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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5 | % filter_tps: make interpolation-smoothing |
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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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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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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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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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59 | % case of input Param set by an xml file (batch mode) |
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60 | if ischar(Param) |
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61 | Param=xml2struct(Param); %if Param is the name of an xml file, read this file as a Matlab structure |
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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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86 | end |
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87 | |
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88 | %% Civ1 |
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89 | if isfield (Param,'Civ1') |
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90 | par_civ1=Param.Civ1; |
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91 | if isfield(par_civ1,'reverse_pair')% A REVOIR |
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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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95 | par_civ1.ImageA=imread(par_civ1.ImageB); |
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96 | end |
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97 | if ischar(temp) |
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98 | par_civ1.ImageB=imread(temp); |
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99 | end |
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100 | end |
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101 | else |
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102 | if isfield(Param.Civ1,'ImageA')%&&... |
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103 | Param.Civ1.ImageA=regexprep(Param.Civ1.ImageA,'''','\'); |
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104 | [par_civ1.ImageA,VideoObject] = read_image(Param.Civ1.ImageA,par_civ1.FileTypeA,[],par_civ1.FrameIndexA); |
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105 | end |
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106 | if isfield(Param.Civ1,'ImageB')%&& ... |
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107 | Param.Civ1.ImageB=regexprep(Param.Civ1.ImageB,'''','\'); |
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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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113 | end |
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114 | end |
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115 | |
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116 | % caluclate velocity data (y and v in indices, reverse to y component) |
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117 | [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ1); |
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118 | |
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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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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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136 | %set the values of all the global attributes in list_param |
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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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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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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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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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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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155 | Data.CivStage=1; |
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156 | else |
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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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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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163 | if isfield(Data,'Txt') |
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164 | errormsg=Data.Txt; |
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165 | return |
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166 | end |
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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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169 | [Data,vardetect,ichoice]=nc2struct(CivFile);%read the variables in the netcdf file |
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170 | else |
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171 | Data=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file |
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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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194 | Data.VarDimName=[Data.VarDimName {'nb_vec_1'}]; |
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195 | nbvar=length(Data.ListVarName); |
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196 | Data.VarAttribute{nbvar}.Role='errorflag'; |
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197 | Data.Civ1_FF=fix(Param.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V); |
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198 | Data.CivStage=2; |
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199 | end |
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200 | end |
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201 | %% Patch1 |
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202 | if isfield (Param,'Patch1') |
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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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207 | |
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208 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch1_Rho','Patch1_Threshold','Patch1_SubDomain'}]; |
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209 | Data.Patch1_Rho=Param.Patch1.FieldSmooth; |
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210 | Data.Patch1_Threshold=Param.Patch1.MaxDiff; |
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211 | Data.Patch1_SubDomain=Param.Patch1.SubdomainSize; |
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212 | nbvar=length(Data.ListVarName); |
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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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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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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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219 | Data.VarAttribute{nbvar+6}.Role='vector_x'; |
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220 | Data.VarAttribute{nbvar+7}.Role='vector_y'; |
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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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223 | if isfield(Data,'Civ1_FF') |
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224 | ind_good=find(Data.Civ1_FF==0); |
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225 | else |
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226 | ind_good=1:numel(Data.Civ1_X); |
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227 | end |
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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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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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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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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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252 | end |
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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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260 | end |
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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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272 | end |
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273 | ibx2=ceil(par_civ2.CorrBoxSize(1)/2); |
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274 | iby2=ceil(par_civ2.CorrBoxSize(2)/2); |
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275 | isx2=ibx2+4;% search ara +-4 pixels around the guess |
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276 | isy2=iby2+4; |
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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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283 | [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy); |
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284 | GridX=reshape(GridX,[],1); |
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285 | GridY=reshape(GridY,[],1); |
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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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295 | NbSubDomain=size(Data.Civ1_SubRange,3); |
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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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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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300 | epoints = [GridX(ind_sel) GridY(ind_sel)];% coordinates of interpolation sites |
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301 | ctrs=Data.Civ1_Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs |
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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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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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317 | end |
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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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323 | if par_civ2.CheckDeformation |
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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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328 | end |
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329 | % caluclate velocity data (y and v in indices, reverse to y component) |
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330 | [xtable ytable utable vtable ctable F] = civ (par_civ2); |
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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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333 | list_param=(fieldnames(Param.Civ2))'; |
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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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342 | Civ2_param{ilist}=['Civ2_' list_param{ilist}]; |
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343 | eval(['Data.Civ2_' list_param{ilist} '=Param.Civ2.' list_param{ilist} ';']) |
---|
344 | end |
---|
345 | if isfield(Data,'Civ2_gridname') && strcmp(Data.Civ1_gridname(1:6),'noFile') |
---|
346 | Data.Civ1_gridname=''; |
---|
347 | end |
---|
348 | if isfield(Data,'Civ2_maskname') && strcmp(Data.Civ1_maskname(1:6),'noFile') |
---|
349 | Data.Civ2_maskname=''; |
---|
350 | end |
---|
351 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param {'Civ2_Time','Civ2_Dt'}]; |
---|
352 | % Data.Civ2_Time=par_civ2.Time; |
---|
353 | % Data.Civ2_Dt=par_civ2.Dt; |
---|
354 | nbvar=numel(Data.ListVarName); |
---|
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 |
---|
356 | Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}]; |
---|
357 | Data.VarAttribute{nbvar+1}.Role='coord_x'; |
---|
358 | Data.VarAttribute{nbvar+2}.Role='coord_y'; |
---|
359 | Data.VarAttribute{nbvar+3}.Role='vector_x'; |
---|
360 | Data.VarAttribute{nbvar+4}.Role='vector_y'; |
---|
361 | Data.VarAttribute{nbvar+5}.Role='warnflag'; |
---|
362 | Data.Civ2_X=reshape(xtable,[],1); |
---|
363 | Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1); |
---|
364 | Data.Civ2_U=reshape(utable,[],1); |
---|
365 | Data.Civ2_V=reshape(-vtable,[],1); |
---|
366 | Data.Civ2_C=reshape(ctable,[],1); |
---|
367 | Data.Civ2_F=reshape(F,[],1); |
---|
368 | Data.CivStage=Data.CivStage+1; |
---|
369 | end |
---|
370 | |
---|
371 | %% Fix2 |
---|
372 | if isfield (Param,'Fix2') |
---|
373 | ListFixParam=fieldnames(Param.Fix2); |
---|
374 | for ilist=1:length(ListFixParam) |
---|
375 | ParamName=ListFixParam{ilist}; |
---|
376 | ListName=['Fix2_' ParamName]; |
---|
377 | eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];']) |
---|
378 | eval(['Data.' ListName '=Param.Fix2.' ParamName ';']) |
---|
379 | end |
---|
380 | if check_civx |
---|
381 | if ~isfield(Data,'fix2') |
---|
382 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix2']; |
---|
383 | Data.fix2=1; |
---|
384 | Data.ListVarName=[Data.ListVarName {'vec2_FixFlag'}]; |
---|
385 | Data.VarDimName=[Data.VarDimName {'nb_vectors2'}]; |
---|
386 | end |
---|
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); |
---|
388 | else |
---|
389 | Data.ListVarName=[Data.ListVarName {'Civ2_FF'}]; |
---|
390 | Data.VarDimName=[Data.VarDimName {'nb_vec_2'}]; |
---|
391 | nbvar=length(Data.ListVarName); |
---|
392 | Data.VarAttribute{nbvar}.Role='errorflag'; |
---|
393 | Data.Civ2_FF=fix(Param.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V); |
---|
394 | Data.CivStage=Data.CivStage+1; |
---|
395 | end |
---|
396 | |
---|
397 | end |
---|
398 | |
---|
399 | %% Patch2 |
---|
400 | if isfield (Param,'Patch2') |
---|
401 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch2_Rho','Patch2_Threshold','Patch2_SubDomain'}]; |
---|
402 | Data.Patch2_Rho=Param.Patch2.FieldSmooth; |
---|
403 | Data.Patch2_Threshold=Param.Patch2.MaxDiff; |
---|
404 | Data.Patch2_SubDomain=Param.Patch2.SubdomainSize; |
---|
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'}]; |
---|
407 | Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},... |
---|
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'; |
---|
411 | Data.VarAttribute{nbvar+2}.Role='vector_y'; |
---|
412 | Data.VarAttribute{nbvar+5}.Role='coord_tps'; |
---|
413 | Data.VarAttribute{nbvar+6}.Role='vector_x'; |
---|
414 | Data.VarAttribute{nbvar+7}.Role='vector_y'; |
---|
415 | Data.Civ2_U_smooth=zeros(size(Data.Civ2_X)); |
---|
416 | Data.Civ2_V_smooth=zeros(size(Data.Civ2_X)); |
---|
417 | if isfield(Data,'Civ2_FF') |
---|
418 | ind_good=find(Data.Civ2_FF==0); |
---|
419 | else |
---|
420 | ind_good=1:numel(Data.Civ2_X); |
---|
421 | end |
---|
422 | [Data.Civ2_SubRange,Data.Civ2_NbSites,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures, Vres,tild,FFres]=... |
---|
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); |
---|
424 | Data.Civ2_U_smooth(ind_good)=Ures; |
---|
425 | Data.Civ2_V_smooth(ind_good)=Vres; |
---|
426 | Data.Civ2_FF(ind_good)=FFres; |
---|
427 | Data.CivStage=Data.CivStage+1; |
---|
428 | end |
---|
429 | |
---|
430 | %% write result in a netcdf file if requested |
---|
431 | if exist('ncfile','var') |
---|
432 | errormsg=struct2nc(ncfile,Data); |
---|
433 | if isempty(errormsg) |
---|
434 | disp([ncfile ' written']) |
---|
435 | else |
---|
436 | disp(errormsg) |
---|
437 | end |
---|
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: |
---|
453 | % par_civ: structure of input parameters, with fields: |
---|
454 | % .CorrBoxSize |
---|
455 | % .SearchBoxSize |
---|
456 | % .SearchBoxShift |
---|
457 | % .ImageHeight |
---|
458 | % .ImageWidth |
---|
459 | % .Dx, Dy |
---|
460 | % .Grid |
---|
461 | % .Mask |
---|
462 | % .MinIma |
---|
463 | % .MaxIma |
---|
464 | % .image1:first image (matrix) |
---|
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 |
---|
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); |
---|
482 | shiftx=round(par_civ.SearchBoxShift(:,1)); |
---|
483 | shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases |
---|
484 | if isfield(par_civ,'Grid') |
---|
485 | if ischar(par_civ.Grid)%read the drid file if the input is a file name |
---|
486 | par_civ.Grid=dlmread(par_civ.Grid); |
---|
487 | par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file) |
---|
488 | end |
---|
489 | else% automatic measurement grid |
---|
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); |
---|
494 | miniy=max(1+isy2+shifty,1+iby2); |
---|
495 | minix=max(1+isx2-shiftx,1+ibx2); |
---|
496 | maxiy=min(par_civ.ImageHeight-isy2+shifty,par_civ.ImageHeight-iby2); |
---|
497 | maxix=min(par_civ.ImageWidth-isx2-shiftx,par_civ.ImageWidth-ibx2); |
---|
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 |
---|
502 | nbvec=size(par_civ.Grid,1); |
---|
503 | if numel(shiftx)==1 |
---|
504 | shiftx=shiftx*ones(nbvec,1); |
---|
505 | shifty=shifty*ones(nbvec,1); |
---|
506 | end |
---|
507 | %% Default output |
---|
508 | xtable=par_civ.Grid(:,1); |
---|
509 | ytable=par_civ.Grid(:,2); |
---|
510 | utable=zeros(nbvec,1); |
---|
511 | vtable=zeros(nbvec,1); |
---|
512 | ctable=zeros(nbvec,1); |
---|
513 | F=zeros(nbvec,1); |
---|
514 | result_conv=[]; |
---|
515 | errormsg=''; |
---|
516 | |
---|
517 | %% prepare mask |
---|
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 |
---|
525 | check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold |
---|
526 | check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma); |
---|
527 | |
---|
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 |
---|
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); |
---|
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 |
---|
556 | % Convention for mask IDEAS TO IMPLEMENT ? |
---|
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 |
---|
560 | % 100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries) |
---|
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 |
---|
570 | check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 ); |
---|
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 |
---|
576 | corrmax=0; |
---|
577 | sum_square=1;% default |
---|
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 |
---|
582 | CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1; |
---|
583 | end |
---|
584 | % vector=[0 0];%default |
---|
585 | for ivec=1:nbvec |
---|
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 |
---|
588 | if ~(checkmask && par_civ.Mask(jref,iref)<=20) %velocity not set to zero by the black mask |
---|
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 |
---|
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 |
---|
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 |
---|
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 |
---|
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 |
---|
605 | end |
---|
606 | if F(ivec)~=3 |
---|
607 | image1_crop=image1_crop-image1_mean;%substract the mean |
---|
608 | image2_crop=image2_crop-image2_mean; |
---|
609 | if CheckDecimal |
---|
610 | xi=(1:mesh:size(image1_crop,2)); |
---|
611 | yi=(1:mesh:size(image1_crop,1))'; |
---|
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 |
---|
620 | xi=(1:mesh:size(image2_crop,2)); |
---|
621 | yi=(1:mesh:size(image2_crop,1))'; |
---|
622 | image2_crop=interp2(image2_crop,xi,yi); |
---|
623 | end |
---|
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 |
---|
633 | if par_civ.CorrSmooth==1 |
---|
634 | [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y); |
---|
635 | elseif par_civ.CorrSmooth==2 |
---|
636 | [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y); |
---|
637 | end |
---|
638 | utable(ivec)=vector(1)*mesh+shiftx(ivec); |
---|
639 | vtable(ivec)=vector(2)*mesh+shifty(ivec); |
---|
640 | xtable(ivec)=iref+utable(ivec)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2) |
---|
641 | ytable(ivec)=jref+vtable(ivec)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge) |
---|
642 | iref=round(xtable(ivec));% image index for the middle of the vector |
---|
643 | jref=round(ytable(ivec)); |
---|
644 | if checkmask && par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100 |
---|
645 | utable(ivec)=0; |
---|
646 | vtable(ivec)=0; |
---|
647 | F(ivec)=3; |
---|
648 | end |
---|
649 | ctable(ivec)=corrmax/sum_square;% correlation value |
---|
650 | catch ME |
---|
651 | F(ivec)=3; |
---|
652 | end |
---|
653 | else |
---|
654 | F(ivec)=3; |
---|
655 | end |
---|
656 | end |
---|
657 | end |
---|
658 | |
---|
659 | %Create the vector matrix x, y, u, v |
---|
660 | end |
---|
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 |
---|
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) |
---|
672 | %the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ᅵ Israel Institute of Technology |
---|
673 | %http://urapiv.wordpress.com |
---|
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 |
---|
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) |
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704 | F=0; |
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705 | for i=-1:1 |
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706 | for j=-1:1 |
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707 | %following 15 lines based on |
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708 | %H. Nobach ᅵ M. Honkanen (2005) |
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709 | %Two-dimensional Gaussian regression for sub-pixel displacement |
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710 | %estimation in particle image velocimetry or particle position |
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711 | %estimation in particle tracking velocimetry |
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712 | %Experiments in Fluids (2005) 38: 511ᅵ515 |
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713 | c10(j+2,i+2)=i*log(result_conv(y+j, x+i)); |
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714 | c01(j+2,i+2)=j*log(result_conv(y+j, x+i)); |
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715 | c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i)); |
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716 | c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i)); |
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717 | c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i)); |
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718 | end |
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719 | end |
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720 | c10=(1/6)*sum(sum(c10)); |
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721 | c01=(1/6)*sum(sum(c01)); |
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722 | c11=(1/4)*sum(sum(c11)); |
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723 | c20=(1/6)*sum(sum(c20)); |
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724 | c02=(1/6)*sum(sum(c02)); |
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725 | deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2); |
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726 | deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2); |
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727 | if abs(deltax)<1 |
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728 | peakx=x+deltax; |
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729 | end |
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730 | if abs(deltay)<1 |
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731 | peaky=y+deltay; |
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732 | end |
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733 | end |
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734 | vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; |
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735 | |
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736 | %'RUN_FIX': function for fixing velocity fields: |
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737 | %----------------------------------------------- |
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738 | % RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref) |
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739 | % |
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740 | %filename: name of the netcdf file (used as input and output) |
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741 | %field: structure specifying the names of the fields to fix (depending on civ1 or civ2) |
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742 | %.vel_type='civ1' or 'civ2'; |
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743 | %.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1); |
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744 | %.fixflag=name of fix flag variable ('vec_FixFlag' for civ1) |
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745 | %flagindex: flag specifying which values of vec_f are removed: |
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746 | % if flagindex(1)=1: vec_f=-2 vectors are removed |
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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) |
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749 | %iter=1 for civ1 fields and iter=2 for civ2 fields |
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750 | %thresh_vecC: threshold in the image correlation vec_C |
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751 | %flag_mask: =1 mask used to remove vectors (0 else) |
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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 |
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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) |
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756 | %fieldref: 'civ1','filter1'...feld used in fileref |
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757 | |
---|
758 | function FF=fix(Param,F,C,U,V,X,Y) |
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759 | FF=zeros(size(F));%default |
---|
760 | |
---|
761 | %criterium on warn flags |
---|
762 | FlagName={'CheckFmin2','CheckF2','CheckF3','CheckF4'}; |
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763 | FlagVal=[-2 2 3 4]; |
---|
764 | for iflag=1:numel(FlagName) |
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765 | if isfield(Param,FlagName{iflag}) && Param.(FlagName{iflag}) |
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766 | FF=(FF==1| F==FlagVal(iflag)); |
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767 | end |
---|
768 | end |
---|
769 | %criterium on correlation values |
---|
770 | if isfield (Param,'MinCorr') |
---|
771 | FF=FF==1 | C<Param.MinCorr; |
---|
772 | end |
---|
773 | if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)) |
---|
774 | Umod= U.*U+V.*V; |
---|
775 | if isfield (Param,'MinVel')&&~isempty(Param.MinVel) |
---|
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 | |
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783 | |
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784 | |
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785 | |
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786 | |
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787 | |
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788 | |
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