paprica.converter

Submodule containing classes and functions relative to converting tiles to APR.

The general workflow is first to parse tiles using a parser object and then convert using the tileConverter class. This class is essentially a wrapper to pyapr which allows to facilitate batch conversions and batch reconstructions.

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© Copyright 2020 Wyss Center for Bio and Neuro Engineering – All rights reserved

class paprica.converter.tileConverter(tiles: paprica.parser.baseParser)[source]

Bases: object

Class to convert tiles to APR or to tiff.

__init__(tiles: paprica.parser.baseParser)[source]

Constructor for the tileConverter class.

Parameters

tiles (baseParser) – parser object referencing tiles to be converted.

batch_convert_to_apr(Ip_th=108, rel_error=0.2, gradient_smoothing=2, dx=1, dy=1, dz=1, path=None, lazy_loading=True, tree_mode='mean', progress_bar=True)[source]

Convert all parsed tiles to APR using auto-parameters.

Parameters

  • Ip_th (int) – Intensity threshold

  • rel_error (float in [0, 1[) – relative error bound

  • gradient_smoothing ((float)) – B-Spline smoothing parameter (typically between 0 (no smoothing) and 10 (LOTS of smoothing)

  • dx (float) – PSF size in x, used to compute the gradient

  • dy (float) – PSF size in y, used to compute the gradient

  • dz (float) – PSF size in z, used to compute the gradient

  • path (str) – path to save the converted APR data (defaut is creating a folder named APR in the raw data directory.

  • lazy_loading (bool) – if lazy_loading is true then the converter save mean tree particle which are necessary for lazy loading of the APR. It will require about 1/7 more storage.

  • tree_mode (str ('mean' or 'max')) – controls how downsampled particles are computed. Either the mean or the max is taken.

Return type

None

batch_reconstruct_pixel(mode='constant', progress_bar=True)[source]

Reconstruct all APR tiles to pixel data.

Parameters

mode (string) – reconstruction mode, can be ‘constant’, ‘smooth’ or ‘level’

Return type

None

deactivate_compression()[source]

Deactivate B3D compression when saving particles.

Return type

None

set_compression(quantization_factor=1, bg=108)[source]

Activate B3D compression for saving tiles.

Parameters

  • quantization_factor (int) – quantization factor: the higher, the more compressed (refer to B3D paper for more detail).

  • bg (int) – background value: any value below this threshold will be set to the background value. This helps save up space by having the same value for the background (refer to B3D paper for more details).

Return type

None