1 | %'civ_series': PIV function activated by the general GUI series |
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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_series(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 2011-2014, LEGI / CNRS UJF G-INP, 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_series(Param) |
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41 | errormsg=''; |
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42 | |
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43 | %% 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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44 | if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN |
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45 | path_series=fileparts(which('series')); |
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46 | addpath(fullfile(path_series,'series')) |
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47 | Data=civ_input(Param);% introduce the civ parameters using the GUI civ_input |
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48 | if isempty(Data) |
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49 | Data=Param;% if civ_input has been cancelled, keep previous parameters |
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50 | end |
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51 | Data.Program=mfilename;%gives the name of the current function |
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52 | Data.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
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53 | Data.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
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54 | if isfield(Data,'ActionInput') && strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2') |
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55 | Data.Desable_j_index='on';% hide the j index in series (set by the pair choice in civ_input) |
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56 | end |
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57 | Data.NbSlice='off'; %nbre of slices ('off' by default) |
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58 | Data.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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59 | Data.FieldName='on';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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60 | Data.FieldTransform = 'off';%can use a transform function |
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61 | Data.ProjObject='off';%can use projection object(option 'off'/'on', |
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62 | Data.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) |
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63 | Data.OutputDirExt='.civ';%set the output dir extension |
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64 | 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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65 | Data.OutputFileMode='NbInput_i';% one output file expected per value of i index (used for waitbar) |
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66 | return |
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67 | end |
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68 | |
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69 | %% read input parameters from an xml file if input is a file name (batch mode) |
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70 | checkrun=1; |
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71 | if ischar(Param) |
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72 | Param=xml2struct(Param);% read Param as input file (batch case) |
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73 | checkrun=0; |
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74 | end |
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75 | if ~isfield(Param,'ActionInput') |
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76 | disp_uvmat('ERROR','no parameter set for PIV',checkrun) |
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77 | return |
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78 | end |
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79 | hseries=findobj(allchild(0),'Tag','series'); |
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80 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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81 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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82 | |
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83 | %% input files and indexing |
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84 | % NbField=1; |
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85 | MaxIndex_i=Param.IndexRange.MaxIndex_i; |
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86 | MinIndex_i=Param.IndexRange.MinIndex_i; |
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87 | MaxIndex_j=ones(size(MaxIndex_i));MinIndex_j=ones(size(MinIndex_i)); |
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88 | if isfield(Param.IndexRange,'MaxIndex_j')&& isfield(Param.IndexRange,'MinIndex_j') |
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89 | MaxIndex_j=Param.IndexRange.MaxIndex_j; |
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90 | MinIndex_j=Param.IndexRange.MinIndex_j; |
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91 | end |
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92 | if isfield(Param,'InputTable') |
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93 | [tild,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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94 | % iview_nc=0;% series index (iview) for an input nc file (for civ2 or patch2) |
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95 | iview_A=0;% series index (iview) for the first image series |
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96 | 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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97 | if Param.ActionInput.CheckCiv1 |
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98 | iview_A=1;% usual PIV, the image series is on the first line of the table |
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99 | elseif Param.ActionInput.CheckCiv2 % civ2 is performed without Civ1, a netcdf file series is needed in the first table line |
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100 | iview_A=2;% the second line is used for the input images of Civ2 |
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101 | end |
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102 | if strcmp(Param.ActionInput.ListCompareMode,'shift') |
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103 | iview_B=iview_A+1; % the second image series is on the next line of the input table |
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104 | end |
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105 | if iview_A~=0 |
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106 | RootPath_A=Param.InputTable{iview_A,1}; |
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107 | RootFile_A=Param.InputTable{iview_A,3}; |
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108 | SubDir_A=Param.InputTable{iview_A,2}; |
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109 | NomType_A=Param.InputTable{iview_A,4}; |
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110 | FileExt_A=Param.InputTable{iview_A,5}; |
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111 | if iview_B==0 |
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112 | iview_B=iview_A;% the second image series is the same as the first |
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113 | end |
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114 | RootPath_B=Param.InputTable{iview_B,1}; |
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115 | RootFile_B=Param.InputTable{iview_B,3}; |
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116 | SubDir_B=Param.InputTable{iview_B,2}; |
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117 | NomType_B=Param.InputTable{iview_B,4}; |
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118 | FileExt_B=Param.InputTable{iview_B,5}; |
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119 | end |
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120 | |
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121 | PairCiv2=''; |
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122 | switch Param.ActionInput.ListCompareMode |
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123 | case 'PIV' |
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124 | PairCiv1=Param.ActionInput.PairIndices.ListPairCiv1; |
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125 | if isfield(Param.ActionInput.PairIndices,'ListPairCiv2') |
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126 | PairCiv2=Param.ActionInput.PairIndices.ListPairCiv2;%string which determines the civ2 pair |
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127 | end |
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128 | if iview_A==1% if Civ1 is performed |
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129 | [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=... |
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130 | find_pair_indices(PairCiv1,i1_series{1},j1_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j); |
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131 | if ~isempty(PairCiv2) |
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132 | [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds_Civ2]=... |
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133 | find_pair_indices(PairCiv2,i1_series{1},j1_series{1},MinIndex_i(1),MaxIndex_i(1),MinIndex_j(1),MaxIndex_j(1)); |
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134 | check_bounds=check_bounds | check_bounds_Civ2; |
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135 | end |
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136 | else% we start from an existing Civ1 file |
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137 | i1_series_Civ1=i1_series{1}; |
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138 | i2_series_Civ1=i2_series{1}; |
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139 | j1_series_Civ1=j1_series{1}; |
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140 | j2_series_Civ1=j2_series{1}; |
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141 | NomTypeNc=Param.InputTable{1,4}; |
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142 | if ~isempty(PairCiv2) |
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143 | [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds,NomTypeNc]=... |
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144 | find_pair_indices(PairCiv2,i1_series{2},j1_series{2},MinIndex_i(2),MaxIndex_i(2),MinIndex_j(2),MaxIndex_j(2)); |
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145 | end |
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146 | end |
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147 | % i1_series_Civ1=i1_series_Civ1(~check_bounds); |
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148 | % i2_series_Civ1=i2_series_Civ1(~check_bounds); |
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149 | % j1_series_Civ1=j1_series_Civ1(~check_bounds); |
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150 | % j2_series_Civ1=j2_series_Civ1(~check_bounds); |
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151 | case 'displacement' |
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152 | i1_series_Civ1=Param.ActionInput.OriginIndex*ones(size(i1_series{1})); |
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153 | i2_series_Civ1=i1_series{1};i2_series_Civ2=i1_series{1}; |
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154 | j1_series_Civ1=ones(size(i1_series{1}));% first j index is 1 |
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155 | if isempty(j1_series_Civ1) |
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156 | j2_series_Civ1=ones(size(i1_series{1})); |
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157 | else |
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158 | j2_series_Civ1=j1_series_Civ1; |
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159 | end |
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160 | i1_series_Civ2=i1_series_Civ1; |
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161 | j1_series_Civ2=j1_series_Civ1; |
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162 | j2_series_Civ2=j2_series_Civ1; |
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163 | NomTypeNc=NomType; |
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164 | case 'shift' |
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165 | i1_series_Civ1=i1_series{1};i1_series_Civ2=i1_series{1}; |
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166 | i2_series_Civ1=i1_series{2};i2_series_Civ2=i1_series{2}; |
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167 | if isempty(j1_series{1}) |
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168 | j1_series_Civ1=ones(size(i1_series{1})); |
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169 | j2_series_Civ1=ones(size(i1_series{2})); |
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170 | else |
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171 | j1_series_Civ1=j1_series{1}; |
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172 | j2_series_Civ1=j1_series{2}; |
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173 | end |
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174 | j1_series_Civ2=j1_series_Civ1; |
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175 | j2_series_Civ2=j2_series_Civ1; |
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176 | NomTypeNc=NomType_A; |
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177 | end |
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178 | if isempty(j1_series_Civ1) |
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179 | FrameIndex_A_Civ1=i1_series_Civ1; |
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180 | FrameIndex_B_Civ1=i2_series_Civ1; |
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181 | j1_series_Civ1=ones(size(i1_series_Civ1)); |
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182 | j2_series_Civ1=ones(size(i1_series_Civ1)); |
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183 | else |
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184 | FrameIndex_A_Civ1=j1_series_Civ1; |
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185 | FrameIndex_B_Civ1=j2_series_Civ1; |
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186 | end |
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187 | if isempty(PairCiv2) |
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188 | FrameIndex_A_Civ2=FrameIndex_A_Civ1; |
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189 | FrameIndex_B_Civ2=FrameIndex_B_Civ1; |
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190 | else |
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191 | if isempty(j1_series_Civ2) |
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192 | FrameIndex_A_Civ2=i1_series_Civ2; |
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193 | FrameIndex_B_Civ2=i2_series_Civ2; |
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194 | j1_series_Civ2=ones(size(i1_series_Civ2)); |
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195 | j2_series_Civ2=ones(size(i1_series_Civ2)); |
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196 | else |
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197 | FrameIndex_A_Civ2=j1_series_Civ2; |
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198 | FrameIndex_B_Civ2=j2_series_Civ2; |
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199 | end |
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200 | end |
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201 | if isempty(i1_series_Civ1)||(~isempty(PairCiv2) && isempty(i1_series_Civ2)) |
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202 | disp_uvmat('ERROR','no image pair fo civ in the input file index range',checkrun) |
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203 | return |
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204 | end |
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205 | end |
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206 | |
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207 | %% check the first image pair |
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208 | try |
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209 | if Param.ActionInput.CheckCiv1% Civ1 is performed |
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210 | ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(1),[],j1_series_Civ1(1)); |
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211 | if ~exist(ImageName_A,'file') |
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212 | disp_uvmat('ERROR',['first input image ' ImageName_A ' does not exist'],checkrun) |
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213 | return |
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214 | end |
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215 | [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A); |
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216 | FileType_A=FileInfo_A.FileType; |
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217 | if strcmp(FileInfo_A.FileType,'netcdf') |
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218 | FieldName_A=Param.InputFields.FieldName; |
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219 | [DataIn,tild,tild,errormsg]=nc2struct(ImageName_A,{FieldName_A}); |
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220 | par_civ1.ImageA=DataIn.(FieldName_A); |
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221 | else |
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222 | [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(1)); |
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223 | end |
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224 | ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(1),[],j2_series_Civ1(1)); |
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225 | if ~exist(ImageName_B,'file') |
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226 | disp_uvmat('ERROR',['first input image ' ImageName_B ' does not exist'],checkrun) |
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227 | return |
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228 | end |
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229 | [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B); |
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230 | FileType_B=FileInfo_B.FileType; |
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231 | if strcmp(FileInfo_B.FileType,'netcdf') |
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232 | FieldName_B=Param.InputFields.FieldName; |
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233 | [DataIn,tild,tild,errormsg]=nc2struct(ImageName_B,{FieldName_B}); |
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234 | par_civ1.ImageB=DataIn.(FieldName_B); |
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235 | else |
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236 | [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(1)); |
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237 | end |
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238 | NbField=numel(i1_series_Civ1); |
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239 | elseif Param.ActionInput.CheckCiv2 % Civ2 is performed without Civ1 |
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240 | ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ2(1),[],j1_series_Civ2(1)); |
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241 | if ~exist(ImageName_A,'file') |
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242 | disp_uvmat('ERROR',['first input image ' ImageName_A ' does not exist'],checkrun) |
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243 | return |
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244 | end |
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245 | [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A); |
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246 | FileType_A=FileInfo_A.FileType; |
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247 | [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileInfo_A.FileType,VideoObject_A,FrameIndex_A_Civ2(1)); |
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248 | ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ2(1),[],j2_series_Civ2(1)); |
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249 | if ~exist(ImageName_B,'file') |
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250 | disp_uvmat('ERROR',['first input image ' ImageName_B ' does not exist'],checkrun) |
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251 | return |
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252 | end |
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253 | [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B); |
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254 | FileType_B=FileInfo_B.FileType; |
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255 | [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ2(1)); |
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256 | NbField=numel(i1_series_Civ2); |
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257 | else |
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258 | NbField=numel(i1_series_Civ1);% no image used (only fix or patch) TO CHECK |
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259 | end |
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260 | catch ME |
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261 | if ~isempty(ME.message) |
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262 | disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun) |
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263 | return |
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264 | end |
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265 | end |
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266 | |
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267 | |
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268 | %% Output directory |
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269 | OutputDir=[Param.OutputSubDir Param.OutputDirExt]; |
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270 | |
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271 | Data.ListGlobalAttribute={'Conventions','Program','CivStage'}; |
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272 | Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes |
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273 | Data.Program='civ_series'; |
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274 | Data.CivStage=0;%default |
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275 | maskname='';%default |
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276 | check_civx=0;%default |
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277 | |
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278 | %% get timing from the ImaDoc file or input video |
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279 | if iview_A~=0 |
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280 | XmlFileName=find_imadoc(RootPath_A,SubDir_A,RootFile_A,FileExt_A); |
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281 | time=[]; |
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282 | if ~isempty(XmlFileName) |
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283 | XmlData=imadoc2struct(XmlFileName); |
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284 | if isfield(XmlData,'Time') |
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285 | time=XmlData.Time; |
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286 | TimeSource='xml'; |
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287 | end |
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288 | if isfield(XmlData,'Camera') |
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289 | if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice) |
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290 | NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform |
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291 | if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) |
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292 | msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); |
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293 | end |
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294 | end |
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295 | if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit) |
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296 | TimeUnit=XmlData.Camera.TimeUnit; |
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297 | end |
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298 | end |
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299 | end |
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300 | if isempty(time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video'})))% case of video input |
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301 | time=zeros(FileInfo_A.NumberOfFrames+1,2); |
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302 | time(:,2)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate)'; |
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303 | TimeSource='video'; |
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304 | ColorType='truecolor'; |
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305 | end |
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306 | if isempty(time)% time = index i +0.001 index j by default |
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307 | %MinIndex_i=min(i1_series_Civ1); |
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308 | MaxIndex_i=max(i2_series_Civ1); |
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309 | %MinIndex_j=min(j1_series_Civ1); |
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310 | MaxIndex_j=max(j2_series_Civ1); |
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311 | time=(1:MaxIndex_i)'*ones(1,MaxIndex_j); |
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312 | time=time+0.001*ones(MaxIndex_i,1)*(1:MaxIndex_j); |
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313 | time=[zeros(1,MaxIndex_j);time];% insert a first line of zeros |
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314 | time=[zeros(MaxIndex_i+1,1) time];% insert a first column of zeros |
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315 | end |
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316 | |
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317 | if length(FileInfo_A) >1 %case of image with multiple frames |
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318 | nbfield=length(FileInfo_A); |
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319 | nbfield_j=1; |
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320 | end |
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321 | end |
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322 | |
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323 | %%%%% MAIN LOOP %%%%%% |
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324 | for ifield=1:NbField |
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325 | update_waitbar(WaitbarHandle,ifield/NbField) |
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326 | if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
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327 | disp('program stopped by user') |
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328 | break |
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329 | end |
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330 | if iview_A==0 |
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331 | ncfile=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},... |
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332 | NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),j1_series_Civ1(ifield),j2_series_Civ1(ifield)); |
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333 | else |
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334 | if iview_A==1% if Civ1 is performed |
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335 | Civ1Dir=OutputDir; |
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336 | else |
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337 | Civ1Dir=Param.InputTable{1,2}; |
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338 | end |
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339 | if strcmp(Param.ActionInput.ListCompareMode,'PIV') |
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340 | ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),... |
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341 | j1_series_Civ1(ifield),j2_series_Civ1(ifield)); |
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342 | else |
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343 | ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],... |
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344 | j1_series_Civ1(ifield),j2_series_Civ1(ifield)); |
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345 | end |
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346 | end |
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347 | %% Civ1 |
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348 | % if Civ1 computation is requested |
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349 | if isfield (Param.ActionInput,'Civ1') |
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350 | par_civ1=Param.ActionInput.Civ1; |
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351 | try |
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352 | ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield)); |
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353 | if strcmp(FileInfo_A.FileType,'netcdf') |
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354 | FieldName_A=Param.InputFields.FieldName; |
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355 | [DataIn,tild,tild,errormsg]=nc2struct(ImageName_A,{FieldName_A}); |
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356 | par_civ1.ImageA=DataIn.(FieldName_A); |
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357 | else |
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358 | [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield)); |
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359 | end |
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360 | ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield)); |
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361 | if strcmp(FileInfo_B.FileType,'netcdf') |
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362 | FieldName_B=Param.InputFields.FieldName; |
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363 | [DataIn,tild,tild,errormsg]=nc2struct(ImageName_B,{FieldName_B}); |
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364 | par_civ1.ImageB=DataIn.(FieldName_B); |
---|
365 | else |
---|
366 | [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield)); |
---|
367 | end |
---|
368 | catch ME |
---|
369 | if ~isempty(ME.message) |
---|
370 | disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun) |
---|
371 | return |
---|
372 | end |
---|
373 | end |
---|
374 | par_civ1.ImageWidth=size(par_civ1.ImageA,2);%FileInfo_A.Width; |
---|
375 | par_civ1.ImageHeight=size(par_civ1.ImageA,1);%FileInfo_A.Height; |
---|
376 | list_param=(fieldnames(Param.ActionInput.Civ1))'; |
---|
377 | Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before each string in list_param |
---|
378 | Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images |
---|
379 | %indicate the values of all the global attributes in the output data |
---|
380 | Data.Civ1_ImageA=ImageName_A; |
---|
381 | Data.Civ1_ImageB=ImageName_B; |
---|
382 | i1=i1_series_Civ1(ifield); |
---|
383 | i2=i1; |
---|
384 | if ~isempty(i2_series_Civ1) |
---|
385 | i2=i2_series_Civ1(ifield); |
---|
386 | end |
---|
387 | j1=1; |
---|
388 | if ~isempty(j1_series_Civ1) |
---|
389 | j1=j1_series_Civ1(ifield); |
---|
390 | end |
---|
391 | j2=j1; |
---|
392 | if ~isempty(j2_series_Civ1) |
---|
393 | j2=j2_series_Civ1(ifield); |
---|
394 | end |
---|
395 | Data.Civ1_Time=(time(i2+1,j2+1)+time(i1+1,j1+1))/2; |
---|
396 | Data.Civ1_Dt=time(i2+1,j2+1)-time(i1+1,j1+1); |
---|
397 | for ilist=1:length(list_param) |
---|
398 | Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist}); |
---|
399 | end |
---|
400 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ1_param]; |
---|
401 | Data.CivStage=1; |
---|
402 | |
---|
403 | % set the list of variables |
---|
404 | Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_F','Civ1_C'};% cell array containing the names of the fields to record |
---|
405 | Data.VarDimName={'nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1'}; |
---|
406 | Data.VarAttribute{1}.Role='coord_x'; |
---|
407 | Data.VarAttribute{2}.Role='coord_y'; |
---|
408 | Data.VarAttribute{3}.Role='vector_x'; |
---|
409 | Data.VarAttribute{4}.Role='vector_y'; |
---|
410 | Data.VarAttribute{5}.Role='warnflag'; |
---|
411 | |
---|
412 | if strcmp(Param.ActionInput.ListCompareMode, 'PIV volume') |
---|
413 | Data.ListVarName=[Data.ListVarName 'Civ1_Z']; |
---|
414 | Data.Civ1_X=[];Data.Civ1_Y=[];Data.Civ1_Z=[]; |
---|
415 | Data.Civ1_U=[];Data.Civ1_V=[];Data.Civ1_C=[];Data.Civ1_F=[]; |
---|
416 | for ivol=1:NbSlice |
---|
417 | % caluclate velocity data (y and v in indices, reverse to y component) |
---|
418 | [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ1); |
---|
419 | if ~isempty(errormsg) |
---|
420 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
421 | return |
---|
422 | end |
---|
423 | Data.Civ1_X=[Data.Civ1_X reshape(xtable,[],1)]; |
---|
424 | Data.Civ1_Y=[Data.Civ1_Y reshape(Param.Civ1.ImageHeight-ytable+1,[],1)]; |
---|
425 | Data.Civ1_Z=[Data.Civ1_Z ivol*ones(numel(xtable),1)];% z=image index in image coordinates |
---|
426 | Data.Civ1_U=[Data.Civ1_U reshape(utable,[],1)]; |
---|
427 | Data.Civ1_V=[Data.Civ1_V reshape(-vtable,[],1)]; |
---|
428 | Data.Civ1_C=[Data.Civ1_C reshape(ctable,[],1)]; |
---|
429 | Data.Civ1_F=[Data.Civ1_C reshape(F,[],1)]; |
---|
430 | end |
---|
431 | else %usual PIV |
---|
432 | % caluclate velocity data (y and v in indices, reverse to y component) |
---|
433 | [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ1); |
---|
434 | if ~isempty(errormsg) |
---|
435 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
436 | return |
---|
437 | end |
---|
438 | Data.Civ1_X=reshape(xtable,[],1); |
---|
439 | Data.Civ1_Y=reshape(par_civ1.ImageHeight-ytable+1,[],1); |
---|
440 | Data.Civ1_U=reshape(utable,[],1); |
---|
441 | Data.Civ1_V=reshape(-vtable,[],1); |
---|
442 | Data.Civ1_C=reshape(ctable,[],1); |
---|
443 | Data.Civ1_F=reshape(F,[],1); |
---|
444 | end |
---|
445 | else% we use existing Civ1 data |
---|
446 | if exist('ncfile','var') |
---|
447 | CivFile=ncfile; |
---|
448 | elseif isfield(Param.Patch1,'CivFile') |
---|
449 | CivFile=Param.Patch1.CivFile; |
---|
450 | end |
---|
451 | [Data,tild,tild,errormsg]=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format |
---|
452 | if ~isempty(errormsg) |
---|
453 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
454 | return |
---|
455 | end |
---|
456 | if ~isempty(Data.absolut_time_T0')%read civx file |
---|
457 | check_civx=1;% test for old civx data format |
---|
458 | [Data,vardetect,ichoice]=nc2struct(CivFile);%read the variables in the netcdf file |
---|
459 | else |
---|
460 | [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file |
---|
461 | end |
---|
462 | end |
---|
463 | |
---|
464 | %% Fix1 |
---|
465 | if isfield (Param.ActionInput,'Fix1') |
---|
466 | if ~isfield (Param.ActionInput,'Civ1')% if we use existing Civ1, remove previous data beyond Civ1 |
---|
467 | Fix1_attr=find(strcmp('Fix1',Data.ListGlobalAttribute)); |
---|
468 | Data.ListGlobalAttribute(Fix1_attr)=[]; |
---|
469 | for ilist=1:numel(Fix1_attr) |
---|
470 | Data=rmfield(Data,Data.ListGlobalAttribute{Fix1_attr(ilist)}); |
---|
471 | end |
---|
472 | end |
---|
473 | ListFixParam=fieldnames(Param.ActionInput.Fix1); |
---|
474 | for ilist=1:length(ListFixParam) |
---|
475 | ParamName=ListFixParam{ilist}; |
---|
476 | ListName=['Fix1_' ParamName]; |
---|
477 | eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];']) |
---|
478 | eval(['Data.' ListName '=Param.ActionInput.Fix1.' ParamName ';']) |
---|
479 | end |
---|
480 | if check_civx |
---|
481 | if ~isfield(Data,'fix') |
---|
482 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix']; |
---|
483 | Data.fix=1; |
---|
484 | Data.ListVarName=[Data.ListVarName {'vec_FixFlag'}]; |
---|
485 | Data.VarDimName=[Data.VarDimName {'nb_vectors'}]; |
---|
486 | end |
---|
487 | Data.vec_FixFlag=fix(Param.ActionInput.Fix1,Data.vec_F,Data.vec_C,Data.vec_U,Data.vec_V,Data.vec_X,Data.vec_Y); |
---|
488 | else |
---|
489 | Data.ListVarName=[Data.ListVarName {'Civ1_FF'}]; |
---|
490 | Data.VarDimName=[Data.VarDimName {'nb_vec_1'}]; |
---|
491 | nbvar=length(Data.ListVarName); |
---|
492 | Data.VarAttribute{nbvar}.Role='errorflag'; |
---|
493 | Data.Civ1_FF=fix(Param.ActionInput.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V); |
---|
494 | Data.CivStage=2; |
---|
495 | end |
---|
496 | end |
---|
497 | %% Patch1 |
---|
498 | if isfield (Param.ActionInput,'Patch1') |
---|
499 | if check_civx |
---|
500 | errormsg='Civ Matlab input needed for patch'; |
---|
501 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
502 | return |
---|
503 | end |
---|
504 | |
---|
505 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch1_Rho','Patch1_Threshold','Patch1_SubDomain'}]; |
---|
506 | Data.Patch1_FieldSmooth=Param.ActionInput.Patch1.FieldSmooth; |
---|
507 | Data.Patch1_MaxDiff=Param.ActionInput.Patch1.MaxDiff; |
---|
508 | Data.Patch1_SubDomainSize=Param.ActionInput.Patch1.SubDomainSize; |
---|
509 | nbvar=length(Data.ListVarName); |
---|
510 | Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbCentres','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}]; |
---|
511 | Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},'nb_subdomain_1',... |
---|
512 | {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}]; |
---|
513 | Data.VarAttribute{nbvar+1}.Role='vector_x'; |
---|
514 | Data.VarAttribute{nbvar+2}.Role='vector_y'; |
---|
515 | Data.VarAttribute{nbvar+5}.Role='coord_tps'; |
---|
516 | Data.VarAttribute{nbvar+6}.Role='vector_x'; |
---|
517 | Data.VarAttribute{nbvar+7}.Role='vector_y'; |
---|
518 | Data.Civ1_U_smooth=zeros(size(Data.Civ1_X)); |
---|
519 | Data.Civ1_V_smooth=zeros(size(Data.Civ1_X)); |
---|
520 | if isfield(Data,'Civ1_FF') |
---|
521 | ind_good=find(Data.Civ1_FF==0); |
---|
522 | else |
---|
523 | ind_good=1:numel(Data.Civ1_X); |
---|
524 | end |
---|
525 | [Data.Civ1_SubRange,Data.Civ1_NbCentres,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=... |
---|
526 | 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); |
---|
527 | Data.Civ1_U_smooth(ind_good)=Ures; |
---|
528 | Data.Civ1_V_smooth(ind_good)=Vres; |
---|
529 | Data.Civ1_FF(ind_good)=FFres; |
---|
530 | Data.CivStage=3; |
---|
531 | end |
---|
532 | |
---|
533 | %% Civ2 |
---|
534 | if isfield (Param.ActionInput,'Civ2') |
---|
535 | par_civ2=Param.ActionInput.Civ2; |
---|
536 | par_civ2.ImageA=[]; |
---|
537 | par_civ2.ImageB=[]; |
---|
538 | % if ~isfield(Param.Civ1,'ImageA') |
---|
539 | i1=i1_series_Civ2(ifield); |
---|
540 | i2=i1; |
---|
541 | if ~isempty(i2_series_Civ2) |
---|
542 | i2=i2_series_Civ2(ifield); |
---|
543 | end |
---|
544 | j1=1; |
---|
545 | if ~isempty(j1_series_Civ2) |
---|
546 | j1=j1_series_Civ2(ifield); |
---|
547 | end |
---|
548 | j2=j1; |
---|
549 | if ~isempty(j2_series_Civ2) |
---|
550 | j2=j2_series_Civ2(ifield); |
---|
551 | end |
---|
552 | ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1,[],j1); |
---|
553 | |
---|
554 | if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield)) |
---|
555 | par_civ2.ImageA=par_civ1.ImageA; |
---|
556 | else |
---|
557 | [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield)); |
---|
558 | end |
---|
559 | ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2,[],j2); |
---|
560 | if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2) |
---|
561 | par_civ2.ImageB=par_civ1.ImageB; |
---|
562 | else |
---|
563 | [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield)); |
---|
564 | end |
---|
565 | |
---|
566 | ncfile=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1,i2,j1,j2); |
---|
567 | par_civ2.ImageWidth=FileInfo_A.Width; |
---|
568 | par_civ2.ImageHeight=FileInfo_A.Height; |
---|
569 | |
---|
570 | if isfield(par_civ2,'Grid')% grid points set as input file |
---|
571 | if ischar(par_civ2.Grid)%read the grid file if the input is a file name |
---|
572 | par_civ2.Grid=dlmread(par_civ2.Grid); |
---|
573 | par_civ2.Grid(1,:)=[];%the first line must be removed (heading in the grid file) |
---|
574 | end |
---|
575 | else% automatic grid |
---|
576 | minix=floor(par_civ2.Dx/2)-0.5; |
---|
577 | maxix=minix+par_civ2.Dx*floor((par_civ2.ImageWidth-1)/par_civ2.Dx); |
---|
578 | miniy=floor(par_civ2.Dy/2)-0.5; |
---|
579 | maxiy=minix+par_civ2.Dy*floor((par_civ2.ImageHeight-1)/par_civ2.Dy); |
---|
580 | [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy); |
---|
581 | par_civ2.Grid(:,1)=reshape(GridX,[],1); |
---|
582 | par_civ2.Grid(:,2)=reshape(GridY,[],1); |
---|
583 | end |
---|
584 | Shiftx=zeros(size(par_civ2.Grid,1),1);% shift expected from civ1 data |
---|
585 | Shifty=zeros(size(par_civ2.Grid,1),1); |
---|
586 | nbval=zeros(size(par_civ2.Grid,1),1); |
---|
587 | if par_civ2.CheckDeformation |
---|
588 | DUDX=zeros(size(par_civ2.Grid,1),1); |
---|
589 | DUDY=zeros(size(par_civ2.Grid,1),1); |
---|
590 | DVDX=zeros(size(par_civ2.Grid,1),1); |
---|
591 | DVDY=zeros(size(par_civ2.Grid,1),1); |
---|
592 | end |
---|
593 | |
---|
594 | % get the guess from patch1 or patch2 (case 'iterate') |
---|
595 | if isfield (par_civ2,'iterate') && strcmp(par_civ2.iterate,'iterate') |
---|
596 | SubRange= Data.Civ2_SubRange; |
---|
597 | NbCentres=Data.Civ2_NbCentres; |
---|
598 | Coord_tps=Data.Civ2_Coord_tps; |
---|
599 | U_tps=Data.Civ2_U_tps; |
---|
600 | V_tps=Data.Civ2_V_tps; |
---|
601 | CivStage=Data.CivStage; |
---|
602 | Civ1_Dt=Data.Civ2_Dt; |
---|
603 | Data=[];%reinitialise the result structure Data |
---|
604 | Data.ListGlobalAttribute={'Conventions','Program','CivStage'}; |
---|
605 | Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes |
---|
606 | Data.Program='civ_series'; |
---|
607 | Data.CivStage=CivStage; |
---|
608 | Data.ListVarName={}; |
---|
609 | Data.VarDimName={}; |
---|
610 | else |
---|
611 | SubRange= Data.Civ1_SubRange; |
---|
612 | NbCentres=Data.Civ1_NbCentres; |
---|
613 | Coord_tps=Data.Civ1_Coord_tps; |
---|
614 | U_tps=Data.Civ1_U_tps; |
---|
615 | V_tps=Data.Civ1_V_tps; |
---|
616 | Civ1_Dt=Data.Civ1_Dt; |
---|
617 | end |
---|
618 | NbSubDomain=size(SubRange,3); |
---|
619 | for isub=1:NbSubDomain% for each sub-domain of Patch1 |
---|
620 | nbvec_sub=NbCentres(isub);% nbre of Civ vectors in the subdomain |
---|
621 | ind_sel=find(par_civ2.Grid(:,1)>=SubRange(1,1,isub) & par_civ2.Grid(:,1)<=SubRange(1,2,isub) &... |
---|
622 | par_civ2.Grid(:,2)>=SubRange(2,1,isub) & par_civ2.Grid(:,2)<=SubRange(2,2,isub)); |
---|
623 | epoints = par_civ2.Grid(ind_sel,:);% coordinates of interpolation sites |
---|
624 | ctrs=Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs |
---|
625 | nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for eacn interpolation point (in case of subdomain overlap) |
---|
626 | EM = tps_eval(epoints,ctrs); |
---|
627 | Shiftx(ind_sel)=Shiftx(ind_sel)+EM*U_tps(1:nbvec_sub+3,isub); |
---|
628 | Shifty(ind_sel)=Shifty(ind_sel)+EM*V_tps(1:nbvec_sub+3,isub); |
---|
629 | if par_civ2.CheckDeformation |
---|
630 | [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs |
---|
631 | DUDX(ind_sel)=DUDX(ind_sel)+EMDX*U_tps(1:nbvec_sub+3,isub); |
---|
632 | DUDY(ind_sel)=DUDY(ind_sel)+EMDY*U_tps(1:nbvec_sub+3,isub); |
---|
633 | DVDX(ind_sel)=DVDX(ind_sel)+EMDX*V_tps(1:nbvec_sub+3,isub); |
---|
634 | DVDY(ind_sel)=DVDY(ind_sel)+EMDY*V_tps(1:nbvec_sub+3,isub); |
---|
635 | end |
---|
636 | end |
---|
637 | mask=''; |
---|
638 | if par_civ2.CheckMask&&~isempty(par_civ2.Mask)&& ~strcmp(maskname,par_civ2.Mask)% mask exist, not already read in civ1 |
---|
639 | mask=imread(par_civ2.Mask); |
---|
640 | end |
---|
641 | ibx2=ceil(par_civ2.CorrBoxSize(1)/2); |
---|
642 | iby2=ceil(par_civ2.CorrBoxSize(2)/2); |
---|
643 | par_civ2.SearchBoxSize(1)=2*ibx2+9;% search ara +-4 pixels around the guess |
---|
644 | par_civ2.SearchBoxSize(2)=2*iby2+9; |
---|
645 | Civ2_Dt=time(i2+1,j2+1)-time(i1+1,j1+1); |
---|
646 | par_civ2.SearchBoxShift=(Civ2_Dt/Civ1_Dt)*[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)]; |
---|
647 | 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];% grid taken at the extrapolated origin of the displacement vectors |
---|
648 | if par_civ2.CheckDeformation |
---|
649 | par_civ2.DUDX=DUDX./nbval; |
---|
650 | par_civ2.DUDY=DUDY./nbval; |
---|
651 | par_civ2.DVDX=DVDX./nbval; |
---|
652 | par_civ2.DVDY=DVDY./nbval; |
---|
653 | end |
---|
654 | % calculate velocity data (y and v in indices, reverse to y component) |
---|
655 | [xtable ytable utable vtable ctable F] = civ (par_civ2); |
---|
656 | list_param=(fieldnames(Param.ActionInput.Civ2))'; |
---|
657 | Civ2_param=regexprep(list_param,'^.+','Civ2_$0');% insert 'Civ2_' before each string in list_param |
---|
658 | Civ2_param=[{'Civ2_ImageA','Civ2_ImageB','Civ2_Time','Civ2_Dt'} Civ2_param]; %insert the names of the two input images |
---|
659 | %indicate the values of all the global attributes in the output data |
---|
660 | Data.Civ2_ImageA=ImageName_A; |
---|
661 | Data.Civ2_ImageB=ImageName_B; |
---|
662 | Data.Civ2_Time=(time(i2+1,j2+1)+time(i1+1,j1+1))/2; |
---|
663 | Data.Civ2_Dt=Civ2_Dt; |
---|
664 | % Data.Civ2_Time=1; |
---|
665 | % Data.Civ2_Dt=1; |
---|
666 | for ilist=1:length(list_param) |
---|
667 | Data.(Civ2_param{4+ilist})=Param.ActionInput.Civ2.(list_param{ilist}); |
---|
668 | end |
---|
669 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param]; |
---|
670 | |
---|
671 | nbvar=numel(Data.ListVarName); |
---|
672 | 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 |
---|
673 | Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}]; |
---|
674 | Data.VarAttribute{nbvar+1}.Role='coord_x'; |
---|
675 | Data.VarAttribute{nbvar+2}.Role='coord_y'; |
---|
676 | Data.VarAttribute{nbvar+3}.Role='vector_x'; |
---|
677 | Data.VarAttribute{nbvar+4}.Role='vector_y'; |
---|
678 | Data.VarAttribute{nbvar+5}.Role='warnflag'; |
---|
679 | Data.Civ2_X=reshape(xtable,[],1); |
---|
680 | Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1); |
---|
681 | Data.Civ2_U=reshape(utable,[],1); |
---|
682 | Data.Civ2_V=reshape(-vtable,[],1); |
---|
683 | Data.Civ2_C=reshape(ctable,[],1); |
---|
684 | Data.Civ2_F=reshape(F,[],1); |
---|
685 | Data.CivStage=Data.CivStage+1; |
---|
686 | end |
---|
687 | |
---|
688 | %% Fix2 |
---|
689 | if isfield (Param.ActionInput,'Fix2') |
---|
690 | ListFixParam=fieldnames(Param.ActionInput.Fix2); |
---|
691 | for ilist=1:length(ListFixParam) |
---|
692 | ParamName=ListFixParam{ilist}; |
---|
693 | ListName=['Fix2_' ParamName]; |
---|
694 | eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];']) |
---|
695 | eval(['Data.' ListName '=Param.ActionInput.Fix2.' ParamName ';']) |
---|
696 | end |
---|
697 | if check_civx |
---|
698 | if ~isfield(Data,'fix2') |
---|
699 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix2']; |
---|
700 | Data.fix2=1; |
---|
701 | Data.ListVarName=[Data.ListVarName {'vec2_FixFlag'}]; |
---|
702 | Data.VarDimName=[Data.VarDimName {'nb_vectors2'}]; |
---|
703 | end |
---|
704 | Data.vec_FixFlag=fix(Param.Fix2,Data.vec2_F,Data.vec2_C,Data.vec2_U,Data.vec2_V,Data.vec2_X,Data.vec2_Y); |
---|
705 | else |
---|
706 | Data.ListVarName=[Data.ListVarName {'Civ2_FF'}]; |
---|
707 | Data.VarDimName=[Data.VarDimName {'nb_vec_2'}]; |
---|
708 | nbvar=length(Data.ListVarName); |
---|
709 | Data.VarAttribute{nbvar}.Role='errorflag'; |
---|
710 | Data.Civ2_FF=double(fix(Param.ActionInput.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V)); |
---|
711 | Data.CivStage=Data.CivStage+1; |
---|
712 | end |
---|
713 | |
---|
714 | end |
---|
715 | |
---|
716 | %% Patch2 |
---|
717 | if isfield (Param.ActionInput,'Patch2') |
---|
718 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch2_Rho','Patch2_Threshold','Patch2_SubDomain'}]; |
---|
719 | Data.Patch2_FieldSmooth=Param.ActionInput.Patch2.FieldSmooth; |
---|
720 | Data.Patch2_MaxDiff=Param.ActionInput.Patch2.MaxDiff; |
---|
721 | Data.Patch2_SubDomainSize=Param.ActionInput.Patch2.SubDomainSize; |
---|
722 | nbvar=length(Data.ListVarName); |
---|
723 | Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbCentres','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}]; |
---|
724 | Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},... |
---|
725 | {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}]; |
---|
726 | |
---|
727 | Data.VarAttribute{nbvar+1}.Role='vector_x'; |
---|
728 | Data.VarAttribute{nbvar+2}.Role='vector_y'; |
---|
729 | Data.VarAttribute{nbvar+5}.Role='coord_tps'; |
---|
730 | Data.VarAttribute{nbvar+6}.Role='vector_x'; |
---|
731 | Data.VarAttribute{nbvar+7}.Role='vector_y'; |
---|
732 | Data.Civ2_U_smooth=zeros(size(Data.Civ2_X)); |
---|
733 | Data.Civ2_V_smooth=zeros(size(Data.Civ2_X)); |
---|
734 | if isfield(Data,'Civ2_FF') |
---|
735 | ind_good=find(Data.Civ2_FF==0); |
---|
736 | else |
---|
737 | ind_good=1:numel(Data.Civ2_X); |
---|
738 | end |
---|
739 | [Data.Civ2_SubRange,Data.Civ2_NbCentres,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures, Vres,tild,FFres]=... |
---|
740 | 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); |
---|
741 | Data.Civ2_U_smooth(ind_good)=Ures; |
---|
742 | Data.Civ2_V_smooth(ind_good)=Vres; |
---|
743 | Data.Civ2_FF(ind_good)=FFres; |
---|
744 | Data.CivStage=Data.CivStage+1; |
---|
745 | end |
---|
746 | |
---|
747 | %% write result in a netcdf file if requested |
---|
748 | if exist('ncfile','var') |
---|
749 | errormsg=struct2nc(ncfile,Data); |
---|
750 | if isempty(errormsg) |
---|
751 | disp([ncfile ' written']) |
---|
752 | else |
---|
753 | disp(errormsg) |
---|
754 | end |
---|
755 | end |
---|
756 | end |
---|
757 | |
---|
758 | % 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/ |
---|
759 | %-------------------------------------------------------------------------- |
---|
760 | % function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi) |
---|
761 | % |
---|
762 | % OUTPUT: |
---|
763 | % xtable: set of x coordinates |
---|
764 | % ytable: set of y coordiantes |
---|
765 | % utable: set of u displacements (along x) |
---|
766 | % vtable: set of v displacements (along y) |
---|
767 | % ctable: max image correlation for each vector |
---|
768 | % typevector: set of flags, =1 for good, =0 for NaN vectors |
---|
769 | % |
---|
770 | %INPUT: |
---|
771 | % par_civ: structure of input parameters, with fields: |
---|
772 | % .CorrBoxSize |
---|
773 | % .SearchBoxSize |
---|
774 | % .SearchBoxShift |
---|
775 | % .ImageHeight |
---|
776 | % .ImageWidth |
---|
777 | % .Dx, Dy |
---|
778 | % .Grid |
---|
779 | % .Mask |
---|
780 | % .MinIma |
---|
781 | % .MaxIma |
---|
782 | % .image1:first image (matrix) |
---|
783 | % image2: second image (matrix) |
---|
784 | % ibx2,iby2: half size of the correlation box along x and y, in px (size=(2*iby2+1,2*ibx2+1) |
---|
785 | % isx2,isy2: half size of the search box along x and y, in px (size=(2*isy2+1,2*isx2+1) |
---|
786 | % shiftx, shifty: shift of the search box (in pixel index, yshift reversed) |
---|
787 | % step: mesh of the measurement points (in px) |
---|
788 | % subpixfinder=1 or 2 controls the curve fitting of the image correlation |
---|
789 | % mask: =[] for no mask |
---|
790 | % roi: 4 element vector defining a region of interest: x position, y position, width, height, (in image indices), for the whole image, roi=[]; |
---|
791 | function [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ) |
---|
792 | %this funtion performs the DCC PIV analysis. Recent window-deformation |
---|
793 | %methods perform better and will maybe be implemented in the future. |
---|
794 | |
---|
795 | %% prepare measurement grid |
---|
796 | if isfield(par_civ,'Grid')% grid points set as input |
---|
797 | if ischar(par_civ.Grid)%read the drid file if the input is a file name |
---|
798 | par_civ.Grid=dlmread(par_civ.Grid); |
---|
799 | par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file) |
---|
800 | end |
---|
801 | else% automatic grid |
---|
802 | minix=floor(par_civ.Dx/2)-0.5; |
---|
803 | maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx); |
---|
804 | miniy=floor(par_civ.Dy/2)-0.5; |
---|
805 | maxiy=minix+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy); |
---|
806 | [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy); |
---|
807 | par_civ.Grid(:,1)=reshape(GridX,[],1); |
---|
808 | par_civ.Grid(:,2)=reshape(GridY,[],1); |
---|
809 | end |
---|
810 | nbvec=size(par_civ.Grid,1); |
---|
811 | |
---|
812 | %% prepare correlation and search boxes |
---|
813 | ibx2=ceil(par_civ.CorrBoxSize(1)/2); |
---|
814 | iby2=ceil(par_civ.CorrBoxSize(2)/2); |
---|
815 | isx2=ceil(par_civ.SearchBoxSize(1)/2); |
---|
816 | isy2=ceil(par_civ.SearchBoxSize(2)/2); |
---|
817 | shiftx=round(par_civ.SearchBoxShift(:,1)); |
---|
818 | shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases |
---|
819 | if numel(shiftx)==1% case of a unique shift for the whole field( civ1) |
---|
820 | shiftx=shiftx*ones(nbvec,1); |
---|
821 | shifty=shifty*ones(nbvec,1); |
---|
822 | end |
---|
823 | |
---|
824 | %% Default output |
---|
825 | xtable=par_civ.Grid(:,1); |
---|
826 | ytable=par_civ.Grid(:,2); |
---|
827 | utable=zeros(nbvec,1); |
---|
828 | vtable=zeros(nbvec,1); |
---|
829 | ctable=zeros(nbvec,1); |
---|
830 | F=zeros(nbvec,1); |
---|
831 | result_conv=[]; |
---|
832 | errormsg=''; |
---|
833 | |
---|
834 | %% prepare mask |
---|
835 | if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) |
---|
836 | if strcmp(par_civ.Mask,'all') |
---|
837 | return % get the grid only, no civ calculation |
---|
838 | elseif ischar(par_civ.Mask) |
---|
839 | par_civ.Mask=imread(par_civ.Mask); |
---|
840 | end |
---|
841 | end |
---|
842 | check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold |
---|
843 | check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma); |
---|
844 | |
---|
845 | % %% prepare images |
---|
846 | % if isfield(par_civ,'reverse_pair') |
---|
847 | % if par_civ.reverse_pair |
---|
848 | % if ischar(par_civ.ImageB) |
---|
849 | % temp=par_civ.ImageA; |
---|
850 | % par_civ.ImageA=imread(par_civ.ImageB); |
---|
851 | % end |
---|
852 | % if ischar(temp) |
---|
853 | % par_civ.ImageB=imread(temp); |
---|
854 | % end |
---|
855 | % end |
---|
856 | % else |
---|
857 | % if ischar(par_civ.ImageA) |
---|
858 | % par_civ.ImageA=imread(par_civ.ImageA); |
---|
859 | % end |
---|
860 | % if ischar(par_civ.ImageB) |
---|
861 | % par_civ.ImageB=imread(par_civ.ImageB); |
---|
862 | % end |
---|
863 | % end |
---|
864 | par_civ.ImageA=sum(double(par_civ.ImageA),3);%sum over rgb component for color images |
---|
865 | par_civ.ImageB=sum(double(par_civ.ImageB),3); |
---|
866 | [npy_ima npx_ima]=size(par_civ.ImageA); |
---|
867 | if ~isequal(size(par_civ.ImageB),[npy_ima npx_ima]) |
---|
868 | errormsg='image pair with unequal size'; |
---|
869 | return |
---|
870 | end |
---|
871 | |
---|
872 | %% Apply mask |
---|
873 | % Convention for mask IDEAS TO IMPLEMENT ? |
---|
874 | % mask >200 : velocity calculated |
---|
875 | % 200 >=mask>150;velocity not calculated, interpolation allowed (bad spots) |
---|
876 | % 150>=mask >100: velocity not calculated, nor interpolated |
---|
877 | % 100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries) |
---|
878 | % 20>=mask: velocity=0 |
---|
879 | checkmask=0; |
---|
880 | MinA=min(min(par_civ.ImageA)); |
---|
881 | MinB=min(min(par_civ.ImageB)); |
---|
882 | if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) |
---|
883 | checkmask=1; |
---|
884 | if ~isequal(size(par_civ.Mask),[npy_ima npx_ima]) |
---|
885 | errormsg='mask must be an image with the same size as the images'; |
---|
886 | return |
---|
887 | end |
---|
888 | % check_noflux=(par_civ.Mask<100) ;%TODO: to implement |
---|
889 | check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 ); |
---|
890 | par_civ.ImageA(check_undefined)=MinA;% put image A to zero (i.e. the min image value) in the undefined area |
---|
891 | par_civ.ImageB(check_undefined)=MinB;% put image B to zero (i.e. the min image value) in the undefined area |
---|
892 | end |
---|
893 | |
---|
894 | %% compute image correlations: MAINLOOP on velocity vectors |
---|
895 | corrmax=0; |
---|
896 | sum_square=1;% default |
---|
897 | mesh=1;% default |
---|
898 | CheckDecimal=isfield(par_civ,'CheckDecimal')&& par_civ.CheckDecimal==1; |
---|
899 | if CheckDecimal |
---|
900 | mesh=0.2;%mesh in pixels for subpixel image interpolation |
---|
901 | CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1; |
---|
902 | end |
---|
903 | % vector=[0 0];%default |
---|
904 | for ivec=1:nbvec |
---|
905 | iref=round(par_civ.Grid(ivec,1)+0.5);% xindex on the image A for the middle of the correlation box |
---|
906 | jref=round(par_civ.ImageHeight-par_civ.Grid(ivec,2)+0.5);% yindex on the image B for the middle of the correlation box |
---|
907 | %if ~(checkmask && par_civ.Mask(jref,iref)<=20) %velocity not set to zero by the black mask |
---|
908 | % if jref-iby2<1 || jref+iby2>par_civ.ImageHeight|| iref-ibx2<1 || iref+ibx2>par_civ.ImageWidth||... |
---|
909 | % 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 |
---|
910 | % F(ivec)=3; |
---|
911 | % else |
---|
912 | F(ivec)=0; |
---|
913 | subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage |
---|
914 | subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage |
---|
915 | subrange2_x=iref+shiftx(ivec)-isx2:iref+shiftx(ivec)+isx2;%x indices defining the second subimage |
---|
916 | subrange2_y=jref+shifty(ivec)-isy2:jref+shifty(ivec)+isy2;%y indices defining the second subimage |
---|
917 | image1_crop=MinA*ones(numel(subrange1_y),numel(subrange1_x));% default value=min of image A |
---|
918 | image2_crop=MinA*ones(numel(subrange2_y),numel(subrange2_x));% default value=min of image A |
---|
919 | check1_x=subrange1_x>=1 & subrange1_x<=par_civ.ImageWidth;% check which points in the subimage 1 are contained in the initial image 1 |
---|
920 | check1_y=subrange1_y>=1 & subrange1_y<=par_civ.ImageHeight; |
---|
921 | check2_x=subrange2_x>=1 & subrange2_x<=par_civ.ImageWidth;% check which points in the subimage 2 are contained in the initial image 2 |
---|
922 | check2_y=subrange2_y>=1 & subrange2_y<=par_civ.ImageHeight; |
---|
923 | |
---|
924 | 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 |
---|
925 | 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 |
---|
926 | image1_mean=mean(mean(image1_crop)); |
---|
927 | image2_mean=mean(mean(image2_crop)); |
---|
928 | %threshold on image minimum |
---|
929 | if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma) |
---|
930 | F(ivec)=3; |
---|
931 | end |
---|
932 | %threshold on image maximum |
---|
933 | if check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma) |
---|
934 | F(ivec)=3; |
---|
935 | end |
---|
936 | % end |
---|
937 | if F(ivec)~=3 |
---|
938 | image1_crop=image1_crop-image1_mean;%substract the mean |
---|
939 | image2_crop=image2_crop-image2_mean; |
---|
940 | if CheckDecimal |
---|
941 | xi=(1:mesh:size(image1_crop,2)); |
---|
942 | yi=(1:mesh:size(image1_crop,1))'; |
---|
943 | if CheckDeformation |
---|
944 | [XI,YI]=meshgrid(xi-ceil(size(image1_crop,2)/2),yi-ceil(size(image1_crop,1)/2)); |
---|
945 | XIant=XI-par_civ.DUDX(ivec)*XI-par_civ.DUDY(ivec)*YI+ceil(size(image1_crop,2)/2); |
---|
946 | YIant=YI-par_civ.DVDX(ivec)*XI-par_civ.DVDY(ivec)*YI+ceil(size(image1_crop,1)/2); |
---|
947 | image1_crop=interp2(image1_crop,XIant,YIant); |
---|
948 | else |
---|
949 | image1_crop=interp2(image1_crop,xi,yi); |
---|
950 | end |
---|
951 | xi=(1:mesh:size(image2_crop,2)); |
---|
952 | yi=(1:mesh:size(image2_crop,1))'; |
---|
953 | image2_crop=interp2(image2_crop,xi,yi); |
---|
954 | end |
---|
955 | sum_square=sum(sum(image1_crop.*image1_crop)); |
---|
956 | %reference: Oliver Pust, PIV: Direct Cross-Correlation |
---|
957 | result_conv= conv2(image2_crop,flipdim(flipdim(image1_crop,2),1),'valid'); |
---|
958 | corrmax= max(max(result_conv)); |
---|
959 | result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255 |
---|
960 | %Find the correlation max, at 255 |
---|
961 | [y,x] = find(result_conv==255,1); |
---|
962 | if ~isempty(y) && ~isempty(x) |
---|
963 | try |
---|
964 | if par_civ.CorrSmooth==1 |
---|
965 | [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y); |
---|
966 | elseif par_civ.CorrSmooth==2 |
---|
967 | [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y); |
---|
968 | end |
---|
969 | utable(ivec)=vector(1)*mesh+shiftx(ivec); |
---|
970 | vtable(ivec)=vector(2)*mesh+shifty(ivec); |
---|
971 | xtable(ivec)=iref+utable(ivec)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2) |
---|
972 | ytable(ivec)=jref+vtable(ivec)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge) |
---|
973 | iref=round(xtable(ivec));% image index for the middle of the vector |
---|
974 | jref=round(ytable(ivec)); |
---|
975 | if checkmask && par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100 |
---|
976 | utable(ivec)=0; |
---|
977 | vtable(ivec)=0; |
---|
978 | F(ivec)=3; |
---|
979 | end |
---|
980 | ctable(ivec)=corrmax/sum_square;% correlation value |
---|
981 | catch ME |
---|
982 | F(ivec)=3; |
---|
983 | end |
---|
984 | else |
---|
985 | F(ivec)=3; |
---|
986 | end |
---|
987 | end |
---|
988 | end |
---|
989 | result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output |
---|
990 | |
---|
991 | %------------------------------------------------------------------------ |
---|
992 | % --- Find the maximum of the correlation function after interpolation |
---|
993 | function [vector,F] = SUBPIXGAUSS (result_conv,x,y) |
---|
994 | %------------------------------------------------------------------------ |
---|
995 | vector=[0 0]; %default |
---|
996 | F=0; |
---|
997 | [npy,npx]=size(result_conv); |
---|
998 | result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log) |
---|
999 | %the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ᅵ Israel Institute of Technology |
---|
1000 | %http://urapiv.wordpress.com |
---|
1001 | peaky = y; |
---|
1002 | if y <= npy-1 && y >= 1 |
---|
1003 | f0 = log(result_conv(y,x)); |
---|
1004 | f1 = log(result_conv(y-1,x)); |
---|
1005 | f2 = log(result_conv(y+1,x)); |
---|
1006 | peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2); |
---|
1007 | else |
---|
1008 | F=-2; % warning flag for vector truncated by the limited search box |
---|
1009 | end |
---|
1010 | peakx=x; |
---|
1011 | if x <= npx-1 && x >= 1 |
---|
1012 | f0 = log(result_conv(y,x)); |
---|
1013 | f1 = log(result_conv(y,x-1)); |
---|
1014 | f2 = log(result_conv(y,x+1)); |
---|
1015 | peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2); |
---|
1016 | else |
---|
1017 | F=-2; % warning flag for vector truncated by the limited search box |
---|
1018 | end |
---|
1019 | vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; |
---|
1020 | |
---|
1021 | %------------------------------------------------------------------------ |
---|
1022 | % --- Find the maximum of the correlation function after interpolation |
---|
1023 | function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y) |
---|
1024 | %------------------------------------------------------------------------ |
---|
1025 | vector=[0 0]; %default |
---|
1026 | F=-2; |
---|
1027 | peaky=y; |
---|
1028 | peakx=x; |
---|
1029 | result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log) |
---|
1030 | [npy,npx]=size(result_conv); |
---|
1031 | if (x <= npx-1) && (y <= npy-1) && (x >= 1) && (y >= 1) |
---|
1032 | F=0; |
---|
1033 | for i=-1:1 |
---|
1034 | for j=-1:1 |
---|
1035 | %following 15 lines based on |
---|
1036 | %H. Nobach ᅵ M. Honkanen (2005) |
---|
1037 | %Two-dimensional Gaussian regression for sub-pixel displacement |
---|
1038 | %estimation in particle image velocimetry or particle position |
---|
1039 | %estimation in particle tracking velocimetry |
---|
1040 | %Experiments in Fluids (2005) 38: 511ᅵ515 |
---|
1041 | c10(j+2,i+2)=i*log(result_conv(y+j, x+i)); |
---|
1042 | c01(j+2,i+2)=j*log(result_conv(y+j, x+i)); |
---|
1043 | c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i)); |
---|
1044 | c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i)); |
---|
1045 | c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i)); |
---|
1046 | end |
---|
1047 | end |
---|
1048 | c10=(1/6)*sum(sum(c10)); |
---|
1049 | c01=(1/6)*sum(sum(c01)); |
---|
1050 | c11=(1/4)*sum(sum(c11)); |
---|
1051 | c20=(1/6)*sum(sum(c20)); |
---|
1052 | c02=(1/6)*sum(sum(c02)); |
---|
1053 | deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2); |
---|
1054 | deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2); |
---|
1055 | if abs(deltax)<1 |
---|
1056 | peakx=x+deltax; |
---|
1057 | end |
---|
1058 | if abs(deltay)<1 |
---|
1059 | peaky=y+deltay; |
---|
1060 | end |
---|
1061 | end |
---|
1062 | vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; |
---|
1063 | |
---|
1064 | %'RUN_FIX': function for fixing velocity fields: |
---|
1065 | %----------------------------------------------- |
---|
1066 | % RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref) |
---|
1067 | % |
---|
1068 | %filename: name of the netcdf file (used as input and output) |
---|
1069 | %field: structure specifying the names of the fields to fix (depending on civ1 or civ2) |
---|
1070 | %.vel_type='civ1' or 'civ2'; |
---|
1071 | %.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1); |
---|
1072 | %.fixflag=name of fix flag variable ('vec_FixFlag' for civ1) |
---|
1073 | %flagindex: flag specifying which values of vec_f are removed: |
---|
1074 | % if flagindex(1)=1: vec_f=-2 vectors are removed |
---|
1075 | % if flagindex(2)=1: vec_f=3 vectors are removed |
---|
1076 | % if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2) |
---|
1077 | %iter=1 for civ1 fields and iter=2 for civ2 fields |
---|
1078 | %thresh_vecC: threshold in the image correlation vec_C |
---|
1079 | %flag_mask: =1 mask used to remove vectors (0 else) |
---|
1080 | %maskname: name of the mask image file for fix |
---|
1081 | %thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists |
---|
1082 | %inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold |
---|
1083 | %fileref: .nc file name for a reference velocity (='': refrence 0 used) |
---|
1084 | %fieldref: 'civ1','filter1'...feld used in fileref |
---|
1085 | |
---|
1086 | function FF=fix(Param,F,C,U,V,X,Y) |
---|
1087 | FF=zeros(size(F));%default |
---|
1088 | |
---|
1089 | %criterium on warn flags |
---|
1090 | FlagName={'CheckFmin2','CheckF2','CheckF3','CheckF4'}; |
---|
1091 | FlagVal=[-2 2 3 4]; |
---|
1092 | for iflag=1:numel(FlagName) |
---|
1093 | if isfield(Param,FlagName{iflag}) && Param.(FlagName{iflag}) |
---|
1094 | FF=(FF==1| F==FlagVal(iflag)); |
---|
1095 | end |
---|
1096 | end |
---|
1097 | %criterium on correlation values |
---|
1098 | if isfield (Param,'MinCorr') |
---|
1099 | FF=FF==1 | C<Param.MinCorr; |
---|
1100 | end |
---|
1101 | if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)) |
---|
1102 | Umod= U.*U+V.*V; |
---|
1103 | if isfield (Param,'MinVel')&&~isempty(Param.MinVel) |
---|
1104 | FF=FF==1 | Umod<(Param.MinVel*Param.MinVel); |
---|
1105 | end |
---|
1106 | if isfield (Param,'MaxVel')&&~isempty(Param.MaxVel) |
---|
1107 | FF=FF==1 | Umod>(Param.MaxVel*Param.MaxVel); |
---|
1108 | end |
---|
1109 | end |
---|
1110 | |
---|
1111 | |
---|
1112 | %------------------------------------------------------------------------ |
---|
1113 | % --- determine the list of index pairs of processing file |
---|
1114 | function [i1_series,i2_series,j1_series,j2_series,check_bounds,NomTypeNc]=... |
---|
1115 | find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j) |
---|
1116 | %------------------------------------------------------------------------ |
---|
1117 | i1_series=i_series;% set of first image indexes |
---|
1118 | i2_series=i_series; |
---|
1119 | j1_series=j_series;%ones(size(i_series));% set of first image numbers |
---|
1120 | j2_series=j_series;%ones(size(i_series)); |
---|
1121 | r=regexp(str_civ,'^\D(?<ind>[i|j])=( -| )(?<num1>\d+)\|(?<num2>\d+)','names'); |
---|
1122 | if ~isempty(r) |
---|
1123 | mode=['D' r.ind]; |
---|
1124 | ind1=str2num(r.num1); |
---|
1125 | ind2=str2num(r.num2); |
---|
1126 | else |
---|
1127 | mode='j1-j2'; |
---|
1128 | r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names'); |
---|
1129 | if ~isempty(r) |
---|
1130 | NomTypeNc='_1ab'; |
---|
1131 | else |
---|
1132 | r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names'); |
---|
1133 | if ~isempty(r) |
---|
1134 | NomTypeNc='_1AB'; |
---|
1135 | else |
---|
1136 | r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names'); |
---|
1137 | if ~isempty(r) |
---|
1138 | NomTypeNc='_1_1-2'; |
---|
1139 | end |
---|
1140 | end |
---|
1141 | end |
---|
1142 | if isempty(r) |
---|
1143 | display('wrong pair mode input option') |
---|
1144 | else |
---|
1145 | ind1=stra2num(r.num1); |
---|
1146 | ind2=stra2num(r.num2); |
---|
1147 | end |
---|
1148 | end |
---|
1149 | switch mode |
---|
1150 | case 'Di' |
---|
1151 | i1_series=i_series-ind1;% set of first image numbers |
---|
1152 | i2_series=i_series+ind2; |
---|
1153 | check_bounds=i1_series<MinIndex_i | i2_series>MaxIndex_i; |
---|
1154 | if isempty(j_series) |
---|
1155 | NomTypeNc='_1-2'; |
---|
1156 | else |
---|
1157 | j1_series=j_series; |
---|
1158 | j2_series=j_series; |
---|
1159 | NomTypeNc='_1-2_1'; |
---|
1160 | end |
---|
1161 | case 'Dj' |
---|
1162 | j1_series=j_series-ind1; |
---|
1163 | j2_series=j_series+ind2; |
---|
1164 | check_bounds=j1_series<MinIndex_j | j2_series>MaxIndex_j; |
---|
1165 | NomTypeNc='_1_1-2'; |
---|
1166 | otherwise %bursts |
---|
1167 | i1_series=i_series(1,:);% do not sweep the j index |
---|
1168 | i2_series=i_series(1,:); |
---|
1169 | j1_series=ind1*ones(1,size(i_series,2));% j index is fixed by pair choice |
---|
1170 | j2_series=ind2*ones(1,size(i_series,2)); |
---|
1171 | check_bounds=zeros(size(i1_series));% no limitations due to min-max indices |
---|
1172 | end |
---|
1173 | |
---|
1174 | |
---|
1175 | |
---|
1176 | |
---|