lumicks.pylake.kymo.Kymo¶

class Kymo(h5py_dset, file)¶

A Kymograph exported from Bluelake

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

__init__(h5py_dset, file)¶: Initialize self. See help(type(self)) for accurate signature.

Methods

`__init__`(h5py_dset, file)	Initialize self.
`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 a full rbg kymograph image
`save_tiff`(filename[, dtype, clip])	Save the RGB photon counts to a TIFF image

Attributes

`blue_image`
`blue_photon_count`
`green_image`
`green_photon_count`
`has_fluorescence`
`has_force`
`infowave`
`pixels_per_line`
`red_image`
`red_photon_count`
`rgb_image`
`timestamps`	Timestamps for image pixels, not for samples

plot_blue(**kwargs)¶

Plot an image of the blue photon channel

Parameters:	**kwargs Forwarded to `~matplotlib.pyplot.imshow`.

plot_green(**kwargs)¶

Plot an image of the green photon channel

Parameters:	**kwargs Forwarded to `~matplotlib.pyplot.imshow`.

plot_red(**kwargs)¶

Plot an image of the red photon channel

Parameters:	**kwargs Forwarded to `~matplotlib.pyplot.imshow`.

plot_rgb(**kwargs)¶

Plot a full rbg kymograph image

Parameters:	**kwargs Forwarded to `~matplotlib.pyplot.imshow`.

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.

timestamps¶

Timestamps for image pixels, not for samples

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