[862] | 1 | %'civ2vel_3C': combine velocity fields from two cameras to get three velocity components
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[839] | 2 | %------------------------------------------------------------------------
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| 3 | % function ParamOut=civ2vel_3C(Param)
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| 4 | %
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| 5 | %OUTPUT
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| 6 | % ParamOut: sets options in the GUI series.fig needed for the function
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| 7 | %
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| 8 | %INPUT:
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| 9 | % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
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| 10 | % In batch mode, Param is the name of the corresponding xml file containing the same information
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| 11 | % when Param.Action.RUN=0 (as activated when the current Action is selected
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| 12 | % in series), the function ouput paramOut set the activation of the needed GUI elements
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| 13 | %
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| 14 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to
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| 15 | % see the current structure Param)
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| 16 | % .InputTable: cell of input file names, (several lines for multiple input)
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| 17 | % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
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| 18 | % .OutputSubDir: name of the subdirectory for data outputs
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| 19 | % .OutputDirExt: directory extension for data outputs
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| 20 | % .Action: .ActionName: name of the current activated function
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| 21 | % .ActionPath: path of the current activated function
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| 22 | % .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled Matlab fct
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| 23 | % .RUN =0 for GUI input, =1 for function activation
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| 24 | % .RunMode='local','background', 'cluster': type of function use
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| 25 | %
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| 26 | % .IndexRange: set the file or frame indices on which the action must be performed
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| 27 | % .InputFields: sub structure describing the input fields withfields
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| 28 | % .FieldName: name(s) of the field
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| 29 | % .VelType: velocity type
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| 30 | % .FieldName_1: name of the second field in case of two input series
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| 31 | % .VelType_1: velocity type of the second field in case of two input series
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| 32 | % .Coord_y: name of y coordinate variable
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| 33 | % .Coord_x: name of x coordinate variable'
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| 34 |
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| 35 | %=======================================================================
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| 36 | % Copyright 2008-2014, LEGI UMR 5519 / CNRS UJF G-INP, Grenoble, France
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| 37 | % http://www.legi.grenoble-inp.fr
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| 38 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
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| 39 | %
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| 40 | % This file is part of the toolbox UVMAT.
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| 41 | %
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| 42 | % UVMAT is free software; you can redistribute it and/or modify
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| 43 | % it under the terms of the GNU General Public License as published
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| 44 | % by the Free Software Foundation; either version 2 of the license,
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| 45 | % or (at your option) any later version.
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| 46 | %
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| 47 | % UVMAT is distributed in the hope that it will be useful,
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| 48 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
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| 49 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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| 50 | % GNU General Public License (see LICENSE.txt) for more details.
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| 51 | %=======================================================================
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| 52 |
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| 53 | function ParamOut=civ2vel_3C(Param)
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| 54 |
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| 55 | %% set the input elements needed on the GUI series when the function is selected in the menu ActionName or InputTable refreshed
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| 56 | if isstruct(Param) && isequal(Param.Action.RUN,0)
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[863] | 57 | ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
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[839] | 58 | ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
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| 59 | ParamOut.NbSlice='off'; %nbre of slices ('off' by default)
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| 60 | ParamOut.VelType='one';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default)
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| 61 | ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
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| 62 | ParamOut.FieldTransform = 'off';%use the phys transform function without choice
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| 63 | %ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only)
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[863] | 64 | ParamOut.ProjObject='on';%can use projection object(option 'off'/'on',
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[839] | 65 | ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default)
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| 66 | ParamOut.OutputDirExt='.vel3C';%set the output dir extension
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[863] | 67 | ParamOut.OutputSubDirMode='two'; % the two first input lines are used to define the output subfolder
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[839] | 68 | ParamOut.OutputFileMode='NbInput';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice
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[863] | 69 | %check the input files
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[839] | 70 | first_j=[];
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[863] | 71 | if size(Param.InputTable,1)<2
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| 72 | msgbox_uvmat('WARNING',['two or three input file series are needed'])
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| 73 | end
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[839] | 74 | if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
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| 75 | PairString='';
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| 76 | if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
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| 77 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
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| 78 | FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
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| 79 | Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
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| 80 | if ~exist(FirstFileName,'file')
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| 81 | msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist'])
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| 82 | elseif isequal(size(Param.InputTable,1),1) && ~isfield(Param,'ProjObject')
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| 83 | msgbox_uvmat('WARNING','You may need a projection object of type plane for merge_proj')
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| 84 | end
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| 85 | return
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| 86 | end
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| 87 |
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| 88 | %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
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| 89 | ParamOut=[]; %default output
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| 90 | %% read input parameters from an xml file if input is a file name (batch mode)
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| 91 | checkrun=1;
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| 92 | if ischar(Param)
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| 93 | Param=xml2struct(Param);% read Param as input file (batch case)
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| 94 | checkrun=0;
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| 95 | end
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| 96 | hseries=findobj(allchild(0),'Tag','series');
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| 97 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
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| 98 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
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| 99 |
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[863] | 100 |
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| 101 | %% root input file(s) name, type and index series
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| 102 | RootPath=Param.InputTable(:,1);
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| 103 | RootFile=Param.InputTable(:,3);
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| 104 | SubDir=Param.InputTable(:,2);
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| 105 | NomType=Param.InputTable(:,4);
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| 106 | FileExt=Param.InputTable(:,5);
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| 107 | hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
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| 108 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
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| 109 | if ~isempty(hdisp),delete(hdisp),end;
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| 110 | %%%%%%%%%%%%
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| 111 | % The cell array filecell is the list of input file names, while
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| 112 | % filecell{iview,fileindex}:
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| 113 | % iview: line in the table corresponding to a given file series
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| 114 | % fileindex: file index within the file series,
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| 115 | % 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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| 116 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
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| 117 | %%%%%%%%%%%%
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| 118 | NbView=numel(i1_series);%number of input file series (lines in InputTable)
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| 119 | NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
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| 120 | NbField_i=size(i1_series{1},2); %nb of fields for the i index
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| 121 | NbField=NbField_j*NbField_i; %total number of fields
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| 122 |
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[839] | 123 | %% define the directory for result file (with path=RootPath{1})
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| 124 | OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
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[863] | 125 | %
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[839] | 126 | % if ~isfield(Param,'InputFields')
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| 127 | % Param.InputFields.FieldName='';
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| 128 | % end
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| 129 |
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| 130 | %% calibration data and timing: read the ImaDoc files
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| 131 | [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
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| 132 | if size(time,1)>1
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| 133 | diff_time=max(max(diff(time)));
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[863] | 134 | if diff_time>0
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[839] | 135 | disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time) ': the mean time is chosen in result'],checkrun)
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[863] | 136 | end
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[839] | 137 | end
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| 138 | if ~isempty(errormsg)
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| 139 | disp_uvmat('WARNING',errormsg,checkrun)
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| 140 | end
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[863] | 141 | time=mean(time,1); %averaged time taken for the merged field
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[839] | 142 | if isfield(XmlData{1},'GeometryCalib')
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[863] | 143 | tsaiA=XmlData{1}.GeometryCalib;
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| 144 | else
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| 145 | disp_uvmat('ERROR','no geometric calibration available for image A',checkrun)
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| 146 | return
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| 147 | end
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| 148 | if isfield(XmlData{2},'GeometryCalib')
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| 149 | tsaiB=XmlData{2}.GeometryCalib;
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| 150 | else
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| 151 | disp_uvmat('ERROR','no geometric calibration available for image B',checkrun)
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| 152 | return
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| 153 | end
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[839] | 154 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
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| 155 |
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[862] | 156 | %% grid of physical positions (given by projection plane)
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| 157 | if ~Param.CheckObject
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[863] | 158 | disp_uvmat('ERROR','a projection plane with interpolation is needed',checkrun)
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| 159 | return
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[862] | 160 | end
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| 161 | ObjectData=Param.ProjObject;
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[863] | 162 | xI=ObjectData.RangeX(1):ObjectData.DX:ObjectData.RangeX(2);
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| 163 | yI=ObjectData.RangeY(1):ObjectData.DY:ObjectData.RangeY(2);
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| 164 | [XI,YI]=meshgrid(xI,yI);
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| 165 | U=zeros(size(XI,1),size(XI,2));
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| 166 | V=zeros(size(XI,1),size(XI,2));
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| 167 | W=zeros(size(XI,1),size(XI,2));
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[862] | 168 |
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[863] | 169 | %% MAIN LOOP ON FIELDS
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| 170 | warning off
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[839] | 171 | for index=1:NbField
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[863] | 172 | update_waitbar(WaitbarHandle,index/NbField)
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[839] | 173 | if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
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| 174 | disp('program stopped by user')
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| 175 | return
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| 176 | end
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| 177 |
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| 178 | %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
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| 179 | Data=cell(1,NbView);%initiate the set Data
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| 180 | timeread=zeros(1,NbView);
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[863] | 181 | [Data{3},tild,errormsg] = nc2struct(filecell{3,index});
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| 182 | ZI=griddata(Data{3}.Xphys,Data{3}.Yphys,Data{3}.Zphys,XI,YI);
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| 183 | [Xa,Ya]=px_XYZ(XmlData{1}.GeometryCalib,XI,YI,ZI);% set of image coordinates on view a
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| 184 | [Xb,Yb]=px_XYZ(XmlData{2}.GeometryCalib,XI,YI,ZI);% set of image coordinates on view b
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| 185 |
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| 186 | %trouver z
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| 187 | % trouver les coordonnées px sur chaque image.
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| 188 | %A=
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| 189 | for iview=1:2
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[839] | 190 | %% reading input file(s)
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[863] | 191 | [Data{iview},tild,errormsg]=read_civdata(filecell{iview,index},{'vec(U,V)'},'*');
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[839] | 192 | if ~isempty(errormsg)
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| 193 | disp_uvmat('ERROR',['ERROR in civ2vel_3C/read_field/' errormsg],checkrun)
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| 194 | return
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| 195 | end
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| 196 | % get the time defined in the current file if not already defined from the xml file
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[863] | 197 | if isfield(Data{iview},'Time')&& isequal(Data{iview}.Time,Data{1}.Time)
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| 198 | Time=Data{iview}.Time;
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| 199 | else
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| 200 | disp_uvmat('ERROR','Time undefined or not synchronous',checkrun)
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| 201 | return
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[839] | 202 | end
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[863] | 203 | if isfield(Data{iview},'Dt')&& isequal(Data{iview}.Dt,Data{1}.Dt)
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| 204 | Dt=Data{iview}.Dt;
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| 205 | else
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| 206 | disp_uvmat('ERROR','Dt undefined or not synchronous',checkrun)
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| 207 | return
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[839] | 208 | end
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| 209 | end
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[863] | 210 | Ua=griddata(Data{1}.X,Data{1}.Y,Data{1}.U,Xa,Ya);
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| 211 | Va=griddata(Data{1}.X,Data{1}.Y,Data{1}.V,Xa,Ya);
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| 212 | A=get_coeff(XmlData{1}.GeometryCalib,Xa,Ya,YI,YI,ZI);
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| 213 |
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| 214 | Ub=griddata(Data{2}.X,Data{2}.Y,Data{1}.U,Xb,Yb);
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| 215 | Vb=griddata(Data{2}.X,Data{2}.Y,Data{2}.V,Xb,Yb);
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| 216 | B=get_coeff(XmlData{2}.GeometryCalib,Xb,Yb,YI,YI,ZI);
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| 217 | S=ones(size(XI,1),size(XI,2),3);
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| 218 | D=ones(size(XI,1),size(XI,2),3,3);
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| 219 | S(:,:,1)=A(:,:,1,1).*Ua+A(:,:,2,1).*Va+B(:,:,1,1).*Ub+B(:,:,2,1).*Vb;
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| 220 | S(:,:,2)=A(:,:,1,2).*Ua+A(:,:,2,2).*Va+B(:,:,1,2).*Ub+B(:,:,2,2).*Vb;
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| 221 | S(:,:,3)=A(:,:,1,3).*Ua+A(:,:,2,3).*Va+B(:,:,1,3).*Ub+B(:,:,2,3).*Vb;
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| 222 | D(:,:,1,1)=A(:,:,1,1).*A(:,:,1,1)+A(:,:,2,1).*A(:,:,2,1)+B(:,:,1,1).*B(:,:,1,1)+B(:,:,2,1).*B(:,:,2,1);
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| 223 | D(:,:,1,2)=A(:,:,1,1).*A(:,:,1,2)+A(:,:,2,1).*A(:,:,2,2)+B(:,:,1,1).*B(:,:,1,2)+B(:,:,2,1).*B(:,:,2,2);
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| 224 | D(:,:,1,3)=A(:,:,1,1).*A(:,:,1,3)+A(:,:,2,1).*A(:,:,2,3)+B(:,:,1,1).*B(:,:,1,3)+B(:,:,2,1).*B(:,:,2,3);
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| 225 | D(:,:,2,1)=A(:,:,1,2).*A(:,:,1,1)+A(:,:,2,2).*A(:,:,2,1)+B(:,:,1,2).*B(:,:,1,1)+B(:,:,2,2).*B(:,:,2,1);
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| 226 | D(:,:,2,2)=A(:,:,1,2).*A(:,:,1,2)+A(:,:,2,2).*A(:,:,2,2)+B(:,:,1,2).*B(:,:,1,2)+B(:,:,2,2).*B(:,:,2,2);
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| 227 | D(:,:,2,3)=A(:,:,1,2).*A(:,:,1,3)+A(:,:,2,2).*A(:,:,2,3)+B(:,:,1,2).*B(:,:,1,3)+B(:,:,2,2).*B(:,:,2,3);
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| 228 | D(:,:,3,1)=A(:,:,1,3).*A(:,:,1,1)+A(:,:,2,3).*A(:,:,2,1)+B(:,:,1,3).*B(:,:,1,1)+B(:,:,2,3).*B(:,:,2,1);
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| 229 | D(:,:,3,2)=A(:,:,1,3).*A(:,:,1,2)+A(:,:,2,3).*A(:,:,2,2)+B(:,:,1,3).*B(:,:,1,2)+B(:,:,2,3).*B(:,:,2,2);
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| 230 | D(:,:,3,3)=A(:,:,1,3).*A(:,:,1,3)+A(:,:,2,3).*A(:,:,2,3)+B(:,:,1,3).*B(:,:,1,3)+B(:,:,2,3).*B(:,:,2,3);
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| 231 | for indj=1:size(XI,1)
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| 232 | for indi=1:size(XI,2)
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| 233 | dxyz=squeeze(S(indj,indi,:))\squeeze(D(indj,indi,:,:));
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| 234 | U(indj,indi)=dxyz(1);
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| 235 | V(indj,indi)=dxyz(2);
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| 236 | W(indj,indi)=dxyz(3);
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| 237 | end
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| 238 | end
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| 239 | Error=zeros(size(XI,1),size(XI,2),4);
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| 240 | Error(:,:,1)=A(:,:,1,1).*U+A(:,:,1,2).*V+A(:,:,1,3).*W-Ua;
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| 241 | Error(:,:,2)=A(:,:,2,1).*U+A(:,:,2,2).*V+A(:,:,2,3).*W-Va;
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| 242 | Error(:,:,3)=B(:,:,1,1).*U+B(:,:,1,2).*V+B(:,:,1,3).*W-Ub;
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| 243 | Error(:,:,4)=B(:,:,2,1).*U+B(:,:,2,2).*V+B(:,:,2,3).*W-Vb;
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| 244 |
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[839] | 245 | %% generating the name of the merged field
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| 246 | i1=i1_series{1}(index);
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| 247 | if ~isempty(i2_series{end})
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| 248 | i2=i2_series{end}(index);
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| 249 | else
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| 250 | i2=i1;
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| 251 | end
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| 252 | j1=1;
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| 253 | j2=1;
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| 254 | if ~isempty(j1_series{1})
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| 255 | j1=j1_series{1}(index);
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| 256 | if ~isempty(j2_series{end})
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| 257 | j2=j2_series{end}(index);
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| 258 | else
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| 259 | j2=j1;
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| 260 | end
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| 261 | end
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[863] | 262 | OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},'.nc','_1-2',i1,i2,j1,j2);
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| 263 |
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[839] | 264 | %% recording the merged field
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[863] | 265 | if index==1% initiate the structure at first index
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| 266 | MergeData.ListGlobalAttribute={'Conventions','Time','Dt'};
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[839] | 267 | MergeData.Conventions='uvmat';
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[863] | 268 | MergeData.Time=Time;
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| 269 | MergeData.Dt=Dt;
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| 270 | MergeData.ListVarName={'coord_x','coord_y','Z','U','V','W','Error'};
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| 271 | MergeData.VarDimName={'coord_x','coord_y',{'coord_y','coord_x'},{'coord_y','coord_x'}...
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| 272 | {'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'}};
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| 273 | MergeData.coord_x=xI;
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| 274 | MergeData.coord_y=yI;
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| 275 | MergeData.Z=ZI;
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| 276 | end
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| 277 | MergeData.U=U/Dt;
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| 278 | MergeData.V=V/Dt;
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| 279 | MergeData.W=W/Dt;
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| 280 | MergeData.Error=sqrt(sum(Error.*Error,3));
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| 281 | errormsg=struct2nc(OutputFile,MergeData);%save result file
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| 282 | if isempty(errormsg)
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| 283 | disp(['output file ' OutputFile ' written'])
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| 284 | else
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| 285 | disp(errormsg)
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| 286 | end
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[839] | 287 | end
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| 288 |
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| 289 |
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[863] | 290 | function A=get_coeff(Calib,X,Y,x,y,z)
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| 291 | R=(Calib.R)';%rotation matrix
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| 292 | T_z=Calib.Tx_Ty_Tz(3);
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| 293 | T=R(7)*x+R(8)*y+R(9)*z+T_z;
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| 294 | A(:,:,1,1)=(R(1)-R(7)*X)./T;
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| 295 | A(:,:,1,2)=(R(2)-R(8)*X)./T;
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| 296 | A(:,:,1,3)=(R(3)-R(9)*X)./T;
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| 297 | A(:,:,2,1)=(R(4)-R(7)*Y)./T;
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| 298 | A(:,:,2,2)=(R(5)-R(8)*Y)./T;
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| 299 | A(:,:,2,3)=(R(6)-R(9)*Y)./T;
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[839] | 300 |
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| 301 |
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| 302 |
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| 303 |
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| 304 |
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| 305 |
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| 306 |
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