rte.h

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/*===========================================================================
  === File description 
  ===========================================================================*/
 
#ifndef rte_h
#define rte_h
 
/*===========================================================================
  === External declarations
  ===========================================================================*/
 
#include "agenda_class.h"
#include "arts.h"
#include "jacobian.h"
#include "matpack_data.h"
#include "matpack_complex.h"
#include "optproperties.h"
#include "ppath.h"
 
 
class Workspace;
 
/*===========================================================================
  === Functions in rte.cc
  ===========================================================================*/
 
void adapt_stepwise_partial_derivatives(
    ArrayOfPropagationMatrix& dK_dx,
    ArrayOfStokesVector& dS_dx,
    const ArrayOfRetrievalQuantity& jacobian_quantities,
    const ConstVectorView& ppath_f_grid,
    const ConstVectorView& ppath_line_of_sight,
    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,
                   const ConstVectorView& f_grid,
                   const Numeric& n,
                   const ArrayOfIndex& i_pol);
 
void apply_iy_unit2(Tensor3View J,
                    const ConstMatrixView& iy,
                    const String& iy_unit,
                    const 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,
                        const Vector& p_grid,
                        const Vector& lat_grid,
                        const Vector& lon_grid,
                        const Tensor3& z_field,
                        const Vector& f_grid,
                        const Vector& refellipsoid,
                        const Matrix& 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,
                        const Vector& p_grid,
                        const Vector& lat_grid,
                        const Vector& lon_grid,
                        const Tensor3& z_field,
                        const Vector& f_grid,
                        const Vector& refellipsoid,
                        const Matrix& z_surface,
                        const Ppath& ppath,
                        const Numeric& ppath_lmax,
                        const Numeric& ppath_lraytrace,
                        const Numeric& dza,
                        const Verbosity& verbosity);
 
Numeric dotprod_with_los(const ConstVectorView& los,
                         const Numeric& u,
                         const Numeric& v,
                         const Numeric& w,
                         const Index& atmosphere_dim);
 
void get_iy(Workspace& ws,
            Matrix& iy,
            const Index& cloudbox_on,
            const Vector& f_grid,
            const EnergyLevelMap& nlte_field,
            const Vector& rte_pos,
            const Vector& rte_los,
            const Vector& rte_pos2,
            const String& iy_unit,
            const Agenda& iy_main_agenda);
 
void get_iy_of_background(Workspace& ws,
                          Matrix& iy,
                          ArrayOfTensor3& diy_dx,
                          const Tensor3& iy_transmittance,
                          const Index& iy_id,
                          const Index& jacobian_do,
                          const ArrayOfRetrievalQuantity& jacobian_quantities,
                          const Ppath& ppath,
                          const Vector& rte_pos2,
                          const Index& atmosphere_dim,
                          const EnergyLevelMap& nlte_field,
                          const Index& cloudbox_on,
                          const Index& stokes_dim,
                          const Vector& f_grid,
                          const String& iy_unit,
                          const Tensor3& 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,
                       const ConstVectorView& p_grid,
                       const ConstTensor3View& t_field,
                       const EnergyLevelMap& nlte_field,
                       const ConstTensor4View& vmr_field,
                       const ConstTensor3View& wind_u_field,
                       const ConstTensor3View& wind_v_field,
                       const ConstTensor3View& wind_w_field,
                       const ConstTensor3View& mag_u_field,
                       const ConstTensor3View& mag_v_field,
                       const 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,
                 const ConstVectorView& f_grid,
                 const Index& atmosphere_dim,
                 const Numeric& rte_alonglos_v,
                 const 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,
                                      const 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,
    const Vector& ppath_f_grid,
    const Vector& ppath_magnetic_field,
    const Vector& ppath_line_of_sight,
    const EnergyLevelMap& ppath_nlte,
    const Vector& ppath_vmrs,
    const Numeric& ppath_temperature,
    const Numeric& ppath_pressure,
    const bool& jacobian_do);
 
Vector get_stepwise_f_partials(const ConstVectorView& ppath_line_of_sight,
                               const ConstVectorView& f_grid,
                               const Jacobian::Atm wind_type,
                               const Index& atmosphere_dim);
 
void get_stepwise_scattersky_propmat(
    StokesVector& ap,
    PropagationMatrix& Kp,
    ArrayOfStokesVector& dap_dx,
    ArrayOfPropagationMatrix& dKp_dx,
    const ArrayOfRetrievalQuantity& jacobian_quantities,
    const 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,
    const ConstVectorView& ppath_line_of_sight,
    const 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,
    const ConstVectorView& ppath_1p_pnd,
    const ArrayOfMatrix& ppath_dpnd_dx,
    const Index ppath_1p_id,
    const ArrayOfArrayOfSingleScatteringData& scat_data,
    const ConstTensor7View& cloudbox_field,
    const ConstVectorView& za_grid,
    const ConstVectorView& aa_grid,
    const 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,
    const 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,
              const Vector& f_grid,
              const Matrix& sensor_pos,
              const Matrix& sensor_los,
              const Matrix& transmitter_pos,
              const Matrix& mblock_dlos,
              const String& iy_unit,
              const Agenda& iy_main_agenda,
              const Index& j_analytical_do,
              const ArrayOfRetrievalQuantity& jacobian_quantities,
              const ArrayOfArrayOfIndex& jacobian_indices,
              const ArrayOfString& iy_aux_vars,
              const Verbosity& verbosity);
 
void iy_transmittance_mult(Tensor3& iy_trans_total,
                          const ConstTensor3View& iy_trans_old,
                          const ConstTensor3View& iy_trans_new);
 
void iy_transmittance_mult(Matrix& iy_new,
                           const ConstTensor3View& iy_trans,
                           const ConstMatrixView& iy_old);
 
void mirror_los(Vector& los_mirrored,
                const ConstVectorView& los,
                const Index& atmosphere_dim);
 
 
void muellersparse_rotation(Sparse& H,
                            const Index& stokes_dim,
                            const Numeric& rotangle);
 
 
void mueller_modif2stokes(Matrix& Cs,
                          const Index& stokes_dim);
 
 
void mueller_rotation(Matrix& L,
                      const Index& stokes_dim,
                      const Numeric& rotangle);
 
 
void mueller_stokes2modif(Matrix& Cm,
                          const Index& stokes_dim);
 
void pos2true_latlon(Numeric& lat,
                     Numeric& lon,
                     const Index& atmosphere_dim,
                     const ConstVectorView& lat_grid,
                     const ConstVectorView& lat_true,
                     const ConstVectorView& lon_true,
                     const ConstVectorView& pos);
 
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_transmittance,
    const Agenda& water_p_eq_agenda,
    const ArrayOfRetrievalQuantity& jacobian_quantities,
    const ArrayOfIndex& jac_species_i);
 
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,
                            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& 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