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.

This tool can
be used for mapping experiments if one considers the slow scan direction
as the rotation. but the \*diff_map\* tool provides in addition a
graphical user interface.

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

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

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