Commit 5097a3d0 authored by Pierre Paleo's avatar Pierre Paleo
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Doc: Add about and v2020.2.0

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# About Nabu
Nabu is a tomography processing software being developed at [ESRF](https://www.esrf.eu) by the Data Analysis Unit. It is part of the [new ESRF tomography software suite](https://tomotools.gitlab-pages.esrf.fr/tomo-bridge-docs/data-proc/projects).
## Why Nabu
The European Synchrotron has several tomography beamlines. Each of them use dedicated software, which over the years led a variety of different tools spread over the beamlines with poor maintainability. This is summarized in [ESRF current situation for tomography software](https://tomotools.gitlab-pages.esrf.fr/tomo-bridge-docs/data-proc/situation/#current-situation-limitations-and-opportunities).
Nabu is an effort to unify tomography software in a new toolkit with the following requirements:
- Library of tomography processing, with "applications" built on top of it, usable by both non-experts and power-users
- High performance processing (parallelization with Cuda/OpenCL, computations distribution, memory re-use)
- Support of [multiple techniques](https://tomotools.gitlab-pages.esrf.fr/tomo-bridge-docs/#tomography-techniques-at-esrf), not only absorption and phase contrast
- Extensively documented
- Focus on maintainability with a [bus factor](https://en.wikipedia.org/wiki/Bus_factor) greater than one
- Compatible with ESRF legacy software, progressively replacing it
Nabu does not aim at being the new universal tomography reconstruction software. Well-established software like [Astra](http://www.astra-toolbox.com), [tomopy](http://tomopy.readthedocs.io), [Savu](https://github.com/DiamondLightSource/Savu) and [UFO](https://github.com/ufo-kit) have an extensive set of features. Nabu foremost focuses on ESRF needs, while being designed so that it can be re-used in other projects.
## Project management
### Development spot
The various projects are hosted on [gitlab.esrf.fr](https://gitlab.esrf.fr/tomotools).
### Members and meeting minutes
The [new ESRF tomography software suite](https://tomotools.gitlab-pages.esrf.fr/tomo-bridge-docs/data-proc/projects) is developed by ESRF Data Analysis Unit.
The weekly meeting minutes [are available here](https://gitlab.esrf.fr/tomotools/minutes/-/tree/master).
### Roadmap
[Roadmap for Nabu developments](https://tomotools.gitlab-pages.esrf.fr/tomo-bridge-docs/data-proc/roadmap)
# 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](features.md).
### 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](features.md#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)
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