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 | % 900 |
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28 | % .IndexRange: set the file or frame indices on which the action must be performseriesed |
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29 | % .FieldTransform: .TransformName: name of the select39ed 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 | % uvmat .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 | % Copyright 2008-2022, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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42 | % http://www.legi.grenoble-inp.fr |
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43 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr |
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44 | % |
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45 | % This file is part of the toolbox UVMAT. |
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46 | % |
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47 | % UVMAT is free software; you can redistribute it and/or modify |
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48 | % it under the terms of the GNU General Public License as published |
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49 | % by the Free Software Foundation; either version 2 of the license, |
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50 | % or (at your option) any later version. |
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51 | % |
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52 | % UVMAT is distributed in the hope that it will be useful, |
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53 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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54 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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55 | % GNU General Public License (see LICENSE.txt) for more details. |
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56 | %======================================================================= |
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57 | |
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58 | function ParamOut=sliding_average(Param) |
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59 | |
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60 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName |
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61 | if isstruct(Param) && isequal(Param.Action.RUN,0) |
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62 | ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
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63 | ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to mseriesax (options 'off'/'on', 'off' by default) |
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64 | ParamOut.NbSlice=1; %nbre of slices ('off' by default) |
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65 | ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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66 | ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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67 | ParamOut.FieldTransform = 'on';%can use a transform function |
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68 | ParamOut.ProjObject='off';%can use projection object39(option 'off'/'on', |
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69 | ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) |
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70 | ParamOut.OutputDirExt='.tfilter';%set the output dir extension |
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71 | 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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72 | % filecell=get_file_series(Param);%check existence of the first input file |
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73 | % if ~exist(filecell{1,1},'file') |
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74 | % msgbox_uvmat('WARNING','the first input file does not exist') |
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75 | % end |
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76 | return |
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77 | end |
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78 | |
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79 | %%%%%%%%%%%% STANDARD PART %%%%%%%%%%%% |
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80 | ParamOut=[];%default output |
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81 | %% read input parameters from an xml file if input is a file name (batch mode) |
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82 | checkrun=1; |
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83 | if ischar(Param) |
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84 | Param=xml2struct(Param);% read Param as input file (batch case) |
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85 | checkrun=0; |
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86 | end |
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87 | |
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88 | hseries=findobj(allchild(0),'Tag','series'); |
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89 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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90 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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91 | |
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92 | %% define the directory for result file (with path=RootPath{1}) |
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93 | OutputDir=[Param.OutputSubDir Param.OutputDirExt]; |
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94 | |
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95 | %% root input file(s) name, type and index series |
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96 | RootPath=Param.InputTable(:,1); |
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97 | RootFile=Param.InputTable(:,3); |
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98 | SubDir=Param.InputTable(:,2); |
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99 | NomType=Param.InputTable(:,4); |
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100 | FileExt=Param.InputTable(:,5); |
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101 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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102 | %%%%%%%%%%%% |
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103 | % The cell array filecell is the list of input file names, while |
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104 | % filecell{iview,fileindex}: |
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105 | % iview: line in the table corresponding to a given file series |
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106 | % fileindex: file index within the file series, |
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107 | % 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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108 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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109 | %%%%%%%%%%%% NbView=1 : a single input series |
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110 | NbView=numel(i1_series);%number of input file series (lines in InputTable) |
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111 | NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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112 | NbField_i=size(i1_series{1},2); %nb of fields for the i index |
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113 | NbField=NbField_j*NbField_i; %total number of fields |
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114 | |
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115 | %% determine the file type on each line from the first input file |
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116 | ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; |
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117 | NcTypeOptions={'netcdf','civx','civdata'}; |
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118 | for iview=1:NbView |
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119 | if ~exist(filecell{iview,1}','file') |
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120 | msgbox_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist']) |
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121 | return |
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122 | end |
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123 | [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1}); |
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124 | FileType{iview}=FileInfo{iview}.FileType; |
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125 | CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images |
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126 | CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files |
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127 | if ~isempty(j1_series{iview}) |
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128 | frame_index{iview}=j1_series{iview}; |
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129 | else |
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130 | frame_index{iview}=i1_series{iview}; |
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131 | end |
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132 | end |
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133 | |
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134 | %% calibration data and timing: read the ImaDoc files |
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135 | XmlData=[]; |
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136 | [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); |
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137 | if size(time,1)>1 |
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138 | diff_time=max(max(diff(time))); |
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139 | if diff_time>0 |
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140 | msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)]) |
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141 | end |
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142 | end |
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143 | |
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144 | %% coordinate transform or other user defined transform |
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145 | transform_fct='';%default |
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146 | if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) |
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147 | addpath(Param.FieldTransform.TransformPath) |
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148 | transform_fct=str2func(Param.FieldTransform.TransformName); |
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149 | rmpath(Param.FieldTransform.TransformPath) |
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150 | end |
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151 | |
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152 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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153 | % EDIT FROM HERE |
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154 | |
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155 | %% check the validity of input file types |
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156 | if CheckImage{1} |
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157 | FileExtOut='.png'; % write result as .png images for image inputs |
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158 | elseif CheckNc{1} |
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159 | FileExtOut='.nc';% write result as .nc files for netcdf inputs |
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160 | else |
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161 | msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}]) |
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162 | return |
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163 | end |
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164 | |
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165 | |
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166 | %% settings for the output file |
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167 | NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file |
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168 | first_i=i1_series{1}(1); |
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169 | last_i=i1_series{1}(end); |
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170 | if isempty(j1_series{1})% if there is no second index j |
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171 | first_j=1;last_j=1; |
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172 | else |
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173 | first_j=j1_series{1}(1); |
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174 | last_j=j1_series{1}(end); |
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175 | end |
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176 | |
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177 | %% Set field names and velocity types |
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178 | InputFields{1}=[];%default (case of images)series |
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179 | if isfield(Param,'InputFields') |
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180 | InputFields{1}=Param.InputFields; |
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181 | end |
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182 | |
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183 | nbfiles=0; |
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184 | nbmissing=0; |
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185 | |
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186 | %% initialisation |
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187 | char_index=regexp(SubDir{1},'waves_L1_'); |
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188 | switch(SubDir{1}(char_index+9)) |
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189 | case '1' |
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190 | amplitude=2.5 %oscillation amplitude |
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191 | T=24.46; |
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192 | t0=3 ;% dt=0.5 s, torus at its max x at the beginning of motion, i0=7 |
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193 | case '2' |
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194 | amplitude=5 %oscillation amplitude |
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195 | T=24.47; |
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196 | t0=8.5; % dt=1/3 s -> image index of starting motion = 26, % torus at its max x at the beginning of motion |
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197 | case '3' |
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198 | amplitude=10 %oscillation amplitude |
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199 | T=24.45; |
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200 | t0=6.5-T/2;% dt=0.25, torus at its minimum x at the beginning of motion |
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201 | case '4' |
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202 | amplitude=15 %oscillation amplitude |
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203 | T=24.48; |
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204 | t0=3.4; %dt=0.2 -> i0=18 image index of starting motion, % torus at its max x at the beginning of motion |
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205 | end |
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206 | %NbPeriod=2; %number of periods for the sliding average |
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207 | NbPeriod=4; %number of periods for the sliding average |
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208 | omega=2*2*pi/T;%harmonic |
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209 | Lscale=15;%diameter of the torus, length scale for normalisation |
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210 | Uscale=amplitude*omega; |
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211 | |
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212 | DataOut.ListGlobalAttribute= {'Conventions','Time'}; |
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213 | DataOut.Conventions='uvmat'; |
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214 | DataOut.ListVarName={'coord_y','coord_x','Umean','Vmean','Ucos','Vcos','Usin','Vsin','DUDXsin','DUDXcos','DUDYsin','DVDXsin','DVDXcos'... |
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215 | ,'DVDYsin','Ustokes','Vstokes'}; |
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216 | DataOut.VarDimName={'coord_y','coord_x',{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},... |
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217 | {'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},... |
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218 | {'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'}}; |
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219 | |
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220 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% |
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221 | % First get time % |
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222 | [Data,tild,errormsg]=nc2struct(filecell{1,1}); |
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223 | Time_1=Data.Time; |
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224 | if ~isempty(errormsg) |
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225 | disp_uvmat('ERROR',errormsg,checkrun) |
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226 | return |
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227 | end |
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228 | [Data,tild,errormsg]=nc2struct(filecell{1,end}); |
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229 | Time_end=Data.Time; |
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230 | dt=(Time_end-Time_1)/(NbField-1); %time interval |
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231 | NpTime=round(NbPeriod*T/dt+1); |
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232 | |
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233 | OutputPath=fullfile(Param.OutputPath,num2str(Param.Experiment),num2str(Param.Device)); |
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234 | RootFileOut=RootFile{1}; |
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235 | NomTypeOut='_1'; |
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236 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% |
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237 | disp('loop for filtering started') |
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238 | for index=1:NbField |
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239 | update_waitbar(WaitbarHandle,index/NbField) |
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240 | if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
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241 | disp('program stopped by user') |
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242 | break |
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243 | end |
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244 | [Field,tild,errormsg] = read_field(filecell{1,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); |
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245 | |
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246 | %%%%%%%%%%% MAIN RUNNING OPERATIONS %%%%%%%%%%%% |
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247 | if index==1 %first field |
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248 | DataOut.coord_x=Field.coord_x/Lscale; |
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249 | DataOut.coord_y=Field.coord_y/Lscale; |
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250 | npy=numel(DataOut.coord_y); |
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251 | npx=numel(DataOut.coord_x); |
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252 | Umean=zeros(NpTime,npy,npx); |
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253 | Vmean=zeros(NpTime,npy,npx); |
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254 | Ucos=zeros(NpTime,npy,npx); |
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255 | Vcos=zeros(NpTime,npy,npx); |
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256 | Usin=zeros(NpTime,npy,npx); |
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257 | Vsin=zeros(NpTime,npy,npx); |
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258 | DUDXcos=zeros(NpTime,npy,npx); |
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259 | DUDXsin=zeros(NpTime,npy,npx); |
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260 | DUDYsin=zeros(NpTime,npy,npx); |
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261 | DVDXcos=zeros(NpTime,npy,npx); |
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262 | DVDXsin=zeros(NpTime,npy,npx); |
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263 | DVDYsin=zeros(NpTime,npy,npx); |
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264 | end |
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265 | Time(index)=Field.Time-t0;%time from the start of the motion |
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266 | Umean=circshift(Umean,[-1 0 0]); %shift U by ishift along the first index |
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267 | Vmean=circshift(Vmean,[-1 0 0]); %shift U by ishift along the first index |
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268 | Ucos=circshift(Ucos,[-1 0 0]); %shift U by ishift along the first index |
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269 | Vcos=circshift(Vcos,[-1 0 0]); %shift U by ishift along the first index |
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270 | Usin=circshift(Usin,[-1 0 0]); %shift U by ishift along the first index |
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271 | Vsin=circshift(Vsin,[-1 0 0]); %shift U by ishift along the first index |
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272 | DUDXcos=circshift(DUDXcos,[-1 0 0]); |
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273 | DUDXsin=circshift(DUDXsin,[-1 0 0]); |
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274 | DUDYsin=circshift(DUDYsin,[-1 0 0]); |
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275 | DVDXcos=circshift(DVDXcos,[-1 0 0]); |
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276 | DVDXsin=circshift(DVDXsin,[-1 0 0]); |
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277 | DVDYsin=circshift(DVDYsin,[-1 0 0]); |
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278 | Umean(end,:,:)=Field.U; |
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279 | Vmean(end,:,:)=Field.V; |
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280 | Ucos(end,:,:)=Field.U*cos(omega*Time(index)); |
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281 | Vcos(end,:,:)=Field.V*cos(omega*Time(index)); |
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282 | Usin(end,:,:)=Field.U*sin(omega*Time(index)); |
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283 | Vsin(end,:,:)=Field.V*sin(omega*Time(index)); |
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284 | DUDXcos(end,:,:)=Field.DUDX*cos(omega*Time(index)); |
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285 | DUDXsin(end,:,:)=Field.DUDX*sin(omega*Time(index)); |
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286 | DUDYsin(end,:,:)=Field.DUDY*sin(omega*Time(index));% ParamOut=[];%default output |
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287 | |
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288 | DVDXcos(end,:,:)=Field.DVDX*cos(omega*Time(index)); |
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289 | DVDXsin(end,:,:)=Field.DVDX*sin(omega*Time(index)); |
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290 | DVDYsin(end,:,:)=Field.DVDY*sin(omega*Time(index)); |
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291 | DataOut.Time=(Time(index)-(NpTime-1)*dt/2)/T;%time inperiods from the beginning of the oscillation (torus at max abscissa) |
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292 | DataOut.Umean=(1/Uscale)*squeeze(nanmean(Umean,1)); |
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293 | DataOut.Vmean=(1/Uscale)*squeeze(nanmean(Vmean,1)); |
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294 | DataOut.Ucos=2*(1/Uscale)*squeeze(nanmean(Ucos,1)); |
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295 | DataOut.Vcos=2*(1/Uscale)*squeeze(nanmean(Vcos,1)); |
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296 | DataOut.Usin=2*(1/Uscale)*squeeze(nanmean(Usin,1)); |
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297 | DataOut.Vsin=2*(1/Uscale)*squeeze(nanmean(Vsin,1)); |
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298 | DataOut.DUDXcos=2*squeeze(nanmean(DUDXcos,1)); |
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299 | DataOut.DUDXsin=2*squeeze(nanmean(DUDXsin,1)); |
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300 | DataOut.DUDYsin=2*squeeze(nanmean(DUDYsin,1)); |
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301 | DataOut.DVDXcos=2*squeeze(nanmean(DVDXcos,1)); |
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302 | DataOut.DVDXsin=2*squeeze(nanmean(DVDXsin,1)); |
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303 | DataOut.DVDYsin=2*squeeze(nanmean(DVDYsin,1)); |
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304 | DataOut.Ustokes=(1/omega)*(1/Uscale)*(DataOut.Ucos.*DataOut.DUDXsin+DataOut.Vcos.*DataOut.DUDYsin); |
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305 | DataOut.Vstokes=(1/omega)*(1/Uscale)*(DataOut.Ucos.*DataOut.DVDXsin+DataOut.Vcos.*DataOut.DVDYsin); |
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306 | |
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307 | % writing the result file as netcdf file |
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308 | i1=i1_series{1}(index); |
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309 | OutputFile=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,'.nc',NomTypeOut,i1); |
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310 | errormsg=struct2nc(OutputFile, DataOut); |
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311 | if isempty(errormsg) |
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312 | disp([OutputFile ' written']) |
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313 | else |
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314 | disp(errormsg) |
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315 | end |
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316 | end |
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317 | |
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