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 | %%%% Use the general syntax for transform fields %%%% |
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4 | % OUTPUT: |
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5 | % DataOut: output field structure |
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6 | % |
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7 | %INPUT: |
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8 | % DataIn: first input field structure |
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9 | % XmlData: first input parameter structure, |
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10 | % .GeometryCalib: substructure of the calibration parameters |
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11 | % DataIn_1: optional second input field structure |
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12 | % XmlData_1: optional second input parameter structure |
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13 | % .GeometryCalib: substructure of the calibration parameters |
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14 | |
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15 | %======================================================================= |
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16 | % Copyright 2008-2014, LEGI UMR 5519 / CNRS UJF G-INP, Grenoble, France |
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17 | % http://www.legi.grenoble-inp.fr |
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18 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr |
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19 | % |
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20 | % This file is part of the toolbox UVMAT. |
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21 | % |
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22 | % UVMAT is free software; you can redistribute it and/or modify |
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23 | % it under the terms of the GNU General Public License as published |
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24 | % by the Free Software Foundation; either version 2 of the license, |
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25 | % or (at your option) any later version. |
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26 | % |
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27 | % UVMAT is distributed in the hope that it will be useful, |
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28 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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29 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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30 | % GNU General Public License (see LICENSE.txt) for more details. |
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31 | %======================================================================= |
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32 | |
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33 | function DataOut=phys(DataIn,XmlData,DataIn_1,XmlData_1) |
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34 | %------------------------------------------------------------------------ |
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35 | |
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36 | % A FAIRE: 1- verifier si DataIn est une 'field structure'(.ListVarName'): |
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37 | % chercher ListVarAttribute, for each field (cell of variables): |
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38 | % .CoordType: 'phys' or 'px' (default==phys, no transform) |
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39 | % .scale_factor: =dt (to transform displacement into velocity) default=1 |
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40 | % .covariance: 'scalar', 'coord', 'D_i': covariant (like velocity), 'D^i': contravariant (like gradient), 'D^jD_i' (like strain tensor) |
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41 | % (default='coord' if .Role='coord_x,_y..., |
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42 | % 'D_i' if '.Role='vector_x,...', |
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43 | % 'scalar', else (thenno change except scale factor) |
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44 | |
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45 | DataOut=[]; |
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46 | DataOut_1=[]; %default second output field |
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47 | if isfield(DataIn,'Action') && isfield(DataIn.Action,'RUN') && isequal(DataIn.Action.RUN,0) |
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48 | if isfield(XmlData,'GeometryCalib')&& isfield(XmlData.GeometryCalib,'CoordUnit') |
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49 | 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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50 | end |
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51 | return |
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52 | end |
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53 | |
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54 | %% analyse input and set default output |
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55 | DataOut=DataIn;%default first output field |
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56 | if nargin>=2 % nargin =nbre of input variables |
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57 | if isfield(XmlData,'GeometryCalib') |
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58 | Calib{1}=XmlData.GeometryCalib; |
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59 | else |
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60 | Calib{1}=[]; |
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61 | end |
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62 | if nargin>=3 %two input fields |
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63 | DataOut_1=DataIn_1;%default second output field |
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64 | if nargin>=4 && isfield(XmlData_1,'GeometryCalib') |
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65 | Calib{2}=XmlData_1.GeometryCalib; |
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66 | else |
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67 | Calib{2}=Calib{1}; |
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68 | end |
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69 | end |
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70 | end |
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71 | |
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72 | %% get the z index defining the section plane |
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73 | if isfield(DataIn,'ZIndex')&&~isempty(DataIn.ZIndex)&&~isnan(DataIn.ZIndex) |
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74 | ZIndex=DataIn.ZIndex; |
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75 | else |
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76 | ZIndex=1; |
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77 | end |
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78 | |
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79 | %% transform first field |
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80 | iscalar=0;% counter of scalar fields |
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81 | if ~isempty(Calib{1}) |
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82 | if ~isfield(Calib{1},'CalibrationType')||~isfield(Calib{1},'CoordUnit') |
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83 | return %bad calib parameter input |
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84 | end |
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85 | if ~(isfield(DataIn,'CoordUnit')&& strcmp(DataIn.CoordUnit,'pixel')) |
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86 | return % transform only fields in pixel coordinates |
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87 | end |
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88 | DataOut=phys_1(DataIn,Calib{1},ZIndex);% transform coordinates and velocity components |
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89 | %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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90 | if isfield(DataIn,'A') && isfield(DataIn,'Coord_x') && ~isempty(DataIn.Coord_x) && isfield(DataIn,'Coord_y')&&... |
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91 | ~isempty(DataIn.Coord_y) && length(DataIn.A)>1 |
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92 | iscalar=1; |
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93 | A{1}=DataIn.A; |
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94 | end |
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95 | end |
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96 | |
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97 | %% document the selected plane position and angle if relevant |
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98 | if isfield(Calib{1},'SliceCoord')&&size(Calib{1}.SliceCoord,1)>=ZIndex |
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99 | DataOut.PlaneCoord=Calib{1}.SliceCoord(ZIndex,:);% transfer the slice position corresponding to index ZIndex |
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100 | if isfield(Calib{1},'SliceAngle') % transfer the slice rotation angles |
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101 | if isequal(size(Calib{1}.SliceAngle,1),1)% case of a unique angle |
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102 | DataOut.PlaneAngle=Calib{1}.SliceAngle; |
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103 | else % case of multiple planes with different angles: select the plane with index ZIndex |
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104 | DataOut.PlaneAngle=Calib{1}.SliceAngle(ZIndex,:); |
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105 | end |
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106 | end |
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107 | end |
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108 | |
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109 | %% transform second field if relevant |
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110 | if ~isempty(DataOut_1) |
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111 | if isfield(DataIn_1,'ZIndex') && ~isequal(DataIn_1.ZIndex,ZIndex) |
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112 | DataOut_1.Txt='different plane indices for the two input fields'; |
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113 | return |
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114 | end |
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115 | if ~isfield(Calib{2},'CalibrationType')||~isfield(Calib{2},'CoordUnit') |
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116 | return %bad calib parameter input |
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117 | end |
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118 | if (isfield(DataIn_1,'CoordUnit')&& strcmp(DataIn_1.CoordUnit,'pixel')) |
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119 | DataOut_1=phys_1(DataOut_1,Calib{2},ZIndex); |
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120 | end |
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121 | if isfield(Calib{1},'SliceCoord') |
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122 | if ~(isfield(Calib{2},'SliceCoord') && isequal(Calib{2}.SliceCoord,Calib{1}.SliceCoord)) |
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123 | DataOut_1.Txt='different plane positions for the two input fields'; |
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124 | return |
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125 | end |
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126 | DataOut_1.PlaneCoord=DataOut.PlaneCoord;% same plane position for the two input fields |
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127 | if isfield(Calib{1},'SliceAngle') |
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128 | if ~(isfield(Calib{2},'SliceAngle') && isequal(Calib{2}.SliceAngle,Calib{1}.SliceAngle)) |
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129 | DataOut_1.Txt='different plane angles for the two input fields'; |
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130 | return |
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131 | end |
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132 | DataOut_1.PlaneAngle=DataOut.PlaneAngle; % same plane angle for the two input fields |
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133 | end |
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134 | end |
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135 | if isfield(DataIn_1,'A')&&isfield(DataIn_1,'Coord_x')&&~isempty(DataIn_1.Coord_x) && isfield(DataIn_1,'Coord_y')&&... |
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136 | ~isempty(DataIn_1.Coord_y)&&length(DataIn_1.A)>1 |
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137 | iscalar=iscalar+1; |
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138 | Calib{iscalar}=Calib{2}; |
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139 | A{iscalar}=DataIn_1.A; |
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140 | end |
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141 | end |
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142 | |
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143 | %% transform the scalar(s) or image(s) |
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144 | if iscalar~=0 |
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145 | [A,Coord_x,Coord_y]=phys_ima(A,XmlData,ZIndex);%TODO : introduire interp2_uvmat ds phys_ima |
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146 | if iscalar==1 && ~isempty(DataOut_1) % case for which only the second field is a scalar |
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147 | DataOut_1.A=A{1}; |
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148 | DataOut_1.Coord_x=Coord_x; |
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149 | DataOut_1.Coord_y=Coord_y; |
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150 | else |
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151 | DataOut.A=A{1}; |
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152 | DataOut.Coord_x=Coord_x; |
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153 | DataOut.Coord_y=Coord_y; |
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154 | end |
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155 | if iscalar==2 |
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156 | DataOut_1.A=A{2}; |
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157 | DataOut_1.Coord_x=Coord_x; |
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158 | DataOut_1.Coord_y=Coord_y; |
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159 | end |
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160 | end |
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161 | |
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162 | % subtract fields |
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163 | if ~isempty(DataOut_1) |
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164 | DataOut=sub_field(DataOut,[],DataOut_1); |
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165 | end |
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166 | %------------------------------------------------ |
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167 | %--- transform a single field |
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168 | function DataOut=phys_1(Data,Calib,ZIndex) |
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169 | %------------------------------------------------ |
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170 | %% set default output |
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171 | DataOut=Data;%default |
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172 | DataOut.CoordUnit=Calib.CoordUnit;% the output coord unit is set by the calibration parameters |
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173 | |
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174 | %% transform X,Y coordinates for velocity fields (transform of an image or scalar done in phys_ima) |
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175 | if isfield(Data,'X') &&isfield(Data,'Y')&&~isempty(Data.X) && ~isempty(Data.Y) |
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176 | [DataOut.X,DataOut.Y]=phys_XYZ(Calib,Data.X,Data.Y,ZIndex); |
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177 | Dt=1; %default |
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178 | if isfield(Data,'dt')&&~isempty(Data.dt) |
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179 | Dt=Data.dt; |
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180 | end |
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181 | if isfield(Data,'Dt')&&~isempty(Data.Dt) |
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182 | Dt=Data.Dt; |
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183 | end |
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184 | if isfield(Data,'U')&&isfield(Data,'V')&&~isempty(Data.U) && ~isempty(Data.V) |
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185 | [XOut_1,YOut_1]=phys_XYZ(Calib,Data.X-Data.U/2,Data.Y-Data.V/2,ZIndex); |
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186 | [XOut_2,YOut_2]=phys_XYZ(Calib,Data.X+Data.U/2,Data.Y+Data.V/2,ZIndex); |
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187 | DataOut.U=(XOut_2-XOut_1)/Dt; |
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188 | DataOut.V=(YOut_2-YOut_1)/Dt; |
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189 | end |
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190 | end |
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191 | |
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192 | %% suppress tps |
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193 | list_tps={'Coord_tps' 'U_tps' 'V_tps' 'SubRange' 'NbSites'}; |
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194 | ind_remove=[]; |
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195 | for ilist=1:numel(list_tps) |
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196 | ind_tps=find(strcmp(list_tps{ilist},Data.ListVarName)); |
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197 | if ~isempty(ind_tps) |
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198 | ind_remove=[ind_remove ind_tps]; |
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199 | DataOut=rmfield(DataOut,list_tps{ilist}); |
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200 | end |
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201 | end |
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202 | if isfield(DataOut,'VarAttribute') && numel(DataOut.VarAttribute)>=3 && isfield(DataOut.VarAttribute{3},'VarIndex_tps') |
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203 | DataOut.VarAttribute{3}=rmfield(DataOut.VarAttribute{3},'VarIndex_tps'); |
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204 | end |
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205 | if isfield(DataOut,'VarAttribute')&& numel(DataOut.VarAttribute)>=4 && isfield(DataOut.VarAttribute{4},'VarIndex_tps') |
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206 | DataOut.VarAttribute{4}=rmfield(DataOut.VarAttribute{4},'VarIndex_tps'); |
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207 | end |
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208 | if ~isempty(ind_remove) |
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209 | DataOut.ListVarName(ind_remove)=[]; |
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210 | DataOut.VarDimName(ind_remove)=[]; |
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211 | DataOut.VarAttribute(ind_remove)=[]; |
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212 | end |
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213 | |
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214 | %% transform of spatial derivatives: TODO check the case with plane angles |
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215 | if isfield(Data,'X') && ~isempty(Data.X) && isfield(Data,'DjUi') && ~isempty(Data.DjUi) |
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216 | % estimate the Jacobian matrix DXpx/DXphys |
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217 | for ip=1:length(Data.X) |
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218 | [Xp1,Yp1]=phys_XYZ(Calib,Data.X(ip)+0.5,Data.Y(ip),ZIndex); |
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219 | [Xm1,Ym1]=phys_XYZ(Calib,Data.X(ip)-0.5,Data.Y(ip),ZIndex); |
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220 | [Xp2,Yp2]=phys_XYZ(Calib,Data.X(ip),Data.Y(ip)+0.5,ZIndex); |
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221 | [Xm2,Ym2]=phys_XYZ(Calib,Data.X(ip),Data.Y(ip)-0.5,ZIndex); |
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222 | %Jacobian matrix DXpphys/DXpx |
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223 | DjXi(1,1)=(Xp1-Xm1); |
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224 | DjXi(2,1)=(Yp1-Ym1); |
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225 | DjXi(1,2)=(Xp2-Xm2); |
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226 | DjXi(2,2)=(Yp2-Ym2); |
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227 | DjUi(:,:)=Data.DjUi(ip,:,:); |
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228 | DjUi=(DjXi*DjUi')/DjXi;% =J-1*M*J , curvature effects (derivatives of J) neglected |
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229 | DataOut.DjUi(ip,:,:)=DjUi'; |
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230 | end |
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231 | DataOut.DjUi = DataOut.DjUi/Dt; % min(Data.DjUi(:,1,1))=DUDX |
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232 | end |
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233 | |
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234 | |
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235 | %%%%%%%%%%%%%%%%%%%% |
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236 | |
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