[751] | 1 | %'aver_stat': calculate Reynolds steress components over time series |
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| 2 | %------------------------------------------------------------------------ |
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| 3 | % function ParamOut=turb_stat(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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[810] | 41 | %======================================================================= |
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[1107] | 42 | % Copyright 2008-2022, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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[810] | 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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[751] | 59 | function ParamOut=turb_stat(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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[1082] | 65 | ParamOut.NbSlice='on'; %nbre of slices ('on' if needed as input, fixed value e.g. 1, 'off' by default) |
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[751] | 66 | ParamOut.VelType='one';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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[1031] | 67 | ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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| 68 | ParamOut.FieldTransform = 'off';%can use a transform function |
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[751] | 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='.staturb';%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 | 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 | NcTypeOptions={'netcdf','civx','civdata'}; |
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| 117 | for iview=1:NbView |
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| 118 | if ~exist(filecell{iview,1}','file') |
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| 119 | msgbox_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist']) |
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| 120 | return |
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| 121 | end |
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[784] | 122 | [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1}); |
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[783] | 123 | FileType{iview}=FileInfo{iview}.FileType; |
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[751] | 124 | CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files |
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| 125 | if ~isempty(j1_series{iview}) |
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| 126 | frame_index{iview}=j1_series{iview}; |
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| 127 | else |
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| 128 | frame_index{iview}=i1_series{iview}; |
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| 129 | end |
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| 130 | end |
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| 131 | |
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| 132 | %% calibration data and timing: read the ImaDoc files |
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| 133 | XmlData=[]; |
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| 134 | [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); |
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| 135 | if size(time,1)>1 |
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| 136 | diff_time=max(max(diff(time))); |
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| 137 | if diff_time>0 |
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| 138 | msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)]) |
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| 139 | end |
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| 140 | end |
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| 141 | |
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| 142 | %% coordinate transform or other user defined transform |
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| 143 | transform_fct='';%default |
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| 144 | if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) |
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| 145 | addpath(Param.FieldTransform.TransformPath) |
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| 146 | transform_fct=str2func(Param.FieldTransform.TransformName); |
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| 147 | rmpath(Param.FieldTransform.TransformPath) |
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| 148 | end |
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| 149 | |
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| 150 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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| 151 | % EDIT FROM HERE |
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| 152 | |
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| 153 | %% settings for the output file |
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[1033] | 154 | FileExtOut='.nc';% write result as .nc files for netcdf inputs |
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[751] | 155 | NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file |
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| 156 | first_i=i1_series{1}(1); |
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| 157 | last_i=i1_series{1}(end); |
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| 158 | if isempty(j1_series{1})% if there is no second index j |
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| 159 | first_j=1;last_j=1; |
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| 160 | else |
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| 161 | first_j=j1_series{1}(1); |
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| 162 | last_j=j1_series{1}(end); |
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| 163 | end |
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| 164 | |
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| 165 | %% Set field names and velocity types |
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| 166 | InputFields{1}=[];%default (case of images) |
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| 167 | if isfield(Param,'InputFields') |
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| 168 | InputFields{1}=Param.InputFields; |
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| 169 | end |
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[1032] | 170 | if isempty(InputFields{1}.FieldName) |
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| 171 | disp('ERROR: input fields U, V and posibly curl and div must be entered by get_field...') |
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| 172 | return |
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| 173 | end |
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[751] | 174 | |
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| 175 | nbfiles=0; |
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| 176 | nbmissing=0; |
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| 177 | |
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| 178 | %initialisation |
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| 179 | DataOut.ListGlobalAttribute= {'Conventions'}; |
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| 180 | DataOut.Conventions= 'uvmat'; |
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[1082] | 181 | DataOut.ListVarName={}; |
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| 182 | DataOut.VarDimName={}; |
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[751] | 183 | DataOut.UMean=0; |
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| 184 | DataOut.VMean=0; |
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| 185 | DataOut.u2Mean=0; |
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| 186 | DataOut.v2Mean=0; |
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| 187 | DataOut.u2Mean_1=0; |
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| 188 | DataOut.v2Mean_1=0; |
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| 189 | DataOut.uvMean=0; |
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| 190 | DataOut.Counter=0; |
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[1032] | 191 | DataOut.CurlMean=0; |
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| 192 | DataOut.DivMean=0; |
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| 193 | DataOut.Curl2Mean=0; |
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| 194 | DataOut.Div2Mean=0; |
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[1077] | 195 | DataOut.KEflux=0; |
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[751] | 196 | U2Mean=0; |
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| 197 | V2Mean=0; |
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| 198 | UVMean=0; |
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| 199 | U2Mean_1=0; |
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| 200 | V2Mean_1=0; |
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[761] | 201 | Counter_1=0; |
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| 202 | |
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[751] | 203 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% |
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[1100] | 204 | % for i_slice=1:Param.IndexRange.NbSlice |
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| 205 | % i_slice |
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| 206 | ind_first=Param.IndexRange.first_i |
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| 207 | for index_i=ind_first:Param.IndexRange.NbSlice:Param.IndexRange.last_i |
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| 208 | if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
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| 209 | disp('program stopped by user') |
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| 210 | break |
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| 211 | end |
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| 212 | for index_j=Param.IndexRange.first_j:Param.IndexRange.last_j |
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| 213 | InputFile=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},index_i,index_i,index_j,index_j); |
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| 214 | [Field,tild,errormsg] = read_field(InputFile,FileType{iview},InputFields{iview}); |
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| 215 | |
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| 216 | %[Field,tild,errormsg] = read_field(filecell{1,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); |
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| 217 | |
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| 218 | %%%%%%%%%%%% MAIN RUNNING OPERATIONS %%%%%%%%%%%% |
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| 219 | if index_i==ind_first && index_j==Param.IndexRange.first_j %initiate the output data structure in the first field |
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| 220 | [CellInfo,NbDim,errormsg]=find_field_cells(Field); |
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| 221 | YName='coord_y';%default |
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| 222 | XName='coord_x';%default |
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| 223 | for icell=1:numel(NbDim) |
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| 224 | if NbDim(icell)==2 && strcmp(CellInfo{icell}.CoordType,'grid') |
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| 225 | YName=CellInfo{icell}.YName; |
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| 226 | XName=CellInfo{icell}.XName; |
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| 227 | break |
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| 228 | end |
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| 229 | end |
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| 230 | DataOut.ListVarName={YName, XName ,'UMean' , 'VMean','u2Mean','v2Mean','u2Mean_1','v2Mean_1','uvMean','CurlMean','DivMean','Curl2Mean','Div2Mean','Counter'}; |
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| 231 | DataOut.VarDimName={YName,XName,{YName,XName},{YName,XName},{YName,XName},{YName,XName},{YName,XName},{YName,XName},... |
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| 232 | {YName,XName},{YName,XName},{YName,XName},{YName,XName},{YName,XName},{YName,XName}}; |
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| 233 | DataOut.(YName)=Field.(YName); |
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| 234 | DataOut.(XName)=Field.(XName); |
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| 235 | Uprev=Field.U;% store the current field for next iteration |
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| 236 | Vprev=Field.V; |
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| 237 | if isfield(Field,'FF') |
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| 238 | FFprev=Field.FF;% possible flag for false data |
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| 239 | else |
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| 240 | %FFprev=true(size(Field.U)); |
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| 241 | FFprev=isnan(Field.U); |
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| 242 | end |
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[1082] | 243 | end |
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[1100] | 244 | FF=isnan(Field.U);%|Field.U<-60|Field.U>30;% threshold on U |
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| 245 | DataOut.Counter=DataOut.Counter+ (~FF);% add 1 to the couter for non NaN point |
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| 246 | Counter_1=Counter_1+(~FF & ~FFprev); |
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| 247 | Field.U(FF)=0;% set to 0 the nan values |
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| 248 | Field.V(FF)=0; |
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| 249 | DataOut.UMean=DataOut.UMean+Field.U; %increment the sum |
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| 250 | DataOut.VMean=DataOut.VMean+Field.V; %increment the sum |
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| 251 | |
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| 252 | U2Mean=U2Mean+(Field.U).*(Field.U); %increment the U squared sum |
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| 253 | V2Mean=V2Mean+(Field.V).*(Field.V); %increment the V squared sum |
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| 254 | UVMean=UVMean+(Field.U).*(Field.V); %increment the sum |
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| 255 | U2Mean_1=U2Mean_1+(Field.U).*Uprev; %increment the U squared sum |
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| 256 | V2Mean_1=V2Mean_1+(Field.V).*Vprev; %increment the V squared sum |
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| 257 | Uprev=Field.U; %store for next iteration |
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| 258 | Vprev=Field.V; |
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| 259 | FFprev=FF; |
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| 260 | if isfield(Field,'curl') && isfield(Field,'div') |
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| 261 | Field.curl(FF)=0;% set to 0 the nan values |
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| 262 | Field.div(FF)=0; |
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| 263 | DataOut.CurlMean=DataOut.CurlMean+Field.curl; |
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| 264 | DataOut.DivMean=DataOut.DivMean+Field.div; |
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| 265 | DataOut.Curl2Mean=DataOut.Curl2Mean+Field.curl.*Field.curl; |
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| 266 | DataOut.Div2Mean=DataOut.Div2Mean+Field.div.*Field.div; |
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| 267 | end |
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[1082] | 268 | end |
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[751] | 269 | end |
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[1100] | 270 | %%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%% |
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[1077] | 271 | |
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[1100] | 272 | DataOut.Counter(DataOut.Counter==0)=1;% put counter to 1 when it is zero |
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| 273 | DataOut.UMean=DataOut.UMean./DataOut.Counter; % normalize the mean |
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| 274 | DataOut.VMean=DataOut.VMean./DataOut.Counter; % normalize the mean |
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| 275 | U2Mean=U2Mean./DataOut.Counter; % normalize the mean |
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| 276 | V2Mean=V2Mean./DataOut.Counter; % normalize the mean |
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| 277 | UVMean=UVMean./DataOut.Counter; % normalize the mean |
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| 278 | U2Mean_1=U2Mean_1./Counter_1; % normalize the mean |
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| 279 | V2Mean_1=V2Mean_1./Counter_1; % normalize the mean |
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| 280 | DataOut.u2Mean=U2Mean-DataOut.UMean.*DataOut.UMean; % normalize the mean |
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| 281 | DataOut.v2Mean=V2Mean-DataOut.VMean.*DataOut.VMean; % normalize the mean |
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| 282 | DataOut.uvMean=UVMean-DataOut.UMean.*DataOut.VMean; % normalize the mean \ |
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| 283 | DataOut.u2Mean_1=U2Mean_1-DataOut.UMean.*DataOut.UMean; % normalize the mean |
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| 284 | DataOut.v2Mean_1=V2Mean_1-DataOut.VMean.*DataOut.VMean; % normalize the mean |
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| 285 | DataOut.CurlMean=DataOut.CurlMean./DataOut.Counter; |
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| 286 | DataOut.DivMean=DataOut.DivMean./DataOut.Counter; |
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| 287 | DataOut.Curl2Mean=DataOut.Curl2Mean./DataOut.Counter-DataOut.CurlMean.*DataOut.CurlMean; |
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| 288 | DataOut.Div2Mean=DataOut.Div2Mean./DataOut.Counter-DataOut.DivMean.*DataOut.DivMean; |
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| 289 | |
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| 290 | %% writing the result file as netcdf file |
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| 291 | OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,ind_first,ind_first,first_j,last_j); |
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| 292 | %case of netcdf input file , determine global attributes |
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| 293 | errormsg=struct2nc(OutputFile,DataOut); %save result file |
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| 294 | if isempty(errormsg) |
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| 295 | disp([OutputFile ' written']); |
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| 296 | else |
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| 297 | disp(['error in writting result file: ' errormsg]) |
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[1032] | 298 | end |
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[1100] | 299 | |
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[751] | 300 | % end |
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| 301 | %% open the result file with uvmat (in RUN mode) |
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[1095] | 302 | if checkrun && isequal(Param.IndexRange.NbSlice,1) |
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[751] | 303 | uvmat(OutputFile)% open the last result file with uvmat |
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| 304 | end |
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