Integration tool: diff_tomo
===========================

Purpose
-------

Azimuthal integration for diffraction tomography.

Diffraction tomography is an experiment where 2D diffraction patterns are recorded
while performing a 2D scan, one (the slowest) in rotation around the sample center
and the other (the fastest) along a translation through the sample.
Diff_tomo is a script (based on pyFAI and h5py) which allows the reduction of this
4D dataset into a 3D dataset containing the rotations angle (hundreds), the translation step (hundreds)
and the many diffraction angles (thousands). The resulting dataset can be opened using PyMca roitool
where the 1d dataset has to be selected as last dimension. This file is not (yet) NeXus compliant.

This tool can be used for mapping experiments if one considers the slow scan
direction as the rotation, but a tool named *diff_map* operates in a similar way,
provides a Graphical interface and is more flexible.

tips: If the number of files is too large, use double quotes around "\*.edf"

Usage:
------

diff_tomo [options] -p ponifile imagefiles*

Options:
--------

  -h, --help            show this help message and exit
  -V, --version         show program's version number and exit
  -o FILE, --output FILE
                        HDF5 File where processed sinogram was saved, by
                        default diff_tomo.h5
  -v, --verbose         switch to verbose/debug mode, defaut: quiet
  -P FILE, --prefix FILE
                        Prefix or common base for all files
  -e EXTENSION, --extension EXTENSION
                        Process all files with this extension
  -t NTRANS, --nTrans NTRANS
                        number of points in translation. Mandatory
  -r NROT, --nRot NROT  number of points in rotation. Mandatory
  -c NDIFF, --nDiff NDIFF
                        number of points in diffraction powder pattern,
                        Mandatory
  -d FILE, --dark FILE  list of dark images to average and subtract
  -f FILE, --flat FILE  list of flat images to average and divide
  -m FILE, --mask FILE  file containing the mask, no mask by default
  -p FILE, --poni FILE  file containing the diffraction parameter (poni-file),
                        Mandatory
  -O OFFSET, --offset OFFSET
                        do not process the first files
  -g, --gpu             process using OpenCL on GPU
  -S, --stats           show statistics at the end


Most of those options are mandatory to define the structure of the dataset.


.. command-output:: diff_tomo --help
    :nostderr: