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.. _dxfile2nxtutorial:
dxfile2nx tutorial
==================
.. article-info::
:read-time: 10 min read
:class-container: sd-p-2 sd-outline-muted sd-rounded-1
the `dxfile2nx` application is used to convert an acquisition stored with the `dxfile format <https://dxfile.readthedocs.io/en/latest/>`_ to the `NXTomo <https://manual.nexusformat.org/classes/applications/NXtomo.html>`_ format.
To call this application you can call directly
.. code-block:: bash
nxtomomill dxfile2nx [input_file] [output_file] [[options]]
You can access help by calling
.. code-block:: bash
$ nxtomomill dxfile2nx --help
usage: nxtomomill dxfile2nx [-h] [--input_entry INPUT_ENTRY]
[--output_entry OUTPUT_ENTRY]
[--file_extension FILE_EXTENSION]
[--scan-range SCAN_RANGE]
[--pixel-size PIXEL_SIZE] [--fov FIELD_OF_VIEW]
[--distance DISTANCE] [--energy ENERGY]
[--overwrite] [--no-data-copy]
input_file output_file
convert acquisition contained in provided dx file to NXTomo entry
positional arguments:
input_file master file of the acquisition
output_file output .nx or .h5 file
optional arguments:
-h, --help show this help message and exit
--input_entry INPUT_ENTRY
h5py group path to be converted
--output_entry OUTPUT_ENTRY
h5py group path to store the NXTomo
--file_extension FILE_EXTENSION
extension of the output file. Valid values are
.h5/.hdf5/.nx
--scan-range SCAN_RANGE
scan range of the projections. Dark and flat will
always be considered with rotation angle ==
scan_range[0]
--pixel-size PIXEL_SIZE
pixel size in meter as (x pixel size, y pixel size)
--fov FIELD_OF_VIEW, --field-of-view FIELD_OF_VIEW
pixel size in meter as (x pixel size, y pixel size)
--distance DISTANCE, --detector-sample-distance DISTANCE
sample to detector distance (in meter)
--energy ENERGY, --incident-beam-energy ENERGY
incident beam energy in keV
--overwrite Do not ask for user permission to overwrite output
files
--no-data-copy Avoid creating any symbolic link between input and
output fileand duplicate the frame datasets to have a
'all-in-one' output file.
Here is an example on how to convert a dxfile.
For it we downloaded the `tomo_00068 dataset <https://tomobank.readthedocs.io/en/latest/source/data/docs.data.phasecontrast.html#wet-sample>`_
To convert it we simply go for
.. code-block:: bash
nxtomomill dxfile2nx tomo_00068.h5 tomo_00068.nx
Here the conversion will set default values to parameters that are not recorded in the dxfile but that tomography software mights need. Such as beam energy ...
Here is an example of providing more information to the converter and requesting the converter to overwrite the output NXtomo entry if it exists
.. code-block:: bash
nxtomomill dxfile2nx tomo_00068.h5 tomo_00068.nx --scan-range 0,180 --distance 0.15 --energy 14 --overwrite
Here is an example of the NXTomo entry generated:
.. image:: img/tomo_00068_nxtomo_entry.png
:width: 600 px
:align: center
From it you can use several tomography tool like `nabu <https://gitlab.esrf.fr/tomotools/nabu>`_ and / or `tomwer <https://gitlab.esrf.fr/tomotools/tomwer>`_.
.. warning:: to have a complete usage of tomwer you will also have to provide the field of view of the detector (Full or Half)
Example of the reconstruction of the middle slice using `nabu <https://gitlab.esrf.fr/tomotools/nabu>`_:
.. image:: img/tomo_00068_nabu_rec.png
:width: 600 px
:align: center
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