%======================================================================

%                    P R E P I N V . M 

%                    doc: Wed Jan  7 16:46:29 2009

%                    dlm: Mon Jun  9 17:03:32 2014

%                    (c) 2009 A.M. Thurnherr

%                    uE-Info: 677 74 NIL 0 0 72 0 2 8 NIL ofnI

%======================================================================

% CHANGES BY ANT:

%   Jan  7, 2009: - tightened use of exist()

%   Oct 27, 2009: - color-coded down/upcast in fig. 6

%   Mar  4, 2010: - BUG: special code for shallow casts (no superensembles)

%			 was broken => removed

%   		  - BUG: down/upcast separation bombed wen no CTD data were

%			 available

%   Jun  9, 2014: - improved messages

function [di,p,d]=prepinv(d,p,dr)

% function [di,p,d]=prepinv(d,p,dr)

% LADCP-2 processing software version 3.0

% prepare for inverse slolve

%

% - average velocities within depth range

% 

%  Martin Visbeck, LDEO, 6/10/99

% average over all ensembles in the depth range avdz 

%  set default avdz to one bin length

p=setdefv(p,'avdz',medianan(abs(diff(d.izm(:,1)))));

p=setdefv(p,'oversample',1.0);

p=setdefv(p,'avpercent',100);

p=setdefv(p,'rotup2down',0);

p=setdefv(p,'offsetup2down',0);

p=setdefv(p,'tilt_weight',10);

p=setdefv(p,'avens',NaN);

p=setdefv(p,'soundcorr',1);

p=setdefv(p,'nav_error',30);

d=setdefv(d,'slon',d.time_jul*NaN);

d=setdefv(d,'slat',d.time_jul*NaN);

p=setdefv(p,'superens_std_min',d.down.Single_Ping_Err/sqrt(d.down.Pings_per_Ensemble));

disp('PREPINV: prepare data for inversion, form Super-Ensembles')

if isfinite(p.avens)

 disp([' average profiles over (p.avens) ',num2str(p.avens),' ensembles'])

else

 disp([' average profiles over (p.avdz) ',num2str(p.avdz),' meter'])

end

% remove bottom "bad" track values 

% This can be because of range 

if isfinite(p.zbottom)

 p=setdefv(p,'btrk_range',[300 50]);

 % backward compatible

 if length(p.btrk_range)<2, p.btrk_range(2)=0; end

 ii=find(abs(d.z+p.zbottom)>max(p.btrk_range) & isfinite(d.bvel(:,1)') );

 if length(ii)>0

  disp([' discarded ',int2str(length(ii)),...

    ' bottom tracks velocities because of height above bottom > ',int2str(max(p.btrk_range))])

  d.bvel(ii,:)=NaN;

  d.bvels(ii,:)=NaN;

 end

 ii=find(abs(d.z+p.zbottom)<min(p.btrk_range) & isfinite(d.bvel(:,1)') );

 if length(ii)>0

  disp([' discarded ',int2str(length(ii)),...

    ' bottom tracks velocities because of height above bottom < ',int2str(min(p.btrk_range))])

  d.bvel(ii,:)=NaN;

  d.bvels(ii,:)=NaN;

 end

 ii=find(abs(d.z+p.zbottom-d.hbot)> 100 );

 if length(ii)>0

  disp([' discarded ',int2str(length(ii)),...

    ' bottom distances because of depth difference > 100'])

  d.hbot(ii)=NaN;

 end

else

 d.bvel(:,:)=NaN;

 d.bvels(:,:)=NaN;

end

% reduce weight for large tilts

if p.tilt_weight>0 & existf(d,'tilt_weight')~=1

 fac=1.-tanh(d.tilt/p.tilt_weight)/2;

 d.weight=d.weight.*meshgrid(fac,d.weight(:,1));

 disp([' reduce weight for larger tilts 0.5 at ',...

        num2str(p.tilt_weight),' degree'])

 d.tilt_weight=p.tilt_weight;

end

% prepare for heading averaging

i=sqrt(-1);

u1d=exp(-i*(d.hdg(1,:))*pi/180); 

if length(d.izu)>1

 u1u=exp(-i*(d.hdg(2,:))*pi/180); 

 % get mean heading offset from COMPASS comparison

 hoff=compoff(u1d,u1u);

 % hoff=angle(u1d/u1u)*180/pi;

 p.up_dn_comp_off=hoff;

 disp([' mean heading offset from compasses = ',num2str(hoff),' deg'])

 % check tilt sensors

 % rotate by compass offset

  diary off

  hoff2=fminsearch('checktilt',0,[],[d.rol(2,:);d.pit(2,:);d.rol(1,:);d.pit(1,:)]);

  diary on

  disp([' mean heading offset from pitch/roll = ',num2str(hoff2),' deg'])

  p.up_dn_pit_rol_comp_off=hoff2;

  [d.rol(3,:),d.pit(3,:)]=uvrot(d.rol(2,:),d.pit(2,:),-hoff2);

  p.up_dn_rol_off=mean(d.rol(1,:)-d.rol(3,:));

  p.up_dn_pit_off=mean(d.pit(1,:)-d.pit(3,:));

% plot compass and tilt meter differences

  figure(6)

  clf

  orient tall

% find downcast/upcast separation

  [btm,btmi] = min(d.z);

% plot compass comparison between up and down instrument

  da=-angle(u1d)+angle(u1u*exp(i*hoff*pi/180));

  ii=find(da>pi);

  da(ii)=da(ii)-2*pi;

  ii=find(da<-pi);

  da(ii)=da(ii)+2*pi;

  subplot(311)

  plot(d.hdg(1,1:btmi),da(1:btmi)*180/pi,'r.')

  hold on

  plot(d.hdg(1,btmi:end),da(btmi:end)*180/pi,'b.')

  ylabel('Heading difference up-down')

  title([' Heading offset : ',num2str(hoff),' (r/b: down-/upcast)'])

  xlabel('Heading down')

  grid

  dhmax=sort(abs(da*180/pi));

  dhmax=dhmax(fix(end*0.95));

  if dhmax > 15 & ~existf(d,'hrot')

   warn=[' Large compass deviation: ',num2str(dhmax)];

   p.warn(size(p.warn,1)+1,1:length(warn))=warn;

  end

  dhmax=max([10 dhmax*1.3]); 

  axis([0 360 [-1 1]*dhmax])

% plot tilt meter difference

  tiltmax=p.tiltmax(1);

  subplot(312)

  pa=d.pit(1,:)-d.pit(3,:)-p.up_dn_pit_off;

  plot(d.pit(1,1:btmi),pa(1:btmi),'r.')

  hold on

  plot(d.pit(1,btmi:end),pa(btmi:end),'b.')

  ylabel('Pitch difference up-down')

  xlabel('Pitch of down instrument')

  title([' Pitch offset : ',num2str(p.up_dn_pit_off)])

  grid;

  axis([[-1 1]*tiltmax [-1 1]*5])

  subplot(313)

  ra=d.rol(1,:)-d.rol(3,:)-p.up_dn_rol_off;

  plot(d.rol(1,1:btmi),ra(1:btmi),'r.')

  hold on

  plot(d.rol(1,btmi:end),ra(btmi:end),'b.')

  ylabel('Roll difference up-down')

  xlabel('Roll of down instrument')

  title(['Roll offset : ',num2str(p.up_dn_rol_off)])

  grid;

  axis([[-1 1]*tiltmax [-1 1]*5])

  streamer([p.name,' Figure 6']);

  pause(0.01)

end

% offset upward looking ADCP to downward looking ADCP

if (p.offsetup2down~=0 & length(d.zd)~=length(d.ru(:,1)) & exist('dr','var'))

  if p.rotup2down==2

   % will not rotate to match velocities and correct offset

   p.rotup2down=1;

  end

  i=sqrt(-1);

  disp(' remove first guess ocean velocity from raw data')

  % OCEAN velocity

  [ib,it]=size(d.ru);

  z=-d.izm+d.ru*0;

  ii=find(z>=min(dr.z) & z<=max(dr.z));

  l.uoce(:,1)=interp1q(dr.z,dr.u,z(ii));

  l.uoce(:,2)=interp1q(dr.z,dr.v,z(ii));

  [prof,bin]=meshgrid(1:it,1:ib);

  l.ru=full(sparse(bin(ii),prof(ii),l.uoce(:,1)));

  l.rv=full(sparse(bin(ii),prof(ii),l.uoce(:,2)));

  l.ru(ib,it)=NaN;

  l.rv(ib,it)=NaN;

  ii=find(~(z>=min(dr.z) & z<=max(dr.z)));

  l.ru(ii)=NaN;

  l.rv(ii)=NaN;

  uu=medianan(d.ru(d.izu,:)+i*d.rv(d.izu,:)...

             -l.ru(d.izu,:)-i*l.rv(d.izu,:)+d.weight(d.izu,:)*0,2);

  ud=medianan(d.ru(d.izd,:)+i*d.rv(d.izd,:)...

             -l.ru(d.izd,:)-i*l.rv(d.izd,:)+d.weight(d.izd,:)*0,2);

  clear l

 ii=find(~isfinite(uu+ud));

 uu(ii)=0;

 ud(ii)=0;

 uoff=(ud-uu)*p.offsetup2down; 

 uoffm(d.izu,:)=meshgrid(uoff/2,d.izu);

 uoffm(d.izd,:)=meshgrid(-uoff/2,d.izd);

 d.ru=d.ru+real(uoffm); 

 d.rv=d.rv+imag(uoffm); 

 if existf(d,'bvel')

  d.bvel(:,1)=d.bvel(:,1)+real(-uoff/2)';

  d.bvel(:,2)=d.bvel(:,2)+imag(-uoff/2)';

 end

 if existf(d,'uoff')

  d.uoff=d.uoff+uoff;

 else

  d.uoff=uoff;

 end

 % estimate tilt error that could explain difference

 % beam velocity ~ W

 wbeam=(abs(d.wm)*cos(d.down.Beam_angle*pi/180));

 ii=find(wbeam<0.4);

 wbeam(ii)=NaN;

 % uerror for 1 degree tilt error

 du=wbeam/sin((d.down.Beam_angle+0.5)*pi/180)-...

    wbeam/sin((d.down.Beam_angle-0.5)*pi/180);

 % linear projection to estimate tilt error

 d.tilterr=abs(d.uoff)./abs(du);

 figure(10), clf

 orient tall

 subplot(311)

 plot(real(d.uoff))

 uoffav=boxav(d.uoff',20);

 hold on

 plot([0.5:length(uoffav)]*20,real(uoffav),'-r')

 grid

 axis tight

 ax=axis;

 ax(3:4)=[-1 1]*max(medianan(abs(real(uoffav)))*6,0.1);

 axis(ax)

 title('U offset [m/s]')

 subplot(312)

 plot(imag(d.uoff))

 hold on

 plot([0.5:length(uoffav)]*20,imag(uoffav),'-r')

 grid

 axis tight

 ax=axis;

 ax(3:4)=[-1 1]*max(medianan(abs(imag(uoffav)))*6,0.1);

 axis(ax)

 title('V offset [m/s]')

 subplot(313)

 plot(d.tilterr)

 hold on

 tilterrav=boxav(d.tilterr',20);

 plot([0.5:length(tilterrav)]*20,tilterrav,'-r')

 axis tight

 ax=axis;

 ax(3:4)=[0 1]*medianan(d.tilterr)*6;

 if isfinite(sum(ax))

  ax(4)=max(3,ax(4));

  axis(ax)

 end

 grid

 title('Tilt error [degree] consistent with offset')

 streamer([p.name,' Figure 10']);

 pause(0.01)

 disp(' adjusted for velocity offset in up and down looking ADCP')

end

if existf(p,'drot')

  if ~isfinite(p.drot)

   warn=[' magnetic deviation given is NAN '];

   p.warnp(size(p.warnp,1)+1,1:length(warn))=warn;

  end

else

   warn=[' NO magnetic deviation given '];

   p.warnp(size(p.warnp,1)+1,1:length(warn))=warn;

end

 % check if rotated already

% rotate upward looking ADCP to downward looking ADCP

if (p.rotup2down~=0 & length(d.zd)~=length(d.ru(:,1)))

  da=angle(u1d)-angle(u1u*exp(-i*hoff*pi/180));

  ii=find(da>pi); da(ii)=da(ii)-2*pi; ii=find(da<-pi); da(ii)=da(ii)+2*pi;

  d.diff_hdg=da;

  u1uc=exp(-i*(d.hdg(2,:)-hoff)*pi/180);

  hrotcomp=angle(u1uc./u1d)*180/pi;

  d.rot_comp=hrotcomp;

  % get mean heading offset from velocities

  if exist('dr','var')

   disp(' remove first guess ocean velocity from raw data')

   % OCEAN velocity

   [ib,it]=size(d.ru);

   z=-d.izm+d.ru*0;

   ii=find(z>=min(dr.z) & z<=max(dr.z));

   l.uoce(:,1)=interp1q(dr.z,dr.u,z(ii));

   l.uoce(:,2)=interp1q(dr.z,dr.v,z(ii));

   [prof,bin]=meshgrid(1:it,1:ib);

   l.ru=full(sparse(bin(ii),prof(ii),l.uoce(:,1)));

   l.rv=full(sparse(bin(ii),prof(ii),l.uoce(:,2)));

   l.ru(ib,it)=NaN;

   l.rv(ib,it)=NaN;

   ii=find(~(z>=min(dr.z) & z<=max(dr.z)));

   l.ru(ii)=NaN;

   l.rv(ii)=NaN;

   uu=medianan(d.ru(d.izu,:)+i*d.rv(d.izu,:)...

              -l.ru(d.izu,:)-i*l.rv(d.izu,:)+d.weight(d.izu,:)*0,2);

   ud=medianan(d.ru(d.izd,:)+i*d.rv(d.izd,:)...

              -l.ru(d.izd,:)-i*l.rv(d.izd,:)+d.weight(d.izd,:)*0,2);

   clear l

  else

   iz=1:4;

   uu=medianan(d.ru(d.izu(iz),:)+i*d.rv(d.izu(iz),:)+d.weight(d.izu(iz),:),1);

   ud=medianan(d.ru(d.izd(iz),:)+i*d.rv(d.izd(iz),:)+d.weight(d.izd(iz),:),1);

  end

%  try to take speed into account

  hrotvel=angle(uu./ud)*180/pi;

  d.rot_vel=hrotvel;

%  decide which to use 

  if p.rotup2down==1

   hrot=hrotcomp;

   disp(' rot up2down use mean up/down compass')

  elseif p.rotup2down==2

   hrot=hrotvel;

   disp(' rot up2down use velocties')

  elseif p.rotup2down==3

   hrot=hrotcomp;

   disp(' rot up2down use down compass')

  elseif p.rotup2down==4

   hrot=hrotcomp;

   disp(' rot up2down use up compass')

  else

   hrot=d.ru(1,:)*0;

   disp(' not sure what you want rot=0')

  end  

% plot what I am about to do

  figure(5)

  clf

  orient tall

  plot([hrotcomp-90;hrotvel-180;hrot]')

  hold on

  ax=axis;

  plot(ax(1:2),[0 0],'-k',ax(1:2),[0 0]-90,'-k',ax(1:2),[0 0]-180,'-k') 

  text(1,20,'rotation used ')

  text(1,-60,'rotation compass')

  text(1,-150,'rotation velocity')

  ax(3)=-250;

  axis(ax)

  ylabel(' heading correction for uplooking')

  streamer([p.name,' Figure 5']);

  pause(.01)

 if existf(d,'hrot')

  disp(' rotated earlier, use difference ')

  oldrot=d.hrot;

 else

  oldrot=0;

 end

 % apply rotation

  hrotm=meshgrid(hrot-oldrot,d.izd);

   % dont rotate NaNs

  ii=find(~isfinite(hrotm));

  hrotm(ii)=meannan(hrot-oldrot);

 % rotate both by half difference

  if p.rotup2down==4

   [ru,rv]=uvrot(d.ru(d.izd,:),d.rv(d.izd,:),-hrotm);

   d.ru(d.izd,:)=ru;

   d.rv(d.izd,:)=rv;

   [bu,bv]=uvrot(d.bvel(:,1),d.bvel(:,2),-(hrot-oldrot)');

   d.bvel(:,1)=bu;

   d.bvel(:,2)=bv;

  elseif p.rotup2down~=3

   [ru,rv]=uvrot(d.ru(d.izd,:),d.rv(d.izd,:),-hrotm/2);

   d.ru(d.izd,:)=ru;

   d.rv(d.izd,:)=rv;

   [bu,bv]=uvrot(d.bvel(:,1),d.bvel(:,2),-(hrot-oldrot)'/2);

   d.bvel(:,1)=bu;

   d.bvel(:,2)=bv;

  end

  hrotm=meshgrid(hrot-oldrot,d.izu);

   % dont rotate NaNs

  ii=find(~isfinite(hrotm));

  hrotm(ii)=meannan(hrot);

 % rotate both by half difference

  if p.rotup2down==4

   [ru,rv]=uvrot(d.ru(d.izu,:),d.rv(d.izu,:),hrotm);

   d.ru(d.izu,:)=ru;

   d.rv(d.izu,:)=rv;

  elseif p.rotup2down~=3

   [ru,rv]=uvrot(d.ru(d.izu,:),d.rv(d.izu,:),hrotm/2);

   d.ru(d.izu,:)=ru;

   d.rv(d.izu,:)=rv;

  end

  d.hrot=hrot;

end

% sound speed correction

if p.soundcorr==1

   if existf(d,'p')~=1

     d.p=press(abs(d.z));

   end

   if existf(d,'ss')~=1

    disp(' make soundspeed based on pressure and ADCP temp')

    d.ss=sounds(d.p,d.temp(1,:),34.5);

   end

   if d.soundc==0

    disp(' correct velocities for sound speed ')

    sc=meshgrid(d.ss./d.sv(1,:),d.izd);

    d.ru(d.izd,:)=d.ru(d.izd,:).*sc;

    d.rv(d.izd,:)=d.rv(d.izd,:).*sc;

    d.rw(d.izd,:)=d.rw(d.izd,:).*sc;

    if length(d.zd)~=length(d.ru(:,1))

     sc=meshgrid(d.ss./d.sv(1,:),d.izu);

     d.ru(d.izu,:)=d.ru(d.izu,:).*sc;

     d.rv(d.izu,:)=d.rv(d.izu,:).*sc;

     d.rw(d.izu,:)=d.rw(d.izu,:).*sc;

    end

    d.soundc=1;

   else

    disp(' will not correct for sound speed twice')

   end

end

if (isnan(p.avdz) | p.avdz<=0 ) & (isnan(p.avens) | p.avens < 2)

 disp(' avdz=NAN  => No pre-averaging done !!!')

 di.ru=d.ru;

 di.rv=d.rv;

 di.ruvs=d.ru*0+p.superens_std_min;

 di.rw=d.rw;

 di.re=d.re;

 di.ts=d.ts;

 di.tg=d.tg;

 di.weight=d.weight;

 di.bvel=d.bvel';

 di.hbot=d.hbot;

% make up std

 di.bvels=d.bvel'*0+p.single_ping_accuracy;

 di.hdg=d.hdg;

 di.pit=d.pit;

 di.rol=d.rol;

 di.temp=d.temp;

 di.tsd=d.ts(d.izd(2),:);

 di.tsd_out=d.ts(d.izd(end),:);

 di.dtiv=d.z*0+1;

 di.time_jul=d.time_jul;

 di.z=d.z;

 di.izm=d.izm;

 di.slat=d.slat;

 di.slon=d.slon;

 di.izd=d.izd;

 di.izu=d.izu;

else

% default reference velocity bin range bin 2 + 3

 if length(d.izd)>2

   izr=[min(d.izd)+[1:2]];

 end

 if length(d.izu)>2

  izr=[izr,max(d.izu)-[1:2]];

 end

 d=setdefv(d,'izr',izr);

 di.izr=d.izr;

 izr=di.izr;

% remove reference velocity and then average ensembles

  disp(' remove reference velocity and average ensembles ')

  ilast=1;

  il=length(d.izm);

  im=0;

  ibin=1:p.nbins;

% big loop

  while ilast<il 

   im=im+1;

   i=ilast;

   if p.avens>0

%  fixed number of ensembles

    i1=ilast+[1:p.avens];

   else

%  set up index for ensembles to average based on depth

    ii=find(abs(d.izm(1,(ilast+1):il)-d.izm(1,ilast))>p.avdz);

    if length(ii)<1, ii=il-ilast; end

    i1=ilast+[1:ii(1)];

   end

   i1l=length(i1)/2*p.oversample;

   i1=round(mean(i1)+[-i1l:i1l]);

   ii=find(i1<1); i1(ii)=[];

   ii=find(i1>il); i1(ii)=[];

   if length(i1)==1, i1=[i1 i1]; end

   ilast=max(i1);

   w=d.weight(izr,i1)*0+1;

   w2=d.weight(:,i1)*0+1;

% U

   ur=medianan(d.ru(izr,i1).*w);

   ruav=meannan(ur);

   i3=find(isnan(ur));