    if isinstance(NewScaleCoordinateRecorder, Initializable) and not getattr(NewScaleCoordinateRecorder, 'initialization', None):
+        NewScaleCoordinateRecorder.initialize()
+    NewScaleCoordinateRecorder.label = img_name
+    NewScaleCoordinateRecorder.start()
+    
+    # remove all but latest file with the current label
+    if img_name and ImageCamera.data_files:
+        views = 2 if ImageCamera.__name__ == 'Cam3d' else 1
+        def files_with_label():
+            return sorted([_ for _ in ImageCamera.data_files if img_name in _.name])
+        while len(files_with_label()) > views:
+            ImageCamera.data_files.remove(files_with_label()[0])
+            
+    return ImageCamera.data_files[-1]
+
+def copy_files(services: Sequence[Service], session_folder: pathlib.Path):
+    """Copy files from raw data storage to session folder for all services."""
+    password = input(f'Enter password for svc_neuropix:')
+    for service in services:
+        match service.__class__.__name__:
+            case "OpenEphys" | "open_ephys":
+                continue # copy ephys after other files
+            case _:
+                with contextlib.suppress(AttributeError):
+                    files = service.data_files or service.get_latest_data('*')
+                    if not files:
+                        continue
+                    files = set(files)
+                    print(files)
+                    for file in files:
+                        shutil.copy2(file, session_folder)
+    
+    password = np_config.fetch('/logins')['svc_neuropix']['password']
+    ssh = fabric.Connection(host=np_services.OpenEphys.host, user='svc_neuropix', connect_kwargs=dict(password=password))
+    for ephys_folder in np_services.OpenEphys.data_files:
+
+        with contextlib.suppress(Exception):
+            with ssh:
+                ssh.run(
+                f'robocopy "{ephys_folder}" "{session_folder / ephys_folder.name}" /j /s /xo' 
+                # /j unbuffered, /s incl non-empty subdirs, /xo exclude src files older than dest
+                )
+            
+            
+import warnings
+
+def hide_warning_lines(msg:str,category:str,*args,**kwargs):
+    print("\n{}: {}\n".format(category.__name__, msg))
+warnings.showwarning = hide_warning_lines
+
+import IPython
+def toggle_tracebacks() -> Generator[None, None, None]:
+    if ipython := IPython.get_ipython():
+        show_traceback = ipython.showtraceback
+        
+        def hide_traceback(exc_tuple=None, filename=None, tb_offset=None,
+                        exception_only=False, running_compiled_code=False):
+            etype, value, tb = sys.exc_info()
+            return ipython._showtraceback(etype, value, ipython.InteractiveTB.get_exception_only(etype, value))
+        
+        hidden = True
+        while True:
+            ipython.showtraceback = hide_traceback if hidden else show_traceback
+            hidden = yield
+    else:
+        raise RuntimeError("Not in IPython")
+    
+with contextlib.suppress(RuntimeError):
+    toggle_tb = toggle_tracebacks()
+
+    toggle_tb.send(None)
+    def show_tracebacks():
+        toggle_tb.send(False)
+    def hide_tracebacks():
+        toggle_tb.send(True)
+        
+def now() -> str:
+    return np_services.utils.normalize_time(time.time())
+
+def validate_or_overwrite(validate: str | pathlib.Path, src: str | pathlib.Path):
+    "Checksum validate against `src`, (over)write `validate` as `src` if different."
+    validate, src = pathlib.Path(validate), pathlib.Path(src)
+    def copy():
+        logger.debug("Copying %s to %s", src, validate)
+        shutil.copy2(src, validate)
+    while (
+        validate.exists() == False
+        or (v := zlib.crc32(validate.read_bytes())) != (c := zlib.crc32(pathlib.Path(src).read_bytes()))
+        ):
+        copy()
+    logger.debug("Validated %s CRC32: %08X", validate, (v & 0xFFFFFFFF) )