`utils_videos`

Helpers for videos

play_video

 play_video (video, figsize=(5, 5), fps=10)

Displays a stack of images as a video inside jupyter notebooks.

	Type	Default	Details
video	ndarray		Stack of images.
figsize	tuple	(5, 5)	Canvas size of the video.
fps	int	10	Video frame rate.
Returns	Video object		Returns a video player with input stack of images.

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convert_uint8

 convert_uint8 (vid, with_vips=False)

Converts a stack of images in to 8bit pixel format.

This is a helper function for transform_to_video

	Type	Default	Details
vid	ndarray		Stack of images.
with_vips	bool	False
Returns	ndarray		Image stack in 8bit.

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psf_width

 psf_width (NA=1.46, wavelength=5e-07, resolution=1e-07)

Computes the PSF full width at half maximum (FWHM).

This is a helper function for transform_to_video

	Type	Default	Details
NA	float	1.46	Numerical aperture.
wavelength	float	5e-07	Wavelength.
resolution	float	1e-07	Resolution of the camera.
Returns	int		PSF width in pixels.

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func_poisson_noise

 func_poisson_noise ()

Applies poisson noise to an image.

This is a custom DeepTrack feature, and a helper function for transform_to_video

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mask

 mask (circle_radius, particle_list=[])

Computes binary masks for particles in microscopy videos.

This is a custom DeepTrack feature, and a helper function for transform_to_video.

`transform_to_video`

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transform_to_video

 transform_to_video (trajectory_data, particle_props={}, optics_props={},
                     background_props={}, get_vip_particles=[],
                     with_masks=False, save_video=False, path='',
                     motion_blur_generator=None)

Transforms trajectory data into microscopy imagery data.

Trajectories generated through phenomenological models in andi-datasets are imaged under a Fluorescence microscope to generate 2D timelapse videos.

	Type	Default	Details
trajectory_data	ndarray		Generated through models_phenom. Array of the shape (T, N, 2) containing the trajectories.
particle_props	dict	{}	Dictionary containing the properties of particles to be simulated as keyword arguments. Valid keys are: ‘`particle_intensity`’ : array_like[int, int] Intensity distribution of particles within a frame given as mean and standard deviations. ‘`intensity_variation`’ : int Intensity variation of particles in subsequent frames given as standard deviation. ‘`z`’ : float Particle positions with respect to the focal plane in pixel units defined by the pixel size in optics_props. For example, particles will be at focus when `z=0`. ‘`refractive_index`’ : float Refractive index of particle.
optics_props	dict	{}	Dictionary containing the properties of microscope as keyword arguments. Valid keys are: ‘`NA`’: float Numerical aperture of the microscope. ‘`wavelength`’ : float Wavelength of light in meters. ‘`resolution`’ : float Effective pixel size of the camera in meters. ‘`magnification`’ : float Magnification of the optical system. ‘`refractive_index_medium`’ : float Refractive index of the medium sorrounding the particles. ‘`output_region`’: array_like[int, int, int, int] ROI of the image to output. Given in the format : [x, y, x + width, y + height].
background_props	dict	{}	Dictionary containing properties related to background intensity as keyword arguments. Valid keys are: ‘`background_mean`’ : int Mean background intensity. ‘`backgound_std`’ : int Standard deviation of the background intesity with subsequent frames of a video.
get_vip_particles	list	[]	List of particles for which the masks are needed in the output.
with_masks	bool	False	If True, particle masks are returned in the output along with the video. If False (default), only the video is returned in the output.
save_video	bool	False	If True, the generated video will be saved at the given path.
path	str		File path for saving the video, the path should be given along the video format. For example: ‘path’ = ‘./video.mp4’ will save the video in the current folder.
motion_blur_generator	NoneType	None
Returns	tuple \| ndarray		Output type I If `with_masks = True`, The function returns a tuple containing: masks : ndarray video : ndarray Note: If `get_vip_particles` is a non-empty list, the masks will contain only the vip particle masks. Output type II If `with_masks = False`, The function returns: video : ndarray Note: If `get_vip_particles` is a non-empty list, the first frame in the output will be the masks of the given vip particles in the first frame, else (default) the output will be a ndarray of just the video.

Usage example

Please check tutorials for more detailed examples

Import packages

from andi_datasets.models_phenom import models_phenom

Generating trajectories and passing them through transform_to_video to generate videos

trajs_test, _ = models_phenom().single_state(N = 50, T = 100, L = 128, Ds = 1)
video, masks = transform_to_video(trajs_test,
                                  with_masks=True,
                                  get_vip_particles=np.arange(55).tolist(),
                                  particle_props = {"z": 0},
                                  background_props = {"background_mean": 0,
                                                      "background_std": 0}, 
                                 optics_props = {'origin': [0,0,20,20]})

Play generated video in jupyter notebook

play_video(video)

Plot the first frames of the video and the masks

fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(10, 5))
img2 = ax1.imshow(video[1], cmap="gray")
ax1.set_title("Frame 0")
ax2.imshow(masks[1], cmap="gray")
ax2.set_title("Mask 0")

Text(0.5, 1.0, 'Mask 0')

Overlay trajectories on the first frame of the video

plt.figure(figsize=(5, 5))
plt.imshow(video[0], cmap="gray", zorder = -1)
for traj in np.moveaxis(trajs_test, 0, 1):
    plt.plot(traj[:,1], traj[:,0], alpha=0.2)
plt.xlim(0,L); plt.ylim(0,L)
plt.show()

Import TIFF video

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import_tiff_video

 import_tiff_video (tiff_file_path:str)

Import a TIFF video file as a NumPy array.

This function reads a multi-frame TIFF file and converts each frame into a NumPy array. All frames are stacked along a new axis, resulting in a 3D array if the frames are 2D (or a 4D array if the frames are 3D).

	Type	Details
tiff_file_path	str	File path of the TIFF video file.
Returns	ndarray	A NumPy array containing the video frames stacked along a new axis. The shape of the array is (N, M, O, …) where N is the number of frames, and M, O, … are the dimensions of each frame.