[40] | 1 | %'phys': transforms image (px) to real world (phys) coordinates using geometric calibration parameters
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| 2 | % DataOut=phys(Data,CalibData) , transform one input field
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| 3 | % [DataOut,DataOut_1]=phys(Data,CalibData,Data_1,CalibData_1), transform two input fields
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| 4 |
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| 5 | % OUTPUT:
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| 6 | % DataOut: structure representing the modified field
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| 7 | % DataOut_1: structure representing the second modified field
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| 8 |
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| 9 | %INPUT:
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| 10 | % Data: structure of input data
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| 11 | % with fields .A (image or scalar matrix), AX, AY
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| 12 | % .X,.Y,.U,.V, .DjUi
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| 13 | % .ZIndex: index of plane in multilevel case
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| 14 | % .CoordType='phys' or 'px', The function ACTS ONLY IF .CoordType='px'
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| 15 | % CalibData: structure containing calibration parameters or a subtree Calib.GeometryCalib =calibration data (tsai parameters)
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| 16 |
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| 17 | function [DataOut,DataOut_1]=phys(varargin)
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| 18 | % A FAIRE: 1- verifier si DataIn est une 'field structure'(.ListVarName'):
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| 19 | % chercher ListVarAttribute, for each field (cell of variables):
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| 20 | % .CoordType: 'phys' or 'px' (default==phys, no transform)
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| 21 | % .scale_factor: =dt (to transform displacement into velocity) default=1
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| 22 | % .covariance: 'scalar', 'coord', 'D_i': covariant (like velocity), 'D^i': contravariant (like gradient), 'D^jD_i' (like strain tensor)
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| 23 | % (default='coord' if .Role='coord_x,_y...,
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| 24 | % 'D_i' if '.Role='vector_x,...',
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| 25 | % 'scalar', else (thenno change except scale factor)
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| 26 | Calib{1}=[];
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| 27 | if nargin==2||nargin==4 % nargin =nbre of input variables
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| 28 | Data=varargin{1};
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| 29 | DataOut=Data;%default
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| 30 | DataOut_1=[];%default
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| 31 | CalibData=varargin{2};
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| 32 | if isfield(CalibData,'GeometryCalib')
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| 33 | Calib{1}=CalibData.GeometryCalib;
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| 34 | end
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| 35 | Calib{2}=Calib{1};
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| 36 | else
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| 37 | DataOut.Txt='wrong input: need two or four structures';
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| 38 | end
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| 39 | test_1=0;
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| 40 | if nargin==4
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| 41 | test_1=1;
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| 42 | Data_1=varargin{3};
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| 43 | DataOut_1=Data_1;%default
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| 44 | CalibData_1=varargin{4};
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| 45 | if isfield(CalibData_1,'GeometryCalib')
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| 46 | Calib{2}=CalibData_1.GeometryCalib;
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| 47 | end
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| 48 | end
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| 49 | iscalar=0;
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| 50 | if ~isempty(Calib{1})
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| 51 | DataOut=phys_1(Data,Calib{1});
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| 52 | %case of images or scalar: in case of two input fields, we need to project the transform of on the same regular grid
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| 53 | if isfield(Data,'A') && isfield(Data,'AX') && ~isempty(Data.AX) && isfield(Data,'AY')&&...
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| 54 | ~isempty(Data.AY) && length(Data.A)>1
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| 55 | iscalar=1;
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| 56 | A{1}=Data.A;
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| 57 | end
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| 58 | end
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| 59 | %transform of X,Y coordinates for vector fields
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[116] | 60 | if isfield(Data,'ZIndex')&&~isempty(Data.ZIndex)&&~isnan(Data.ZIndex)
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[40] | 61 | ZIndex=Data.ZIndex;
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| 62 | else
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[116] | 63 | ZIndex=1;
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[40] | 64 | end
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| 65 | if test_1
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| 66 | DataOut_1=phys_1(Data_1,Calib{2});
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| 67 | if isfield(Data_1,'A')&&isfield(Data_1,'AX')&&~isempty(Data_1.AX) && isfield(Data_1,'AY')&&...
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| 68 | ~isempty(Data_1.AY)&&length(Data_1.A)>1
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| 69 | iscalar=iscalar+1;
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| 70 | Calib{iscalar}=Calib{2};
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| 71 | A{iscalar}=Data_1.A;
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| 72 | if isfield(Data_1,'ZIndex') && ~isequal(Data_1.ZIndex,ZIndex)
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| 73 | DataOut.Txt='inconsistent plane indexes in the two input fields';
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| 74 | end
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| 75 | if iscalar==1% case for which only the second field is a scalar
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| 76 | [A,AX,AY]=phys_Ima(A,Calib,ZIndex);
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| 77 | DataOut_1.A=A{1};
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| 78 | DataOut_1.AX=AX;
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| 79 | DataOut_1.AY=AY;
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| 80 | return
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| 81 | end
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| 82 | end
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| 83 | end
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| 84 | if iscalar~=0
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| 85 | [A,AX,AY]=phys_Ima(A,Calib,ZIndex);%TODO : introduire interp2_uvmat ds phys_ima
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| 86 | DataOut.A=A{1};
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| 87 | DataOut.AX=AX;
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| 88 | DataOut.AY=AY;
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| 89 | if iscalar==2
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| 90 | DataOut_1.A=A{2};
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| 91 | DataOut_1.AX=AX;
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| 92 | DataOut_1.AY=AY;
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| 93 | end
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| 94 | end
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| 95 |
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[209] | 96 | % DataOut.VarDimName{2}
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| 97 | % DataOut.VarDimName{3}
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| 98 | % DataOut.VarDimName{4}
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| 99 | % DataOut.VarDimName{5}
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| 100 | % DataOut.VarDimName{6}
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| 101 | % DataOut.VarDimName{7}
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| 102 | % DataOut.VarAttribute{1}
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| 103 | % DataOut.VarAttribute{2}
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| 104 | % DataOut.VarAttribute{3}
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| 105 | % DataOut.VarAttribute{4}
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| 106 | % DataOut.VarAttribute{5}
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| 107 | % DataOut.VarAttribute{6}
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| 108 | % DataOut.VarAttribute{7}
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[40] | 109 | %------------------------------------------------
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| 110 | function DataOut=phys_1(Data,Calib)
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| 111 | % for icell=1:length(Data)
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| 112 |
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| 113 | DataOut=Data;%default
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[167] | 114 | % DataOut.CoordUnit=Calib.CoordUnit; %put flag for physical coordinates
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[209] | 115 | if isfield(Calib,'SliceCoord') && isfield(Data,'ZIndex')&&~isempty(Data.ZIndex)&&~isnan(Data.ZIndex)
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| 116 | DataOut.PlaneCoord=Calib.SliceCoord(Data.ZIndex,:);% transfer the slice position
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| 117 | if isfield(Calib,'SliceAngle') % transfer the slice rotation angles
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[250] | 118 | if isequal(size(Calib.SliceAngle,1),1)
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| 119 | DataOut.PlaneAngle=Calib.SliceAngle;
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| 120 | else
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| 121 | DataOut.PlaneAngle=Calib.SliceAngle(Data.ZIndex,:);
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| 122 | end
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[209] | 123 | end
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[151] | 124 | end
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[40] | 125 | % The transform ACTS ONLY IF .CoordType='px'and Calib defined
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[158] | 126 | if isfield(Data,'CoordUnit')%&& isequal(Data.CoordType,'px')&& ~isempty(Calib)
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[40] | 127 | if isfield(Calib,'CoordUnit')
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| 128 | DataOut.CoordUnit=Calib.CoordUnit;
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| 129 | else
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| 130 | DataOut.CoordUnit='cm'; %default
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| 131 | end
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| 132 | DataOut.TimeUnit='s';
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| 133 | %transform of X,Y coordinates for vector fields
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[209] | 134 | test_z=0;
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[116] | 135 | if isfield(Data,'ZIndex') && ~isempty(Data.ZIndex)&&~isnan(Data.ZIndex)
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[157] | 136 | Z=Data.ZIndex;
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[209] | 137 | test_z=1;
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[40] | 138 | else
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| 139 | Z=0;
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| 140 | end
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| 141 | if isfield(Data,'X') &&isfield(Data,'Y')&&~isempty(Data.X) && ~isempty(Data.Y)
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| 142 | [DataOut.X,DataOut.Y,DataOut.Z]=phys_XYZ(Calib,Data.X,Data.Y,Z);
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[209] | 143 | if test_z
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| 144 | DataOut.ListVarName=[DataOut.ListVarName(1:2) {'Z'} DataOut.ListVarName(3:end)];
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| 145 | DataOut.VarDimName=[DataOut.VarDimName(1:2) DataOut.VarDimName(1) DataOut.VarDimName(3:end)];
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| 146 | ZAttribute{1}.Role='coord_z';
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| 147 | DataOut.VarAttribute=[DataOut.VarAttribute(1:2) ZAttribute DataOut.VarAttribute(3:end)];
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| 148 | end
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[40] | 149 | if isfield(Data,'U')&&isfield(Data,'V')&&~isempty(Data.U) && ~isempty(Data.V)&& isfield(Data,'dt')
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| 150 | if ~isempty(Data.dt)
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| 151 | [XOut_1,YOut_1]=phys_XYZ(Calib,Data.X-Data.U/2,Data.Y-Data.V/2,Z);
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| 152 | [XOut_2,YOut_2]=phys_XYZ(Calib,Data.X+Data.U/2,Data.Y+Data.V/2,Z);
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| 153 | DataOut.U=(XOut_2-XOut_1)/Data.dt;
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| 154 | DataOut.V=(YOut_2-YOut_1)/Data.dt;
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| 155 | end
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| 156 | end
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| 157 | end
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| 158 | %transform of an image or scalar: done in phys_ima
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| 159 |
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| 160 | %transform of spatial derivatives
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| 161 | if isfield(Data,'X') && ~isempty(Data.X) && isfield(Data,'DjUi') && ~isempty(Data.DjUi)...
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| 162 | && isfield(Data,'dt')
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| 163 | if ~isempty(Data.dt)
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| 164 | % estimate the Jacobian matrix DXpx/DXphys
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| 165 | for ip=1:length(Data.X)
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| 166 | [Xp1,Yp1]=phys_XYZ(Calib,Data.X(ip)+0.5,Data.Y(ip),Z);
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| 167 | [Xm1,Ym1]=phys_XYZ(Calib,Data.X(ip)-0.5,Data.Y(ip),Z);
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| 168 | [Xp2,Yp2]=phys_XYZ(Calib,Data.X(ip),Data.Y(ip)+0.5,Z);
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| 169 | [Xm2,Ym2]=phys_XYZ(Calib,Data.X(ip),Data.Y(ip)-0.5,Z);
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| 170 | %Jacobian matrix DXpphys/DXpx
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| 171 | DjXi(1,1)=(Xp1-Xm1);
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| 172 | DjXi(2,1)=(Yp1-Ym1);
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| 173 | DjXi(1,2)=(Xp2-Xm2);
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| 174 | DjXi(2,2)=(Yp2-Ym2);
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| 175 | DjUi(:,:)=Data.DjUi(ip,:,:);
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| 176 | DjUi=(DjXi*DjUi')/DjXi;% =J-1*M*J , curvature effects (derivatives of J) neglected
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| 177 | DataOut.DjUi(ip,:,:)=DjUi';
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| 178 | end
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| 179 | DataOut.DjUi = DataOut.DjUi/Data.dt; % min(Data.DjUi(:,1,1))=DUDX
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| 180 | end
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| 181 | end
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| 182 | end
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| 183 |
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| 184 | %%%%%%%%%%%%%%%%%%%%
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| 185 | function [A_out,Rangx,Rangy]=phys_Ima(A,CalibIn,ZIndex)
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| 186 | xcorner=[];
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| 187 | ycorner=[];
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| 188 | npx=[];
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| 189 | npy=[];
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[116] | 190 | dx=ones(1,length(A));
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| 191 | dy=ones(1,length(A));
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[40] | 192 | for icell=1:length(A)
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| 193 | siz=size(A{icell});
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| 194 | npx=[npx siz(2)];
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| 195 | npy=[npy siz(1)];
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| 196 | Calib=CalibIn{icell};
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[116] | 197 | xima=[0.5 siz(2)-0.5 0.5 siz(2)-0.5];%image coordinates of corners
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[40] | 198 | yima=[0.5 0.5 siz(1)-0.5 siz(1)-0.5];
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| 199 | [xcorner_new,ycorner_new]=phys_XYZ(Calib,xima,yima,ZIndex);%corresponding physical coordinates
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[79] | 200 | dx(icell)=(max(xcorner_new)-min(xcorner_new))/(siz(2)-1);
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| 201 | dy(icell)=(max(ycorner_new)-min(ycorner_new))/(siz(1)-1);
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[40] | 202 | xcorner=[xcorner xcorner_new];
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| 203 | ycorner=[ycorner ycorner_new];
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| 204 | end
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| 205 | Rangx(1)=min(xcorner);
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| 206 | Rangx(2)=max(xcorner);
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| 207 | Rangy(2)=min(ycorner);
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| 208 | Rangy(1)=max(ycorner);
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[116] | 209 | test_multi=(max(npx)~=min(npx)) || (max(npy)~=min(npy)); %different image lengths
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[79] | 210 | npX=1+round((Rangx(2)-Rangx(1))/min(dx));% nbre of pixels in the new image (use the finest resolution min(dx) in the set of images)
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| 211 | npY=1+round((Rangy(1)-Rangy(2))/min(dy));
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| 212 | x=linspace(Rangx(1),Rangx(2),npX);
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| 213 | y=linspace(Rangy(1),Rangy(2),npY);
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[40] | 214 | [X,Y]=meshgrid(x,y);%grid in physical coordiantes
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| 215 | vec_B=[];
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| 216 | A_out={};
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| 217 | for icell=1:length(A)
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| 218 | Calib=CalibIn{icell};
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[116] | 219 | if isfield(Calib,'R') || isfield(Calib,'kc')|| test_multi ||~isequal(Calib,CalibIn{1})% the image needs to be interpolated to the new coordinates
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[40] | 220 | zphys=0; %default
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| 221 | if isfield(Calib,'SliceCoord') %.Z= index of plane
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| 222 | SliceCoord=Calib.SliceCoord(ZIndex,:);
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| 223 | zphys=SliceCoord(3); %to generalize for non-parallel planes
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[202] | 224 | if isfield(Calib,'InterfaceCoord') && isfield(Calib,'RefractionIndex')
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| 225 | H=Calib.InterfaceCoord(3);
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| 226 | if H>zphys
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| 227 | zphys=H-(H-zphys)/Calib.RefractionIndex; %corrected z (virtual object)
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| 228 | end
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| 229 | end
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[40] | 230 | end
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[79] | 231 | [XIMA,YIMA]=px_XYZ(CalibIn{icell},X,Y,zphys);% image coordinates for each point in the real space grid
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| 232 | XIMA=reshape(round(XIMA),1,npX*npY);%indices reorganized in 'line'
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| 233 | YIMA=reshape(round(YIMA),1,npX*npY);
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| 234 | flagin=XIMA>=1 & XIMA<=npx(icell) & YIMA >=1 & YIMA<=npy(icell);%flagin=1 inside the original image
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[40] | 235 | testuint8=isa(A{icell},'uint8');
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| 236 | testuint16=isa(A{icell},'uint16');
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| 237 | if numel(siz)==2 %(B/W images)
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[79] | 238 | vec_A=reshape(A{icell},1,npx(icell)*npy(icell));%put the original image in line
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[209] | 239 | %ind_in=find(flagin);
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[40] | 240 | ind_out=find(~flagin);
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[79] | 241 | ICOMB=((XIMA-1)*npy(icell)+(npy(icell)+1-YIMA));
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[40] | 242 | ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A
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[209] | 243 | %vec_B(ind_in)=vec_A(ICOMB);
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| 244 | vec_B(flagin)=vec_A(ICOMB);
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| 245 | vec_B(~flagin)=zeros(size(ind_out));
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| 246 | % vec_B(ind_out)=zeros(size(ind_out));
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[79] | 247 | A_out{icell}=reshape(vec_B,npY,npX);%new image in real coordinates
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[40] | 248 | elseif numel(siz)==3
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| 249 | for icolor=1:siz(3)
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| 250 | vec_A=reshape(A{icell}(:,:,icolor),1,npx*npy);%put the original image in line
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[209] | 251 | % ind_in=find(flagin);
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[40] | 252 | ind_out=find(~flagin);
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| 253 | ICOMB=((XIMA-1)*npy+(npy+1-YIMA));
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| 254 | ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A
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[209] | 255 | vec_B(flagin)=vec_A(ICOMB);
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| 256 | vec_B(~flagin)=zeros(size(ind_out));
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[40] | 257 | A_out{icell}(:,:,icolor)=reshape(vec_B,npy,npx);%new image in real coordinates
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| 258 | end
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| 259 | end
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| 260 | if testuint8
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| 261 | A_out{icell}=uint8(A_out{icell});
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| 262 | end
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| 263 | if testuint16
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| 264 | A_out{icell}=uint16(A_out{icell});
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| 265 | end
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[116] | 266 | else%
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[40] | 267 | A_out{icell}=A{icell};%no transform
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| 268 | Rangx=[0.5 npx-0.5];%image coordiantes of corners
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| 269 | Rangy=[npy-0.5 0.5];
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[116] | 270 | [Rangx]=phys_XYZ(Calib,Rangx,[0.5 0.5],ZIndex);%case of translations without rotation and quadratic deformation
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| 271 | [xx,Rangy]=phys_XYZ(Calib,[0.5 0.5],Rangy,ZIndex);
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[40] | 272 | end
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| 273 | end
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| 274 |
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