nxtomomill.converter.hdf5.post_processing.dark_flat_copy.ZSeriesDarkFlatCopy

class nxtomomill.converter.hdf5.post_processing.dark_flat_copy.ZSeriesDarkFlatCopy(series, acquisition_to_nxtomo)

Bases: object

z-series version 3 can require to reuse dark-flat from a bliss scan done at the start or at the end of the series.

This class is an helper to do this processing.

__init__(series, acquisition_to_nxtomo)

Parameters:

• series (list[BaseAcquisition]) – list of acquisition part of the series. warning: we expect this list to be ordered.

• acquisition_to_nxtomo (dict[BaseAcquisition, tuple | None]) – for each acquisition in “series” this dict can provide the nxtomo created during conversion. The value is expected to the None if the conversion failed or (file_path, data_path)

Warning

even if list contains BaseAcquisition; those are sub_acquisitions of ZSeriesBaseAcquisition

Methods

__init__(series, acquisition_to_nxtomo)	type series: list[BaseAcquisition]
build_edition_to_do(darks_start_urls, ...)	build all the edition to do to complete the dark and flat copy according to z-series v3 configuration.
build_mapping_to_dark_flat_source()	Build the list of DataUrl that can be used for copy.
process_edition(editions_to_do[, ...])	do edition
run()	rtype: None

Attributes

first_acquisition	rtype: BaseAcquisition
last_acquisition	rtype: BaseAcquisition

build_edition_to_do(darks_start_urls, flats_start_urls, darks_end_urls, flats_end_urls)

build all the edition to do to complete the dark and flat copy according to z-series v3 configuration.

Return type:

dict[tuple, dict]

build_mapping_to_dark_flat_source()

Build the list of DataUrl that can be used for copy.

Output looks like: {

file_path_first_nxtomo, data_path_first_nxtomo: {

ImageKey.DARK_FIELD: (DataUrlSeries1, DataUrlSeries2), ImageKey.FLAT_FIELD: (DataUrlSeries1, …),

}, file_path_last_nxtomo, data_path_last_nxtomo: {

ImageKey.DARK_FIELD: (DataUrlSeries1, DataUrlSeries2), ImageKey.FLAT_FIELD: (DataUrlSeries1, …),

},

}

Return type:

dict[tuple, dict[ImageKey, list[DataUrl]]]

process_edition(editions_to_do, embed_dark_flat=True)

do edition