lumicks.pylake.scan.Scan

class Scan(name, file, start, stop, json)

A confocal scan exported from Bluelake

Parameters

namestr

Scan name

filelumicks.pylake.File

Parent file. Contains the channel data.

startint

Start point in the relevant info wave.

stopint

End point in the relevant info wave.

jsondict

Dictionary containing scan-specific metadata.

__init__(name, file, start, stop, json)

Methods

__getitem__(item)	All indexing is in frames
_export_video(plot_type, file_name, ...[, ...])	Export a video of a particular scan plot
_fix_incorrect_start()	Resolve error when confocal scan starts before the timeline information.
_get_laser_power(name)
_get_photon_count(name)	Grab the portion of the photon count that overlaps with the scan.
_get_plot_data(channel[, adjustment, frame])	Get image data for plotting requested channel.
_has_default_factories()
_image(channel)
_ordered_axes()	Returns axis indices in spatial order
_plot(channel, axes[, frame, image_handle, ...])	Plot a scan frame for requested color channel(s).
_timestamps(channel[, reduce])
_to_spatial(data)	If the first axis of the reconstruction has a higher physical axis number than the second, we flip the axes.
export_video_blue(file_name[, start_frame, ...])	Export multi-frame scan as video.
export_video_green(file_name[, start_frame, ...])	Export multi-frame scan as video.
export_video_red(file_name[, start_frame, ...])	Export multi-frame scan as video.
export_video_rgb(file_name[, start_frame, ...])	Export multi-frame scan as video.
frame_timestamp_ranges([exclude])	Get start and stop timestamp of each frame in the scan.
from_dataset(h5py_dset, file)	Construct a confocal class from dataset.
get_image([channel])	Get image data for the full stack as an np.ndarray.
plot(channel[, axes])	Show a formatted plot for the requested color channel.
plot_blue(**kwargs)	Plot an image of the blue photon channel
plot_correlated(channel_slice[, frame, ...])	Downsample channel on a frame by frame basis and plot the results.
plot_green(**kwargs)	Plot an image of the green photon channel
plot_red(**kwargs)	Plot an image of the red photon channel
plot_rgb(**kwargs)	Plot an image of all color channels.
save_tiff(filename[, dtype, clip])	Save the RGB photon counts to a TIFF image

Attributes

_num_pixels
_scan_order	Order in which the axes are scanned.
_shape	The shape of the image ([optional: pixels on slow axis], pixels on fast axis)
blue_image	Deprecated since version 0.12.0.
blue_photon_count
blue_power
center_point_um	Returns a dictionary of the x/y/z center coordinates of the scan (w.r.t.
fast_axis
green_image	Deprecated since version 0.12.0.
green_photon_count
green_power
infowave
lines_per_frame
num_frames
pixels_per_line
pixelsize_um	Returns a List of axes dimensions in um.
red_image	Deprecated since version 0.12.0.
red_photon_count
red_power
rgb_image	Deprecated since version 0.12.0.
size_um	Returns a List of scan sizes in um along axes.
sted_power
timestamps	Timestamps for image pixels, not for samples