[598] | 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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[597] | 6 | %------------------------------------------------------------------------ |
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[598] | 7 | % function [Data,errormsg,result_conv]= civ_series(Param,ncfile) |
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[597] | 8 | % |
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| 9 | %OUTPUT |
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[598] | 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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[597] | 13 | % |
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| 14 | %INPUT: |
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[598] | 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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[597] | 23 | % |
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[819] | 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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[598] | 29 | % UVMAT is free software; you can redistribute it and/or modify |
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[819] | 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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[598] | 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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[819] | 37 | % GNU General Public License (open UVMAT/COPYING.txt) for more details. |
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| 38 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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[597] | 39 | |
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[724] | 40 | function [Data,errormsg,result_conv]= civ_series(Param) |
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[598] | 41 | errormsg=''; |
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[763] | 42 | |
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[606] | 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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[716] | 44 | if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN |
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[763] | 45 | path_series=fileparts(which('series')); |
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| 46 | addpath(fullfile(path_series,'series')) |
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[598] | 47 | Data=civ_input(Param);% introduce the civ parameters using the GUI civ_input |
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[668] | 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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[606] | 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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[774] | 54 | if isfield(Data,'ActionInput') && strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2') |
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[721] | 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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[606] | 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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[781] | 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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[606] | 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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[711] | 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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[645] | 65 | Data.OutputFileMode='NbInput_i';% one output file expected per value of i index (used for waitbar) |
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[758] | 66 | % check the existence of the first file in the series: suppressed |
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| 67 | % first_j=[]; |
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| 68 | % if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end |
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| 69 | % last_j=[]; |
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| 70 | % if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end |
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| 71 | % PairString=''; |
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| 72 | % if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end |
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[598] | 73 | return |
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[597] | 74 | end |
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| 75 | |
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| 76 | %% read input parameters from an xml file if input is a file name (batch mode) |
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| 77 | checkrun=1; |
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| 78 | if ischar(Param) |
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| 79 | Param=xml2struct(Param);% read Param as input file (batch case) |
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| 80 | checkrun=0; |
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| 81 | end |
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[668] | 82 | if ~isfield(Param,'ActionInput') |
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| 83 | disp_uvmat('ERROR','no parameter set for PIV',checkrun) |
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| 84 | return |
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| 85 | end |
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[624] | 86 | hseries=findobj(allchild(0),'Tag','series'); |
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| 87 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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| 88 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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[597] | 89 | |
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[605] | 90 | %% input files and indexing |
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[758] | 91 | % NbField=1; |
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[635] | 92 | MaxIndex_i=Param.IndexRange.MaxIndex_i; |
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| 93 | MinIndex_i=Param.IndexRange.MinIndex_i; |
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[763] | 94 | MaxIndex_j=ones(size(MaxIndex_i));MinIndex_j=ones(size(MinIndex_i)); |
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[635] | 95 | if isfield(Param.IndexRange,'MaxIndex_j')&& isfield(Param.IndexRange,'MinIndex_j') |
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| 96 | MaxIndex_j=Param.IndexRange.MaxIndex_j; |
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| 97 | MinIndex_j=Param.IndexRange.MinIndex_j; |
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| 98 | end |
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[598] | 99 | if isfield(Param,'InputTable') |
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[761] | 100 | [tild,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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[758] | 101 | % iview_nc=0;% series index (iview) for an input nc file (for civ2 or patch2) |
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| 102 | iview_A=0;% series index (iview) for the first image series |
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| 103 | 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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| 104 | if Param.ActionInput.CheckCiv1 |
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| 105 | iview_A=1;% usual PIV, the image series is on the first line of the table |
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| 106 | elseif Param.ActionInput.CheckCiv2 % civ2 is performed without Civ1, a netcdf file series is needed in the first table line |
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| 107 | iview_A=2;% the second line is used for the input images of Civ2 |
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[609] | 108 | end |
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[758] | 109 | if strcmp(Param.ActionInput.ListCompareMode,'shift') |
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[761] | 110 | iview_B=iview_A+1; % the second image series is on the next line of the input table |
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[758] | 111 | end |
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[610] | 112 | if iview_A~=0 |
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[758] | 113 | RootPath_A=Param.InputTable{iview_A,1}; |
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| 114 | RootFile_A=Param.InputTable{iview_A,3}; |
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| 115 | SubDir_A=Param.InputTable{iview_A,2}; |
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| 116 | NomType_A=Param.InputTable{iview_A,4}; |
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| 117 | FileExt_A=Param.InputTable{iview_A,5}; |
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| 118 | if iview_B==0 |
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| 119 | iview_B=iview_A;% the second image series is the same as the first |
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[610] | 120 | end |
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[758] | 121 | RootPath_B=Param.InputTable{iview_B,1}; |
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| 122 | RootFile_B=Param.InputTable{iview_B,3}; |
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| 123 | SubDir_B=Param.InputTable{iview_B,2}; |
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| 124 | NomType_B=Param.InputTable{iview_B,4}; |
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| 125 | FileExt_B=Param.InputTable{iview_B,5}; |
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[597] | 126 | end |
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[758] | 127 | |
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| 128 | PairCiv2=''; |
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| 129 | switch Param.ActionInput.ListCompareMode |
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| 130 | case 'PIV' |
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| 131 | PairCiv1=Param.ActionInput.PairIndices.ListPairCiv1; |
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| 132 | if isfield(Param.ActionInput.PairIndices,'ListPairCiv2') |
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[824] | 133 | PairCiv2=Param.ActionInput.PairIndices.ListPairCiv2;%string which determines the civ2 pair |
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[758] | 134 | end |
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[761] | 135 | if iview_A==1% if Civ1 is performed |
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| 136 | [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=... |
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| 137 | find_pair_indices(PairCiv1,i1_series{1},j1_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j); |
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| 138 | if ~isempty(PairCiv2) |
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| 139 | [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds_Civ2]=... |
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[763] | 140 | 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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[761] | 141 | check_bounds=check_bounds | check_bounds_Civ2; |
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| 142 | end |
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| 143 | else% we start from an existing Civ1 file |
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| 144 | i1_series_Civ1=i1_series{1}; |
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| 145 | i2_series_Civ1=i2_series{1}; |
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| 146 | j1_series_Civ1=j1_series{1}; |
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| 147 | j2_series_Civ1=j2_series{1}; |
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| 148 | NomTypeNc=Param.InputTable{1,4}; |
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| 149 | if ~isempty(PairCiv2) |
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| 150 | [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds,NomTypeNc]=... |
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[763] | 151 | 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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[761] | 152 | end |
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[758] | 153 | end |
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[761] | 154 | % i1_series_Civ1=i1_series_Civ1(~check_bounds); |
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| 155 | % i2_series_Civ1=i2_series_Civ1(~check_bounds); |
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| 156 | % j1_series_Civ1=j1_series_Civ1(~check_bounds); |
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| 157 | % j2_series_Civ1=j2_series_Civ1(~check_bounds); |
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[758] | 158 | case 'displacement' |
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[824] | 159 | i1_series_Civ1=Param.ActionInput.OriginIndex*ones(size(i1_series{1})); |
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| 160 | i2_series_Civ1=i1_series{1};i2_series_Civ2=i1_series{1}; |
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| 161 | j1_series_Civ1=ones(size(i1_series{1}));% first j index is 1 |
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[761] | 162 | if isempty(j1_series_Civ1) |
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[824] | 163 | j2_series_Civ1=ones(size(i1_series{1})); |
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[610] | 164 | else |
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[761] | 165 | j2_series_Civ1=j1_series_Civ1; |
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[610] | 166 | end |
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[758] | 167 | i1_series_Civ2=i1_series_Civ1; |
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| 168 | j1_series_Civ2=j1_series_Civ1; |
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| 169 | j2_series_Civ2=j2_series_Civ1; |
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| 170 | NomTypeNc=NomType; |
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| 171 | case 'shift' |
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[824] | 172 | i1_series_Civ1=i1_series{1};i1_series_Civ2=i1_series{1}; |
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| 173 | i2_series_Civ1=i1_series{2};i2_series_Civ2=i1_series{2}; |
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| 174 | if isempty(j1_series{1}) |
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| 175 | j1_series_Civ1=ones(size(i1_series{1})); |
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| 176 | j2_series_Civ1=ones(size(i1_series{2})); |
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[758] | 177 | else |
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[824] | 178 | j1_series_Civ1=j1_series{1}; |
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| 179 | j2_series_Civ1=j1_series{2}; |
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[758] | 180 | end |
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| 181 | j1_series_Civ2=j1_series_Civ1; |
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| 182 | j2_series_Civ2=j2_series_Civ1; |
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| 183 | NomTypeNc=NomType_A; |
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[597] | 184 | end |
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[761] | 185 | if isempty(j1_series_Civ1) |
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[661] | 186 | FrameIndex_A_Civ1=i1_series_Civ1; |
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| 187 | FrameIndex_B_Civ1=i2_series_Civ1; |
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[761] | 188 | j1_series_Civ1=ones(size(i1_series_Civ1)); |
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| 189 | j2_series_Civ1=ones(size(i1_series_Civ1)); |
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[661] | 190 | else |
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| 191 | FrameIndex_A_Civ1=j1_series_Civ1; |
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| 192 | FrameIndex_B_Civ1=j2_series_Civ1; |
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| 193 | end |
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[824] | 194 | if isempty(PairCiv2) |
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| 195 | FrameIndex_A_Civ2=FrameIndex_A_Civ1; |
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| 196 | FrameIndex_B_Civ2=FrameIndex_B_Civ1; |
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| 197 | else |
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[761] | 198 | if isempty(j1_series_Civ2) |
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[758] | 199 | FrameIndex_A_Civ2=i1_series_Civ2; |
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| 200 | FrameIndex_B_Civ2=i2_series_Civ2; |
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[822] | 201 | j1_series_Civ2=ones(size(i1_series_Civ2)); |
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| 202 | j2_series_Civ2=ones(size(i1_series_Civ2)); |
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[758] | 203 | else |
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| 204 | FrameIndex_A_Civ2=j1_series_Civ2; |
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| 205 | FrameIndex_B_Civ2=j2_series_Civ2; |
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| 206 | end |
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| 207 | end |
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| 208 | if isempty(i1_series_Civ1)||(~isempty(PairCiv2) && isempty(i1_series_Civ2)) |
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| 209 | disp_uvmat('ERROR','no image pair fo civ in the input file index range',checkrun) |
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| 210 | return |
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| 211 | end |
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[597] | 212 | end |
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| 213 | |
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[758] | 214 | %% check the first image pair |
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| 215 | try |
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| 216 | if Param.ActionInput.CheckCiv1% Civ1 is performed |
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| 217 | 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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| 218 | if ~exist(ImageName_A,'file') |
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| 219 | disp_uvmat('ERROR',['first input image ' ImageName_A ' does not exist'],checkrun) |
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| 220 | return |
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| 221 | end |
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[784] | 222 | [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A); |
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[783] | 223 | FileType_A=FileInfo_A.FileType; |
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[781] | 224 | if strcmp(FileInfo_A.FileType,'netcdf') |
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| 225 | FieldName_A=Param.InputFields.FieldName; |
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| 226 | [DataIn,tild,tild,errormsg]=nc2struct(ImageName_A,{FieldName_A}); |
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| 227 | par_civ1.ImageA=DataIn.(FieldName_A); |
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[819] | 228 | else |
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| 229 | [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(1)); |
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[781] | 230 | end |
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[758] | 231 | 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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| 232 | if ~exist(ImageName_B,'file') |
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| 233 | disp_uvmat('ERROR',['first input image ' ImageName_B ' does not exist'],checkrun) |
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| 234 | return |
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| 235 | end |
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[784] | 236 | [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B); |
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[783] | 237 | FileType_B=FileInfo_B.FileType; |
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[781] | 238 | if strcmp(FileInfo_B.FileType,'netcdf') |
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| 239 | FieldName_B=Param.InputFields.FieldName; |
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[819] | 240 | [DataIn,tild,tild,errormsg]=nc2struct(ImageName_B,{FieldName_B}); |
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| 241 | par_civ1.ImageB=DataIn.(FieldName_B); |
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[781] | 242 | else |
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[819] | 243 | [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(1)); |
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[781] | 244 | end |
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[758] | 245 | NbField=numel(i1_series_Civ1); |
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| 246 | elseif Param.ActionInput.CheckCiv2 % Civ2 is performed without Civ1 |
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| 247 | 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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| 248 | if ~exist(ImageName_A,'file') |
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| 249 | disp_uvmat('ERROR',['first input image ' ImageName_A ' does not exist'],checkrun) |
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| 250 | return |
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| 251 | end |
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[822] | 252 | [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A); |
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| 253 | FileType_A=FileInfo_A.FileType; |
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[781] | 254 | [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileInfo_A.FileType,VideoObject_A,FrameIndex_A_Civ2(1)); |
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[758] | 255 | 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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| 256 | if ~exist(ImageName_B,'file') |
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| 257 | disp_uvmat('ERROR',['first input image ' ImageName_B ' does not exist'],checkrun) |
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| 258 | return |
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| 259 | end |
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[784] | 260 | [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B); |
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[783] | 261 | FileType_B=FileInfo_B.FileType; |
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[758] | 262 | [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ2(1)); |
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| 263 | NbField=numel(i1_series_Civ2); |
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[822] | 264 | else |
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| 265 | NbField=numel(i1_series_Civ1);% no image used (only fix or patch) TO CHECK |
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[758] | 266 | end |
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| 267 | catch ME |
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| 268 | if ~isempty(ME.message) |
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| 269 | disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun) |
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| 270 | return |
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| 271 | end |
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| 272 | end |
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| 273 | |
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| 274 | |
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[605] | 275 | %% Output directory |
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| 276 | OutputDir=[Param.OutputSubDir Param.OutputDirExt]; |
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| 277 | |
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| 278 | Data.ListGlobalAttribute={'Conventions','Program','CivStage'}; |
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| 279 | Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes |
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| 280 | Data.Program='civ_series'; |
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| 281 | Data.CivStage=0;%default |
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| 282 | maskname='';%default |
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| 283 | check_civx=0;%default |
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| 284 | |
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[606] | 285 | %% get timing from the ImaDoc file or input video |
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[822] | 286 | if iview_A~=0 |
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[833] | 287 | XmlFileName=find_imadoc(RootPath_A,SubDir_A,RootFile_A,FileExt_A); |
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| 288 | time=[]; |
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| 289 | if ~isempty(XmlFileName) |
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| 290 | XmlData=imadoc2struct(XmlFileName); |
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[609] | 291 | if isfield(XmlData,'Time') |
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| 292 | time=XmlData.Time; |
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| 293 | TimeSource='xml'; |
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| 294 | end |
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| 295 | if isfield(XmlData,'Camera') |
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| 296 | if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice) |
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| 297 | NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform |
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| 298 | if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) |
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| 299 | msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); |
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| 300 | end |
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| 301 | end |
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| 302 | if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit) |
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| 303 | TimeUnit=XmlData.Camera.TimeUnit; |
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| 304 | end |
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| 305 | end |
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[833] | 306 | end |
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| 307 | if isempty(time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video'})))% case of video input |
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| 308 | time=zeros(FileInfo_A.NumberOfFrames+1,2); |
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| 309 | time(:,2)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate)'; |
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| 310 | TimeSource='video'; |
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| 311 | ColorType='truecolor'; |
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| 312 | end |
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| 313 | if isempty(time)% time = index i +0.001 index j by default |
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| 314 | %MinIndex_i=min(i1_series_Civ1); |
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| 315 | MaxIndex_i=max(i2_series_Civ1); |
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| 316 | %MinIndex_j=min(j1_series_Civ1); |
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| 317 | MaxIndex_j=max(j2_series_Civ1); |
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| 318 | time=(1:MaxIndex_i)'*ones(1,MaxIndex_j); |
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| 319 | time=time+0.001*ones(MaxIndex_i,1)*(1:MaxIndex_j); |
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| 320 | time=[zeros(1,MaxIndex_j);time];% insert a first line of zeros |
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| 321 | time=[zeros(MaxIndex_i+1,1) time];% insert a first column of zeros |
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| 322 | end |
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[637] | 323 | |
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[833] | 324 | if length(FileInfo_A) >1 %case of image with multiple frames |
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| 325 | nbfield=length(FileInfo_A); |
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| 326 | nbfield_j=1; |
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| 327 | end |
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[610] | 328 | end |
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[609] | 329 | |
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[598] | 330 | %%%%% MAIN LOOP %%%%%% |
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| 331 | for ifield=1:NbField |
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[635] | 332 | update_waitbar(WaitbarHandle,ifield/NbField) |
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| 333 | if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
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[624] | 334 | disp('program stopped by user') |
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| 335 | break |
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| 336 | end |
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[822] | 337 | if iview_A==0 |
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| 338 | ncfile=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},... |
---|
| 339 | NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),j1_series_Civ1(ifield),j2_series_Civ1(ifield)); |
---|
[761] | 340 | else |
---|
[822] | 341 | if iview_A==1% if Civ1 is performed |
---|
| 342 | Civ1Dir=OutputDir; |
---|
| 343 | else |
---|
| 344 | Civ1Dir=Param.InputTable{1,2}; |
---|
| 345 | end |
---|
| 346 | if strcmp(Param.ActionInput.ListCompareMode,'PIV') |
---|
| 347 | ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),... |
---|
| 348 | j1_series_Civ1(ifield),j2_series_Civ1(ifield)); |
---|
| 349 | else |
---|
| 350 | ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],... |
---|
| 351 | j1_series_Civ1(ifield),j2_series_Civ1(ifield)); |
---|
| 352 | end |
---|
[761] | 353 | end |
---|
[598] | 354 | %% Civ1 |
---|
[707] | 355 | % if Civ1 computation is requested |
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[598] | 356 | if isfield (Param.ActionInput,'Civ1') |
---|
| 357 | par_civ1=Param.ActionInput.Civ1; |
---|
[758] | 358 | try |
---|
[661] | 359 | ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield)); |
---|
[781] | 360 | if strcmp(FileInfo_A.FileType,'netcdf') |
---|
| 361 | FieldName_A=Param.InputFields.FieldName; |
---|
| 362 | [DataIn,tild,tild,errormsg]=nc2struct(ImageName_A,{FieldName_A}); |
---|
| 363 | par_civ1.ImageA=DataIn.(FieldName_A); |
---|
| 364 | else |
---|
| 365 | [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield)); |
---|
| 366 | end |
---|
[661] | 367 | ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield)); |
---|
[781] | 368 | if strcmp(FileInfo_B.FileType,'netcdf') |
---|
| 369 | FieldName_B=Param.InputFields.FieldName; |
---|
| 370 | [DataIn,tild,tild,errormsg]=nc2struct(ImageName_B,{FieldName_B}); |
---|
| 371 | par_civ1.ImageB=DataIn.(FieldName_B); |
---|
| 372 | else |
---|
| 373 | [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield)); |
---|
| 374 | end |
---|
[758] | 375 | catch ME |
---|
| 376 | if ~isempty(ME.message) |
---|
| 377 | disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun) |
---|
| 378 | return |
---|
| 379 | end |
---|
[597] | 380 | end |
---|
[781] | 381 | par_civ1.ImageWidth=size(par_civ1.ImageA,2);%FileInfo_A.Width; |
---|
| 382 | par_civ1.ImageHeight=size(par_civ1.ImageA,1);%FileInfo_A.Height; |
---|
[598] | 383 | list_param=(fieldnames(Param.ActionInput.Civ1))'; |
---|
[606] | 384 | Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before each string in list_param |
---|
| 385 | Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images |
---|
| 386 | %indicate the values of all the global attributes in the output data |
---|
| 387 | Data.Civ1_ImageA=ImageName_A; |
---|
| 388 | Data.Civ1_ImageB=ImageName_B; |
---|
[610] | 389 | i1=i1_series_Civ1(ifield); |
---|
| 390 | i2=i1; |
---|
| 391 | if ~isempty(i2_series_Civ1) |
---|
| 392 | i2=i2_series_Civ1(ifield); |
---|
| 393 | end |
---|
| 394 | j1=1; |
---|
| 395 | if ~isempty(j1_series_Civ1) |
---|
| 396 | j1=j1_series_Civ1(ifield); |
---|
| 397 | end |
---|
| 398 | j2=j1; |
---|
| 399 | if ~isempty(j2_series_Civ1) |
---|
| 400 | j2=j2_series_Civ1(ifield); |
---|
| 401 | end |
---|
[637] | 402 | Data.Civ1_Time=(time(i2+1,j2+1)+time(i1+1,j1+1))/2; |
---|
| 403 | Data.Civ1_Dt=time(i2+1,j2+1)-time(i1+1,j1+1); |
---|
[598] | 404 | for ilist=1:length(list_param) |
---|
[606] | 405 | Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist}); |
---|
[597] | 406 | end |
---|
[604] | 407 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ1_param]; |
---|
[598] | 408 | Data.CivStage=1; |
---|
[597] | 409 | |
---|
[598] | 410 | % set the list of variables |
---|
| 411 | Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_F','Civ1_C'};% cell array containing the names of the fields to record |
---|
| 412 | Data.VarDimName={'nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1'}; |
---|
| 413 | Data.VarAttribute{1}.Role='coord_x'; |
---|
| 414 | Data.VarAttribute{2}.Role='coord_y'; |
---|
| 415 | Data.VarAttribute{3}.Role='vector_x'; |
---|
| 416 | Data.VarAttribute{4}.Role='vector_y'; |
---|
| 417 | Data.VarAttribute{5}.Role='warnflag'; |
---|
[597] | 418 | |
---|
[598] | 419 | if strcmp(Param.ActionInput.ListCompareMode, 'PIV volume') |
---|
| 420 | Data.ListVarName=[Data.ListVarName 'Civ1_Z']; |
---|
| 421 | Data.Civ1_X=[];Data.Civ1_Y=[];Data.Civ1_Z=[]; |
---|
| 422 | Data.Civ1_U=[];Data.Civ1_V=[];Data.Civ1_C=[];Data.Civ1_F=[]; |
---|
| 423 | for ivol=1:NbSlice |
---|
| 424 | % caluclate velocity data (y and v in indices, reverse to y component) |
---|
| 425 | [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ1); |
---|
| 426 | if ~isempty(errormsg) |
---|
[703] | 427 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
[598] | 428 | return |
---|
| 429 | end |
---|
| 430 | Data.Civ1_X=[Data.Civ1_X reshape(xtable,[],1)]; |
---|
| 431 | Data.Civ1_Y=[Data.Civ1_Y reshape(Param.Civ1.ImageHeight-ytable+1,[],1)]; |
---|
| 432 | Data.Civ1_Z=[Data.Civ1_Z ivol*ones(numel(xtable),1)];% z=image index in image coordinates |
---|
| 433 | Data.Civ1_U=[Data.Civ1_U reshape(utable,[],1)]; |
---|
| 434 | Data.Civ1_V=[Data.Civ1_V reshape(-vtable,[],1)]; |
---|
| 435 | Data.Civ1_C=[Data.Civ1_C reshape(ctable,[],1)]; |
---|
| 436 | Data.Civ1_F=[Data.Civ1_C reshape(F,[],1)]; |
---|
| 437 | end |
---|
| 438 | else %usual PIV |
---|
| 439 | % caluclate velocity data (y and v in indices, reverse to y component) |
---|
| 440 | [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ1); |
---|
[597] | 441 | if ~isempty(errormsg) |
---|
[703] | 442 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
[597] | 443 | return |
---|
| 444 | end |
---|
[598] | 445 | Data.Civ1_X=reshape(xtable,[],1); |
---|
| 446 | Data.Civ1_Y=reshape(par_civ1.ImageHeight-ytable+1,[],1); |
---|
| 447 | Data.Civ1_U=reshape(utable,[],1); |
---|
| 448 | Data.Civ1_V=reshape(-vtable,[],1); |
---|
| 449 | Data.Civ1_C=reshape(ctable,[],1); |
---|
| 450 | Data.Civ1_F=reshape(F,[],1); |
---|
[597] | 451 | end |
---|
[707] | 452 | else% we use existing Civ1 data |
---|
[598] | 453 | if exist('ncfile','var') |
---|
| 454 | CivFile=ncfile; |
---|
| 455 | elseif isfield(Param.Patch1,'CivFile') |
---|
| 456 | CivFile=Param.Patch1.CivFile; |
---|
| 457 | end |
---|
[761] | 458 | [Data,tild,tild,errormsg]=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format |
---|
| 459 | if ~isempty(errormsg) |
---|
[703] | 460 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
[598] | 461 | return |
---|
| 462 | end |
---|
| 463 | if ~isempty(Data.absolut_time_T0')%read civx file |
---|
| 464 | check_civx=1;% test for old civx data format |
---|
| 465 | [Data,vardetect,ichoice]=nc2struct(CivFile);%read the variables in the netcdf file |
---|
| 466 | else |
---|
[761] | 467 | [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file |
---|
[598] | 468 | end |
---|
[597] | 469 | end |
---|
| 470 | |
---|
[598] | 471 | %% Fix1 |
---|
| 472 | if isfield (Param.ActionInput,'Fix1') |
---|
[822] | 473 | if ~isfield (Param.ActionInput,'Civ1')% if we use existing Civ1, remove previous data beyond Civ1 |
---|
| 474 | Fix1_attr=find(strcmp('Fix1',Data.ListGlobalAttribute)); |
---|
| 475 | Data.ListGlobalAttribute(Fix1_attr)=[]; |
---|
| 476 | for ilist=1:numel(Fix1_attr) |
---|
| 477 | Data=rmfield(Data,Data.ListGlobalAttribute{Fix1_attr(ilist)}); |
---|
| 478 | end |
---|
| 479 | end |
---|
[598] | 480 | ListFixParam=fieldnames(Param.ActionInput.Fix1); |
---|
| 481 | for ilist=1:length(ListFixParam) |
---|
| 482 | ParamName=ListFixParam{ilist}; |
---|
| 483 | ListName=['Fix1_' ParamName]; |
---|
| 484 | eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];']) |
---|
| 485 | eval(['Data.' ListName '=Param.ActionInput.Fix1.' ParamName ';']) |
---|
| 486 | end |
---|
| 487 | if check_civx |
---|
| 488 | if ~isfield(Data,'fix') |
---|
| 489 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix']; |
---|
| 490 | Data.fix=1; |
---|
| 491 | Data.ListVarName=[Data.ListVarName {'vec_FixFlag'}]; |
---|
| 492 | Data.VarDimName=[Data.VarDimName {'nb_vectors'}]; |
---|
| 493 | end |
---|
| 494 | 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); |
---|
| 495 | else |
---|
| 496 | Data.ListVarName=[Data.ListVarName {'Civ1_FF'}]; |
---|
| 497 | Data.VarDimName=[Data.VarDimName {'nb_vec_1'}]; |
---|
| 498 | nbvar=length(Data.ListVarName); |
---|
| 499 | Data.VarAttribute{nbvar}.Role='errorflag'; |
---|
| 500 | Data.Civ1_FF=fix(Param.ActionInput.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V); |
---|
| 501 | Data.CivStage=2; |
---|
| 502 | end |
---|
[597] | 503 | end |
---|
[598] | 504 | %% Patch1 |
---|
| 505 | if isfield (Param.ActionInput,'Patch1') |
---|
| 506 | if check_civx |
---|
| 507 | errormsg='Civ Matlab input needed for patch'; |
---|
[703] | 508 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
[598] | 509 | return |
---|
| 510 | end |
---|
| 511 | |
---|
| 512 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch1_Rho','Patch1_Threshold','Patch1_SubDomain'}]; |
---|
| 513 | Data.Patch1_FieldSmooth=Param.ActionInput.Patch1.FieldSmooth; |
---|
| 514 | Data.Patch1_MaxDiff=Param.ActionInput.Patch1.MaxDiff; |
---|
| 515 | Data.Patch1_SubDomainSize=Param.ActionInput.Patch1.SubDomainSize; |
---|
| 516 | nbvar=length(Data.ListVarName); |
---|
| 517 | Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbCentres','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}]; |
---|
| 518 | Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},'nb_subdomain_1',... |
---|
| 519 | {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}]; |
---|
| 520 | Data.VarAttribute{nbvar+1}.Role='vector_x'; |
---|
| 521 | Data.VarAttribute{nbvar+2}.Role='vector_y'; |
---|
| 522 | Data.VarAttribute{nbvar+5}.Role='coord_tps'; |
---|
| 523 | Data.VarAttribute{nbvar+6}.Role='vector_x'; |
---|
| 524 | Data.VarAttribute{nbvar+7}.Role='vector_y'; |
---|
| 525 | Data.Civ1_U_smooth=zeros(size(Data.Civ1_X)); |
---|
| 526 | Data.Civ1_V_smooth=zeros(size(Data.Civ1_X)); |
---|
| 527 | if isfield(Data,'Civ1_FF') |
---|
| 528 | ind_good=find(Data.Civ1_FF==0); |
---|
[597] | 529 | else |
---|
[598] | 530 | ind_good=1:numel(Data.Civ1_X); |
---|
[597] | 531 | end |
---|
[598] | 532 | [Data.Civ1_SubRange,Data.Civ1_NbCentres,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=... |
---|
| 533 | 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); |
---|
| 534 | Data.Civ1_U_smooth(ind_good)=Ures; |
---|
| 535 | Data.Civ1_V_smooth(ind_good)=Vres; |
---|
| 536 | Data.Civ1_FF(ind_good)=FFres; |
---|
| 537 | Data.CivStage=3; |
---|
[597] | 538 | end |
---|
| 539 | |
---|
[598] | 540 | %% Civ2 |
---|
| 541 | if isfield (Param.ActionInput,'Civ2') |
---|
| 542 | par_civ2=Param.ActionInput.Civ2; |
---|
| 543 | par_civ2.ImageA=[]; |
---|
| 544 | par_civ2.ImageB=[]; |
---|
| 545 | % if ~isfield(Param.Civ1,'ImageA') |
---|
[819] | 546 | i1=i1_series_Civ2(ifield); |
---|
| 547 | i2=i1; |
---|
| 548 | if ~isempty(i2_series_Civ2) |
---|
| 549 | i2=i2_series_Civ2(ifield); |
---|
| 550 | end |
---|
| 551 | j1=1; |
---|
| 552 | if ~isempty(j1_series_Civ2) |
---|
| 553 | j1=j1_series_Civ2(ifield); |
---|
| 554 | end |
---|
| 555 | j2=j1; |
---|
| 556 | if ~isempty(j2_series_Civ2) |
---|
| 557 | j2=j2_series_Civ2(ifield); |
---|
| 558 | end |
---|
| 559 | ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1,[],j1); |
---|
[598] | 560 | |
---|
[635] | 561 | if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield)) |
---|
[598] | 562 | par_civ2.ImageA=par_civ1.ImageA; |
---|
| 563 | else |
---|
[768] | 564 | [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield)); |
---|
[597] | 565 | end |
---|
[819] | 566 | ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2,[],j2); |
---|
[601] | 567 | if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2) |
---|
[598] | 568 | par_civ2.ImageB=par_civ1.ImageB; |
---|
[597] | 569 | else |
---|
[768] | 570 | [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield)); |
---|
[598] | 571 | end |
---|
| 572 | |
---|
[819] | 573 | ncfile=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1,i2,... |
---|
| 574 | j1,j2); |
---|
[635] | 575 | par_civ2.ImageWidth=FileInfo_A.Width; |
---|
| 576 | par_civ2.ImageHeight=FileInfo_A.Height; |
---|
[598] | 577 | |
---|
| 578 | if isfield(par_civ2,'Grid')% grid points set as input file |
---|
| 579 | if ischar(par_civ2.Grid)%read the grid file if the input is a file name |
---|
| 580 | par_civ2.Grid=dlmread(par_civ2.Grid); |
---|
| 581 | par_civ2.Grid(1,:)=[];%the first line must be removed (heading in the grid file) |
---|
| 582 | end |
---|
| 583 | else% automatic grid |
---|
| 584 | minix=floor(par_civ2.Dx/2)-0.5; |
---|
| 585 | maxix=minix+par_civ2.Dx*floor((par_civ2.ImageWidth-1)/par_civ2.Dx); |
---|
| 586 | miniy=floor(par_civ2.Dy/2)-0.5; |
---|
| 587 | maxiy=minix+par_civ2.Dy*floor((par_civ2.ImageHeight-1)/par_civ2.Dy); |
---|
| 588 | [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy); |
---|
| 589 | par_civ2.Grid(:,1)=reshape(GridX,[],1); |
---|
| 590 | par_civ2.Grid(:,2)=reshape(GridY,[],1); |
---|
[597] | 591 | end |
---|
[598] | 592 | Shiftx=zeros(size(par_civ2.Grid,1),1);% shift expected from civ1 data |
---|
| 593 | Shifty=zeros(size(par_civ2.Grid,1),1); |
---|
| 594 | nbval=zeros(size(par_civ2.Grid,1),1); |
---|
| 595 | if par_civ2.CheckDeformation |
---|
| 596 | DUDX=zeros(size(par_civ2.Grid,1),1); |
---|
| 597 | DUDY=zeros(size(par_civ2.Grid,1),1); |
---|
| 598 | DVDX=zeros(size(par_civ2.Grid,1),1); |
---|
| 599 | DVDY=zeros(size(par_civ2.Grid,1),1); |
---|
[597] | 600 | end |
---|
[598] | 601 | NbSubDomain=size(Data.Civ1_SubRange,3); |
---|
| 602 | % get the guess from patch1 |
---|
[761] | 603 | for isub=1:NbSubDomain% for each sub-domain of Patch1 |
---|
| 604 | nbvec_sub=Data.Civ1_NbCentres(isub);% nbre of Civ1 vectors in the subdomain |
---|
| 605 | ind_sel=find(par_civ2.Grid(:,1)>=Data.Civ1_SubRange(1,1,isub) & par_civ2.Grid(:,1)<=Data.Civ1_SubRange(1,2,isub) &... |
---|
| 606 | par_civ2.Grid(:,2)>=Data.Civ1_SubRange(2,1,isub) & par_civ2.Grid(:,2)<=Data.Civ1_SubRange(2,2,isub)); |
---|
| 607 | epoints = par_civ2.Grid(ind_sel,:);% coordinates of interpolation sites |
---|
[598] | 608 | ctrs=Data.Civ1_Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs |
---|
| 609 | nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for eacn interpolation point (in case of subdomain overlap) |
---|
| 610 | EM = tps_eval(epoints,ctrs); |
---|
| 611 | Shiftx(ind_sel)=Shiftx(ind_sel)+EM*Data.Civ1_U_tps(1:nbvec_sub+3,isub); |
---|
| 612 | Shifty(ind_sel)=Shifty(ind_sel)+EM*Data.Civ1_V_tps(1:nbvec_sub+3,isub); |
---|
| 613 | if par_civ2.CheckDeformation |
---|
| 614 | [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs |
---|
| 615 | DUDX(ind_sel)=DUDX(ind_sel)+EMDX*Data.Civ1_U_tps(1:nbvec_sub+3,isub); |
---|
| 616 | DUDY(ind_sel)=DUDY(ind_sel)+EMDY*Data.Civ1_U_tps(1:nbvec_sub+3,isub); |
---|
| 617 | DVDX(ind_sel)=DVDX(ind_sel)+EMDX*Data.Civ1_V_tps(1:nbvec_sub+3,isub); |
---|
| 618 | DVDY(ind_sel)=DVDY(ind_sel)+EMDY*Data.Civ1_V_tps(1:nbvec_sub+3,isub); |
---|
[597] | 619 | end |
---|
| 620 | end |
---|
[598] | 621 | mask=''; |
---|
| 622 | if par_civ2.CheckMask&&~isempty(par_civ2.Mask)&& ~strcmp(maskname,par_civ2.Mask)% mask exist, not already read in civ1 |
---|
| 623 | mask=imread(par_civ2.Mask); |
---|
| 624 | end |
---|
| 625 | ibx2=ceil(par_civ2.CorrBoxSize(1)/2); |
---|
| 626 | iby2=ceil(par_civ2.CorrBoxSize(2)/2); |
---|
| 627 | par_civ2.SearchBoxSize(1)=2*ibx2+9;% search ara +-4 pixels around the guess |
---|
| 628 | par_civ2.SearchBoxSize(2)=2*iby2+9; |
---|
[768] | 629 | Civ2_Dt=time(i2+1,j2+1)-time(i1+1,j1+1); |
---|
| 630 | par_civ2.SearchBoxShift=(Civ2_Dt/Data.Civ1_Dt)*[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)]; |
---|
[761] | 631 | 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 |
---|
[598] | 632 | if par_civ2.CheckDeformation |
---|
| 633 | par_civ2.DUDX=DUDX./nbval; |
---|
| 634 | par_civ2.DUDY=DUDY./nbval; |
---|
| 635 | par_civ2.DVDX=DVDX./nbval; |
---|
| 636 | par_civ2.DVDY=DVDY./nbval; |
---|
| 637 | end |
---|
| 638 | % caluclate velocity data (y and v in indices, reverse to y component) |
---|
| 639 | [xtable ytable utable vtable ctable F] = civ (par_civ2); |
---|
| 640 | list_param=(fieldnames(Param.ActionInput.Civ2))'; |
---|
[606] | 641 | Civ2_param=regexprep(list_param,'^.+','Civ2_$0');% insert 'Civ2_' before each string in list_param |
---|
| 642 | Civ2_param=[{'Civ2_ImageA','Civ2_ImageB','Civ2_Time','Civ2_Dt'} Civ2_param]; %insert the names of the two input images |
---|
| 643 | %indicate the values of all the global attributes in the output data |
---|
| 644 | Data.Civ2_ImageA=ImageName_A; |
---|
| 645 | Data.Civ2_ImageB=ImageName_B; |
---|
[676] | 646 | Data.Civ2_Time=(time(i2+1,j2+1)+time(i1+1,j1+1))/2; |
---|
[768] | 647 | Data.Civ2_Dt=Civ2_Dt; |
---|
[676] | 648 | % Data.Civ2_Time=1; |
---|
| 649 | % Data.Civ2_Dt=1; |
---|
[598] | 650 | for ilist=1:length(list_param) |
---|
[606] | 651 | Data.(Civ2_param{4+ilist})=Param.ActionInput.Civ2.(list_param{ilist}); |
---|
[598] | 652 | end |
---|
[606] | 653 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param]; |
---|
| 654 | |
---|
[598] | 655 | nbvar=numel(Data.ListVarName); |
---|
| 656 | 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 |
---|
| 657 | Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}]; |
---|
| 658 | Data.VarAttribute{nbvar+1}.Role='coord_x'; |
---|
| 659 | Data.VarAttribute{nbvar+2}.Role='coord_y'; |
---|
| 660 | Data.VarAttribute{nbvar+3}.Role='vector_x'; |
---|
| 661 | Data.VarAttribute{nbvar+4}.Role='vector_y'; |
---|
| 662 | Data.VarAttribute{nbvar+5}.Role='warnflag'; |
---|
| 663 | Data.Civ2_X=reshape(xtable,[],1); |
---|
| 664 | Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1); |
---|
| 665 | Data.Civ2_U=reshape(utable,[],1); |
---|
| 666 | Data.Civ2_V=reshape(-vtable,[],1); |
---|
| 667 | Data.Civ2_C=reshape(ctable,[],1); |
---|
| 668 | Data.Civ2_F=reshape(F,[],1); |
---|
| 669 | Data.CivStage=Data.CivStage+1; |
---|
| 670 | end |
---|
| 671 | |
---|
| 672 | %% Fix2 |
---|
| 673 | if isfield (Param.ActionInput,'Fix2') |
---|
| 674 | ListFixParam=fieldnames(Param.ActionInput.Fix2); |
---|
| 675 | for ilist=1:length(ListFixParam) |
---|
| 676 | ParamName=ListFixParam{ilist}; |
---|
| 677 | ListName=['Fix2_' ParamName]; |
---|
| 678 | eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];']) |
---|
| 679 | eval(['Data.' ListName '=Param.ActionInput.Fix2.' ParamName ';']) |
---|
| 680 | end |
---|
| 681 | if check_civx |
---|
| 682 | if ~isfield(Data,'fix2') |
---|
| 683 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix2']; |
---|
| 684 | Data.fix2=1; |
---|
| 685 | Data.ListVarName=[Data.ListVarName {'vec2_FixFlag'}]; |
---|
| 686 | Data.VarDimName=[Data.VarDimName {'nb_vectors2'}]; |
---|
| 687 | end |
---|
| 688 | Data.vec_FixFlag=fix(Param.Fix2,Data.vec2_F,Data.vec2_C,Data.vec2_U,Data.vec2_V,Data.vec2_X,Data.vec2_Y); |
---|
[597] | 689 | else |
---|
[598] | 690 | Data.ListVarName=[Data.ListVarName {'Civ2_FF'}]; |
---|
| 691 | Data.VarDimName=[Data.VarDimName {'nb_vec_2'}]; |
---|
| 692 | nbvar=length(Data.ListVarName); |
---|
| 693 | Data.VarAttribute{nbvar}.Role='errorflag'; |
---|
[822] | 694 | Data.Civ2_FF=double(fix(Param.ActionInput.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V)); |
---|
[598] | 695 | Data.CivStage=Data.CivStage+1; |
---|
[597] | 696 | end |
---|
[598] | 697 | |
---|
| 698 | end |
---|
| 699 | |
---|
| 700 | %% Patch2 |
---|
| 701 | if isfield (Param.ActionInput,'Patch2') |
---|
| 702 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch2_Rho','Patch2_Threshold','Patch2_SubDomain'}]; |
---|
| 703 | Data.Patch2_FieldSmooth=Param.ActionInput.Patch2.FieldSmooth; |
---|
| 704 | Data.Patch2_MaxDiff=Param.ActionInput.Patch2.MaxDiff; |
---|
| 705 | Data.Patch2_SubDomainSize=Param.ActionInput.Patch2.SubDomainSize; |
---|
| 706 | nbvar=length(Data.ListVarName); |
---|
| 707 | Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbCentres','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}]; |
---|
| 708 | Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},... |
---|
| 709 | {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}]; |
---|
| 710 | |
---|
| 711 | Data.VarAttribute{nbvar+1}.Role='vector_x'; |
---|
| 712 | Data.VarAttribute{nbvar+2}.Role='vector_y'; |
---|
| 713 | Data.VarAttribute{nbvar+5}.Role='coord_tps'; |
---|
| 714 | Data.VarAttribute{nbvar+6}.Role='vector_x'; |
---|
| 715 | Data.VarAttribute{nbvar+7}.Role='vector_y'; |
---|
| 716 | Data.Civ2_U_smooth=zeros(size(Data.Civ2_X)); |
---|
| 717 | Data.Civ2_V_smooth=zeros(size(Data.Civ2_X)); |
---|
| 718 | if isfield(Data,'Civ2_FF') |
---|
| 719 | ind_good=find(Data.Civ2_FF==0); |
---|
[597] | 720 | else |
---|
[598] | 721 | ind_good=1:numel(Data.Civ2_X); |
---|
[597] | 722 | end |
---|
[598] | 723 | [Data.Civ2_SubRange,Data.Civ2_NbCentres,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures, Vres,tild,FFres]=... |
---|
| 724 | 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); |
---|
| 725 | Data.Civ2_U_smooth(ind_good)=Ures; |
---|
| 726 | Data.Civ2_V_smooth(ind_good)=Vres; |
---|
| 727 | Data.Civ2_FF(ind_good)=FFres; |
---|
| 728 | Data.CivStage=Data.CivStage+1; |
---|
[597] | 729 | end |
---|
[598] | 730 | |
---|
| 731 | %% write result in a netcdf file if requested |
---|
| 732 | if exist('ncfile','var') |
---|
| 733 | errormsg=struct2nc(ncfile,Data); |
---|
| 734 | if isempty(errormsg) |
---|
| 735 | disp([ncfile ' written']) |
---|
| 736 | else |
---|
| 737 | disp(errormsg) |
---|
| 738 | end |
---|
| 739 | end |
---|
[597] | 740 | end |
---|
| 741 | |
---|
[598] | 742 | % 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/ |
---|
| 743 | %-------------------------------------------------------------------------- |
---|
| 744 | % function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi) |
---|
| 745 | % |
---|
| 746 | % OUTPUT: |
---|
| 747 | % xtable: set of x coordinates |
---|
| 748 | % ytable: set of y coordiantes |
---|
| 749 | % utable: set of u displacements (along x) |
---|
| 750 | % vtable: set of v displacements (along y) |
---|
| 751 | % ctable: max image correlation for each vector |
---|
| 752 | % typevector: set of flags, =1 for good, =0 for NaN vectors |
---|
| 753 | % |
---|
| 754 | %INPUT: |
---|
| 755 | % par_civ: structure of input parameters, with fields: |
---|
| 756 | % .CorrBoxSize |
---|
| 757 | % .SearchBoxSize |
---|
| 758 | % .SearchBoxShift |
---|
| 759 | % .ImageHeight |
---|
| 760 | % .ImageWidth |
---|
| 761 | % .Dx, Dy |
---|
| 762 | % .Grid |
---|
| 763 | % .Mask |
---|
| 764 | % .MinIma |
---|
| 765 | % .MaxIma |
---|
| 766 | % .image1:first image (matrix) |
---|
| 767 | % image2: second image (matrix) |
---|
| 768 | % ibx2,iby2: half size of the correlation box along x and y, in px (size=(2*iby2+1,2*ibx2+1) |
---|
| 769 | % isx2,isy2: half size of the search box along x and y, in px (size=(2*isy2+1,2*isx2+1) |
---|
| 770 | % shiftx, shifty: shift of the search box (in pixel index, yshift reversed) |
---|
| 771 | % step: mesh of the measurement points (in px) |
---|
| 772 | % subpixfinder=1 or 2 controls the curve fitting of the image correlation |
---|
| 773 | % mask: =[] for no mask |
---|
| 774 | % roi: 4 element vector defining a region of interest: x position, y position, width, height, (in image indices), for the whole image, roi=[]; |
---|
| 775 | function [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ) |
---|
| 776 | %this funtion performs the DCC PIV analysis. Recent window-deformation |
---|
| 777 | %methods perform better and will maybe be implemented in the future. |
---|
| 778 | |
---|
| 779 | %% prepare measurement grid |
---|
| 780 | if isfield(par_civ,'Grid')% grid points set as input |
---|
| 781 | if ischar(par_civ.Grid)%read the drid file if the input is a file name |
---|
| 782 | par_civ.Grid=dlmread(par_civ.Grid); |
---|
| 783 | par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file) |
---|
| 784 | end |
---|
| 785 | else% automatic grid |
---|
| 786 | minix=floor(par_civ.Dx/2)-0.5; |
---|
| 787 | maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx); |
---|
| 788 | miniy=floor(par_civ.Dy/2)-0.5; |
---|
| 789 | maxiy=minix+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy); |
---|
| 790 | [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy); |
---|
| 791 | par_civ.Grid(:,1)=reshape(GridX,[],1); |
---|
| 792 | par_civ.Grid(:,2)=reshape(GridY,[],1); |
---|
[597] | 793 | end |
---|
[598] | 794 | nbvec=size(par_civ.Grid,1); |
---|
| 795 | |
---|
| 796 | %% prepare correlation and search boxes |
---|
| 797 | ibx2=ceil(par_civ.CorrBoxSize(1)/2); |
---|
| 798 | iby2=ceil(par_civ.CorrBoxSize(2)/2); |
---|
| 799 | isx2=ceil(par_civ.SearchBoxSize(1)/2); |
---|
| 800 | isy2=ceil(par_civ.SearchBoxSize(2)/2); |
---|
| 801 | shiftx=round(par_civ.SearchBoxShift(:,1)); |
---|
| 802 | shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases |
---|
| 803 | if numel(shiftx)==1% case of a unique shift for the whole field( civ1) |
---|
| 804 | shiftx=shiftx*ones(nbvec,1); |
---|
| 805 | shifty=shifty*ones(nbvec,1); |
---|
| 806 | end |
---|
| 807 | |
---|
| 808 | %% Default output |
---|
| 809 | xtable=par_civ.Grid(:,1); |
---|
| 810 | ytable=par_civ.Grid(:,2); |
---|
| 811 | utable=zeros(nbvec,1); |
---|
| 812 | vtable=zeros(nbvec,1); |
---|
| 813 | ctable=zeros(nbvec,1); |
---|
| 814 | F=zeros(nbvec,1); |
---|
| 815 | result_conv=[]; |
---|
| 816 | errormsg=''; |
---|
| 817 | |
---|
| 818 | %% prepare mask |
---|
| 819 | if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) |
---|
| 820 | if strcmp(par_civ.Mask,'all') |
---|
| 821 | return % get the grid only, no civ calculation |
---|
| 822 | elseif ischar(par_civ.Mask) |
---|
| 823 | par_civ.Mask=imread(par_civ.Mask); |
---|
| 824 | end |
---|
| 825 | end |
---|
| 826 | check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold |
---|
| 827 | check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma); |
---|
| 828 | |
---|
| 829 | % %% prepare images |
---|
| 830 | % if isfield(par_civ,'reverse_pair') |
---|
| 831 | % if par_civ.reverse_pair |
---|
| 832 | % if ischar(par_civ.ImageB) |
---|
| 833 | % temp=par_civ.ImageA; |
---|
| 834 | % par_civ.ImageA=imread(par_civ.ImageB); |
---|
| 835 | % end |
---|
| 836 | % if ischar(temp) |
---|
| 837 | % par_civ.ImageB=imread(temp); |
---|
| 838 | % end |
---|
| 839 | % end |
---|
| 840 | % else |
---|
| 841 | % if ischar(par_civ.ImageA) |
---|
| 842 | % par_civ.ImageA=imread(par_civ.ImageA); |
---|
| 843 | % end |
---|
| 844 | % if ischar(par_civ.ImageB) |
---|
| 845 | % par_civ.ImageB=imread(par_civ.ImageB); |
---|
| 846 | % end |
---|
| 847 | % end |
---|
| 848 | par_civ.ImageA=sum(double(par_civ.ImageA),3);%sum over rgb component for color images |
---|
| 849 | par_civ.ImageB=sum(double(par_civ.ImageB),3); |
---|
| 850 | [npy_ima npx_ima]=size(par_civ.ImageA); |
---|
| 851 | if ~isequal(size(par_civ.ImageB),[npy_ima npx_ima]) |
---|
| 852 | errormsg='image pair with unequal size'; |
---|
[597] | 853 | return |
---|
| 854 | end |
---|
| 855 | |
---|
[598] | 856 | %% Apply mask |
---|
| 857 | % Convention for mask IDEAS TO IMPLEMENT ? |
---|
| 858 | % mask >200 : velocity calculated |
---|
| 859 | % 200 >=mask>150;velocity not calculated, interpolation allowed (bad spots) |
---|
| 860 | % 150>=mask >100: velocity not calculated, nor interpolated |
---|
| 861 | % 100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries) |
---|
| 862 | % 20>=mask: velocity=0 |
---|
| 863 | checkmask=0; |
---|
| 864 | MinA=min(min(par_civ.ImageA)); |
---|
| 865 | MinB=min(min(par_civ.ImageB)); |
---|
| 866 | if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) |
---|
| 867 | checkmask=1; |
---|
| 868 | if ~isequal(size(par_civ.Mask),[npy_ima npx_ima]) |
---|
| 869 | errormsg='mask must be an image with the same size as the images'; |
---|
| 870 | return |
---|
| 871 | end |
---|
| 872 | % check_noflux=(par_civ.Mask<100) ;%TODO: to implement |
---|
| 873 | check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 ); |
---|
| 874 | par_civ.ImageA(check_undefined)=MinA;% put image A to zero (i.e. the min image value) in the undefined area |
---|
| 875 | par_civ.ImageB(check_undefined)=MinB;% put image B to zero (i.e. the min image value) in the undefined area |
---|
| 876 | end |
---|
| 877 | |
---|
| 878 | %% compute image correlations: MAINLOOP on velocity vectors |
---|
| 879 | corrmax=0; |
---|
| 880 | sum_square=1;% default |
---|
| 881 | mesh=1;% default |
---|
| 882 | CheckDecimal=isfield(par_civ,'CheckDecimal')&& par_civ.CheckDecimal==1; |
---|
| 883 | if CheckDecimal |
---|
| 884 | mesh=0.2;%mesh in pixels for subpixel image interpolation |
---|
| 885 | CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1; |
---|
| 886 | end |
---|
| 887 | % vector=[0 0];%default |
---|
| 888 | for ivec=1:nbvec |
---|
| 889 | iref=round(par_civ.Grid(ivec,1)+0.5);% xindex on the image A for the middle of the correlation box |
---|
| 890 | jref=round(par_civ.ImageHeight-par_civ.Grid(ivec,2)+0.5);% yindex on the image B for the middle of the correlation box |
---|
| 891 | %if ~(checkmask && par_civ.Mask(jref,iref)<=20) %velocity not set to zero by the black mask |
---|
| 892 | % if jref-iby2<1 || jref+iby2>par_civ.ImageHeight|| iref-ibx2<1 || iref+ibx2>par_civ.ImageWidth||... |
---|
| 893 | % 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 |
---|
| 894 | % F(ivec)=3; |
---|
| 895 | % else |
---|
| 896 | F(ivec)=0; |
---|
| 897 | subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage |
---|
| 898 | subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage |
---|
| 899 | subrange2_x=iref+shiftx(ivec)-isx2:iref+shiftx(ivec)+isx2;%x indices defining the second subimage |
---|
| 900 | subrange2_y=jref+shifty(ivec)-isy2:jref+shifty(ivec)+isy2;%y indices defining the second subimage |
---|
| 901 | image1_crop=MinA*ones(numel(subrange1_y),numel(subrange1_x));% default value=min of image A |
---|
| 902 | image2_crop=MinA*ones(numel(subrange2_y),numel(subrange2_x));% default value=min of image A |
---|
| 903 | check1_x=subrange1_x>=1 & subrange1_x<=par_civ.ImageWidth;% check which points in the subimage 1 are contained in the initial image 1 |
---|
| 904 | check1_y=subrange1_y>=1 & subrange1_y<=par_civ.ImageHeight; |
---|
| 905 | check2_x=subrange2_x>=1 & subrange2_x<=par_civ.ImageWidth;% check which points in the subimage 2 are contained in the initial image 2 |
---|
| 906 | check2_y=subrange2_y>=1 & subrange2_y<=par_civ.ImageHeight; |
---|
| 907 | |
---|
| 908 | 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 |
---|
| 909 | 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 |
---|
| 910 | image1_mean=mean(mean(image1_crop)); |
---|
| 911 | image2_mean=mean(mean(image2_crop)); |
---|
| 912 | %threshold on image minimum |
---|
| 913 | if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma) |
---|
| 914 | F(ivec)=3; |
---|
[597] | 915 | end |
---|
[598] | 916 | %threshold on image maximum |
---|
| 917 | if check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma) |
---|
| 918 | F(ivec)=3; |
---|
[597] | 919 | end |
---|
[598] | 920 | % end |
---|
| 921 | if F(ivec)~=3 |
---|
| 922 | image1_crop=image1_crop-image1_mean;%substract the mean |
---|
| 923 | image2_crop=image2_crop-image2_mean; |
---|
| 924 | if CheckDecimal |
---|
| 925 | xi=(1:mesh:size(image1_crop,2)); |
---|
| 926 | yi=(1:mesh:size(image1_crop,1))'; |
---|
| 927 | if CheckDeformation |
---|
| 928 | [XI,YI]=meshgrid(xi-ceil(size(image1_crop,2)/2),yi-ceil(size(image1_crop,1)/2)); |
---|
| 929 | XIant=XI-par_civ.DUDX(ivec)*XI-par_civ.DUDY(ivec)*YI+ceil(size(image1_crop,2)/2); |
---|
| 930 | YIant=YI-par_civ.DVDX(ivec)*XI-par_civ.DVDY(ivec)*YI+ceil(size(image1_crop,1)/2); |
---|
| 931 | image1_crop=interp2(image1_crop,XIant,YIant); |
---|
| 932 | else |
---|
| 933 | image1_crop=interp2(image1_crop,xi,yi); |
---|
[597] | 934 | end |
---|
[598] | 935 | xi=(1:mesh:size(image2_crop,2)); |
---|
| 936 | yi=(1:mesh:size(image2_crop,1))'; |
---|
| 937 | image2_crop=interp2(image2_crop,xi,yi); |
---|
[597] | 938 | end |
---|
[598] | 939 | sum_square=sum(sum(image1_crop.*image1_crop)); |
---|
| 940 | %reference: Oliver Pust, PIV: Direct Cross-Correlation |
---|
| 941 | result_conv= conv2(image2_crop,flipdim(flipdim(image1_crop,2),1),'valid'); |
---|
| 942 | corrmax= max(max(result_conv)); |
---|
| 943 | result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255 |
---|
| 944 | %Find the correlation max, at 255 |
---|
| 945 | [y,x] = find(result_conv==255,1); |
---|
| 946 | if ~isempty(y) && ~isempty(x) |
---|
| 947 | try |
---|
| 948 | if par_civ.CorrSmooth==1 |
---|
| 949 | [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y); |
---|
| 950 | elseif par_civ.CorrSmooth==2 |
---|
| 951 | [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y); |
---|
[597] | 952 | end |
---|
[598] | 953 | utable(ivec)=vector(1)*mesh+shiftx(ivec); |
---|
| 954 | vtable(ivec)=vector(2)*mesh+shifty(ivec); |
---|
| 955 | xtable(ivec)=iref+utable(ivec)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2) |
---|
| 956 | ytable(ivec)=jref+vtable(ivec)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge) |
---|
| 957 | iref=round(xtable(ivec));% image index for the middle of the vector |
---|
| 958 | jref=round(ytable(ivec)); |
---|
| 959 | if checkmask && par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100 |
---|
| 960 | utable(ivec)=0; |
---|
| 961 | vtable(ivec)=0; |
---|
| 962 | F(ivec)=3; |
---|
| 963 | end |
---|
| 964 | ctable(ivec)=corrmax/sum_square;% correlation value |
---|
| 965 | catch ME |
---|
| 966 | F(ivec)=3; |
---|
[597] | 967 | end |
---|
[598] | 968 | else |
---|
| 969 | F(ivec)=3; |
---|
[597] | 970 | end |
---|
[598] | 971 | end |
---|
| 972 | end |
---|
| 973 | result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output |
---|
| 974 | |
---|
| 975 | %------------------------------------------------------------------------ |
---|
| 976 | % --- Find the maximum of the correlation function after interpolation |
---|
| 977 | function [vector,F] = SUBPIXGAUSS (result_conv,x,y) |
---|
| 978 | %------------------------------------------------------------------------ |
---|
| 979 | vector=[0 0]; %default |
---|
| 980 | F=0; |
---|
| 981 | [npy,npx]=size(result_conv); |
---|
[731] | 982 | result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log) |
---|
| 983 | %the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ï¿œ Israel Institute of Technology |
---|
| 984 | %http://urapiv.wordpress.com |
---|
| 985 | peaky = y; |
---|
| 986 | if y <= npy-1 && y >= 1 |
---|
| 987 | f0 = log(result_conv(y,x)); |
---|
| 988 | f1 = log(result_conv(y-1,x)); |
---|
| 989 | f2 = log(result_conv(y+1,x)); |
---|
| 990 | peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2); |
---|
| 991 | else |
---|
| 992 | F=-2; % warning flag for vector truncated by the limited search box |
---|
| 993 | end |
---|
| 994 | peakx=x; |
---|
| 995 | if x <= npx-1 && x >= 1 |
---|
| 996 | f0 = log(result_conv(y,x)); |
---|
| 997 | f1 = log(result_conv(y,x-1)); |
---|
| 998 | f2 = log(result_conv(y,x+1)); |
---|
| 999 | peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2); |
---|
| 1000 | else |
---|
| 1001 | F=-2; % warning flag for vector truncated by the limited search box |
---|
| 1002 | end |
---|
| 1003 | vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; |
---|
[598] | 1004 | |
---|
| 1005 | %------------------------------------------------------------------------ |
---|
| 1006 | % --- Find the maximum of the correlation function after interpolation |
---|
| 1007 | function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y) |
---|
| 1008 | %------------------------------------------------------------------------ |
---|
| 1009 | vector=[0 0]; %default |
---|
| 1010 | F=-2; |
---|
| 1011 | peaky=y; |
---|
| 1012 | peakx=x; |
---|
[731] | 1013 | result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log) |
---|
[598] | 1014 | [npy,npx]=size(result_conv); |
---|
| 1015 | if (x <= npx-1) && (y <= npy-1) && (x >= 1) && (y >= 1) |
---|
| 1016 | F=0; |
---|
| 1017 | for i=-1:1 |
---|
| 1018 | for j=-1:1 |
---|
| 1019 | %following 15 lines based on |
---|
| 1020 | %H. Nobach ï¿œ M. Honkanen (2005) |
---|
| 1021 | %Two-dimensional Gaussian regression for sub-pixel displacement |
---|
| 1022 | %estimation in particle image velocimetry or particle position |
---|
| 1023 | %estimation in particle tracking velocimetry |
---|
| 1024 | %Experiments in Fluids (2005) 38: 511ï¿œ515 |
---|
| 1025 | c10(j+2,i+2)=i*log(result_conv(y+j, x+i)); |
---|
| 1026 | c01(j+2,i+2)=j*log(result_conv(y+j, x+i)); |
---|
| 1027 | c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i)); |
---|
| 1028 | c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i)); |
---|
| 1029 | c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i)); |
---|
| 1030 | end |
---|
| 1031 | end |
---|
| 1032 | c10=(1/6)*sum(sum(c10)); |
---|
| 1033 | c01=(1/6)*sum(sum(c01)); |
---|
| 1034 | c11=(1/4)*sum(sum(c11)); |
---|
| 1035 | c20=(1/6)*sum(sum(c20)); |
---|
| 1036 | c02=(1/6)*sum(sum(c02)); |
---|
| 1037 | deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2); |
---|
| 1038 | deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2); |
---|
| 1039 | if abs(deltax)<1 |
---|
| 1040 | peakx=x+deltax; |
---|
| 1041 | end |
---|
| 1042 | if abs(deltay)<1 |
---|
| 1043 | peaky=y+deltay; |
---|
| 1044 | end |
---|
| 1045 | end |
---|
| 1046 | vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; |
---|
| 1047 | |
---|
| 1048 | %'RUN_FIX': function for fixing velocity fields: |
---|
| 1049 | %----------------------------------------------- |
---|
| 1050 | % RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref) |
---|
| 1051 | % |
---|
| 1052 | %filename: name of the netcdf file (used as input and output) |
---|
| 1053 | %field: structure specifying the names of the fields to fix (depending on civ1 or civ2) |
---|
| 1054 | %.vel_type='civ1' or 'civ2'; |
---|
| 1055 | %.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1); |
---|
| 1056 | %.fixflag=name of fix flag variable ('vec_FixFlag' for civ1) |
---|
| 1057 | %flagindex: flag specifying which values of vec_f are removed: |
---|
| 1058 | % if flagindex(1)=1: vec_f=-2 vectors are removed |
---|
| 1059 | % if flagindex(2)=1: vec_f=3 vectors are removed |
---|
| 1060 | % if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2) |
---|
| 1061 | %iter=1 for civ1 fields and iter=2 for civ2 fields |
---|
| 1062 | %thresh_vecC: threshold in the image correlation vec_C |
---|
| 1063 | %flag_mask: =1 mask used to remove vectors (0 else) |
---|
| 1064 | %maskname: name of the mask image file for fix |
---|
| 1065 | %thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists |
---|
| 1066 | %inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold |
---|
| 1067 | %fileref: .nc file name for a reference velocity (='': refrence 0 used) |
---|
| 1068 | %fieldref: 'civ1','filter1'...feld used in fileref |
---|
| 1069 | |
---|
| 1070 | function FF=fix(Param,F,C,U,V,X,Y) |
---|
| 1071 | FF=zeros(size(F));%default |
---|
| 1072 | |
---|
| 1073 | %criterium on warn flags |
---|
| 1074 | FlagName={'CheckFmin2','CheckF2','CheckF3','CheckF4'}; |
---|
| 1075 | FlagVal=[-2 2 3 4]; |
---|
| 1076 | for iflag=1:numel(FlagName) |
---|
| 1077 | if isfield(Param,FlagName{iflag}) && Param.(FlagName{iflag}) |
---|
| 1078 | FF=(FF==1| F==FlagVal(iflag)); |
---|
| 1079 | end |
---|
| 1080 | end |
---|
| 1081 | %criterium on correlation values |
---|
| 1082 | if isfield (Param,'MinCorr') |
---|
| 1083 | FF=FF==1 | C<Param.MinCorr; |
---|
| 1084 | end |
---|
| 1085 | if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)) |
---|
| 1086 | Umod= U.*U+V.*V; |
---|
| 1087 | if isfield (Param,'MinVel')&&~isempty(Param.MinVel) |
---|
| 1088 | FF=FF==1 | Umod<(Param.MinVel*Param.MinVel); |
---|
| 1089 | end |
---|
| 1090 | if isfield (Param,'MaxVel')&&~isempty(Param.MaxVel) |
---|
| 1091 | FF=FF==1 | Umod>(Param.MaxVel*Param.MaxVel); |
---|
| 1092 | end |
---|
| 1093 | end |
---|
| 1094 | |
---|
| 1095 | |
---|
| 1096 | %------------------------------------------------------------------------ |
---|
| 1097 | % --- determine the list of index pairs of processing file |
---|
| 1098 | function [i1_series,i2_series,j1_series,j2_series,check_bounds,NomTypeNc]=... |
---|
[635] | 1099 | find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j) |
---|
[598] | 1100 | %------------------------------------------------------------------------ |
---|
[610] | 1101 | i1_series=i_series;% set of first image indexes |
---|
[598] | 1102 | i2_series=i_series; |
---|
[819] | 1103 | j1_series=j_series;%ones(size(i_series));% set of first image numbers |
---|
| 1104 | j2_series=j_series;%ones(size(i_series)); |
---|
[610] | 1105 | r=regexp(str_civ,'^\D(?<ind>[i|j])=( -| )(?<num1>\d+)\|(?<num2>\d+)','names'); |
---|
[598] | 1106 | if ~isempty(r) |
---|
| 1107 | mode=['D' r.ind]; |
---|
| 1108 | ind1=str2num(r.num1); |
---|
| 1109 | ind2=str2num(r.num2); |
---|
| 1110 | else |
---|
[668] | 1111 | mode='j1-j2'; |
---|
[598] | 1112 | r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names'); |
---|
| 1113 | if ~isempty(r) |
---|
| 1114 | NomTypeNc='_1ab'; |
---|
| 1115 | else |
---|
| 1116 | r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names'); |
---|
| 1117 | if ~isempty(r) |
---|
| 1118 | NomTypeNc='_1AB'; |
---|
[597] | 1119 | else |
---|
[598] | 1120 | r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names'); |
---|
| 1121 | if ~isempty(r) |
---|
| 1122 | NomTypeNc='_1_1-2'; |
---|
| 1123 | end |
---|
[597] | 1124 | end |
---|
| 1125 | end |
---|
[598] | 1126 | if isempty(r) |
---|
| 1127 | display('wrong pair mode input option') |
---|
| 1128 | else |
---|
| 1129 | ind1=stra2num(r.num1); |
---|
| 1130 | ind2=stra2num(r.num2); |
---|
| 1131 | end |
---|
[597] | 1132 | end |
---|
[819] | 1133 | switch mode |
---|
| 1134 | case 'Di' |
---|
| 1135 | i1_series=i_series-ind1;% set of first image numbers |
---|
| 1136 | i2_series=i_series+ind2; |
---|
| 1137 | check_bounds=i1_series<MinIndex_i | i2_series>MaxIndex_i; |
---|
| 1138 | if isempty(j_series) |
---|
| 1139 | NomTypeNc='_1-2'; |
---|
| 1140 | else |
---|
| 1141 | j1_series=j_series; |
---|
| 1142 | j2_series=j_series; |
---|
| 1143 | NomTypeNc='_1-2_1'; |
---|
| 1144 | end |
---|
| 1145 | case 'Dj' |
---|
| 1146 | j1_series=j_series-ind1; |
---|
| 1147 | j2_series=j_series+ind2; |
---|
| 1148 | check_bounds=j1_series<MinIndex_j | j2_series>MaxIndex_j; |
---|
| 1149 | NomTypeNc='_1_1-2'; |
---|
| 1150 | otherwise %bursts |
---|
| 1151 | i1_series=i_series(1,:);% do not sweep the j index |
---|
| 1152 | i2_series=i_series(1,:); |
---|
| 1153 | j1_series=ind1*ones(1,size(i_series,2));% j index is fixed by pair choice |
---|
| 1154 | j2_series=ind2*ones(1,size(i_series,2)); |
---|
| 1155 | check_bounds=zeros(size(i1_series));% no limitations due to min-max indices |
---|
[598] | 1156 | end |
---|
[597] | 1157 | |
---|
[598] | 1158 | |
---|
| 1159 | |
---|
| 1160 | |
---|