1 | %transform LIF images to concentration images
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2 |
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3 | %=======================================================================
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4 | % Copyright 2008-2016, 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,DataOut_1,DataMask]=concentration(Data,XmlData,Data_1,XmlData_1,Ref)
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22 | cpath=which('uvmat');
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23 | addpath(fullfile(fileparts(cpath),'transform_field'))% define path for phys_polar.m
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24 | DataOut_1=[];
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25 |
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26 | %% for use in uvmat
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27 | num_level=Data.ZIndex;
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28 | if ~exist('Ref','var')
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29 | huvmat=findobj(allchild(0),'tag','uvmat');
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30 | hhuvmat=guidata(huvmat);
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31 | RootPath=get(hhuvmat.RootPath,'String');
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32 |
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33 | %reference file
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34 | RootPath=fullfile(RootPath,'LIF_REF');
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35 | file_ref=fullfile(RootPath,['lif_ref_' num2str(num_level) '.nc']);
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36 | Ref=nc2struct(file_ref);
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37 | end
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38 |
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39 | %% Parameters
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40 | XmlData.GeometryCalib.PolarCentre=Ref.IlluminationOrigin;%[-515 -175]; %position of the laser origin [x, y]
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41 | XmlData_1.GeometryCalib.PolarCentre=Ref.IlluminationOrigin;%[-515 -175]; %position of the laser origin [x, y]
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42 | ImageOffset=Ref.ImageOffset; %237;% image value for black background
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43 | nfilt=64;
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44 |
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45 | %% concentration image
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46 | Data.A(Ref.CoverIndex:end,:)=Ref.CoverCoeff*(double(Data.A(Ref.CoverIndex:end,:))-ImageOffset(1))+ImageOffset(1);% COMPENSATION OF BRIGHTNESS UNDER THE COVER
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47 | [DataOut,DataOut_1]=phys_polar(Data,XmlData,Data_1,XmlData_1);
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48 | A=Ref.Aref;%default
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49 | ind_good=find(Ref.Aref~=0);
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50 | ind_bad=find(Ref.Aref==0);
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51 | 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
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52 | %filtering and decimate
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53 | Afilt=filter2(ones(nfilt,nfilt),A);
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54 | Mask=filter2(ones(nfilt,nfilt),double(Ref.Aref~=0));
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55 | B=Afilt./Mask;
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56 | A(ind_bad)=B(ind_bad);
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57 | [npy,npx]=size(A);
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58 | DataMask=DataOut;
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59 | DataMask.A=2*ones(npy,npx);%mask=2 for good data
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60 |
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61 | DataMask.A(Ref.Aref==0)=1;%mask=0 for undefined data
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62 |
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63 |
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64 |
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65 | C=filter2(ones(nfilt,nfilt),Ref.Aref);
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66 | D=C./Mask;
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67 | Ref.Aref(ind_bad)=D(ind_bad);
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68 | DataOut_1=[];
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69 | Coord_x=DataOut.Coord_x;
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70 | Coord_y=DataOut.Coord_y;
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71 |
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72 | dX=(Coord_x(2)-Coord_x(1))/(npx-1);
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73 | dY=(Coord_y(1)-Coord_y(2))/(npy-1);%mesh of new pixels
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74 | [R,Y]=meshgrid(linspace(Coord_x(1),Coord_x(2),npx),linspace(Coord_y(1),Coord_y(2),npy));
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75 | r=Coord_x(1)+[0:npx-1]*dX;%distance from laser
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76 | %A(ind_good)=(A(ind_good)>=0).*A(ind_good); %replaces negative values by zeros
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77 | A=A./Ref.Aref;% luminosity normalised by the reference (value at the edge of the box)
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78 |
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79 | %% Interpolation
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80 | % [Rindex,Yindex]=meshgrid(linspace(0.5,npx-0.5,npx),linspace(npy-0.5,0.5,npy));
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81 | % Rgood=Rindex(ind_good);
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82 | % Ygood=Yindex(ind_good);
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83 | %F=TriScatteredInterp(Rgood,Ygood,A(ind_good));
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84 | %A=F(Rindex,Yindex);
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85 |
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86 |
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87 | DataMask.A(isnan(A)|isinf(A)|A>1.5)=0;% mask=1 for interpolated data
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88 | r_edge=Ref.r_edge*ones(1,npx);
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89 | 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
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90 | yedge=min(min(Y(Edge_ind)));
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91 | jmax=round(-(yedge-Coord_y(1))/dY+1);
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92 | DataMask.A(jmax:end,:)=0;
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93 |
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94 | A(isnan(A)|isinf(A))=0;
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95 |
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96 | % radius along the reference line
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97 | Theta=(linspace(Coord_y(1),Coord_y(2),npy)*pi/180)'*ones(1,npx);%theta in radians
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98 |
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99 | gamma_coeff=Ref.GammaCoeff*ones(1,npx);
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100 |
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101 | A(R<r_edge)=0;
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102 | I=(r_edge-dX*gamma_coeff.*cumsum(R.*A,2))./R;% expected laser intensity along the line
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103 |
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104 | DataOut.A=A./I;%concentration
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105 | DataOut.A(I<=0)=0;% eliminate values obtained with I<=0
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106 | DataOut.A(jmax:end,:)=0;%put to zeros points for which the e laser ray is not visible from the edge
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107 | RangeX=Ref.RangeX-XmlData.GeometryCalib.PolarCentre(1);
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108 | RangeY=Ref.RangeY-XmlData.GeometryCalib.PolarCentre(2);
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109 |
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110 | DataOut=polar2phys(DataOut,RangeX,RangeY);
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111 | DataOut.Coord_x=DataOut.Coord_x+XmlData.GeometryCalib.PolarCentre(1);
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112 | DataOut.Coord_y=DataOut.Coord_y+XmlData.GeometryCalib.PolarCentre(2);
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113 | DataMask=polar2phys(DataMask,RangeX,RangeY);
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114 | DataMask.Coord_x=DataMask.Coord_x+XmlData.GeometryCalib.PolarCentre(1);
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115 | DataMask.Coord_y=DataMask.Coord_y+XmlData.GeometryCalib.PolarCentre(2);
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116 |
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117 |
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118 | function DataOut=polar2phys(DataIn,RangeX,RangeY)
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119 | %%%%%%%%%%%%%%%%%%%%
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120 | DataOut=DataIn; %fdefault
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121 | [npy,npx]=size(DataIn.A);
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122 | dx=(DataIn.Coord_x(2)-DataIn.Coord_x(1))/(npx-1);
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123 | dy=(DataIn.Coord_y(2)-DataIn.Coord_y(1))/(npy-1);%mesh
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124 | 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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125 | 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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126 | thetacorner=pi*ycorner/180;% azimuth in radians
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127 | [Xcorner,Ycorner] = pol2cart(thetacorner,rcorner);% cartesian coordinates of the corners (with respect to lser source)
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128 | if ~exist('RangeX','var')
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129 | RangeX(1)=min(Xcorner);
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130 | RangeX(2)=max(Xcorner);
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131 | end
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132 | if ~exist('RangeY','var')
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133 | RangeY(2)=min(Ycorner);
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134 | RangeY(1)=max(Ycorner);
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135 | end
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136 | %Rangx=[-100 100];%bounds of the initial box
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137 | %Rangy=[75 -150];
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138 | % Rangy(1)=min(Ycorner);
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139 | % Rangy(2)=max(Ycorner);
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140 | x=linspace(RangeX(1),RangeX(2),npx);%coordinates of the new pixels
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141 | y=linspace(RangeY(2),RangeY(1),npy);
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142 | [X,Y]=meshgrid(x,y);%grid for new pixels in cartesian coordiantes
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143 |
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144 | [Theta,R] = cart2pol(X,Y);%corresponding polar coordiantes
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145 | Theta=Theta*180/pi;
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146 | %Theta=1+round((Theta-DataIn.Coord_y(1))/dy); %index along y (dy negative)
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147 | Theta=1-round((Theta-DataIn.Coord_y(2))/dy); %index along y (dy negative)
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148 | R=1+round((R-DataIn.Coord_x(1))/dx); %index along x
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149 | R=reshape(R,1,npx*npy);%indices reorganized in 'line'
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150 | Theta=reshape(Theta,1,npx*npy);
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151 | flagin=R>=1 & R<=npx & Theta >=1 & Theta<=npy;%flagin=1 inside the original image
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152 | vec_A=reshape(DataIn.A,1,npx*npy);%put the original image in line
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153 | ind_in=find(flagin);
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154 | ind_out=find(~flagin);
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155 | ICOMB=((R-1)*npy+(npy+1-Theta));
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156 | ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A
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157 | vec_B(ind_in)=vec_A(ICOMB);
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158 | vec_B(ind_out)=zeros(size(ind_out));
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159 | DataOut.A=flipdim(reshape(vec_B,npy,npx),1);%new image in real coordinates
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160 |
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161 | %Rangx=Rangx-radius_ref;
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162 | DataOut.Coord_x=RangeX;
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163 | DataOut.Coord_y=RangeY;
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164 |
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