Source code for magscope.utils

from __future__ import annotations

from datetime import datetime
from enum import IntEnum, StrEnum
from typing import TYPE_CHECKING, Callable, Type

import magtrack
import numpy as np
from PyQt6.QtGui import QImage

from magscope.ipc_commands import Command



[docs]
class AcquisitionMode(StrEnum):
    """ Enum for the different acquisition modes """

[docs]
    TRACK = 'track'


[docs]
    TRACK_AND_CROP_VIDEO = 'track & video (cropped)'


[docs]
    TRACK_AND_FULL_VIDEO = 'track & video (full)'


[docs]
    CROP_VIDEO = 'video (cropped)'


[docs]
    FULL_VIDEO = 'video (full)'




[docs]
def crop_stack_to_rois(stack, rois):
    rois = np.asarray(rois, dtype=np.int64)

    # Pre-allocate space for cropped_stack
    n_images = stack.shape[2]
    n_rois = len(rois)
    width = rois[0, 1] - rois[0, 0]
    shape = (width, width, n_images, n_rois)
    cropped_stack = np.ndarray(
        shape, dtype=stack.dtype
    )  # width, width, frames, rois

    # Crop
    for i, roi in enumerate(rois):
        cropped_stack[:, :, :, i] = (
            stack[roi[0]:roi[1], roi[2]:roi[3], :]
        )

    return cropped_stack



[docs]
def numpy_type_to_qt_image_type(numpy_type):
    NP2QT = {
        np.uint8: QImage.Format.Format_Grayscale8,
        np.uint16: QImage.Format.Format_Grayscale16
    }

    if numpy_type not in NP2QT:
        raise ValueError(f"Unsupported bit type: {numpy_type}")
    return NP2QT[numpy_type]



[docs]
def date_timestamp_str(timestamp):
    date_str = datetime.today().strftime('%Y-%m-%d')
    hour = (timestamp // 3600 % 24 - 5) % 24
    minutes = timestamp // 60 % 60
    seconds = timestamp // 1 % 60
    milliseconds = timestamp % 1 * 1000
    return f'{date_str} {hour:02.0f}-{minutes:02.0f}-{seconds:02.0f}.{milliseconds:03.0f}'



[docs]
class PoolVideoFlag(IntEnum):

[docs]
    READY = 0


[docs]
    RUNNING = 1


[docs]
    FINISHED = 2




[docs]
class Units:
    # Meters

[docs]
    m = 1.


[docs]
    cm = 1e-2


[docs]
    mm = 1e-3


[docs]
    um = 1e-6


[docs]
    nm = 1e-9


    # Newtons

[docs]
    N = 1.


[docs]
    mN = 1e-3


[docs]
    uN = 1e-6


[docs]
    nN = 1e-9


[docs]
    pN = 1e-12


[docs]
    fN = 1e-15


    # Seconds
    sec = s = 1.

[docs]
    ms = 1e-3


[docs]
    us = 1e-6


[docs]
    ns = 1e-9


[docs]
    ps = 1e-12


[docs]
    fs = 1e-15


    # Directions
    clockwise = cw = 1.
    counterclockwise = ccw = -1.



[docs]
def register_script_command(command_type: type[Command]):
    """Decorator marking a method as callable from a MagScope script.

    Each script command must be paired with the IPC :class:`~magscope.ipc_commands.Command`
    that will be dispatched when the script executes that step. The decorator mirrors
    :func:`magscope.ipc_commands.command_handler` by attaching metadata to the wrapped
    function without constraining how it is collected.
    """

    def decorator(meth: callable):
        meth._scriptable = True
        meth._script_command_type = command_type
        return meth

    return decorator



[docs]
def check_cupy() -> bool:
    """Return ``True`` when the CuPy package is usable."""
    return magtrack.check_cupy()