1 | %'imadoc2struct': reads the xml file for image documentation
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2 | %------------------------------------------------------------------------
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3 | % function [s,errormsg]=imadoc2struct(ImaDoc,option)
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4 | %
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5 | % OUTPUT:
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6 | % s: structure representing ImaDoc
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7 | % s.Heading: information about the data hierarchical structure
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8 | % s.Time: matrix of times
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9 | % s.TimeUnit
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10 | % s.GeometryCalib: substructure containing the parameters for geometric calibration
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11 | % errormsg: error message
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12 | %
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13 | % INPUT:
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14 | % ImaDoc: full name of the xml input file with head key ImaDoc
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15 | % option: ='GeometryCalib': read the data of GeometryCalib, including source point coordinates
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16 |
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17 | function [s,errormsg]=imadoc2struct(ImaDoc,option)
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18 | %% default input and output
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19 | if ~exist('option','var')
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20 | option='*';
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21 | end
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22 | errormsg=[];%default
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23 | s.Heading=[];%default
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24 | s.Time=[]; %default
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25 | s.TimeUnit=[]; %default
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26 | s.GeometryCalib=[];
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27 | tsai=[];%default
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28 |
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29 | %% opening the xml file
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30 | if exist(ImaDoc,'file')~=2, errormsg=[ ImaDoc ' does not exist']; return;end;%input file does not exist
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31 | try
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32 | t=xmltree(ImaDoc);
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33 | catch
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34 | errormsg={[ImaDoc ' is not a valid xml file']; lasterr};
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35 | display(errormsg);
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36 | return
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37 | end
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38 | uid_root=find(t,'/ImaDoc');
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39 | if isempty(uid_root), errormsg=[ImaDoc ' is not an image documentation file ImaDoc']; return; end;%not an ImaDoc .xml file
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40 |
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41 |
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42 | %% Heading
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43 | uid_Heading=find(t,'/ImaDoc/Heading');
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44 | if ~isempty(uid_Heading),
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45 | uid_Campaign=find(t,'/ImaDoc/Heading/Campaign');
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46 | uid_Exp=find(t,'/ImaDoc/Heading/Experiment');
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47 | uid_Device=find(t,'/ImaDoc/Heading/Device');
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48 | uid_Record=find(t,'/ImaDoc/Heading/Record');
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49 | uid_FirstImage=find(t,'/ImaDoc/Heading/ImageName');
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50 | s.Heading.Campaign=get(t,children(t,uid_Campaign),'value');
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51 | s.Heading.Experiment=get(t,children(t,uid_Exp),'value');
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52 | s.Heading.Device=get(t,children(t,uid_Device),'value');
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53 | if ~isempty(uid_Record)
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54 | s.Heading.Record=get(t,children(t,uid_Record),'value');
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55 | end
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56 | s.Heading.ImageName=get(t,children(t,uid_FirstImage),'value');
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57 | end
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58 |
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59 | %% Camera and timing
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60 | if strcmp(option,'*') || strcmp(option,'Camera')
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61 | uid_Camera=find(t,'/ImaDoc/Camera');
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62 | if ~isempty(uid_Camera)
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63 | uid_ImageSize=find(t,'/ImaDoc/Camera/ImageSize');
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64 | if ~isempty(uid_ImageSize);
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65 | ImageSize=get(t,children(t,uid_ImageSize),'value');
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66 | xindex=findstr(ImageSize,'x');
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67 | if length(xindex)>=2
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68 | s.Npx=str2double(ImageSize(1:xindex(1)-1));
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69 | s.Npy=str2double(ImageSize(xindex(1)+1:xindex(2)-1));
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70 | end
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71 | end
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72 | uid_TimeUnit=find(t,'/ImaDoc/Camera/TimeUnit');
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73 | if ~isempty(uid_TimeUnit)
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74 | s.TimeUnit=get(t,children(t,uid_TimeUnit),'value');
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75 | end
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76 | uid_BurstTiming=find(t,'/ImaDoc/Camera/BurstTiming');
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77 | if ~isempty(uid_BurstTiming)
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78 | for k=1:length(uid_BurstTiming)
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79 | subt=branch(t,uid_BurstTiming(k));%subtree under BurstTiming
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80 | % reading Dtk
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81 | Frequency=get_value(subt,'/BurstTiming/FrameFrequency',1);
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82 | Dtj=get_value(subt,'/BurstTiming/Dtj',[]);
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83 | Dtj=Dtj/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's')
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84 | NbDtj=get_value(subt,'/BurstTiming/NbDtj',1);
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85 | Dti=get_value(subt,'/BurstTiming/Dti',[]);
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86 | Dti=Dti/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's')
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87 | NbDti=get_value(subt,'/BurstTiming/NbDti',1);
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88 | Time_val=get_value(subt,'/BurstTiming/Time',0);%time in TimeUnit
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89 | if ~isempty(Dti)
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90 | Dti=reshape(Dti'*ones(1,NbDti),NbDti*numel(Dti),1); %concatene Dti vector NbDti times
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91 | Time_val=[Time_val;Time_val(end)+cumsum(Dti)];%append the times defined by the intervals Dti
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92 | end
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93 | if ~isempty(Dtj)
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94 | Dtj=reshape(Dtj'*ones(1,NbDtj),1,NbDtj*numel(Dtj)); %concatene Dtj vector NbDtj times
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95 | Dtj=[0 Dtj];
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96 | Time_val=Time_val*ones(1,numel(Dtj))+ones(numel(Time_val),1)*cumsum(Dtj);% produce a time matrix with Dtj
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97 | end
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98 | % reading Dtk
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99 | Dtk=get_value(subt,'/BurstTiming/Dtk',[]);
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100 | NbDtk=get_value(subt,'/BurstTiming/NbDtk',1);
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101 | if isempty(Dtk)
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102 | s.Time=[s.Time;Time_val];
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103 | else
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104 | for kblock=1:NbDtk+1
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105 | Time_val_k=Time_val+(kblock-1)*Dtk;
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106 | s.Time=[s.Time;Time_val_k];
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107 | end
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108 | end
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109 | end
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110 | end
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111 | end
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112 | end
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113 |
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114 | %% motor
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115 | if strcmp(option,'*') || strcmp(option,'GeometryCalib')
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116 | uid_subtree=find(t,'/ImaDoc/TranslationMotor');
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117 | if length(uid_subtree)==1
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118 | subt=branch(t,uid_subtree);%subtree under GeometryCalib
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119 | [s.TranslationMotor,errormsg]=read_subtree(subt,{'Nbslice','ZStart','ZEnd'},[1 1 1],[1 1 1]);
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120 | end
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121 | end
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122 | %% geometric calibration
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123 | if strcmp(option,'*') || strcmp(option,'GeometryCalib')
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124 | uid_GeometryCalib=find(t,'/ImaDoc/GeometryCalib');
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125 | if ~isempty(uid_GeometryCalib)
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126 | if length(uid_GeometryCalib)>1
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127 | errormsg=['More than one GeometryCalib in ' filecivxml];
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128 | return
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129 | end
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130 | subt=branch(t,uid_GeometryCalib);%subtree under GeometryCalib
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131 | cont=get(subt,1,'contents');
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132 | if ~isempty(cont)
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133 | uid_CalibrationType=find(subt,'/GeometryCalib/CalibrationType');
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134 | if isequal(length(uid_CalibrationType),1)
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135 | tsai.CalibrationType=get(subt,children(subt,uid_CalibrationType),'value');
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136 | end
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137 | uid_CoordUnit=find(subt,'/GeometryCalib/CoordUnit');
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138 | if isequal(length(uid_CoordUnit),1)
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139 | tsai.CoordUnit=get(subt,children(subt,uid_CoordUnit),'value');
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140 | end
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141 | uid_fx_fy=find(subt,'/GeometryCalib/fx_fy');
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142 | focal=[];%default fro old convention (Reg Wilson)
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143 | if isequal(length(uid_fx_fy),1)
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144 | tsai.fx_fy=str2num(get(subt,children(subt,uid_fx_fy),'value'));
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145 | else %old convention (Reg Wilson)
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146 | uid_focal=find(subt,'/GeometryCalib/focal');
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147 | uid_dpx_dpy=find(subt,'/GeometryCalib/dpx_dpy');
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148 | uid_sx=find(subt,'/GeometryCalib/sx');
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149 | if ~isempty(uid_focal) && ~isempty(uid_dpx_dpy) && ~isempty(uid_sx)
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150 | dpx_dpy=str2num(get(subt,children(subt,uid_dpx_dpy),'value'));
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151 | sx=str2num(get(subt,children(subt,uid_sx),'value'));
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152 | focal=str2num(get(subt,children(subt,uid_focal),'value'));
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153 | tsai.fx_fy(1)=sx*focal/dpx_dpy(1);
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154 | tsai.fx_fy(2)=focal/dpx_dpy(2);
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155 | end
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156 | end
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157 | uid_Cx_Cy=find(subt,'/GeometryCalib/Cx_Cy');
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158 | if ~isempty(uid_Cx_Cy)
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159 | tsai.Cx_Cy=str2num(get(subt,children(subt,uid_Cx_Cy),'value'));
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160 | end
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161 | uid_kc=find(subt,'/GeometryCalib/kc');
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162 | if ~isempty(uid_kc)
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163 | tsai.kc=str2double(get(subt,children(subt,uid_kc),'value'));
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164 | else %old convention (Reg Wilson)
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165 | uid_kappa1=find(subt,'/GeometryCalib/kappa1');
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166 | if ~isempty(uid_kappa1)&& ~isempty(focal)
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167 | kappa1=str2double(get(subt,children(subt,uid_kappa1),'value'));
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168 | tsai.kc=-kappa1*focal*focal;
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169 | end
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170 | end
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171 | uid_Tx_Ty_Tz=find(subt,'/GeometryCalib/Tx_Ty_Tz');
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172 | if ~isempty(uid_Tx_Ty_Tz)
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173 | tsai.Tx_Ty_Tz=str2num(get(subt,children(subt,uid_Tx_Ty_Tz),'value'));
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174 | end
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175 | uid_R=find(subt,'/GeometryCalib/R');
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176 | if ~isempty(uid_R)
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177 | RR=get(subt,children(subt,uid_R),'value');
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178 | if length(RR)==3
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179 | tsai.R=[str2num(RR{1});str2num(RR{2});str2num(RR{3})];
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180 | end
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181 | end
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182 |
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183 | %look for laser plane definitions
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184 | uid_Angle=find(subt,'/GeometryCalib/PlaneAngle');
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185 | uid_Pos=find(subt,'/GeometryCalib/SliceCoord');
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186 | if isempty(uid_Pos)
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187 | uid_Pos=find(subt,'/GeometryCalib/PlanePos');%old convention
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188 | end
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189 | if ~isempty(uid_Angle)
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190 | tsai.PlaneAngle=str2num(get(subt,children(subt,uid_Angle),'value'));
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191 | end
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192 | if ~isempty(uid_Pos)
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193 | for j=1:length(uid_Pos)
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194 | tsai.SliceCoord(j,:)=str2num(get(subt,children(subt,uid_Pos(j)),'value'));
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195 | end
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196 | uid_DZ=find(subt,'/GeometryCalib/SliceDZ');
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197 | uid_NbSlice=find(subt,'/GeometryCalib/NbSlice');
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198 | if ~isempty(uid_DZ) && ~isempty(uid_NbSlice)
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199 | DZ=str2double(get(subt,children(subt,uid_DZ),'value'));
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200 | NbSlice=get(subt,children(subt,uid_NbSlice),'value');
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201 | if isequal(NbSlice,'volume')
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202 | tsai.NbSlice='volume';
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203 | NbSlice=NbDtj+1;
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204 | else
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205 | tsai.NbSlice=str2double(NbSlice);
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206 | end
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207 | tsai.SliceCoord=ones(NbSlice,1)*tsai.SliceCoord+DZ*(0:NbSlice-1)'*[0 0 1];
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208 | end
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209 | end
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210 | tsai.SliceAngle=get_value(subt,'/GeometryCalib/SliceAngle',[0 0 0]);
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211 | tsai.VolumeScan=get_value(subt,'/GeometryCalib/VolumeScan','n');
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212 | tsai.InterfaceCoord=get_value(subt,'/GeometryCalib/InterfaceCoord',[0 0 0]);
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213 | tsai.RefractionIndex=get_value(subt,'/GeometryCalib/RefractionIndex',1);
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214 |
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215 | if strcmp(option,'GeometryCalib')
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216 | tsai.PointCoord=get_value(subt,'/GeometryCalib/SourceCalib/PointCoord',[0 0 0 0 0]);
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217 | end
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218 | s.GeometryCalib=tsai;
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219 | end
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220 | end
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221 | end
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222 |
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223 | %--------------------------------------------------
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224 | % read a subtree
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225 | % INPUT:
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226 | % t: xltree
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227 | % head_element: head elelemnt of the subtree
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228 | % Data, structure containing
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229 | % .Key: element name
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230 | % .Type: type of element ('charg', 'float'....)
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231 | % .NbOccur: nbre of occurrence, NaN for un specified number
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232 | function [s,errormsg]=read_subtree(subt,Data,NbOccur,NumTest)
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233 | %--------------------------------------------------
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234 | s=[];%default
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235 | errormsg='';
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236 | head_element=get(subt,1,'name');
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237 | cont=get(subt,1,'contents');
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238 | if ~isempty(cont)
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239 | for ilist=1:length(Data)
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240 | uid_key=find(subt,[head_element '/' Data{ilist}]);
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241 | if ~isequal(length(uid_key),NbOccur(ilist))
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242 | errormsg=['wrong number of occurence for ' Data{ilist}];
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243 | return
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244 | end
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245 | for ival=1:length(uid_key)
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246 | val=get(subt,children(subt,uid_key(ival)),'value');
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247 | if ~NumTest(ilist)
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248 | eval(['s.' Data{ilist} '=val;']);
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249 | else
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250 | eval(['s.' Data{ilist} '=str2double(val);'])
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251 | end
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252 | end
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253 | end
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254 | end
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255 |
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256 |
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257 | %--------------------------------------------------
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258 | % read an xml element
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259 | function val=get_value(t,label,default)
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260 | %--------------------------------------------------
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261 | val=default;
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262 | uid=find(t,label);%find the element iud(s)
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263 | if ~isempty(uid) %if the element named label exists
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264 | uid_child=children(t,uid);%find the children
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265 | if ~isempty(uid_child)
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266 | data=get(t,uid_child,'type');%get the type of child
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267 | if iscell(data)% case of multiple element
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268 | for icell=1:numel(data)
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269 | val_read=str2num(get(t,uid_child(icell),'value'));
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270 | if ~isempty(val_read)
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271 | val(icell,:)=val_read;
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272 | end
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273 | end
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274 | % val=val';
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275 | else % case of unique element value
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276 | val_read=str2num(get(t,uid_child,'value'));
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277 | if ~isempty(val_read)
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278 | val=val_read;
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279 | else
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280 | val=get(t,uid_child,'value');%char string data
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281 | end
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282 | end
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283 | end
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284 | end
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