%transform LIF images to concentration images

function [DataOut,DataOut_1,DataMask]=concentration(Data,XmlData,Data_1,XmlData_1,Ref)
cpath=which('uvmat');
addpath(fullfile(fileparts(cpath),'transform_field'))% define path for phys_polar.m
DataOut_1=[];

%%  for use in uvmat
num_level=Data.ZIndex;
if ~exist('Ref','var')
    huvmat=findobj(allchild(0),'tag','uvmat');
    hhuvmat=guidata(huvmat);
    RootPath=get(hhuvmat.RootPath,'String');
    
    %reference file
    RootPath=fullfile(RootPath,'LIF_REF');
    file_ref=fullfile(RootPath,['lif_ref_' num2str(num_level) '.nc']);
    Ref=nc2struct(file_ref);
end

%% Parameters
XmlData.GeometryCalib.PolarCentre=Ref.IlluminationOrigin;%[-515 -175]; %position of the laser origin [x, y]
XmlData_1.GeometryCalib.PolarCentre=Ref.IlluminationOrigin;%[-515 -175]; %position of the laser origin [x, y]
ImageOffset=Ref.ImageOffset; %237;% image value for black background 
nfilt=64;

%% concentration image
Data.A(Ref.CoverIndex:end,:)=Ref.CoverCoeff*(double(Data.A(Ref.CoverIndex:end,:))-ImageOffset(1))+ImageOffset(1);% COMPENSATION OF BRIGHTNESS UNDER THE COVER
[DataOut,DataOut_1]=phys_polar(Data,XmlData,Data_1,XmlData_1);
A=Ref.Aref;%default
ind_good=find(Ref.Aref~=0);
ind_bad=find(Ref.Aref==0);
A(ind_good)=double(DataOut.A(ind_good))-ImageOffset(1)-0.07*(double(DataOut_1.A(ind_good))-ImageOffset(2));%substract PIV image information for removing particles
%filtering and decimate
Afilt=filter2(ones(nfilt,nfilt),A);
Mask=filter2(ones(nfilt,nfilt),double(Ref.Aref~=0));
B=Afilt./Mask;
A(ind_bad)=B(ind_bad);
[npy,npx]=size(A);
DataMask=DataOut;
DataMask.A=2*ones(npy,npx);%mask=2 for good data

DataMask.A(Ref.Aref==0)=1;%mask=0 for undefined data



C=filter2(ones(nfilt,nfilt),Ref.Aref);
D=C./Mask;
Ref.Aref(ind_bad)=D(ind_bad);
DataOut_1=[];
Coord_x=DataOut.Coord_x;
Coord_y=DataOut.Coord_y;

dX=(Coord_x(2)-Coord_x(1))/(npx-1);
dY=(Coord_y(1)-Coord_y(2))/(npy-1);%mesh of new pixels
[R,Y]=meshgrid(linspace(Coord_x(1),Coord_x(2),npx),linspace(Coord_y(1),Coord_y(2),npy));
r=Coord_x(1)+[0:npx-1]*dX;%distance from laser
%A(ind_good)=(A(ind_good)>=0).*A(ind_good); %replaces negative values  by zeros
A=A./Ref.Aref;% luminosity normalised by the reference (value at the edge of the box)

%% Interpolation
% [Rindex,Yindex]=meshgrid(linspace(0.5,npx-0.5,npx),linspace(npy-0.5,0.5,npy));
% Rgood=Rindex(ind_good);
% Ygood=Yindex(ind_good);
%F=TriScatteredInterp(Rgood,Ygood,A(ind_good));
%A=F(Rindex,Yindex);


DataMask.A(isnan(A)|isinf(A)|A>1.5)=0;% mask=1 for interpolated data
r_edge=Ref.r_edge*ones(1,npx);
Edge_ind=find((abs(R-r_edge)/dX)<=1 & DataMask.A~=0);%indies of positions close to r_edge, values greater than 1 are not expected
yedge=min(min(Y(Edge_ind)));
jmax=round(-(yedge-Coord_y(1))/dY+1);
DataMask.A(jmax:end,:)=0;

A(isnan(A)|isinf(A))=0;

% radius along the reference line
Theta=(linspace(Coord_y(1),Coord_y(2),npy)*pi/180)'*ones(1,npx);%theta in radians

gamma_coeff=Ref.GammaCoeff*ones(1,npx);

A(R<r_edge)=0;
I=(r_edge-dX*gamma_coeff.*cumsum(R.*A,2))./R;% expected laser intensity along the line

DataOut.A=A./I;%concentration
DataOut.A(I<=0)=0;% eliminate values obtained with I<=0
DataOut.A(jmax:end,:)=0;%put to zeros points for which the e laser ray is not visible from the edge
RangeX=Ref.RangeX-XmlData.GeometryCalib.PolarCentre(1);
RangeY=Ref.RangeY-XmlData.GeometryCalib.PolarCentre(2);

DataOut=polar2phys(DataOut,RangeX,RangeY);
DataOut.Coord_x=DataOut.Coord_x+XmlData.GeometryCalib.PolarCentre(1);
DataOut.Coord_y=DataOut.Coord_y+XmlData.GeometryCalib.PolarCentre(2);
DataMask=polar2phys(DataMask,RangeX,RangeY);
DataMask.Coord_x=DataMask.Coord_x+XmlData.GeometryCalib.PolarCentre(1);
DataMask.Coord_y=DataMask.Coord_y+XmlData.GeometryCalib.PolarCentre(2);


function DataOut=polar2phys(DataIn,RangeX,RangeY)
%%%%%%%%%%%%%%%%%%%%
DataOut=DataIn; %fdefault
[npy,npx]=size(DataIn.A);
dx=(DataIn.Coord_x(2)-DataIn.Coord_x(1))/(npx-1); 
dy=(DataIn.Coord_y(2)-DataIn.Coord_y(1))/(npy-1);%mesh
rcorner=[DataIn.Coord_x(1) DataIn.Coord_x(2) DataIn.Coord_x(1) DataIn.Coord_x(2)];% radius of the corners
ycorner=[DataIn.Coord_y(2) DataIn.Coord_y(2) DataIn.Coord_y(1) DataIn.Coord_y(1)];% azimuth of the corners
thetacorner=pi*ycorner/180;% azimuth in radians
[Xcorner,Ycorner] = pol2cart(thetacorner,rcorner);% cartesian coordinates of the corners (with respect to lser source)
if ~exist('RangeX','var')
RangeX(1)=min(Xcorner);
RangeX(2)=max(Xcorner);
end
if ~exist('RangeY','var')
RangeY(2)=min(Ycorner);
RangeY(1)=max(Ycorner);
end
%Rangx=[-100 100];%bounds of the initial box 
%Rangy=[75 -150];
% Rangy(1)=min(Ycorner);
% Rangy(2)=max(Ycorner);
x=linspace(RangeX(1),RangeX(2),npx);%coordinates of the new pixels
y=linspace(RangeY(2),RangeY(1),npy);
[X,Y]=meshgrid(x,y);%grid for new pixels in cartesian coordiantes

[Theta,R] = cart2pol(X,Y);%corresponding polar coordiantes
Theta=Theta*180/pi;
%Theta=1+round((Theta-DataIn.Coord_y(1))/dy); %index along y (dy negative)
Theta=1-round((Theta-DataIn.Coord_y(2))/dy); %index along y (dy negative)
R=1+round((R-DataIn.Coord_x(1))/dx); %index along x 
R=reshape(R,1,npx*npy);%indices reorganized in 'line'
Theta=reshape(Theta,1,npx*npy);
flagin=R>=1 & R<=npx & Theta >=1 & Theta<=npy;%flagin=1 inside the original image
vec_A=reshape(DataIn.A,1,npx*npy);%put the original image in line
ind_in=find(flagin);
ind_out=find(~flagin);
ICOMB=((R-1)*npy+(npy+1-Theta));
ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A
vec_B(ind_in)=vec_A(ICOMB);
vec_B(ind_out)=zeros(size(ind_out));
DataOut.A=flipdim(reshape(vec_B,npy,npx),1);%new image in real coordinates

     %Rangx=Rangx-radius_ref;
DataOut.Coord_x=RangeX;
DataOut.Coord_y=RangeY;  

