Convert EDF files to HDF5
=========================

Since Darfix 4.0, raw data needs to be supplied in HDF5. This means images stored in EDF need to be converted to HDF5 before we can load them in Darfix.

Conversion is handled by the utility ``silx convert`` from `silx <https://www.silx.org/doc/silx/latest/index.html>`_. 

.. note::

    ``silx`` should be installed with Darfix. If not, it can installed by running

    .. code-block::

        pip install silx


To give an example of use of ``silx convert``, we will consider that all the images are stored as EDF files in a folder ``my_edf_scan/``.

To convert them, we can run

.. code-block::

    silx convert my_edf_scan/*.edf -o converted.h5

This will produce an HDF5 file called ``converted.h5`` in the current folder. This file can then be loaded in Darfix.

.. seealso::

    The `silx convert <https://www.silx.org/doc/silx/latest/applications/convert.html#silx-convert>`_ page gathers lot of useful information on how to convert files.
    
    For example, see the `Merging a stack of images <https://www.silx.org/doc/silx/latest/Tutorials/convert.html#merging-a-stack-of-images>`_.