pencil.tool_kit.field_skeleton
==============================

.. py:module:: pencil.tool_kit.field_skeleton

.. autoapi-nested-parse::

   Classes for determining the structure of the field's skeleton, i.e. null points,
   separatrix layers and separators using the trilinear method by
   Haynes-Parnell-2007-14-8-PhysPlasm (http://dx.doi.org/10.1063/1.2756751) and
   Haynes-Parnell-2010-17-9-PhysPlasm (http://dx.doi.org/10.1063/1.3467499).



Classes
-------

.. autoapisummary::

   pencil.tool_kit.field_skeleton.NullPoint
   pencil.tool_kit.field_skeleton.Separatrix
   pencil.tool_kit.field_skeleton.Spine


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

.. py:class:: NullPoint

   Bases: :py:obj:`object`


   Contains the position of the null points and the finding routine.

   Fill members with default values.


   .. py:attribute:: nulls
      :value: None



   .. py:attribute:: eigen_values
      :value: None



   .. py:attribute:: eigen_vectors
      :value: None



   .. py:attribute:: sign_trace
      :value: None



   .. py:attribute:: fan_vectors
      :value: None



   .. py:attribute:: normals
      :value: None



   .. py:method:: find_nullpoints(var, field)

      find_nullpoints(var, field)

      Find the null points to the field 'field' with information from 'var'.

      :param var: The var object from the read.var routine.
      :type var: obj
      :param field: The vector field name.
      :type field: string



   .. py:method:: write_vtk(datadir='data', file_name='nulls.vtk', binary=False)

      write_vtk(datadir='data', file_name='nulls.vtk', binary=False)

      Write the null point into a vtk file.

      :param datadir: Target data directory.
      :type datadir: string
      :param file_name: Target file name.
      :type file_name: string
      :param binary: Write file in binary or ASCII format.
      :type binary: bool



   .. py:method:: read_vtk(datadir='data', file_name='nulls.vtk')

      read_vtk(datadir='data', file_name='nulls.vtk')

      Read the null point from a vtk file.

      :param datadir: Origin data directory.
      :type datadir: string
      :param file_name: Origin file name.
      :type file_name: string



.. py:class:: Separatrix

   Bases: :py:obj:`object`


   Contains the separatrix layers and methods to find them.

   Fill members with default values.


   .. py:attribute:: lines
      :value: []



   .. py:attribute:: eigen_values
      :value: []



   .. py:attribute:: eigen_vectors
      :value: []



   .. py:attribute:: sign_trace
      :value: []



   .. py:attribute:: fan_vectors
      :value: []



   .. py:attribute:: normals
      :value: []



   .. py:attribute:: separatrices
      :value: []



   .. py:attribute:: connectivity
      :value: []



   .. py:method:: find_separatrices(var, field, null_point, delta=0.1, iter_max=100, ring_density=8)

      find_separatrices(var, field, null_point, delta=0.1,
                        iter_max=100, ring_density=8)

      Find the separatrices to the field 'field' with information from 'var'.

      :param var: The var object from the read_var routine.
      :type var: obj
      :param field: The vector field.
      :type field: string
      :param null_point: NullPoint object containing the magnetic null points.
      :type null_point: obj
      :param delta: Step length for the field line tracing.
      :type delta: float
      :param iter_max: Maximum iteration steps for the fiel line tracing.
      :type iter_max: int
      :param ring_density: Density of the tracer rings.
      :type ring_density: float



   .. py:method:: write_vtk(datadir='data', file_name='separatrices.vtk', binary=False)

      write_vtk(datadir='data', file_name='separatrices.vtk', binary=False)

      Write the separatrices into a vtk file.

      :param datadir: Target data directory.
      :type datadir: string
      :param file_name: Target file name.
      :type file_name: string
      :param binary: Write file in binary or ASCII format.
      :type binary: bool



   .. py:method:: read_vtk(datadir='data', file_name='separatrices.vtk')

      read_vtk(datadir='data', file_name='separatrices.vtk')

      Read the separatrices from a vtk file.

      :param datadir: Origin data directory.
      :type datadir: string
      :param file_name: Origin file name.
      :type file_name: string



.. py:class:: Spine

   Bases: :py:obj:`object`


   Contains the spines of the null points and their finding routines.

   Fill members with default values.


   .. py:attribute:: spines
      :value: []



   .. py:method:: find_spines(var, field, null_point, delta=0.1, iter_max=100)

      find_spines(var, field, null_point, delta=0.1, iter_max=100)

      Find the spines to the field 'field' with information from 'var'.


      :param var: The var object from the read_var routine.
      :type var: obj
      :param field: The vector field.
      :type field: string
      :param null_point: NullPoint object containing the magnetic null points.
      :type null_point: obj
      :param delta: Step length for the field line tracing.
      :type delta: float
      :param iter_max: Maximum iteration steps for the fiel line tracing.
      :type iter_max: int



   .. py:method:: write_vtk(datadir='data', file_name='spines.vtk', binary=False)

      write_vtk(datadir='data', file_name='spines.vtk', binary=False)

      Write the spines into a vtk file.

      :param datadir: Target data directory.
      :type datadir: string
      :param file_name: Target file name.
      :type file_name: string
      :param binary: Write file in binary or ASCII format.
      :type binary: bool



   .. py:method:: read_vtk(datadir='data', file_name='spines.vtk')

      read_vtk(datadir='data', file_name='spines.vtk')

      Read the spines from a vtk file.

      :param datadir: Target data directory.
      :type datadir: string
      :param file_name: Target file name.
      :type file_name: string