1 | %'merge_proj': concatene several fields from series, can project them on a regular grid in phys coordinates |
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2 | %------------------------------------------------------------------------ |
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3 | % function ParamOut=merge_proj(Param) |
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4 | %------------------------------------------------------------------------ |
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5 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% |
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6 | % |
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7 | %OUTPUT |
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8 | % ParamOut: sets options in the GUI series.fig needed for the function |
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9 | % |
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10 | %INPUT: |
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11 | % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. |
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12 | % In batch mode, Param is the name of the corresponding xml file containing the same information |
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13 | % when Param.Action.RUN=0 (as activated when the current Action is selected |
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14 | % in series), the function ouput paramOut set the activation of the needed GUI elements |
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15 | % |
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16 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to |
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17 | % see the current structure Param) |
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18 | % .InputTable: cell of input file names, (several lines for multiple input) |
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19 | % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} |
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20 | % .OutputSubDir: name of the subdirectory for data outputs |
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21 | % .OutputDirExt: directory extension for data outputs |
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22 | % .Action: .ActionName: name of the current activated function |
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23 | % .ActionPath: path of the current activated function |
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24 | % .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled Matlab fct |
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25 | % .RUN =0 for GUI input, =1 for function activation |
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26 | % .RunMode='local','background', 'cluster': type of function use |
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27 | % |
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28 | % .IndexRange: set the file or frame indices on which the action must be performed |
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29 | % .FieldTransform: .TransformName: name of the selected transform function |
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30 | % .TransformPath: path of the selected transform function |
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31 | % .InputFields: sub structure describing the input fields withfields |
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32 | % .FieldName: name(s) of the field |
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33 | % .VelType: velocity type |
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34 | % .FieldName_1: name of the second field in case of two input series |
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35 | % .VelType_1: velocity type of the second field in case of two input series |
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36 | % .Coord_y: name of y coordinate variable |
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37 | % .Coord_x: name of x coordinate variable |
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38 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) |
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39 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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40 | |
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41 | %======================================================================= |
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42 | % Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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43 | % http://www.legi.grenoble-inp.fr |
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44 | % Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.fr |
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45 | % |
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46 | % This file is part of the toolbox UVMAT. |
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47 | % |
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48 | % UVMAT is free software; you can redistribute it and/or modify |
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49 | % it under the terms of the GNU General Public License as published |
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50 | % by the Free Software Foundation; either version 2 of the license, |
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51 | % or (at your option) any later version. |
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52 | % |
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53 | % UVMAT is distributed in the hope that it will be useful, |
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54 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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55 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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56 | % GNU General Public License (see LICENSE.txt) for more details. |
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57 | %======================================================================= |
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58 | |
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59 | function ParamOut=merge_proj(Param) |
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60 | |
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61 | %% set the input elements needed on the GUI series when the function is selected in the menu ActionName or InputTable refreshed |
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62 | if isstruct(Param) && isequal(Param.Action.RUN,0) |
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63 | ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
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64 | ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
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65 | ParamOut.NbSlice='off'; %nbre of slices ('off' by default) |
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66 | ParamOut.VelType='one';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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67 | ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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68 | ParamOut.FieldTransform = 'on';%can use a transform function |
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69 | %%%%% list of possible transform functions (needed only for compilation) |
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70 | % ListTransform={'phys','phys_polar','sub_field'};%list of possible transform functions (needed only for compilation) |
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71 | % if 0==1 %never satisfied but trigger compilation with the appropriate transform functions |
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72 | % phys |
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73 | % phys_polar |
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74 | % sub_field |
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75 | try |
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76 | for ilist=1:numel(ListTransform) |
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77 | eval(ListTransform{ilist}) |
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78 | end |
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79 | end |
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80 | |
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81 | ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions |
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82 | %%%%%%%% |
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83 | ParamOut.ProjObject='on';%can use projection object(option 'off'/'on', |
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84 | ParamOut.Mask='on';%can use mask option (option 'off'/'on', 'off' by default) |
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85 | ParamOut.OutputDirExt='.mproj';%set the output dir extension |
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86 | ParamOut.OutputFileMode='NbInput';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice |
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87 | %check the input files |
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88 | ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) |
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89 | first_j=[]; |
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90 | if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end |
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91 | PairString=''; |
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92 | if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end |
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93 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString); |
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94 | FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... |
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95 | Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); |
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96 | if ~exist(FirstFileName,'file') |
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97 | msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist']) |
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98 | end |
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99 | return |
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100 | end |
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101 | |
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102 | %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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103 | ParamOut=[]; %default output |
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104 | RUNHandle=[]; |
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105 | WaitbarHandle=[]; |
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106 | %% read input parameters from an xml file if input is a file name (batch mode) |
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107 | checkrun=1; |
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108 | if ischar(Param) |
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109 | Param=xml2struct(Param);% read Param as input file (batch case) |
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110 | checkrun=0; |
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111 | else |
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112 | hseries=findobj(allchild(0),'Tag','series'); |
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113 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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114 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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115 | end |
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116 | |
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117 | %% define the directory for result file (with path=RootPath{1}) |
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118 | OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files |
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119 | |
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120 | if ~isfield(Param,'InputFields') |
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121 | Param.InputFields.FieldName=''; |
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122 | end |
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123 | |
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124 | %% root input file(s) name, type and index series |
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125 | RootPath=Param.InputTable(:,1); |
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126 | RootFile=Param.InputTable(:,3); |
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127 | SubDir=Param.InputTable(:,2); |
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128 | FileExt=Param.InputTable(:,5); |
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129 | |
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130 | hdisp=disp_uvmat('WAITING...','checking the file series',checkrun); |
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131 | % gives the series of input file names and indices set by the input parameters: |
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132 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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133 | % filecell{iview,fileindex}: |
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134 | % iview: line in the table corresponding to a given file series |
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135 | % fileindex: file index with i and j reshaped as a 1D array |
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136 | % i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j |
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137 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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138 | if ~isempty(hdisp),delete(hdisp),end %end the waiting display |
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139 | |
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140 | NbView=numel(i1_series);%number of input file series (lines in InputTable) |
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141 | NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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142 | NbField_i=size(i1_series{1},2); %nb of fields for the i index |
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143 | NbField=NbField_j*NbField_i; %total number of fields |
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144 | |
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145 | %% determine the file type on each line from the first input file |
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146 | NcTypeOptions={'netcdf','civx','civdata','pivdata_fluidimage'}; |
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147 | for iview=1:NbView |
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148 | if ~exist(filecell{iview,1}','file') |
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149 | disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun) |
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150 | return |
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151 | end |
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152 | [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1}); |
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153 | FileType{iview}=FileInfo{iview}.FileType; |
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154 | if strcmp(FileType{iview},'civdata')&& ~isfield(Param.InputFields,'VelType') |
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155 | FileType{iview}='netcdf'; |
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156 | end |
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157 | CheckImage{iview}=strcmp(FileInfo{iview}.FieldType,'image');% =1 for images |
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158 | if CheckImage{iview} |
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159 | ParamIn{iview}=MovieObject{iview}; |
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160 | else |
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161 | ParamIn{iview}=Param.InputFields; |
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162 | end |
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163 | CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files |
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164 | if ~isempty(j1_series{iview}) |
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165 | frame_index{iview}=j1_series{iview}; |
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166 | else |
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167 | frame_index{iview}=i1_series{iview}; |
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168 | end |
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169 | end |
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170 | if NbView >1 && max(cell2mat(CheckImage))>0 && ~isfield(Param,'ProjObject') |
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171 | disp_uvmat('ERROR','projection on a common grid is needed to concatene images: use a Projection Object of type ''plane'' with ProjMode=''interp_lin''',checkrun) |
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172 | return |
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173 | end |
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174 | |
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175 | %% calibration data and timing: read the ImaDoc files |
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176 | [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); |
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177 | if size(time,1)>1 |
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178 | diff_time=max(max(diff(time))); |
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179 | if diff_time>0 |
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180 | disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time) ': the mean time is chosen in result'],checkrun) |
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181 | end |
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182 | end |
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183 | if ~isempty(errormsg) |
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184 | disp_uvmat('WARNING',errormsg,checkrun) |
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185 | end |
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186 | time=mean(time,1); %averaged time taken for the merged field |
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187 | |
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188 | %% coordinate transform or other user defined transform |
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189 | transform_fct='';%default fct handle |
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190 | checksub=0; |
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191 | if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) |
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192 | currentdir=pwd; |
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193 | cd(Param.FieldTransform.TransformPath) |
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194 | transform_fct=str2func(Param.FieldTransform.TransformName); |
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195 | cd (currentdir) |
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196 | if isfield(Param,'TransformInput') |
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197 | for iview=1:NbView |
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198 | XmlData{iview}.TransformInput=Param.TransformInput; |
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199 | end |
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200 | end |
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201 | checksub=nargin(transform_fct);% number of input arguments for the selected transform fct |
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202 | if checksub>2 && NbView>2 |
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203 | disp_uvmat('WARNING',['only the two first input file series will be combined by ' Param.FieldTransform.TransformName],checkrun) |
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204 | end |
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205 | end |
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206 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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207 | % EDIT FROM HERE |
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208 | |
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209 | %% check the validity of input file types |
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210 | for iview=1:NbView |
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211 | if ~isequal(CheckImage{iview},1)&&~isequal(CheckNc{iview},1) |
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212 | disp_uvmat('ERROR','input set of input series: need either netcdf either image series',checkrun) |
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213 | return |
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214 | end |
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215 | end |
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216 | |
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217 | %% output file type |
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218 | if min(cell2mat(CheckImage))==1 && (~Param.CheckObject || strcmp(Param.ProjObject.Type,'plane')) |
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219 | FileExtOut='.png'; %image output (input and proj result = image) |
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220 | else |
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221 | FileExtOut='.nc'; %netcdf output |
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222 | end |
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223 | if isempty(j1_series{1}) |
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224 | NomTypeOut='_1'; |
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225 | else |
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226 | NomTypeOut='_1_1'; |
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227 | end |
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228 | %NomTypeOut=NomType;% output file index will indicate the first and last ref index in the series |
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229 | RootFileOut=RootFile{1}; |
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230 | for iview=2:NbView |
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231 | if ~strcmp(RootFile{iview},RootFile{1}) |
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232 | RootFileOut='mproj'; |
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233 | break |
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234 | end |
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235 | end |
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236 | |
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237 | %% mask (TODO: case of multilevels) |
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238 | MaskData=cell(NbView,1); |
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239 | if Param.CheckMask |
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240 | if ischar(Param.MaskTable)% case of a single mask (char chain) |
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241 | Param.MaskTable={Param.MaskTable}; |
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242 | end |
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243 | for iview=1:numel(Param.MaskTable) |
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244 | if exist(Param.MaskTable{iview},'file') |
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245 | [MaskData{iview},tild,errormsg] = read_field(Param.MaskTable{iview},'image'); |
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246 | if ~isempty(transform_fct) && nargin(transform_fct)>=2 |
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247 | MaskData{iview}=transform_fct(MaskData{iview},XmlData{iview}); |
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248 | end |
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249 | end |
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250 | end |
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251 | end |
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252 | |
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253 | %% Set field names and velocity types |
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254 | %use Param.InputFields for all views |
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255 | |
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256 | %% MAIN LOOP ON FIELDS |
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257 | %%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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258 | |
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259 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% |
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260 | tstart=tic; %used to record the computing time |
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261 | CheckOverwrite=1;%default |
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262 | if isfield(Param,'CheckOverwrite') |
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263 | CheckOverwrite=Param.CheckOverwrite; |
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264 | end |
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265 | OutputPath=fullfile(Param.OutputPath,num2str(Param.Experiment),num2str(Param.Device)); |
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266 | |
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267 | for index=1:NbField |
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268 | update_waitbar(WaitbarHandle,index/NbField) |
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269 | if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
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270 | disp('program stopped by user') |
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271 | return |
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272 | end |
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273 | |
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274 | %% generating the name of the merged field |
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275 | i1=i1_series{1}(index); |
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276 | if ~isempty(i2_series{end}) |
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277 | i2=i2_series{end}(index); |
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278 | else |
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279 | i2=i1; |
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280 | end |
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281 | j1=1; |
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282 | j2=1; |
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283 | if ~isempty(j1_series{1}) |
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284 | j1=j1_series{1}(index); |
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285 | if ~isempty(j2_series{end}) |
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286 | j2=j2_series{end}(index); |
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287 | else |
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288 | j2=j1; |
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289 | end |
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290 | end |
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291 | OutputFile=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,FileExtOut,NomTypeOut,i1,i2,j1,j2); |
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292 | if ~CheckOverwrite && exist(OutputFile,'file') |
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293 | disp(['existing output file ' OutputFile ' already exists, skip to next field']) |
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294 | continue% skip iteration if the mode overwrite is desactivated and the result file already exists |
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295 | end |
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296 | |
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297 | %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%% |
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298 | Data=cell(1,NbView);%initiate the set Data |
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299 | timeread=zeros(1,NbView); |
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300 | for iview=1:NbView |
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301 | %% reading input file(s) |
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302 | [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},ParamIn{iview},frame_index{iview}(index)); |
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303 | if isempty(errormsg) |
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304 | disp([filecell{iview,index} ' read OK']) |
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305 | else |
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306 | disp_uvmat('ERROR',['ERROR in merge_proj/read_field/' errormsg],checkrun) |
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307 | return |
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308 | end |
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309 | |
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310 | ListVar=Data{iview}.ListVarName; |
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311 | for ilist=1:numel(ListVar) |
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312 | Data{iview}.(ListVar{ilist})=double(Data{iview}.(ListVar{ilist}));% transform all fields in double before all operations |
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313 | end |
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314 | % get the time defined in the current file if not already defined from the xml file |
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315 | if isempty(time) && isfield(Data{iview},'Time') |
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316 | timeread(iview)=Data{iview}.Time; |
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317 | end |
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318 | if ~isempty(NbSlice_calib) |
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319 | Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform |
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320 | end |
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321 | |
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322 | %% transform the input field iview (e.g; phys) if requested (no transform involving two input fields at this stage) |
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323 | checksub=0; |
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324 | if ~isempty(transform_fct) |
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325 | checksub=nargin(transform_fct); |
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326 | if checksub>=2 |
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327 | Data{iview}=transform_fct(Data{iview},XmlData{iview}); |
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328 | elseif checksub==1 |
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329 | Data{iview}=transform_fct(Data{iview}); |
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330 | end |
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331 | end |
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332 | |
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333 | %% calculate tps coefficients if needed |
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334 | |
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335 | check_proj_tps= strcmp(FileType{iview},'civdata') && isfield(Param,'ProjObject')&&~isempty(Param.ProjObject)... |
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336 | && strcmp(Param.ProjObject.ProjMode,'interp_tps')&&~isfield(Data{iview},'Coord_tps'); |
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337 | if check_proj_tps |
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338 | Data{iview}=tps_coeff_field(Data{iview},check_proj_tps); |
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339 | end |
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340 | |
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341 | %% projection on object (gridded plane) |
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342 | if Param.CheckObject |
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343 | [Data{iview},errormsg]=proj_field(Data{iview},Param.ProjObject); |
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344 | if ~isempty(errormsg) |
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345 | disp_uvmat('ERROR',['ERROR in merge_proge/proj_field: ' errormsg],checkrun) |
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346 | return |
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347 | end |
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348 | end |
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349 | |
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350 | %% mask |
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351 | if Param.CheckMask && ~isempty(MaskData{iview}) |
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352 | [Data{iview},errormsg]=mask_proj(Data{iview},MaskData{iview}); |
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353 | end |
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354 | end |
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355 | %%%%%%%%%%%%%%%% END LOOP ON VIEWS %%%%%%%%%%%%%%%% |
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356 | |
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357 | %% merge the NbView fields |
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358 | % if checksub<=2 |
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359 | [MergeData,errormsg]=merge_field(Data);%concatene all the input field series by fct merge_data |
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360 | % elseif checksub==3 |
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361 | % MergeData=transform_fct(Data{1},XmlData{1},Data{2}); %combine the two input file series |
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362 | % else |
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363 | % MergeData=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2});%combine the two input file series with calibration parameters |
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364 | % end |
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365 | if ~isempty(errormsg) |
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366 | disp_uvmat('ERROR',errormsg,checkrun); |
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367 | return |
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368 | end |
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369 | |
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370 | %% time of the merged field: take the average of the different views |
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371 | if ~isempty(time) |
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372 | timeread=time(index); |
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373 | elseif ~isempty(find(timeread))% time defined from ImaDoc |
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374 | timeread=mean(timeread(timeread~=0));% take average over times form the files (when defined) |
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375 | else |
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376 | timeread=index;% take time=file index |
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377 | end |
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378 | |
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379 | |
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380 | %% recording the merged field |
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381 | if strcmp(FileExtOut,'.png') %output as image |
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382 | if index==1 |
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383 | if strcmp(class(MergeData.A),'uint8') |
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384 | BitDepth=8; |
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385 | else |
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386 | BitDepth=16; |
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387 | end |
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388 | %write xml calibration file, using the first file |
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389 | siz=size(MergeData.A); |
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390 | npy=siz(1); |
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391 | npx=siz(2); |
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392 | if isfield(MergeData,'Coord_x') && isfield(MergeData,'Coord_y') |
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393 | Rangx=MergeData.Coord_x; |
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394 | Rangy=MergeData.Coord_y; |
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395 | elseif isfield(MergeData,'AX')&& isfield(MergeData,'AY') |
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396 | Rangx=[MergeData.AX(1) MergeData.AX(end)]; |
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397 | Rangy=[MergeData.AY(1) MergeData.AY(end)]; |
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398 | else |
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399 | Rangx=[0.5 npx-0.5]; |
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400 | Rangy=[npy-0.5 0.5];%default |
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401 | end |
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402 | pxcmx=(npx-1)/(Rangx(2)-Rangx(1)); |
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403 | pxcmy=(npy-1)/(Rangy(1)-Rangy(2)); |
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404 | T_x=-pxcmx*Rangx(1)+0.5; |
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405 | T_y=-pxcmy*Rangy(2)+0.5; |
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406 | GeometryCal.CalibrationType='rescale'; |
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407 | GeometryCal.CoordUnit=MergeData.CoordUnit; |
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408 | GeometryCal.focal=1; |
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409 | GeometryCal.R=[pxcmx,0,0;0,pxcmy,0;0,0,1]; |
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410 | GeometryCal.Tx_Ty_Tz=[T_x T_y 1]; |
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411 | ImaDoc.GeometryCalib=GeometryCal; |
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412 | t=struct2xml(ImaDoc); |
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413 | t=set(t,1,'name','ImaDoc'); |
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414 | save(t,[fileparts(OutputFile) '.xml']) |
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415 | end |
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416 | if BitDepth==8 |
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417 | imwrite(uint8(MergeData.A),OutputFile,'BitDepth',8) |
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418 | else |
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419 | imwrite(uint16(MergeData.A),OutputFile,'BitDepth',16) |
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420 | end |
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421 | else %output as netcdf files |
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422 | MergeData.ListGlobalAttribute={'Conventions','Project','InputFile_1','InputFile_end','NbCoord','NbDim'}; |
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423 | MergeData.Conventions='uvmat'; |
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424 | MergeData.NbCoord=2; |
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425 | MergeData.NbDim=2; |
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426 | % time interval of PIV |
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427 | Dt=[]; |
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428 | if isfield(Data{1},'Dt')&& isnumeric(Data{1}.Dt) |
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429 | Dt=Data{1}.Dt; |
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430 | end |
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431 | for iview =2:numel(Data) |
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432 | if ~(isfield(Data{iview},'Dt')&& isequal(Data{iview}.Dt,Dt)) |
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433 | Dt=[];%dt not the same for all fields |
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434 | end |
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435 | end |
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436 | if ~isempty(timeread) |
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437 | MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'Time'}]; |
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438 | MergeData.Time=timeread; |
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439 | end |
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440 | % position of projection plane |
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441 | if isfield(Data{1},'ProjObjectCoord')&& isfield(Data{1},'ProjObjectAngle') |
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442 | ProjObjectCoord=Data{1}.ProjObjectCoord; |
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443 | ProjObjectAngle=Data{1}.ProjObjectAngle; |
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444 | for iview =2:numel(Data) |
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445 | if ~(isfield(Data{iview},'ProjObjectCoord')&& isequal(Data{iview}.ProjObjectCoord,ProjObjectCoord))... |
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446 | ||~(isfield(Data{iview},'ProjObjectAngle')&& isequal(Data{iview}.ProjObjectAngle,ProjObjectAngle)) |
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447 | ProjObjectCoord=[];%dt not the same for all fields |
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448 | end |
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449 | end |
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450 | if ~isempty(ProjObjectCoord) |
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451 | MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'ProjObjectCoord'} {'ProjObjectAngle'}]; |
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452 | MergeData.ProjObjectCoord=ProjObjectCoord; |
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453 | MergeData.ProjObjectAngle=ProjObjectAngle; |
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454 | end |
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455 | end |
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456 | % coord unit |
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457 | if isfield(Data{1},'CoordUnit') |
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458 | CoordUnit=Data{1}.CoordUnit; |
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459 | for iview =2:numel(Data) |
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460 | if ~(isfield(Data{iview},'CoordUnit')&& isequal(Data{iview}.CoordUnit,CoordUnit)) |
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461 | CoordUnit=[];%CoordUnit not the same for all fields |
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462 | end |
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463 | end |
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464 | if ~isempty(CoordUnit) |
---|
465 | MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'CoordUnit'}]; |
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466 | MergeData.CoordUnit=CoordUnit; |
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467 | end |
---|
468 | end |
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469 | % time unit |
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470 | if isfield(Data{1},'TimeUnit') |
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471 | TimeUnit=Data{1}.TimeUnit; |
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472 | for iview =2:numel(Data) |
---|
473 | if ~(isfield(Data{iview},'TimeUnit')&& isequal(Data{iview}.TimeUnit,TimeUnit)) |
---|
474 | TimeUnit=[];%TimeUnit not the same for all fields |
---|
475 | end |
---|
476 | end |
---|
477 | if ~isempty(TimeUnit) |
---|
478 | MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'TimeUnit'}]; |
---|
479 | MergeData.TimeUnit=TimeUnit; |
---|
480 | end |
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481 | end |
---|
482 | error=struct2nc(OutputFile,MergeData);%save result file |
---|
483 | if isempty(error) |
---|
484 | disp(['output file ' OutputFile ' written']) |
---|
485 | else |
---|
486 | disp(error) |
---|
487 | end |
---|
488 | end |
---|
489 | end |
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490 | ellapsed_time=toc(tstart); |
---|
491 | disp(['total ellapsed time ' num2str(ellapsed_time/60,2) ' minutes']) |
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492 | disp([ num2str(ellapsed_time/(60*NbField),3) ' minutes per iteration']) |
---|
493 | |
---|
494 | %'merge_field': concatene fields |
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495 | %------------------------------------------------------------------------ |
---|
496 | function [MergeData,errormsg]=merge_field(Data) |
---|
497 | %% default output |
---|
498 | if isempty(Data)||~iscell(Data) |
---|
499 | MergeData=[]; |
---|
500 | return |
---|
501 | end |
---|
502 | errormsg=''; |
---|
503 | MergeData=Data{1};% merged field= first field by default, reproduces the global attributes of the first field |
---|
504 | NbView=length(Data); |
---|
505 | if NbView==1% if there is only one field, just reproduce it in MergeData |
---|
506 | return |
---|
507 | end |
---|
508 | |
---|
509 | %% group the variables (fields of 'Data') in cells of variables with the same dimensions |
---|
510 | [CellInfo,NbDim,errormsg]=find_field_cells(Data{1}); |
---|
511 | if ~isempty(errormsg) |
---|
512 | return |
---|
513 | end |
---|
514 | |
---|
515 | %LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS |
---|
516 | for icell=1:length(CellInfo) |
---|
517 | if NbDim(icell)~=1 % skip field cells which are of dim 1 |
---|
518 | switch CellInfo{icell}.CoordType |
---|
519 | case 'scattered' %case of input fields with unstructured coordinates: just concatene data |
---|
520 | for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName |
---|
521 | VarName=Data{1}.ListVarName{ivar}; |
---|
522 | for iview=2:NbView |
---|
523 | MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)]; |
---|
524 | end |
---|
525 | end |
---|
526 | case 'grid' %case of fields defined on a structured grid |
---|
527 | FFName=''; |
---|
528 | if isfield(CellInfo{icell},'VarIndex_errorflag') && ~isempty(CellInfo{icell}.VarIndex_errorflag) |
---|
529 | FFName=Data{1}.ListVarName{CellInfo{icell}.VarIndex_errorflag};% name of errorflag variable |
---|
530 | MergeData.ListVarName(CellInfo{icell}.VarIndex_errorflag)=[];%remove error flag variable in MergeData (will use NaN instead) |
---|
531 | MergeData.VarDimName(CellInfo{icell}.VarIndex_errorflag)=[]; |
---|
532 | MergeData.VarAttribute(CellInfo{icell}.VarIndex_errorflag)=[]; |
---|
533 | end |
---|
534 | % select good data on each view |
---|
535 | for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName |
---|
536 | VarName=Data{1}.ListVarName{ivar}; |
---|
537 | for iview=1:NbView |
---|
538 | if isempty(FFName) |
---|
539 | check_bad=isnan(Data{iview}.(VarName));%=0 for NaN data values, 1 else |
---|
540 | else |
---|
541 | check_bad=isnan(Data{iview}.(VarName)) | Data{iview}.(FFName)~=0;%=0 for NaN or error flagged data values, 1 else |
---|
542 | end |
---|
543 | Data{iview}.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag |
---|
544 | if iview==1 |
---|
545 | %MergeData.(VarName)=Data{1}.(VarName);% initiate MergeData with the first field |
---|
546 | MergeData.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag |
---|
547 | NbAver=~check_bad;% initiate NbAver: the nbre of good data for each point |
---|
548 | elseif size(Data{iview}.(VarName))~=size(MergeData.(VarName)) |
---|
549 | errormsg='sizes of the input matrices do not agree, need to interpolate on a common grid using a projection object'; |
---|
550 | return |
---|
551 | else |
---|
552 | MergeData.(VarName)=MergeData.(VarName) +double(Data{iview}.(VarName));%add data |
---|
553 | NbAver=NbAver + ~check_bad;% add 1 for good data, 0 else |
---|
554 | end |
---|
555 | end |
---|
556 | MergeData.(VarName)(NbAver~=0)=MergeData.(VarName)(NbAver~=0)./NbAver(NbAver~=0);% take average of defined data at each point |
---|
557 | MergeData.(VarName)(NbAver==0)=NaN;% set to NaN the points with no good data |
---|
558 | end |
---|
559 | end |
---|
560 | end |
---|
561 | end |
---|
562 | |
---|
563 | |
---|
564 | |
---|