lumicks.pylake.scan.Scan¶
- class Scan(name, file, start, stop, metadata)¶
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.
- metadataScanMetaData
Metadata.
- __init__(name, file, start, stop, metadata)¶
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)_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
_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
pixel_time_seconds
Pixel dwell time in seconds
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