[695] | 1 | %'phys': transforms image (Unit='pixel') to real world (phys) coordinates using geometric calibration parameters. It acts if the input field contains the tag 'CoordTUnit' with value 'pixel' |
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| 2 | |
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| 3 | %------------------------------------------------------------------------ |
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| 4 | %%%% Use the general syntax for transform fields %%%% |
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| 5 | % OUTPUT: |
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| 6 | % DataOut: output field structure |
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| 7 | |
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| 8 | %INPUT: |
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| 9 | % DataIn: first input field structure |
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| 10 | % XmlData: first input parameter structure, |
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| 11 | % .GeometryCalib: substructure of the calibration parameters |
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| 12 | % DataIn_1: optional second input field structure |
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| 13 | % XmlData_1: optional second input parameter structure |
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| 14 | % .GeometryCalib: substructure of the calibration parameters |
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| 15 | %------------------------------------------------------------------------ |
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| 16 | function DataOut=phys(DataIn,XmlData,DataIn_1,XmlData_1) |
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| 17 | %------------------------------------------------------------------------ |
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| 18 | |
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| 19 | % A FAIRE: 1- verifier si DataIn est une 'field structure'(.ListVarName'): |
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| 20 | % chercher ListVarAttribute, for each field (cell of variables): |
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| 21 | % .CoordType: 'phys' or 'px' (default==phys, no transform) |
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| 22 | % .scale_factor: =dt (to transform displacement into velocity) default=1 |
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| 23 | % .covariance: 'scalar', 'coord', 'D_i': covariant (like velocity), 'D^i': contravariant (like gradient), 'D^jD_i' (like strain tensor) |
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| 24 | % (default='coord' if .Role='coord_x,_y..., |
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| 25 | % 'D_i' if '.Role='vector_x,...', |
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| 26 | % 'scalar', else (thenno change except scale factor) |
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| 27 | |
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| 28 | DataOut=[]; |
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| 29 | DataOut_1=[]; %default second output field |
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| 30 | if strcmp(DataIn,'*') |
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| 31 | if isfield(XmlData,'GeometryCalib')&& isfield(XmlData.GeometryCalib,'CoordUnit') |
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| 32 | DataOut.CoordUnit=XmlData.GeometryCalib.CoordUnit;% states that the output is in unit defined by GeometryCalib, then erased all projection objects with different units |
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| 33 | end |
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| 34 | return |
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| 35 | end |
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| 36 | |
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| 37 | %% analyse input and set default output |
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| 38 | DataOut=DataIn;%default first output field |
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| 39 | if nargin>=2 % nargin =nbre of input variables |
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| 40 | if isfield(XmlData,'GeometryCalib') |
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| 41 | Calib{1}=XmlData.GeometryCalib; |
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| 42 | else |
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| 43 | Calib{1}=[]; |
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| 44 | end |
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| 45 | if nargin>=3 %two input fields |
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| 46 | DataOut_1=DataIn_1;%default second output field |
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| 47 | if nargin>=4 && isfield(XmlData_1,'GeometryCalib') |
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| 48 | Calib{2}=XmlData_1.GeometryCalib; |
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| 49 | else |
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| 50 | Calib{2}=Calib{1}; |
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| 51 | end |
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| 52 | end |
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| 53 | end |
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| 54 | |
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| 55 | %% get the z index defining the section plane |
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| 56 | if isfield(DataIn,'ZIndex')&&~isempty(DataIn.ZIndex)&&~isnan(DataIn.ZIndex) |
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| 57 | ZIndex=DataIn.ZIndex; |
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| 58 | else |
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| 59 | ZIndex=1; |
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| 60 | end |
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| 61 | |
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| 62 | %% transform first field |
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| 63 | iscalar=0;% counter of scalar fields |
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| 64 | if ~isempty(Calib{1}) |
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| 65 | if ~isfield(Calib{1},'CalibrationType')||~isfield(Calib{1},'CoordUnit') |
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| 66 | return %bad calib parameter input |
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| 67 | end |
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| 68 | if ~(isfield(DataIn,'CoordUnit')&& strcmp(DataIn.CoordUnit,'pixel')) |
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| 69 | return % transform only fields in pixel coordinates |
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| 70 | end |
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| 71 | DataOut=phys_1(DataIn,Calib{1},ZIndex);% transform coordiantes and velocity components |
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| 72 | %case of images or scalar: in case of two input fields, we need to project the transform on the same regular grid |
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| 73 | if isfield(DataIn,'A') && isfield(DataIn,'AX') && ~isempty(DataIn.AX) && isfield(DataIn,'AY')&&... |
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| 74 | ~isempty(DataIn.AY) && length(DataIn.A)>1 |
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| 75 | iscalar=1; |
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| 76 | A{1}=DataIn.A; |
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| 77 | end |
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| 78 | end |
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| 79 | |
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| 80 | %% document the selected plane position and angle if relevant |
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| 81 | if isfield(Calib{1},'SliceCoord')&&size(Calib{1}.SliceCoord,1)>=ZIndex |
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| 82 | DataOut.PlaneCoord=Calib{1}.SliceCoord(ZIndex,:);% transfer the slice position corresponding to index ZIndex |
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| 83 | if isfield(Calib{1},'SliceAngle') % transfer the slice rotation angles |
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| 84 | if isequal(size(Calib{1}.SliceAngle,1),1)% case of a unique angle |
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| 85 | DataOut.PlaneAngle=Calib{1}.SliceAngle; |
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| 86 | else % case of multiple planes with different angles: select the plane with index ZIndex |
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| 87 | DataOut.PlaneAngle=Calib{1}.SliceAngle(ZIndex,:); |
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| 88 | end |
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| 89 | end |
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| 90 | end |
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| 91 | |
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| 92 | %% transform second field if relevant |
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| 93 | if ~isempty(DataOut_1) |
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| 94 | if isfield(DataIn_1,'ZIndex') && ~isequal(DataIn_1.ZIndex,ZIndex) |
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| 95 | DataOut_1.Txt='different plane indices for the two input fields'; |
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| 96 | return |
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| 97 | end |
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| 98 | if ~isfield(Calib{2},'CalibrationType')||~isfield(Calib{2},'CoordUnit') |
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| 99 | return %bad calib parameter input |
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| 100 | end |
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| 101 | if ~(isfield(DataIn_1,'CoordUnit')&& strcmp(DataIn_1.CoordUnit,'pixel')) |
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| 102 | return % transform only fields in pixel coordinates |
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| 103 | end |
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| 104 | DataOut_1=phys_1(DataOut_1,Calib{2},ZIndex); |
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| 105 | if isfield(Calib{1},'SliceCoord') |
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| 106 | if ~(isfield(Calib{2},'SliceCoord') && isequal(Calib{2}.SliceCoord,Calib{1}.SliceCoord)) |
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| 107 | DataOut_1.Txt='different plane positions for the two input fields'; |
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| 108 | return |
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| 109 | end |
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| 110 | DataOut_1.PlaneCoord=DataOut.PlaneCoord;% same plane position for the two input fields |
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| 111 | if isfield(Calib{1},'SliceAngle') |
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| 112 | if ~(isfield(Calib{2},'SliceAngle') && isequal(Calib{2}.SliceAngle,Calib{1}.SliceAngle)) |
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| 113 | DataOut_1.Txt='different plane angles for the two input fields'; |
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| 114 | return |
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| 115 | end |
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| 116 | DataOut_1.PlaneAngle=DataOut.PlaneAngle; % same plane angle for the two input fields |
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| 117 | end |
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| 118 | end |
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| 119 | if isfield(DataIn_1,'A')&&isfield(DataIn_1,'AX')&&~isempty(DataIn_1.AX) && isfield(DataIn_1,'AY')&&... |
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| 120 | ~isempty(DataIn_1.AY)&&length(DataIn_1.A)>1 |
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| 121 | iscalar=iscalar+1; |
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| 122 | Calib{iscalar}=Calib{2}; |
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| 123 | A{iscalar}=DataIn_1.A; |
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| 124 | end |
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| 125 | end |
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| 126 | |
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| 127 | %% transform the scalar(s) or image(s) |
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| 128 | if iscalar~=0 |
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| 129 | [A,AX,AY]=phys_Ima(A,Calib,ZIndex);%TODO : introduire interp2_uvmat ds phys_ima |
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| 130 | if iscalar==1 && ~isempty(DataOut_1) % case for which only the second field is a scalar |
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| 131 | DataOut_1.A=A{1}; |
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| 132 | DataOut_1.AX=AX; |
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| 133 | DataOut_1.AY=AY; |
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| 134 | else |
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| 135 | DataOut.A=A{1}; |
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| 136 | DataOut.AX=AX; |
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| 137 | DataOut.AY=AY; |
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| 138 | end |
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| 139 | if iscalar==2 |
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| 140 | DataOut_1.A=A{2}; |
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| 141 | DataOut_1.AX=AX; |
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| 142 | DataOut_1.AY=AY; |
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| 143 | end |
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| 144 | end |
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| 145 | |
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| 146 | % subtract fields |
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| 147 | if ~isempty(DataOut_1) |
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| 148 | DataOut=sub_field(DataOut,[],DataOut_1); |
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| 149 | end |
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| 150 | %------------------------------------------------ |
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| 151 | %--- transform a single field |
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| 152 | function DataOut=phys_1(Data,Calib,ZIndex) |
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| 153 | %------------------------------------------------ |
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| 154 | %% set default output |
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| 155 | DataOut=Data;%default |
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| 156 | DataOut.CoordUnit=Calib.CoordUnit;% the output coord unit is set by the calibration parameters |
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| 157 | |
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| 158 | %% transform X,Y coordinates for velocity fields (transform of an image or scalar done in phys_ima) |
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| 159 | if isfield(Data,'X') &&isfield(Data,'Y')&&~isempty(Data.X) && ~isempty(Data.Y) |
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| 160 | [DataOut.X,DataOut.Y]=phys_XYZ(Calib,Data.X,Data.Y,ZIndex); |
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| 161 | Dt=1; %default |
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| 162 | if isfield(Data,'dt')&&~isempty(Data.dt) |
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| 163 | Dt=Data.dt; |
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| 164 | end |
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| 165 | if isfield(Data,'Dt')&&~isempty(Data.Dt) |
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| 166 | Dt=Data.Dt; |
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| 167 | end |
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| 168 | if isfield(Data,'U')&&isfield(Data,'V')&&~isempty(Data.U) && ~isempty(Data.V) |
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| 169 | [XOut_1,YOut_1]=phys_XYZ(Calib,Data.X-Data.U/2,Data.Y-Data.V/2,ZIndex); |
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| 170 | [XOut_2,YOut_2]=phys_XYZ(Calib,Data.X+Data.U/2,Data.Y+Data.V/2,ZIndex); |
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| 171 | DataOut.U=(XOut_2-XOut_1)/Dt; |
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| 172 | DataOut.V=(YOut_2-YOut_1)/Dt; |
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| 173 | end |
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| 174 | % if ~strcmp(Calib.CalibrationType,'rescale') && isfield(Data,'X_tps') && isfield(Data,'Y_tps') |
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| 175 | % [DataOut.X_tps,DataOut.Y_tps]=phys_XYZ(Calib,Data.X,Data.Y,ZIndex); |
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| 176 | % end |
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| 177 | end |
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| 178 | |
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| 179 | %% suppress tps |
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| 180 | list_tps={'Coord_tps' 'U_tps' 'V_tps' 'SubRange' 'NbSites'}; |
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| 181 | ind_remove=[]; |
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| 182 | for ilist=1:numel(list_tps) |
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| 183 | ind_tps=find(strcmp(list_tps{ilist},Data.ListVarName)); |
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| 184 | if ~isempty(ind_tps) |
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| 185 | ind_remove=[ind_remove ind_tps]; |
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| 186 | DataOut=rmfield(DataOut,list_tps{ilist}); |
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| 187 | end |
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| 188 | end |
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| 189 | if isfield(DataOut,'VarAttribute') && numel(DataOut.VarAttribute)>=3 && isfield(DataOut.VarAttribute{3},'VarIndex_tps') |
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| 190 | DataOut.VarAttribute{3}=rmfield(DataOut.VarAttribute{3},'VarIndex_tps'); |
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| 191 | end |
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| 192 | if isfield(DataOut,'VarAttribute')&& numel(DataOut.VarAttribute)>=4 && isfield(DataOut.VarAttribute{4},'VarIndex_tps') |
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| 193 | DataOut.VarAttribute{4}=rmfield(DataOut.VarAttribute{4},'VarIndex_tps'); |
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| 194 | end |
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| 195 | if ~isempty(ind_remove) |
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| 196 | DataOut.ListVarName(ind_remove)=[]; |
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| 197 | DataOut.VarDimName(ind_remove)=[]; |
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| 198 | DataOut.VarAttribute(ind_remove)=[]; |
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| 199 | end |
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| 200 | |
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| 201 | %% transform of spatial derivatives: TODO check the case with plane angles |
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| 202 | if isfield(Data,'X') && ~isempty(Data.X) && isfield(Data,'DjUi') && ~isempty(Data.DjUi) |
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| 203 | % estimate the Jacobian matrix DXpx/DXphys |
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| 204 | for ip=1:length(Data.X) |
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| 205 | [Xp1,Yp1]=phys_XYZ(Calib,Data.X(ip)+0.5,Data.Y(ip),ZIndex); |
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| 206 | [Xm1,Ym1]=phys_XYZ(Calib,Data.X(ip)-0.5,Data.Y(ip),ZIndex); |
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| 207 | [Xp2,Yp2]=phys_XYZ(Calib,Data.X(ip),Data.Y(ip)+0.5,ZIndex); |
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| 208 | [Xm2,Ym2]=phys_XYZ(Calib,Data.X(ip),Data.Y(ip)-0.5,ZIndex); |
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| 209 | %Jacobian matrix DXpphys/DXpx |
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| 210 | DjXi(1,1)=(Xp1-Xm1); |
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| 211 | DjXi(2,1)=(Yp1-Ym1); |
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| 212 | DjXi(1,2)=(Xp2-Xm2); |
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| 213 | DjXi(2,2)=(Yp2-Ym2); |
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| 214 | DjUi(:,:)=Data.DjUi(ip,:,:); |
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| 215 | DjUi=(DjXi*DjUi')/DjXi;% =J-1*M*J , curvature effects (derivatives of J) neglected |
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| 216 | DataOut.DjUi(ip,:,:)=DjUi'; |
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| 217 | end |
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| 218 | DataOut.DjUi = DataOut.DjUi/Dt; % min(Data.DjUi(:,1,1))=DUDX |
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| 219 | end |
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| 220 | |
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| 221 | |
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| 222 | %%%%%%%%%%%%%%%%%%%% |
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| 223 | function [A_out,Rangx,Rangy]=phys_Ima(A,CalibIn,ZIndex) |
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| 224 | xcorner=[]; |
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| 225 | ycorner=[]; |
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| 226 | npx=[]; |
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| 227 | npy=[]; |
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| 228 | dx=ones(1,numel(A)); |
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| 229 | dy=ones(1,numel(A)); |
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| 230 | for icell=1:numel(A) |
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| 231 | siz=size(A{icell}); |
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| 232 | npx=[npx siz(2)]; |
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| 233 | npy=[npy siz(1)]; |
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| 234 | Calib=CalibIn{icell}; |
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| 235 | xima=[0.5 siz(2)-0.5 0.5 siz(2)-0.5];%image coordinates of corners |
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| 236 | yima=[0.5 0.5 siz(1)-0.5 siz(1)-0.5]; |
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| 237 | [xcorner_new,ycorner_new]=phys_XYZ(Calib,xima,yima,ZIndex);%corresponding physical coordinates |
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| 238 | dx(icell)=(max(xcorner_new)-min(xcorner_new))/(siz(2)-1); |
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| 239 | dy(icell)=(max(ycorner_new)-min(ycorner_new))/(siz(1)-1); |
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| 240 | xcorner=[xcorner xcorner_new]; |
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| 241 | ycorner=[ycorner ycorner_new]; |
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| 242 | end |
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| 243 | Rangx(1)=min(xcorner); |
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| 244 | Rangx(2)=max(xcorner); |
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| 245 | Rangy(2)=min(ycorner); |
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| 246 | Rangy(1)=max(ycorner); |
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| 247 | test_multi=(max(npx)~=min(npx)) || (max(npy)~=min(npy)); %different image lengths |
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| 248 | 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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| 249 | npY=1+round((Rangy(1)-Rangy(2))/min(dy)); |
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| 250 | x=linspace(Rangx(1),Rangx(2),npX); |
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| 251 | y=linspace(Rangy(1),Rangy(2),npY); |
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| 252 | [X,Y]=meshgrid(x,y);%grid in physical coordiantes |
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| 253 | %vec_B=[]; |
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| 254 | A_out=cell(1,numel(A)); |
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| 255 | for icell=1:length(A) |
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| 256 | Calib=CalibIn{icell}; |
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| 257 | % rescaling of the image coordinates without change of the image array |
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| 258 | if strcmp(Calib.CalibrationType,'rescale') && isequal(Calib,CalibIn{1}) |
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| 259 | A_out{icell}=A{icell};%no transform |
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| 260 | Rangx=[0.5 npx-0.5];%image coordiantes of corners |
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| 261 | Rangy=[npy-0.5 0.5]; |
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| 262 | [Rangx]=phys_XYZ(Calib,Rangx,[0.5 0.5],ZIndex);%case of translations without rotation and quadratic deformation |
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| 263 | [xx,Rangy]=phys_XYZ(Calib,[0.5 0.5],Rangy,ZIndex); |
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| 264 | else |
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| 265 | % the image needs to be interpolated to the new coordinates |
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| 266 | zphys=0; %default |
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| 267 | if isfield(Calib,'SliceCoord') %.Z= index of plane |
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| 268 | SliceCoord=Calib.SliceCoord(ZIndex,:); |
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| 269 | zphys=SliceCoord(3); %to generalize for non-parallel planes |
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| 270 | if isfield(Calib,'InterfaceCoord') && isfield(Calib,'RefractionIndex') |
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| 271 | H=Calib.InterfaceCoord(3); |
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| 272 | if H>zphys |
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| 273 | zphys=H-(H-zphys)/Calib.RefractionIndex; %corrected z (virtual object) |
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| 274 | end |
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| 275 | end |
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| 276 | end |
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[742] | 277 | xima=0.5:npx-0.5;%image coordinates of corners |
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[695] | 278 | yima=npy-0.5:-1:0.5; |
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[742] | 279 | [XIMA_init,YIMA_init]=meshgrid(xima,yima);%grid of initial image in px coordinates |
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[695] | 280 | [XIMA,YIMA]=px_XYZ(CalibIn{icell},X,Y,zphys);% image coordinates for each point in the real |
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| 281 | %[XPHYS_init,YPHYS_init]=phys_XYZ(Calib,XIMA_init,YIMA_init,ZIndex); |
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[742] | 282 | testuint8=isa(A{icell},'uint8'); |
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| 283 | testuint16=isa(A{icell},'uint16'); |
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[695] | 284 | if ndims(A{icell})==2 %(B/W images) |
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| 285 | A_out{icell}=interp2(XIMA_init,YIMA_init,double(A{icell}),XIMA,YIMA); |
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| 286 | % [Rangx]=phys_XYZ(Calib,Rangx,[0.5 0.5],ZIndex);%case of translations without rotation and quadratic deformation |
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| 287 | % [XIMA_init,YIMA_init]=px_XYZ(CalibIn{icell},X,Y,zphys);% image coordinates for each point in the real space grid |
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| 288 | % |
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| 289 | % XIMA=reshape(round(XIMA),1,npX*npY);%indices reorganized in 'line' |
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| 290 | % YIMA=reshape(round(YIMA),1,npX*npY); |
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| 291 | % flagin=XIMA>=1 & XIMA<=npx(icell) & YIMA >=1 & YIMA<=npy(icell);%flagin=1 inside the original image |
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| 292 | |
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| 293 | % if numel(siz)==2 %(B/W images) |
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| 294 | % vec_A=reshape(A{icell},1,npx(icell)*npy(icell));%put the original image in line |
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| 295 | % %ind_in=find(flagin); |
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| 296 | % ind_out=find(~flagin); |
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| 297 | % ICOMB=((XIMA-1)*npy(icell)+(npy(icell)+1-YIMA)); |
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| 298 | % ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A |
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| 299 | % %vec_B(ind_in)=vec_A(ICOMB); |
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| 300 | % vec_B(flagin)=vec_A(ICOMB); |
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| 301 | % vec_B(~flagin)=zeros(size(ind_out)); |
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| 302 | % % vec_B(ind_out)=zeros(size(ind_out)); |
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| 303 | % A_out{icell}=reshape(vec_B,npY,npX);%new image in real coordinates |
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| 304 | elseif ndims(A{icell})==3 |
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| 305 | for icolor=1:size(A{icell},3) |
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| 306 | A{icell}=double(A{icell}); |
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| 307 | A_out{icell}(:,:,icolor)=interp2(XIMA_init,YIMA_init,A{icell}(:,:,icolor),XIMA,YIMA); |
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| 308 | % vec_A=reshape(A{icell}(:,:,icolor),1,npx*npy);%put the original image in line |
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| 309 | % % ind_in=find(flagin); |
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| 310 | % ind_out=find(~flagin); |
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| 311 | % ICOMB=((XIMA-1)*npy+(npy+1-YIMA)); |
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| 312 | % ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A |
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| 313 | % vec_B(flagin)=vec_A(ICOMB); |
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| 314 | % vec_B(~flagin)=zeros(size(ind_out)); |
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| 315 | % A_out{icell}(:,:,icolor)=reshape(vec_B,npy,npx);%new image in real coordinates |
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| 316 | end |
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| 317 | end |
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| 318 | if testuint8 |
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| 319 | A_out{icell}=uint8(A_out{icell}); |
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| 320 | end |
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| 321 | if testuint16 |
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| 322 | A_out{icell}=uint16(A_out{icell}); |
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| 323 | end |
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| 324 | end |
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| 325 | end |
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| 326 | |
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