[958] | 1 | %'read_civdata': reads new civ data from netcdf files
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| 2 | %------------------------------------------------------------------
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| 3 | %
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| 4 | % function [Field,VelTypeOut]=read_civdata(FileName,FieldNames,VelType)
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| 5 | %
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| 6 | % OUTPUT:
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| 7 | % Field: structure representing the selected field, containing
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| 8 | % .Txt: (char string) error message if any
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| 9 | % .ListGlobalAttribute: list of global attributes containing:
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| 10 | % .NbCoord: number of vector components
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| 11 | % .NbDim: number of dimensions (=2 or 3)
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| 12 | % .Dt: time interval for the corresponding image pair
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| 13 | % .Time: absolute time (average of the initial image pair)
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| 14 | % .CivStage: =0,
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| 15 | % =1, civ1 has been performed only
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| 16 | % =2, fix1 has been performed
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| 17 | % =3, pacth1 has been performed
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| 18 | % =4, civ2 has been performed
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| 19 | % =5, fix2 has been performed
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| 20 | % =6, pacth2 has been performed
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| 21 | % .CoordUnit: 'pixel'
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| 22 | % .ListVarName: {'X' 'Y' 'U' 'V' 'F' 'FF'}
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| 23 | % .X, .Y, .Z: set of vector coordinates
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| 24 | % .U,.V,.W: corresponding set of vector components
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| 25 | % .F: warning flags
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| 26 | % .FF: error flag, =0 for good vectors
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| 27 | % .C: scalar associated with velocity (used for vector colors)
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| 28 | %
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| 29 | % VelTypeOut: velocity type corresponding to the selected field: ='civ1','interp1','interp2','civ2'....
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| 30 | %
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| 31 | % INPUT:
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| 32 | % FileName: file name (string).
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| 33 | % FieldNames =cell of field names to get, which can contain the strings:
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| 34 | % 'ima_cor': image correlation, vec_c or vec2_C
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| 35 | % 'vort','div','strain': requires velocity derivatives DUDX...
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| 36 | % 'error': error estimate (vec_E or vec2_E)
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| 37 | %
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| 38 | % VelType : character string indicating the types of velocity fields to read ('civ1','civ2'...)
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| 39 | % if vel_type=[] or'*', a priority choice, given by vel_type_out{1,2}, is done depending
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| 40 | % if vel_type='filter'; a structured field is sought (filter2 in priority, then filter1)
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| 41 | %
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| 42 | % FUNCTIONS called:
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| 43 | % 'varcivx_generator':, sets the names of vaiables to read in the netcdf file
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| 44 | % 'nc2struct': reads a netcdf file
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| 45 |
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| 46 | %=======================================================================
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[1071] | 47 | % Copyright 2008-2020, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
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[958] | 48 | % http://www.legi.grenoble-inp.fr
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| 49 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
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| 50 | %
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| 51 | % This file is part of the toolbox UVMAT.
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| 52 | %
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| 53 | % UVMAT is free software; you can redistribute it and/or modify
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| 54 | % it under the terms of the GNU General Public License as published
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| 55 | % by the Free Software Foundation; either version 2 of the license,
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| 56 | % or (at your option) any later version.
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| 57 | %
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| 58 | % UVMAT is distributed in the hope that it will be useful,
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| 59 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
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| 60 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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| 61 | % GNU General Public License (see LICENSE.txt) for more details.
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| 62 | %=======================================================================
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| 63 |
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| 64 | function [Field,VelTypeOut,errormsg]=read_pivdata_fluidimage(FileName,FieldNames,VelType)
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| 65 |
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| 66 | %% default input
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| 67 | if ~exist('VelType','var')
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| 68 | VelType='';
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| 69 | end
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| 70 | if isequal(VelType,'*')
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| 71 | VelType='';
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| 72 | end
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| 73 | if isempty(VelType)
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| 74 | VelType='';
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| 75 | end
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| 76 | if ~exist('FieldNames','var')
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| 77 | FieldNames=[]; %default
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| 78 | end
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| 79 | Field=[];
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| 80 | VelTypeOut=VelType;
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| 81 | errormsg='';
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| 82 | if ~exist(FileName,'file')
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| 83 | errormsg=['input file ' FileName ' does not exist'];
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| 84 | return
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| 85 | end
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| 86 | if ischar(FieldNames), FieldNames={FieldNames}; end;
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| 87 | ProjModeRequest='';
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| 88 | for ilist=1:length(FieldNames)
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| 89 | if ~isempty(FieldNames{ilist})
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| 90 | switch FieldNames{ilist}
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[987] | 91 | case {'U','V','norm(U,V)'}
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[958] | 92 | if ~strcmp(FieldNames{1},'vec(U,V)')% if the scalar is not used as color of vectors
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| 93 | ProjModeRequest='interp_lin';
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| 94 | end
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| 95 | case {'curl(U,V)','div(U,V)','strain(U,V)'}
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| 96 | ProjModeRequest='interp_tps';
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| 97 | end
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| 98 | end
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| 99 | end
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| 100 |
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| 101 | %% reading data
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| 102 |
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| 103 |
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| 104 | % Data=nc2struct(FileName,'ListGlobalAttribute','CivStage');
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| 105 | % if isfield(Data,'Txt')
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| 106 | % erromsg=['error in read_civdata: ' Data.Txt];
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| 107 | % return
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| 108 | % end
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| 109 | % % set the list of variables to read and their role
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| 110 | %[varlist,role,VelTypeOut]=varcivx_generator(ProjModeRequest,VelType,Datasets.CivStage);
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| 111 | % if isempty(varlist)
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| 112 | % erromsg=['error in read_civdata: unknow velocity type ' VelType];
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| 113 | % return
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| 114 | % else
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| 115 | Datasets=hdf5load(FileName);%read the variables in the netcdf file
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| 116 | %[varlist,role,VelTypeOut]=varcivx_generator(ProjModeRequest,VelType,Datasets.CivStage);
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| 117 | role={'coord_x','coord_y','vector_x','vector_y','ancillary','warnflag','errorflag'};
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| 118 | vardetect=ones(size(role));
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| 119 | Field.ListGlobalAttribute= {'Dt','Time','CivStage'};
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| 120 | Field.Dt=1;
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| 121 | Field.Time=0;
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| 122 | if isfield(Datasets, 'piv1')
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| 123 | Field.CivStage=6;
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| 124 | else
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| 125 | Field.CivStage=3;
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| 126 | end
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| 127 | VelTypeOut=VelType;
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| 128 | switch VelType
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| 129 | case {'civ1','filter1'}
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| 130 | Data=Datasets.piv0;
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| 131 | VelTypeOut='filter1';
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| 132 | case {'civ2','filter2'}
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| 133 | Data=Datasets.piv1;
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| 134 | VelTypeOut='filter2';
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| 135 | case ''
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| 136 | if isfield(Datasets, 'piv1')
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| 137 | Data=Datasets.piv1;
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| 138 | VelTypeOut='filter2';
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| 139 | else
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| 140 | Data=Datasets.piv0;
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| 141 | VelTypeOut='filter1';
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| 142 | end
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| 143 | end
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| 144 | switch VelType
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| 145 | case {'civ1','civ2'}
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| 146 | Field.X= double(Data.xs);
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| 147 | Field.Y= double(Data.ys);
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| 148 | Field.U= double(Data.deltaxs);
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| 149 | Field.U(isnan(Field.U)) = 0;
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| 150 | Field.V= double(Data.deltays);
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| 151 | Field.V(isnan(Field.V)) = 0;
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| 152 | case {'filter1','filter2',''}
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[1003] | 153 | Field.X= double(Data.ixvecs_final);
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| 154 | Field.Y= double(Data.iyvecs_final);
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| 155 | Field.U= double(Data.deltaxs_final);
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[958] | 156 | Field.U(isnan(Field.U)) = 0;
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[1003] | 157 | Field.V= double(Data.deltays_final);
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[958] | 158 | Field.V(isnan(Field.V)) = 0;
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| 159 | end
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| 160 | Field.ListVarName={'X' 'Y' 'U' 'V' 'C' 'F' 'FF'};
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| 161 | Field.VarDimName={'nb_vec' 'nb_vec' 'nb_vec' 'nb_vec' 'nb_vec' 'nb_vec' 'nb_vec'};
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| 162 | Field.C = double(Data.correls_max);
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| 163 | Field.F=zeros(size(Field.U)); Field.F(Data.errors.keys + 1)=1; % !!! convention matlab vs python
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| 164 | Field.FF=zeros(size(Field.U)); Field.FF(Data.errors.keys + 1)=1;
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| 165 | % if vardetect(1)==0
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| 166 | % errormsg=[ 'requested field not available in ' FileName '/' VelType ': need to run patch'];
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| 167 | % return
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| 168 | % end
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| 169 | switch VelTypeOut
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[987] | 170 | case {'civ1','filter1'}
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[958] | 171 | if isfield(Field,'Patch1_SubDomain')
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| 172 | Field.SubDomain=Field.Patch1_SubDomain;
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| 173 | Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'SubDomain'}];
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| 174 | end
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| 175 | if isfield(Field,'Civ1_Dt')
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| 176 | Field.Dt=Field.Civ1_Dt;
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| 177 | end
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| 178 | if isfield(Field,'Civ1_Time')
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| 179 | Field.Time=Field.Civ1_Time;
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| 180 | end
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[987] | 181 | case {'civ2','filter2'}
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[958] | 182 | if isfield(Field,'Patch2_SubDomain')
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| 183 | Field.SubDomain=Field.Patch2_SubDomain;
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| 184 | Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'SubDomain'}];
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| 185 | end
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| 186 | if isfield(Field,'Civ2_Dt')
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| 187 | Field.Dt=Field.Civ2_Dt;
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| 188 | end
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| 189 | if isfield(Field,'Civ2_Time')
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| 190 | Field.Time=Field.Civ2_Time;
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| 191 | end
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| 192 | end
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| 193 | %Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'Dt','Time'}];
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| 194 | ivar_U_tps=[];
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| 195 | ivar_V_tps=[];
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| 196 | var_ind=find(vardetect);
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| 197 | for ivar=1:numel(var_ind)
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| 198 | Field.VarAttribute{ivar}.Role=role{var_ind(ivar)};
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| 199 | %Field.VarAttribute{ivar}.Mesh=0.025;%typical mesh for histograms O.025 pixel (used in series)
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| 200 | Field.VarAttribute{ivar}.ProjModeRequest=ProjModeRequest;
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| 201 | if strcmp(role{var_ind(ivar)},'vector_x')
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| 202 | Field.VarAttribute{ivar}.FieldName=FieldNames;
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| 203 | ivar_U=ivar;
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| 204 | end
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| 205 | if strcmp(role{var_ind(ivar)},'vector_x_tps')
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| 206 | Field.VarAttribute{ivar}.FieldName=FieldNames;
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| 207 | ivar_U_tps=ivar;
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| 208 | end
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| 209 | if strcmp(role{var_ind(ivar)},'vector_y')
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| 210 | Field.VarAttribute{ivar}.FieldName=FieldNames;
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| 211 | ivar_V=ivar;
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| 212 | end
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| 213 | if strcmp(role{var_ind(ivar)},'vector_y_tps')
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| 214 | Field.VarAttribute{ivar}.FieldName=FieldNames;
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| 215 | ivar_V_tps=ivar;
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| 216 | end
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| 217 | end
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| 218 | if ~isempty(ivar_U_tps)
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| 219 | Field.VarAttribute{ivar_U}.VarIndex_tps=ivar_U_tps;
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| 220 | end
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| 221 | if ~isempty(ivar_V_tps)
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| 222 | Field.VarAttribute{ivar_V}.VarIndex_tps=ivar_V_tps;
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| 223 | end
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| 224 |
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| 225 | %% update list of global attributes
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| 226 | Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'NbCoord','NbDim','TimeUnit','CoordUnit'}];
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| 227 | Field.NbCoord=2;
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| 228 | Field.NbDim=2;
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| 229 | Field.TimeUnit='s';
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| 230 | Field.CoordUnit='pixel';
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