1 | %'civ_3D': 3D PIV from image scan in a volume |
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2 | |
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3 | %------------------------------------------------------------------------ |
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4 | % function [Data,errormsg,result_conv]= civ_3D(Param) |
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5 | % |
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6 | %OUTPUT |
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7 | % Data=structure containing the PIV results and information on the processing parameters |
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8 | % errormsg=error message char string, decd ..fault='' |
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9 | % resul_conv: image inter-correlation function for the last grid point (used for tests) |
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10 | % |
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11 | %INPUT: |
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12 | % Param: Matlab structure of input parameters |
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13 | % Param contains info of the GUI series using the fct read_GUI. |
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14 | % Param.Action.RUN = 0 (to set the status of the GUI series) or =1 to RUN the computation |
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15 | % Param.InputTable: sets the input file(s) |
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16 | % if absent, the fct looks for input data in Param.ActionInput (test mode) |
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17 | % Param.OutputSubDir: sets the folder name of output file(s, |
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18 | % if absent no file is produced, result in the output structure Data (test mode) |
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19 | % Param.ActionInput: substructure with the parameters provided by the GUI civ_input |
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20 | % .Civ1: parameters for civ1cc |
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21 | % .Fix1: parameters for detect_false1 |
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22 | % .Patch1: |
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23 | % .Civ2: for civ2 |
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24 | % .Fix2: |
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25 | % .Patch2: |
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26 | |
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27 | %======================================================================= |
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28 | % Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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29 | % http://www.legi.grenoble-inp.fr |
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30 | % Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.fr |
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31 | % |
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32 | % This file is part of the toolbox UVMAT. |
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33 | % |
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34 | % UVMAT is free software; you can redistribute it and/or modify |
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35 | % it under the terms of the GNU General Public License as published |
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36 | % by the Free Software Foundation; either version 2 of the license, |
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37 | % or (at your option) any later version. |
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38 | % |
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39 | % UVMAT is distributed in the hope that it will be useful, |
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40 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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41 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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42 | % GNU General Public License (see LICENSE.txt) for more details. |
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43 | %======================================================================= |
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44 | |
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45 | function [Data,errormsg,result_conv]= civ_3D(Param) |
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46 | errormsg=''; |
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47 | |
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48 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed |
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49 | if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN |
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50 | path_series=fileparts(which('series')); |
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51 | addpath(fullfile(path_series,'series')) |
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52 | |
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53 | Data=civ_input(Param) |
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54 | |
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55 | Data.Program=mfilename;%gives the name of the current function |
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56 | Data.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
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57 | Data.IndexRange_j='whole';% prescribes the file index ranges j from min to max (options 'off'/'on'/'whole', 'on' by default) |
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58 | Data.NbSlice='off'; %nbre of slices ('off' by default) |
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59 | Data.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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60 | Data.FieldName='on';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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61 | Data.FieldTransform = 'off';%can use a transform function |
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62 | Data.ProjObject='off';%can use projection object(option 'off'/'on', |
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63 | Data.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) |
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64 | Data.OutputDirExt='.civ_3D';%set the output dir extension |
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65 | Data.OutputSubDirMode='last'; %select the last subDir in the input table as root of the output subdir name (option 'all'/'first'/'last', 'all' by default) |
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66 | Data.OutputFileMode='NbInput_i';% one output file expected per value of i index (used for waitbar) |
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67 | Data.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) |
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68 | if isfield(Data,'ActionInput') && isfield(Data.ActionInput,'PairIndices') && strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2') |
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69 | if isfield(Data.ActionInput.PairIndices,'ListPairCiv2') |
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70 | str_civ=Data.ActionInput.PairIndices.ListPairCiv2; |
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71 | else |
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72 | str_civ=Data.ActionInput.PairIndices.ListPairCiv1; |
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73 | end |
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74 | r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names'); |
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75 | if isempty(r) |
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76 | r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names'); |
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77 | if isempty(r) |
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78 | r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names'); |
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79 | end |
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80 | end |
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81 | if ~isempty(r) |
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82 | Data.j_index_1=stra2num(r.num1); |
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83 | Data.j_index_2=stra2num(r.num2); |
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84 | end |
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85 | end |
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86 | |
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87 | |
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88 | return |
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89 | end |
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90 | %% END OF ENTERING INPUT PARAMETER MODE |
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91 | |
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92 | %% RUN MODE: read input parameters from an xml file if input is a file name (batch mode) |
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93 | if ischar(Param) |
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94 | Param=xml2struct(Param);% read Param as input file (batch case) |
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95 | checkrun=0; |
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96 | RUNHandle=[]; |
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97 | else |
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98 | hseries=findobj(allchild(0),'Tag','series'); |
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99 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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100 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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101 | checkrun=1; |
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102 | end |
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103 | |
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104 | %% test input Param |
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105 | if ~isfield(Param,'InputTable') |
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106 | disp('ERROR: no input file entered') |
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107 | return |
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108 | end |
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109 | if ~isfield(Param,'ActionInput') |
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110 | disp_uvmat('ERROR','no parameter set for PIV',checkrun) |
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111 | return |
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112 | end |
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113 | iview_A=0;%default values |
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114 | |
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115 | if isfield(Param,'OutputSubDir')&& isfield(Param,'OutputDirExt') |
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116 | OutputDir=[Param.OutputSubDir Param.OutputDirExt]; |
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117 | OutputPath=fullfile(Param.OutputPath,num2str(Param.Experiment),num2str(Param.Device)); |
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118 | else |
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119 | disp_uvmat('ERROR','no output folder defined',checkrun) |
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120 | return |
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121 | end |
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122 | |
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123 | %% input files and indexing |
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124 | MaxIndex_i=Param.IndexRange.MaxIndex_i; |
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125 | MinIndex_i=Param.IndexRange.MinIndex_i; |
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126 | MaxIndex_j=ones(size(MaxIndex_i));MinIndex_j=ones(size(MinIndex_i)); |
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127 | if isfield(Param.IndexRange,'MaxIndex_j')&& isfield(Param.IndexRange,'MinIndex_j') |
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128 | MaxIndex_j=Param.IndexRange.MaxIndex_j; |
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129 | MinIndex_j=Param.IndexRange.MinIndex_j; |
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130 | end |
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131 | |
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132 | [~,i1_series,~,j1_series,~]=get_file_series(Param); |
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133 | iview_A=0;% series index (iview) for the first image series |
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134 | iview_B=0;% series index (iview) for the second image series (only non zero for option 'shift' comparing two image series ) |
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135 | if Param.ActionInput.CheckCiv1 |
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136 | iview_A=1;% usual PIV, the image series is on the first line of the table |
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137 | elseif Param.ActionInput.CheckCiv2 % civ2 is performed without Civ1, a netcdf file series is needed in the first table line |
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138 | iview_A=2;% the second line is used for the input images of Civ2 |
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139 | end |
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140 | if iview_A~=0 |
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141 | RootPath_A=Param.InputTable{iview_A,1}; |
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142 | RootFile_A=Param.InputTable{iview_A,3}; |
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143 | SubDir_A=Param.InputTable{iview_A,2}; |
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144 | NomType_A=Param.InputTable{iview_A,4}; |
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145 | FileExt_A=Param.InputTable{iview_A,5}; |
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146 | if iview_B==0 |
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147 | iview_B=iview_A;% the second image series is the same as the first |
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148 | end |
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149 | RootPath_B=Param.InputTable{iview_B,1}; |
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150 | RootFile_B=Param.InputTable{iview_B,3}; |
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151 | SubDir_B=Param.InputTable{iview_B,2}; |
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152 | NomType_B=Param.InputTable{iview_B,4}; |
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153 | FileExt_B=Param.InputTable{iview_B,5}; |
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154 | end |
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155 | |
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156 | PairCiv1=Param.ActionInput.PairIndices.ListPairCiv1; |
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157 | |
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158 | [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,~,NomTypeNc]=... |
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159 | find_pair_indices(PairCiv1,i1_series{1},j1_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j); |
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160 | |
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161 | if isempty(i1_series_Civ1) |
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162 | disp_uvmat('ERROR','no image pair for civ in the input file index range',checkrun) |
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163 | return |
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164 | end |
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165 | NbField_i=size(i1_series_Civ1,2); |
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166 | NbSlice=size(i1_series_Civ1,1); |
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167 | |
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168 | %% prepare output Data |
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169 | ListGlobalAttribute={'Conventions','Program','CivStage'}; |
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170 | Data.Conventions='uvmat/civdata_3D';% states the conventions used for the description of field variables and attributes |
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171 | Data.Program='civ_3D'; |
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172 | if isfield(Param,'UvmatRevision') |
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173 | Data.Program=[Data.Program ', uvmat r' Param.UvmatRevision]; |
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174 | end |
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175 | Data.CivStage=0;%default |
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176 | list_param=(fieldnames(Param.ActionInput.Civ1))'; |
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177 | list_param(strcmp('TestCiv1',list_param))=[];% remove the parameter TestCiv1 from the list |
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178 | Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before each string in list_param |
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179 | Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images |
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180 | Data.ListGlobalAttribute=[ListGlobalAttribute Civ1_param]; |
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181 | % set the list of variables |
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182 | Data.ListVarName={'Coord_z','Coord_y','Coord_x','Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_W','Civ1_C','Civ1_FF'};% cell array containing the names of the fields to record |
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183 | Data.VarDimName={'npz','npy','npx',{'npz','npy','npx'},{'npz','npy','npx'},{'npz','npy','npx'},{'npz','npy','npx'},... |
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184 | {'npz','npy','npx'},{'npz','npy','npx'},{'npz','npy','npx'}}; |
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185 | Data.VarAttribute{1}.Role='coord_x'; |
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186 | Data.VarAttribute{2}.Role='coord_y'; |
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187 | Data.VarAttribute{3}.Role='vector_x'; |
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188 | Data.VarAttribute{4}.Role='vector_y'; |
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189 | Data.VarAttribute{5}.Role='vector_z'; |
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190 | Data.VarAttribute{6}.Role='ancillary'; |
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191 | Data.VarAttribute{7}.Role='errorflag'; |
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192 | Data.Coord_z=j1_series_Civ1; |
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193 | % path for output nc file |
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194 | OutputPath=fullfile(Param.OutputPath,num2str(Param.Experiment),num2str(Param.Device),[Param.OutputSubDir Param.OutputDirExt]); |
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195 | |
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196 | %% get timing from the ImaDoc file or input video |
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197 | if iview_A~=0 |
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198 | XmlFileName=find_imadoc(RootPath_A,SubDir_A); |
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199 | Time=[]; |
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200 | if ~isempty(XmlFileName) |
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201 | XmlData=imadoc2struct(XmlFileName); |
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202 | if isfield(XmlData,'Time') |
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203 | Time=XmlData.Time; |
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204 | end |
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205 | if isfield(XmlData,'Camera') |
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206 | if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice) |
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207 | NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform |
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208 | if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) |
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209 | msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); |
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210 | end |
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211 | end |
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212 | if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit) |
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213 | TimeUnit=XmlData.Camera.TimeUnit; |
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214 | end |
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215 | end |
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216 | end |
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217 | end |
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218 | |
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219 | maskoldname='';% initiate the mask name |
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220 | FileType_A=''; |
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221 | FileType_B=''; |
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222 | CheckOverwrite=1;%default |
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223 | if isfield(Param,'CheckOverwrite') |
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224 | CheckOverwrite=Param.CheckOverwrite; |
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225 | end |
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226 | Data.Civ1_ImageA=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(1),[],j1_series_Civ1(1,1)); |
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227 | Data.Civ1_ImageB=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i1_series_Civ1(1),[],j2_series_Civ1(1,1)); |
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228 | FileInfo=get_file_info(Data.Civ1_ImageA); |
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229 | par_civ1=Param.ActionInput.Civ1;% parameters for civ1 |
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230 | par_civ1.ImageHeight=FileInfo.Height;npy=FileInfo.Height; |
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231 | par_civ1.ImageWidth=FileInfo.Width;npx=FileInfo.Width; |
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232 | SearchRange_z=floor(Param.ActionInput.Civ1.SearchBoxSize(3)/2); |
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233 | par_civ1.Dz=Param.ActionInput.Civ1.Dz; |
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234 | par_civ1.ImageA=zeros(2*SearchRange_z+1,npy,npx); |
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235 | par_civ1.ImageB=zeros(2*SearchRange_z+1,npy,npx); |
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236 | |
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237 | |
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238 | |
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239 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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240 | %%%%% MAIN LOOP %%%%%% |
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241 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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242 | for ifield=1:NbField_i |
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243 | tstart=tic; |
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244 | time_civ1=0; |
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245 | time_patch1=0; |
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246 | time_civ2=0; |
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247 | time_patch2=0; |
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248 | if checkrun% update the waitbar in interactive mode with GUI series (checkrun=1) |
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249 | update_waitbar(WaitbarHandle,ifield/NbField_i) |
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250 | if checkrun && ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
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251 | disp('program stopped by user') |
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252 | break |
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253 | end |
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254 | end |
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255 | |
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256 | %indicate the values of all the global attributes in the output data |
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257 | i1=i1_series_Civ1(ifield); |
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258 | i2=i1; |
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259 | if ~isempty(i2_series_Civ1) |
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260 | i2=i2_series_Civ1(ifield); |
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261 | end |
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262 | j1=1; |
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263 | if ~isempty(j1_series_Civ1) |
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264 | j1=j1_series_Civ1(ifield); |
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265 | end |
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266 | j2=j1; |
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267 | if ~isempty(j2_series_Civ1) |
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268 | j2=j2_series_Civ1(ifield); |
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269 | end |
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270 | |
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271 | Data.Civ1_Time=(Time(i2+1,j2+1)+Time(i1+1,j1+1))/2;% the Time is the Time at the middle of the image pair |
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272 | Data.Civ1_Dt=Time(i2+1,j2+1)-Time(i1+1,j1+1); |
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273 | |
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274 | for ilist=1:length(list_param) |
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275 | Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist}); |
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276 | end |
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277 | |
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278 | Data.CivStage=1; |
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279 | |
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280 | ncfile_out=fullfile_uvmat(OutputPath,'',Param.InputTable{1,3},'.nc',... |
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281 | '_1-1',i1_series_Civ1(ifield),i2_series_Civ1(ifield)); %output file name |
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282 | |
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283 | if ~CheckOverwrite && exist(ncfile_out,'file') |
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284 | disp(['existing output file ' ncfile_out ' already exists, skip to next field']) |
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285 | continue% skip iteration if the mode overwrite is desactivated and the result file already exists |
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286 | end |
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287 | |
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288 | |
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289 | %% Civ1 |
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290 | % if Civ1 computation is requested |
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291 | if isfield (Param.ActionInput,'Civ1') |
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292 | |
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293 | disp('civ1 started') |
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294 | |
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295 | % read input images by vertical blocks with nbre of images equal to 2*SearchRange+1, |
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296 | par_civ1.ImageA=zeros(2*SearchRange_z+1,npy,npx);%image block initiation |
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297 | par_civ1.ImageB=zeros(2*SearchRange_z+1,npy,npx); |
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298 | |
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299 | z_index=1;%first vertical block centered at image index z_index=par_civ1.Dz |
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300 | for iz=1:par_civ1.Dz+SearchRange_z |
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301 | j_image_index=j1_series_Civ1(iz,1)% j index of the current image |
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302 | ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(1,ifield),[],j_image_index);% |
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303 | A= read_image(ImageName_A,FileType_A); |
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304 | ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(1,ifield),[],j_image_index); |
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305 | B= read_image(ImageName_B,FileType_B); |
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306 | par_civ1.ImageA(iz+par_civ1.Dz-1,:,:) = A; |
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307 | par_civ1.ImageB(iz+par_civ1.Dz-1,:,:) = B; |
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308 | end |
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309 | % calculate velocity data at the first position z, corresponding to j_index=par_civ1.Dz |
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310 | [Data.Civ1_X(1,:,:),Data.Civ1_Y(1,:,:), Data.Civ1_U(1,:,:), Data.Civ1_V(1,:,:),Data.Civ1_W(1,:,:),... |
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311 | Data.Civ1_C(1,:,:), Data.Civ1_FF(1,:,:), result_conv, errormsg] = civ3D (par_civ1); |
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312 | if ~isempty(errormsg) |
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313 | disp_uvmat('ERROR',errormsg,checkrun) |
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314 | return |
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315 | end |
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316 | for z_index=2:floor((NbSlice-1)/par_civ1.Dz)% loop on slices |
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317 | par_civ1.ImageA=circshift(par_civ1.ImageA,-par_civ1.Dz);%shift the indices in the image block upward by par_civ1.Dz |
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318 | par_civ1.ImageB=circshift(par_civ1.ImageA,-par_civ1.Dz); |
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319 | for iz=1:par_civ1.Dz %read the new images at the end of the image block |
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320 | j_image_index=j1_series_Civ1(z_index*par_civ1.Dz+SearchRange_z-par_civ1.Dz+iz,1) |
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321 | ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(1,ifield),[],j_image_index);% |
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322 | A= read_image(ImageName_A,FileType_A); |
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323 | ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(1,ifield),[],j_image_index); |
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324 | B= read_image(ImageName_B,FileType_B); |
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325 | par_civ1.ImageA(2*SearchRange_z+1-par_civ1.Dz+iz,:,:) = A; |
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326 | par_civ1.ImageB(2*SearchRange_z+1-par_civ1.Dz+iz,:,:) = B; |
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327 | end |
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328 | % caluclate velocity data (y and v in indices, reverse to y component) |
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329 | [Data.Civ1_X(z_index,:,:),Data.Civ1_Y(z_index,:,:), Data.Civ1_U(z_index,:,:), Data.Civ1_V(z_index,:,:),Data.Civ1_W(z_index,:,:),... |
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330 | Data.Civ1_C(z_index,:,:), Data.Civ1_FF(z_index,:,:), result_conv, errormsg] = civ3D (par_civ1); |
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331 | |
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332 | if ~isempty(errormsg) |
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333 | disp_uvmat('ERROR',errormsg,checkrun) |
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334 | return |
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335 | end |
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336 | end |
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337 | Data.Civ1_C=double(Data.Civ1_C); |
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338 | Data.Civ1_C(Data.Civ1_C==Inf)=0; |
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339 | [npz,npy,npx]=size(Data.Civ1_X); |
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340 | Data.Coord_z=1:npz; |
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341 | Data.Coord_y=1:npy; |
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342 | Data.Coord_x=1:npx; |
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343 | % case of mask TO ADAPT |
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344 | if par_civ1.CheckMask&&~isempty(par_civ1.Mask) |
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345 | if isfield(par_civ1,'NbSlice') |
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346 | [RootPath_mask,SubDir_mask,RootFile_mask,i1_mask,i2_mask,j1_mask,j2_mask,Ext_mask]=fileparts_uvmat(Param.ActionInput.Civ1.Mask); |
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347 | i1_mask=mod(i1-1,par_civ1.NbSlice)+1; |
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348 | maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',i1_mask); |
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349 | else |
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350 | maskname=Param.ActionInput.Civ1.Mask; |
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351 | end |
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352 | if strcmp(maskoldname,maskname)% mask exist, not already read in civ1 |
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353 | par_civ1.Mask=mask; %use mask already opened |
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354 | else |
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355 | if ~isempty(regexp(maskname,'(^http://)|(^https://)'))|| exist(maskname,'file') |
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356 | try |
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357 | par_civ1.Mask=imread(maskname);%update the mask, an store it for future use |
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358 | catch ME |
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359 | if ~isempty(ME.message) |
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360 | errormsg=['error reading input image: ' ME.message]; |
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361 | disp_uvmat('ERROR',errormsg,checkrun) |
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362 | return |
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363 | end |
---|
364 | end |
---|
365 | else |
---|
366 | par_civ1.Mask=[]; |
---|
367 | end |
---|
368 | mask=par_civ1.Mask; |
---|
369 | maskoldname=maskname; |
---|
370 | end |
---|
371 | end |
---|
372 | % Data.ListVarName=[Data.ListVarName 'Civ1_Z']; |
---|
373 | % Data.Civ1_X=[];Data.Civ1_Y=[];Data.Civ1_Z=[]; |
---|
374 | % Data.Civ1_U=[];Data.Civ1_V=[];Data.Civ1_C=[]; |
---|
375 | % |
---|
376 | % |
---|
377 | % Data.Civ1_X=[Data.Civ1_X reshape(xtable,[],1)]; |
---|
378 | % Data.Civ1_Y=[Data.Civ1_Y reshape(Param.Civ1.ImageHeight-ytable+1,[],1)]; |
---|
379 | % Data.Civ1_Z=[Data.Civ1_Z ivol*ones(numel(xtable),1)];% z=image index in image coordinates |
---|
380 | % Data.Civ1_U=[Data.Civ1_U reshape(utable,[],1)]; |
---|
381 | % Data.Civ1_V=[Data.Civ1_V reshape(-vtable,[],1)]; |
---|
382 | % Data.Civ1_C=[Data.Civ1_C reshape(ctable,[],1)]; |
---|
383 | % Data.Civ1_FF=[Data.Civ1_FF reshape(F,[],1)]; |
---|
384 | |
---|
385 | end |
---|
386 | |
---|
387 | %% Fix1 |
---|
388 | if isfield (Param.ActionInput,'Fix1') |
---|
389 | disp('detect_false1 started') |
---|
390 | if ~isfield (Param.ActionInput,'Civ1')% if we use existing Civ1, remove previous data beyond Civ1 |
---|
391 | Fix1_attr=find(strcmp('Fix1',Data.ListGlobalAttribute)); |
---|
392 | Data.ListGlobalAttribute(Fix1_attr)=[]; |
---|
393 | for ilist=1:numel(Fix1_attr) |
---|
394 | Data=rmfield(Data,Data.ListGlobalAttribute{Fix1_attr(ilist)}); |
---|
395 | end |
---|
396 | end |
---|
397 | list_param=fieldnames(Param.ActionInput.Fix1)'; |
---|
398 | Fix1_param=regexprep(list_param,'^.+','Fix1_$0');% insert 'Fix1_' before each string in ListFixParam |
---|
399 | %indicate the values of all the global attributes in the output data |
---|
400 | for ilist=1:length(list_param) |
---|
401 | Data.(Fix1_param{ilist})=Param.ActionInput.Fix1.(list_param{ilist}); |
---|
402 | end |
---|
403 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix1_param]; |
---|
404 | Data.Civ1_FF=uint8(detect_false(Param.ActionInput.Fix1,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V,Data.Civ1_FF)); |
---|
405 | Data.CivStage=2; |
---|
406 | end |
---|
407 | %% Patch1 |
---|
408 | if isfield (Param.ActionInput,'Patch1') |
---|
409 | disp('patch1 started') |
---|
410 | tstart_patch1=tic; |
---|
411 | |
---|
412 | % record the processing parameters of Patch1 as global attributes in the result nc file |
---|
413 | list_param=fieldnames(Param.ActionInput.Patch1)'; |
---|
414 | list_param(strcmp('TestPatch1',list_param))=[];% remove 'TestPatch1' from the list of parameters |
---|
415 | Patch1_param=regexprep(list_param,'^.+','Patch1_$0');% insert 'Patch1_' before each parameter name |
---|
416 | for ilist=1:length(list_param) |
---|
417 | Data.(Patch1_param{ilist})=Param.ActionInput.Patch1.(list_param{ilist}); |
---|
418 | end |
---|
419 | Data.CivStage=3;% record the new state of processing |
---|
420 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch1_param]; |
---|
421 | |
---|
422 | % list the variables to record |
---|
423 | nbvar=length(Data.ListVarName); |
---|
424 | Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbCentres','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}]; |
---|
425 | Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},'nb_subdomain_1',... |
---|
426 | {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}]; |
---|
427 | Data.VarAttribute{nbvar+1}.Role='vector_x'; |
---|
428 | Data.VarAttribute{nbvar+2}.Role='vector_y'; |
---|
429 | Data.VarAttribute{nbvar+5}.Role='coord_tps'; |
---|
430 | Data.VarAttribute{nbvar+6}.Role='vector_x'; |
---|
431 | Data.VarAttribute{nbvar+7}.Role='vector_y'; |
---|
432 | Data.Civ1_U_smooth=Data.Civ1_U; % zeros(size(Data.Civ1_X)); |
---|
433 | Data.Civ1_V_smooth=Data.Civ1_V; %zeros(size(Data.Civ1_X)); |
---|
434 | if isfield(Data,'Civ1_FF') |
---|
435 | ind_good=find(Data.Civ1_FF==0); |
---|
436 | else |
---|
437 | ind_good=1:numel(Data.Civ1_X); |
---|
438 | end |
---|
439 | if isempty(ind_good) |
---|
440 | disp_uvmat('ERROR','all vectors of civ1 are bad, check input parameters' ,checkrun) |
---|
441 | return |
---|
442 | end |
---|
443 | |
---|
444 | % perform Patch calculation using the UVMAT fct 'filter_tps' |
---|
445 | |
---|
446 | [Data.Civ1_SubRange,Data.Civ1_NbCentres,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=... |
---|
447 | 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); |
---|
448 | Data.Civ1_U_smooth(ind_good)=Ures;% take the interpolated (smoothed) velocity values for good vectors, keep civ1 data for the other |
---|
449 | Data.Civ1_V_smooth(ind_good)=Vres; |
---|
450 | Data.Civ1_FF(ind_good)=uint8(FFres); |
---|
451 | time_patch1=toc(tstart_patch1); |
---|
452 | disp('patch1 performed') |
---|
453 | end |
---|
454 | |
---|
455 | %% Civ2 |
---|
456 | if isfield (Param.ActionInput,'Civ2') |
---|
457 | disp('civ2 started') |
---|
458 | tstart_civ2=tic; |
---|
459 | par_civ2=Param.ActionInput.Civ2; |
---|
460 | % read input images |
---|
461 | par_civ2.ImageA=[]; |
---|
462 | par_civ2.ImageB=[]; |
---|
463 | if strcmp(Param.ActionInput.ListCompareMode,'displacement') |
---|
464 | ImageName_A_Civ2=Param.ActionInput.RefFile; |
---|
465 | else |
---|
466 | ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_civ2,[],j1_civ2); |
---|
467 | end |
---|
468 | if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield)) |
---|
469 | par_civ2.ImageA=par_civ1.ImageA; |
---|
470 | else |
---|
471 | [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield)); |
---|
472 | end |
---|
473 | ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_civ2,[],j2_civ2); |
---|
474 | if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2) |
---|
475 | par_civ2.ImageB=par_civ1.ImageB; |
---|
476 | else |
---|
477 | [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield)); |
---|
478 | end |
---|
479 | [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A_Civ2); |
---|
480 | par_civ2.ImageWidth=FileInfo_A.Width; |
---|
481 | par_civ2.ImageHeight=FileInfo_A.Height; |
---|
482 | if isfield(par_civ2,'Grid')% grid points set as input file |
---|
483 | if ischar(par_civ2.Grid)%read the grid file if the input is a file name |
---|
484 | par_civ2.Grid=dlmread(par_civ2.Grid); |
---|
485 | par_civ2.Grid(1,:)=[];%the first line must be removed (heading in the grid file) |
---|
486 | end |
---|
487 | else% automatic grid |
---|
488 | minix=floor(par_civ2.Dx/2)-0.5; |
---|
489 | maxix=minix+par_civ2.Dx*floor((par_civ2.ImageWidth-1)/par_civ2.Dx); |
---|
490 | miniy=floor(par_civ2.Dy/2)-0.5; |
---|
491 | maxiy=minix+par_civ2.Dy*floor((par_civ2.ImageHeight-1)/par_civ2.Dy); |
---|
492 | [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy); |
---|
493 | par_civ2.Grid(:,1)=reshape(GridX,[],1); |
---|
494 | par_civ2.Grid(:,2)=reshape(GridY,[],1); |
---|
495 | end |
---|
496 | % end |
---|
497 | |
---|
498 | % get the guess from patch1 or patch2 (case 'CheckCiv3') |
---|
499 | |
---|
500 | if isfield (par_civ2,'CheckCiv3') && par_civ2.CheckCiv3 %get the guess from patch2 |
---|
501 | SubRange= Data.Civ2_SubRange; |
---|
502 | NbCentres=Data.Civ2_NbCentres; |
---|
503 | Coord_tps=Data.Civ2_Coord_tps; |
---|
504 | U_tps=Data.Civ2_U_tps; |
---|
505 | V_tps=Data.Civ2_V_tps; |
---|
506 | CivStage=Data.CivStage;%store the current CivStage |
---|
507 | Civ1_Dt=Data.Civ2_Dt; |
---|
508 | Data=[];%reinitialise the result structure Data |
---|
509 | Data.ListGlobalAttribute={'Conventions','Program','CivStage'}; |
---|
510 | Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes |
---|
511 | Data.Program='civ_series'; |
---|
512 | Data.CivStage=CivStage+1;%update the current civStage after reinitialisation of Data |
---|
513 | Data.ListVarName={}; |
---|
514 | Data.VarDimName={}; |
---|
515 | else % get the guess from patch1 |
---|
516 | SubRange= Data.Civ1_SubRange; |
---|
517 | NbCentres=Data.Civ1_NbCentres; |
---|
518 | Coord_tps=Data.Civ1_Coord_tps; |
---|
519 | U_tps=Data.Civ1_U_tps; |
---|
520 | V_tps=Data.Civ1_V_tps; |
---|
521 | Civ1_Dt=Data.Civ1_Dt; |
---|
522 | Data.CivStage=4; |
---|
523 | end |
---|
524 | % else |
---|
525 | % SubRange= par_civ2.Civ1_SubRange; |
---|
526 | % NbCentres=par_civ2.Civ1_NbCentres; |
---|
527 | % Coord_tps=par_civ2.Civ1_Coord_tps; |
---|
528 | % U_tps=par_civ2.Civ1_U_tps; |
---|
529 | % V_tps=par_civ2.Civ1_V_tps; |
---|
530 | % Civ1_Dt=par_civ2.Civ1_Dt; |
---|
531 | % Civ2_Dt=par_civ2.Civ1_Dt; |
---|
532 | % Data.ListVarName={}; |
---|
533 | % Data.VarDimName={}; |
---|
534 | % end |
---|
535 | Shiftx=zeros(size(par_civ2.Grid,1),1);% shift expected from civ1 data |
---|
536 | Shifty=zeros(size(par_civ2.Grid,1),1); |
---|
537 | nbval=zeros(size(par_civ2.Grid,1),1);% nbre of interpolated values at each grid point (from the different patch subdomains) |
---|
538 | if par_civ2.CheckDeformation |
---|
539 | DUDX=zeros(size(par_civ2.Grid,1),1); |
---|
540 | DUDY=zeros(size(par_civ2.Grid,1),1); |
---|
541 | DVDX=zeros(size(par_civ2.Grid,1),1); |
---|
542 | DVDY=zeros(size(par_civ2.Grid,1),1); |
---|
543 | end |
---|
544 | NbSubDomain=size(SubRange,3); |
---|
545 | for isub=1:NbSubDomain% for each sub-domain of Patch1 |
---|
546 | nbvec_sub=NbCentres(isub);% nbre of Civ vectors in the subdomain |
---|
547 | ind_sel=find(par_civ2.Grid(:,1)>=SubRange(1,1,isub) & par_civ2.Grid(:,1)<=SubRange(1,2,isub) &... |
---|
548 | par_civ2.Grid(:,2)>=SubRange(2,1,isub) & par_civ2.Grid(:,2)<=SubRange(2,2,isub));% grid points in the subdomain |
---|
549 | if ~isempty(ind_sel) |
---|
550 | epoints = par_civ2.Grid(ind_sel,:);% coordinates of interpolation sites (measurement grids) |
---|
551 | ctrs=Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs |
---|
552 | nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for each interpolation point (in case of subdomain overlap) |
---|
553 | EM = tps_eval(epoints,ctrs);% thin plate spline (tps) coefficient |
---|
554 | Shiftx(ind_sel)=Shiftx(ind_sel)+EM*U_tps(1:nbvec_sub+3,isub);%velocity shift estimated by tps from civ1 |
---|
555 | Shifty(ind_sel)=Shifty(ind_sel)+EM*V_tps(1:nbvec_sub+3,isub); |
---|
556 | if par_civ2.CheckDeformation |
---|
557 | [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs |
---|
558 | DUDX(ind_sel)=DUDX(ind_sel)+EMDX*U_tps(1:nbvec_sub+3,isub); |
---|
559 | DUDY(ind_sel)=DUDY(ind_sel)+EMDY*U_tps(1:nbvec_sub+3,isub); |
---|
560 | DVDX(ind_sel)=DVDX(ind_sel)+EMDX*V_tps(1:nbvec_sub+3,isub); |
---|
561 | DVDY(ind_sel)=DVDY(ind_sel)+EMDY*V_tps(1:nbvec_sub+3,isub); |
---|
562 | end |
---|
563 | end |
---|
564 | end |
---|
565 | if par_civ2.CheckMask&&~isempty(par_civ2.Mask) |
---|
566 | if isfield(par_civ2,'NbSlice') |
---|
567 | [RootPath_mask,SubDir_mask,RootFile_mask,i1_mask,i2_mask,j1_mask,j2_mask,Ext_mask]=fileparts_uvmat(Param.ActionInput.Civ2.Mask); |
---|
568 | i1_mask=mod(i1-1,par_civ2.NbSlice)+1; |
---|
569 | maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',i1_mask); |
---|
570 | else |
---|
571 | maskname=Param.ActionInput.Civ2.Mask; |
---|
572 | end |
---|
573 | if strcmp(maskoldname,maskname)% mask exist, not already read in civ1 |
---|
574 | par_civ2.Mask=mask; %use mask already opened |
---|
575 | else |
---|
576 | if exist(maskname,'file') |
---|
577 | try |
---|
578 | par_civ2.Mask=imread(maskname);%update the mask, an store it for future use |
---|
579 | catch ME |
---|
580 | if ~isempty(ME.message) |
---|
581 | errormsg=['error reading input image: ' ME.message]; |
---|
582 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
583 | return |
---|
584 | end |
---|
585 | end |
---|
586 | else |
---|
587 | par_civ2.Mask=[]; |
---|
588 | end |
---|
589 | mask=par_civ2.Mask; |
---|
590 | maskoldname=maskname; |
---|
591 | end |
---|
592 | end |
---|
593 | |
---|
594 | |
---|
595 | if strcmp(Param.ActionInput.ListCompareMode,'displacement') |
---|
596 | Civ1_Dt=1; |
---|
597 | Civ2_Dt=1; |
---|
598 | else |
---|
599 | Civ2_Dt=Time(i2_civ2+1,j2_civ2+1)-Time(i1_civ2+1,j1_civ2+1); |
---|
600 | end |
---|
601 | |
---|
602 | par_civ2.SearchBoxShift=(Civ2_Dt/Civ1_Dt)*[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)]; |
---|
603 | % shift the grid points by half the expected shift to provide the correlation box position in image A |
---|
604 | par_civ2.Grid=[par_civ2.Grid(nbval>=1,1)-par_civ2.SearchBoxShift(:,1)/2 par_civ2.Grid(nbval>=1,2)-par_civ2.SearchBoxShift(:,2)/2]; |
---|
605 | if par_civ2.CheckDeformation |
---|
606 | par_civ2.DUDX=DUDX(nbval>=1)./nbval(nbval>=1); |
---|
607 | par_civ2.DUDY=DUDY(nbval>=1)./nbval(nbval>=1); |
---|
608 | par_civ2.DVDX=DVDX(nbval>=1)./nbval(nbval>=1); |
---|
609 | par_civ2.DVDY=DVDY(nbval>=1)./nbval(nbval>=1); |
---|
610 | end |
---|
611 | |
---|
612 | % calculate velocity data (y and v in image indices, reverse to y component) |
---|
613 | |
---|
614 | [xtable, ytable, utable, vtable, ctable, F,result_conv,errormsg] = civ (par_civ2); |
---|
615 | |
---|
616 | list_param=(fieldnames(Param.ActionInput.Civ2))'; |
---|
617 | list_param(strcmp('TestCiv2',list_param))=[];% remove the parameter TestCiv2 from the list |
---|
618 | Civ2_param=regexprep(list_param,'^.+','Civ2_$0');% insert 'Civ2_' before each string in list_param |
---|
619 | Civ2_param=[{'Civ2_ImageA','Civ2_ImageB','Civ2_Time','Civ2_Dt'} Civ2_param]; %insert the names of the two input images |
---|
620 | %indicate the values of all the global attributes in the output data |
---|
621 | if exist('ImageName_A','var') |
---|
622 | Data.Civ2_ImageA=ImageName_A; |
---|
623 | Data.Civ2_ImageB=ImageName_B; |
---|
624 | if strcmp(Param.ActionInput.ListCompareMode,'displacement') |
---|
625 | Data.Civ2_Time=Time(i2_civ2+1,j2_civ2+1);% the Time is the Time of the secodn image |
---|
626 | Data.Civ2_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading |
---|
627 | else |
---|
628 | Data.Civ2_Time=(Time(i2_civ2+1,j2_civ2+1)+Time(i1_civ2+1,j1_civ2+1))/2; |
---|
629 | Data.Civ2_Dt=Civ2_Dt; |
---|
630 | end |
---|
631 | end |
---|
632 | for ilist=1:length(list_param) |
---|
633 | Data.(Civ2_param{4+ilist})=Param.ActionInput.Civ2.(list_param{ilist}); |
---|
634 | end |
---|
635 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param]; |
---|
636 | |
---|
637 | nbvar=numel(Data.ListVarName); |
---|
638 | % define the Civ2 variable (if Civ2 data are not replaced from previous calculation) |
---|
639 | if isempty(find(strcmp('Civ2_X',Data.ListVarName),1)) |
---|
640 | Data.ListVarName=[Data.ListVarName {'Civ2_X','Civ2_Y','Civ2_U','Civ2_V','Civ2_C','Civ2_FF'}];% cell array containing the names of the fields to record |
---|
641 | Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}]; |
---|
642 | Data.VarAttribute{nbvar+1}.Role='coord_x'; |
---|
643 | Data.VarAttribute{nbvar+2}.Role='coord_y'; |
---|
644 | Data.VarAttribute{nbvar+3}.Role='vector_x'; |
---|
645 | Data.VarAttribute{nbvar+4}.Role='vector_y'; |
---|
646 | Data.VarAttribute{nbvar+5}.Role='ancillary'; |
---|
647 | Data.VarAttribute{nbvar+6}.Role='errorflag'; |
---|
648 | end |
---|
649 | Data.Civ2_X=reshape(xtable,[],1); |
---|
650 | Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1); |
---|
651 | Data.Civ2_U=reshape(utable,[],1); |
---|
652 | Data.Civ2_V=reshape(-vtable,[],1); |
---|
653 | Data.Civ2_C=reshape(ctable,[],1); |
---|
654 | Data.Civ2_FF=reshape(F,[],1); |
---|
655 | disp('civ2 performed') |
---|
656 | time_civ2=toc(tstart_civ2); |
---|
657 | elseif ~isfield(Data,'ListVarName') % we start there, using existing Civ2 data |
---|
658 | if exist('ncfile','var') |
---|
659 | CivFile=ncfile; |
---|
660 | [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and detect_false1 data in the existing netcdf file |
---|
661 | if ~isempty(errormsg) |
---|
662 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
663 | return |
---|
664 | end |
---|
665 | % elseif isfield(Param,'Civ2_X')% use Civ2 data as input in Param (test mode) |
---|
666 | % Data.ListGlobalAttribute={}; |
---|
667 | % Data.ListVarName={}; |
---|
668 | % Data.VarDimName={}; |
---|
669 | % Data.Civ2_X=Param.Civ2_X; |
---|
670 | % Data.Civ2_Y=Param.Civ2_Y; |
---|
671 | % Data.Civ2_U=Param.Civ2_U; |
---|
672 | % Data.Civ2_V=Param.Civ2_V; |
---|
673 | % Data.Civ2_FF=Param.Civ2_FF; |
---|
674 | end |
---|
675 | end |
---|
676 | |
---|
677 | %% Fix2 |
---|
678 | if isfield (Param.ActionInput,'Fix2') |
---|
679 | disp('detect_false2 started') |
---|
680 | list_param=fieldnames(Param.ActionInput.Fix2)'; |
---|
681 | Fix2_param=regexprep(list_param,'^.+','Fix2_$0');% insert 'Fix1_' before each string in ListFixParam |
---|
682 | %indicate the values of all the global attributes in the output data |
---|
683 | for ilist=1:length(list_param) |
---|
684 | Data.(Fix2_param{ilist})=Param.ActionInput.Fix2.(list_param{ilist}); |
---|
685 | end |
---|
686 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix2_param]; |
---|
687 | Data.Civ2_FF=detect_false(Param.ActionInput.Fix2,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V,Data.Civ2_FF); |
---|
688 | Data.CivStage=Data.CivStage+1; |
---|
689 | end |
---|
690 | |
---|
691 | %% Patch2 |
---|
692 | if isfield (Param.ActionInput,'Patch2') |
---|
693 | disp('patch2 started') |
---|
694 | tstart_patch2=tic; |
---|
695 | list_param=fieldnames(Param.ActionInput.Patch2)'; |
---|
696 | list_param(strcmp('TestPatch2',list_param))=[];% remove the parameter TestCiv1 from the list |
---|
697 | Patch2_param=regexprep(list_param,'^.+','Patch2_$0');% insert 'Fix1_' before each string in ListFixParam |
---|
698 | %indicate the values of all the global attributes in the output data |
---|
699 | for ilist=1:length(list_param) |
---|
700 | Data.(Patch2_param{ilist})=Param.ActionInput.Patch2.(list_param{ilist}); |
---|
701 | end |
---|
702 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch2_param]; |
---|
703 | |
---|
704 | nbvar=length(Data.ListVarName); |
---|
705 | Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbCentres','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}]; |
---|
706 | Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},... |
---|
707 | {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}]; |
---|
708 | |
---|
709 | Data.VarAttribute{nbvar+1}.Role='vector_x'; |
---|
710 | Data.VarAttribute{nbvar+2}.Role='vector_y'; |
---|
711 | Data.VarAttribute{nbvar+5}.Role='coord_tps'; |
---|
712 | Data.VarAttribute{nbvar+6}.Role='vector_x'; |
---|
713 | Data.VarAttribute{nbvar+7}.Role='vector_y'; |
---|
714 | Data.Civ2_U_smooth=Data.Civ2_U; |
---|
715 | Data.Civ2_V_smooth=Data.Civ2_V; |
---|
716 | if isfield(Data,'Civ2_FF') |
---|
717 | ind_good=find(Data.Civ2_FF==0); |
---|
718 | else |
---|
719 | ind_good=1:numel(Data.Civ2_X); |
---|
720 | end |
---|
721 | if isempty(ind_good) |
---|
722 | disp_uvmat('ERROR','all vectors of civ2 are bad, check input parameters' ,checkrun) |
---|
723 | return |
---|
724 | end |
---|
725 | |
---|
726 | [Data.Civ2_SubRange,Data.Civ2_NbCentres,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures,Vres,tild,FFres]=... |
---|
727 | 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); |
---|
728 | Data.Civ2_U_smooth(ind_good)=Ures; |
---|
729 | Data.Civ2_V_smooth(ind_good)=Vres; |
---|
730 | Data.Civ2_FF(ind_good)=FFres; |
---|
731 | Data.CivStage=Data.CivStage+1; |
---|
732 | time_patch2=toc(tstart_patch2); |
---|
733 | disp('patch2 performed') |
---|
734 | end |
---|
735 | |
---|
736 | %% write result in a netcdf file if requested |
---|
737 | % if CheckOutputFile |
---|
738 | errormsg=struct2nc(ncfile_out,Data); |
---|
739 | if isempty(errormsg) |
---|
740 | disp([ncfile_out ' written']) |
---|
741 | %[success,msg] = fileattrib(ncfile_out ,'+w','g');% done in struct2nc |
---|
742 | else |
---|
743 | disp(errormsg) |
---|
744 | end |
---|
745 | time_total=toc(tstart); |
---|
746 | disp(['ellapsed time ' num2str(time_total/60,2) ' minutes']) |
---|
747 | disp(['time civ1 ' num2str(time_civ1,2) ' s']) |
---|
748 | disp(['time patch1 ' num2str(time_patch1,2) ' s']) |
---|
749 | disp(['time civ2 ' num2str(time_civ2,2) ' s']) |
---|
750 | disp(['time patch2 ' num2str(time_patch2,2) ' s']) |
---|
751 | |
---|
752 | end |
---|
753 | |
---|
754 | |
---|
755 | % 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/ |
---|
756 | %-------------------------------------------------------------------------- |
---|
757 | % function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi) |
---|
758 | % |
---|
759 | % OUTPUT: |
---|
760 | % xtable: set of x coordinates |
---|
761 | % ytable: set of y coordiantes |
---|
762 | % utable: set of u displacements (along x) |
---|
763 | % vtable: set of v displacements (along y) |
---|
764 | % ctable: max image correlation for each vector |
---|
765 | % typevector: set of flags, =1 for good, =0 for NaN vectors |
---|
766 | % |
---|
767 | %INPUT: |
---|
768 | % par_civ: structure of input parameters, with fields: |
---|
769 | % .ImageA: first image for correlation (matrix) |
---|
770 | % .ImageB: second image for correlation(matrix) |
---|
771 | % .CorrBoxSize: 1,2 vector giving the size of the correlation box in x and y |
---|
772 | % .SearchBoxSize: 1,2 vector giving the size of the search box in x and y |
---|
773 | % .SearchBoxShift: 1,2 vector or 2 column matrix (for civ2) giving the shift of the search box in x and y |
---|
774 | % .CorrSmooth: =1 or 2 determines the choice of the sub-pixel determination of the correlation max |
---|
775 | % .ImageWidth: nb of pixels of the image in x |
---|
776 | % .Dx, Dy: mesh for the PIV calculation |
---|
777 | % .Grid: grid giving the PIV calculation points (alternative to .Dx .Dy): centres of the correlation boxes in Image A |
---|
778 | % .Mask: name of a mask file or mask image matrix itself |
---|
779 | % .MinIma: thresholds for image luminosity |
---|
780 | % .MaxIma |
---|
781 | % .CheckDeformation=1 for subpixel interpolation and image deformation (linear transform) |
---|
782 | % .DUDX: matrix of deformation obtained from patch at each grid point |
---|
783 | % .DUDY |
---|
784 | % .DVDX: |
---|
785 | % .DVDY |
---|
786 | |
---|
787 | function [xtable,ytable,utable,vtable,wtable,ctable,FF,result_conv,errormsg] = civ3D (par_civ) |
---|
788 | |
---|
789 | %% prepare measurement grid |
---|
790 | |
---|
791 | minix=floor(par_civ.Dx/2)-0.5; |
---|
792 | maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx); |
---|
793 | miniy=floor(par_civ.Dy/2)-0.5;% first automatic grid point at half the mesh Dy |
---|
794 | maxiy=miniy+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy); |
---|
795 | [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy); |
---|
796 | par_civ.Grid(:,:,1)=GridX; |
---|
797 | par_civ.Grid(:,:,2)=GridY;% increases with array index, |
---|
798 | [nbvec_y,nbvec_x,~]=size(par_civ.Grid); |
---|
799 | % |
---|
800 | % |
---|
801 | % minix=floor(par_civ.Dx/2)-0.5; |
---|
802 | % maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx); |
---|
803 | % miniy=floor(par_civ.Dy/2)-0.5;% first automatic grid point at half the mesh Dy |
---|
804 | % maxiy=miniy+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy); |
---|
805 | % [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy); |
---|
806 | % par_civ.Grid(:,1)=reshape(GridX,[],1); |
---|
807 | % par_civ.Grid(:,2)=reshape(GridY,[],1);% increases with array index |
---|
808 | |
---|
809 | %% prepare correlation and search boxes |
---|
810 | ibx2=floor(par_civ.CorrBoxSize(1)/2); |
---|
811 | iby2=floor(par_civ.CorrBoxSize(2)/2); |
---|
812 | isx2=floor(par_civ.SearchBoxSize(1)/2); |
---|
813 | isy2=floor(par_civ.SearchBoxSize(2)/2); |
---|
814 | isz2=floor(par_civ.SearchBoxSize(3)/2); |
---|
815 | kref=isz2+1;%middle index of the z slice |
---|
816 | shiftx=round(par_civ.SearchBoxShift(:,1));%use the input shift estimate, rounded to the next integer value |
---|
817 | shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases |
---|
818 | if numel(shiftx)==1% case of a unique shift for the whole field( civ1) |
---|
819 | shiftx=shiftx*ones(nbvec_y,nbvec_x,1); |
---|
820 | shifty=shifty*ones(nbvec_y,nbvec_x,1); |
---|
821 | end |
---|
822 | |
---|
823 | %% Array initialisation and default output if par_civ.CorrSmooth=0 (just the grid calculated, no civ computation) |
---|
824 | xtable=round(par_civ.Grid(:,:,1)+0.5)-0.5; |
---|
825 | ytable=round(par_civ.ImageHeight-par_civ.Grid(:,:,2)+0.5)-0.5;% y index corresponding to the position in image coordiantes |
---|
826 | utable=shiftx;%zeros(nbvec,1); |
---|
827 | vtable=shifty;%zeros(nbvec,1); |
---|
828 | wtable=zeros(size(utable)); |
---|
829 | ctable=zeros(nbvec_y,nbvec_x,1); |
---|
830 | FF=zeros(nbvec_y,nbvec_x,1); |
---|
831 | result_conv=[]; |
---|
832 | errormsg=''; |
---|
833 | |
---|
834 | %% prepare mask |
---|
835 | check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold |
---|
836 | check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma); |
---|
837 | |
---|
838 | [npz,npy_ima,npx_ima]=size(par_civ.ImageA); |
---|
839 | if ~isequal(size(par_civ.ImageB),[npz npy_ima npx_ima]) |
---|
840 | errormsg='image pair with unequal size'; |
---|
841 | return |
---|
842 | end |
---|
843 | |
---|
844 | %% Apply mask |
---|
845 | % Convention for mask, IDEAS NOT IMPLEMENTED |
---|
846 | % mask >200 : velocity calculated |
---|
847 | % 200 >=mask>150;velocity not calculated, interpolation allowed (bad spots) |
---|
848 | % 150>=mask >100: velocity not calculated, nor interpolated |
---|
849 | % 100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries) |
---|
850 | % 20>=mask: velocity=0 |
---|
851 | checkmask=0; |
---|
852 | MinA=min(min(min(par_civ.ImageA))); |
---|
853 | %MinB=min(min(par_civ.ImageB)); |
---|
854 | %check_undefined=false(size(par_civ.ImageA)); |
---|
855 | if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) |
---|
856 | checkmask=1; |
---|
857 | if ~isequal(size(par_civ.Mask),[npy_ima npx_ima]) |
---|
858 | errormsg='mask must be an image with the same size as the images'; |
---|
859 | return |
---|
860 | end |
---|
861 | check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 ); |
---|
862 | end |
---|
863 | |
---|
864 | %% compute image correlations: MAINLOOP on velocity vectors |
---|
865 | corrmax=0; |
---|
866 | sum_square=1;% default |
---|
867 | mesh=1;% default |
---|
868 | CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1; |
---|
869 | if CheckDeformation |
---|
870 | mesh=0.25;%mesh in pixels for subpixel image interpolation (x 4 in each direction) |
---|
871 | par_civ.CorrSmooth=2;% use SUBPIX2DGAUSS (take into account more points near the max) |
---|
872 | end |
---|
873 | |
---|
874 | if par_civ.CorrSmooth~=0 % par_civ.CorrSmooth=0 implies no civ computation (just input image and grid points given) |
---|
875 | for ivec_x=1:nbvec_x |
---|
876 | for ivec_y=1:nbvec_y |
---|
877 | iref=round(par_civ.Grid(ivec_y,ivec_x,1)+0.5);% xindex on the image A for the middle of the correlation box |
---|
878 | jref=round(par_civ.ImageHeight-par_civ.Grid(ivec_y,ivec_x,2)+0.5);% j index for the middle of the correlation box in the image A |
---|
879 | subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage |
---|
880 | subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage |
---|
881 | subrange2_x=iref+shiftx(ivec_y,ivec_x)-isx2:iref+shiftx(ivec_y,ivec_x)+isx2;%x indices defining the second subimage |
---|
882 | subrange2_y=jref+shifty(ivec_y,ivec_x)-isy2:jref+shifty(ivec_y,ivec_x)+isy2;%y indices defining the second subimage |
---|
883 | image1_crop=MinA*ones(npz,numel(subrange1_y),numel(subrange1_x));% default value=min of image A |
---|
884 | image2_crop=MinA*ones(npz,numel(subrange2_y),numel(subrange2_x));% default value=min of image A |
---|
885 | check1_x=subrange1_x>=1 & subrange1_x<=par_civ.ImageWidth;% check which points in the subimage 1 are contained in the initial image 1 |
---|
886 | check1_y=subrange1_y>=1 & subrange1_y<=par_civ.ImageHeight; |
---|
887 | check2_x=subrange2_x>=1 & subrange2_x<=par_civ.ImageWidth;% check which points in the subimage 2 are contained in the initial image 2 |
---|
888 | check2_y=subrange2_y>=1 & subrange2_y<=par_civ.ImageHeight; |
---|
889 | 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 |
---|
890 | 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 |
---|
891 | if checkmask |
---|
892 | mask1_crop=ones(numel(subrange1_y),numel(subrange1_x));% default value=1 for mask |
---|
893 | mask2_crop=ones(numel(subrange2_y),numel(subrange2_x));% default value=1 for mask |
---|
894 | mask1_crop(check1_y,check1_x)=check_undefined(subrange1_y(check1_y),subrange1_x(check1_x));%extract a mask subimage (correlation box) from image A |
---|
895 | mask2_crop(check2_y,check2_x)=check_undefined(subrange2_y(check2_y),subrange2_x(check2_x));%extract a mask subimage (search box) from image B |
---|
896 | sizemask=sum(sum(mask1_crop))/(numel(subrange1_y)*numel(subrange1_x));%size of the masked part relative to the correlation sub-image |
---|
897 | if sizemask > 1/2% eliminate point if more than half of the correlation box is masked |
---|
898 | FF(ivec_y,ivec_x)=1; % |
---|
899 | utable(ivec_y,ivec_x)=NaN; |
---|
900 | vtable(ivec_y,ivec_x)=NaN; |
---|
901 | else |
---|
902 | FF(ivec_y,ivec_x)=0; |
---|
903 | image1_crop=image1_crop.*~mask1_crop;% put to zero the masked pixels (mask1_crop='true'=1) |
---|
904 | image2_crop=image2_crop.*~mask2_crop; |
---|
905 | image1_mean=mean(mean(image1_crop))/(1-sizemask); |
---|
906 | image2_mean=mean(mean(image2_crop))/(1-sizemask); |
---|
907 | end |
---|
908 | else |
---|
909 | image1_mean=mean(mean(image1_crop)); |
---|
910 | image2_mean=mean(mean(image2_crop)); |
---|
911 | end |
---|
912 | %threshold on image minimum |
---|
913 | if FF(ivec_y,ivec_x)==0 |
---|
914 | if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma) |
---|
915 | FF(ivec_y,ivec_x)=1; |
---|
916 | %threshold on image maximum |
---|
917 | elseif check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma) |
---|
918 | FF(ivec_y,ivec_x)=1; |
---|
919 | end |
---|
920 | if FF(ivec_y,ivec_x)==1 |
---|
921 | utable(ivec_y,ivec_x)=NaN; |
---|
922 | vtable(ivec_y,ivec_x)=NaN; |
---|
923 | else |
---|
924 | %mask |
---|
925 | if checkmask |
---|
926 | image1_crop=(image1_crop-image1_mean).*~mask1_crop;%substract the mean, put to zero the masked parts |
---|
927 | image2_crop=(image2_crop-image2_mean).*~mask2_crop; |
---|
928 | else |
---|
929 | image1_crop=(image1_crop-image1_mean); |
---|
930 | image2_crop=(image2_crop-image2_mean); |
---|
931 | end |
---|
932 | |
---|
933 | |
---|
934 | |
---|
935 | for kz=1:par_civ.SearchBoxSize(3) |
---|
936 | subima2=squeeze(image2_crop(kz,:,:)); |
---|
937 | subima1=squeeze(image1_crop(kref,:,:)); |
---|
938 | correl_xy=conv2(subima2,flip(flip(subima1,2),1),'valid'); |
---|
939 | result_conv(kz,:,:)= correl_xy; |
---|
940 | max_xy(kz)=max(max(correl_xy)); |
---|
941 | [xk(kz),yk(kz)]=find(correl_xy==max_xy(kz),1); |
---|
942 | |
---|
943 | end |
---|
944 | [corrmax,zmax]=max(max_xy); |
---|
945 | |
---|
946 | x=xk(zmax); |
---|
947 | y=yk(zmax); |
---|
948 | result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255 |
---|
949 | subimage2_crop=squeeze(image2_crop(zmax,y:y+2*iby2/mesh,x:x+2*ibx2/mesh));%subimage of image 2 corresponding to the optimum displacement of first image |
---|
950 | sum_square=sum(sum(squeeze(image1_crop(zmax,:,:).*image1_crop(zmax,:,:)))); |
---|
951 | sum_square=sum_square*sum(sum(subimage2_crop.*subimage2_crop));% product of variances of image 1 and 2 |
---|
952 | sum_square=sqrt(sum_square);% srt of the variance product to normalise correlation |
---|
953 | if ~isempty(y) && ~isempty(x) |
---|
954 | |
---|
955 | if par_civ.CorrSmooth==1 |
---|
956 | [vector,FF(ivec_y,ivec_x)] = SUBPIXGAUSS (squeeze(result_conv(zmax,:,:)),x,y);%TODO: improve by max optimisation along z |
---|
957 | elseif par_civ.CorrSmooth==2 |
---|
958 | [vector,FF(ivec_y,ivec_x)] = SUBPIX2DGAUSS (squeeze(result_conv(zmax,:,:)),x,y); |
---|
959 | else |
---|
960 | [vector,FF(ivec_y,ivec_x)] = quadr_fit(squeeze(result_conv(zmax,:,:)),x,y); |
---|
961 | end |
---|
962 | utable(ivec_y,ivec_x)=vector(1)*mesh+shiftx(ivec_y,ivec_x); |
---|
963 | vtable(ivec_y,ivec_x)=vector(2)*mesh+shifty(ivec_y,ivec_x); |
---|
964 | xtable(ivec_y,ivec_x)=iref+utable(ivec_y,ivec_x)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2) |
---|
965 | ytable(ivec_y,ivec_x)=jref+vtable(ivec_y,ivec_x)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge) |
---|
966 | iref=round(xtable(ivec_y,ivec_x)+0.5);% nearest image index for the middle of the vector |
---|
967 | jref=round(ytable(ivec_y,ivec_x)+0.5); |
---|
968 | wtable(ivec_y,ivec_x)=zmax-kref; |
---|
969 | % eliminate vectors located in the mask |
---|
970 | if checkmask && (iref<1 || jref<1 ||iref>npx_ima || jref>npy_ima ||( par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100)) |
---|
971 | utable(ivec_y,ivec_x)=0; |
---|
972 | vtable(ivec_y,ivec_x)=0; |
---|
973 | FF(ivec_y,ivec_x)=1; |
---|
974 | end |
---|
975 | ctable(ivec_y,ivec_x)=corrmax/sum_square;% correlation value |
---|
976 | |
---|
977 | else |
---|
978 | FF(ivec_y,ivec_x)=true; |
---|
979 | end |
---|
980 | end |
---|
981 | end |
---|
982 | end |
---|
983 | end |
---|
984 | end |
---|
985 | result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output |
---|
986 | |
---|
987 | %------------------------------------------------------------------------ |
---|
988 | % --- Find the maximum of the correlation function after interpolation |
---|
989 | % OUPUT: |
---|
990 | % vector = optimum displacement vector with subpixel correction |
---|
991 | % FF =flag: ='true' max too close to the edge of the search box (1 pixel margin) |
---|
992 | % INPUT: |
---|
993 | % x,y: position of the maximum correlation at integer values |
---|
994 | |
---|
995 | function [vector,FF] = SUBPIXGAUSS (result_conv,x,y) |
---|
996 | %------------------------------------------------------------------------ |
---|
997 | vector=[0 0]; %default |
---|
998 | [npy,npx]=size(result_conv); |
---|
999 | result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (=0 by discretisation, to avoid divergence in the log) |
---|
1000 | %the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ??? Israel Institute of Technology |
---|
1001 | %http://urapiv.wordpress.com |
---|
1002 | FF=false; |
---|
1003 | peaky = y; |
---|
1004 | if y < npy && y > 1 |
---|
1005 | f0 = log(result_conv(y,x)); |
---|
1006 | f1 = log(result_conv(y-1,x)); |
---|
1007 | f2 = log(result_conv(y+1,x)); |
---|
1008 | peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2); |
---|
1009 | else |
---|
1010 | FF=true; % error flag for vector truncated by the limited search box in y |
---|
1011 | end |
---|
1012 | peakx=x; |
---|
1013 | if x < npx-1 && x > 1 |
---|
1014 | f0 = log(result_conv(y,x)); |
---|
1015 | f1 = log(result_conv(y,x-1)); |
---|
1016 | f2 = log(result_conv(y,x+1)); |
---|
1017 | peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2); |
---|
1018 | else |
---|
1019 | FF=true; % warning flag for vector truncated by the limited search box in x |
---|
1020 | end |
---|
1021 | vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; |
---|
1022 | |
---|
1023 | %------------------------------------------------------------------------ |
---|
1024 | % --- Find the maximum of the correlation function after interpolation |
---|
1025 | function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y) |
---|
1026 | %------------------------------------------------------------------------ |
---|
1027 | % vector=[0 0]; %default |
---|
1028 | F=1; |
---|
1029 | peaky=y; |
---|
1030 | peakx=x; |
---|
1031 | result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log) |
---|
1032 | [npy,npx]=size(result_conv); |
---|
1033 | if (x < npx) && (y < npy) && (x > 1) && (y > 1) |
---|
1034 | F=0; |
---|
1035 | for i=-1:1 |
---|
1036 | for j=-1:1 |
---|
1037 | %following 15 lines based on |
---|
1038 | %H. Nobach ??? M. Honkanen (2005) |
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1039 | %Two-dimensional Gaussian regression for sub-pixel displacement |
---|
1040 | %estimation in particle image velocimetry or particle position |
---|
1041 | %estimation in particle tracking velocimetry |
---|
1042 | %Experiments in Fluids (2005) 38: 511???515 |
---|
1043 | c10(j+2,i+2)=i*log(result_conv(y+j, x+i)); |
---|
1044 | c01(j+2,i+2)=j*log(result_conv(y+j, x+i)); |
---|
1045 | c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i)); |
---|
1046 | c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i)); |
---|
1047 | c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i)); |
---|
1048 | end |
---|
1049 | end |
---|
1050 | c10=(1/6)*sum(sum(c10)); |
---|
1051 | c01=(1/6)*sum(sum(c01)); |
---|
1052 | c11=(1/4)*sum(sum(c11)); |
---|
1053 | c20=(1/6)*sum(sum(c20)); |
---|
1054 | c02=(1/6)*sum(sum(c02)); |
---|
1055 | deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2); |
---|
1056 | deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2); |
---|
1057 | if abs(deltax)<1 |
---|
1058 | peakx=x+deltax; |
---|
1059 | end |
---|
1060 | if abs(deltay)<1 |
---|
1061 | peaky=y+deltay; |
---|
1062 | end |
---|
1063 | end |
---|
1064 | vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; |
---|
1065 | |
---|
1066 | %------------------------------------------------------------------------ |
---|
1067 | % --- Find the maximum of the correlation function after quadratic interpolation |
---|
1068 | function [vector,F] = quadr_fit(result_conv,x,y) |
---|
1069 | [npy,npx]=size(result_conv); |
---|
1070 | if x<4 || y<4 || npx-x<4 ||npy-y <4 |
---|
1071 | F=1; |
---|
1072 | vector=[x y]; |
---|
1073 | else |
---|
1074 | F=0; |
---|
1075 | x_ind=x-4:x+4; |
---|
1076 | y_ind=y-4:y+4; |
---|
1077 | x_vec=0.25*(x_ind-x); |
---|
1078 | y_vec=0.25*(y_ind-y); |
---|
1079 | [X,Y]=meshgrid(x_vec,y_vec); |
---|
1080 | coord=[reshape(X,[],1) reshape(Y,[],1)]; |
---|
1081 | result_conv=reshape(result_conv(y_ind,x_ind),[],1); |
---|
1082 | |
---|
1083 | |
---|
1084 | % n=numel(X); |
---|
1085 | % x=[X Y]; |
---|
1086 | % X=X-0.5; |
---|
1087 | % Y=Y+0.5; |
---|
1088 | % y = (X.*X+2*Y.*Y+X.*Y+6) + 0.1*rand(n,1); |
---|
1089 | p = polyfitn(coord,result_conv,2); |
---|
1090 | A(1,1)=2*p.Coefficients(1); |
---|
1091 | A(1,2)=p.Coefficients(2); |
---|
1092 | A(2,1)=p.Coefficients(2); |
---|
1093 | A(2,2)=2*p.Coefficients(4); |
---|
1094 | vector=[x y]'-A\[p.Coefficients(3) p.Coefficients(5)]'; |
---|
1095 | vector=vector'-[floor(npx/2) floor(npy/2)]-1 ; |
---|
1096 | % zg = polyvaln(p,coord); |
---|
1097 | % figure |
---|
1098 | % surf(x_vec,y_vec,reshape(zg,9,9)) |
---|
1099 | % hold on |
---|
1100 | % plot3(X,Y,reshape(result_conv,9,9),'o') |
---|
1101 | % hold off |
---|
1102 | end |
---|
1103 | |
---|
1104 | |
---|
1105 | function FF=detect_false(Param,C,U,V,FFIn) |
---|
1106 | FF=FFIn;%default, good vectors |
---|
1107 | % FF=1, for correlation max at edge, not set in this function |
---|
1108 | % FF=2, for too small correlation |
---|
1109 | % FF=3, for velocity outside bounds |
---|
1110 | % FF=4 for exclusion by difference with the smoothed field, not set in this function |
---|
1111 | |
---|
1112 | if isfield (Param,'MinCorr') |
---|
1113 | FF(C<Param.MinCorr & FFIn==0)=2; |
---|
1114 | end |
---|
1115 | if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)) |
---|
1116 | Umod= U.*U+V.*V; |
---|
1117 | if isfield (Param,'MinVel')&&~isempty(Param.MinVel) |
---|
1118 | U2Min=Param.MinVel*Param.MinVel; |
---|
1119 | FF(Umod<U2Min & FFIn==0)=3; |
---|
1120 | end |
---|
1121 | if isfield (Param,'MaxVel')&&~isempty(Param.MaxVel) |
---|
1122 | U2Max=Param.MaxVel*Param.MaxVel; |
---|
1123 | FF(Umod>U2Max & FFIn==0)=3; |
---|
1124 | end |
---|
1125 | end |
---|
1126 | |
---|
1127 | %------------------------------------------------------------------------ |
---|
1128 | % --- determine the list of index pairs of processing file |
---|
1129 | function [i1_series,i2_series,j1_series,j2_series,check_bounds,NomTypeNc]=... |
---|
1130 | find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j) |
---|
1131 | %------------------------------------------------------------------------ |
---|
1132 | i1_series=i_series;% set of first image indexes |
---|
1133 | i2_series=i_series; |
---|
1134 | j1_series=j_series;%ones(size(i_series));% set of first image numbers |
---|
1135 | j2_series=j_series;%ones(size(i_series)); |
---|
1136 | r=regexp(str_civ,'^\D(?<ind>[i|j])=( -| )(?<num1>\d+)\|(?<num2>\d+)','names'); |
---|
1137 | if ~isempty(r) |
---|
1138 | mode=['D' r.ind]; |
---|
1139 | ind1=str2num(r.num1); |
---|
1140 | ind2=str2num(r.num2); |
---|
1141 | else |
---|
1142 | mode='j1-j2'; |
---|
1143 | r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names'); |
---|
1144 | if ~isempty(r) |
---|
1145 | NomTypeNc='_1ab'; |
---|
1146 | else |
---|
1147 | r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names'); |
---|
1148 | if ~isempty(r) |
---|
1149 | NomTypeNc='_1AB'; |
---|
1150 | else |
---|
1151 | r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names'); |
---|
1152 | if ~isempty(r) |
---|
1153 | NomTypeNc='_1_1-2'; |
---|
1154 | end |
---|
1155 | end |
---|
1156 | end |
---|
1157 | if isempty(r) |
---|
1158 | display('wrong pair mode input option') |
---|
1159 | else |
---|
1160 | ind1=stra2num(r.num1); |
---|
1161 | ind2=stra2num(r.num2); |
---|
1162 | end |
---|
1163 | end |
---|
1164 | switch mode |
---|
1165 | case 'Di' |
---|
1166 | i1_series=i_series-ind1;% set of first image numbers |
---|
1167 | i2_series=i_series+ind2; |
---|
1168 | check_bounds=i1_series<MinIndex_i | i2_series>MaxIndex_i; |
---|
1169 | if isempty(j_series) |
---|
1170 | NomTypeNc='_1-2'; |
---|
1171 | else |
---|
1172 | j1_series=j_series; |
---|
1173 | j2_series=j_series; |
---|
1174 | NomTypeNc='_1-2_1'; |
---|
1175 | end |
---|
1176 | case 'Dj' |
---|
1177 | j1_series=j_series-ind1; |
---|
1178 | j2_series=j_series+ind2; |
---|
1179 | check_bounds=j1_series<MinIndex_j | j2_series>MaxIndex_j; |
---|
1180 | NomTypeNc='_1_1-2'; |
---|
1181 | otherwise %bursts |
---|
1182 | i1_series=i_series(1,:);% do not sweep the j index |
---|
1183 | i2_series=i_series(1,:); |
---|
1184 | j1_series=ind1*ones(1,size(i_series,2));% j index is fixed by pair choice |
---|
1185 | j2_series=ind2*ones(1,size(i_series,2)); |
---|
1186 | check_bounds=zeros(size(i1_series));% no limitations due to min-max indices |
---|
1187 | end |
---|
1188 | |
---|
1189 | |
---|
1190 | |
---|
1191 | |
---|