calc_Cd

  Calc_cd Setup a covariance model to account for borehole imperfections

  Call: Cd=calc_Cd(ant_pos,var_uncor,var_cor1,var_cor2,L)
  This function sets up a data covariance matrix that accounts for static
  (i.e. correlated) data errors.

  Inputs:
  * ant_pos: A N x 4 array that contains N combinations of transmitter/source 
  and receiver positions. The first two columns are the x- and y-coordinates
  of the transmitter/source position. The last two columns are the x- and 
  y-coordiantes of the receiver position.
  * var_uncor: The variance of the uncorrelated data errors.
  * var_cor1: The variance of the correlated data errors
  related to the transmitter/source positions.
  * var_cor2: The variance of the correlated data errors
  related to the receiver positions.
  * L: The correlation length for the correlation between the individual
  transmitter/source or receiver positions using an exponential covariance 
  function. For typical static errors the correlation length is set to a 
  small number (e.g. 10^-6).

  For more details and practical examples see:
  Cordua et al., 2008 in Vadose zone journal.
  Cordua et al., 2009 in Journal of applied geophysics.

  Knud S. Cordua (2012)

eikonal

  eikonal Traveltime computation by solving the eikonal equation

  tmap=eikonal(x,y,z,V,Sources,type);

   x,y,z : arrays defining the x, y, and z axis
   V: velocity field, with size (length(y),length(x),length(z));
   Sources [ndata,ndim] : Source positions
   type (optional): type of eikonal solver: [1]:Fast Marching(default), [2]:FD

   tmap [size(V)]: travel times computed everywhere in the velocity grid

 %Example (2D):
    x=[1:1:100];
    y=1:1:100;
    z=1;
    V=ones(100,100);V(:,1:50)=2;
    Sources = [10 50;75 50];
    t=eikonal(x,y,z,V,Sources);
    subplot(1,2,1);imagesc(x,y,t(:,:,1,1));axis image;colorbar
    subplot(1,2,2);imagesc(x,y,t(:,:,1,2));axis image;colorbar

  See also eikonal_traveltime

eikonal_raylength

  eikonal_raylength : Computes the raylength from S to R using the eikonal equaiton

  Call:
    raylength=eikonal_raylength(x,y,v,S,R,tS,doPlot)

eikonal_traveltime

  eikonal_traveltime Computes traveltime between sources and receivers by solving the eikonal equation

  t=eikonal_traveltime(x,y,z,V,Sources,Receivers,iuse,type);

   x,y,z : arrays defining the x, y, and z axis
   V: velocity field, with size (length(y),length(x),length(z));
   Sources [ndata,ndim] : Source positions
   Receivers [ndata,ndim] : Receiver positions
   iuse (optional): optionally only use subset of data. eg.g i_use=[1 2 4];
   type (optional): type of eikonal solver: [1]:Fast Marching(default), [2]:FD

   tmap [size(V)]: travel times computed everywhere in the velocity grid

 %Example (2%

  Example 2d traveltime compuation

  Example (2D):
    x=[1:1:100];
    y=1:1:100;
    z=1;
    V=ones(100,100);V(:,1:50)=2;
    S=[50 50 1;50 50 1];
    R=[90 90 1; 90 80 1];
    t=eikonal_traveltime(x,y,z,V,S,R)

  Example (3D):
    nx=50;ny=50;nz=50;
    x=1:1:nx;
    y=1:1:ny;
    z=1:1:nz;
    V=ones(ny,nx,nz);V(:,1:50,:)=2;
    S=[10 10 1;10 10 1;10 9 1];
    R=[40 40 40; 40 39 40; 40 40 40];
    t=eikonal_traveltime(x,y,z,V,S,R)


  See also eikonal

kernel_buursink_2d

  kernel_buursink_2k Computes 2D Sensitivity kernel based on 1st order EM scattering theory

  See 
    Buursink et al. 2008. Crosshole radar velocity tomography 
                          with finite-frequency Fresnel. Geophys J. Int.
                          (172) 117;

   CALL : 
      % specify a source trace (dt, wf_trace):
      [kernel,L,L1_all,L2_all]=kernel_buursink_2d(model,x,z,S,R,dt,wf_trace);
      % Use a ricker wavelet with center frequency 'f0'
      [kernel,L,L1_all,L2_all]=kernel_buursink_2d(model,x,z,S,R,f0));


  Knud Cordua, 2009, 
  Thomas Mejer Hansen (small edits, 2009)

kernel_finite_2d

  kernel_finite_2d 2D sensitivity kernels

   Call:
     [Knorm,K,dt,options]=kernel_finite_2d(v_ref,x,y,S,R,freq,options);

kernel_fresnel_2d

  kernel_fresnel_2d Sensitivity kernel for amplitude and first arrival

  Call:
    [kernel_t,kernel_a,P_omega,omega]=kernel_fresnel_2d(v,x,y,S,R,omega,P_omega);


  Based on Liu, Dong, Wang, Zhu and Ma, 2009, Sensitivity kernels for
  seismic Fresenl volume Tomography, Geophysics, 75(5), U35-U46

  See also kernel_fresnel_monochrome_2d

  Run with no argument for an example.

kernel_fresnel_monochrome_2d

  kernel_fresnel_monochrome_2d 2D monchrome kernel for amplitude and first arrival

  Call:
    [kernel_t,kernel_a]=kernel_fresnel_monochrome_2d(v,x,y,S,R,omega);
  or
    [kernel_t,kernel_a]=kernel_fresnel_monochrome_2d(v,x,y,S,R,omega,L,L1,L2);

  Based on Liu, Dong, Wang, Zhu and Ma, 2009, Sensitivity kernels for
  seismic Fresenl volume Tomography, Geophysics, 75(5), U35-U46

  See also, kernel_fresnel_2d

kernel_multiple

  kernel_multiple Computes the sensitivity kernel for a wave traveling
  from S to R.

  CALL : 
     [K,RAY,Gk,Gray,timeS,timeR,raypath]=kernel_multiple(Vel,x,y,z,S,R,T,alpha,Knorm);

  IN : 
     Vel [ny,nx] : Velocity field
     x [1:nx] :
     y [1:ny] :
     z [1:nz] :
     S [1,3] : Location of Source
     R [1,3] : Location of Receiver
     T : Donminant period
     alpha: controls exponential decay away ray path
     Knorm [1] : normaliztion of K [0]:none, K:[1]:vertical

  OUT :
     K : Sensitivity kernel
     R : Ray sensitivity kernel (High Frequency approx)
     timeS : travel computed form Source
     timeR : travel computed form Receiver
     raypath [nraydata,ndim] : the center of the raypath 

  The sensitivity is the length travelled in each cell.


  See also : fast_fd_2d

  TMH/2006

kernel_slowness_to_velocity

  kernel_slowness_to_velocity Converts from slowness to velocity parameterizations

  G : kernel [1,nkernels]
  V : Velocity field (


  CALL:
    G_vel=kernel_slowness_to_velocity(G,V);
  or 
    [G_vel,v_obs]=kernel_slowness_to_velocity(G,V,t);
  or
    [G_vel,v_obs,Cd_v]=kernel_slowness_to_velocity(G,V,t,Cd);

mspectrum

  mspectrum : Amplitude and Power spectrum
  Call  :
      function [A,P,smoothP,kx]=mspectrum(x,dx)

  1D (A)mplitude and (P)owerspectrum of x-series with spacing dx

munk_fresnel_2d

  2D frechet kernel, First Fresnel Zone 

  See Jensen, Jacobsen, Christensen-Dalsgaard (2000) Solar Physics 192.

  Call :
  S=munk_fresnel_2d(T,dt,alpha,As,Ar,K);

  T : dominant period
  dt : 
  alpha : degree of cancellation 
  As : Amplitude fo the wavefield propagating from the source
  Ar : Amplitude fo the wavefield propagating from the receiver
  K : normalization factor

munk_fresnel_3d

  3D frechet kernel, First Fresnel Zone 

  See Jensen, Jacobsen, Christensen-Dalsgaard (2000) Solar Physics 192.

  Call :

pick_first_arrival

  pick_first_arrival : pick first arrival travel time data using simple
                       correlation

  Call 
    [tt_pick]=pick_first_arrival(wf_data,ref_trace,ref_t0,doPlot,wf_time);

plot_traveltime_sr

  plot_traveltime_sr

  Call 
     plot_traveltime(S,R)
     S: [n,2] : source locattion
     R: [n,2] : reveiver locattion
     or (3d)
     S: [n,3] : source locattion
     R: [n,3] : reveiver locattion


  EX:
   % 2D
   D=load('AM13_data.mat');
   plot_traveltime_sr(D.S,D.R);
   or
   ant_pos=[D.S,D.R];
   plot_traveltime_sr(ant_pos);

   % 3D
   D=load('AM1234_data.mat');
   plot_traveltime_sr(D.S,D.R);

sippi_forward_traveltime

  sippi_forward_traveltime Traveltime computation in SIPPI

  Call :
    [d,forward,prior,data]=sippi_forward_traveltime(m,forward,prior,data)

    forward.type determines the method used to compute travel times
    forward.type='ray';
    forward.type='fat';
    forward.type='eikonal';
    forward.type='born';
    forward.type='fd';

    forward.sources [ndata,ndim]: Source locations
    forward.receivers [ndata,ndim]: Receiver locations

    % the following options does not apply to 'eikonal' type modeling
    forward.linear : [0] a linear kernel is computed, based on the current velocity model
                     [1] a linear kenrel is computed only once, based on
                     the velocity field defined in forward.linear_m;

    forward.linear_m: the reference velocity field, for a linear forward
                      operator (forward.G) will be computed.
                      Can be eithe a scalar (constant velocity field) or
                      the same size as the the velcity model 'm'.

    forward.normalize_vertical [1]: Normalize sensitivitykernel by
                                    in vertical slices
                               [0]: No normalization

    forward.alpha [1]: alpha value for munk_fresnel_2d, munk_fresnel_3f

sippi_forward_traveltime_example

  sippi_forward_traveltime_example: Different examples of travel time
       computation

  See also: sippi_forward_traveltime

 % load some data

tomography_kernel

  tomography_kernel Computes the sensitivity kernel for a wave traveling from S to R.

  CALL :
     [K,RAY,Gk,Gray,timeS,timeR,raypath]=tomography_kernel(Vel,x,y,z,S,R,T,alpha,Knorm);

  IN :
     Vel [ny,nx] : Velocity field
     x [1:nx] :
     y [1:ny] :
     z [1:nz] :
     S [1,3] : Location of Source
     R [1,3] : Location of Receiver
     T : Donminant period
     alpha: controls exponential decay away ray path
     Knorm [1] : normaliztion of K [0]:none, K:[1]:vertical

  OUT :
     K : Sensitivity kernel
     R : Ray sensitivity kernel (High Frequency approx)
     timeS : travel computed form Source
     timeR : travel computed form Receiver
     raypath [nraydata,ndim] : the center of the raypath

  The sensitivity is the length travelled in each cell.

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