[1085] | 1 | %'aver_stat': calculate field average over a time series |
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| 2 | %------------------------------------------------------------------------ |
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| 3 | % function ParamOut=aver_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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| 41 | %======================================================================= |
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[1107] | 42 | % Copyright 2008-2022, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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[1085] | 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=aver_synchro(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='on'; %nbre of slices ('off' by default) |
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| 66 | ParamOut.VelType='two';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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| 67 | ParamOut.FieldName='two';% 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='on';%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='.synchro_multi';%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 | def={''}; |
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| 78 | if isfield (Param,'ActionInput')&& isfield(Param.ActionInput,'WavePeriod') |
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| 79 | def=Param.ActionInput.WavePeriod; |
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| 80 | |
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| 81 | def={num2str(def)}; |
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| 82 | end |
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| 83 | prompt={'wave period'}; |
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| 84 | dlgTitle='primary period'; |
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| 85 | lineNo=1; |
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| 86 | answer=inputdlg(prompt,dlgTitle,lineNo,def); |
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| 87 | ParamOut.ActionInput.WavePeriod=str2num(answer{1}); |
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| 88 | return |
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| 89 | end |
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| 90 | |
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| 91 | %%%%%%%%%%%% STANDARD PART %%%%%%%%%%%% |
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| 92 | ParamOut=[];%default output |
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| 93 | %% read input parameters from an xml file if input is a file name (batch mode) |
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| 94 | checkrun=1; |
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| 95 | if ischar(Param) |
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| 96 | Param=xml2struct(Param);% read Param as input file (batch case) |
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| 97 | checkrun=0; |
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| 98 | end |
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| 99 | hseries=findobj(allchild(0),'Tag','series'); |
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| 100 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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| 101 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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| 102 | |
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| 103 | %% define the directory for result file (with path=RootPath{1}) |
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| 104 | OutputDir=[Param.OutputSubDir Param.OutputDirExt]; |
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| 105 | |
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| 106 | %% root input file(s) name, type and index series |
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| 107 | RootPath=Param.InputTable(:,1); |
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| 108 | RootFile=Param.InputTable(:,3); |
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| 109 | SubDir=Param.InputTable(:,2); |
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| 110 | NomType=Param.InputTable(:,4); |
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| 111 | FileExt=Param.InputTable(:,5); |
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| 112 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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| 113 | FileInfo=get_file_info(filecell{1,1}); |
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| 114 | FileType=FileInfo.FileType; |
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| 115 | %%%%%%%%%%%% |
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| 116 | % The cell array filecell is the list of input file names, while |
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| 117 | % filecell{iview,fileindex}: |
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| 118 | % iview: line in the table corresponding to a given file series |
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| 119 | % fileindex: file index within the file series, |
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| 120 | % 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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| 121 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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| 122 | %%%%%%%%%%%% |
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| 123 | nbview=numel(i1_series);%number of input file series (lines in InputTable) |
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| 124 | nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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| 125 | nbfield_i=size(i1_series{1},2); %nb of fields for the i index |
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| 126 | nbfield=nbfield_j*nbfield_i; %total number of fields |
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| 127 | |
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| 128 | %% determine the input file type |
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| 129 | % if ~strcmp(FileType{1},'netcdf') |
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| 130 | % displ_uvmat('ERROR','netcdf file series with field projected on a regular mesh must be put as input') |
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| 131 | % return |
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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,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); |
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| 136 | % if size(time,1)>1 |
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| 137 | % diff_time=max(max(diff(time))); |
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| 138 | % if diff_time>0 |
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| 139 | % msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)]) |
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| 140 | % end |
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| 141 | % end |
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| 142 | |
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| 143 | %% coordinate transform or other user defined transform |
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| 144 | transform_fct='';%default |
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| 145 | if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) |
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| 146 | addpath(Param.FieldTransform.TransformPath) |
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| 147 | transform_fct=str2func(Param.FieldTransform.TransformName); |
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| 148 | rmpath(Param.FieldTransform.TransformPath) |
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| 149 | end |
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| 150 | |
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| 151 | %% settings for the output file |
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| 152 | NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file |
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| 153 | first_i=i1_series{1}(1); |
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| 154 | last_i=i1_series{1}(end); |
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| 155 | if isempty(j1_series{1})% if there is no second index j |
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| 156 | first_j=1;last_j=1; |
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| 157 | else |
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| 158 | first_j=j1_series{1}(1); |
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| 159 | last_j=j1_series{1}(end); |
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| 160 | end |
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| 161 | |
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| 162 | %% Set field names and velocity types |
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| 163 | InputFields{1}=[];%default (case of images) |
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| 164 | if isfield(Param,'InputFields') |
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| 165 | InputFields{1}=Param.InputFields; |
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| 166 | end |
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| 167 | |
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| 168 | main_period=Param.ActionInput.WavePeriod; |
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| 169 | main_frequency=2*pi/main_period; |
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| 170 | frequency=(0:main_frequency/16:3*main_frequency)'; |
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| 171 | nbfrequency=numel(frequency); |
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| 172 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% |
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| 173 | for index=1:nbfield |
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| 174 | index |
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| 175 | update_waitbar(WaitbarHandle,index/nbfield) |
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| 176 | if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
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| 177 | disp('program stopped by user') |
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| 178 | break |
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| 179 | end |
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| 180 | |
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| 181 | % reading input file(s) |
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| 182 | [Data,tild,errormsg] = read_field(filecell{1,index},FileType,InputFields{1}); |
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| 183 | if ~isempty(errormsg) |
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| 184 | displ_uvmat('ERROR',['error of input reading: ' errormsg],checkrun); |
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| 185 | break |
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| 186 | end |
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| 187 | if ~isempty(NbSlice_calib) |
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| 188 | Data.ZIndex=mod(i1_series{1}(index)-1,NbSlice_calib{1})+1;%Zindex for phys transform |
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| 189 | end |
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| 190 | %initiate average |
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| 191 | if index==1 |
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| 192 | nby=numel(Data.coord_y); |
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| 193 | nbx=numel(Data.coord_x); |
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| 194 | cos_U=zeros(nbfrequency,numel(Data.coord_y),numel(Data.coord_x)); |
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| 195 | sin_U=zeros(nbfrequency,numel(Data.coord_y),numel(Data.coord_x)); |
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| 196 | cos_V=zeros(nbfrequency,numel(Data.coord_y),numel(Data.coord_x)); |
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| 197 | sin_V=zeros(nbfrequency,numel(Data.coord_y),numel(Data.coord_x)); |
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| 198 | NbField=zeros(nbfrequency,numel(Data.coord_y),numel(Data.coord_x)); |
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| 199 | end |
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| 200 | %update average |
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| 201 | FF=isnan(Data.U)|isnan(Data.V);% check NaN values |
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| 202 | Data.U(FF)=0;% set to zero the NaN values |
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| 203 | Data.V(FF)=0; |
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| 204 | for ifreq=1:nbfrequency |
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| 205 | NbField(ifreq,:,:)=NbField(ifreq,:,:)+reshape(~FF,1,nby,nbx);%count the NaN values |
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| 206 | cos_U(ifreq,:,:)=cos_U(ifreq,:,:)+reshape(Data.U,1,nby,nbx)*cos(Data.Time*frequency(ifreq)); |
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| 207 | sin_U(ifreq,:,:)=sin_U(ifreq,:,:)+reshape(Data.U,1,nby,nbx)*sin(Data.Time*frequency(ifreq)); |
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| 208 | cos_V(ifreq,:,:)=cos_V(ifreq,:,:)+reshape(Data.V,1,nby,nbx)*cos(Data.Time*frequency(ifreq)); |
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| 209 | sin_V(ifreq,:,:)=sin_V(ifreq,:,:)+reshape(Data.V,1,nby,nbx)*sin(Data.Time*frequency(ifreq)); |
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| 210 | end |
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| 211 | end |
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| 212 | |
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| 213 | %%%%%%%%%%%%%%%%%%%%%%%% |
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| 214 | Data.ListVarName={'coord_x','coord_y','frequency','cos_U','cos_V','sin_U','sin_V','a_U','a_V','phase_U','phase_V'}; |
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| 215 | %Data.ListVarName=[{'coord_y','coord_x'} Data.ListVarName]; |
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| 216 | Data.VarDimName={'coord_x', 'coord_y','frequency'}; |
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| 217 | for ilist=1:numel(Data.ListVarName)-3 |
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| 218 | Data.VarDimName{ilist+3}={'frequency','coord_y','coord_x'}; |
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| 219 | end |
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| 220 | Data.frequency=frequency; |
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| 221 | Data.cos_U=cos_U./NbField; |
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| 222 | Data.sin_U=sin_U./NbField; |
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| 223 | Data.cos_V=cos_V./NbField; |
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| 224 | Data.sin_V=sin_V./NbField; |
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| 225 | Data.a_U=sqrt(2)*sqrt(Data.cos_U.*Data.cos_U+Data.sin_U.*Data.sin_U); |
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| 226 | Data.a_V=sqrt(2)*sqrt(Data.cos_V.*Data.cos_V+Data.sin_V.*Data.sin_V); |
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| 227 | Data.phase_U=angle(Data.cos_U+1i*Data.sin_U); |
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| 228 | Data.phase_V=angle(Data.cos_V+1i*Data.sin_V); |
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| 229 | |
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| 230 | |
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| 231 | %% write the results |
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| 232 | OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},'.nc','',1); |
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| 233 | errormsg=struct2nc(OutputFile,Data);% write the output file |
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| 234 | if isempty(errormsg) |
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| 235 | disp_uvmat('CONFIRMATION',[OutputFile ' successfully written'],checkrun) |
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| 236 | else |
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| 237 | disp_uvmat('ERROR',errormsg,checkrun) |
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| 238 | end |
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| 239 | |
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| 240 | |
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| 241 | %% open the result file with uvmat (in RUN mode) |
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| 242 | % if checkrun |
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| 243 | % uvmat(OutputFile)% open the last result file with uvmat |
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| 244 | % end |
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| 245 | '#### THE END ####' |
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