lumicks.pylake.point_scan.PointScan¶

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

A confocal point scan exported from Bluelake

Parameters:	name : str point 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.
`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_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.

Attributes

`blue_photon_count`
`blue_power`
`center_point_um`	Returns a dictionary of the x/y/z center coordinates of the scan (w.r.t.
`green_photon_count`
`green_power`
`has_fluorescence`	Deprecated since version 0.8.0.
`has_force`	Deprecated since version 0.8.0.
`json`	Deprecated since version 0.8.0.
`red_photon_count`
`red_power`
`sted_power`

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_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.

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)