Commit b94a7613 authored by Pierre Paleo's avatar Pierre Paleo

[doc] Add whatsnew for 2020.5.0

parent 42b4ad44
# 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](features.md).
### 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.
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