1 | %transform LIF images to concentration images
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2 |
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3 | %=======================================================================
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4 | % Copyright 2008-2019, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
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5 | % http://www.legi.grenoble-inp.fr
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6 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
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7 | %
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8 | % This file is part of the toolbox UVMAT.
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9 | %
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10 | % UVMAT is free software; you can redistribute it and/or modify
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11 | % it under the terms of the GNU General Public License as published
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12 | % by the Free Software Foundation; either version 2 of the license,
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13 | % or (at your option) any later version.
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14 | %
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15 | % UVMAT is distributed in the hope that it will be useful,
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16 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
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17 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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18 | % GNU General Public License (see LICENSE.txt) for more details.
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19 | %=======================================================================
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20 |
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21 | function [DataOut]=ima2concentration(DataIn,XmlData)
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22 |
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23 | %% request input parameters
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24 | DataOut=[];
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25 | if (isfield(DataIn,'Action') && isfield(DataIn.Action,'RUN') && isequal(DataIn.Action.RUN,0))
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26 | return
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27 | end
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28 | if ~isfield(XmlData,'LIFCalib')
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29 | msgbox_uvmat('ERROR','no LIF calibration data available, first run LIFCalib in uvmat')
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30 | return
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31 | end
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32 | cpath=which('uvmat');
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33 | addpath(fullfile(fileparts(cpath),'transform_field'))% define path for phys_polar.m
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34 |
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35 | %% rescale the image
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36 | [nby,nbx]=size(DataIn.A);
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37 | x=linspace(DataIn.Coord_x(1),DataIn.Coord_x(2),nbx)-nbx/2;
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38 | y=linspace(DataIn.Coord_y(1),DataIn.Coord_y(2),nby)-nby/2;
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39 | [X,Y]=meshgrid(x,y);
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40 | coeff_quad=0.15*4/(nbx*nbx);% image luminosity reduced by 10% at the edge
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41 | DataIn.A=double(DataIn.A).*(1+coeff_quad*(X.*X+Y.*Y));
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42 |
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43 | %% Transform images to polar coordinates with origin at the light source position
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44 | XmlData.TransformInput.PolarCentre=XmlData.LIFCalib.LightOrigin; %position of the laser origin [x, y]
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45 | DataIn.Action.RUN=1;% avoid input menu in phys_polar
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46 | DataOut=phys_polar(DataIn,XmlData);
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47 | [npangle,npr]=size(DataOut.A);%size of the image in polar coordinates
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48 | dX=(DataOut.Coord_x(2)-DataOut.Coord_x(1))/(npr-1);% radial step
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49 |
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50 | %% introduce the reference line where the laser enters the fluid region
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51 | r_edge=XmlData.LIFCalib.RefLineRadius'*ones(1,npr);% radial position of the reference line extended as a matrix (npx,npy)
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52 | A_ref=XmlData.LIFCalib.RefLineLum'*ones(1,npr);% luminosity on the reference line extended as a matrix (npx,npy)
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53 | R=ones(npangle,1)*linspace(DataOut.Coord_x(1), DataOut.Coord_x(2),npr);%radial coordinate extended as a matrix (npx,npy)
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54 |
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55 | %gamma_coeff=XmlData.LIFCalib.DecayRate;
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56 | DataOut.A(R<r_edge)=0;
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57 | DataOut.A=double(DataOut.A)./A_ref;% renormalize the luminosity with the reference luminosity at the same azimuth on the reference line
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58 | I=(r_edge-dX*XmlData.LIFCalib.DecayRate.*cumsum(R.*DataOut.A,2))./R;% expected laser intensity along the line
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59 | DataOut.A=DataOut.A./I;%concentration normalized by the uniform concentration assumed in the ref image used for calibration
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60 | DataOut.A(I<=0)=0;% eliminate values obtained with I<=0
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61 |
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62 | DataOut=polar2phys(DataOut);% back to phys cartesian coordinates with origin at the light source
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63 | DataOut.A=uint16(1000*DataOut.A);% concentration multiplied by 1000 to get an image
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64 | DataOut.Coord_x=DataOut.Coord_x+XmlData.LIFCalib.LightOrigin(1);%shift to original cartesian coordinates
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65 | DataOut.Coord_y=DataOut.Coord_y+XmlData.LIFCalib.LightOrigin(2);
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66 |
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67 |
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68 | function DataOut=polar2phys(DataIn)
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69 | %%%%%%%%%%%%%%%%%%%%
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70 | DataOut=DataIn; %default
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71 | [npy,npx]=size(DataIn.A);
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72 | dx=(DataIn.Coord_x(2)-DataIn.Coord_x(1))/(npx-1); %mesh along radius
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73 | dy=(DataIn.Coord_y(2)-DataIn.Coord_y(1))/(npy-1);%mesh along azimuth
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74 |
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75 | %% create cartesian coordinates in the domain defined by the four image corners
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76 | rcorner=[DataIn.Coord_x(1) DataIn.Coord_x(2) DataIn.Coord_x(1) DataIn.Coord_x(2)];% radius of the corners
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77 | ycorner=[DataIn.Coord_y(2) DataIn.Coord_y(2) DataIn.Coord_y(1) DataIn.Coord_y(1)];% azimuth of the corners
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78 | thetacorner=pi*ycorner/180;% azimuth in radians
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79 | [Xcorner,Ycorner] = pol2cart(thetacorner,rcorner);% cartesian coordinates of the corners (with respect to lser source)
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80 | RangeX(1)=min(Xcorner);
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81 | RangeX(2)=max(Xcorner);
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82 | RangeY(2)=min(Ycorner);
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83 | RangeY(1)=max(Ycorner);
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84 | x=linspace(RangeX(1),RangeX(2),npx);%coordinates of the new pixels
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85 | y=linspace(RangeY(2),RangeY(1),npy);
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86 | [X,Y]=meshgrid(x,y);%grid for new pixels in cartesian coordinates
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87 |
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88 | %% image indices corresponding to the cartesian grid
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89 | [Theta,R] = cart2pol(X,Y);%corresponding polar coordiantes
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90 | Theta=180*Theta/pi;%angles in degrees
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91 | Theta=1-round((Theta-DataIn.Coord_y(2))/dy); %angular index along y (dy negative)
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92 | R=1+round((R-DataIn.Coord_x(1))/dx); %angular index along x
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93 | R=reshape(R,1,npx*npy);%indices reorganized in 'line'
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94 | Theta=reshape(Theta,1,npx*npy);
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95 | flagin=R>=1 & R<=npx & Theta >=1 & Theta<=npy;%flagin=1 inside the original image
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96 | vec_A=reshape(DataIn.A,1,npx*npy);%put the original image in line
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97 | ind_in=find(flagin);
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98 | ind_out=find(~flagin);
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99 | ICOMB=((R-1)*npy+(npy+1-Theta));
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100 | ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A
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101 | vec_B(ind_in)=vec_A(ICOMB);
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102 | vec_B(ind_out)=zeros(size(ind_out));
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103 | DataOut.A=flipdim(reshape(vec_B,npy,npx),1);%new image in real coordinates
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104 | DataOut.Coord_x=RangeX;
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105 | DataOut.Coord_y=RangeY;
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106 |
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