opengate.postprocessors.base
============================

.. py:module:: opengate.postprocessors.base


Attributes
----------

.. autoapisummary::

   opengate.postprocessors.base.__run_group_prefix__


Classes
-------

.. autoapisummary::

   opengate.postprocessors.base.ProcessingGroupBase
   opengate.postprocessors.base.PostProcessor
   opengate.postprocessors.base.ManagedExternalLink


Module Contents
---------------

.. py:data:: __run_group_prefix__
   :value: 'data_from_run'


.. py:class:: ProcessingGroupBase(*args, **kwargs)

   Bases: :py:obj:`opengate.base.GateObject`


   This is the base class used for all objects that handle user input in GATE.

   The class is assumed to be processed by process_cls(), either explicitly
   or via the metaclass MetaUserInfo, before any instances of the class are created.
   Some class attributes, e.g. inherited_user_info_defaults, are created as part of this processing.


   .. py:attribute:: processing_units


   .. py:attribute:: _need_tree_update
      :value: True



   .. py:method:: close()

      Dummy implementation for inherited classes which do not implement this method.



   .. py:method:: to_dictionary()


   .. py:property:: last_added_processing_unit


   .. py:method:: add_processing_unit(processing_unit, **kwargs)


   .. py:method:: get_processing_unit(name)


   .. py:property:: all_processing_units


   .. py:property:: is_post_processor


   .. py:property:: tree_roots


   .. py:method:: get_output_groups()


   .. py:method:: update_processing_tree()


   .. py:method:: update_processing_tree_if_needed()


   .. py:property:: processing_groups


.. py:class:: PostProcessor(*args, **kwargs)

   Bases: :py:obj:`ProcessingGroupBase`


   This is the base class used for all objects that handle user input in GATE.

   The class is assumed to be processed by process_cls(), either explicitly
   or via the metaclass MetaUserInfo, before any instances of the class are created.
   Some class attributes, e.g. inherited_user_info_defaults, are created as part of this processing.


   .. py:attribute:: output_file_handle
      :value: None



   .. py:attribute:: extra_file_handles


   .. py:method:: initialize()


   .. py:method:: initialize_output_file()


   .. py:property:: output_directory_external_files


   .. py:property:: output_directory


   .. py:method:: get_extra_file_handle(identifier)


   .. py:method:: get_or_register_extra_file_handle(file_handle)

      Register a handle if it is not known yet.



   .. py:method:: has_extra_file_handle(identifier)


   .. py:method:: create_external_link(where, name, target, createparents=False)

      Create an external link.

      Create an external link to a *target* node with the given *name*
      in *where* location.  *target* can be a node object in another
      file or a path string in the form 'file:/path/to/node'.  If
      *createparents* is true, the intermediate groups required for
      reaching *where* are created (the default is not doing so).

      The returned node is an :class:`ExternalLink` instance.




   .. py:method:: release_file_handles()


   .. py:method:: close()

      Dummy implementation for inherited classes which do not implement this method.



   .. py:method:: run()


   .. py:property:: hdf5_group


   .. py:method:: initialize_hdf5_groups()


   .. py:property:: all_initial_units

      Get all



.. py:class:: ManagedExternalLink(post_processor, parentnode, name, target=None, _log=False)

   Bases: :py:obj:`tables.linkextension.ExternalLink`, :py:obj:`tables.link.Link`


   Variant of the ExternalLink class from PyTables.


   .. py:attribute:: _c_classid
      :value: 'MANAGEDEXTERNALLINK'



   .. py:attribute:: post_processor

      The external file handler, if the link has been dereferenced.
      In case the link has not been dereferenced yet, its value is
      None.



   .. py:property:: extfile


   .. py:method:: _get_filename_node()

      Return the external filename and nodepath from `self.target`.



   .. py:method:: __call__(**kwargs)

      Dereference self.target and return the object.

      You can pass all the arguments supported by the :func:`open_file`
      function (except filename, of course) so as to open the referenced
      external file.



   .. py:method:: umount()

      Safely unmount self.extfile, if opened.



   .. py:method:: __str__()

      Return a short string representation of the link.