pyfibre.addons.shg_pl_trans.shg_reader module

class pyfibre.addons.shg_pl_trans.shg_reader.SHGReader(*args, **kwargs)

Bases: pyfibre.core.base_multi_image_reader.BaseMultiImageReader

Reader class for a combined SHG file

can_load(filename)

Perform check to see whether file is formatted correctly to be loaded

get_filenames(file_set)

From a collection of files in a FileSet, yield each file that should be used

get_multi_image_class()

Returns class of IMultiImage that will be loaded.

get_supported_file_sets()

Returns class of IFileSets that will be supported.

load_image(filename)

Load a single image from a file

pyfibre.addons.shg_pl_trans.shg_reader.get_accumulation_number(file_name)

Extrct accumulation from file name if present. Return default value of 1 if not present.

Parameters

file_name (str) – File name of Tiff image

Returns

acc_number – Accumulation number for image

Return type

int

Notes

Expects the following file formatting:

<prefix>-acc<number>.ext

pyfibre.addons.shg_pl_trans.shg_reader.get_fluoview_param(description, xy_dim, shape)

pyfibre.addons.shg_pl_trans.shg_reader.get_imagej_param(description, xy_dim, shape)

pyfibre.addons.shg_pl_trans.shg_reader.get_tiff_param(tiff_file)

Obtain relevant parameters of TiffFile object

pyfibre.addons.shg_pl_trans.shg_reader.lookup_page(tiff_page)

Obtain relevant information from a TiffPage object