lumicks.pylake.scan.Scan¶

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

A confocal scan exported from Bluelake

Parameters:	name : str Scan name file : lumicks.pylake.File Parent file. Contains the channel data. start : int Start point in the relevant info wave. stop : int End point in the relevant info wave. json : dict Dictionary containing scan-specific metadata.

__init__(name, file, start, stop, json)¶: Initialize self. See help(type(self)) for accurate signature.

Methods

`__init__`(name, file, start, stop, json)	Initialize self.
`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.
`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

`blue_image`
`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`
`green_photon_count`
`green_power`
`has_fluorescence`	Deprecated since version 0.8.0.
`has_force`	Deprecated since version 0.8.0.
`infowave`
`json`	Deprecated since version 0.8.0.
`lines_per_frame`
`num_frames`
`pixels_per_line`
`pixelsize_um`	Returns a `List` of axes dimensions in um.
`red_image`
`red_photon_count`
`red_power`
`rgb_image`
`scan_width_um`	Returns a `List` of scan widths as configured in the Bluelake UI. The length of the list
`size_um`	Returns a `List` of scan sizes in um along axes.
`sted_power`
`timestamps`	Timestamps for image pixels, not for samples

__getitem__(item)¶: All indexing is in frames

export_video_blue(file_name, start_frame=None, end_frame=None, fps=15, **kwargs)¶

Export multi-frame scan as video.

Parameters:	file_name : str File name to export to. start_frame : int Initial frame. end_frame : int Last frame. fps : int Frames per second. **kwargs Forwarded to `matplotlib.pyplot.imshow()`.

export_video_green(file_name, start_frame=None, end_frame=None, fps=15, **kwargs)¶

Export multi-frame scan as video.

Parameters:	file_name : str File name to export to. start_frame : int Initial frame. end_frame : int Last frame. fps : int Frames per second. **kwargs Forwarded to `matplotlib.pyplot.imshow()`.

export_video_red(file_name, start_frame=None, end_frame=None, fps=15, **kwargs)¶

Export multi-frame scan as video.

Parameters:	file_name : str File name to export to. start_frame : int Initial frame. end_frame : int Last frame. fps : int Frames per second. **kwargs Forwarded to `matplotlib.pyplot.imshow()`.

export_video_rgb(file_name, start_frame=None, end_frame=None, fps=15, **kwargs)¶

Export multi-frame scan as video.

Parameters:	file_name : str File name to export to. start_frame : int Initial frame. end_frame : int Last frame. fps : int Frames per second. **kwargs Forwarded to `matplotlib.pyplot.imshow()`.

frame_timestamp_ranges(exclude=True)¶

Get start and stop timestamp of each frame in the scan.

Parameters:	exclude : bool Exclude dead time at the end of each frame.

classmethod from_dataset(h5py_dset, file)¶

Construct a confocal class from dataset.

Parameters:	h5py_dset : h5py.Dataset The original HDF5 dataset containing confocal scan information file : lumicks.pylake.File The parent file. Used to loop up channel data

plot(channel, axes=None, **kwargs)¶

Show a formatted plot for the requested color channel.

Parameters:	channel : {‘red’, ‘green’, ‘blue’, ‘rgb’} Color channel to plot. axes : mpl.axes.Axes or None If supplied, the axes instance in which to plot. **kwargs Forwarded to `matplotlib.pyplot.plot()` or `matplotlib.pyplot.imshow()`

plot_blue(**kwargs)¶

Plot an image of the blue photon channel

Parameters:	kwargs Forwarded to `matplotlib.pyplot.imshow()`. .. deprecated:: 0.11.1** `plot_blue()` is deprecated. Use `plot(channel=’blue’) instead.

plot_correlated(channel_slice, frame=0, reduce=<function mean>, channel='rgb', figure_scale=0.75)¶

Downsample channel on a frame by frame basis and plot the results. The downsampling function (e.g. np.mean) is evaluated for the time between a start and end time of a frame. Note: In environments which support interactive figures (e.g. jupyter notebook with ipywidgets or interactive python) this plot will be interactive.

Parameters:

channel_slice : pylake.channel.Slice: Data slice that we with to downsample.
frame : int: Frame to show.
reduce : callable: The function which is going to reduce multiple samples into one. The default is numpy.mean(), but numpy.sum() could also be appropriate for some cases e.g. photon counts.
channel : ‘rgb’, ‘red’, ‘green’, ‘blue’, None; optional: Channel to plot for RGB images (None defaults to ‘rgb’) Not used for grayscale images
figure_scale : float: Scaling of the figure width and height. Values greater than one increase the size of the figure.

Examples

from lumicks import pylake

file = pylake.File("example.h5")
scan = file.scans["my scan"]
scan.plot_correlated(file.force1x, channel="red")

plot_green(**kwargs)¶

Plot an image of the green photon channel

Parameters:	kwargs Forwarded to `matplotlib.pyplot.imshow()`. .. deprecated:: 0.11.1** `plot_green()` is deprecated. Use `plot(channel=’green’) instead.

plot_red(**kwargs)¶

Plot an image of the red photon channel

Parameters:	kwargs Forwarded to `matplotlib.pyplot.imshow()`. .. deprecated:: 0.11.1** `plot_red()` is deprecated. Use `plot(channel=’red’) instead.

plot_rgb(**kwargs)¶

Plot an image of all color channels.

Parameters:	kwargs Forwarded to `matplotlib.pyplot.imshow()`. .. deprecated:: 0.11.1** `plot_rgb()` is deprecated. Use `plot(channel=’rgb’) instead.

save_tiff(filename, dtype=<class 'numpy.float32'>, clip=False)¶

Save the RGB photon counts to a TIFF image

Parameters:	filename : str The name of the TIFF file where the image will be saved. dtype : np.dtype The data type of a single color channel in the resulting image. clip : bool If enabled, the photon count data will be clipped to fit into the desired `dtype`. This option is disabled by default: an error will be raise if the data does not fit.

center_point_um¶: Returns a dictionary of the x/y/z center coordinates of the scan (w.r.t. brightfield field of view)

has_fluorescence¶: Deprecated since version 0.8.0: By definition, confocal images always have fluorescence data.

has_force¶: Deprecated since version 0.8.0: This property is always False and therefore not needed.

json¶: Deprecated since version 0.8.0: Access to raw metadata will be removed in a future release. Use accessor properties instead. (see docs)

pixelsize_um¶: Returns a List of axes dimensions in um. The length of the list corresponds to the number of scan axes.

scan_width_um¶

Returns a List of scan widths as configured in the Bluelake UI. The length of the list: corresponds to the number of scan axes. Note that these widths can deviate from the actual scan widths performed in practice

Deprecated since version 0.8.2: The property scan_width_um has been deprecated. Use size_um to get the actual size of the scan. When performing a scan, Bluelake determines an appropriate scan width based on the desired pixel size and the desired scan width. This means that the size of the performed scan could deviate from the width provided in this property.

size_um¶: Returns a List of scan sizes in um along axes. The length of the list corresponds to the number of scan axes.

timestamps¶

Timestamps for image pixels, not for samples

The returned array has the same shape as the *_image arrays.