Atomic Data
===========

.. list-table::
   :widths: 28 50 22
   :header-rows: 1

   * - Name
     - Description
     - Preview
   * - :ref:`Photon Emissivity Coefficients <photon_emissivity_coefficients>`
     - Sampling and plotting PEC rates provided by OPEN-ADAS.
     - .. image:: ./atomic_data/D_alpha_PECs.png
          :height: 150px
          :width: 150px
   * - :ref:`Beam-Plasma Interaction Rates <beam_plasma_interaction_rates>`
     - Sampling and plotting various beam-plasma interaction rates provided by OPEN-ADAS.
     - .. image:: ./atomic_data/effective_cx_rates.png
          :height: 150px
          :width: 150px
   * - :ref:`Fractional Abundances <fractional_abundances>`
     - Sampling and plotting Neon fractional abundances with the ADAS subscription package.
     - .. image:: ./atomic_data/fractional_abundance.png
          :height: 150px
          :width: 150px
   * - :ref:`Radiated Powers <radiated_powers>`
     - Sampling and plotting total and stage resolved radiated powers with the ADAS
       subscription package.
     - .. image:: ./atomic_data/stage_resolved_radiation.png
          :height: 150px
          :width: 150px


Creating Plasmas
================

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   :header-rows: 1

   * - Name
     - Description
     - Preview
   * - :ref:`Analytic Functions <analytic_function_plasma>`
     - Specifying plasma distributions with analytic functions.
     - .. image:: ./plasmas/analytic_plasma.png
          :height: 150px
          :width: 150px
   * - :ref:`Flux Function Plasmas <flux_function_plasmas>`
     - Loading the example EFIT equilibrium and making 1D flux functions.
     - .. image:: ./plasmas/equilibrium_surfaces.png
          :height: 150px
          :width: 150px
   * - :ref:`2D Mesh Plasmas <mesh2d_plasma>`
     - Specifying a plasma distribution with a 2D r-z triangular mesh.
     - .. image:: ./plasmas/mesh_plasma_column.png
          :height: 150px
          :width: 150px
   * - :ref:`Slab Plasma <slab_plasma>`
     - Constructing a slab of plasma defined along +ve x.
     - .. image:: ./plasmas/slab_plasma.png
          :height: 150px
          :width: 150px
   * - :ref:`Beams into Plasmas <beams_into_plasmas>`
     - Specifying a mono-energetic neutral beam that interacts with a plasma.
     - .. image:: ./plasmas/beam_into_plasma.png
          :height: 150px
          :width: 150px


Surface Radiation Loads
=======================

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   :widths: 28 50 22
   :header-rows: 1

   * - Name
     - Description
     - Preview
   * - :ref:`Defining A Radiation Function <radiation_function>`
     - Defining an example radiation function.
     - .. image:: ./radiation_loads/radiation_function.png
          :height: 150px
          :width: 150px
   * - :ref:`Defining A Wall From A 2D Polygon <wall_from_polygon>`
     - A toroidal mesh representing the tokamak wall is made from a
       2D polygon outline.
     - .. image:: ./radiation_loads/toroidal_wall.png
          :height: 150px
          :width: 150px
   * - :ref:`Symmetric Power Load Calculation <symmetric_power_load>`
     - Calculating the power load by exploiting symmetry. We manually
       create an array of detectors for sampling.
     - .. image:: ./radiation_loads/symmetric_power_load.png
          :height: 150px
          :width: 150px
   * - `Mesh Observer <https://raysect.github.io/documentation/demonstrations/observers/mesh_observers.html>`_
     - Calculating powers on an arbitrary 3D surface (Raysect docs).
     - .. image:: https://raysect.github.io/documentation/_images/mesh_observers.jpg
          :height: 150px
          :width: 150px
   * - :ref:`AUG - SOLPS radiation load example <aug_solps_radiation_load>`
     - An older demonstration of the tutorials above using a SOLPS simulation
       and an AUG wall outline.
     - .. image:: ./radiation_loads/AUG_wall_outline.png
          :height: 150px
          :width: 150px


Active Spectroscopy
===================

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   :widths: 28 50 22
   :header-rows: 1

   * - Name
     - Description
     - Preview
   * - :ref:`Charge Exchange Spectroscopy (CXS) <beam_cxs>`
     - A simple CXS model for a beam into a plasma slab.
     - .. image:: ./active_spectroscopy/CXS_multi_sightlines.png
          :height: 150px
          :width: 150px
   * - :ref:`Beam Emission Spectroscopy <beam_bes>`
     - A simple Beam Emission Spectroscopy (BES) model for a beam into a plasma slab.
     - .. image:: ./active_spectroscopy/BES_spectrum_zoomed.png
          :height: 150px
          :width: 150px


Passive Spectroscopy
====================

.. list-table::
   :widths: 28 50 22
   :header-rows: 1

   * - Name
     - Description
     - Preview
   * - :ref:`Impact Excitation and Recombination <impact_recom_lines>`
     - Modelling background lines due to electron impact excitation and recombination.
     - .. image:: ./passive_spectroscopy/BalmerSeries_camera.png
          :height: 150px
          :width: 150px
   * - :ref:`Multiplet Line Ratios <multiplet_lines>`
     - Including experimentally determined multiplet line ratios.
     - .. image:: ./passive_spectroscopy/multiplet_spectrum.png
          :height: 150px
          :width: 150px
   * - :ref:`Stark Broadened Lines <stark_broadening>`
     - Specifying a Stark broadened lineshape instead of Doppler broadening.
     - .. image:: ./passive_spectroscopy/stark_line_zoomed.png
          :height: 150px
          :width: 150px
   * - :ref:`Zeeman Spectroscopy <zeeman_spectroscopy>`
     - Specifying a Zeeman triplet or multiplet line shapes.
     - .. image:: ./passive_spectroscopy/zeeman_spectrum_45deg.png
          :height: 150px
          :width: 150px   


Bolometry
=========

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   :widths: 28 50 22
   :header-rows: 1

   * - Name
     - Description
     - Preview
   * - :ref:`Camera From Primitives <bolometer_from_primitives>`
     - Designing a simple bolometer camera using raysect primitives
     - .. image:: ./bolometry/camera_from_primitives.svg
          :height: 150px
          :width: 150px
   * - :ref:`Camera From Mesh and Coordinates <bolometer_from_mesh>`
     - Designing a simple bolometer camera using a mesh file and vertex coordinates
     - .. image:: ./bolometry/camera_from_mesh_and_coordinates.svg
          :height: 150px
          :width: 150px
   * - :ref:`Observing a Radiation Function <bolometer_observing_radiation>`
     - Calculating the measured power and radiance on bolometer from a 3D radiation function
     - .. image:: ./bolometry/bolometer_and_radiation_function.png
          :height: 150px
          :width: 150px
   * - :ref:`Calculating the Etendue <bolometer_etendue>`
     - Calculating the etendue of a bolometer detector
     - .. image:: ./bolometry/bolometer_etendues.svg
          :height: 150px
          :width: 150px
   * - :ref:`Geometry Matrix Calculation Using Voxels <bolometer_geometry_voxels>`
     - Calculating the geometry matrix for a bolometer system using the voxel framework
     - .. image:: ./bolometry/bolometer_voxel_sensitivities.png
          :height: 150px
          :width: 150px
   * - :ref:`Bolometer Inversions Using Voxels <bolometer_voxel_inversion>`
     - Performing inversions using geometry matrices and the voxel framework
     - .. image:: ./bolometry/inversion_with_voxels_profile.png
          :height: 150px
          :width: 150px
   * - :ref:`Geometry Matrix Calculation Using Ray Transfer Objects <bolometer_geometry_raytransfer>`
     - Calculating the geometry matrix for a bolometer system using ray transfer objects
     - .. image:: ./bolometry/bolometer_raytransfer_sensitivities.png
          :height: 150px
          :width: 150px
   * - :ref:`Bolometer Inversions Using Ray Transfer Objects <bolometer_raytransfer_inversion>`
     - Performing inversions using geometry matrices from a ray transfer object
     - .. image:: ./bolometry/inversion_with_raytransfer_profile.png
          :height: 150px
          :width: 150px


Geometry Matrices
=================
.. list-table::
   :widths: 28 50 22
   :header-rows: 1

   * - Name
     - Description
     - Preview
   * - :ref:`Rectangular regular grid <ray_transfer_box>`
     - Calculating the geometry matrix for a rectangular emitter defined on a regular grid.
     - .. image:: ./ray_transfer/ray_transfer_box_demo.png
          :height: 150px
          :width: 150px
   * - :ref:`Cylindrical regular grid <ray_transfer_cylinder>`
     - Calculating the geometry matrix for a cylindrical emitter defined on a regular grid.
     - .. image:: ./ray_transfer/ray_transfer_cylinder_demo.gif
          :height: 150px
          :width: 150px
   * - :ref:`Axisymmetrical (toroidal) regular grid <ray_transfer_mask>`
     - Calculating the geometry matrix for an axisymmetrical toroidal emitter defined on a regular grid. Applying a mask to filter out extra grid cells.
     - .. image:: ./ray_transfer/ray_transfer_mask_demo.gif
          :height: 150px
          :width: 150px
   * - :ref:`Axisymmetrical (toroidal) regular grid with custom mapping of light sources <ray_transfer_map>`
     - Mapping multiple grid cells into a single light source.
     - .. image:: ./ray_transfer/ray_transfer_map_demo.gif
          :height: 150px
          :width: 150px


Code examples gallery
=====================

.. note::
   These code examples are included for historical reasons.
   They may require specific (sometimes older) versions of Cherab's submodules to work.
   Many also require access to specific machine data.

.. list-table::
   :widths: 28 50 22
   :header-rows: 1

   * - Name
     - Description
     - Preview
   * - :ref:`CXRS Quickstart <jet_cxrs_quickstart>`
     - Commented demo file about how to use Cherab for JET CX simulations.
     - .. image:: ./jet_cxrs/JET_CXRS_d5lines.png
          :height: 150px
          :width: 150px
   * - :ref:`#76666 sample analysis <jet_cxrs_76666>`
     - Demo CX analysis for pulse 76666 at t=61s
     -
   * - :ref:`MAST-U filtered cameras <mastu_forward_cameras>`
     - Example of using SOLPS simulation and ADAS rates to model filtered cameras.
     - .. image:: ./line_emission/mastu_bulletb_midplane_dgamma.png
          :height: 150px
          :width: 150px
   * - :ref:`MAST-U SOLPS plasma <mastu_solps_plasma>`
     - Example of loading a plasma from a SOLPS simulation and inspecting the various
       plasma species parameters.
     - .. image:: ./solps/species_narrow.png
          :height: 150px
          :width: 150px
   * - :ref:`Custom Emission Model <custom_emitter>`
     - Example of making a custom emitter class in Cherab. D-alpha impact excitation
       is used for the example.
     - .. image:: ./line_emission/mastu_bulletb_midplane_dalpha.png
          :height: 150px
          :width: 150px
   * - :ref:`Measuring line of sight spectra <balmer_series_spectra>`
     - Basic balmer series measurement in the MAST-U divertor with an optical fibre.
       Localisation of the plasma emission is examined by plotting profiles of parameters
       such as density and temperature along the ray trajectory.
     - .. image:: ./line_emission/balmer_series_spectra.png
          :height: 150px
          :width: 150px