End to end reconstruction tests

About

Unit test verify that the basic building blocks work as expected when used "alone". On the other hand, the full-field pipeline comes with a variety of options, and combining them together quickly gives many possible code paths.

Automating end-to-end reconstruction tests might be a tedious task, so for now they will consist in several configuration files with various processing options. The configuration files target our reconstruction datasets.

The files are located in /data/scisofttmp/paleo/nabu_end2end_tests.

Default options

Unless told otherwise, the following parameters are used with default values:

take_logarithm = True
flatfield_enabled = True
ccd_filter_enabled = False
Output format: HDF5

Bamboo

`bamboo_simple`

paganin
CoR: "growing-window"

`bamboo_dff_unsharp_binning`

DFF
Binning
Projections subsampling
Paganin
Unsharp mask
CoR: "centered"

Big

This is a dataset in the legacy EDF format.

`big_unsharp_tif`

paganin
unsharp mask
CoR : 2262
enable_halftomo = True
Output format: tiff
Histogram