[315] | 1 | %'civ_matlab': Matlab version of the PIV programs CivX |
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| 2 | % --- call the sub-functions: |
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| 3 | % civ: PIV function itself |
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| 4 | % fix: removes false vectors after detection by various criteria |
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[382] | 5 | % filter_tps: make interpolation-smoothing |
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[315] | 6 | %------------------------------------------------------------------------ |
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| 7 | % function [Data,errormsg,result_conv]= civ_uvmat(Param,ncfile) |
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| 8 | % |
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| 9 | %OUTPUT |
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| 10 | % Data=structure containing the PIV results and information on the processing parameters |
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| 11 | % errormsg=error message char string, default='' |
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| 12 | % resul_conv: image inter-correlation function for the last grid point (used for tests) |
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| 13 | % |
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| 14 | %INPUT: |
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| 15 | % Param: input images and processing parameters |
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[387] | 16 | % .Civ1: for civ1 |
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| 17 | % .Fix1: |
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| 18 | % .Patch1: |
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| 19 | % .Civ2: for civ2 |
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| 20 | % .Fix2: |
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| 21 | % .Patch2: |
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[315] | 22 | % ncfile: name of a netcdf file to be created for the result (extension .nc) |
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| 23 | % |
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| 24 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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| 25 | % Copyright 2011, LEGI / CNRS-UJF-INPG, joel.sommeria@legi.grenoble-inp.fr. |
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| 26 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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| 27 | % This is part of the toolbox UVMAT. |
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| 28 | % |
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| 29 | % UVMAT is free software; you can redistribute it and/or modify |
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| 30 | % it under the terms of the GNU General Public License as published by |
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| 31 | % the Free Software Foundation; either version 2 of the License, or |
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| 32 | % (at your option) any later version. |
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| 33 | % |
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| 34 | % UVMAT is distributed in the hope that it will be useful, |
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| 35 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 36 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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| 37 | % GNU General Public License (open UVMAT/COPYING.txt) for more details. |
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| 38 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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| 39 | |
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| 40 | function [Data,errormsg,result_conv]= civ_matlab(Param,ncfile) |
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| 41 | errormsg=''; |
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| 42 | Data.ListGlobalAttribute={'Conventions','Program','CivStage'}; |
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| 43 | Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes |
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| 44 | Data.Program='civ_matlab'; |
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| 45 | Data.CivStage=0;%default |
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| 46 | ListVarCiv1={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F'}; %variables to read |
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| 47 | ListVarFix1={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F','Civ1_FF'}; |
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| 48 | mask=''; |
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| 49 | maskname='';%default |
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| 50 | check_civx=0;%default |
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| 51 | check_civ1=0;%default |
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| 52 | check_patch1=0;%default |
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[466] | 53 | % ImageFileA=Param.Civ1.ImageA; |
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| 54 | % ImageFileB=Param.Civ1.ImageB; |
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| 55 | % if isfield(Param,'Civ2') |
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| 56 | % ImageFileA_civ2=Param.Civ2.ImageA; |
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| 57 | % ImageFileB_civ2=Param.Civ2.ImageB; |
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| 58 | % end |
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[435] | 59 | % case of input Param set by an xml file (batch mode) |
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[319] | 60 | if ischar(Param) |
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[387] | 61 | Param=xml2struct(Param); %if Param is the name of an xml file, read this file as a Matlab structure |
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[493] | 62 | % if isfield(Param,'Civ1') |
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| 63 | % if strcmp(Param.Civ1.FileTypeA,'video') |
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| 64 | % Param.Civ1.ImageA=VideoReader(regexprep(Param.Civ1.ImageA,'''','\'));% remove spurious ' appearing in Windows; |
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| 65 | % elseif strcmp(Param.Civ1.FileTypeA,'mmreader') |
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| 66 | % Param.Civ1.ImageA=mmreader(regexprep(Param.Civ1.ImageA,'''','\'));% remove spurious ' appearing in Windows |
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| 67 | % end |
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| 68 | % if strcmp(Param.Civ1.FileTypeB,'video') |
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| 69 | % Param.Civ1.ImageB=VideoReader(regexprep(Param.Civ1.ImageB,'''','\'));% remove spurious ' appearing in Windows |
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| 70 | % elseif strcmp(Param.Civ1.FileTypeB,'mmreader') |
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| 71 | % Param.Civ1.ImageB=mmreader(regexprep(Param.Civ1.ImageB,'''','\'));% remove spurious ' appearing in Windows |
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| 72 | % end |
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| 73 | % end |
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| 74 | % if isfield(Param,'Civ2') |
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| 75 | % if strcmp(Param.Civ2.FileTypeA,'video') |
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| 76 | % Param.Civ2.ImageA=VideoReader(regexprep(Param.Civ2.ImageA,'''','\'));% remove spurious ' appearing in Windows; |
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| 77 | % elseif strcmp(Param.Civ2.FileTypeA,'mmreader') |
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| 78 | % Param.Civ2.ImageA=mmreader(regexprep(Param.Civ2.ImageA,'''','\'));% remove spurious ' appearing in Windows |
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| 79 | % if strcmp(Param.Civ2.FileTypeB,'video') |
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| 80 | % Param.Civ2.ImageB=VideoReader(regexprep(Param.Civ2.ImageB,'''','\'));% remove spurious ' appearing in Windows |
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| 81 | % elseif strcmp(Param.Civ2.FileTypeB,'mmreader') |
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| 82 | % Param.Civ2.ImageB=mmreader(regexprep(Param.Civ2.ImageB,'''','\'));% remove spurious ' appearing in Windows |
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| 83 | % end; |
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| 84 | % end |
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| 85 | % end |
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[319] | 86 | end |
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| 87 | |
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[315] | 88 | %% Civ1 |
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| 89 | if isfield (Param,'Civ1') |
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[364] | 90 | par_civ1=Param.Civ1; |
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[494] | 91 | if isfield(par_civ1,'reverse_pair')% A REVOIR |
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[364] | 92 | if par_civ1.reverse_pair |
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| 93 | if ischar(par_civ1.ImageB) |
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| 94 | temp=par_civ1.ImageA; |
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[388] | 95 | par_civ1.ImageA=imread(par_civ1.ImageB); |
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[364] | 96 | end |
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| 97 | if ischar(temp) |
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[388] | 98 | par_civ1.ImageB=imread(temp); |
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[364] | 99 | end |
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| 100 | end |
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| 101 | else |
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[548] | 102 | if isfield(Param.Civ1,'ImageA') && ischar(Param.Civ1.ImageA) |
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[493] | 103 | Param.Civ1.ImageA=regexprep(Param.Civ1.ImageA,'''','\'); |
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[494] | 104 | [par_civ1.ImageA,VideoObject] = read_image(Param.Civ1.ImageA,par_civ1.FileTypeA,[],par_civ1.FrameIndexA); |
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[364] | 105 | end |
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[548] | 106 | if isfield(Param.Civ1,'ImageB')&& ischar(Param.Civ1.ImageB) |
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[493] | 107 | Param.Civ1.ImageB=regexprep(Param.Civ1.ImageB,'''','\'); |
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[494] | 108 | if strcmp(Param.Civ1.ImageA,Param.Civ1.ImageB)% use the same movie object |
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| 109 | [par_civ1.ImageB,VideoObject] = read_image(Param.Civ1.ImageB,par_civ1.FileTypeB,VideoObject,par_civ1.FrameIndexB); |
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| 110 | else |
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| 111 | [par_civ1.ImageB,VideoObject] = read_image(Param.Civ1.ImageB,par_civ1.FileTypeB,par_civ1.ImageB,par_civ1.FrameIndexB); |
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| 112 | end |
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[364] | 113 | end |
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| 114 | end |
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| 115 | |
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[315] | 116 | % caluclate velocity data (y and v in indices, reverse to y component) |
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[364] | 117 | [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ1); |
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[337] | 118 | |
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[364] | 119 | % to try the reverse_pair method, uncomment below |
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| 120 | % [xtable1 ytable1 utable1 vtable1 ctable1 F1 result_conv1 errormsg1] = civ (Param.Civ1); |
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| 121 | % Param.Civ1.reverse_pair=1; |
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| 122 | % [xtable2 ytable2 utable2 vtable2 ctable2 F2 result_conv2 errormsg2] = civ (Param.Civ1); |
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| 123 | % xtable=[xtable1; xtable2]; |
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| 124 | % ytable=[ytable1; ytable2]; |
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| 125 | % utable=[utable1; -utable2]; |
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| 126 | % vtable=[vtable1; -vtable2]; |
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| 127 | % ctable=[ctable1; ctable2]; |
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| 128 | % F=[F1; F2]; |
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| 129 | % result_conv=[result_conv1; result_conv2]; |
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| 130 | % errormsg=[errormsg1; errormsg2]; |
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[315] | 131 | if ~isempty(errormsg) |
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| 132 | return |
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| 133 | end |
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| 134 | list_param=(fieldnames(Param.Civ1))'; |
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| 135 | Civ1_param=list_param;%default |
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[406] | 136 | %set the values of all the global attributes in list_param |
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[315] | 137 | for ilist=1:length(list_param) |
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| 138 | Civ1_param{ilist}=['Civ1_' list_param{ilist}]; |
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| 139 | Data.(['Civ1_' list_param{ilist}])=Param.Civ1.(list_param{ilist}); |
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| 140 | end |
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| 141 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ1_param];% {'Civ1_Time','Civ1_Dt'}]; |
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[364] | 142 | Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_F','Civ1_C'};% cell array containing the names of the fields to record |
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[399] | 143 | Data.VarDimName={'nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1'}; |
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[319] | 144 | Data.VarAttribute{1}.Role='coord_x'; |
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| 145 | Data.VarAttribute{2}.Role='coord_y'; |
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| 146 | Data.VarAttribute{3}.Role='vector_x'; |
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| 147 | Data.VarAttribute{4}.Role='vector_y'; |
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| 148 | Data.VarAttribute{5}.Role='warnflag'; |
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[315] | 149 | Data.Civ1_X=reshape(xtable,[],1); |
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| 150 | Data.Civ1_Y=reshape(Param.Civ1.ImageHeight-ytable+1,[],1); |
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| 151 | Data.Civ1_U=reshape(utable,[],1); |
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| 152 | Data.Civ1_V=reshape(-vtable,[],1); |
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| 153 | Data.Civ1_C=reshape(ctable,[],1); |
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| 154 | Data.Civ1_F=reshape(F,[],1); |
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[435] | 155 | Data.CivStage=1; |
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[315] | 156 | else |
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[319] | 157 | if exist('ncfile','var') |
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| 158 | CivFile=ncfile; |
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| 159 | elseif isfield(Param.Patch1,'CivFile') |
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| 160 | CivFile=Param.Patch1.CivFile; |
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| 161 | end |
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[363] | 162 | Data=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format |
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[317] | 163 | if isfield(Data,'Txt') |
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[319] | 164 | errormsg=Data.Txt; |
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[317] | 165 | return |
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| 166 | end |
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[315] | 167 | if ~isempty(Data.absolut_time_T0')%read civx file |
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| 168 | check_civx=1;% test for old civx data format |
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[319] | 169 | [Data,vardetect,ichoice]=nc2struct(CivFile);%read the variables in the netcdf file |
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[315] | 170 | else |
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[363] | 171 | Data=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file |
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[315] | 172 | end |
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| 173 | end |
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| 174 | |
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| 175 | %% Fix1 |
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| 176 | if isfield (Param,'Fix1') |
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| 177 | ListFixParam=fieldnames(Param.Fix1); |
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| 178 | for ilist=1:length(ListFixParam) |
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| 179 | ParamName=ListFixParam{ilist}; |
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| 180 | ListName=['Fix1_' ParamName]; |
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| 181 | eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];']) |
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| 182 | eval(['Data.' ListName '=Param.Fix1.' ParamName ';']) |
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| 183 | end |
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| 184 | if check_civx |
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| 185 | if ~isfield(Data,'fix') |
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| 186 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix']; |
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| 187 | Data.fix=1; |
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| 188 | Data.ListVarName=[Data.ListVarName {'vec_FixFlag'}]; |
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| 189 | Data.VarDimName=[Data.VarDimName {'nb_vectors'}]; |
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| 190 | end |
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| 191 | Data.vec_FixFlag=fix(Param.Fix1,Data.vec_F,Data.vec_C,Data.vec_U,Data.vec_V,Data.vec_X,Data.vec_Y); |
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| 192 | else |
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| 193 | Data.ListVarName=[Data.ListVarName {'Civ1_FF'}]; |
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[399] | 194 | Data.VarDimName=[Data.VarDimName {'nb_vec_1'}]; |
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[315] | 195 | nbvar=length(Data.ListVarName); |
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[435] | 196 | Data.VarAttribute{nbvar}.Role='errorflag'; |
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[315] | 197 | Data.Civ1_FF=fix(Param.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V); |
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[435] | 198 | Data.CivStage=2; |
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[315] | 199 | end |
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[435] | 200 | end |
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[315] | 201 | %% Patch1 |
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| 202 | if isfield (Param,'Patch1') |
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[326] | 203 | if check_civx |
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| 204 | errormsg='Civ Matlab input needed for patch'; |
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| 205 | return |
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| 206 | end |
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[389] | 207 | |
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[315] | 208 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch1_Rho','Patch1_Threshold','Patch1_SubDomain'}]; |
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[437] | 209 | Data.Patch1_Rho=Param.Patch1.FieldSmooth; |
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[316] | 210 | Data.Patch1_Threshold=Param.Patch1.MaxDiff; |
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| 211 | Data.Patch1_SubDomain=Param.Patch1.SubdomainSize; |
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[397] | 212 | nbvar=length(Data.ListVarName); |
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[389] | 213 | Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbSites','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}]; |
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[435] | 214 | Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},{'nb_subdomain_1'},... |
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| 215 | {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}]; |
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[397] | 216 | Data.VarAttribute{nbvar+1}.Role='vector_x'; |
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| 217 | Data.VarAttribute{nbvar+2}.Role='vector_y'; |
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| 218 | Data.VarAttribute{nbvar+5}.Role='coord_tps'; |
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[492] | 219 | Data.VarAttribute{nbvar+6}.Role='vector_x'; |
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| 220 | Data.VarAttribute{nbvar+7}.Role='vector_y'; |
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[389] | 221 | Data.Civ1_U_smooth=zeros(size(Data.Civ1_X)); |
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| 222 | Data.Civ1_V_smooth=zeros(size(Data.Civ1_X)); |
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[315] | 223 | if isfield(Data,'Civ1_FF') |
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| 224 | ind_good=find(Data.Civ1_FF==0); |
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[435] | 225 | else |
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[315] | 226 | ind_good=1:numel(Data.Civ1_X); |
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| 227 | end |
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[382] | 228 | [Data.Civ1_SubRange,Data.Civ1_NbSites,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=... |
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[435] | 229 | filter_tps([Data.Civ1_X(ind_good) Data.Civ1_Y(ind_good)],Data.Civ1_U(ind_good),Data.Civ1_V(ind_good),[],Data.Patch1_SubDomain,Data.Patch1_Rho,Data.Patch1_Threshold); |
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| 230 | Data.Civ1_U_smooth(ind_good)=Ures; |
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| 231 | Data.Civ1_V_smooth(ind_good)=Vres; |
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| 232 | Data.Civ1_FF(ind_good)=FFres; |
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| 233 | Data.CivStage=3; |
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| 234 | end |
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[315] | 235 | |
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| 236 | %% Civ2 |
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| 237 | if isfield (Param,'Civ2') |
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| 238 | par_civ2=Param.Civ2; |
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[494] | 239 | par_civ2.ImageA=[]; |
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| 240 | par_civ2.ImageB=[]; |
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| 241 | if isfield(Param.Civ2,'ImageA') && isfield(Param.Civ2,'ImageB') |
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| 242 | Param.Civ2.ImageA=regexprep(Param.Civ2.ImageA,'''','\'); |
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| 243 | Param.Civ2.ImageB=regexprep(Param.Civ2.ImageB,'''','\'); |
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| 244 | if isfield (Param,'Civ1') |
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| 245 | Param.Civ2.ImageA=regexprep(Param.Civ2.ImageA,'''','\'); |
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| 246 | if strcmp(Param.Civ1.ImageA,Param.Civ2.ImageA) |
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| 247 | if isequal(Param.Civ1.FrameIndexA,Param.Civ2.FrameIndexA) |
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| 248 | par_civ2.ImageA=par_civ1.ImageA; |
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| 249 | else % read another frame of the same movie object |
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| 250 | par_civ2.ImageA = read_image(Param.Civ2.ImageA,Param.Civ2.FileTypeA,VideoObject,Param.Civ2.FrameIndexA); |
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| 251 | end |
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[435] | 252 | end |
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[494] | 253 | Param.Civ2.ImageB=regexprep(Param.Civ2.ImageB,'''','\'); |
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| 254 | if strcmp(Param.Civ1.ImageB,Param.Civ2.ImageB) |
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| 255 | if isequal(Param.Civ1.FrameIndexB,Param.Civ2.FrameIndexB) |
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| 256 | par_civ2.ImageB=par_civ1.ImageB; |
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| 257 | else % read another frame of the same movie object |
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| 258 | par_civ2.ImageB = read_image(Param.Civ2.ImageB,Param.Civ2.FileTypeB,VideoObject,Param.Civ2.FrameIndexB); |
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| 259 | end |
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[435] | 260 | end |
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[494] | 261 | end |
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| 262 | if isempty(par_civ2.ImageA) && isfield(Param.Civ2,'ImageA') |
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| 263 | [par_civ2.ImageA,VideoObject] = read_image(Param.Civ2.ImageA,Param.Civ2.FileTypeA,[],Param.Civ2.FrameIndexA); |
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| 264 | end |
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| 265 | if isempty(par_civ2.ImageB)&& isfield(Param.Civ2,'ImageB') |
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| 266 | if strcmp(Param.Civ2.ImageA,Param.Civ2.ImageB) |
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| 267 | par_civ2.ImageB = read_image(Param.Civ2.ImageB,Param.Civ2.FileTypeB,VideoObject,Param.Civ2.FrameIndexB); |
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| 268 | else |
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| 269 | par_civ2.ImageB = read_image(Param.Civ2.ImageB,Param.Civ2.FileTypeB,[],Param.Civ2.FrameIndexB); |
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| 270 | end |
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| 271 | end |
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[315] | 272 | end |
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[437] | 273 | ibx2=ceil(par_civ2.CorrBoxSize(1)/2); |
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| 274 | iby2=ceil(par_civ2.CorrBoxSize(2)/2); |
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[389] | 275 | isx2=ibx2+4;% search ara +-4 pixels around the guess |
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| 276 | isy2=iby2+4; |
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[363] | 277 | % shift from par_civ2.filename_nc1 |
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| 278 | % shiftx=velocity interpolated at position |
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| 279 | miniy=max(1+isy2,1+iby2); |
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| 280 | minix=max(1+isx2,1+ibx2); |
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| 281 | maxiy=min(size(par_civ2.ImageA,1)-isy2,size(par_civ2.ImageA,1)-iby2); |
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| 282 | maxix=min(size(par_civ2.ImageA,2)-isx2,size(par_civ2.ImageA,2)-ibx2); |
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[315] | 283 | [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy); |
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[363] | 284 | GridX=reshape(GridX,[],1); |
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[435] | 285 | GridY=reshape(GridY,[],1); |
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[363] | 286 | Shiftx=zeros(size(GridX));% shift expected from civ1 data |
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| 287 | Shifty=zeros(size(GridX)); |
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| 288 | nbval=zeros(size(GridX)); |
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| 289 | if par_civ2.CheckDeformation |
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| 290 | DUDX=zeros(size(GridX)); |
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| 291 | DUDY=zeros(size(GridX)); |
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| 292 | DVDX=zeros(size(GridX)); |
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| 293 | DVDY=zeros(size(GridX)); |
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| 294 | end |
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[383] | 295 | NbSubDomain=size(Data.Civ1_SubRange,3); |
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[363] | 296 | % get the guess from patch1 |
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| 297 | for isub=1:NbSubDomain |
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| 298 | nbvec_sub=Data.Civ1_NbSites(isub); |
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[383] | 299 | ind_sel=find(GridX>=Data.Civ1_SubRange(1,1,isub) & GridX<=Data.Civ1_SubRange(1,2,isub) & GridY>=Data.Civ1_SubRange(2,1,isub) & GridY<=Data.Civ1_SubRange(2,2,isub)); |
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[363] | 300 | epoints = [GridX(ind_sel) GridY(ind_sel)];% coordinates of interpolation sites |
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[383] | 301 | ctrs=Data.Civ1_Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs |
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[363] | 302 | nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for eacn interpolation point (in case of subdomain overlap) |
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| 303 | EM = tps_eval(epoints,ctrs); |
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| 304 | Shiftx(ind_sel)=Shiftx(ind_sel)+EM*Data.Civ1_U_tps(1:nbvec_sub+3,isub); |
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| 305 | Shifty(ind_sel)=Shifty(ind_sel)+EM*Data.Civ1_V_tps(1:nbvec_sub+3,isub); |
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| 306 | if par_civ2.CheckDeformation |
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| 307 | [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs |
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| 308 | DUDX(ind_sel)=DUDX(ind_sel)+EMDX*Data.Civ1_U_tps(1:nbvec_sub+3,isub); |
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| 309 | DUDY(ind_sel)=DUDY(ind_sel)+EMDY*Data.Civ1_U_tps(1:nbvec_sub+3,isub); |
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| 310 | DVDX(ind_sel)=DVDX(ind_sel)+EMDX*Data.Civ1_V_tps(1:nbvec_sub+3,isub); |
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| 311 | DVDY(ind_sel)=DVDY(ind_sel)+EMDY*Data.Civ1_V_tps(1:nbvec_sub+3,isub); |
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| 312 | end |
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| 313 | end |
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| 314 | mask=''; |
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[387] | 315 | if par_civ2.CheckMask&&~isempty(par_civ2.Mask)&& ~strcmp(maskname,par_civ2.Mask)% mask exist, not already read in civ1 |
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| 316 | mask=imread(par_civ2.Mask); |
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[315] | 317 | end |
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[437] | 318 | par_civ2.SearchBoxSize(1)=2*isx2+1; |
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| 319 | par_civ2.SearchBoxSize(2)=2*isy2+1; |
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| 320 | par_civ2.SearchBoxShift=[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)]; |
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| 321 | % par_civ2.SearchBoxShift(2)=Shifty(nbval>=1)./nbval(nbval>=1); |
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| 322 | par_civ2.Grid=[GridX(nbval>=1)-par_civ2.SearchBoxShift(:,1)/2 GridY(nbval>=1)-par_civ2.SearchBoxShift(:,2)/2];% grid taken at the extrapolated origin of the displacement vectors |
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[363] | 323 | if par_civ2.CheckDeformation |
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[370] | 324 | par_civ2.DUDX=DUDX./nbval; |
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| 325 | par_civ2.DUDY=DUDY./nbval; |
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| 326 | par_civ2.DVDX=DVDX./nbval; |
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| 327 | par_civ2.DVDY=DVDY./nbval; |
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[363] | 328 | end |
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[315] | 329 | % caluclate velocity data (y and v in indices, reverse to y component) |
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[363] | 330 | [xtable ytable utable vtable ctable F] = civ (par_civ2); |
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[435] | 331 | % diff_squared=(utable-par_civ2.Shiftx).*(utable-par_civ2.Shiftx)+(vtable+par_civ2.Shifty).*(vtable+par_civ2.Shifty); |
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| 332 | % F(diff_squared>=4)=4; %flag vectors whose distance to the guess exceeds 2 pixels |
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[363] | 333 | list_param=(fieldnames(Param.Civ2))'; |
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[315] | 334 | list_remove={'pxcmx','pxcmy','npx','npy','gridflag','maskflag','term_a','term_b','T0'}; |
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| 335 | for ilist=1:length(list_remove) |
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| 336 | index=strcmp(list_remove{ilist},list_param); |
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| 337 | if ~isempty(find(index,1)) |
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| 338 | list_param(index)=[]; |
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| 339 | end |
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| 340 | end |
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| 341 | for ilist=1:length(list_param) |
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[363] | 342 | Civ2_param{ilist}=['Civ2_' list_param{ilist}]; |
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| 343 | eval(['Data.Civ2_' list_param{ilist} '=Param.Civ2.' list_param{ilist} ';']) |
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[315] | 344 | end |
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[363] | 345 | if isfield(Data,'Civ2_gridname') && strcmp(Data.Civ1_gridname(1:6),'noFile') |
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[315] | 346 | Data.Civ1_gridname=''; |
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| 347 | end |
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[363] | 348 | if isfield(Data,'Civ2_maskname') && strcmp(Data.Civ1_maskname(1:6),'noFile') |
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| 349 | Data.Civ2_maskname=''; |
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[315] | 350 | end |
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[363] | 351 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param {'Civ2_Time','Civ2_Dt'}]; |
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[435] | 352 | % Data.Civ2_Time=par_civ2.Time; |
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| 353 | % Data.Civ2_Dt=par_civ2.Dt; |
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[364] | 354 | nbvar=numel(Data.ListVarName); |
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| 355 | Data.ListVarName=[Data.ListVarName {'Civ2_X','Civ2_Y','Civ2_U','Civ2_V','Civ2_F','Civ2_C'}];% cell array containing the names of the fields to record |
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[399] | 356 | Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}]; |
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[364] | 357 | Data.VarAttribute{nbvar+1}.Role='coord_x'; |
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| 358 | Data.VarAttribute{nbvar+2}.Role='coord_y'; |
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| 359 | Data.VarAttribute{nbvar+3}.Role='vector_x'; |
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| 360 | Data.VarAttribute{nbvar+4}.Role='vector_y'; |
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| 361 | Data.VarAttribute{nbvar+5}.Role='warnflag'; |
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[363] | 362 | Data.Civ2_X=reshape(xtable,[],1); |
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| 363 | Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1); |
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| 364 | Data.Civ2_U=reshape(utable,[],1); |
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| 365 | Data.Civ2_V=reshape(-vtable,[],1); |
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| 366 | Data.Civ2_C=reshape(ctable,[],1); |
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| 367 | Data.Civ2_F=reshape(F,[],1); |
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[315] | 368 | Data.CivStage=Data.CivStage+1; |
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| 369 | end |
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| 370 | |
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| 371 | %% Fix2 |
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| 372 | if isfield (Param,'Fix2') |
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| 373 | ListFixParam=fieldnames(Param.Fix2); |
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| 374 | for ilist=1:length(ListFixParam) |
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| 375 | ParamName=ListFixParam{ilist}; |
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[364] | 376 | ListName=['Fix2_' ParamName]; |
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[315] | 377 | eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];']) |
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| 378 | eval(['Data.' ListName '=Param.Fix2.' ParamName ';']) |
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| 379 | end |
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| 380 | if check_civx |
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| 381 | if ~isfield(Data,'fix2') |
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| 382 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix2']; |
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| 383 | Data.fix2=1; |
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| 384 | Data.ListVarName=[Data.ListVarName {'vec2_FixFlag'}]; |
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| 385 | Data.VarDimName=[Data.VarDimName {'nb_vectors2'}]; |
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| 386 | end |
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| 387 | Data.vec_FixFlag=fix(Param.Fix2,Data.vec2_F,Data.vec2_C,Data.vec2_U,Data.vec2_V,Data.vec2_X,Data.vec2_Y); |
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| 388 | else |
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| 389 | Data.ListVarName=[Data.ListVarName {'Civ2_FF'}]; |
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[399] | 390 | Data.VarDimName=[Data.VarDimName {'nb_vec_2'}]; |
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[315] | 391 | nbvar=length(Data.ListVarName); |
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[435] | 392 | Data.VarAttribute{nbvar}.Role='errorflag'; |
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[315] | 393 | Data.Civ2_FF=fix(Param.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V); |
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[435] | 394 | Data.CivStage=Data.CivStage+1; |
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[315] | 395 | end |
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| 396 | |
---|
[435] | 397 | end |
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[315] | 398 | |
---|
| 399 | %% Patch2 |
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| 400 | if isfield (Param,'Patch2') |
---|
| 401 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch2_Rho','Patch2_Threshold','Patch2_SubDomain'}]; |
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[437] | 402 | Data.Patch2_Rho=Param.Patch2.FieldSmooth; |
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[364] | 403 | Data.Patch2_Threshold=Param.Patch2.MaxDiff; |
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| 404 | Data.Patch2_SubDomain=Param.Patch2.SubdomainSize; |
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[397] | 405 | nbvar=length(Data.ListVarName); |
---|
| 406 | Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbSites','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}]; |
---|
[399] | 407 | Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},... |
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[435] | 408 | {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}]; |
---|
| 409 | |
---|
| 410 | Data.VarAttribute{nbvar+1}.Role='vector_x'; |
---|
[397] | 411 | Data.VarAttribute{nbvar+2}.Role='vector_y'; |
---|
| 412 | Data.VarAttribute{nbvar+5}.Role='coord_tps'; |
---|
[492] | 413 | Data.VarAttribute{nbvar+6}.Role='vector_x'; |
---|
| 414 | Data.VarAttribute{nbvar+7}.Role='vector_y'; |
---|
[397] | 415 | Data.Civ2_U_smooth=zeros(size(Data.Civ2_X)); |
---|
| 416 | Data.Civ2_V_smooth=zeros(size(Data.Civ2_X)); |
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[315] | 417 | if isfield(Data,'Civ2_FF') |
---|
| 418 | ind_good=find(Data.Civ2_FF==0); |
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| 419 | else |
---|
| 420 | ind_good=1:numel(Data.Civ2_X); |
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[435] | 421 | end |
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[382] | 422 | [Data.Civ2_SubRange,Data.Civ2_NbSites,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures, Vres,tild,FFres]=... |
---|
[435] | 423 | filter_tps([Data.Civ2_X(ind_good) Data.Civ2_Y(ind_good)],Data.Civ2_U(ind_good),Data.Civ2_V(ind_good),[],Data.Patch2_SubDomain,Data.Patch2_Rho,Data.Patch2_Threshold); |
---|
[397] | 424 | Data.Civ2_U_smooth(ind_good)=Ures; |
---|
| 425 | Data.Civ2_V_smooth(ind_good)=Vres; |
---|
| 426 | Data.Civ2_FF(ind_good)=FFres; |
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[435] | 427 | Data.CivStage=Data.CivStage+1; |
---|
| 428 | end |
---|
[315] | 429 | |
---|
| 430 | %% write result in a netcdf file if requested |
---|
[319] | 431 | if exist('ncfile','var') |
---|
[315] | 432 | errormsg=struct2nc(ncfile,Data); |
---|
[494] | 433 | if isempty(errormsg) |
---|
| 434 | disp([ncfile ' written']) |
---|
| 435 | else |
---|
| 436 | disp(errormsg) |
---|
| 437 | end |
---|
[315] | 438 | end |
---|
| 439 | |
---|
| 440 | % 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/ |
---|
| 441 | %-------------------------------------------------------------------------- |
---|
| 442 | % function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi) |
---|
| 443 | % |
---|
| 444 | % OUTPUT: |
---|
| 445 | % xtable: set of x coordinates |
---|
| 446 | % ytable: set of y coordiantes |
---|
| 447 | % utable: set of u displacements (along x) |
---|
| 448 | % vtable: set of v displacements (along y) |
---|
| 449 | % ctable: max image correlation for each vector |
---|
| 450 | % typevector: set of flags, =1 for good, =0 for NaN vectors |
---|
| 451 | % |
---|
| 452 | %INPUT: |
---|
[493] | 453 | % par_civ: structure of input parameters, with fields: |
---|
| 454 | % .CorrBoxSize |
---|
| 455 | % .SearchBoxSize |
---|
| 456 | % .SearchBoxShift |
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| 457 | % .ImageHeight |
---|
| 458 | % .ImageWidth |
---|
| 459 | % .Dx, Dy |
---|
| 460 | % .Grid |
---|
| 461 | % .Mask |
---|
| 462 | % .MinIma |
---|
| 463 | % .MaxIma |
---|
| 464 | % .image1:first image (matrix) |
---|
[315] | 465 | % image2: second image (matrix) |
---|
| 466 | % ibx2,iby2: half size of the correlation box along x and y, in px (size=(2*iby2+1,2*ibx2+1) |
---|
| 467 | % isx2,isy2: half size of the search box along x and y, in px (size=(2*isy2+1,2*isx2+1) |
---|
| 468 | % shiftx, shifty: shift of the search box (in pixel index, yshift reversed) |
---|
| 469 | % step: mesh of the measurement points (in px) |
---|
| 470 | % subpixfinder=1 or 2 controls the curve fitting of the image correlation |
---|
| 471 | % mask: =[] for no mask |
---|
| 472 | % roi: 4 element vector defining a region of interest: x position, y position, width, height, (in image indices), for the whole image, roi=[]; |
---|
| 473 | function [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ) |
---|
| 474 | %this funtion performs the DCC PIV analysis. Recent window-deformation |
---|
| 475 | %methods perform better and will maybe be implemented in the future. |
---|
| 476 | |
---|
| 477 | %% prepare grid |
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[437] | 478 | ibx2=ceil(par_civ.CorrBoxSize(1)/2); |
---|
| 479 | iby2=ceil(par_civ.CorrBoxSize(2)/2); |
---|
| 480 | isx2=ceil(par_civ.SearchBoxSize(1)/2); |
---|
| 481 | isy2=ceil(par_civ.SearchBoxSize(2)/2); |
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| 482 | shiftx=round(par_civ.SearchBoxShift(:,1)); |
---|
| 483 | shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases |
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[315] | 484 | if isfield(par_civ,'Grid') |
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[364] | 485 | if ischar(par_civ.Grid)%read the drid file if the input is a file name |
---|
[315] | 486 | par_civ.Grid=dlmread(par_civ.Grid); |
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| 487 | par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file) |
---|
| 488 | end |
---|
| 489 | else% automatic measurement grid |
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[437] | 490 | % ibx2=ceil(par_civ.Bx/2); |
---|
| 491 | % iby2=ceil(par_civ.By/2); |
---|
| 492 | % isx2=ceil(par_civ.Searchx/2); |
---|
| 493 | % isy2=ceil(par_civ.Searchy/2); |
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[315] | 494 | miniy=max(1+isy2+shifty,1+iby2); |
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| 495 | minix=max(1+isx2-shiftx,1+ibx2); |
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| 496 | maxiy=min(par_civ.ImageHeight-isy2+shifty,par_civ.ImageHeight-iby2); |
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| 497 | maxix=min(par_civ.ImageWidth-isx2-shiftx,par_civ.ImageWidth-ibx2); |
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| 498 | [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy); |
---|
| 499 | par_civ.Grid(:,1)=reshape(GridX,[],1); |
---|
| 500 | par_civ.Grid(:,2)=reshape(GridY,[],1); |
---|
| 501 | end |
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[363] | 502 | nbvec=size(par_civ.Grid,1); |
---|
| 503 | if numel(shiftx)==1 |
---|
[365] | 504 | shiftx=shiftx*ones(nbvec,1); |
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| 505 | shifty=shifty*ones(nbvec,1); |
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[363] | 506 | end |
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[315] | 507 | %% Default output |
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| 508 | xtable=par_civ.Grid(:,1); |
---|
| 509 | ytable=par_civ.Grid(:,2); |
---|
| 510 | utable=zeros(nbvec,1); |
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| 511 | vtable=zeros(nbvec,1); |
---|
| 512 | ctable=zeros(nbvec,1); |
---|
| 513 | F=zeros(nbvec,1); |
---|
| 514 | result_conv=[]; |
---|
| 515 | errormsg=''; |
---|
| 516 | |
---|
| 517 | %% prepare mask |
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| 518 | if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) |
---|
| 519 | if strcmp(par_civ.Mask,'all') |
---|
| 520 | return % get the grid only, no civ calculation |
---|
| 521 | elseif ischar(par_civ.Mask) |
---|
| 522 | par_civ.Mask=imread(par_civ.Mask); |
---|
| 523 | end |
---|
| 524 | end |
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| 525 | check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold |
---|
| 526 | check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma); |
---|
| 527 | |
---|
[364] | 528 | % %% prepare images |
---|
| 529 | % if isfield(par_civ,'reverse_pair') |
---|
| 530 | % if par_civ.reverse_pair |
---|
| 531 | % if ischar(par_civ.ImageB) |
---|
| 532 | % temp=par_civ.ImageA; |
---|
| 533 | % par_civ.ImageA=imread(par_civ.ImageB); |
---|
| 534 | % end |
---|
| 535 | % if ischar(temp) |
---|
| 536 | % par_civ.ImageB=imread(temp); |
---|
| 537 | % end |
---|
| 538 | % end |
---|
| 539 | % else |
---|
| 540 | % if ischar(par_civ.ImageA) |
---|
| 541 | % par_civ.ImageA=imread(par_civ.ImageA); |
---|
| 542 | % end |
---|
| 543 | % if ischar(par_civ.ImageB) |
---|
| 544 | % par_civ.ImageB=imread(par_civ.ImageB); |
---|
| 545 | % end |
---|
| 546 | % end |
---|
[388] | 547 | par_civ.ImageA=sum(double(par_civ.ImageA),3);%sum over rgb component for color images |
---|
| 548 | par_civ.ImageB=sum(double(par_civ.ImageB),3); |
---|
[315] | 549 | [npy_ima npx_ima]=size(par_civ.ImageA); |
---|
| 550 | if ~isequal(size(par_civ.ImageB),[npy_ima npx_ima]) |
---|
| 551 | errormsg='image pair with unequal size'; |
---|
| 552 | return |
---|
| 553 | end |
---|
| 554 | |
---|
| 555 | %% Apply mask |
---|
[411] | 556 | % Convention for mask IDEAS TO IMPLEMENT ? |
---|
[315] | 557 | % mask >200 : velocity calculated |
---|
| 558 | % 200 >=mask>150;velocity not calculated, interpolation allowed (bad spots) |
---|
| 559 | % 150>=mask >100: velocity not calculated, nor interpolated |
---|
[411] | 560 | % 100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries) |
---|
[315] | 561 | % 20>=mask: velocity=0 |
---|
| 562 | checkmask=0; |
---|
| 563 | if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) |
---|
| 564 | checkmask=1; |
---|
| 565 | if ~isequal(size(par_civ.Mask),[npy_ima npx_ima]) |
---|
| 566 | errormsg='mask must be an image with the same size as the images'; |
---|
| 567 | return |
---|
| 568 | end |
---|
| 569 | % check_noflux=(par_civ.Mask<100) ;%TODO: to implement |
---|
[411] | 570 | check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 ); |
---|
[315] | 571 | par_civ.ImageA(check_undefined)=min(min(par_civ.ImageA));% put image A to zero (i.e. the min image value) in the undefined area |
---|
| 572 | par_civ.ImageB(check_undefined)=min(min(par_civ.ImageB));% put image B to zero (i.e. the min image value) in the undefined area |
---|
| 573 | end |
---|
| 574 | |
---|
| 575 | %% compute image correlations: MAINLOOP on velocity vectors |
---|
[317] | 576 | corrmax=0; |
---|
| 577 | sum_square=1;% default |
---|
[368] | 578 | mesh=1;% default |
---|
| 579 | CheckDecimal=isfield(par_civ,'CheckDecimal')&& par_civ.CheckDecimal==1; |
---|
| 580 | if CheckDecimal |
---|
| 581 | mesh=0.2;%mesh in pixels for subpixel image interpolation |
---|
[370] | 582 | CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1; |
---|
[368] | 583 | end |
---|
[315] | 584 | % vector=[0 0];%default |
---|
| 585 | for ivec=1:nbvec |
---|
[370] | 586 | iref=round(par_civ.Grid(ivec,1)+0.5);% xindex on the image A for the middle of the correlation box |
---|
| 587 | jref=round(par_civ.ImageHeight-par_civ.Grid(ivec,2)+0.5);% yindex on the image B for the middle of the correlation box |
---|
[315] | 588 | if ~(checkmask && par_civ.Mask(jref,iref)<=20) %velocity not set to zero by the black mask |
---|
[363] | 589 | if jref-iby2<1 || jref+iby2>par_civ.ImageHeight|| iref-ibx2<1 || iref+ibx2>par_civ.ImageWidth||... |
---|
| 590 | jref+shifty(ivec)-isy2<1||jref+shifty(ivec)+isy2>par_civ.ImageHeight|| iref+shiftx(ivec)-isx2<1 || iref+shiftx(ivec)+isx2>par_civ.ImageWidth % we are outside the image |
---|
[315] | 591 | F(ivec)=3; |
---|
| 592 | else |
---|
| 593 | image1_crop=par_civ.ImageA(jref-iby2:jref+iby2,iref-ibx2:iref+ibx2);%extract a subimage (correlation box) from image A |
---|
[363] | 594 | image2_crop=par_civ.ImageB(jref+shifty(ivec)-isy2:jref+shifty(ivec)+isy2,iref+shiftx(ivec)-isx2:iref+shiftx(ivec)+isx2);%extract a larger subimage (search box) from image B |
---|
[315] | 595 | image1_mean=mean(mean(image1_crop)); |
---|
| 596 | image2_mean=mean(mean(image2_crop)); |
---|
| 597 | %threshold on image minimum |
---|
| 598 | if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma) |
---|
| 599 | F(ivec)=3; |
---|
| 600 | end |
---|
[319] | 601 | %threshold on image maximum |
---|
| 602 | if check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma) |
---|
| 603 | F(ivec)=3; |
---|
| 604 | end |
---|
[366] | 605 | end |
---|
[315] | 606 | if F(ivec)~=3 |
---|
| 607 | image1_crop=image1_crop-image1_mean;%substract the mean |
---|
| 608 | image2_crop=image2_crop-image2_mean; |
---|
[370] | 609 | if CheckDecimal |
---|
[368] | 610 | xi=(1:mesh:size(image1_crop,2)); |
---|
| 611 | yi=(1:mesh:size(image1_crop,1))'; |
---|
[370] | 612 | if CheckDeformation |
---|
| 613 | [XI,YI]=meshgrid(xi-ceil(size(image1_crop,2)/2),yi-ceil(size(image1_crop,1)/2)); |
---|
| 614 | XIant=XI-par_civ.DUDX(ivec)*XI-par_civ.DUDY(ivec)*YI+ceil(size(image1_crop,2)/2); |
---|
| 615 | YIant=YI-par_civ.DVDX(ivec)*XI-par_civ.DVDY(ivec)*YI+ceil(size(image1_crop,1)/2); |
---|
| 616 | image1_crop=interp2(image1_crop,XIant,YIant); |
---|
| 617 | else |
---|
| 618 | image1_crop=interp2(image1_crop,xi,yi); |
---|
| 619 | end |
---|
[369] | 620 | xi=(1:mesh:size(image2_crop,2)); |
---|
| 621 | yi=(1:mesh:size(image2_crop,1))'; |
---|
[368] | 622 | image2_crop=interp2(image2_crop,xi,yi); |
---|
| 623 | end |
---|
[315] | 624 | sum_square=sum(sum(image1_crop.*image1_crop)); |
---|
| 625 | %reference: Oliver Pust, PIV: Direct Cross-Correlation |
---|
| 626 | result_conv= conv2(image2_crop,flipdim(flipdim(image1_crop,2),1),'valid'); |
---|
| 627 | corrmax= max(max(result_conv)); |
---|
| 628 | result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255 |
---|
| 629 | %Find the correlation max, at 255 |
---|
| 630 | [y,x] = find(result_conv==255,1); |
---|
| 631 | if ~isempty(y) && ~isempty(x) |
---|
| 632 | try |
---|
[437] | 633 | if par_civ.CorrSmooth==1 |
---|
[315] | 634 | [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y); |
---|
[437] | 635 | elseif par_civ.CorrSmooth==2 |
---|
[315] | 636 | [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y); |
---|
| 637 | end |
---|
[368] | 638 | utable(ivec)=vector(1)*mesh+shiftx(ivec); |
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| 639 | vtable(ivec)=vector(2)*mesh+shifty(ivec); |
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[370] | 640 | xtable(ivec)=iref+utable(ivec)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2) |
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| 641 | ytable(ivec)=jref+vtable(ivec)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge) |
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[315] | 642 | iref=round(xtable(ivec));% image index for the middle of the vector |
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| 643 | jref=round(ytable(ivec)); |
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| 644 | if checkmask && par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100 |
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| 645 | utable(ivec)=0; |
---|
| 646 | vtable(ivec)=0; |
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| 647 | F(ivec)=3; |
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| 648 | end |
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| 649 | ctable(ivec)=corrmax/sum_square;% correlation value |
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| 650 | catch ME |
---|
| 651 | F(ivec)=3; |
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| 652 | end |
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| 653 | else |
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| 654 | F(ivec)=3; |
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| 655 | end |
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| 656 | end |
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| 657 | end |
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| 658 | |
---|
| 659 | %Create the vector matrix x, y, u, v |
---|
| 660 | end |
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| 661 | result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output |
---|
| 662 | |
---|
| 663 | %------------------------------------------------------------------------ |
---|
| 664 | % --- Find the maximum of the correlation function after interpolation |
---|
| 665 | function [vector,F] = SUBPIXGAUSS (result_conv,x,y) |
---|
| 666 | %------------------------------------------------------------------------ |
---|
| 667 | vector=[0 0]; %default |
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| 668 | F=0; |
---|
| 669 | [npy,npx]=size(result_conv); |
---|
| 670 | |
---|
| 671 | % if (x <= (size(result_conv,1)-1)) && (y <= (size(result_conv,1)-1)) && (x >= 1) && (y >= 1) |
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[337] | 672 | %the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ï¿œ Israel Institute of Technology |
---|
[315] | 673 | %http://urapiv.wordpress.com |
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| 674 | peaky = y; |
---|
| 675 | if y <= npy-1 && y >= 1 |
---|
| 676 | f0 = log(result_conv(y,x)); |
---|
| 677 | f1 = real(log(result_conv(y-1,x))); |
---|
| 678 | f2 = real(log(result_conv(y+1,x))); |
---|
| 679 | peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2); |
---|
| 680 | else |
---|
| 681 | F=-2; % warning flag for vector truncated by the limited search box |
---|
| 682 | end |
---|
| 683 | peakx=x; |
---|
| 684 | if x <= npx-1 && x >= 1 |
---|
| 685 | f0 = log(result_conv(y,x)); |
---|
| 686 | f1 = real(log(result_conv(y,x-1))); |
---|
| 687 | f2 = real(log(result_conv(y,x+1))); |
---|
| 688 | peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2); |
---|
| 689 | else |
---|
| 690 | F=-2; % warning flag for vector truncated by the limited search box |
---|
| 691 | end |
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| 692 | vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; |
---|
| 693 | |
---|
| 694 | %------------------------------------------------------------------------ |
---|
| 695 | % --- Find the maximum of the correlation function after interpolation |
---|
| 696 | function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y) |
---|
| 697 | %------------------------------------------------------------------------ |
---|
| 698 | vector=[0 0]; %default |
---|
| 699 | F=-2; |
---|
| 700 | peaky=y; |
---|
| 701 | peakx=x; |
---|
| 702 | [npy,npx]=size(result_conv); |
---|
| 703 | if (x <= npx-1) && (y <= npy-1) && (x >= 1) && (y >= 1) |
---|
| 704 | F=0; |
---|
| 705 | for i=-1:1 |
---|
| 706 | for j=-1:1 |
---|
| 707 | %following 15 lines based on |
---|
[337] | 708 | %H. Nobach ï¿œ M. Honkanen (2005) |
---|
[315] | 709 | %Two-dimensional Gaussian regression for sub-pixel displacement |
---|
| 710 | %estimation in particle image velocimetry or particle position |
---|
| 711 | %estimation in particle tracking velocimetry |
---|
[337] | 712 | %Experiments in Fluids (2005) 38: 511ï¿œ515 |
---|
[315] | 713 | c10(j+2,i+2)=i*log(result_conv(y+j, x+i)); |
---|
| 714 | c01(j+2,i+2)=j*log(result_conv(y+j, x+i)); |
---|
| 715 | c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i)); |
---|
| 716 | c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i)); |
---|
| 717 | c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i)); |
---|
| 718 | end |
---|
| 719 | end |
---|
| 720 | c10=(1/6)*sum(sum(c10)); |
---|
| 721 | c01=(1/6)*sum(sum(c01)); |
---|
| 722 | c11=(1/4)*sum(sum(c11)); |
---|
| 723 | c20=(1/6)*sum(sum(c20)); |
---|
| 724 | c02=(1/6)*sum(sum(c02)); |
---|
| 725 | deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2); |
---|
| 726 | deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2); |
---|
| 727 | if abs(deltax)<1 |
---|
| 728 | peakx=x+deltax; |
---|
| 729 | end |
---|
| 730 | if abs(deltay)<1 |
---|
| 731 | peaky=y+deltay; |
---|
| 732 | end |
---|
| 733 | end |
---|
| 734 | vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; |
---|
| 735 | |
---|
| 736 | %'RUN_FIX': function for fixing velocity fields: |
---|
| 737 | %----------------------------------------------- |
---|
| 738 | % RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref) |
---|
| 739 | % |
---|
| 740 | %filename: name of the netcdf file (used as input and output) |
---|
| 741 | %field: structure specifying the names of the fields to fix (depending on civ1 or civ2) |
---|
| 742 | %.vel_type='civ1' or 'civ2'; |
---|
| 743 | %.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1); |
---|
| 744 | %.fixflag=name of fix flag variable ('vec_FixFlag' for civ1) |
---|
| 745 | %flagindex: flag specifying which values of vec_f are removed: |
---|
| 746 | % if flagindex(1)=1: vec_f=-2 vectors are removed |
---|
| 747 | % if flagindex(2)=1: vec_f=3 vectors are removed |
---|
| 748 | % if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2) |
---|
| 749 | %iter=1 for civ1 fields and iter=2 for civ2 fields |
---|
| 750 | %thresh_vecC: threshold in the image correlation vec_C |
---|
| 751 | %flag_mask: =1 mask used to remove vectors (0 else) |
---|
| 752 | %maskname: name of the mask image file for fix |
---|
| 753 | %thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists |
---|
| 754 | %inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold |
---|
| 755 | %fileref: .nc file name for a reference velocity (='': refrence 0 used) |
---|
| 756 | %fieldref: 'civ1','filter1'...feld used in fileref |
---|
| 757 | |
---|
| 758 | function FF=fix(Param,F,C,U,V,X,Y) |
---|
| 759 | FF=zeros(size(F));%default |
---|
| 760 | |
---|
| 761 | %criterium on warn flags |
---|
| 762 | FlagName={'CheckFmin2','CheckF2','CheckF3','CheckF4'}; |
---|
| 763 | FlagVal=[-2 2 3 4]; |
---|
| 764 | for iflag=1:numel(FlagName) |
---|
| 765 | if isfield(Param,FlagName{iflag}) && Param.(FlagName{iflag}) |
---|
| 766 | FF=(FF==1| F==FlagVal(iflag)); |
---|
| 767 | end |
---|
| 768 | end |
---|
| 769 | %criterium on correlation values |
---|
| 770 | if isfield (Param,'MinCorr') |
---|
| 771 | FF=FF==1 | C<Param.MinCorr; |
---|
| 772 | end |
---|
[316] | 773 | if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)) |
---|
[315] | 774 | Umod= U.*U+V.*V; |
---|
[316] | 775 | if isfield (Param,'MinVel')&&~isempty(Param.MinVel) |
---|
[315] | 776 | FF=FF==1 | Umod<(Param.MinVel*Param.MinVel); |
---|
| 777 | end |
---|
| 778 | if isfield (Param,'MaxVel')&&~isempty(Param.MaxVel) |
---|
| 779 | FF=FF==1 | Umod>(Param.MaxVel*Param.MaxVel); |
---|
| 780 | end |
---|
| 781 | end |
---|
| 782 | |
---|
| 783 | |
---|
| 784 | |
---|
[326] | 785 | |
---|
[315] | 786 | |
---|
| 787 | |
---|
| 788 | |
---|