1  %transform LIF images to concentration images


2 


3  %=======================================================================


4  % Copyright 20082020, LEGI UMR 5519 / CNRS UGA GINP, Grenoble, France


5  % http://www.legi.grenobleinp.fr


6  % Joel.Sommeria  Joel.Sommeria (A) legi.cnrs.fr


7  %


8  % This file is part of the toolbox UVMAT.


9  %


10  % UVMAT is free software; you can redistribute it and/or modify


11  % it under the terms of the GNU General Public License as published


12  % by the Free Software Foundation; either version 2 of the license,


13  % or (at your option) any later version.


14  %


15  % UVMAT is distributed in the hope that it will be useful,


16  % but WITHOUT ANY WARRANTY; without even the implied warranty of


17  % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the


18  % GNU General Public License (see LICENSE.txt) for more details.


19  %=======================================================================


20 


21  function [DataOut]=ima2concentration(DataIn,XmlData)


22 


23  %% request input parameters


24  DataOut=[];


25  if (isfield(DataIn,'Action') && isfield(DataIn.Action,'RUN') && isequal(DataIn.Action.RUN,0))


26  return


27  end


28  if ~isfield(XmlData,'LIFCalib')


29  msgbox_uvmat('ERROR','no LIF calibration data available, first run LIFCalib in uvmat')


30  return


31  end


32  cpath=which('uvmat');


33  addpath(fullfile(fileparts(cpath),'transform_field'))% define path for phys_polar.m


34 


35  %% rescale the image


36  [nby,nbx]=size(DataIn.A);


37  x=linspace(DataIn.Coord_x(1),DataIn.Coord_x(2),nbx)nbx/2;


38  y=linspace(DataIn.Coord_y(1),DataIn.Coord_y(2),nby)nby/2;


39  [X,Y]=meshgrid(x,y);


40  coeff_quad=0.15*4/(nbx*nbx);% image luminosity reduced by 10% at the edge


41  DataIn.A=double(DataIn.A).*(1+coeff_quad*(X.*X+Y.*Y));


42 


43  %% Transform images to polar coordinates with origin at the light source position


44  XmlData.TransformInput.PolarCentre=XmlData.LIFCalib.LightOrigin; %position of the laser origin [x, y]


45  DataIn.Action.RUN=1;% avoid input menu in phys_polar


46  DataOut=phys_polar(DataIn,XmlData);


47  [npangle,npr]=size(DataOut.A);%size of the image in polar coordinates


48  dX=(DataOut.Coord_x(2)DataOut.Coord_x(1))/(npr1);% radial step


49 


50  %% introduce the reference line where the laser enters the fluid region


51  r_edge=XmlData.LIFCalib.RefLineRadius'*ones(1,npr);% radial position of the reference line extended as a matrix (npx,npy)


52  A_ref=XmlData.LIFCalib.RefLineLum'*ones(1,npr);% luminosity on the reference line extended as a matrix (npx,npy)


53  R=ones(npangle,1)*linspace(DataOut.Coord_x(1), DataOut.Coord_x(2),npr);%radial coordinate extended as a matrix (npx,npy)


54 


55  %gamma_coeff=XmlData.LIFCalib.DecayRate;


56  DataOut.A(R<r_edge)=0;


57  DataOut.A=double(DataOut.A)./A_ref;% renormalize the luminosity with the reference luminosity at the same azimuth on the reference line


58  I=(r_edgedX*XmlData.LIFCalib.DecayRate.*cumsum(R.*DataOut.A,2))./R;% expected laser intensity along the line


59  DataOut.A=DataOut.A./I;%concentration normalized by the uniform concentration assumed in the ref image used for calibration


60  DataOut.A(I<=0)=0;% eliminate values obtained with I<=0


61 


62  DataOut=polar2phys(DataOut);% back to phys cartesian coordinates with origin at the light source


63  DataOut.A=uint16(1000*DataOut.A);% concentration multiplied by 1000 to get an image


64  DataOut.Coord_x=DataOut.Coord_x+XmlData.LIFCalib.LightOrigin(1);%shift to original cartesian coordinates


65  DataOut.Coord_y=DataOut.Coord_y+XmlData.LIFCalib.LightOrigin(2);


66 


67 


68  function DataOut=polar2phys(DataIn)


69  %%%%%%%%%%%%%%%%%%%%


70  DataOut=DataIn; %default


71  [npy,npx]=size(DataIn.A);


72  dx=(DataIn.Coord_x(2)DataIn.Coord_x(1))/(npx1); %mesh along radius


73  dy=(DataIn.Coord_y(2)DataIn.Coord_y(1))/(npy1);%mesh along azimuth


74 


75  %% create cartesian coordinates in the domain defined by the four image corners


76  rcorner=[DataIn.Coord_x(1) DataIn.Coord_x(2) DataIn.Coord_x(1) DataIn.Coord_x(2)];% radius of the corners


77  ycorner=[DataIn.Coord_y(2) DataIn.Coord_y(2) DataIn.Coord_y(1) DataIn.Coord_y(1)];% azimuth of the corners


78  thetacorner=pi*ycorner/180;% azimuth in radians


79  [Xcorner,Ycorner] = pol2cart(thetacorner,rcorner);% cartesian coordinates of the corners (with respect to lser source)


80  RangeX(1)=min(Xcorner);


81  RangeX(2)=max(Xcorner);


82  RangeY(2)=min(Ycorner);


83  RangeY(1)=max(Ycorner);


84  x=linspace(RangeX(1),RangeX(2),npx);%coordinates of the new pixels


85  y=linspace(RangeY(2),RangeY(1),npy);


86  [X,Y]=meshgrid(x,y);%grid for new pixels in cartesian coordinates


87 


88  %% image indices corresponding to the cartesian grid


89  [Theta,R] = cart2pol(X,Y);%corresponding polar coordiantes


90  Theta=180*Theta/pi;%angles in degrees


91  Theta=1round((ThetaDataIn.Coord_y(2))/dy); %angular index along y (dy negative)


92  R=1+round((RDataIn.Coord_x(1))/dx); %angular index along x


93  R=reshape(R,1,npx*npy);%indices reorganized in 'line'


94  Theta=reshape(Theta,1,npx*npy);


95  flagin=R>=1 & R<=npx & Theta >=1 & Theta<=npy;%flagin=1 inside the original image


96  vec_A=reshape(DataIn.A,1,npx*npy);%put the original image in line


97  ind_in=find(flagin);


98  ind_out=find(~flagin);


99  ICOMB=((R1)*npy+(npy+1Theta));


100  ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A


101  vec_B(ind_in)=vec_A(ICOMB);


102  vec_B(ind_out)=zeros(size(ind_out));


103  DataOut.A=flipdim(reshape(vec_B,npy,npx),1);%new image in real coordinates


104  DataOut.Coord_x=RangeX;


105  DataOut.Coord_y=RangeY;


106 

