Description of RUN

0001 %'RUN_STLIN': combine velocity fields for stereo PIV
0002 % file_A,file_B: input velocity files
0003 %vel_type: string ='civ1' or 'civ2'
0004 function RUN_STLIN(file_A,file_B,vel_type,file_st,nx_patch,ny_patch,thresh_patch,fileAxml,fileBxml)
0005                 
0006  [XmlDataA,error]=imadoc2struct(fileAxml); 
0007  [XmlDataB,error]=imadoc2struct(fileBxml);
0008  npxA=[]; npyA=[]; pxB=[]; npyB=[];
0009  if isfield(XmlDataA,'Camera') && isfield(XmlDataB,'Camera')
0010       if isfield(XmlDataA.Camera,'ImageSize')&& isfield(XmlDataB.Camera,'ImageSize')
0011           ImageSizeA=XmlDataA.Camera.ImageSize;
0012           ImageSizeB=XmlDataB.Camera.ImageSize;
0013           if ~isempty(ImageSizeA)&& ~isempty(ImageSizeB)
0014                xindex=findstr(ImageSizeA,'x');
0015                if length(xindex)>=2
0016                     npxA=str2num(ImageSizeA(1:xindex(1)-1));
0017                     npyA=str2num(ImageSizeA(xindex(1)+1:xindex(2)-1));
0018                end
0019                xindex=findstr(ImageSizeB,'x');
0020                if length(xindex)>=2
0021                     npxB=str2num(ImageSizeB(1:xindex(1)-1));
0022                     npyB=str2num(ImageSizeB(xindex(1)+1:xindex(2)-1));
0023                end
0024           end
0025      end
0026  end
0027  if isempty(npxA) ||isempty(npxB)
0028      warndlg_uvmat('The size of image A needs to be defined in the xml file ImaDoc','ERROR')
0029      return
0030  elseif isempty(npxB) || isempty(npyB)
0031       warndlg_uvmat('The size of image B needs to be defined in the xml file ImaDoc','ERROR')
0032      return
0033  end
0034  if isfield(XmlDataA,'GeometryCalib')
0035      tsaiA=XmlDataA.GeometryCalib;
0036  else
0037      warndlg_uvmat('no geometric calibration available for image A','ERROR')
0038      return
0039  end
0040  if isfield(XmlDataB,'GeometryCalib')
0041      tsaiB=XmlDataB.GeometryCalib;
0042  else
0043      warndlg_uvmat('no geometric calibration available for image B','ERROR')
0044      return
0045  end
0046  
0047  %corners of each image in real coordinates:
0048  cornerA(:,1)=[0 0 npxA npxA]';%x positions
0049  cornerA(:,2)=[0 npyA 0 npyA]';%y positions
0050  cornerB(:,1)=[0 0 npxB npxB]';%x positions
0051  cornerB(:,2)=[0 npyB 0 npyB]';%y positions
0052 [xyA(:,1),xyA(:,2)]=phys_XYZ(tsaiA,cornerA(:,1),cornerA(:,2));
0053 [xyB(:,1),xyB(:,2)]=phys_XYZ(tsaiB,cornerB(:,1),cornerB(:,2));
0054  max_x=max(max(xyA(:,1)),max(xyB(:,1)));%maximum on the 4 corners of the the images
0055  min_x=min(min(xyA(:,1)),min(xyB(:,1)));%minimum on the 4 corners of the the images
0056  max_y=max(max(xyA(:,2)),max(xyB(:,2)));
0057  min_y=min(min(xyA(:,2)),min(xyB(:,2)));
0058  array_realx=[min_x:(max_x-min_x)/(nx_patch-1):max_x];
0059  array_realy=[min_y:(max_y-min_y)/(ny_patch-1):max_y];
0060  [grid_realx,grid_realy]=meshgrid(array_realx,array_realy);
0061  grid_real(:,1)=reshape(grid_realx,nx_patch*ny_patch,1);
0062  grid_real(:,2)=reshape(grid_realy,nx_patch*ny_patch,1);
0063  grid_real(:,3)=zeros(nx_patch*ny_patch,1);
0064 [grid_imaA(:,1),grid_imaA(:,2)]=px_XYZ(tsaiA,grid_real(:,1),grid_real(:,2));
0065 [grid_imaB(:,1),grid_imaB(:,2)]=px_XYZ(tsaiB,grid_real(:,1),grid_real(:,2));
0066 
0067  flagA=grid_imaA(:,1)>0 & grid_imaA(:,1)<npxA & grid_imaA(:,2)>0 & grid_imaA(:,2)<npyA;
0068  flagB=grid_imaB(:,1)>0 & grid_imaB(:,1)<npxB & grid_imaB(:,2)>0 & grid_imaB(:,2)<npyB;
0069  ind_good=find(flagA==1&flagB==1);
0070  XimaA=grid_imaA(ind_good,1);
0071  YimaA=grid_imaA(ind_good,2);
0072  XimaB=grid_imaB(ind_good,1);
0073  YimaB=grid_imaB(ind_good,2);
0074  grid_real_x=grid_real(ind_good,1);
0075  grid_real_y=grid_real(ind_good,2);
0076 
0077 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0078 % %read the velocity fields
0079 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0080 %
0081 % [dt,time1,pixcmx,pixcmy,vec_X,vec_Y,vec_Z,vec_U,vec_V,vec_W,vec_C,vec_F,fixflag,vel_type_out,error,nb_coord,nb_dim]...
0082 %     =read_vel({filecell_ncA},{vel_type});
0083 %read field A
0084 [Field,VelTypeOut]=read_civxdata(file_A,[],vel_type);
0085 %interpolate on XimaA
0086 Field.X=Field.X(find(Field.FF==0));
0087 Field.Y=Field.Y(find(Field.FF==0));
0088 Field.U=Field.U(find(Field.FF==0));
0089 Field.V=Field.V(find(Field.FF==0));
0090 dXa= griddata_uvmat(Field.X,Field.Y,Field.U,XimaA,YimaA);
0091 dYa= griddata_uvmat(Field.X,Field.Y,Field.V,XimaA,YimaA);
0092 dt=Field.dt;
0093 time=Field.Time;
0094 
0095 %read field B
0096 % [dt,time2,pixcmx,pixcmy,vec_X,vec_Y,vec_Z,vec_U,vec_V,vec_W,vec_C,vec_F,fixflag,vel_type_out,error,nb_coord,nb_dim]...
0097 %     =read_vel({file_B},{vel_type});
0098 [Field,VelTypeOut]=read_civxdata(file_B,FieldNames,vel_type);
0099 if ~isequal(Field.dt,dt)
0100     warndlg_uvmat('different time intervals for the two velocity fields ','ERROR')
0101      return
0102 end
0103 if ~isequal(Field.Time,time)
0104     warndlg_uvmat('different times for the two velocity fields ','ERROR')
0105      return
0106 end
0107 %interpolate on XimaB
0108 Field.X=Field.X(find(Field.FF==0));
0109 Field.Y=Field.Y(find(Field.FF==0));
0110 Field.U=Field.U(find(Field.FF==0));
0111 Field.V=Field.V(find(Field.FF==0));
0112 dXb=griddata_uvmat(Field.X,Field.Y,Field.U,XimaB,YimaB);
0113 dYb=griddata_uvmat(Field.X,Field.Y,Field.V,XimaB,YimaB);
0114 %eliminate Not-a-Number
0115 ind_Nan=find(and(~isnan(dXa),~isnan(dXb)));
0116 dXa=dXa(ind_Nan);
0117 dYa=dYa(ind_Nan);
0118 dXb=dXb(ind_Nan);
0119 dYb=dYb(ind_Nan); 
0120 grid_phys1(:,1)=grid_real_x(ind_Nan);
0121 grid_phys1(:,2)=grid_real_y(ind_Nan);
0122  
0123 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0124 %compute the coefficients
0125 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0126 
0127 
0128 [A11,A12,A13,A21,A22,A23]=pxcm_tsai(tsaiA,grid_phys1);
0129 [B11,B12,B13,B21,B22,B23]=pxcm_tsai(tsaiB,grid_phys1);
0130 
0131 C1=A11.*A22-A12.*A21;
0132 C2=A13.*A22-A12.*A23;
0133 C3=A13.*A21-A11.*A23;
0134 D1=B11.*B22-B12.*B21;
0135 D2=B13.*B22-B12.*B23;
0136 D3=B13.*B21-B11.*B23;
0137 A1=(A22.*D1.*(C1.*D3-C3.*D1)+A21.*D1.*(C2.*D1-C1.*D2));
0138 A2=(A12.*D1.*(C3.*D1-C1.*D3)+A11.*D1.*(C1.*D2-C2.*D1));
0139 B1=(B22.*C1.*(C3.*D1-C1.*D3)+B21.*C1.*(C1.*D2-C2.*D1));
0140 B2=(B12.*C1.*(C1.*D3-C3.*D1)+B11.*C1.*(C2.*D1-C1.*D2));
0141 Lambda=(A1.*dXa+A2.*dYa+B1.*dXb+B2.*dYb)./(A1.*A1+A2.*A2+B1.*B1+B2.*B2);
0142 
0143 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0144 %Projection for compatible displacements
0145 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0146 Ua=dXa-Lambda.*A1;
0147 Va=dYa-Lambda.*A2;
0148 Ub=dXb-Lambda.*B1;
0149 Vb=dYb-Lambda.*B2;
0150 
0151 %%%%%%%%%%%%%%%%%%%%%%%%%%%%
0152 %Calculations of displacements and error
0153 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0154 U=(A22.*D2.*Ua-A12.*D2.*Va-B22.*C2.*Ub+B12.*C2.*Vb)./(C1.*D2-C2.*D1);
0155 V=(A21.*D3.*Ua-A11.*D3.*Va-B21.*C3.*Ub+B11.*C3.*Vb)./(C3.*D1-C1.*D3);
0156 W=(A22.*D1.*Ua-A12.*D1.*Va-B22.*C1.*Ub+B12.*C1.*Vb)./(C2.*D1-C1.*D2);
0157 W1=(-A21.*D1.*Ua+A11.*D1.*Va+B21.*C1.*Ub-B11.*C1.*Vb)./(C1.*D3-C3.*D1);
0158 
0159 error=sqrt((A1.*dXa+A2.*dYa+B1.*dXb+B2.*dYb).*(A1.*dXa+A2.*dYa+B1.*dXb+B2.*dYb)./(A1.*A1+A2.*A2+B1.*B1+B2.*B2));
0160 
0161 ind_error=(find(error<thresh_patch));
0162 U=U(ind_error);
0163 V=V(ind_error);
0164 W=W(ind_error);%correction for water interface
0165 error=error(ind_error);
0166 
0167 %create nc grid file
0168 Result.ListGlobalAttribute={'nb_coord','nb_dim','constant_pixcm','absolut_time_T0','hart','dt','civ'};
0169 Result.nb_coord=3;%grid file, no velocity
0170 Result.nb_dim=2;
0171 Result.constant_pixcm=0;%no linear correspondance with images
0172 Result.absolut_time_T0=time;%absolute time of the field
0173 Result.hart=0;
0174 Result.dt=dt;%time interval for image correlation (put  by default)
0175 % cte.title='grid';
0176 Result.civ=0;%not a civ file (no direct correspondance with an image)
0177 Result.ListDimName={'nb_vectors'}
0178 Result.DimValue=length(U);
0179 Result.ListVarName={'vec_X';'vec_Y';'vec_U';'vec_V';'vec_W';'vec_E'};
0180 Result.VarDimIndex: {[1]  [1]  [1]  [1]  [1]  [1]}
0181 Result.vec_X= grid_phys1(ind_error,1);
0182 Result.vec_Y= grid_phys1(ind_error,2);
0183 Result.vec_U=U/dt;
0184 Result.vec_V=V/dt;
0185 Result.vec_W=W/dt;
0186 Result.vec_E=error; 
0187 % error=write_netcdf(file_st,cte,fieldlabels,grid_phys);
0188 error=struct2nc(file_st,Result);
0189 display([file_st ' written'])
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RUN_STLIN

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