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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60 | if isfield(Data,'ZIndex')&&~isempty(Data.ZIndex)&&~isnan(Data.ZIndex)
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61 | ZIndex=Data.ZIndex;
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62 | else
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63 | ZIndex=1;
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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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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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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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114 | % DataOut.CoordUnit=Calib.CoordUnit; %put flag for physical coordinates
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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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118 | DataOut.PlaneAngle=Calib.SliceAngle(Data.ZIndex,:);
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119 | end
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120 | end
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121 | % The transform ACTS ONLY IF .CoordType='px'and Calib defined
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122 | if isfield(Data,'CoordUnit')%&& isequal(Data.CoordType,'px')&& ~isempty(Calib)
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123 | if isfield(Calib,'CoordUnit')
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124 | DataOut.CoordUnit=Calib.CoordUnit;
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125 | else
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126 | DataOut.CoordUnit='cm'; %default
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127 | end
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128 | DataOut.TimeUnit='s';
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129 | %transform of X,Y coordinates for vector fields
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130 | test_z=0;
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131 | if isfield(Data,'ZIndex') && ~isempty(Data.ZIndex)&&~isnan(Data.ZIndex)
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132 | Z=Data.ZIndex;
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133 | test_z=1;
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134 | else
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135 | Z=0;
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136 | end
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137 | if isfield(Data,'X') &&isfield(Data,'Y')&&~isempty(Data.X) && ~isempty(Data.Y)
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138 | [DataOut.X,DataOut.Y,DataOut.Z]=phys_XYZ(Calib,Data.X,Data.Y,Z);
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139 | if test_z
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140 | DataOut.ListVarName=[DataOut.ListVarName(1:2) {'Z'} DataOut.ListVarName(3:end)];
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141 | DataOut.VarDimName=[DataOut.VarDimName(1:2) DataOut.VarDimName(1) DataOut.VarDimName(3:end)];
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142 | ZAttribute{1}.Role='coord_z';
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143 | DataOut.VarAttribute=[DataOut.VarAttribute(1:2) ZAttribute DataOut.VarAttribute(3:end)];
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144 | end
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145 | if isfield(Data,'U')&&isfield(Data,'V')&&~isempty(Data.U) && ~isempty(Data.V)&& isfield(Data,'dt')
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146 | if ~isempty(Data.dt)
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147 | [XOut_1,YOut_1]=phys_XYZ(Calib,Data.X-Data.U/2,Data.Y-Data.V/2,Z);
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148 | [XOut_2,YOut_2]=phys_XYZ(Calib,Data.X+Data.U/2,Data.Y+Data.V/2,Z);
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149 | DataOut.U=(XOut_2-XOut_1)/Data.dt;
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150 | DataOut.V=(YOut_2-YOut_1)/Data.dt;
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151 | end
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152 | end
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153 | end
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154 | %transform of an image or scalar: done in phys_ima
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155 |
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156 | %transform of spatial derivatives
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157 | if isfield(Data,'X') && ~isempty(Data.X) && isfield(Data,'DjUi') && ~isempty(Data.DjUi)...
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158 | && isfield(Data,'dt')
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159 | if ~isempty(Data.dt)
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160 | % estimate the Jacobian matrix DXpx/DXphys
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161 | for ip=1:length(Data.X)
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162 | [Xp1,Yp1]=phys_XYZ(Calib,Data.X(ip)+0.5,Data.Y(ip),Z);
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163 | [Xm1,Ym1]=phys_XYZ(Calib,Data.X(ip)-0.5,Data.Y(ip),Z);
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164 | [Xp2,Yp2]=phys_XYZ(Calib,Data.X(ip),Data.Y(ip)+0.5,Z);
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165 | [Xm2,Ym2]=phys_XYZ(Calib,Data.X(ip),Data.Y(ip)-0.5,Z);
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166 | %Jacobian matrix DXpphys/DXpx
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167 | DjXi(1,1)=(Xp1-Xm1);
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168 | DjXi(2,1)=(Yp1-Ym1);
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169 | DjXi(1,2)=(Xp2-Xm2);
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170 | DjXi(2,2)=(Yp2-Ym2);
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171 | DjUi(:,:)=Data.DjUi(ip,:,:);
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172 | DjUi=(DjXi*DjUi')/DjXi;% =J-1*M*J , curvature effects (derivatives of J) neglected
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173 | DataOut.DjUi(ip,:,:)=DjUi';
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174 | end
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175 | DataOut.DjUi = DataOut.DjUi/Data.dt; % min(Data.DjUi(:,1,1))=DUDX
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176 | end
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177 | end
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178 | end
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179 |
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180 | %%%%%%%%%%%%%%%%%%%%
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181 | function [A_out,Rangx,Rangy]=phys_Ima(A,CalibIn,ZIndex)
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182 | xcorner=[];
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183 | ycorner=[];
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184 | npx=[];
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185 | npy=[];
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186 | dx=ones(1,length(A));
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187 | dy=ones(1,length(A));
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188 | for icell=1:length(A)
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189 | siz=size(A{icell});
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190 | npx=[npx siz(2)];
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191 | npy=[npy siz(1)];
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192 | Calib=CalibIn{icell};
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193 | xima=[0.5 siz(2)-0.5 0.5 siz(2)-0.5];%image coordinates of corners
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194 | yima=[0.5 0.5 siz(1)-0.5 siz(1)-0.5];
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195 | [xcorner_new,ycorner_new]=phys_XYZ(Calib,xima,yima,ZIndex);%corresponding physical coordinates
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196 | dx(icell)=(max(xcorner_new)-min(xcorner_new))/(siz(2)-1);
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197 | dy(icell)=(max(ycorner_new)-min(ycorner_new))/(siz(1)-1);
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198 | xcorner=[xcorner xcorner_new];
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199 | ycorner=[ycorner ycorner_new];
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200 | end
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201 | Rangx(1)=min(xcorner);
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202 | Rangx(2)=max(xcorner);
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203 | Rangy(2)=min(ycorner);
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204 | Rangy(1)=max(ycorner);
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205 | test_multi=(max(npx)~=min(npx)) || (max(npy)~=min(npy)); %different image lengths
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206 | 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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207 | npY=1+round((Rangy(1)-Rangy(2))/min(dy));
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208 | x=linspace(Rangx(1),Rangx(2),npX);
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209 | y=linspace(Rangy(1),Rangy(2),npY);
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210 | [X,Y]=meshgrid(x,y);%grid in physical coordiantes
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211 | vec_B=[];
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212 | A_out={};
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213 | for icell=1:length(A)
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214 | Calib=CalibIn{icell};
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215 | 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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216 | zphys=0; %default
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217 | if isfield(Calib,'SliceCoord') %.Z= index of plane
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218 | SliceCoord=Calib.SliceCoord(ZIndex,:);
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219 | zphys=SliceCoord(3); %to generalize for non-parallel planes
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220 | if isfield(Calib,'InterfaceCoord') && isfield(Calib,'RefractionIndex')
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221 | H=Calib.InterfaceCoord(3);
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222 | if H>zphys
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223 | zphys=H-(H-zphys)/Calib.RefractionIndex; %corrected z (virtual object)
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224 | end
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225 | end
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226 | end
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227 | [XIMA,YIMA]=px_XYZ(CalibIn{icell},X,Y,zphys);% image coordinates for each point in the real space grid
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228 | XIMA=reshape(round(XIMA),1,npX*npY);%indices reorganized in 'line'
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229 | YIMA=reshape(round(YIMA),1,npX*npY);
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230 | flagin=XIMA>=1 & XIMA<=npx(icell) & YIMA >=1 & YIMA<=npy(icell);%flagin=1 inside the original image
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231 | testuint8=isa(A{icell},'uint8');
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232 | testuint16=isa(A{icell},'uint16');
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233 | if numel(siz)==2 %(B/W images)
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234 | vec_A=reshape(A{icell},1,npx(icell)*npy(icell));%put the original image in line
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235 | %ind_in=find(flagin);
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236 | ind_out=find(~flagin);
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237 | ICOMB=((XIMA-1)*npy(icell)+(npy(icell)+1-YIMA));
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238 | ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A
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239 | %vec_B(ind_in)=vec_A(ICOMB);
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240 | vec_B(flagin)=vec_A(ICOMB);
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241 | vec_B(~flagin)=zeros(size(ind_out));
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242 | % vec_B(ind_out)=zeros(size(ind_out));
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243 | A_out{icell}=reshape(vec_B,npY,npX);%new image in real coordinates
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244 | elseif numel(siz)==3
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245 | for icolor=1:siz(3)
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246 | vec_A=reshape(A{icell}(:,:,icolor),1,npx*npy);%put the original image in line
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247 | % ind_in=find(flagin);
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248 | ind_out=find(~flagin);
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249 | ICOMB=((XIMA-1)*npy+(npy+1-YIMA));
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250 | ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A
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251 | vec_B(flagin)=vec_A(ICOMB);
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252 | vec_B(~flagin)=zeros(size(ind_out));
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253 | A_out{icell}(:,:,icolor)=reshape(vec_B,npy,npx);%new image in real coordinates
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254 | end
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255 | end
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256 | if testuint8
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257 | A_out{icell}=uint8(A_out{icell});
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258 | end
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259 | if testuint16
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260 | A_out{icell}=uint16(A_out{icell});
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261 | end
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262 | else%
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263 | A_out{icell}=A{icell};%no transform
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264 | Rangx=[0.5 npx-0.5];%image coordiantes of corners
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265 | Rangy=[npy-0.5 0.5];
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266 | [Rangx]=phys_XYZ(Calib,Rangx,[0.5 0.5],ZIndex);%case of translations without rotation and quadratic deformation
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267 | [xx,Rangy]=phys_XYZ(Calib,[0.5 0.5],Rangy,ZIndex);
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268 | end
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269 | end
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270 |
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