[575] | 1 | %'civ_matlab': main PIV function, calleed by the GUI civ |
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[315] | 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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[596] | 7 | % function [Data,errormsg,result_conv]= civ_matlab(Param,ncfile) |
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[315] | 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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[809] | 23 | |
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| 24 | %======================================================================= |
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| 25 | % Copyright 2008-2014, LEGI UMR 5519 / CNRS UJF G-INP, Grenoble, France |
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| 26 | % http://www.legi.grenoble-inp.fr |
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| 27 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr |
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[315] | 28 | % |
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[809] | 29 | % This file is part of the toolbox UVMAT. |
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| 30 | % |
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[315] | 31 | % UVMAT is free software; you can redistribute it and/or modify |
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[809] | 32 | % it under the terms of the GNU General Public License as published |
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| 33 | % by the Free Software Foundation; either version 2 of the license, |
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| 34 | % or (at your option) any later version. |
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| 35 | % |
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[315] | 36 | % UVMAT is distributed in the hope that it will be useful, |
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| 37 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 38 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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[809] | 39 | % GNU General Public License (see LICENSE.txt) for more details. |
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| 40 | %======================================================================= |
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[315] | 41 | |
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| 42 | function [Data,errormsg,result_conv]= civ_matlab(Param,ncfile) |
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| 43 | errormsg=''; |
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| 44 | Data.ListGlobalAttribute={'Conventions','Program','CivStage'}; |
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| 45 | Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes |
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| 46 | Data.Program='civ_matlab'; |
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| 47 | Data.CivStage=0;%default |
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| 48 | ListVarCiv1={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F'}; %variables to read |
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| 49 | ListVarFix1={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F','Civ1_FF'}; |
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| 50 | mask=''; |
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| 51 | maskname='';%default |
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| 52 | check_civx=0;%default |
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| 53 | check_civ1=0;%default |
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| 54 | check_patch1=0;%default |
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[576] | 55 | |
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[435] | 56 | % case of input Param set by an xml file (batch mode) |
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[319] | 57 | if ischar(Param) |
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[387] | 58 | Param=xml2struct(Param); %if Param is the name of an xml file, read this file as a Matlab structure |
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[319] | 59 | end |
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| 60 | |
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[315] | 61 | %% Civ1 |
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| 62 | if isfield (Param,'Civ1') |
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[364] | 63 | par_civ1=Param.Civ1; |
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[772] | 64 | if isfield(Param.Civ1,'ImageA') && ischar(Param.Civ1.ImageA)% the input is a char string, read the corresponding image name (else Param.Civ1.ImageA is already an image) |
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| 65 | Param.Civ1.ImageA=regexprep(Param.Civ1.ImageA,'''','\'); |
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| 66 | [par_civ1.ImageA,VideoObject] = read_image(Param.Civ1.ImageA,par_civ1.FileTypeA,[],par_civ1.FrameIndexA); |
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| 67 | end |
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| 68 | if isfield(Param.Civ1,'ImageB')&& ischar(Param.Civ1.ImageB)% the input is a char string, read the corresponding image name (else Param.Civ1.ImageB is already an image) |
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| 69 | Param.Civ1.ImageB=regexprep(Param.Civ1.ImageB,'''','\'); |
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| 70 | if strcmp(Param.Civ1.ImageA,Param.Civ1.ImageB)% use the same movie object |
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| 71 | [par_civ1.ImageB,VideoObject] = read_image(Param.Civ1.ImageB,par_civ1.FileTypeB,VideoObject,par_civ1.FrameIndexB); |
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| 72 | else |
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[494] | 73 | [par_civ1.ImageB,VideoObject] = read_image(Param.Civ1.ImageB,par_civ1.FileTypeB,par_civ1.ImageB,par_civ1.FrameIndexB); |
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[364] | 74 | end |
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| 75 | end |
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[315] | 76 | list_param=(fieldnames(Param.Civ1))'; |
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| 77 | Civ1_param=list_param;%default |
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[591] | 78 | |
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[406] | 79 | %set the values of all the global attributes in list_param |
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[315] | 80 | for ilist=1:length(list_param) |
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| 81 | Civ1_param{ilist}=['Civ1_' list_param{ilist}]; |
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| 82 | Data.(['Civ1_' list_param{ilist}])=Param.Civ1.(list_param{ilist}); |
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| 83 | end |
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[604] | 84 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ1_param]; |
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[591] | 85 | Data.CivStage=1; |
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| 86 | |
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| 87 | % set the list of variables |
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[364] | 88 | 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] | 89 | 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] | 90 | Data.VarAttribute{1}.Role='coord_x'; |
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| 91 | Data.VarAttribute{2}.Role='coord_y'; |
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| 92 | Data.VarAttribute{3}.Role='vector_x'; |
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| 93 | Data.VarAttribute{4}.Role='vector_y'; |
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| 94 | Data.VarAttribute{5}.Role='warnflag'; |
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[591] | 95 | |
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[604] | 96 | if isfield(Param,'ListCompareMode') && strcmp(Param.ListCompareMode, 'PIV volume') |
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[591] | 97 | Data.ListVarName=[Data.ListVarName 'Civ1_Z']; |
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| 98 | Data.Civ1_X=[];Data.Civ1_Y=[];Data.Civ1_Z=[]; |
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| 99 | Data.Civ1_U=[];Data.Civ1_V=[];Data.Civ1_C=[];Data.Civ1_F=[]; |
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| 100 | for ivol=1:NbSlice |
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| 101 | % caluclate velocity data (y and v in indices, reverse to y component) |
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| 102 | [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ1); |
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| 103 | if ~isempty(errormsg) |
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| 104 | return |
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| 105 | end |
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| 106 | Data.Civ1_X=[Data.Civ1_X reshape(xtable,[],1)]; |
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| 107 | Data.Civ1_Y=[Data.Civ1_Y reshape(Param.Civ1.ImageHeight-ytable+1,[],1)]; |
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| 108 | Data.Civ1_Z=[Data.Civ1_Z ivol*ones(numel(xtable),1)];% z=image index in image coordinates |
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| 109 | Data.Civ1_U=[Data.Civ1_U reshape(utable,[],1)]; |
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| 110 | Data.Civ1_V=[Data.Civ1_V reshape(-vtable,[],1)]; |
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| 111 | Data.Civ1_C=[Data.Civ1_C reshape(ctable,[],1)]; |
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| 112 | Data.Civ1_F=[Data.Civ1_C reshape(F,[],1)]; |
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| 113 | end |
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| 114 | else %usual PIV |
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| 115 | % caluclate velocity data (y and v in indices, reverse to y component) |
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| 116 | [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ1); |
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| 117 | if ~isempty(errormsg) |
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| 118 | return |
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| 119 | end |
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| 120 | Data.Civ1_X=reshape(xtable,[],1); |
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| 121 | Data.Civ1_Y=reshape(Param.Civ1.ImageHeight-ytable+1,[],1); |
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| 122 | Data.Civ1_U=reshape(utable,[],1); |
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| 123 | Data.Civ1_V=reshape(-vtable,[],1); |
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| 124 | Data.Civ1_C=reshape(ctable,[],1); |
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| 125 | Data.Civ1_F=reshape(F,[],1); |
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| 126 | end |
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[315] | 127 | else |
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[319] | 128 | if exist('ncfile','var') |
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| 129 | CivFile=ncfile; |
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| 130 | elseif isfield(Param.Patch1,'CivFile') |
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| 131 | CivFile=Param.Patch1.CivFile; |
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| 132 | end |
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[772] | 133 | [Data,tild,tild,erromsg]=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format |
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| 134 | if ~isempty(errormsg) |
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[317] | 135 | return |
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| 136 | end |
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[315] | 137 | if ~isempty(Data.absolut_time_T0')%read civx file |
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| 138 | check_civx=1;% test for old civx data format |
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[319] | 139 | [Data,vardetect,ichoice]=nc2struct(CivFile);%read the variables in the netcdf file |
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[315] | 140 | else |
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[363] | 141 | Data=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file |
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[315] | 142 | end |
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| 143 | end |
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| 144 | |
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| 145 | %% Fix1 |
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| 146 | if isfield (Param,'Fix1') |
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| 147 | ListFixParam=fieldnames(Param.Fix1); |
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| 148 | for ilist=1:length(ListFixParam) |
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| 149 | ParamName=ListFixParam{ilist}; |
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| 150 | ListName=['Fix1_' ParamName]; |
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| 151 | eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];']) |
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| 152 | eval(['Data.' ListName '=Param.Fix1.' ParamName ';']) |
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| 153 | end |
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| 154 | if check_civx |
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| 155 | if ~isfield(Data,'fix') |
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| 156 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix']; |
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| 157 | Data.fix=1; |
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| 158 | Data.ListVarName=[Data.ListVarName {'vec_FixFlag'}]; |
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| 159 | Data.VarDimName=[Data.VarDimName {'nb_vectors'}]; |
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| 160 | end |
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| 161 | 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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| 162 | else |
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| 163 | Data.ListVarName=[Data.ListVarName {'Civ1_FF'}]; |
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[399] | 164 | Data.VarDimName=[Data.VarDimName {'nb_vec_1'}]; |
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[315] | 165 | nbvar=length(Data.ListVarName); |
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[435] | 166 | Data.VarAttribute{nbvar}.Role='errorflag'; |
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[315] | 167 | Data.Civ1_FF=fix(Param.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V); |
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[435] | 168 | Data.CivStage=2; |
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[315] | 169 | end |
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[435] | 170 | end |
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[315] | 171 | %% Patch1 |
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| 172 | if isfield (Param,'Patch1') |
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[326] | 173 | if check_civx |
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| 174 | errormsg='Civ Matlab input needed for patch'; |
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| 175 | return |
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| 176 | end |
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[389] | 177 | |
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[315] | 178 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch1_Rho','Patch1_Threshold','Patch1_SubDomain'}]; |
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[581] | 179 | Data.Patch1_FieldSmooth=Param.Patch1.FieldSmooth; |
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| 180 | Data.Patch1_MaxDiff=Param.Patch1.MaxDiff; |
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| 181 | Data.Patch1_SubDomainSize=Param.Patch1.SubDomainSize; |
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[397] | 182 | nbvar=length(Data.ListVarName); |
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[651] | 183 | Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbCentre','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}]; |
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| 184 | Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bound','nb_subdomain_1'},'nb_subdomain_1',... |
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[435] | 185 | {'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] | 186 | Data.VarAttribute{nbvar+1}.Role='vector_x'; |
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| 187 | Data.VarAttribute{nbvar+2}.Role='vector_y'; |
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| 188 | Data.VarAttribute{nbvar+5}.Role='coord_tps'; |
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[492] | 189 | Data.VarAttribute{nbvar+6}.Role='vector_x'; |
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| 190 | Data.VarAttribute{nbvar+7}.Role='vector_y'; |
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[389] | 191 | Data.Civ1_U_smooth=zeros(size(Data.Civ1_X)); |
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| 192 | Data.Civ1_V_smooth=zeros(size(Data.Civ1_X)); |
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[315] | 193 | if isfield(Data,'Civ1_FF') |
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| 194 | ind_good=find(Data.Civ1_FF==0); |
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[435] | 195 | else |
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[315] | 196 | ind_good=1:numel(Data.Civ1_X); |
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| 197 | end |
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[651] | 198 | [Data.Civ1_SubRange,Data.Civ1_NbCentre,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=... |
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[581] | 199 | filter_tps([Data.Civ1_X(ind_good) Data.Civ1_Y(ind_good)],Data.Civ1_U(ind_good),Data.Civ1_V(ind_good),[],Data.Patch1_SubDomainSize,Data.Patch1_FieldSmooth,Data.Patch1_MaxDiff); |
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[435] | 200 | Data.Civ1_U_smooth(ind_good)=Ures; |
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| 201 | Data.Civ1_V_smooth(ind_good)=Vres; |
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| 202 | Data.Civ1_FF(ind_good)=FFres; |
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| 203 | Data.CivStage=3; |
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| 204 | end |
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[315] | 205 | |
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| 206 | %% Civ2 |
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| 207 | if isfield (Param,'Civ2') |
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| 208 | par_civ2=Param.Civ2; |
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[494] | 209 | par_civ2.ImageA=[]; |
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| 210 | par_civ2.ImageB=[]; |
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| 211 | if isfield(Param.Civ2,'ImageA') && isfield(Param.Civ2,'ImageB') |
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| 212 | Param.Civ2.ImageA=regexprep(Param.Civ2.ImageA,'''','\'); |
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| 213 | Param.Civ2.ImageB=regexprep(Param.Civ2.ImageB,'''','\'); |
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| 214 | if isfield (Param,'Civ1') |
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| 215 | Param.Civ2.ImageA=regexprep(Param.Civ2.ImageA,'''','\'); |
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| 216 | if strcmp(Param.Civ1.ImageA,Param.Civ2.ImageA) |
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| 217 | if isequal(Param.Civ1.FrameIndexA,Param.Civ2.FrameIndexA) |
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| 218 | par_civ2.ImageA=par_civ1.ImageA; |
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| 219 | else % read another frame of the same movie object |
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| 220 | par_civ2.ImageA = read_image(Param.Civ2.ImageA,Param.Civ2.FileTypeA,VideoObject,Param.Civ2.FrameIndexA); |
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| 221 | end |
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[435] | 222 | end |
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[494] | 223 | Param.Civ2.ImageB=regexprep(Param.Civ2.ImageB,'''','\'); |
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| 224 | if strcmp(Param.Civ1.ImageB,Param.Civ2.ImageB) |
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| 225 | if isequal(Param.Civ1.FrameIndexB,Param.Civ2.FrameIndexB) |
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| 226 | par_civ2.ImageB=par_civ1.ImageB; |
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| 227 | else % read another frame of the same movie object |
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| 228 | par_civ2.ImageB = read_image(Param.Civ2.ImageB,Param.Civ2.FileTypeB,VideoObject,Param.Civ2.FrameIndexB); |
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| 229 | end |
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[435] | 230 | end |
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[494] | 231 | end |
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| 232 | if isempty(par_civ2.ImageA) && isfield(Param.Civ2,'ImageA') |
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| 233 | [par_civ2.ImageA,VideoObject] = read_image(Param.Civ2.ImageA,Param.Civ2.FileTypeA,[],Param.Civ2.FrameIndexA); |
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| 234 | end |
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| 235 | if isempty(par_civ2.ImageB)&& isfield(Param.Civ2,'ImageB') |
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| 236 | if strcmp(Param.Civ2.ImageA,Param.Civ2.ImageB) |
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| 237 | par_civ2.ImageB = read_image(Param.Civ2.ImageB,Param.Civ2.FileTypeB,VideoObject,Param.Civ2.FrameIndexB); |
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| 238 | else |
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| 239 | par_civ2.ImageB = read_image(Param.Civ2.ImageB,Param.Civ2.FileTypeB,[],Param.Civ2.FrameIndexB); |
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| 240 | end |
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| 241 | end |
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[315] | 242 | end |
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[576] | 243 | % ibx2=ceil(par_civ2.CorrBoxSize(1)/2); |
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| 244 | % iby2=ceil(par_civ2.CorrBoxSize(2)/2); |
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| 245 | % isx2=ibx2+4;% search ara +-4 pixels around the guess |
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| 246 | % isy2=iby2+4; |
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| 247 | % % shift from par_civ2.filename_nc1 |
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| 248 | % % shiftx=velocity interpolated at position |
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| 249 | % miniy=max(1+isy2,1+iby2); |
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| 250 | % minix=max(1+isx2,1+ibx2); |
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| 251 | % maxiy=min(size(par_civ2.ImageA,1)-isy2,size(par_civ2.ImageA,1)-iby2); |
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| 252 | % maxix=min(size(par_civ2.ImageA,2)-isx2,size(par_civ2.ImageA,2)-ibx2); |
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| 253 | % [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy); |
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| 254 | % GridX=reshape(GridX,[],1); |
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| 255 | % GridY=reshape(GridY,[],1); |
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| 256 | if isfield(par_civ2,'Grid')% grid points set as input file |
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| 257 | if ischar(par_civ2.Grid)%read the grid file if the input is a file name |
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| 258 | par_civ2.Grid=dlmread(par_civ2.Grid); |
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| 259 | par_civ2.Grid(1,:)=[];%the first line must be removed (heading in the grid file) |
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| 260 | end |
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| 261 | else% automatic grid |
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| 262 | minix=floor(par_civ2.Dx/2)-0.5; |
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| 263 | maxix=minix+par_civ2.Dx*floor((par_civ2.ImageWidth-1)/par_civ2.Dx); |
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| 264 | miniy=floor(par_civ2.Dy/2)-0.5; |
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| 265 | maxiy=minix+par_civ2.Dy*floor((par_civ2.ImageHeight-1)/par_civ2.Dy); |
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| 266 | [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy); |
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| 267 | par_civ2.Grid(:,1)=reshape(GridX,[],1); |
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| 268 | par_civ2.Grid(:,2)=reshape(GridY,[],1); |
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| 269 | end |
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[578] | 270 | Shiftx=zeros(size(par_civ2.Grid,1),1);% shift expected from civ1 data |
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| 271 | Shifty=zeros(size(par_civ2.Grid,1),1); |
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| 272 | nbval=zeros(size(par_civ2.Grid,1),1); |
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[363] | 273 | if par_civ2.CheckDeformation |
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[578] | 274 | DUDX=zeros(size(par_civ2.Grid,1),1); |
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| 275 | DUDY=zeros(size(par_civ2.Grid,1),1); |
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| 276 | DVDX=zeros(size(par_civ2.Grid,1),1); |
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| 277 | DVDY=zeros(size(par_civ2.Grid,1),1); |
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[363] | 278 | end |
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[383] | 279 | NbSubDomain=size(Data.Civ1_SubRange,3); |
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[363] | 280 | % get the guess from patch1 |
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| 281 | for isub=1:NbSubDomain |
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[651] | 282 | nbvec_sub=Data.Civ1_NbCentre(isub); |
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[383] | 283 | 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] | 284 | epoints = [GridX(ind_sel) GridY(ind_sel)];% coordinates of interpolation sites |
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[383] | 285 | ctrs=Data.Civ1_Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs |
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[363] | 286 | 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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| 287 | EM = tps_eval(epoints,ctrs); |
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| 288 | Shiftx(ind_sel)=Shiftx(ind_sel)+EM*Data.Civ1_U_tps(1:nbvec_sub+3,isub); |
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| 289 | Shifty(ind_sel)=Shifty(ind_sel)+EM*Data.Civ1_V_tps(1:nbvec_sub+3,isub); |
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| 290 | if par_civ2.CheckDeformation |
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| 291 | [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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| 292 | DUDX(ind_sel)=DUDX(ind_sel)+EMDX*Data.Civ1_U_tps(1:nbvec_sub+3,isub); |
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| 293 | DUDY(ind_sel)=DUDY(ind_sel)+EMDY*Data.Civ1_U_tps(1:nbvec_sub+3,isub); |
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| 294 | DVDX(ind_sel)=DVDX(ind_sel)+EMDX*Data.Civ1_V_tps(1:nbvec_sub+3,isub); |
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| 295 | DVDY(ind_sel)=DVDY(ind_sel)+EMDY*Data.Civ1_V_tps(1:nbvec_sub+3,isub); |
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| 296 | end |
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| 297 | end |
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| 298 | mask=''; |
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[387] | 299 | if par_civ2.CheckMask&&~isempty(par_civ2.Mask)&& ~strcmp(maskname,par_civ2.Mask)% mask exist, not already read in civ1 |
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| 300 | mask=imread(par_civ2.Mask); |
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[315] | 301 | end |
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[576] | 302 | ibx2=ceil(par_civ2.CorrBoxSize(1)/2); |
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| 303 | iby2=ceil(par_civ2.CorrBoxSize(2)/2); |
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| 304 | % isx2=ibx2+4;% search ara +-4 pixels around the guess |
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| 305 | % isy2=iby2+4; |
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| 306 | par_civ2.SearchBoxSize(1)=2*ibx2+9;% search ara +-4 pixels around the guess |
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| 307 | par_civ2.SearchBoxSize(2)=2*iby2+9; |
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| 308 | %par_civ2.SearchBoxSize(1)=2*isx2+1; |
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| 309 | %par_civ2.SearchBoxSize(2)=2*isy2+1; |
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[437] | 310 | par_civ2.SearchBoxShift=[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)]; |
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| 311 | 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] | 312 | if par_civ2.CheckDeformation |
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[370] | 313 | par_civ2.DUDX=DUDX./nbval; |
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| 314 | par_civ2.DUDY=DUDY./nbval; |
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| 315 | par_civ2.DVDX=DVDX./nbval; |
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| 316 | par_civ2.DVDY=DVDY./nbval; |
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[363] | 317 | end |
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[315] | 318 | % caluclate velocity data (y and v in indices, reverse to y component) |
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[363] | 319 | [xtable ytable utable vtable ctable F] = civ (par_civ2); |
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| 320 | list_param=(fieldnames(Param.Civ2))'; |
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[315] | 321 | list_remove={'pxcmx','pxcmy','npx','npy','gridflag','maskflag','term_a','term_b','T0'}; |
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| 322 | for ilist=1:length(list_remove) |
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| 323 | index=strcmp(list_remove{ilist},list_param); |
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| 324 | if ~isempty(find(index,1)) |
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| 325 | list_param(index)=[]; |
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| 326 | end |
---|
| 327 | end |
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| 328 | for ilist=1:length(list_param) |
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[363] | 329 | Civ2_param{ilist}=['Civ2_' list_param{ilist}]; |
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| 330 | eval(['Data.Civ2_' list_param{ilist} '=Param.Civ2.' list_param{ilist} ';']) |
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[315] | 331 | end |
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[363] | 332 | if isfield(Data,'Civ2_gridname') && strcmp(Data.Civ1_gridname(1:6),'noFile') |
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[315] | 333 | Data.Civ1_gridname=''; |
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| 334 | end |
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[363] | 335 | if isfield(Data,'Civ2_maskname') && strcmp(Data.Civ1_maskname(1:6),'noFile') |
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| 336 | Data.Civ2_maskname=''; |
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[315] | 337 | end |
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[363] | 338 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param {'Civ2_Time','Civ2_Dt'}]; |
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[364] | 339 | nbvar=numel(Data.ListVarName); |
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| 340 | 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] | 341 | 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] | 342 | Data.VarAttribute{nbvar+1}.Role='coord_x'; |
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| 343 | Data.VarAttribute{nbvar+2}.Role='coord_y'; |
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| 344 | Data.VarAttribute{nbvar+3}.Role='vector_x'; |
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| 345 | Data.VarAttribute{nbvar+4}.Role='vector_y'; |
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| 346 | Data.VarAttribute{nbvar+5}.Role='warnflag'; |
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[363] | 347 | Data.Civ2_X=reshape(xtable,[],1); |
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| 348 | Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1); |
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| 349 | Data.Civ2_U=reshape(utable,[],1); |
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| 350 | Data.Civ2_V=reshape(-vtable,[],1); |
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| 351 | Data.Civ2_C=reshape(ctable,[],1); |
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| 352 | Data.Civ2_F=reshape(F,[],1); |
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[315] | 353 | Data.CivStage=Data.CivStage+1; |
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| 354 | end |
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| 355 | |
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| 356 | %% Fix2 |
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| 357 | if isfield (Param,'Fix2') |
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| 358 | ListFixParam=fieldnames(Param.Fix2); |
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| 359 | for ilist=1:length(ListFixParam) |
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| 360 | ParamName=ListFixParam{ilist}; |
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[364] | 361 | ListName=['Fix2_' ParamName]; |
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[315] | 362 | eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];']) |
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| 363 | eval(['Data.' ListName '=Param.Fix2.' ParamName ';']) |
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| 364 | end |
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| 365 | if check_civx |
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| 366 | if ~isfield(Data,'fix2') |
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| 367 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix2']; |
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| 368 | Data.fix2=1; |
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| 369 | Data.ListVarName=[Data.ListVarName {'vec2_FixFlag'}]; |
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| 370 | Data.VarDimName=[Data.VarDimName {'nb_vectors2'}]; |
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| 371 | end |
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| 372 | 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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| 373 | else |
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| 374 | Data.ListVarName=[Data.ListVarName {'Civ2_FF'}]; |
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[399] | 375 | Data.VarDimName=[Data.VarDimName {'nb_vec_2'}]; |
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[315] | 376 | nbvar=length(Data.ListVarName); |
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[435] | 377 | Data.VarAttribute{nbvar}.Role='errorflag'; |
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[315] | 378 | Data.Civ2_FF=fix(Param.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V); |
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[435] | 379 | Data.CivStage=Data.CivStage+1; |
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[315] | 380 | end |
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| 381 | |
---|
[435] | 382 | end |
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[315] | 383 | |
---|
| 384 | %% Patch2 |
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| 385 | if isfield (Param,'Patch2') |
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| 386 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch2_Rho','Patch2_Threshold','Patch2_SubDomain'}]; |
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[581] | 387 | Data.Patch2_FieldSmooth=Param.Patch2.FieldSmooth; |
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| 388 | Data.Patch2_MaxDiff=Param.Patch2.MaxDiff; |
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[582] | 389 | Data.Patch2_SubDomainSize=Param.Patch2.SubDomainSize; |
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[397] | 390 | nbvar=length(Data.ListVarName); |
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[651] | 391 | Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbCentre','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}]; |
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| 392 | Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bound','nb_subdomain_2'},{'nb_subdomain_2'},... |
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[435] | 393 | {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}]; |
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| 394 | |
---|
| 395 | Data.VarAttribute{nbvar+1}.Role='vector_x'; |
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[397] | 396 | Data.VarAttribute{nbvar+2}.Role='vector_y'; |
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| 397 | Data.VarAttribute{nbvar+5}.Role='coord_tps'; |
---|
[492] | 398 | Data.VarAttribute{nbvar+6}.Role='vector_x'; |
---|
| 399 | Data.VarAttribute{nbvar+7}.Role='vector_y'; |
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[397] | 400 | Data.Civ2_U_smooth=zeros(size(Data.Civ2_X)); |
---|
| 401 | Data.Civ2_V_smooth=zeros(size(Data.Civ2_X)); |
---|
[315] | 402 | if isfield(Data,'Civ2_FF') |
---|
| 403 | ind_good=find(Data.Civ2_FF==0); |
---|
| 404 | else |
---|
| 405 | ind_good=1:numel(Data.Civ2_X); |
---|
[435] | 406 | end |
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[651] | 407 | [Data.Civ2_SubRange,Data.Civ2_NbCentre,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures, Vres,tild,FFres]=... |
---|
[581] | 408 | filter_tps([Data.Civ2_X(ind_good) Data.Civ2_Y(ind_good)],Data.Civ2_U(ind_good),Data.Civ2_V(ind_good),[],Data.Patch2_SubDomainSize,Data.Patch2_FieldSmooth,Data.Patch2_MaxDiff); |
---|
[397] | 409 | Data.Civ2_U_smooth(ind_good)=Ures; |
---|
| 410 | Data.Civ2_V_smooth(ind_good)=Vres; |
---|
| 411 | Data.Civ2_FF(ind_good)=FFres; |
---|
[435] | 412 | Data.CivStage=Data.CivStage+1; |
---|
| 413 | end |
---|
[315] | 414 | |
---|
| 415 | %% write result in a netcdf file if requested |
---|
[319] | 416 | if exist('ncfile','var') |
---|
[315] | 417 | errormsg=struct2nc(ncfile,Data); |
---|
[494] | 418 | if isempty(errormsg) |
---|
| 419 | disp([ncfile ' written']) |
---|
| 420 | else |
---|
| 421 | disp(errormsg) |
---|
| 422 | end |
---|
[315] | 423 | end |
---|
| 424 | |
---|
| 425 | % 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/ |
---|
| 426 | %-------------------------------------------------------------------------- |
---|
| 427 | % function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi) |
---|
| 428 | % |
---|
| 429 | % OUTPUT: |
---|
| 430 | % xtable: set of x coordinates |
---|
| 431 | % ytable: set of y coordiantes |
---|
| 432 | % utable: set of u displacements (along x) |
---|
| 433 | % vtable: set of v displacements (along y) |
---|
| 434 | % ctable: max image correlation for each vector |
---|
| 435 | % typevector: set of flags, =1 for good, =0 for NaN vectors |
---|
| 436 | % |
---|
| 437 | %INPUT: |
---|
[493] | 438 | % par_civ: structure of input parameters, with fields: |
---|
| 439 | % .CorrBoxSize |
---|
| 440 | % .SearchBoxSize |
---|
| 441 | % .SearchBoxShift |
---|
| 442 | % .ImageHeight |
---|
| 443 | % .ImageWidth |
---|
| 444 | % .Dx, Dy |
---|
| 445 | % .Grid |
---|
| 446 | % .Mask |
---|
| 447 | % .MinIma |
---|
| 448 | % .MaxIma |
---|
| 449 | % .image1:first image (matrix) |
---|
[315] | 450 | % image2: second image (matrix) |
---|
| 451 | % ibx2,iby2: half size of the correlation box along x and y, in px (size=(2*iby2+1,2*ibx2+1) |
---|
| 452 | % isx2,isy2: half size of the search box along x and y, in px (size=(2*isy2+1,2*isx2+1) |
---|
| 453 | % shiftx, shifty: shift of the search box (in pixel index, yshift reversed) |
---|
| 454 | % step: mesh of the measurement points (in px) |
---|
| 455 | % subpixfinder=1 or 2 controls the curve fitting of the image correlation |
---|
| 456 | % mask: =[] for no mask |
---|
| 457 | % roi: 4 element vector defining a region of interest: x position, y position, width, height, (in image indices), for the whole image, roi=[]; |
---|
| 458 | function [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ) |
---|
| 459 | %this funtion performs the DCC PIV analysis. Recent window-deformation |
---|
| 460 | %methods perform better and will maybe be implemented in the future. |
---|
| 461 | |
---|
[576] | 462 | %% prepare measurement grid |
---|
| 463 | if isfield(par_civ,'Grid')% grid points set as input |
---|
[364] | 464 | if ischar(par_civ.Grid)%read the drid file if the input is a file name |
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[315] | 465 | par_civ.Grid=dlmread(par_civ.Grid); |
---|
| 466 | par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file) |
---|
| 467 | end |
---|
[576] | 468 | else% automatic grid |
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| 469 | minix=floor(par_civ.Dx/2)-0.5; |
---|
| 470 | maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx); |
---|
| 471 | miniy=floor(par_civ.Dy/2)-0.5; |
---|
| 472 | maxiy=minix+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy); |
---|
[315] | 473 | [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy); |
---|
| 474 | par_civ.Grid(:,1)=reshape(GridX,[],1); |
---|
| 475 | par_civ.Grid(:,2)=reshape(GridY,[],1); |
---|
| 476 | end |
---|
[363] | 477 | nbvec=size(par_civ.Grid,1); |
---|
[576] | 478 | |
---|
| 479 | %% prepare correlation and search boxes |
---|
| 480 | ibx2=ceil(par_civ.CorrBoxSize(1)/2); |
---|
| 481 | iby2=ceil(par_civ.CorrBoxSize(2)/2); |
---|
| 482 | isx2=ceil(par_civ.SearchBoxSize(1)/2); |
---|
| 483 | isy2=ceil(par_civ.SearchBoxSize(2)/2); |
---|
| 484 | shiftx=round(par_civ.SearchBoxShift(:,1)); |
---|
| 485 | shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases |
---|
| 486 | if numel(shiftx)==1% case of a unique shift for the whole field( civ1) |
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[365] | 487 | shiftx=shiftx*ones(nbvec,1); |
---|
| 488 | shifty=shifty*ones(nbvec,1); |
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[363] | 489 | end |
---|
[576] | 490 | |
---|
[315] | 491 | %% Default output |
---|
| 492 | xtable=par_civ.Grid(:,1); |
---|
| 493 | ytable=par_civ.Grid(:,2); |
---|
| 494 | utable=zeros(nbvec,1); |
---|
| 495 | vtable=zeros(nbvec,1); |
---|
| 496 | ctable=zeros(nbvec,1); |
---|
| 497 | F=zeros(nbvec,1); |
---|
| 498 | result_conv=[]; |
---|
| 499 | errormsg=''; |
---|
| 500 | |
---|
| 501 | %% prepare mask |
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| 502 | if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) |
---|
| 503 | if strcmp(par_civ.Mask,'all') |
---|
| 504 | return % get the grid only, no civ calculation |
---|
| 505 | elseif ischar(par_civ.Mask) |
---|
| 506 | par_civ.Mask=imread(par_civ.Mask); |
---|
| 507 | end |
---|
| 508 | end |
---|
| 509 | check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold |
---|
| 510 | check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma); |
---|
| 511 | |
---|
[364] | 512 | % %% prepare images |
---|
| 513 | % if isfield(par_civ,'reverse_pair') |
---|
| 514 | % if par_civ.reverse_pair |
---|
| 515 | % if ischar(par_civ.ImageB) |
---|
| 516 | % temp=par_civ.ImageA; |
---|
| 517 | % par_civ.ImageA=imread(par_civ.ImageB); |
---|
| 518 | % end |
---|
| 519 | % if ischar(temp) |
---|
| 520 | % par_civ.ImageB=imread(temp); |
---|
| 521 | % end |
---|
| 522 | % end |
---|
| 523 | % else |
---|
| 524 | % if ischar(par_civ.ImageA) |
---|
| 525 | % par_civ.ImageA=imread(par_civ.ImageA); |
---|
| 526 | % end |
---|
| 527 | % if ischar(par_civ.ImageB) |
---|
| 528 | % par_civ.ImageB=imread(par_civ.ImageB); |
---|
| 529 | % end |
---|
| 530 | % end |
---|
[388] | 531 | par_civ.ImageA=sum(double(par_civ.ImageA),3);%sum over rgb component for color images |
---|
| 532 | par_civ.ImageB=sum(double(par_civ.ImageB),3); |
---|
[315] | 533 | [npy_ima npx_ima]=size(par_civ.ImageA); |
---|
| 534 | if ~isequal(size(par_civ.ImageB),[npy_ima npx_ima]) |
---|
| 535 | errormsg='image pair with unequal size'; |
---|
| 536 | return |
---|
| 537 | end |
---|
| 538 | |
---|
| 539 | %% Apply mask |
---|
[411] | 540 | % Convention for mask IDEAS TO IMPLEMENT ? |
---|
[315] | 541 | % mask >200 : velocity calculated |
---|
| 542 | % 200 >=mask>150;velocity not calculated, interpolation allowed (bad spots) |
---|
| 543 | % 150>=mask >100: velocity not calculated, nor interpolated |
---|
[411] | 544 | % 100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries) |
---|
[315] | 545 | % 20>=mask: velocity=0 |
---|
| 546 | checkmask=0; |
---|
[576] | 547 | MinA=min(min(par_civ.ImageA)); |
---|
| 548 | MinB=min(min(par_civ.ImageB)); |
---|
[315] | 549 | if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) |
---|
| 550 | checkmask=1; |
---|
| 551 | if ~isequal(size(par_civ.Mask),[npy_ima npx_ima]) |
---|
| 552 | errormsg='mask must be an image with the same size as the images'; |
---|
| 553 | return |
---|
| 554 | end |
---|
| 555 | % check_noflux=(par_civ.Mask<100) ;%TODO: to implement |
---|
[411] | 556 | check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 ); |
---|
[576] | 557 | par_civ.ImageA(check_undefined)=MinA;% put image A to zero (i.e. the min image value) in the undefined area |
---|
| 558 | par_civ.ImageB(check_undefined)=MinB;% put image B to zero (i.e. the min image value) in the undefined area |
---|
[315] | 559 | end |
---|
| 560 | |
---|
| 561 | %% compute image correlations: MAINLOOP on velocity vectors |
---|
[317] | 562 | corrmax=0; |
---|
| 563 | sum_square=1;% default |
---|
[368] | 564 | mesh=1;% default |
---|
| 565 | CheckDecimal=isfield(par_civ,'CheckDecimal')&& par_civ.CheckDecimal==1; |
---|
| 566 | if CheckDecimal |
---|
| 567 | mesh=0.2;%mesh in pixels for subpixel image interpolation |
---|
[370] | 568 | CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1; |
---|
[368] | 569 | end |
---|
[315] | 570 | % vector=[0 0];%default |
---|
| 571 | for ivec=1:nbvec |
---|
[370] | 572 | iref=round(par_civ.Grid(ivec,1)+0.5);% xindex on the image A for the middle of the correlation box |
---|
| 573 | jref=round(par_civ.ImageHeight-par_civ.Grid(ivec,2)+0.5);% yindex on the image B for the middle of the correlation box |
---|
[596] | 574 | %if ~(checkmask && par_civ.Mask(jref,iref)<=20) %velocity not set to zero by the black mask |
---|
| 575 | % if jref-iby2<1 || jref+iby2>par_civ.ImageHeight|| iref-ibx2<1 || iref+ibx2>par_civ.ImageWidth||... |
---|
| 576 | % 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 |
---|
| 577 | % F(ivec)=3; |
---|
| 578 | % else |
---|
| 579 | F(ivec)=0; |
---|
| 580 | subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage |
---|
| 581 | subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage |
---|
| 582 | subrange2_x=iref+shiftx(ivec)-isx2:iref+shiftx(ivec)+isx2;%x indices defining the second subimage |
---|
| 583 | subrange2_y=jref+shifty(ivec)-isy2:jref+shifty(ivec)+isy2;%y indices defining the second subimage |
---|
| 584 | image1_crop=MinA*ones(numel(subrange1_y),numel(subrange1_x));% default value=min of image A |
---|
| 585 | image2_crop=MinA*ones(numel(subrange2_y),numel(subrange2_x));% default value=min of image A |
---|
| 586 | check1_x=subrange1_x>=1 & subrange1_x<=par_civ.ImageWidth;% check which points in the subimage 1 are contained in the initial image 1 |
---|
| 587 | check1_y=subrange1_y>=1 & subrange1_y<=par_civ.ImageHeight; |
---|
| 588 | check2_x=subrange2_x>=1 & subrange2_x<=par_civ.ImageWidth;% check which points in the subimage 2 are contained in the initial image 2 |
---|
| 589 | check2_y=subrange2_y>=1 & subrange2_y<=par_civ.ImageHeight; |
---|
| 590 | |
---|
| 591 | image1_crop(check1_y,check1_x)=par_civ.ImageA(subrange1_y(check1_y),subrange1_x(check1_x));%extract a subimage (correlation box) from image A |
---|
| 592 | image2_crop(check2_y,check2_x)=par_civ.ImageB(subrange2_y(check2_y),subrange2_x(check2_x));%extract a larger subimage (search box) from image B |
---|
| 593 | image1_mean=mean(mean(image1_crop)); |
---|
| 594 | image2_mean=mean(mean(image2_crop)); |
---|
| 595 | %threshold on image minimum |
---|
| 596 | if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma) |
---|
| 597 | F(ivec)=3; |
---|
| 598 | end |
---|
| 599 | %threshold on image maximum |
---|
| 600 | if check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma) |
---|
| 601 | F(ivec)=3; |
---|
| 602 | end |
---|
| 603 | % end |
---|
| 604 | if F(ivec)~=3 |
---|
| 605 | image1_crop=image1_crop-image1_mean;%substract the mean |
---|
| 606 | image2_crop=image2_crop-image2_mean; |
---|
| 607 | if CheckDecimal |
---|
| 608 | xi=(1:mesh:size(image1_crop,2)); |
---|
| 609 | yi=(1:mesh:size(image1_crop,1))'; |
---|
| 610 | if CheckDeformation |
---|
| 611 | [XI,YI]=meshgrid(xi-ceil(size(image1_crop,2)/2),yi-ceil(size(image1_crop,1)/2)); |
---|
| 612 | XIant=XI-par_civ.DUDX(ivec)*XI-par_civ.DUDY(ivec)*YI+ceil(size(image1_crop,2)/2); |
---|
| 613 | YIant=YI-par_civ.DVDX(ivec)*XI-par_civ.DVDY(ivec)*YI+ceil(size(image1_crop,1)/2); |
---|
| 614 | image1_crop=interp2(image1_crop,XIant,YIant); |
---|
| 615 | else |
---|
| 616 | image1_crop=interp2(image1_crop,xi,yi); |
---|
[315] | 617 | end |
---|
[596] | 618 | xi=(1:mesh:size(image2_crop,2)); |
---|
| 619 | yi=(1:mesh:size(image2_crop,1))'; |
---|
| 620 | image2_crop=interp2(image2_crop,xi,yi); |
---|
| 621 | end |
---|
| 622 | sum_square=sum(sum(image1_crop.*image1_crop)); |
---|
| 623 | %reference: Oliver Pust, PIV: Direct Cross-Correlation |
---|
| 624 | result_conv= conv2(image2_crop,flipdim(flipdim(image1_crop,2),1),'valid'); |
---|
| 625 | corrmax= max(max(result_conv)); |
---|
| 626 | result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255 |
---|
| 627 | %Find the correlation max, at 255 |
---|
| 628 | [y,x] = find(result_conv==255,1); |
---|
| 629 | if ~isempty(y) && ~isempty(x) |
---|
| 630 | try |
---|
| 631 | if par_civ.CorrSmooth==1 |
---|
| 632 | [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y); |
---|
| 633 | elseif par_civ.CorrSmooth==2 |
---|
| 634 | [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y); |
---|
[370] | 635 | end |
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[596] | 636 | utable(ivec)=vector(1)*mesh+shiftx(ivec); |
---|
| 637 | vtable(ivec)=vector(2)*mesh+shifty(ivec); |
---|
| 638 | xtable(ivec)=iref+utable(ivec)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2) |
---|
| 639 | ytable(ivec)=jref+vtable(ivec)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge) |
---|
| 640 | iref=round(xtable(ivec));% image index for the middle of the vector |
---|
| 641 | jref=round(ytable(ivec)); |
---|
| 642 | if checkmask && par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100 |
---|
| 643 | utable(ivec)=0; |
---|
| 644 | vtable(ivec)=0; |
---|
[315] | 645 | F(ivec)=3; |
---|
| 646 | end |
---|
[596] | 647 | ctable(ivec)=corrmax/sum_square;% correlation value |
---|
| 648 | catch ME |
---|
[315] | 649 | F(ivec)=3; |
---|
| 650 | end |
---|
[596] | 651 | else |
---|
| 652 | F(ivec)=3; |
---|
[315] | 653 | end |
---|
| 654 | end |
---|
| 655 | end |
---|
| 656 | result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output |
---|
| 657 | |
---|
| 658 | %------------------------------------------------------------------------ |
---|
| 659 | % --- Find the maximum of the correlation function after interpolation |
---|
| 660 | function [vector,F] = SUBPIXGAUSS (result_conv,x,y) |
---|
| 661 | %------------------------------------------------------------------------ |
---|
| 662 | vector=[0 0]; %default |
---|
| 663 | F=0; |
---|
| 664 | [npy,npx]=size(result_conv); |
---|
| 665 | |
---|
| 666 | % if (x <= (size(result_conv,1)-1)) && (y <= (size(result_conv,1)-1)) && (x >= 1) && (y >= 1) |
---|
[337] | 667 | %the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ᅵ Israel Institute of Technology |
---|
[315] | 668 | %http://urapiv.wordpress.com |
---|
| 669 | peaky = y; |
---|
| 670 | if y <= npy-1 && y >= 1 |
---|
| 671 | f0 = log(result_conv(y,x)); |
---|
| 672 | f1 = real(log(result_conv(y-1,x))); |
---|
| 673 | f2 = real(log(result_conv(y+1,x))); |
---|
| 674 | peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2); |
---|
| 675 | else |
---|
| 676 | F=-2; % warning flag for vector truncated by the limited search box |
---|
| 677 | end |
---|
| 678 | peakx=x; |
---|
| 679 | if x <= npx-1 && x >= 1 |
---|
| 680 | f0 = log(result_conv(y,x)); |
---|
| 681 | f1 = real(log(result_conv(y,x-1))); |
---|
| 682 | f2 = real(log(result_conv(y,x+1))); |
---|
| 683 | peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2); |
---|
| 684 | else |
---|
| 685 | F=-2; % warning flag for vector truncated by the limited search box |
---|
| 686 | end |
---|
| 687 | vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; |
---|
| 688 | |
---|
| 689 | %------------------------------------------------------------------------ |
---|
| 690 | % --- Find the maximum of the correlation function after interpolation |
---|
| 691 | function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y) |
---|
| 692 | %------------------------------------------------------------------------ |
---|
| 693 | vector=[0 0]; %default |
---|
| 694 | F=-2; |
---|
| 695 | peaky=y; |
---|
| 696 | peakx=x; |
---|
| 697 | [npy,npx]=size(result_conv); |
---|
| 698 | if (x <= npx-1) && (y <= npy-1) && (x >= 1) && (y >= 1) |
---|
| 699 | F=0; |
---|
| 700 | for i=-1:1 |
---|
| 701 | for j=-1:1 |
---|
| 702 | %following 15 lines based on |
---|
[337] | 703 | %H. Nobach ᅵ M. Honkanen (2005) |
---|
[315] | 704 | %Two-dimensional Gaussian regression for sub-pixel displacement |
---|
| 705 | %estimation in particle image velocimetry or particle position |
---|
| 706 | %estimation in particle tracking velocimetry |
---|
[337] | 707 | %Experiments in Fluids (2005) 38: 511ᅵ515 |
---|
[315] | 708 | c10(j+2,i+2)=i*log(result_conv(y+j, x+i)); |
---|
| 709 | c01(j+2,i+2)=j*log(result_conv(y+j, x+i)); |
---|
| 710 | c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i)); |
---|
| 711 | c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i)); |
---|
| 712 | c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i)); |
---|
| 713 | end |
---|
| 714 | end |
---|
| 715 | c10=(1/6)*sum(sum(c10)); |
---|
| 716 | c01=(1/6)*sum(sum(c01)); |
---|
| 717 | c11=(1/4)*sum(sum(c11)); |
---|
| 718 | c20=(1/6)*sum(sum(c20)); |
---|
| 719 | c02=(1/6)*sum(sum(c02)); |
---|
| 720 | deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2); |
---|
| 721 | deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2); |
---|
| 722 | if abs(deltax)<1 |
---|
| 723 | peakx=x+deltax; |
---|
| 724 | end |
---|
| 725 | if abs(deltay)<1 |
---|
| 726 | peaky=y+deltay; |
---|
| 727 | end |
---|
| 728 | end |
---|
| 729 | vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; |
---|
| 730 | |
---|
| 731 | %'RUN_FIX': function for fixing velocity fields: |
---|
| 732 | %----------------------------------------------- |
---|
| 733 | % RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref) |
---|
| 734 | % |
---|
| 735 | %filename: name of the netcdf file (used as input and output) |
---|
| 736 | %field: structure specifying the names of the fields to fix (depending on civ1 or civ2) |
---|
| 737 | %.vel_type='civ1' or 'civ2'; |
---|
| 738 | %.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1); |
---|
| 739 | %.fixflag=name of fix flag variable ('vec_FixFlag' for civ1) |
---|
| 740 | %flagindex: flag specifying which values of vec_f are removed: |
---|
| 741 | % if flagindex(1)=1: vec_f=-2 vectors are removed |
---|
| 742 | % if flagindex(2)=1: vec_f=3 vectors are removed |
---|
| 743 | % if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2) |
---|
| 744 | %iter=1 for civ1 fields and iter=2 for civ2 fields |
---|
| 745 | %thresh_vecC: threshold in the image correlation vec_C |
---|
| 746 | %flag_mask: =1 mask used to remove vectors (0 else) |
---|
| 747 | %maskname: name of the mask image file for fix |
---|
| 748 | %thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists |
---|
| 749 | %inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold |
---|
| 750 | %fileref: .nc file name for a reference velocity (='': refrence 0 used) |
---|
| 751 | %fieldref: 'civ1','filter1'...feld used in fileref |
---|
| 752 | |
---|
| 753 | function FF=fix(Param,F,C,U,V,X,Y) |
---|
| 754 | FF=zeros(size(F));%default |
---|
| 755 | |
---|
| 756 | %criterium on warn flags |
---|
| 757 | FlagName={'CheckFmin2','CheckF2','CheckF3','CheckF4'}; |
---|
| 758 | FlagVal=[-2 2 3 4]; |
---|
| 759 | for iflag=1:numel(FlagName) |
---|
| 760 | if isfield(Param,FlagName{iflag}) && Param.(FlagName{iflag}) |
---|
| 761 | FF=(FF==1| F==FlagVal(iflag)); |
---|
| 762 | end |
---|
| 763 | end |
---|
| 764 | %criterium on correlation values |
---|
| 765 | if isfield (Param,'MinCorr') |
---|
| 766 | FF=FF==1 | C<Param.MinCorr; |
---|
| 767 | end |
---|
[316] | 768 | if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)) |
---|
[315] | 769 | Umod= U.*U+V.*V; |
---|
[316] | 770 | if isfield (Param,'MinVel')&&~isempty(Param.MinVel) |
---|
[315] | 771 | FF=FF==1 | Umod<(Param.MinVel*Param.MinVel); |
---|
| 772 | end |
---|
| 773 | if isfield (Param,'MaxVel')&&~isempty(Param.MaxVel) |
---|
| 774 | FF=FF==1 | Umod>(Param.MaxVel*Param.MaxVel); |
---|
| 775 | end |
---|
| 776 | end |
---|
| 777 | |
---|
| 778 | |
---|
| 779 | |
---|
[326] | 780 | |
---|
[315] | 781 | |
---|
| 782 | |
---|
| 783 | |
---|