rte.h

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/* Copyright (C) 2002-2012
   Patrick Eriksson <Patrick.Eriksson@chalmers.se>
   Stefan Buehler   <sbuehler@ltu.se>
                            
   This program is free software; you can redistribute it and/or modify it
   under the terms of the GNU General Public License as published by the
   Free Software Foundation; either version 2, or (at your option) any
   later version.

   This program is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.

   You should have received a copy of the GNU General Public License
   along with this program; if not, write to the Free Software
   Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307,
   USA. */

/*===========================================================================
  === File description 
  ===========================================================================*/

#ifndef rte_h
#define rte_h

/*===========================================================================
  === External declarations
  ===========================================================================*/

#include "agenda_class.h"
#include "arts.h"
#include "auto_md.h"
#include "complex.h"
#include "jacobian.h"
#include "matpackI.h"
#include "matpackII.h"
#include "matpackIII.h"
#include "optproperties.h"
#include "ppath.h"

/*===========================================================================
  === Functions in rte.cc
  ===========================================================================*/

void adapt_stepwise_partial_derivatives(
    ArrayOfPropagationMatrix& dK_dx,
    ArrayOfStokesVector& dS_dx,
    const ArrayOfRetrievalQuantity& jacobian_quantities,
    ConstVectorView ppath_f_grid,
    ConstVectorView ppath_line_of_sight,
    ConstVectorView ppath_vmrs,
    const Numeric& ppath_temperature,
    const Numeric& ppath_pressure,
    const ArrayOfIndex& jacobian_species,
    const ArrayOfIndex& jacobian_wind,
    const Index& lte,
    const Index& atmosphere_dim,
    const bool& jacobian_do);

void adjust_los(VectorView los, const Index& atmosphere_dim);

void apply_iy_unit(MatrixView iy,
                   const String& iy_unit,
                   ConstVectorView f_grid,
                   const Numeric& n,
                   const ArrayOfIndex& i_pol);

void apply_iy_unit2(Tensor3View J,
                    ConstMatrixView iy,
                    const String& iy_unit,
                    ConstVectorView f_grid,
                    const Numeric& n,
                    const ArrayOfIndex& i_pol);

void bending_angle1d(Numeric& alpha, const Ppath& ppath);

void defocusing_general(Workspace& ws,
                        Numeric& dlf,
                        const Agenda& ppath_step_agenda,
                        const Index& atmosphere_dim,
                        ConstVectorView p_grid,
                        ConstVectorView lat_grid,
                        ConstVectorView lon_grid,
                        ConstTensor3View z_field,
                        ConstVectorView f_grid,
                        ConstVectorView refellipsoid,
                        ConstMatrixView z_surface,
                        const Ppath& ppath,
                        const Numeric& ppath_lmax,
                        const Numeric& ppath_lraytrace,
                        const Numeric& dza,
                        const Verbosity& verbosity);

void defocusing_sat2sat(Workspace& ws,
                        Numeric& dlf,
                        const Agenda& ppath_step_agenda,
                        const Index& atmosphere_dim,
                        ConstVectorView p_grid,
                        ConstVectorView lat_grid,
                        ConstVectorView lon_grid,
                        ConstTensor3View z_field,
                        ConstVectorView f_grid,
                        ConstVectorView refellipsoid,
                        ConstMatrixView z_surface,
                        const Ppath& ppath,
                        const Numeric& ppath_lmax,
                        const Numeric& ppath_lraytrace,
                        const Numeric& dza,
                        const Verbosity& verbosity);

Numeric dotprod_with_los(ConstVectorView los,
                         const Numeric& u,
                         const Numeric& v,
                         const Numeric& w,
                         const Index& atmosphere_dim);

void ext2trans(MatrixView trans_mat,
               Index& icase,
               ConstMatrixView ext_mat_av,
               const Numeric& l_step);

void get_iy(Workspace& ws,
            Matrix& iy,
            const Index& cloudbox_on,
            ConstVectorView f_grid,
            const EnergyLevelMap& nlte_field,
            ConstVectorView rte_pos,
            ConstVectorView rte_los,
            ConstVectorView rte_pos2,
            const String& iy_unit,
            const Agenda& iy_main_agenda);

void get_iy_of_background(Workspace& ws,
                          Matrix& iy,
                          ArrayOfTensor3& diy_dx,
                          ConstTensor3View iy_transmission,
                          const Index& iy_id,
                          const Index& jacobian_do,
                          const ArrayOfRetrievalQuantity& jacobian_quantities,
                          const Ppath& ppath,
                          ConstVectorView rte_pos2,
                          const Index& atmosphere_dim,
                          const EnergyLevelMap& nlte_field,
                          const Index& cloudbox_on,
                          const Index& stokes_dim,
                          ConstVectorView f_grid,
                          const String& iy_unit,
                          ConstTensor3View surface_props_data,
                          const Agenda& iy_main_agenda,
                          const Agenda& iy_space_agenda,
                          const Agenda& iy_surface_agenda,
                          const Agenda& iy_cloudbox_agenda,
                          const Index& iy_agenda_call1,
                          const Verbosity& verbosity);

void get_ppath_atmvars(Vector& ppath_p,
                       Vector& ppath_t,
                       EnergyLevelMap& ppath_nlte,
                       Matrix& ppath_vmr,
                       Matrix& ppath_wind,
                       Matrix& ppath_mag,
                       const Ppath& ppath,
                       const Index& atmosphere_dim,
                       ConstVectorView p_grid,
                       ConstTensor3View t_field,
                       const EnergyLevelMap& nlte_field,
                       ConstTensor4View vmr_field,
                       ConstTensor3View wind_u_field,
                       ConstTensor3View wind_v_field,
                       ConstTensor3View wind_w_field,
                       ConstTensor3View mag_u_field,
                       ConstTensor3View mag_v_field,
                       ConstTensor3View mag_w_field);

void get_ppath_cloudvars(ArrayOfIndex& clear2cloudy,
                         Matrix& ppath_pnd,
                         ArrayOfMatrix& ppath_dpnd_dx,
                         const Ppath& ppath,
                         const Index& atmosphere_dim,
                         const ArrayOfIndex& cloudbox_limits,
                         const Tensor4& pnd_field,
                         const ArrayOfTensor4& dpnd_field_dx);

void get_ppath_f(Matrix& ppath_f,
                 const Ppath& ppath,
                 ConstVectorView f_grid,
                 const Index& atmosphere_dim,
                 const Numeric& rte_alonglos_v,
                 ConstMatrixView ppath_wind);

Range get_rowindex_for_mblock(const Sparse& sensor_response,
                              const Index& imblock);

void get_stepwise_blackbody_radiation(VectorView B,
                                      VectorView dB_dT,
                                      ConstVectorView ppath_f_grid,
                                      const Numeric& ppath_temperature,
                                      const bool& do_temperature_derivative);

void get_stepwise_clearsky_propmat(
  Workspace& ws,
  PropagationMatrix& K,
  StokesVector& S,
  Index& lte,
  ArrayOfPropagationMatrix& dK_dx,
  ArrayOfStokesVector& dS_dx,
  const Agenda& propmat_clearsky_agenda,
  const ArrayOfRetrievalQuantity& jacobian_quantities,
  ConstVectorView ppath_f_grid,
  ConstVectorView ppath_magnetic_field,
  ConstVectorView ppath_line_of_sight,
  const EnergyLevelMap& ppath_nlte,
  ConstVectorView ppath_vmrs,
  const Numeric& ppath_temperature,
  const Numeric& ppath_pressure,
  const ArrayOfIndex& jacobian_species,
  const bool& jacobian_do);

void get_stepwise_effective_source(
    MatrixView J,
    Tensor3View dJ_dx,
    const PropagationMatrix& K,
    const StokesVector& a,
    const StokesVector& S,
    const ArrayOfPropagationMatrix& dK_dx,
    const ArrayOfStokesVector& da_dx,
    const ArrayOfStokesVector& dS_dx,
    ConstVectorView B,
    ConstVectorView dB_dT,
    const ArrayOfRetrievalQuantity& jacobian_quantities,
    const bool& jacobian_do);

void get_stepwise_frequency_grid(VectorView ppath_f_grid,
                                 ConstVectorView f_grid,
                                 ConstVectorView ppath_wind,
                                 ConstVectorView ppath_line_of_sight,
                                 const Numeric& rte_alonglos_v,
                                 const Index& atmosphere_dim);

void get_stepwise_f_partials(Vector& f_partials,
                             const Index& component,
                             ConstVectorView& ppath_line_of_sight,
                             ConstVectorView f_grid,
                             const Index& atmosphere_dim);

void get_stepwise_scattersky_propmat(
    StokesVector& ap,
    PropagationMatrix& Kp,
    ArrayOfStokesVector& dap_dx,
    ArrayOfPropagationMatrix& dKp_dx,
    const ArrayOfRetrievalQuantity& jacobian_quantities,
    ConstMatrixView ppath_1p_pnd,  // the ppath_pnd at this ppath point
    const ArrayOfMatrix&
        ppath_dpnd_dx,  // the full ppath_dpnd_dx, ie all ppath points
    const Index ppath_1p_id,
    const ArrayOfArrayOfSingleScatteringData& scat_data,
    ConstVectorView ppath_line_of_sight,
    ConstVectorView ppath_temperature,
    const Index& atmosphere_dim,
    const bool& jacobian_do);

void get_stepwise_scattersky_source(
    StokesVector& Sp,
    ArrayOfStokesVector& dSp_dx,
    const ArrayOfRetrievalQuantity& jacobian_quantities,
    ConstVectorView ppath_1p_pnd,
    const ArrayOfMatrix& ppath_dpnd_dx,
    const Index ppath_1p_id,
    const ArrayOfArrayOfSingleScatteringData& scat_data,
    ConstTensor7View cloudbox_field,
    ConstVectorView za_grid,
    ConstVectorView aa_grid,
    ConstMatrixView ppath_line_of_sight,
    const GridPos& ppath_pressure,
    const Vector& temperature,
    const Index& atmosphere_dim,
    const bool& jacobian_do,
    const Index& t_interp_order = 1);

void get_stepwise_transmission_matrix(
    Tensor3View cumulative_transmission,
    Tensor3View T,
    Tensor4View dT_dx_close,
    Tensor4View dT_dx_far,
    ConstTensor3View cumulative_transmission_close,
    const PropagationMatrix& K_close,
    const PropagationMatrix& K_far,
    const ArrayOfPropagationMatrix& dK_close_dx,
    const ArrayOfPropagationMatrix& dK_far_dx,
    const Numeric& ppath_distance,
    const bool& first_level,
    const Numeric& dr_dT_close = 0,
    const Numeric& dr_dT_far = 0,
    const Index& it = -1);

void iyb_calc(Workspace& ws,
              Vector& iyb,
              ArrayOfVector& iyb_aux,
              ArrayOfMatrix& diyb_dx,
              Matrix& geo_pos_matrix,
              const Index& imblock,
              const Index& atmosphere_dim,
              const EnergyLevelMap& nlte_field,
              const Index& cloudbox_on,
              const Index& stokes_dim,
              ConstVectorView f_grid,
              ConstMatrixView sensor_pos,
              ConstMatrixView sensor_los,
              ConstMatrixView transmitter_pos,
              ConstMatrixView mblock_dlos_grid,
              const String& iy_unit,
              const Agenda& iy_main_agenda,
              const Agenda& geo_pos_agenda,
              const Index& j_analytical_do,
              const ArrayOfRetrievalQuantity& jacobian_quantities,
              const ArrayOfArrayOfIndex& jacobian_indices,
              const ArrayOfString& iy_aux_vars,
              const Verbosity& verbosity);

void iy_transmission_mult(Tensor3& iy_trans_total,
                          ConstTensor3View iy_trans_old,
                          ConstTensor3View iy_trans_new);

void iy_transmission_mult(Matrix& iy_new,
                          ConstTensor3View iy_trans,
                          ConstMatrixView iy_old);

void mirror_los(Vector& los_mirrored,
                ConstVectorView los,
                const Index& atmosphere_dim);

void pos2true_latlon(Numeric& lat,
                     Numeric& lon,
                     const Index& atmosphere_dim,
                     ConstVectorView lat_grid,
                     ConstVectorView lat_true,
                     ConstVectorView lon_true,
                     ConstVectorView pos);

void rtmethods_jacobian_init(
    ArrayOfIndex& jac_species_i,
    ArrayOfIndex& jac_scat_i,
    ArrayOfIndex& jac_is_t,
    ArrayOfIndex& jac_wind_i,
    ArrayOfIndex& jac_mag_i,
    ArrayOfIndex& jac_other,
    ArrayOfTensor3& diy_dx,
    ArrayOfTensor3& diy_dpath,
    const Index& ns,
    const Index& nf,
    const Index& np,
    const Index& nq,
    const ArrayOfArrayOfSpeciesTag& abs_species,
    const Index& cloudbox_on,
    const ArrayOfString& scat_species,
    const ArrayOfTensor4& dpnd_field_dx,
    const ArrayOfRetrievalQuantity& jacobian_quantities,
    const Index& iy_agenda_call1,
    const bool is_active = false);

void rtmethods_jacobian_finalisation(
    Workspace& ws,
    ArrayOfTensor3& diy_dx,
    ArrayOfTensor3& diy_dpath,
    const Index& ns,
    const Index& nf,
    const Index& np,
    const Index& atmosphere_dim,
    const Ppath& ppath,
    const Vector& ppvar_p,
    const Vector& ppvar_t,
    const Matrix& ppvar_vmr,
    const Index& iy_agenda_call1,
    const Tensor3& iy_transmission,
    const Agenda& water_p_eq_agenda,
    const ArrayOfRetrievalQuantity& jacobian_quantities,
    const ArrayOfIndex jac_species_i,
    const ArrayOfIndex jac_is_t);

void rtmethods_unit_conversion(
    Matrix& iy,
    ArrayOfTensor3& diy_dx,
    Tensor3& ppvar_iy,
    const Index& ns,
    const Index& np,
    const Vector& f_grid,
    const Ppath& ppath,
    const ArrayOfRetrievalQuantity& jacobian_quantities,
    const Index& j_analytical_do,
    const String& iy_unit);

void yCalc_mblock_loop_body(bool& failed,
                            String& fail_msg,
                            ArrayOfArrayOfVector& iyb_aux_array,
                            Workspace& ws,
                            Vector& y,
                            Vector& y_f,
                            ArrayOfIndex& y_pol,
                            Matrix& y_pos,
                            Matrix& y_los,
                            Matrix& y_geo,
                            Matrix& jacobian,
                            const Index& atmosphere_dim,
                            const EnergyLevelMap& nlte_field,
                            const Index& cloudbox_on,
                            const Index& stokes_dim,
                            const Vector& f_grid,
                            const Matrix& sensor_pos,
                            const Matrix& sensor_los,
                            const Matrix& transmitter_pos,
                            const Matrix& mblock_dlos_grid,
                            const Sparse& sensor_response,
                            const Vector& sensor_response_f,
                            const ArrayOfIndex& sensor_response_pol,
                            const Matrix& sensor_response_dlos,
                            const String& iy_unit,
                            const Agenda& iy_main_agenda,
                            const Agenda& geo_pos_agenda,
                            const Agenda& jacobian_agenda,
                            const Index& jacobian_do,
                            const ArrayOfRetrievalQuantity& jacobian_quantities,
                            const ArrayOfArrayOfIndex& jacobian_indices,
                            const ArrayOfString& iy_aux_vars,
                            const Verbosity& verbosity,
                            const Index& mblock_index,
                            const Index& n1y,
                            const Index& j_analytical_do);

void ze_cfac(Vector& fac,
             const Vector& f_grid,
             const Numeric& ze_tref,
             const Numeric& k2);

#endif  // rte_h