lumicks.pylake.scan.Scan

class Scan(h5py_dset, file)

A confocal scan 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
lines_per_frame
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.