Index: trunk/src/transform_field/ima2concentration.m
===================================================================
--- trunk/src/transform_field/ima2concentration.m	(revision 1073)
+++ trunk/src/transform_field/ima2concentration.m	(revision 1073)
@@ -0,0 +1,168 @@
+%transform LIF images to concentration images
+
+%=======================================================================
+% Copyright 2008-2019, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
+%   http://www.legi.grenoble-inp.fr
+%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
+%
+%     This file is part of the toolbox UVMAT.
+%
+%     UVMAT 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 of the license,
+%     or (at your option) any later version.
+%
+%     UVMAT 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 (see LICENSE.txt) for more details.
+%=======================================================================
+
+function [DataOut]=ima2concentration(DataIn,XmlData)
+%% request input parameters
+if isfield(DataIn,'Action') && isfield(DataIn.Action,'RUN') && isequal(DataIn.Action.RUN,0)
+    if ~isfield(XmlData,'LIFCalib')
+        msgbox_uvmat('ERROR','no LIF calibration data available, first run LIFCalib in uvmat')
+    return
+    end
+end
+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.TransformInput.PolarCentre=XmlData.LIFCalib.LightOrigin; %position of the laser origin [x, y]
+
+%         if isfield(XmlData.TransformInput,'PolarReferenceRadius')
+%             def{2}=num2str(XmlData.TransformInput.PolarReferenceRadius);
+%         end
+%         if isfield(XmlData.TransformInput,'PolarReferenceAngle')
+%             def{3}=num2str(XmlData.TransformInput.PolarReferenceAngle);
+
+%% concentration image
+DataIn.Action.RUN=1;% avoid input menu in phys_polar
+DataOut=phys_polar(DataIn,XmlData);
+% 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)
+% %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)
+
+[npangle,npr]=size(DataOut.A);
+dX=(DataOut.Coord_x(2)-DataOut.Coord_x(1))/(npr-1);
+r_edge=XmlData.LIFCalib.RefLineRadius'*ones(1,npr);% radial position of the reference line extended as a matrix (npx,npy)
+A_ref=XmlData.LIFCalib.RefLineLum'*ones(1,npr);% luminosity on the reference line at the edge of the box,extended as a matrix (npx,npy)
+R=ones(npangle,1)*linspace(DataOut.Coord_x(1), DataOut.Coord_x(2),npr);%radial coordinate extended as a matrix (npx,npy)
+%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=XmlData.LIFCalib.DecayRate;
+
+
+DataOut.A(R<r_edge)=0;
+DataOut.A=double(DataOut.A)./A_ref;
+I=(r_edge-dX*gamma_coeff.*cumsum(R.*DataOut.A,2))./R;% expected laser intensity along the line
+DataOut.A=DataOut.A./I;%concentration
+DataOut.A(I<=0)=0;% eliminate values obtained with I<=0
+
+RangeX=DataIn.Coord_x-XmlData.LIFCalib.LightOrigin(1);
+RangeY=DataIn.Coord_y-XmlData.LIFCalib.LightOrigin(2);
+% 
+DataOut=polar2phys(DataOut,RangeX,RangeY);
+DataOut.A=uint16(DataOut.A);
+DataOut.Coord_x=DataOut.Coord_x+XmlData.LIFCalib.LightOrigin(1);
+DataOut.Coord_y=DataOut.Coord_y+XmlData.LIFCalib.LightOrigin(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;  
+