1 | %'turb_correlation_time': calculate the time correlation function at each point |
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2 | %------------------------------------------------------------------------ |
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3 | % function ParamOut=turb_correlation_time(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 2008-2021, 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) legi.cnrs.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=turb_correlation_time(Param) |
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60 | |
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61 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName |
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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=1; %nbre of slices ('off' by default) |
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66 | ParamOut.VelType='off';% 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 | ParamOut.ProjObject='off';%can use projection object(option 'off'/'on', |
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70 | ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) |
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71 | ParamOut.OutputDirExt='.corr_t';%set the output dir extension |
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72 | ParamOut.OutputFileMode='NbSlice';% '=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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73 | % filecell=get_file_series(Param);%check existence of the first input file |
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74 | % if ~exist(filecell{1,1},'file') |
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75 | % msgbox_uvmat('WARNING','the first input file does not exist') |
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76 | % end |
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77 | return |
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78 | end |
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79 | |
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80 | %%%%%%%%%%%% STANDARD PART %%%%%%%%%%%% |
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81 | ParamOut=[];%default output |
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82 | %% read input parameters from an xml file if input is a file name (batch mode) |
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83 | checkrun=1; |
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84 | if ischar(Param) |
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85 | Param=xml2struct(Param);% read Param as input file (batch case) |
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86 | checkrun=0; |
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87 | end |
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88 | |
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89 | hseries=findobj(allchild(0),'Tag','series'); |
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90 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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91 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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92 | |
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93 | %% define the directory for result file (with path=RootPath{1}) |
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94 | OutputDir=[Param.OutputSubDir Param.OutputDirExt]; |
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95 | |
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96 | %% root input file(s) name, type and index series |
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97 | RootPath=Param.InputTable(:,1); |
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98 | RootFile=Param.InputTable(:,3); |
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99 | SubDir=Param.InputTable(:,2); |
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100 | NomType=Param.InputTable(:,4); |
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101 | FileExt=Param.InputTable(:,5); |
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102 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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103 | %%%%%%%%%%%% |
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104 | % The cell array filecell is the list of input file names, while |
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105 | % filecell{iview,fileindex}: |
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106 | % iview: line in the table corresponding to a given file series |
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107 | % fileindex: file index within the file series, |
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108 | % 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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109 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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110 | %%%%%%%%%%%% NbView=1 : a single input series |
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111 | NbView=numel(i1_series);%number of input file series (lines in InputTable) |
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112 | NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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113 | NbField_i=size(i1_series{1},2); %nb of fields for the i index |
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114 | NbField=NbField_j*NbField_i; %total number of fields |
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115 | NpTime=256;% max number of times for each side of the time correlation fct |
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116 | NpTime=min(NpTime,floor(NbField/4)); %nbre of points for the correlation fct on each side of 0 |
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117 | |
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118 | %% determine the file type on each line from the first input file |
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119 | ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; |
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120 | NcTypeOptions={'netcdf','civx','civdata'}; |
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121 | for iview=1:NbView |
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122 | if ~exist(filecell{iview,1}','file') |
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123 | msgbox_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist']) |
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124 | return |
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125 | end |
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126 | [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1}); |
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127 | FileType{iview}=FileInfo{iview}.FileType; |
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128 | CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images |
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129 | CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files |
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130 | if ~isempty(j1_series{iview}) |
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131 | frame_index{iview}=j1_series{iview}; |
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132 | else |
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133 | frame_index{iview}=i1_series{iview}; |
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134 | end |
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135 | end |
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136 | |
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137 | %% calibration data and timing: read the ImaDoc files |
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138 | XmlData=[]; |
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139 | [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); |
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140 | if size(time,1)>1 |
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141 | diff_time=max(max(diff(time))); |
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142 | if diff_time>0 |
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143 | msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)]) |
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144 | end |
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145 | end |
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146 | |
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147 | %% coordinate transform or other user defined transform |
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148 | transform_fct='';%default |
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149 | if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) |
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150 | addpath(Param.FieldTransform.TransformPath) |
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151 | transform_fct=str2func(Param.FieldTransform.TransformName); |
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152 | rmpath(Param.FieldTransform.TransformPath) |
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153 | end |
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154 | |
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155 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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156 | % EDIT FROM HERE |
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157 | |
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158 | %% check the validity of input file types |
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159 | if CheckImage{1} |
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160 | FileExtOut='.png'; % write result as .png images for image inputs |
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161 | elseif CheckNc{1} |
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162 | FileExtOut='.nc';% write result as .nc files for netcdf inputs |
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163 | else |
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164 | msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}]) |
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165 | return |
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166 | end |
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167 | |
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168 | |
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169 | %% settings for the output file |
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170 | NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file |
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171 | first_i=i1_series{1}(1); |
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172 | last_i=i1_series{1}(end); |
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173 | if isempty(j1_series{1})% if there is no second index j |
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174 | first_j=1;last_j=1; |
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175 | else |
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176 | first_j=j1_series{1}(1); |
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177 | last_j=j1_series{1}(end); |
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178 | end |
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179 | |
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180 | %% Set field names and velocity types |
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181 | InputFields{1}=[];%default (case of images) |
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182 | if isfield(Param,'InputFields') |
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183 | InputFields{1}=Param.InputFields; |
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184 | end |
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185 | |
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186 | nbfiles=0; |
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187 | nbmissing=0; |
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188 | |
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189 | %initialisation |
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190 | DataOut.ListGlobalAttribute= {'Conventions'}; |
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191 | DataOut.Conventions='uvmat'; |
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192 | DataOut.ListVarName={'delta_t','coord_y','coord_x','UUCorr' , 'VVCorr','UVCorr','Counter'}; |
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193 | DataOut.VarDimName={'delta_t','coord_y','coord_x',... |
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194 | {'delta_t','coord_y','coord_x'},{'delta_t','coord_y','coord_x'},{'delta_t','coord_y','coord_x'},{'delta_t','coord_y','coord_x'}}; |
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195 | |
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196 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% |
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197 | % First get mean values % |
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198 | disp('loop for mean started') |
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199 | Time=zeros(1,NbField); |
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200 | for index=1:NbField |
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201 | update_waitbar(WaitbarHandle,index/NbField) |
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202 | if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
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203 | disp('program stopped by user') |
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204 | break |
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205 | end |
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206 | [Field,tild,errormsg] = read_field(filecell{1,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); |
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207 | if index==1 %first field |
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208 | if ~isempty(errormsg) |
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209 | disp_uvmat('ERROR',errormsg,checkrun) |
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210 | return |
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211 | elseif ~isfield(Field,'U')||~isfield(Field,'V') |
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212 | disp_uvmat('ERROR','this function requires the velocity components U and V as input',checkrun) |
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213 | return |
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214 | elseif ~isfield(Field,'Time') |
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215 | disp_uvmat('ERROR','the attribute Time needs to be defined as input',checkrun) |
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216 | return |
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217 | end |
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218 | [npy,npx]=size(Field.U); |
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219 | UMean=zeros(npy,npx); |
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220 | VMean=zeros(npy,npx); |
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221 | Counter=false(npy,npx); |
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222 | % transcripts the global attributes |
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223 | if isfield(Field,'ListGlobalAttribute') |
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224 | DataOut.ListGlobalAttribute= Field.ListGlobalAttribute; |
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225 | for ilist=1:numel(Field.ListGlobalAttribute) |
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226 | AttrName=Field.ListGlobalAttribute{ilist}; |
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227 | DataOut.(AttrName)=Field.(AttrName); |
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228 | end |
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229 | end |
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230 | end |
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231 | Time(index)=Field.Time; |
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232 | FF=isnan(Field.U);%|Field.U<-60|Field.U>30;% threshold on U |
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233 | Field.U(FF)=0;% set to 0 the nan values, |
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234 | Field.V(FF)=0; |
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235 | UMean=UMean+Field.U; |
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236 | VMean=VMean+Field.V; |
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237 | Counter=Counter+~FF; |
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238 | end |
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239 | UMean=UMean./Counter; |
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240 | VMean=VMean./Counter; |
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241 | |
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242 | |
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243 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% |
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244 | disp('loop for correlation started') |
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245 | for index=1:NbField |
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246 | update_waitbar(WaitbarHandle,index/NbField) |
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247 | if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
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248 | disp('program stopped by user') |
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249 | break |
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250 | end |
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251 | [Field,tild,errormsg] = read_field(filecell{1,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); |
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252 | |
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253 | %%%%%%%%%%%% MAIN RUNNING OPERATIONS %%%%%%%%%%%% |
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254 | if index==1 %first field |
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255 | [npy,npx]=size(Field.U); |
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256 | dt=diff(Time); |
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257 | Maxdt=max(dt); Mindt=min(dt); |
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258 | if Maxdt-Mindt>0.001*Maxdt |
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259 | disp_uvmat('ERROR','the time increment between fields is not constant',checkrun) |
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260 | return |
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261 | else |
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262 | dt=(Maxdt+Mindt)/2; |
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263 | end |
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264 | DataOut.delta_t=(0:dt:dt*NpTime)'; |
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265 | DataOut.coord_x=Field.coord_x; |
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266 | DataOut.coord_y=Field.coord_y; |
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267 | DataOut.UUCorr=zeros(NpTime+1,npy,npx); |
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268 | DataOut.VVCorr=zeros(NpTime+1,npy,npx); |
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269 | DataOut.UVCorr=zeros(NpTime+1,npy,npx); |
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270 | DataOut.Counter=zeros(NpTime+1,npy,npx); |
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271 | U_shift=zeros(NpTime+1,npy,npx); |
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272 | V_shift=zeros(NpTime+1,npy,npx); |
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273 | FF_shift=zeros(NpTime+1,npy,npx); |
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274 | UUCorr=zeros(NpTime+1,npy,npx); |
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275 | VVCorr=zeros(NpTime+1,npy,npx); |
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276 | UVCorr=zeros(NpTime+1,npy,npx); |
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277 | FFCorr=false(NpTime+1,npy,npx); |
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278 | end |
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279 | Field.U=Field.U-UMean; |
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280 | Field.V=Field.V-VMean; |
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281 | FF=isnan(Field.U);%|Field.U<-60|Field.U>30;% threshold on U |
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282 | Field.U(FF)=0;% set to 0 the nan values,'delta_x' |
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283 | Field.V(FF)=0; |
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284 | if index<=NpTime+1 |
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285 | U_shift(NpTime+2-index,:,:)=Field.U; |
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286 | V_shift(NpTime+2-index,:,:)=Field.V; |
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287 | FF_shift(NpTime+2-index,:,:)=FF; |
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288 | else |
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289 | U_shift=circshift(U_shift,[1 0 0]); %shift U by ishift along the first index |
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290 | V_shift=circshift(V_shift,[1 0 0]); %shift U by ishift along the first index |
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291 | FF_shift=circshift(FF_shift,[1 0 0]); %shift U by ishift along the first index |
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292 | U_shift(1,:,:)=Field.U; |
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293 | V_shift(1,:,:)=Field.V; |
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294 | FF_shift(1,:,:)=FF; |
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295 | end |
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296 | for ishift=1:NpTime+1% calculate the field U shifted |
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297 | UUCorr(ishift,:,:)=Field.U.*squeeze(U_shift(ishift,:,:)); |
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298 | VVCorr(ishift,:,:)=Field.V.*squeeze(V_shift(ishift,:,:)); |
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299 | UVCorr(ishift,:,:)=Field.U.*squeeze(V_shift(ishift,:,:)); |
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300 | FFCorr(ishift,:,:)=FF | squeeze(FF_shift(ishift,:,:)); |
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301 | end |
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302 | DataOut.UUCorr=DataOut.UUCorr+UUCorr; |
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303 | DataOut.VVCorr=DataOut.VVCorr+VVCorr; |
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304 | DataOut.UVCorr=DataOut.UVCorr+UVCorr; |
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305 | DataOut.Counter=DataOut.Counter+~FFCorr; |
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306 | end |
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307 | %%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%% |
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308 | DataOut.Counter(DataOut.Counter==0)=1;% put counter to 1 when it is zero (to avoid NaN) |
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309 | DataOut.UUCorr=DataOut.UUCorr./DataOut.Counter; |
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310 | DataOut.VVCorr=DataOut.VVCorr./DataOut.Counter; |
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311 | DataOut.UVCorr=DataOut.UVCorr./DataOut.Counter; |
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312 | |
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313 | % DataOut.UMean=DataOut.UMean./DataOut.Counter; % normalize the mean |
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314 | % DataOut.VMean=DataOut.VMean./DataOut.Counter; % normalize the mean |
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315 | % U2Mean=U2Mean./DataOut.Counter; % normalize the mean |
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316 | % V2Mean=V2Mean./DataOut.Counter; % normalize the mean |
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317 | % UVMean=UVMean./DataOut.Counter; % normalize the mean |
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318 | % U2Mean_1=U2Mean_1./Counter_1; % normalize the mean |
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319 | % V2Mean_1=V2Mean_1./Counter_1; % normalize the mean |
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320 | % DataOut.u2Mean=U2Mean-DataOut.UMean.*DataOut.UMean; % normalize the meanFFCorr |
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321 | % DataOut.v2Mean=V2Mean-DataOut.VMean.*DataOut.VMean; % normalize the mean |
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322 | % DataOut.uvMean=UVMean-DataOut.UMean.*DataOut.VMean; % normalize the mean \ |
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323 | % DataOut.u2Mean_1=U2Mean_1-DataOut.UMean.*DataOut.UMean; % normalize the mean |
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324 | % DataOut.v2Mean_1=V2Mean_1-DataOut.VMean.*DataOut.VMean; % normalize the mean |
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325 | |
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326 | |
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327 | %% calculate the profiles |
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328 | % npx=numel(DataOut.coord_x); |
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329 | % band=ceil(npx/5) :floor(4*npx/5);% keep only the central band |
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330 | % for ivar=3:numel(DataOut.ListVarName)-1 |
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331 | % VarName=DataOut.ListVarName{ivar};% name of the variable |
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332 | % DataOut.ListVarName=[DataOut.ListVarName {[VarName 'Profile']}];%append the name of the profile variable |
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333 | % DataOut.VarDimName=[DataOut.VarDimName {'coord_y'}]; |
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334 | % DataOut.([VarName 'Profile'])=mean(DataOut.(VarName)(:,band),2); %take the mean profile of U, excluding the edges |
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335 | % end |
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336 | |
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337 | %% writing the result file as netcdf file |
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338 | OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j,last_j); |
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339 | %case of netcdf input file , determine global attributes |
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340 | errormsg=struct2nc(OutputFile,DataOut); %save result file |
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341 | if isempty(errormsg) |
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342 | disp([OutputFile ' written']); |
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343 | else |
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344 | disp(['error in writting result file: ' errormsg]) |
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345 | end |
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346 | |
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347 | |
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348 | %% open the result file with uvmat (in RUN mode) |
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349 | if checkrun |
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350 | uvmat(OutputFile)% open the last result file with uvmat |
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351 | end |
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