Version 2020.5.0

Version 2020.5.0 is a major version aiming at stabilizing fixes and features added over weeks.

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.

New methods for estimating the center of rotation

In the configuration, nabu now provides four methods for estimating the Center Of Rotation (CoR):

  • centered: a fast and simple auto-CoR method. It only works when the CoR is not far from the middle of the detector. It does not work for half-tomography.

  • global: a slow but robust auto-CoR.

  • sliding-window: semi-automatically find the CoR with a sliding window. You have to specify on which side the CoR is (left, center, right).

  • growing-window : automatically find the CoR with a sliding-and-growing window. You can tune the option with the parameter ‘cor_options’.

Advanced options for each of these methods can be tuned with the cor_options parameter.

Histogram improvements

  • When the slice/volume histogram is computed, the processing is now done on GPU, dramatically speeding up this step.

  • The histogram can now be computed for output file formats other than HDF5.

Excluding projections

Sometimes it is useful to exclude certain projection images from being processes. It can be done with two different means:

  • The CLI tool nxtomomill patch-nx (available since nxtomomill 0.4.0) can patch a HDF5-Nexus dataset inplace.

  • In the nabu configuration, you can provide exclude_projections = excluded.txt were the text file contains one radio index to ignore per line.

Changes

Unique files nabu_processes.h5 and nabu.log

The files nabu_processes.h5 (containing various processing steps dumped for further reuse) and nabu.log (default file name for logs) are now named dataset_prefix_nabu_processes.h5 and dataset_prefix_nabu.log.

The reason is, sometimes several reconstruction are launched simultaneously on dataset files placed in the same folder, giving conflicts in both files.

Use of “magnified pixel size”

The HDF5-NX file used as an input contains two pixel sizes: detector pixel size, and “magnified pixel size” accounting for optics effects. Until version 2020.4.1, the former was taken for scaling the reconstruction and computing the Paganin filter. From 2020.4.1 and on, the magnified pixel size will be used. This has mainly two effects:

  • For phase retrieval, this change impacts the “blurring effect” but not the gray values scale. When using a smaller pixel size, the delta/beta value will have to be much smaller to obtain a result similar to the output of previous versions. More precisely, if magnified_pixel_size = pixel_size/10, then a result obtained with the parameters (pixel_size, delta_beta) using nabu < 2020.4.1 can be obtained by using parameters (magnified_pixel_size, delta_beta/100) in nabu >= 2020.4.1.

  • For reconstruction, this change impacts the final gray values range, as the reconstructions values are normalized with (horizontal) pixel size.