Version 2020.2.0

Version 2020.2.0 is a “preview” of a major release foreseen for September 2020. It brings new features since 2020.1.0.

Note

The changelog is available at https://gitlab.esrf.fr/tomotools/nabu/-/blob/master/CHANGELOG.md

Highlights

This section highlights some of the available features.

Binning

For a quick reconstruction, you can perform binning on the data. There are three parameters in the configuration file:

  • binning: binning in the horizontal direction. Each reconstructed slice will have its dimensions divided by this factor. For now only factors 2 and 3 are supported.

  • binning_z: binning in the vertical direction. The number of reconstructed slices will be divided by this number. For now only factors 2 and 3 are supported.

  • projections_subsampling: read one projection out of 2 or 3. This accelerates the processing but results in lower quality data.

Automatic center of rotation estimation

The default rotation_axis_position value (if left blank) is half of the detector width. The value rotation_axis_position = auto can now be provided, so that the value will be automatically estimated.

In the current version, automatic estimation lacks robustness and does not work for half tomography.

Half tomography

Half tomography reconstruction is supported by setting the parameter enable_halftomo to 1.

Double flat-field

Double flat-field is a projections-based rings artefacts removal. The relevant configuration key is double_flatfield_enabled.

Foreseen developments

Most of the following foreseen developments should materialize for “September Milestone”.

Input/output

  • “merge” HDF5 reconstructions by creating a master file

  • Allow other formats than HDF5 (ex. tiff, jp2k, npy)

  • Enable to dump intermediate results (pre-processed radios/sinograms) and run the processing from a previous intermediate result

  • Generate flats/darks instead of relying on a tomwer_processes.h5 file

Reconstruction

  • Determine the minimum number of detector rows to read (“Paganin margin”)

  • Reconstruction with overlapping vertical regions for phase retrieval

  • More robust Center of Rotation estimation methods (notably for half-tomography)

  • Sample/detector shifts. This is theoretically already implemented, but real datasets for tests are missing.

  • Sinogram normalization (background subtraction)

  • Iterative reconstruction (need a forward projector implementation)

Computations distribution

Distributing the computation will be a crucial feature of Nabu.

  • Distribution on the local machine

  • Distribution on the computing cluster (via the SLURM task dispatcher)