1 | |
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2 | %'merge_proj': project and concatene fields, used with series.fig |
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3 | %------------------------------------------------------------------------ |
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4 | % function GUI_input=merge_proj(num_i1,num_i2,num_j1,num_j2,Series) |
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5 | % |
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6 | %OUTPUT |
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7 | % GUI_input=list of options in the GUI series.fig needed for the function |
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8 | % |
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9 | %INPUT: |
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10 | %num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) |
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11 | %num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) |
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12 | %num_j1: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ ) |
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13 | %num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ) |
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14 | %Series: Matlab structure containing information set by the series interface |
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15 | % |
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16 | function GUI_input=merge_proj(num_i1,num_i2,num_j1,num_j2,Series) |
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17 | |
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18 | %requests for the visibility of input windows in the GUI series (activated directly by the selection in the menu ACTION) |
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19 | if ~exist('num_i1','var') |
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20 | GUI_input={'RootPath';'two';...%nbre of possible input series (options 'on'/'two'/'many', default:'one') |
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21 | 'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default) |
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22 | 'RootFile';'on';... %root input file name ('on' by default) |
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23 | 'FileExt';'on';... %input file extension ('on' by default) |
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24 | 'NomType';'on';...%type of file indexing ('on' by default) |
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25 | 'NbSlice';'on'; ...%nbre of slices ('off' by default) |
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26 | 'VelTypeMenu';'one';...% menu for selecting the velocity type (civ1,..) options 'off'/'one'/'two', 'off' by default) |
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27 | 'FieldMenu';'one';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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28 | 'CoordType';'on';...%can use a transform function 'off' by default |
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29 | 'GetObject';'on';...%can use projection object ,'off' by default |
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30 | %'GetMask';'on'...%can use mask option ,'off' by default |
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31 | %'PARAMETER'; options: name of the user defined parameter',repeat a line for each parameter |
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32 | ''}; |
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33 | return %exit the function |
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34 | end |
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35 | |
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36 | %------------------------------------------------- |
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37 | hseries=guidata(Series.hseries);%handles of the GUI series |
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38 | WaitbarPos=get(hseries.waitbar_frame,'Position'); %positiopn of waitbar frame |
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39 | %------------------------------------------------- |
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40 | |
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41 | |
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42 | %% projection object |
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43 | test_object=get(hseries.GetObject,'Value'); |
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44 | if test_object |
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45 | hset_object=findobj(allchild(0),'tag','set_object'); |
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46 | ProjObject=read_set_object(guidata(hset_object)); |
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47 | if ~isfield(ProjObject,'Style') |
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48 | msgbox_uvmat('ERROR','Undefined projection object style') |
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49 | return |
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50 | end |
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51 | if ~isequal(ProjObject.Style,'plane')|| isequal(ProjObject.ProjMode,'projection') |
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52 | msgbox_uvmat('ERROR','The projection object must be a plane with projection mode interp or filter') |
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53 | return |
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54 | end |
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55 | answeryes=msgbox_uvmat('INPUT_Y-N',['field series projected on ' ProjObject.Style]); |
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56 | if ~isequal(answeryes,'Yes') |
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57 | return |
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58 | end |
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59 | end |
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60 | |
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61 | %% numbers of view fields (nbre of inputs in RootPath) |
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62 | testcell=iscell(Series.RootFile); |
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63 | if ~testcell |
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64 | Series.RootPath={Series.RootPath}; |
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65 | Series.RootFile={Series.RootFile}; |
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66 | Series.SubDir={Series.SubDir}; |
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67 | Series.FileExt={Series.FileExt}; |
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68 | Series.NomType={Series.NomType}; |
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69 | num_i1={num_i1}; |
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70 | num_i2={num_i2}; |
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71 | num_j1={num_j1}; |
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72 | num_j2={num_j2}; |
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73 | end |
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74 | nbview=length(Series.RootFile);%number of views (file series to merge) |
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75 | nbfield=size(num_i1{1},1)*size(num_i1{1},2);%number of fields in the time series |
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76 | hhh=which('mmreader'); |
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77 | for iview=1:nbview |
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78 | test_movie(iview)=0; |
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79 | if ~isequal(hhh,'')&& mmreader.isPlatformSupported() |
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80 | if isequal(lower(Series.FileExt{iview}),'.avi') |
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81 | MovieObject{iview}=mmreader(fullfile(Series.RootPath{iview},[Series.RootFile{iview} Series.FileExt{iview}])); |
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82 | test_movie(iview)=1; |
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83 | end |
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84 | end |
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85 | end |
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86 | |
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87 | %% Calibration data and timing: read the ImaDoc files |
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88 | timecell={}; |
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89 | itime=0; |
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90 | NbSlice_calib={}; %test for z index |
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91 | for iview=1:nbview%Loop on views |
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92 | XmlData{iview}=[];%default |
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93 | filebase{iview}=fullfile(Series.RootPath{iview},Series.RootFile{iview}); |
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94 | if exist([filebase{iview} '.xml'],'file') |
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95 | [XmlData{iview},error]=imadoc2struct([filebase{iview} '.xml']); |
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96 | if isfield(XmlData{iview},'Time') |
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97 | itime=itime+1; |
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98 | timecell{itime}=XmlData{iview}.Time; |
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99 | end |
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100 | if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord') |
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101 | NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1); |
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102 | if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) |
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103 | msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); |
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104 | end |
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105 | end |
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106 | elseif exist([filebase{iview} '.civ'],'file') |
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107 | [error,time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([filebase{iview} '.civ']); |
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108 | itime=itime+1; |
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109 | timecell{itime}=time; |
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110 | XmlData{iview}.Time=time; |
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111 | GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0]; |
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112 | GeometryCalib.Tx=0; |
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113 | GeometryCalib.Ty=0; |
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114 | GeometryCalib.Tz=1; |
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115 | GeometryCalib.dpx=1; |
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116 | GeometryCalib.dpy=1; |
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117 | GeometryCalib.sx=1; |
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118 | GeometryCalib.Cx=0; |
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119 | GeometryCalib.Cy=0; |
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120 | GeometryCalib.f=1; |
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121 | GeometryCalib.kappa1=0; |
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122 | GeometryCalib.CoordUnit='cm'; |
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123 | XmlData{iview}.GeometryCalib=GeometryCalib; |
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124 | if error==1 |
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125 | msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file'); |
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126 | end |
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127 | end |
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128 | end |
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129 | |
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130 | %% check coincidence in time |
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131 | multitime=0; |
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132 | if isempty(timecell) |
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133 | time=[]; |
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134 | elseif length(timecell)==1 |
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135 | time=timecell{1}; |
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136 | elseif length(timecell)>1 |
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137 | multitime=1; |
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138 | for icell=1:length(timecell) |
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139 | if ~isequal(size(timecell{icell}),size(timecell{1})) |
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140 | msgbox_uvmat('WARNING','inconsistent time array dimensions in ImaDoc fields, the time for the first series is used') |
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141 | time=timecell{1}; |
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142 | multitime=0; |
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143 | break |
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144 | end |
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145 | end |
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146 | end |
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147 | if multitime |
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148 | for icell=1:length(timecell) |
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149 | time(icell,:,:)=timecell{icell}; |
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150 | end |
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151 | diff_time=max(max(diff(time))); |
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152 | if diff_time>0 |
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153 | msgbox_uvmat('WARNING',['times of series differ by more than ' num2str(diff_time)]) |
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154 | end |
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155 | end |
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156 | if size(time,2) < num_i2{1}(end) || size(time,3) < num_j2{1}(end)% ime array absent or too short in ImaDoc xml file' |
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157 | time=[]; |
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158 | end |
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159 | |
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160 | %% coordinate transform or other user defined transform |
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161 | transform_fct=[];%default |
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162 | if isfield(Series,'transform_fct') |
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163 | transform_fct=Series.transform_fct; |
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164 | end |
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165 | |
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166 | %% Field and velocity type (the same for all views) |
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167 | FieldName=''; |
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168 | if strcmp(get(hseries.FieldMenu,'Visible'),'on') |
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169 | Field_str=get(hseries.FieldMenu,'String'); |
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170 | val=get(hseries.FieldMenu,'Value'); |
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171 | FieldName=Field_str(val);%the same set of fields for all views |
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172 | VelType_str=get(hseries.VelTypeMenu,'String'); |
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173 | VelType_val=get(hseries.VelTypeMenu,'Value'); |
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174 | VelType=VelType_str{VelType_val}; %the same for all views |
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175 | if strcmp(FieldName,'') |
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176 | msgbox_uvmat('ERROR','no input field defined in FieldMenu') |
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177 | elseif strcmp(FieldName,'get_field...') |
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178 | hget_field=findobj(allchild(0),'Name','get_field');%find the get_field... GUI |
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179 | SubField=get_field('read_get_field',hObject,eventdata,hget_field); %read the names of the variables to plot in the get_field GUI |
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180 | end |
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181 | end |
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182 | %detect whether all the files are 'images' or 'netcdf' |
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183 | testima=0; |
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184 | testvol=0; |
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185 | testcivx=0; |
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186 | testnc=0; |
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187 | FileExt=get(hseries.FileExt,'String'); |
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188 | for iview=1:nbview |
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189 | ext=FileExt{iview}; |
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190 | form=imformats(ext(2:end)); |
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191 | if isequal(lower(ext),'.vol') |
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192 | testvol=testvol+1; |
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193 | elseif ~isempty(form)||isequal(lower(ext),'.avi')% if the extension corresponds to an image format recognized by Matlab |
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194 | testima=testima+1; |
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195 | elseif isequal(ext,'.nc') |
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196 | testnc=testnc+1; |
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197 | end |
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198 | end |
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199 | if testvol |
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200 | msgbox_uvmat('ERROR','volume images not implemented yet') |
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201 | return |
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202 | end |
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203 | if testnc~=nbview && testima~=nbview && testvol~=nbview |
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204 | msgbox_uvmat('ERROR','need a set of images or a set of netcdf files with the same fields as input') |
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205 | return |
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206 | end |
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207 | if ~isequal(FieldName,'get_field...') |
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208 | testcivx=testnc; |
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209 | end |
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210 | |
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211 | %% name of output files and directory: |
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212 | ProjectDir=fileparts(fileparts(Series.RootPath{1}));% preoject directory (GERK) |
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213 | prompt={['result directory (in' ProjectDir ')']}; |
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214 | RootPath=get(hseries.RootPath,'String'); |
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215 | SubDir=get(hseries.SubDir,'String'); |
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216 | if isequal(length(RootPath),1) |
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217 | fulldir=RootPath{1}; |
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218 | subdir='merge_proj'; |
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219 | res_subdir=fullfile(fulldir,subdir); |
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220 | else |
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221 | def={fullfile(ProjectDir,'0_RESULTS')}; |
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222 | dlgTitle='result directory'; |
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223 | lineNo=1; |
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224 | answer=msgbox_uvmat('INPUT_TXT',dlgTitle,def); |
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225 | fulldir=answer{1}; |
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226 | subdir=[]; |
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227 | dirlist=sort(Series.RootFile); |
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228 | for iview=1:nbview |
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229 | if ~isempty(subdir) |
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230 | subdir=[subdir '-']; |
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231 | end |
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232 | subdir=[subdir dirlist{iview}]; |
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233 | end |
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234 | res_subdir=fullfile(fulldir,subdir); |
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235 | end |
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236 | ext=FileExt{1}; |
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237 | if ~exist(fulldir,'dir') |
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238 | msgbox_uvmat('ERROR',['directory ' fulldir ' needs to be created']) |
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239 | return |
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240 | end |
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241 | if ~exist(res_subdir,'dir') |
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242 | dircur=pwd; |
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243 | cd(fulldir); |
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244 | succeed=mkdir(subdir); |
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245 | if succeed |
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246 | [xx,msg2] = fileattrib(res_subdir,'+w','g'); %yield writing access (+w) to user group (g) |
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247 | if ~strcmp(msg2,'') |
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248 | msgbox_uvmat('ERROR',['pb of permission for ' res_subdir ': ' msg2])%error message for directory creation |
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249 | cd(dircur) |
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250 | return |
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251 | end |
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252 | cd(dircur); |
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253 | else |
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254 | msgbox_uvmat('ERROR',['Cannot create directory ' fulldir]) |
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255 | return |
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256 | end |
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257 | end |
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258 | filebasesub=fullfile(res_subdir,Series.RootFile{1}); |
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259 | filebase_merge=fullfile(res_subdir,'merged');%root name for the merged files |
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260 | |
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261 | %% MAIN LOOP |
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262 | for ifile=1:nbfield |
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263 | stopstate=get(hseries.RUN,'BusyAction'); |
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264 | if isequal(stopstate,'queue')% enable STOP command from the 'series' interface |
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265 | update_waitbar(hseries.waitbar,WaitbarPos,ifile/nbfield) |
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266 | |
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267 | %% ----------LOOP ON VIEWS---------------------- |
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268 | nbtime=0; |
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269 | for iview=1:nbview |
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270 | %name of the current file |
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271 | filename=name_generator(filebase{iview},num_i1{iview}(ifile),num_j1{iview}(ifile),Series.FileExt{iview},Series.NomType{iview},1,num_i2{iview}(ifile),num_j2{iview}(ifile),SubDir{iview}); |
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272 | if ~exist(filename,'file') |
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273 | msgbox_uvmat('ERROR',['missing input file' filename]) |
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274 | break |
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275 | end |
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276 | %reading the current file |
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277 | if testima |
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278 | if test_movie(iview) |
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279 | Field{iview}.A=read(MovieObject{iview},num_i1{iview}(ifile)); |
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280 | else |
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281 | Field{iview}.A=imread(filename); |
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282 | end % TODO: introduce ListVarName |
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283 | npxy=size(Field{iview}.A); |
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284 | Field{iview}.ListVarName={'AX','AY','A'}; |
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285 | Field{iview}.VarDimName={'AX','AY',{'AY','AX'}}; |
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286 | Field{iview}.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers |
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287 | Field{iview}.AY=[npxy(1)-0.5 0.5]; |
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288 | Field{iview}.CoordUnit='pixel'; |
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289 | Field{iview}.AName='image'; |
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290 | timeread(iview)=0; |
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291 | else |
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292 | if testcivx |
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293 | [Field{iview},VelTypeOut]=read_civxdata(filename,FieldName,VelType); |
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294 | else |
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295 | [Field{iview},var_detect]=nc2struct(filename,SubField.ListVarName); %read the corresponding input data |
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296 | Field{iview}.VarAttribute=SubField.VarAttribute; |
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297 | end |
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298 | if isfield(Field{iview},'Txt') |
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299 | msgbox_uvmat('ERROR',Field{iview}.Txt) |
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300 | return |
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301 | end |
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302 | if isfield(Field{iview},'Time') |
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303 | timeread(iview)=Field{iview}.Time; |
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304 | nbtime=nbtime+1; |
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305 | end |
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306 | end |
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307 | if ~isempty(NbSlice_calib) |
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308 | Field{iview}.ZIndex=mod(num_i1{iview}(ifile)-1,NbSlice_calib{1})+1; |
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309 | end |
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310 | %transform the input field (e.g; phys) if requested |
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311 | if ~isempty(transform_fct) |
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312 | Field{iview}=transform_fct(Field{iview},XmlData{iview}); %transform to phys if requested |
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313 | end |
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314 | if testcivx |
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315 | Field{iview}=calc_field(FieldName,Field{iview}); |
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316 | end |
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317 | %projection on object (gridded plane) |
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318 | if test_object |
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319 | Field{iview}=proj_field(Field{iview},ProjObject); |
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320 | end |
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321 | end |
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322 | %----------END LOOP ON VIEWS---------------------- |
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323 | |
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324 | %% merge the nbview fields |
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325 | MergeData=merge_field(Field); |
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326 | if isfield(MergeData,'Txt') |
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327 | msgbox_uvmat('ERROR',MergeData.Txt) |
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328 | return |
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329 | end |
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330 | % generating the name of the merged field |
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331 | mergename=name_generator(filebase_merge,num_i1{iview}(ifile),num_j1{iview}(ifile),Series.FileExt{iview},Series.NomType{iview},1,num_i2{iview}(ifile),num_j2{iview}(ifile)); |
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332 | |
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333 | % time of the merged field: |
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334 | time_i=0;%default |
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335 | if isempty(time)% time from ImaDoc prevails |
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336 | time_i=sum(timeread)/nbtime; |
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337 | else |
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338 | time_i=(time(iview,num_i1{iview}(ifile),num_j1{iview}(ifile))+time(iview,num_i2{iview}(ifile),num_j2{iview}(ifile)))/2; |
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339 | end |
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340 | |
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341 | % recording the merged field |
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342 | if testima %in case of input images an image is produced |
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343 | if isa(MergeData.A,'uint8') |
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344 | bitdepth=8; |
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345 | elseif isa(MergeData.A,'uint16') |
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346 | bitdepth=16; |
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347 | end |
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348 | imwrite(MergeData.A,mergename,'BitDepth',bitdepth); |
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349 | %write xml calibration file |
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350 | siz=size(MergeData.A); |
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351 | npy=siz(1); |
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352 | npx=siz(2); |
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353 | if isfield(MergeData,'VarAttribute')&&isfield(MergeData.VarAttribute{1},'Coord_2')&&isfield(MergeData.VarAttribute{1},'Coord_1') |
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354 | Rangx=MergeData.VarAttribute{1}.Coord_2; |
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355 | Rangy=MergeData.VarAttribute{1}.Coord_1; |
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356 | elseif isfield(MergeData,'AX')&& isfield(MergeData,'AY') |
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357 | Rangx=[MergeData.AX(1) MergeData.AX(end)]; |
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358 | Rangy=[MergeData.AY(1) MergeData.AY(end)]; |
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359 | else |
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360 | Rangx=[0.5 npx-0.5]; |
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361 | Rangy=[npy-0.5 0.5];%default |
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362 | end |
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363 | pxcmx=(npx-1)/(Rangx(2)-Rangx(1)); |
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364 | pxcmy=(npy-1)/(Rangy(1)-Rangy(2)); |
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365 | T_x=-pxcmx*Rangx(1)+0.5; |
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366 | T_y=-pxcmy*Rangy(2)+0.5; |
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367 | GeometryCal.focal=1; |
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368 | GeometryCal.R=[pxcmx,0,0;0,pxcmy,0;0,0,1]; |
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369 | GeometryCal.Tx_Ty_Tz=[T_x T_y 1]; |
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370 | ImaDoc.GeometryCalib=GeometryCal; |
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371 | t=struct2xml(ImaDoc); |
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372 | t=set(t,1,'name','ImaDoc'); |
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373 | save(t,[filebase_merge '.xml']) |
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374 | display([filebase_merge '.xml saved']) |
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375 | else |
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376 | MergeData.ListGlobalAttribute={'Project','InputFile_1','InputFile_end','nb_coord','nb_dim','dt','Time','civ'}; |
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377 | MergeData.nb_coord=2; |
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378 | MergeData.nb_dim=2; |
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379 | dt=[]; |
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380 | if isfield(Field{1},'dt')&& isnumeric(Field{1}.dt) |
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381 | dt=Field{1}.dt; |
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382 | end |
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383 | for iview =2:numel(Field) |
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384 | if ~(isfield(Field{iview},'dt')&& isequal(Field{iview}.dt,dt)) |
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385 | dt=[];%dt not the same for all fields |
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386 | end |
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387 | end |
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388 | if isempty(dt) |
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389 | MergeData.ListGlobalAttribute(6)=[]; |
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390 | else |
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391 | MergeData.dt=dt; |
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392 | end |
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393 | MergeData.Time=time_i; |
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394 | error=struct2nc(mergename,MergeData);%save result file |
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395 | if isempty(error) |
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396 | display(['output file ' mergename ' written']) |
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397 | else |
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398 | display(error) |
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399 | end |
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400 | end |
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401 | end |
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402 | end |
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403 | |
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404 | %'merge_field': concatene fields |
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405 | %------------------------------------------------------------------------ |
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406 | function MergeData=merge_field(Data) |
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407 | %% default output |
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408 | if isempty(Data)||~iscell(Data) |
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409 | MergeData=[]; |
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410 | return |
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411 | end |
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412 | MergeData=Data{1};%default |
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413 | error=0; |
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414 | nbview=length(Data); |
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415 | if nbview==1 |
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416 | return |
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417 | end |
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418 | |
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419 | %% group the variables (fields of 'FieldData') in cells of variables with the same dimensions |
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420 | [CellVarIndex,NbDim,VarTypeCell]=find_field_indices(Data{1}); |
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421 | %LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS |
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422 | % CellVarIndex=cells of variable index arrays |
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423 | ivar_new=0; % index of the current variable in the projected field |
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424 | for icell=1:length(CellVarIndex) |
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425 | if NbDim(icell)==1 |
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426 | continue |
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427 | end |
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428 | VarIndex=CellVarIndex{icell};% indices of the selected variables in the list FieldData.ListVarName |
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429 | VarType=VarTypeCell{icell}; |
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430 | ivar_X=VarType.coord_x; |
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431 | ivar_Y=VarType.coord_y; |
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432 | ivar_FF=VarType.errorflag; |
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433 | if isempty(ivar_X) |
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434 | test_grid=1;%test for input data on regular grid (e.g. image)coordinates |
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435 | else |
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436 | if length(ivar_Y)~=1 |
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437 | msgbox_uvmat('ERROR','y coordinate missing in proj_field.m') |
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438 | return |
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439 | end |
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440 | test_grid=0; |
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441 | end |
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442 | %case of input fields with unstructured coordinates |
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443 | if ~test_grid |
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444 | for ivar=VarIndex |
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445 | VarName=MergeData.ListVarName{ivar}; |
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446 | for iview=1:nbview |
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447 | eval(['MergeData.' VarName '=[MergeData.' VarName '; Data{iview}.' VarName '];']) |
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448 | end |
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449 | end |
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450 | %case of fields defined on a structured grid |
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451 | else |
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452 | testFF=0; |
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453 | for iview=2:nbview |
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454 | for ivar=VarIndex |
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455 | VarName=MergeData.ListVarName{ivar}; |
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456 | if isfield(MergeData,'VarAttribute') |
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457 | if length(MergeData.VarAttribute)>=ivar && isfield(MergeData.VarAttribute{ivar},'Role') && isequal(MergeData.VarAttribute{ivar}.Role,'errorflag') |
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458 | testFF=1; |
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459 | end |
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460 | end |
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461 | eval(['MergeData.' VarName '=MergeData.' VarName '+ Data{iview}.' VarName ';']) |
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462 | end |
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463 | end |
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464 | if testFF |
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465 | nbaver=nbview-MergeData.FF; |
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466 | indgood=find(nbaver>0); |
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467 | for ivar=VarIndex |
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468 | VarName=MergeData.ListVarName{ivar}; |
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469 | eval(['MergeData.' VarName '(indgood)=double(MergeData.' VarName '(indgood))./nbaver(indgood);']) |
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470 | end |
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471 | else |
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472 | for ivar=VarIndex |
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473 | VarName=MergeData.ListVarName{ivar}; |
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474 | eval(['MergeData.' VarName '=double(MergeData.' VarName ')./nbview;']) |
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475 | end |
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476 | end |
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477 | end |
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478 | end |
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479 | |
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480 | |
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