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caosdb
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CaosDB Crawler
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f3e8ec1e
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f3e8ec1e
authored
1 year ago
by
Florian Spreckelsen
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DOC: Document the individual HDF5 converter classes
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ENH: HDF5 Converter
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@@ -18,6 +18,8 @@ Relevant sources in:
- ``src/structure_elements.py``
.. _ConceptConverters:
Converters
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HDF5 Converters
===============
For treating `HDF5 Files
<https://docs.hdfgroup.org/hdf5/develop/_s_p_e_c.html>`_, there are in total
four indivdual converters corresponding to the internal structure of HDF5 files:
the :ref:`H5FileConverter` which opens the file itself and creates further
structure elements from HDF5 groups, datasets, and included multi-dimensional
arrays that are in turn treated by the :ref:`H5GroupConverter`, the
:ref:`H5DatasetConverter`, and the :ref:`H5NdarrayConverter`, respectively. You
need to install the LinkAhead crawler with its optional ``h5crawler`` dependency
for using these converters.
H5FileConverter
---------------
This is an extension of the
:py:class:`~caoscrawler.converters.SimpleFileConverter` class. It opens the HDF5
file and creates children for any contained group or dataset. Additionaly, the
root-level attributes of the HDF5 file are accessible as children.
H5GroupConverter
----------------
This is an extension of the
:py:class:`~caoscrawler.converters.DictElementConverter` class. Children are
created for all subgroups and datasets in this HDF5 group. Additionally, the
group-level attributes are accessible as children.
H5DatasetConverter
------------------
This is an extension of the
:py:class:`~caoscrawler.converters.DictElementConverter` class. Most
importantly, it stores the array data in HDF5 dataset into
:py:class:`~caoscrawler.hdf5_converters.H5NdarrayElement` which is added to its
children, as well as the dataset attributes.
H5NdarrayConverter
------------------
This converter creates a wrapper record for the contained dataset. The name of
this record needs to be specified in the cfood definition of this converter via
the ``recordname`` option. The RecordType of this record can be configured with
the ``array_recordtype_name`` option and defaults to ``H5Ndarray``. Via the
given ``recordname``, this record can be used within the cfood. Most
importantly, this record stores the internal path of this array within the HDF5
file in a text property, the name of which can be configured with the
``internal_path_property_name`` option which defaults to ``internal_hdf5_path``.
Custom Converters
+++++++++++++++++
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