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diff_tomo - Online in the Cloud

Run diff_tomo in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command diff_tomo that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


diff_tomo - diffraction tomography sinogram construction

DESCRIPTION


usage: diff_tomo [options] -p ponifile imagefiles* If the number of files is too large,
use double quotes like "*.edf"

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.

positional arguments:
FILE List of files to calibrate

optional arguments:
-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"

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