[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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[855] | 7 | % function [Data,errormsg,result_conv]= civ_series(Param) |
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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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[855] | 15 | % Param: Matlab structure of input parameters |
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| 16 | % Param contains info of the GUI series using the fct read_GUI. |
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| 17 | % Param.Action.RUN = 0 (to set the status of the GUI series) or =1 to RUN the computation |
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| 18 | % Param.InputTable: sets the input file(s) |
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| 19 | % if absent, the fct looks for input data in Param.ActionInput (test mode) |
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| 20 | % Param.OutputSubDir: sets the folder name of output file(s, |
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| 21 | % if absent no file is produced, result in the output structure Data (test mode) |
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[859] | 22 | % Param.ActionInput: substructure with the parameters provided by the GUI civ_input |
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[855] | 23 | % .Civ1: parameters for civ1 |
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| 24 | % .Fix1: parameters for fix1 |
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[859] | 25 | % .Patch1: |
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[855] | 26 | % .Civ2: for civ2 |
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[859] | 27 | % .Fix2: |
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[855] | 28 | % .Patch2: |
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| 29 | |
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[924] | 30 | %======================================================================= |
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| 31 | % Copyright 2008-2016, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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| 32 | % http://www.legi.grenoble-inp.fr |
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| 33 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr |
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[859] | 34 | % |
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[924] | 35 | % This file is part of the toolbox UVMAT. |
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| 36 | % |
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[598] | 37 | % UVMAT is free software; you can redistribute it and/or modify |
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[924] | 38 | % it under the terms of the GNU General Public License as published |
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| 39 | % by the Free Software Foundation; either version 2 of the license, |
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| 40 | % or (at your option) any later version. |
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[859] | 41 | % |
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[598] | 42 | % UVMAT is distributed in the hope that it will be useful, |
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| 43 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 44 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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[924] | 45 | % GNU General Public License (see LICENSE.txt) for more details. |
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| 46 | %======================================================================= |
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[597] | 47 | |
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[724] | 48 | function [Data,errormsg,result_conv]= civ_series(Param) |
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[598] | 49 | errormsg=''; |
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[763] | 50 | |
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[606] | 51 | %% 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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[859] | 52 | if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN |
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[763] | 53 | path_series=fileparts(which('series')); |
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| 54 | addpath(fullfile(path_series,'series')) |
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[598] | 55 | Data=civ_input(Param);% introduce the civ parameters using the GUI civ_input |
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[668] | 56 | if isempty(Data) |
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| 57 | Data=Param;% if civ_input has been cancelled, keep previous parameters |
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| 58 | end |
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[606] | 59 | Data.Program=mfilename;%gives the name of the current function |
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| 60 | Data.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
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| 61 | Data.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
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[856] | 62 | if isfield(Data,'ActionInput') && isfield(Data.ActionInput,'PairIndices')&& strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2') |
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[721] | 63 | Data.Desable_j_index='on';% hide the j index in series (set by the pair choice in civ_input) |
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| 64 | end |
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[606] | 65 | Data.NbSlice='off'; %nbre of slices ('off' by default) |
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| 66 | Data.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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[781] | 67 | 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] | 68 | Data.FieldTransform = 'off';%can use a transform function |
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| 69 | Data.ProjObject='off';%can use projection object(option 'off'/'on', |
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| 70 | Data.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) |
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| 71 | Data.OutputDirExt='.civ';%set the output dir extension |
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[711] | 72 | 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] | 73 | Data.OutputFileMode='NbInput_i';% one output file expected per value of i index (used for waitbar) |
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[904] | 74 | Data.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) |
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[598] | 75 | return |
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[597] | 76 | end |
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| 77 | |
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| 78 | %% read input parameters from an xml file if input is a file name (batch mode) |
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| 79 | checkrun=1; |
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| 80 | if ischar(Param) |
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| 81 | Param=xml2struct(Param);% read Param as input file (batch case) |
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| 82 | checkrun=0; |
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| 83 | end |
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[855] | 84 | |
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| 85 | %% test input |
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[668] | 86 | if ~isfield(Param,'ActionInput') |
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[859] | 87 | disp_uvmat('ERROR','no parameter set for PIV',checkrun) |
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| 88 | return |
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[668] | 89 | end |
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[855] | 90 | iview_A=0;%default values |
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| 91 | NbField=1; |
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| 92 | RUNHandle=[]; |
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| 93 | CheckInputFile=isfield(Param,'InputTable');%= 1 in test use for TestCiv (no nc file involved) |
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| 94 | CheckOutputFile=isfield(Param,'OutputSubDir');%= 1 in test use for TestPatch (no nc file produced) |
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[597] | 95 | |
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[855] | 96 | %% input files and indexing (skipped in Test mode) |
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| 97 | if CheckInputFile |
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| 98 | hseries=findobj(allchild(0),'Tag','series'); |
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| 99 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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| 100 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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| 101 | MaxIndex_i=Param.IndexRange.MaxIndex_i; |
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| 102 | MinIndex_i=Param.IndexRange.MinIndex_i; |
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| 103 | MaxIndex_j=ones(size(MaxIndex_i));MinIndex_j=ones(size(MinIndex_i)); |
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| 104 | if isfield(Param.IndexRange,'MaxIndex_j')&& isfield(Param.IndexRange,'MinIndex_j') |
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| 105 | MaxIndex_j=Param.IndexRange.MaxIndex_j; |
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| 106 | MinIndex_j=Param.IndexRange.MinIndex_j; |
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[609] | 107 | end |
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[855] | 108 | if isfield(Param,'InputTable') |
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| 109 | [tild,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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| 110 | iview_A=0;% series index (iview) for the first image series |
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| 111 | 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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| 112 | if Param.ActionInput.CheckCiv1 |
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| 113 | iview_A=1;% usual PIV, the image series is on the first line of the table |
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| 114 | elseif Param.ActionInput.CheckCiv2 % civ2 is performed without Civ1, a netcdf file series is needed in the first table line |
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| 115 | iview_A=2;% the second line is used for the input images of Civ2 |
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[610] | 116 | end |
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[855] | 117 | if strcmp(Param.ActionInput.ListCompareMode,'shift') |
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| 118 | iview_B=iview_A+1; % the second image series is on the next line of the input table |
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| 119 | end |
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| 120 | if iview_A~=0 |
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| 121 | RootPath_A=Param.InputTable{iview_A,1}; |
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| 122 | RootFile_A=Param.InputTable{iview_A,3}; |
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| 123 | SubDir_A=Param.InputTable{iview_A,2}; |
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| 124 | NomType_A=Param.InputTable{iview_A,4}; |
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| 125 | FileExt_A=Param.InputTable{iview_A,5}; |
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| 126 | if iview_B==0 |
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| 127 | iview_B=iview_A;% the second image series is the same as the first |
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[758] | 128 | end |
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[855] | 129 | RootPath_B=Param.InputTable{iview_B,1}; |
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| 130 | RootFile_B=Param.InputTable{iview_B,3}; |
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| 131 | SubDir_B=Param.InputTable{iview_B,2}; |
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| 132 | NomType_B=Param.InputTable{iview_B,4}; |
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| 133 | FileExt_B=Param.InputTable{iview_B,5}; |
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| 134 | end |
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| 135 | |
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| 136 | PairCiv2=''; |
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| 137 | switch Param.ActionInput.ListCompareMode |
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| 138 | case 'PIV' |
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| 139 | PairCiv1=Param.ActionInput.PairIndices.ListPairCiv1; |
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| 140 | if isfield(Param.ActionInput.PairIndices,'ListPairCiv2') |
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| 141 | PairCiv2=Param.ActionInput.PairIndices.ListPairCiv2;%string which determines the civ2 pair |
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[761] | 142 | end |
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[855] | 143 | if iview_A==1% if Civ1 is performed |
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| 144 | [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=... |
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| 145 | find_pair_indices(PairCiv1,i1_series{1},j1_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j); |
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| 146 | if ~isempty(PairCiv2) |
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| 147 | [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds_Civ2]=... |
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| 148 | 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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| 149 | check_bounds=check_bounds | check_bounds_Civ2; |
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| 150 | end |
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| 151 | else% we start from an existing Civ1 file |
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| 152 | i1_series_Civ1=i1_series{1}; |
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| 153 | i2_series_Civ1=i2_series{1}; |
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| 154 | j1_series_Civ1=j1_series{1}; |
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| 155 | j2_series_Civ1=j2_series{1}; |
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| 156 | NomTypeNc=Param.InputTable{1,4}; |
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| 157 | if ~isempty(PairCiv2) |
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| 158 | [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds,NomTypeNc]=... |
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| 159 | 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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| 160 | end |
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[761] | 161 | end |
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[855] | 162 | case 'displacement' |
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| 163 | i1_series_Civ1=Param.ActionInput.OriginIndex*ones(size(i1_series{1})); |
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| 164 | i2_series_Civ1=i1_series{1};i2_series_Civ2=i1_series{1}; |
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| 165 | j1_series_Civ1=ones(size(i1_series{1}));% first j index is 1 |
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| 166 | if isempty(j1_series_Civ1) |
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| 167 | j2_series_Civ1=ones(size(i1_series{1})); |
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| 168 | else |
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| 169 | j2_series_Civ1=j1_series_Civ1; |
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| 170 | end |
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| 171 | i1_series_Civ2=i1_series_Civ1; |
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| 172 | j1_series_Civ2=j1_series_Civ1; |
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| 173 | j2_series_Civ2=j2_series_Civ1; |
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[856] | 174 | NomTypeNc=Param.InputTable{1,4}; |
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[855] | 175 | case 'PIV volume' |
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| 176 | % TODO, TODO |
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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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[824] | 188 | FrameIndex_A_Civ2=FrameIndex_A_Civ1; |
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| 189 | FrameIndex_B_Civ2=FrameIndex_B_Civ1; |
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[758] | 190 | else |
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[855] | 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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[758] | 200 | end |
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[855] | 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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[758] | 203 | return |
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| 204 | end |
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[855] | 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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[819] | 257 | else |
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[855] | 258 | NbField=numel(i1_series_Civ1);% no image used (only fix or patch) TO CHECK |
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[781] | 259 | end |
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[855] | 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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[758] | 263 | return |
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| 264 | end |
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| 265 | end |
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[855] | 266 | |
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| 267 | |
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| 268 | %% Output directory |
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| 269 | OutputDir=''; |
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| 270 | if CheckOutputFile |
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[859] | 271 | OutputDir=[Param.OutputSubDir Param.OutputDirExt]; |
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[758] | 272 | end |
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| 273 | end |
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| 274 | |
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[855] | 275 | %% prepare output Data |
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[886] | 276 | ListGlobalAttribute={'Conventions','Program','CivStage'}; |
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[605] | 277 | Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes |
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| 278 | Data.Program='civ_series'; |
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| 279 | Data.CivStage=0;%default |
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| 280 | check_civx=0;%default |
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| 281 | |
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[606] | 282 | %% get timing from the ImaDoc file or input video |
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[822] | 283 | if iview_A~=0 |
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[833] | 284 | XmlFileName=find_imadoc(RootPath_A,SubDir_A,RootFile_A,FileExt_A); |
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| 285 | time=[]; |
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| 286 | if ~isempty(XmlFileName) |
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| 287 | XmlData=imadoc2struct(XmlFileName); |
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[609] | 288 | if isfield(XmlData,'Time') |
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| 289 | time=XmlData.Time; |
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| 290 | TimeSource='xml'; |
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| 291 | end |
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| 292 | if isfield(XmlData,'Camera') |
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| 293 | if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice) |
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| 294 | NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform |
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| 295 | if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) |
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| 296 | msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); |
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| 297 | end |
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| 298 | end |
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| 299 | if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit) |
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| 300 | TimeUnit=XmlData.Camera.TimeUnit; |
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| 301 | end |
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| 302 | end |
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[833] | 303 | end |
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| 304 | if isempty(time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video'})))% case of video input |
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| 305 | time=zeros(FileInfo_A.NumberOfFrames+1,2); |
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| 306 | time(:,2)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate)'; |
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| 307 | TimeSource='video'; |
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| 308 | ColorType='truecolor'; |
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| 309 | end |
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| 310 | if isempty(time)% time = index i +0.001 index j by default |
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| 311 | %MinIndex_i=min(i1_series_Civ1); |
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| 312 | MaxIndex_i=max(i2_series_Civ1); |
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| 313 | %MinIndex_j=min(j1_series_Civ1); |
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| 314 | MaxIndex_j=max(j2_series_Civ1); |
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| 315 | time=(1:MaxIndex_i)'*ones(1,MaxIndex_j); |
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| 316 | time=time+0.001*ones(MaxIndex_i,1)*(1:MaxIndex_j); |
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| 317 | time=[zeros(1,MaxIndex_j);time];% insert a first line of zeros |
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| 318 | time=[zeros(MaxIndex_i+1,1) time];% insert a first column of zeros |
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| 319 | end |
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[637] | 320 | |
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[833] | 321 | if length(FileInfo_A) >1 %case of image with multiple frames |
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| 322 | nbfield=length(FileInfo_A); |
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| 323 | nbfield_j=1; |
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| 324 | end |
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[610] | 325 | end |
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[609] | 326 | |
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[598] | 327 | %%%%% MAIN LOOP %%%%%% |
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[856] | 328 | maskname='';% initiate the mask name |
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[895] | 329 | tic; |
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[904] | 330 | CheckOverwrite=1;%default |
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| 331 | if isfield(Param,'CheckOverwrite') |
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| 332 | CheckOverwrite=Param.CheckOverwrite; |
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| 333 | end |
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[598] | 334 | for ifield=1:NbField |
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[855] | 335 | if ~isempty(RUNHandle)% update the waitbar in interactive mode with GUI series (checkrun=1) |
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| 336 | update_waitbar(WaitbarHandle,ifield/NbField) |
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[905] | 337 | if checkrun && ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
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[855] | 338 | disp('program stopped by user') |
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| 339 | break |
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| 340 | end |
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[624] | 341 | end |
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[855] | 342 | if CheckInputFile |
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| 343 | if iview_A==0 % no nc file has been entered |
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| 344 | ncfile=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},... |
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| 345 | NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),j1_series_Civ1(ifield),j2_series_Civ1(ifield)); |
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| 346 | else% an existing nc file has been entered |
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| 347 | if iview_A==1% if Civ1 is performed |
---|
| 348 | Civ1Dir=OutputDir; |
---|
| 349 | else |
---|
| 350 | Civ1Dir=Param.InputTable{1,2}; |
---|
| 351 | end |
---|
| 352 | if strcmp(Param.ActionInput.ListCompareMode,'PIV') |
---|
| 353 | ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),... |
---|
| 354 | j1_series_Civ1(ifield),j2_series_Civ1(ifield)); |
---|
| 355 | else |
---|
| 356 | ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],... |
---|
| 357 | j1_series_Civ1(ifield),j2_series_Civ1(ifield)); |
---|
| 358 | end |
---|
[822] | 359 | end |
---|
[912] | 360 | ncfile_out=ncfile;% by default |
---|
| 361 | if isfield (Param.ActionInput,'Civ2') |
---|
| 362 | i1_civ2=i1_series_Civ2(ifield); |
---|
| 363 | i2_civ2=i1_civ2; |
---|
| 364 | if ~isempty(i2_series_Civ2) |
---|
| 365 | i2_civ2=i2_series_Civ2(ifield); |
---|
| 366 | end |
---|
| 367 | j1_civ2=1; |
---|
| 368 | if ~isempty(j1_series_Civ2) |
---|
| 369 | j1_civ2=j1_series_Civ2(ifield); |
---|
| 370 | end |
---|
| 371 | j2_civ2=i1_civ2; |
---|
| 372 | if ~isempty(j2_series_Civ2) |
---|
| 373 | j2_civ2=j2_series_Civ2(ifield); |
---|
| 374 | end |
---|
| 375 | if strcmp(Param.ActionInput.ListCompareMode,'PIV') |
---|
| 376 | ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1_civ2,i2_civ2,j1_civ2,j2_civ2); |
---|
| 377 | else % displacement |
---|
| 378 | ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i2_civ2,[],j2_civ2); |
---|
| 379 | end |
---|
[904] | 380 | end |
---|
[912] | 381 | if ~CheckOverwrite && exist(ncfile_out,'file') |
---|
| 382 | disp(['existing output file ' ncfile_out ' already exists, skip to next field']) |
---|
| 383 | continue% skip iteration if the mode overwrite is desactivated and the result file already exists |
---|
| 384 | end |
---|
[761] | 385 | end |
---|
[598] | 386 | %% Civ1 |
---|
[707] | 387 | % if Civ1 computation is requested |
---|
[598] | 388 | if isfield (Param.ActionInput,'Civ1') |
---|
[897] | 389 | if CheckInputFile |
---|
[896] | 390 | disp('civ1 started') |
---|
[897] | 391 | end |
---|
[598] | 392 | par_civ1=Param.ActionInput.Civ1; |
---|
[856] | 393 | if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) |
---|
[855] | 394 | try |
---|
| 395 | ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield)); |
---|
| 396 | if strcmp(FileInfo_A.FileType,'netcdf')% case of input images in format netcdf |
---|
| 397 | FieldName_A=Param.InputFields.FieldName; |
---|
| 398 | [DataIn,tild,tild,errormsg]=nc2struct(ImageName_A,{FieldName_A}); |
---|
| 399 | par_civ1.ImageA=DataIn.(FieldName_A); |
---|
| 400 | else % usual image formats for image A |
---|
| 401 | [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield)); |
---|
| 402 | end |
---|
| 403 | ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield)); |
---|
| 404 | if strcmp(FileInfo_B.FileType,'netcdf') % case of input images in format netcdf |
---|
| 405 | FieldName_B=Param.InputFields.FieldName; |
---|
| 406 | [DataIn,tild,tild,errormsg]=nc2struct(ImageName_B,{FieldName_B}); |
---|
| 407 | par_civ1.ImageB=DataIn.(FieldName_B); |
---|
| 408 | else % usual image formats for image B |
---|
| 409 | [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield)); |
---|
| 410 | end |
---|
| 411 | catch ME % display errors in reading input images |
---|
| 412 | if ~isempty(ME.message) |
---|
| 413 | disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun) |
---|
| 414 | return |
---|
| 415 | end |
---|
[781] | 416 | end |
---|
[855] | 417 | par_civ1.ImageWidth=size(par_civ1.ImageA,2);%FileInfo_A.Width; |
---|
| 418 | par_civ1.ImageHeight=size(par_civ1.ImageA,1);%FileInfo_A.Height; |
---|
| 419 | list_param=(fieldnames(Param.ActionInput.Civ1))'; |
---|
| 420 | list_param(strcmp('TestCiv1',list_param))=[];% remove the parameter TestCiv1 from the list |
---|
| 421 | Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before each string in list_param |
---|
| 422 | Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images |
---|
| 423 | %indicate the values of all the global attributes in the output data |
---|
| 424 | Data.Civ1_ImageA=ImageName_A; |
---|
| 425 | Data.Civ1_ImageB=ImageName_B; |
---|
| 426 | i1=i1_series_Civ1(ifield); |
---|
| 427 | i2=i1; |
---|
| 428 | if ~isempty(i2_series_Civ1) |
---|
| 429 | i2=i2_series_Civ1(ifield); |
---|
[781] | 430 | end |
---|
[855] | 431 | j1=1; |
---|
| 432 | if ~isempty(j1_series_Civ1) |
---|
| 433 | j1=j1_series_Civ1(ifield); |
---|
[758] | 434 | end |
---|
[855] | 435 | j2=j1; |
---|
| 436 | if ~isempty(j2_series_Civ1) |
---|
| 437 | j2=j2_series_Civ1(ifield); |
---|
| 438 | end |
---|
[861] | 439 | if strcmp(Param.ActionInput.ListCompareMode,'displacement') |
---|
| 440 | Data.Civ1_Time=time(i2+1,j2+1);% the time is the time of the secodn image |
---|
| 441 | Data.Civ1_Dt=1;% time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading |
---|
| 442 | else |
---|
| 443 | Data.Civ1_Time=(time(i2+1,j2+1)+time(i1+1,j1+1))/2;% the time is the time at the middle of the image pair |
---|
[855] | 444 | Data.Civ1_Dt=time(i2+1,j2+1)-time(i1+1,j1+1); |
---|
[861] | 445 | end |
---|
[855] | 446 | for ilist=1:length(list_param) |
---|
| 447 | Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist}); |
---|
| 448 | end |
---|
[886] | 449 | Data.ListGlobalAttribute=[ListGlobalAttribute Civ1_param]; |
---|
[855] | 450 | Data.CivStage=1; |
---|
[597] | 451 | end |
---|
[598] | 452 | % set the list of variables |
---|
| 453 | Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_F','Civ1_C'};% cell array containing the names of the fields to record |
---|
| 454 | Data.VarDimName={'nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1'}; |
---|
| 455 | Data.VarAttribute{1}.Role='coord_x'; |
---|
| 456 | Data.VarAttribute{2}.Role='coord_y'; |
---|
| 457 | Data.VarAttribute{3}.Role='vector_x'; |
---|
| 458 | Data.VarAttribute{4}.Role='vector_y'; |
---|
| 459 | Data.VarAttribute{5}.Role='warnflag'; |
---|
[856] | 460 | if par_civ1.CheckMask&&~isempty(par_civ1.Mask) |
---|
| 461 | if strcmp(maskname,par_civ1.Mask)% mask exist, not already read in civ1 |
---|
| 462 | par_civ1.Mask=mask; %use mask already opened |
---|
| 463 | else |
---|
[861] | 464 | try |
---|
| 465 | par_civ1.Mask=imread(par_civ1.Mask);%update the mask, an store it for future use |
---|
| 466 | catch ME |
---|
| 467 | if ~isempty(ME.message) |
---|
| 468 | errormsg=['error reading input image: ' ME.message]; |
---|
| 469 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
| 470 | return |
---|
| 471 | end |
---|
| 472 | end |
---|
[856] | 473 | mask=par_civ1.Mask; |
---|
| 474 | maskname=par_civ1.Mask; |
---|
| 475 | end |
---|
| 476 | end |
---|
[598] | 477 | if strcmp(Param.ActionInput.ListCompareMode, 'PIV volume') |
---|
| 478 | Data.ListVarName=[Data.ListVarName 'Civ1_Z']; |
---|
| 479 | Data.Civ1_X=[];Data.Civ1_Y=[];Data.Civ1_Z=[]; |
---|
| 480 | Data.Civ1_U=[];Data.Civ1_V=[];Data.Civ1_C=[];Data.Civ1_F=[]; |
---|
| 481 | for ivol=1:NbSlice |
---|
| 482 | % caluclate velocity data (y and v in indices, reverse to y component) |
---|
[856] | 483 | [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1); |
---|
[598] | 484 | if ~isempty(errormsg) |
---|
[859] | 485 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
[598] | 486 | return |
---|
| 487 | end |
---|
| 488 | Data.Civ1_X=[Data.Civ1_X reshape(xtable,[],1)]; |
---|
| 489 | Data.Civ1_Y=[Data.Civ1_Y reshape(Param.Civ1.ImageHeight-ytable+1,[],1)]; |
---|
| 490 | Data.Civ1_Z=[Data.Civ1_Z ivol*ones(numel(xtable),1)];% z=image index in image coordinates |
---|
| 491 | Data.Civ1_U=[Data.Civ1_U reshape(utable,[],1)]; |
---|
| 492 | Data.Civ1_V=[Data.Civ1_V reshape(-vtable,[],1)]; |
---|
| 493 | Data.Civ1_C=[Data.Civ1_C reshape(ctable,[],1)]; |
---|
| 494 | Data.Civ1_F=[Data.Civ1_C reshape(F,[],1)]; |
---|
| 495 | end |
---|
| 496 | else %usual PIV |
---|
| 497 | % caluclate velocity data (y and v in indices, reverse to y component) |
---|
[856] | 498 | [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1); |
---|
[597] | 499 | if ~isempty(errormsg) |
---|
[703] | 500 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
[597] | 501 | return |
---|
| 502 | end |
---|
[598] | 503 | Data.Civ1_X=reshape(xtable,[],1); |
---|
| 504 | Data.Civ1_Y=reshape(par_civ1.ImageHeight-ytable+1,[],1); |
---|
| 505 | Data.Civ1_U=reshape(utable,[],1); |
---|
| 506 | Data.Civ1_V=reshape(-vtable,[],1); |
---|
| 507 | Data.Civ1_C=reshape(ctable,[],1); |
---|
| 508 | Data.Civ1_F=reshape(F,[],1); |
---|
[597] | 509 | end |
---|
[707] | 510 | else% we use existing Civ1 data |
---|
[598] | 511 | if exist('ncfile','var') |
---|
| 512 | CivFile=ncfile; |
---|
[855] | 513 | [Data,tild,tild,errormsg]=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format |
---|
| 514 | if ~isempty(errormsg) |
---|
| 515 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
| 516 | return |
---|
| 517 | end |
---|
[859] | 518 | [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file |
---|
[856] | 519 | elseif isfield(Param,'Civ1_X') |
---|
[855] | 520 | Data.ListGlobalAttribute={}; |
---|
| 521 | Data.ListVarName={}; |
---|
| 522 | Data.VarDimName={}; |
---|
| 523 | Data.Civ1_X=Param.Civ1_X; |
---|
| 524 | Data.Civ1_Y=Param.Civ1_Y; |
---|
| 525 | Data.Civ1_U=Param.Civ1_U; |
---|
| 526 | Data.Civ1_V=Param.Civ1_V; |
---|
[859] | 527 | Data.Civ1_FF=Param.Civ1_FF; |
---|
[598] | 528 | end |
---|
[597] | 529 | end |
---|
| 530 | |
---|
[598] | 531 | %% Fix1 |
---|
| 532 | if isfield (Param.ActionInput,'Fix1') |
---|
[896] | 533 | disp('fix1 started') |
---|
[822] | 534 | if ~isfield (Param.ActionInput,'Civ1')% if we use existing Civ1, remove previous data beyond Civ1 |
---|
| 535 | Fix1_attr=find(strcmp('Fix1',Data.ListGlobalAttribute)); |
---|
| 536 | Data.ListGlobalAttribute(Fix1_attr)=[]; |
---|
| 537 | for ilist=1:numel(Fix1_attr) |
---|
| 538 | Data=rmfield(Data,Data.ListGlobalAttribute{Fix1_attr(ilist)}); |
---|
| 539 | end |
---|
[859] | 540 | end |
---|
[852] | 541 | list_param=fieldnames(Param.ActionInput.Fix1)'; |
---|
| 542 | Fix1_param=regexprep(list_param,'^.+','Fix1_$0');% insert 'Fix1_' before each string in ListFixParam |
---|
[859] | 543 | %indicate the values of all the global attributes in the output data |
---|
[852] | 544 | for ilist=1:length(list_param) |
---|
| 545 | Data.(Fix1_param{ilist})=Param.ActionInput.Fix1.(list_param{ilist}); |
---|
[598] | 546 | end |
---|
[852] | 547 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix1_param]; |
---|
[859] | 548 | Data.ListVarName=[Data.ListVarName {'Civ1_FF'}]; |
---|
| 549 | Data.VarDimName=[Data.VarDimName {'nb_vec_1'}]; |
---|
| 550 | nbvar=length(Data.ListVarName); |
---|
| 551 | Data.VarAttribute{nbvar}.Role='errorflag'; |
---|
| 552 | Data.Civ1_FF=fix(Param.ActionInput.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V); |
---|
| 553 | Data.CivStage=2; |
---|
[597] | 554 | end |
---|
[598] | 555 | %% Patch1 |
---|
| 556 | if isfield (Param.ActionInput,'Patch1') |
---|
[896] | 557 | disp('patch1 started') |
---|
[598] | 558 | if check_civx |
---|
| 559 | errormsg='Civ Matlab input needed for patch'; |
---|
[703] | 560 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
[598] | 561 | return |
---|
| 562 | end |
---|
[855] | 563 | |
---|
| 564 | % record the processing parameters of Patch1 as global attributes in the result nc file |
---|
[852] | 565 | list_param=fieldnames(Param.ActionInput.Patch1)'; |
---|
[855] | 566 | list_param(strcmp('TestPatch1',list_param))=[];% remove 'TestPatch1' from the list of parameters |
---|
| 567 | Patch1_param=regexprep(list_param,'^.+','Patch1_$0');% insert 'Patch1_' before each parameter name |
---|
[852] | 568 | for ilist=1:length(list_param) |
---|
| 569 | Data.(Patch1_param{ilist})=Param.ActionInput.Patch1.(list_param{ilist}); |
---|
| 570 | end |
---|
[855] | 571 | Data.CivStage=3;% record the new state of processing |
---|
[852] | 572 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch1_param]; |
---|
[598] | 573 | |
---|
[855] | 574 | % list the variables to record |
---|
[598] | 575 | nbvar=length(Data.ListVarName); |
---|
| 576 | Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbCentres','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}]; |
---|
| 577 | Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},'nb_subdomain_1',... |
---|
| 578 | {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}]; |
---|
| 579 | Data.VarAttribute{nbvar+1}.Role='vector_x'; |
---|
| 580 | Data.VarAttribute{nbvar+2}.Role='vector_y'; |
---|
| 581 | Data.VarAttribute{nbvar+5}.Role='coord_tps'; |
---|
| 582 | Data.VarAttribute{nbvar+6}.Role='vector_x'; |
---|
| 583 | Data.VarAttribute{nbvar+7}.Role='vector_y'; |
---|
[855] | 584 | Data.Civ1_U_smooth=Data.Civ1_U; % zeros(size(Data.Civ1_X)); |
---|
| 585 | Data.Civ1_V_smooth=Data.Civ1_V; %zeros(size(Data.Civ1_X)); |
---|
[598] | 586 | if isfield(Data,'Civ1_FF') |
---|
| 587 | ind_good=find(Data.Civ1_FF==0); |
---|
[597] | 588 | else |
---|
[598] | 589 | ind_good=1:numel(Data.Civ1_X); |
---|
[597] | 590 | end |
---|
[855] | 591 | |
---|
[859] | 592 | % perform Patch calculation using the UVMAT fct 'filter_tps' |
---|
[598] | 593 | [Data.Civ1_SubRange,Data.Civ1_NbCentres,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=... |
---|
| 594 | 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); |
---|
[855] | 595 | Data.Civ1_U_smooth(ind_good)=Ures;% take the interpolated (smoothed) velocity values for good vectors, keep 0 for the others |
---|
[598] | 596 | Data.Civ1_V_smooth(ind_good)=Vres; |
---|
| 597 | Data.Civ1_FF(ind_good)=FFres; |
---|
[896] | 598 | disp('patch1 performed') |
---|
[597] | 599 | end |
---|
| 600 | |
---|
[598] | 601 | %% Civ2 |
---|
| 602 | if isfield (Param.ActionInput,'Civ2') |
---|
[896] | 603 | disp('civ2 started') |
---|
[598] | 604 | par_civ2=Param.ActionInput.Civ2; |
---|
[856] | 605 | if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) |
---|
| 606 | par_civ2.ImageA=[]; |
---|
| 607 | par_civ2.ImageB=[]; |
---|
[912] | 608 | % i1_civ2=i1_series_Civ2(ifield); |
---|
| 609 | % i2_civ2=i1_civ2; |
---|
| 610 | % if ~isempty(i2_series_Civ2) |
---|
| 611 | % i2_civ2=i2_series_Civ2(ifield); |
---|
| 612 | % end |
---|
| 613 | % j1_civ2=1; |
---|
| 614 | % if ~isempty(j1_series_Civ2) |
---|
| 615 | % j1_civ2=j1_series_Civ2(ifield); |
---|
| 616 | % end |
---|
| 617 | % j2_civ2=i1_civ2; |
---|
| 618 | % if ~isempty(j2_series_Civ2) |
---|
| 619 | % j2_civ2=j2_series_Civ2(ifield); |
---|
| 620 | % end |
---|
| 621 | ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_civ2,[],j1_civ2); |
---|
[856] | 622 | |
---|
| 623 | if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield)) |
---|
| 624 | par_civ2.ImageA=par_civ1.ImageA; |
---|
| 625 | else |
---|
| 626 | [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield)); |
---|
| 627 | end |
---|
[912] | 628 | ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_civ2,[],j2_civ2); |
---|
[856] | 629 | if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2) |
---|
| 630 | par_civ2.ImageB=par_civ1.ImageB; |
---|
| 631 | else |
---|
| 632 | [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield)); |
---|
| 633 | end |
---|
[912] | 634 | % if strcmp(Param.ActionInput.ListCompareMode,'PIV') |
---|
| 635 | % ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1,i2,j1,j2); |
---|
| 636 | % else % displacement |
---|
| 637 | % ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i2,[],j2); |
---|
| 638 | % end |
---|
[856] | 639 | par_civ2.ImageWidth=FileInfo_A.Width; |
---|
| 640 | par_civ2.ImageHeight=FileInfo_A.Height; |
---|
| 641 | if isfield(par_civ2,'Grid')% grid points set as input file |
---|
| 642 | if ischar(par_civ2.Grid)%read the grid file if the input is a file name |
---|
| 643 | par_civ2.Grid=dlmread(par_civ2.Grid); |
---|
| 644 | par_civ2.Grid(1,:)=[];%the first line must be removed (heading in the grid file) |
---|
| 645 | end |
---|
| 646 | else% automatic grid |
---|
| 647 | minix=floor(par_civ2.Dx/2)-0.5; |
---|
| 648 | maxix=minix+par_civ2.Dx*floor((par_civ2.ImageWidth-1)/par_civ2.Dx); |
---|
| 649 | miniy=floor(par_civ2.Dy/2)-0.5; |
---|
| 650 | maxiy=minix+par_civ2.Dy*floor((par_civ2.ImageHeight-1)/par_civ2.Dy); |
---|
| 651 | [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy); |
---|
| 652 | par_civ2.Grid(:,1)=reshape(GridX,[],1); |
---|
| 653 | par_civ2.Grid(:,2)=reshape(GridY,[],1); |
---|
| 654 | end |
---|
[597] | 655 | end |
---|
[851] | 656 | |
---|
[856] | 657 | % get the guess from patch1 or patch2 (case 'CheckCiv3') |
---|
| 658 | if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) |
---|
| 659 | if isfield (par_civ2,'CheckCiv3') && par_civ2.CheckCiv3 %get the guess from patch2 |
---|
| 660 | SubRange= Data.Civ2_SubRange; |
---|
| 661 | NbCentres=Data.Civ2_NbCentres; |
---|
| 662 | Coord_tps=Data.Civ2_Coord_tps; |
---|
| 663 | U_tps=Data.Civ2_U_tps; |
---|
| 664 | V_tps=Data.Civ2_V_tps; |
---|
[859] | 665 | CivStage=Data.CivStage;%store the current CivStage |
---|
[856] | 666 | Civ1_Dt=Data.Civ2_Dt; |
---|
| 667 | Data=[];%reinitialise the result structure Data |
---|
| 668 | Data.ListGlobalAttribute={'Conventions','Program','CivStage'}; |
---|
| 669 | Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes |
---|
| 670 | Data.Program='civ_series'; |
---|
[859] | 671 | Data.CivStage=CivStage+1;%update the current civStage after reinitialisation of Data |
---|
[856] | 672 | Data.ListVarName={}; |
---|
| 673 | Data.VarDimName={}; |
---|
| 674 | else % get the guess from patch1 |
---|
| 675 | SubRange= Data.Civ1_SubRange; |
---|
| 676 | NbCentres=Data.Civ1_NbCentres; |
---|
| 677 | Coord_tps=Data.Civ1_Coord_tps; |
---|
| 678 | U_tps=Data.Civ1_U_tps; |
---|
| 679 | V_tps=Data.Civ1_V_tps; |
---|
| 680 | Civ1_Dt=Data.Civ1_Dt; |
---|
[859] | 681 | Data.CivStage=4; |
---|
[856] | 682 | end |
---|
| 683 | else |
---|
| 684 | SubRange= par_civ2.Civ1_SubRange; |
---|
| 685 | NbCentres=par_civ2.Civ1_NbCentres; |
---|
| 686 | Coord_tps=par_civ2.Civ1_Coord_tps; |
---|
| 687 | U_tps=par_civ2.Civ1_U_tps; |
---|
| 688 | V_tps=par_civ2.Civ1_V_tps; |
---|
| 689 | Civ1_Dt=par_civ2.Civ1_Dt; |
---|
[858] | 690 | Civ2_Dt=par_civ2.Civ1_Dt; |
---|
[859] | 691 | Data.ListVarName={}; |
---|
| 692 | Data.VarDimName={}; |
---|
[851] | 693 | end |
---|
[856] | 694 | Shiftx=zeros(size(par_civ2.Grid,1),1);% shift expected from civ1 data |
---|
| 695 | Shifty=zeros(size(par_civ2.Grid,1),1); |
---|
| 696 | nbval=zeros(size(par_civ2.Grid,1),1);% nbre of interpolated values at each grid point (from the different patch subdomains) |
---|
[862] | 697 | if par_civ2.CheckDeformation |
---|
| 698 | DUDX=zeros(size(par_civ2.Grid,1),1); |
---|
| 699 | DUDY=zeros(size(par_civ2.Grid,1),1); |
---|
| 700 | DVDX=zeros(size(par_civ2.Grid,1),1); |
---|
| 701 | DVDY=zeros(size(par_civ2.Grid,1),1); |
---|
| 702 | end |
---|
[856] | 703 | NbSubDomain=size(SubRange,3); |
---|
[761] | 704 | for isub=1:NbSubDomain% for each sub-domain of Patch1 |
---|
[851] | 705 | nbvec_sub=NbCentres(isub);% nbre of Civ vectors in the subdomain |
---|
| 706 | ind_sel=find(par_civ2.Grid(:,1)>=SubRange(1,1,isub) & par_civ2.Grid(:,1)<=SubRange(1,2,isub) &... |
---|
[862] | 707 | par_civ2.Grid(:,2)>=SubRange(2,1,isub) & par_civ2.Grid(:,2)<=SubRange(2,2,isub));% grid points in the subdomain |
---|
[859] | 708 | if ~isempty(ind_sel) |
---|
[862] | 709 | epoints = par_civ2.Grid(ind_sel,:);% coordinates of interpolation sites (measurement grids) |
---|
[859] | 710 | ctrs=Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs |
---|
| 711 | nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for each interpolation point (in case of subdomain overlap) |
---|
[862] | 712 | EM = tps_eval(epoints,ctrs);% thin plate spline (tps) coefficient |
---|
| 713 | Shiftx(ind_sel)=Shiftx(ind_sel)+EM*U_tps(1:nbvec_sub+3,isub);%velocity shift estimated by tps from civ1 |
---|
[859] | 714 | Shifty(ind_sel)=Shifty(ind_sel)+EM*V_tps(1:nbvec_sub+3,isub); |
---|
| 715 | if par_civ2.CheckDeformation |
---|
| 716 | [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs |
---|
| 717 | DUDX(ind_sel)=DUDX(ind_sel)+EMDX*U_tps(1:nbvec_sub+3,isub); |
---|
| 718 | DUDY(ind_sel)=DUDY(ind_sel)+EMDY*U_tps(1:nbvec_sub+3,isub); |
---|
| 719 | DVDX(ind_sel)=DVDX(ind_sel)+EMDX*V_tps(1:nbvec_sub+3,isub); |
---|
| 720 | DVDY(ind_sel)=DVDY(ind_sel)+EMDY*V_tps(1:nbvec_sub+3,isub); |
---|
| 721 | end |
---|
[597] | 722 | end |
---|
| 723 | end |
---|
[856] | 724 | if par_civ2.CheckMask&&~isempty(par_civ2.Mask) |
---|
| 725 | if strcmp(maskname,par_civ2.Mask)% mask exist, not already read in civ1 |
---|
| 726 | par_civ2.Mask=mask; %use mask already opened |
---|
| 727 | else |
---|
| 728 | par_civ2.Mask=imread(par_civ2.Mask);%update the mask, and store it for future use |
---|
| 729 | mask=par_civ2.Mask; |
---|
| 730 | maskname=par_civ2.Mask; |
---|
| 731 | end |
---|
[598] | 732 | end |
---|
[858] | 733 | if CheckInputFile % else Dt given by par_civ2 |
---|
| 734 | if strcmp(Param.ActionInput.ListCompareMode,'displacement') |
---|
| 735 | Civ1_Dt=1; |
---|
| 736 | Civ2_Dt=1; |
---|
| 737 | else |
---|
[912] | 738 | Civ2_Dt=time(i2_civ2+1,j2_civ2+1)-time(i1_civ2+1,j1_civ2+1); |
---|
[858] | 739 | end |
---|
[856] | 740 | end |
---|
[851] | 741 | par_civ2.SearchBoxShift=(Civ2_Dt/Civ1_Dt)*[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)]; |
---|
[862] | 742 | % shift the grid points by half the expected shift to provide the correlation box position in image A |
---|
[873] | 743 | 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]; |
---|
[598] | 744 | if par_civ2.CheckDeformation |
---|
[876] | 745 | par_civ2.DUDX=DUDX(nbval>=1)./nbval(nbval>=1); |
---|
| 746 | par_civ2.DUDY=DUDY(nbval>=1)./nbval(nbval>=1); |
---|
| 747 | par_civ2.DVDX=DVDX(nbval>=1)./nbval(nbval>=1); |
---|
| 748 | par_civ2.DVDY=DVDY(nbval>=1)./nbval(nbval>=1); |
---|
[598] | 749 | end |
---|
[859] | 750 | |
---|
[862] | 751 | % calculate velocity data (y and v in image indices, reverse to y component) |
---|
[856] | 752 | [xtable, ytable, utable, vtable, ctable, F,result_conv,errormsg] = civ (par_civ2); |
---|
| 753 | |
---|
[598] | 754 | list_param=(fieldnames(Param.ActionInput.Civ2))'; |
---|
[859] | 755 | list_param(strcmp('TestCiv2',list_param))=[];% remove the parameter TestCiv2 from the list |
---|
[606] | 756 | Civ2_param=regexprep(list_param,'^.+','Civ2_$0');% insert 'Civ2_' before each string in list_param |
---|
| 757 | Civ2_param=[{'Civ2_ImageA','Civ2_ImageB','Civ2_Time','Civ2_Dt'} Civ2_param]; %insert the names of the two input images |
---|
[856] | 758 | %indicate the values of all the global attributes in the output data |
---|
| 759 | if exist('ImageName_A','var') |
---|
[859] | 760 | Data.Civ2_ImageA=ImageName_A; |
---|
| 761 | Data.Civ2_ImageB=ImageName_B; |
---|
[861] | 762 | if strcmp(Param.ActionInput.ListCompareMode,'displacement') |
---|
[912] | 763 | Data.Civ2_Time=time(i2_civ2+1,j2_civ2+1);% the time is the time of the secodn image |
---|
[861] | 764 | Data.Civ2_Dt=1;% time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading |
---|
| 765 | else |
---|
[912] | 766 | Data.Civ2_Time=(time(i2_civ2+1,j2_civ2+1)+time(i1_civ2+1,j1_civ2+1))/2; |
---|
[859] | 767 | Data.Civ2_Dt=Civ2_Dt; |
---|
[861] | 768 | end |
---|
[856] | 769 | end |
---|
[598] | 770 | for ilist=1:length(list_param) |
---|
[606] | 771 | Data.(Civ2_param{4+ilist})=Param.ActionInput.Civ2.(list_param{ilist}); |
---|
[598] | 772 | end |
---|
[606] | 773 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param]; |
---|
| 774 | |
---|
[598] | 775 | nbvar=numel(Data.ListVarName); |
---|
[859] | 776 | % define the Civ2 variable (if Civ2 data are not replaced from previous calculation) |
---|
| 777 | if isempty(find(strcmp('Civ2_X',Data.ListVarName),1)) |
---|
| 778 | 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 |
---|
| 779 | Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}]; |
---|
| 780 | Data.VarAttribute{nbvar+1}.Role='coord_x'; |
---|
| 781 | Data.VarAttribute{nbvar+2}.Role='coord_y'; |
---|
| 782 | Data.VarAttribute{nbvar+3}.Role='vector_x'; |
---|
| 783 | Data.VarAttribute{nbvar+4}.Role='vector_y'; |
---|
| 784 | Data.VarAttribute{nbvar+5}.Role='warnflag'; |
---|
| 785 | end |
---|
[598] | 786 | Data.Civ2_X=reshape(xtable,[],1); |
---|
| 787 | Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1); |
---|
| 788 | Data.Civ2_U=reshape(utable,[],1); |
---|
| 789 | Data.Civ2_V=reshape(-vtable,[],1); |
---|
| 790 | Data.Civ2_C=reshape(ctable,[],1); |
---|
| 791 | Data.Civ2_F=reshape(F,[],1); |
---|
[896] | 792 | disp('civ2 performed') |
---|
[860] | 793 | elseif ~isfield(Data,'ListVarName') % we start there, using existing Civ2 data |
---|
| 794 | if exist('ncfile','var') |
---|
| 795 | CivFile=ncfile; |
---|
| 796 | [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file |
---|
| 797 | if ~isempty(errormsg) |
---|
| 798 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
| 799 | return |
---|
| 800 | end |
---|
| 801 | elseif isfield(Param,'Civ2_X')% use Civ2 data as input in Param (test mode) |
---|
| 802 | Data.ListGlobalAttribute={}; |
---|
| 803 | Data.ListVarName={}; |
---|
| 804 | Data.VarDimName={}; |
---|
| 805 | Data.Civ2_X=Param.Civ2_X; |
---|
| 806 | Data.Civ2_Y=Param.Civ2_Y; |
---|
| 807 | Data.Civ2_U=Param.Civ2_U; |
---|
| 808 | Data.Civ2_V=Param.Civ2_V; |
---|
| 809 | Data.Civ2_FF=Param.Civ2_FF; |
---|
| 810 | end |
---|
[598] | 811 | end |
---|
| 812 | |
---|
| 813 | %% Fix2 |
---|
| 814 | if isfield (Param.ActionInput,'Fix2') |
---|
[896] | 815 | disp('fix2 started') |
---|
[856] | 816 | list_param=fieldnames(Param.ActionInput.Fix2)'; |
---|
[852] | 817 | Fix2_param=regexprep(list_param,'^.+','Fix2_$0');% insert 'Fix1_' before each string in ListFixParam |
---|
[859] | 818 | %indicate the values of all the global attributes in the output data |
---|
[852] | 819 | for ilist=1:length(list_param) |
---|
| 820 | Data.(Fix2_param{ilist})=Param.ActionInput.Fix2.(list_param{ilist}); |
---|
[598] | 821 | end |
---|
[859] | 822 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix2_param]; |
---|
| 823 | % |
---|
| 824 | % ListFixParam=fieldnames(Param.ActionInput.Fix2); |
---|
| 825 | % for ilist=1:length(ListFixParam) |
---|
| 826 | % ParamName=ListFixParam{ilist}; |
---|
| 827 | % ListName=['Fix2_' ParamName]; |
---|
| 828 | % eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];']) |
---|
| 829 | % eval(['Data.' ListName '=Param.ActionInput.Fix2.' ParamName ';']) |
---|
| 830 | % end |
---|
[598] | 831 | if check_civx |
---|
| 832 | if ~isfield(Data,'fix2') |
---|
| 833 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix2']; |
---|
| 834 | Data.fix2=1; |
---|
| 835 | Data.ListVarName=[Data.ListVarName {'vec2_FixFlag'}]; |
---|
| 836 | Data.VarDimName=[Data.VarDimName {'nb_vectors2'}]; |
---|
| 837 | end |
---|
| 838 | 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] | 839 | else |
---|
[598] | 840 | Data.ListVarName=[Data.ListVarName {'Civ2_FF'}]; |
---|
| 841 | Data.VarDimName=[Data.VarDimName {'nb_vec_2'}]; |
---|
| 842 | nbvar=length(Data.ListVarName); |
---|
| 843 | Data.VarAttribute{nbvar}.Role='errorflag'; |
---|
[822] | 844 | Data.Civ2_FF=double(fix(Param.ActionInput.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V)); |
---|
[598] | 845 | Data.CivStage=Data.CivStage+1; |
---|
[597] | 846 | end |
---|
[598] | 847 | end |
---|
| 848 | |
---|
| 849 | %% Patch2 |
---|
| 850 | if isfield (Param.ActionInput,'Patch2') |
---|
[896] | 851 | disp('patch2 started') |
---|
[859] | 852 | list_param=fieldnames(Param.ActionInput.Patch2)'; |
---|
| 853 | list_param(strcmp('TestPatch2',list_param))=[];% remove the parameter TestCiv1 from the list |
---|
[852] | 854 | Patch2_param=regexprep(list_param,'^.+','Patch2_$0');% insert 'Fix1_' before each string in ListFixParam |
---|
[859] | 855 | %indicate the values of all the global attributes in the output data |
---|
[852] | 856 | for ilist=1:length(list_param) |
---|
| 857 | Data.(Patch2_param{ilist})=Param.ActionInput.Patch2.(list_param{ilist}); |
---|
| 858 | end |
---|
| 859 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch2_param]; |
---|
| 860 | |
---|
[598] | 861 | nbvar=length(Data.ListVarName); |
---|
| 862 | Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbCentres','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}]; |
---|
| 863 | Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},... |
---|
| 864 | {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}]; |
---|
| 865 | |
---|
| 866 | Data.VarAttribute{nbvar+1}.Role='vector_x'; |
---|
| 867 | Data.VarAttribute{nbvar+2}.Role='vector_y'; |
---|
| 868 | Data.VarAttribute{nbvar+5}.Role='coord_tps'; |
---|
| 869 | Data.VarAttribute{nbvar+6}.Role='vector_x'; |
---|
| 870 | Data.VarAttribute{nbvar+7}.Role='vector_y'; |
---|
[860] | 871 | Data.Civ2_U_smooth=Data.Civ2_U; % zeros(size(Data.Civ2_X)); |
---|
| 872 | Data.Civ2_V_smooth=Data.Civ2_V; %zeros(size(Data.Civ2_X)); |
---|
[598] | 873 | if isfield(Data,'Civ2_FF') |
---|
| 874 | ind_good=find(Data.Civ2_FF==0); |
---|
[597] | 875 | else |
---|
[598] | 876 | ind_good=1:numel(Data.Civ2_X); |
---|
[597] | 877 | end |
---|
[598] | 878 | [Data.Civ2_SubRange,Data.Civ2_NbCentres,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures, Vres,tild,FFres]=... |
---|
| 879 | 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); |
---|
| 880 | Data.Civ2_U_smooth(ind_good)=Ures; |
---|
| 881 | Data.Civ2_V_smooth(ind_good)=Vres; |
---|
| 882 | Data.Civ2_FF(ind_good)=FFres; |
---|
| 883 | Data.CivStage=Data.CivStage+1; |
---|
[896] | 884 | disp('patch2 performed') |
---|
[597] | 885 | end |
---|
[598] | 886 | |
---|
| 887 | %% write result in a netcdf file if requested |
---|
[859] | 888 | if CheckOutputFile |
---|
[912] | 889 | errormsg=struct2nc(ncfile_out,Data); |
---|
[598] | 890 | if isempty(errormsg) |
---|
[912] | 891 | disp([ncfile_out ' written']) |
---|
[598] | 892 | else |
---|
| 893 | disp(errormsg) |
---|
| 894 | end |
---|
[904] | 895 | disp(['ellapsed time ' num2str(toc/60,2) ' minutes']) |
---|
[598] | 896 | end |
---|
[597] | 897 | end |
---|
| 898 | |
---|
[894] | 899 | |
---|
[598] | 900 | % 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/ |
---|
| 901 | %-------------------------------------------------------------------------- |
---|
| 902 | % function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi) |
---|
| 903 | % |
---|
| 904 | % OUTPUT: |
---|
| 905 | % xtable: set of x coordinates |
---|
| 906 | % ytable: set of y coordiantes |
---|
| 907 | % utable: set of u displacements (along x) |
---|
| 908 | % vtable: set of v displacements (along y) |
---|
| 909 | % ctable: max image correlation for each vector |
---|
| 910 | % typevector: set of flags, =1 for good, =0 for NaN vectors |
---|
| 911 | % |
---|
| 912 | %INPUT: |
---|
| 913 | % par_civ: structure of input parameters, with fields: |
---|
[856] | 914 | % .ImageA: first image for correlation (matrix) |
---|
| 915 | % .ImageB: second image for correlation(matrix) |
---|
| 916 | % .CorrBoxSize: 1,2 vector giving the size of the correlation box in x and y |
---|
| 917 | % .SearchBoxSize: 1,2 vector giving the size of the search box in x and y |
---|
| 918 | % .SearchBoxShift: 1,2 vector or 2 column matrix (for civ2) giving the shift of the search box in x and y |
---|
| 919 | % .CorrSmooth: =1 or 2 determines the choice of the sub-pixel determination of the correlation max |
---|
| 920 | % .ImageWidth: nb of pixels of the image in x |
---|
| 921 | % .Dx, Dy: mesh for the PIV calculation |
---|
[862] | 922 | % .Grid: grid giving the PIV calculation points (alternative to .Dx .Dy): centres of the correlation boxes in Image A |
---|
[856] | 923 | % .Mask: name of a mask file or mask image matrix itself |
---|
| 924 | % .MinIma: thresholds for image luminosity |
---|
[598] | 925 | % .MaxIma |
---|
[856] | 926 | % .CheckDeformation=1 for subpixel interpolation and image deformation (linear transform) |
---|
| 927 | % .DUDX: matrix of deformation obtained from patch at each grid point |
---|
| 928 | % .DUDY |
---|
| 929 | % .DVDX: |
---|
| 930 | % .DVDY |
---|
| 931 | |
---|
[855] | 932 | function [xtable,ytable,utable,vtable,ctable,F,result_conv,errormsg] = civ (par_civ) |
---|
[598] | 933 | |
---|
| 934 | %% prepare measurement grid |
---|
[862] | 935 | if isfield(par_civ,'Grid')% grid points set as input, central positions of the sub-images in image A |
---|
| 936 | if ischar(par_civ.Grid)%read the grid file if the input is a file name (grid in x, y image coordinates) |
---|
[598] | 937 | par_civ.Grid=dlmread(par_civ.Grid); |
---|
| 938 | par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file) |
---|
| 939 | end |
---|
[862] | 940 | % else par_civ.Grid is already an array, no action here |
---|
| 941 | else% automatic grid in x, y image coordinates |
---|
[598] | 942 | minix=floor(par_civ.Dx/2)-0.5; |
---|
| 943 | maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx); |
---|
[862] | 944 | miniy=floor(par_civ.Dy/2)-0.5;% first automatic grid point at half the mesh Dy |
---|
[598] | 945 | maxiy=minix+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy); |
---|
| 946 | [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy); |
---|
| 947 | par_civ.Grid(:,1)=reshape(GridX,[],1); |
---|
[862] | 948 | par_civ.Grid(:,2)=reshape(GridY,[],1);% increases with array index |
---|
[597] | 949 | end |
---|
[598] | 950 | nbvec=size(par_civ.Grid,1); |
---|
| 951 | |
---|
[859] | 952 | %% prepare correlation and search boxes |
---|
[876] | 953 | ibx2=floor(par_civ.CorrBoxSize(1)/2); |
---|
| 954 | iby2=floor(par_civ.CorrBoxSize(2)/2); |
---|
| 955 | isx2=floor(par_civ.SearchBoxSize(1)/2); |
---|
| 956 | isy2=floor(par_civ.SearchBoxSize(2)/2); |
---|
[862] | 957 | shiftx=round(par_civ.SearchBoxShift(:,1));%use the input shift estimate, rounded to the next integer value |
---|
[598] | 958 | shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases |
---|
| 959 | if numel(shiftx)==1% case of a unique shift for the whole field( civ1) |
---|
| 960 | shiftx=shiftx*ones(nbvec,1); |
---|
| 961 | shifty=shifty*ones(nbvec,1); |
---|
| 962 | end |
---|
| 963 | |
---|
[862] | 964 | %% Array initialisation and default output if par_civ.CorrSmooth=0 (just the grid calculated, no civ computation) |
---|
| 965 | xtable=round(par_civ.Grid(:,1)+0.5)-0.5; |
---|
| 966 | ytable=round(par_civ.ImageHeight-par_civ.Grid(:,2)+0.5)-0.5;% y index corresponding to the position in image coordiantes |
---|
| 967 | utable=shiftx;%zeros(nbvec,1); |
---|
| 968 | vtable=shifty;%zeros(nbvec,1); |
---|
[598] | 969 | ctable=zeros(nbvec,1); |
---|
| 970 | F=zeros(nbvec,1); |
---|
| 971 | result_conv=[]; |
---|
| 972 | errormsg=''; |
---|
[859] | 973 | |
---|
[598] | 974 | %% prepare mask |
---|
| 975 | if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) |
---|
| 976 | if strcmp(par_civ.Mask,'all') |
---|
| 977 | return % get the grid only, no civ calculation |
---|
| 978 | elseif ischar(par_civ.Mask) |
---|
[856] | 979 | par_civ.Mask=imread(par_civ.Mask);% read the mask if not allready done |
---|
[598] | 980 | end |
---|
| 981 | end |
---|
| 982 | check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold |
---|
| 983 | check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma); |
---|
| 984 | |
---|
| 985 | par_civ.ImageA=sum(double(par_civ.ImageA),3);%sum over rgb component for color images |
---|
| 986 | par_civ.ImageB=sum(double(par_civ.ImageB),3); |
---|
| 987 | [npy_ima npx_ima]=size(par_civ.ImageA); |
---|
| 988 | if ~isequal(size(par_civ.ImageB),[npy_ima npx_ima]) |
---|
| 989 | errormsg='image pair with unequal size'; |
---|
[597] | 990 | return |
---|
| 991 | end |
---|
| 992 | |
---|
[598] | 993 | %% Apply mask |
---|
[859] | 994 | % Convention for mask IDEAS TO IMPLEMENT ? |
---|
| 995 | % mask >200 : velocity calculated |
---|
| 996 | % 200 >=mask>150;velocity not calculated, interpolation allowed (bad spots) |
---|
| 997 | % 150>=mask >100: velocity not calculated, nor interpolated |
---|
| 998 | % 100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries) |
---|
| 999 | % 20>=mask: velocity=0 |
---|
[598] | 1000 | checkmask=0; |
---|
| 1001 | MinA=min(min(par_civ.ImageA)); |
---|
[873] | 1002 | %MinB=min(min(par_civ.ImageB)); |
---|
[879] | 1003 | %check_undefined=false(size(par_civ.ImageA)); |
---|
[598] | 1004 | if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) |
---|
[859] | 1005 | checkmask=1; |
---|
| 1006 | if ~isequal(size(par_civ.Mask),[npy_ima npx_ima]) |
---|
[598] | 1007 | errormsg='mask must be an image with the same size as the images'; |
---|
| 1008 | return |
---|
[859] | 1009 | end |
---|
[598] | 1010 | check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 ); |
---|
[876] | 1011 | % par_civ.ImageA(check_undefined)=0;% put image A to zero (i.e. the min image value) in the undefined area |
---|
| 1012 | % par_civ.ImageB(check_undefined)=0;% put image B to zero (i.e. the min image value) in the undefined area |
---|
[598] | 1013 | end |
---|
| 1014 | |
---|
| 1015 | %% compute image correlations: MAINLOOP on velocity vectors |
---|
| 1016 | corrmax=0; |
---|
| 1017 | sum_square=1;% default |
---|
| 1018 | mesh=1;% default |
---|
[856] | 1019 | CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1; |
---|
| 1020 | if CheckDeformation |
---|
| 1021 | mesh=0.25;%mesh in pixels for subpixel image interpolation (x 4 in each direction) |
---|
[885] | 1022 | par_civ.CorrSmooth=2;% use SUBPIX2DGAUSS (take into account more points near the max) |
---|
[598] | 1023 | end |
---|
[862] | 1024 | |
---|
| 1025 | if par_civ.CorrSmooth~=0 % par_civ.CorrSmooth=0 implies no civ computation (just input image and grid points given) |
---|
[856] | 1026 | for ivec=1:nbvec |
---|
| 1027 | iref=round(par_civ.Grid(ivec,1)+0.5);% xindex on the image A for the middle of the correlation box |
---|
[862] | 1028 | jref=round(par_civ.ImageHeight-par_civ.Grid(ivec,2)+0.5);% j index for the middle of the correlation box in the image A |
---|
[856] | 1029 | F(ivec)=0; |
---|
| 1030 | subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage |
---|
| 1031 | subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage |
---|
| 1032 | subrange2_x=iref+shiftx(ivec)-isx2:iref+shiftx(ivec)+isx2;%x indices defining the second subimage |
---|
| 1033 | subrange2_y=jref+shifty(ivec)-isy2:jref+shifty(ivec)+isy2;%y indices defining the second subimage |
---|
| 1034 | image1_crop=MinA*ones(numel(subrange1_y),numel(subrange1_x));% default value=min of image A |
---|
| 1035 | image2_crop=MinA*ones(numel(subrange2_y),numel(subrange2_x));% default value=min of image A |
---|
| 1036 | check1_x=subrange1_x>=1 & subrange1_x<=par_civ.ImageWidth;% check which points in the subimage 1 are contained in the initial image 1 |
---|
| 1037 | check1_y=subrange1_y>=1 & subrange1_y<=par_civ.ImageHeight; |
---|
| 1038 | check2_x=subrange2_x>=1 & subrange2_x<=par_civ.ImageWidth;% check which points in the subimage 2 are contained in the initial image 2 |
---|
[859] | 1039 | check2_y=subrange2_y>=1 & subrange2_y<=par_civ.ImageHeight; |
---|
[856] | 1040 | 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 |
---|
| 1041 | 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 |
---|
[879] | 1042 | if checkmask |
---|
| 1043 | mask1_crop=ones(numel(subrange1_y),numel(subrange1_x));% default value=1 for mask |
---|
| 1044 | mask2_crop=ones(numel(subrange2_y),numel(subrange2_x));% default value=1 for mask |
---|
| 1045 | mask1_crop(check1_y,check1_x)=check_undefined(subrange1_y(check1_y),subrange1_x(check1_x));%extract a mask subimage (correlation box) from image A |
---|
| 1046 | mask2_crop(check2_y,check2_x)=check_undefined(subrange2_y(check2_y),subrange2_x(check2_x));%extract a mask subimage (search box) from image B |
---|
| 1047 | sizemask=sum(sum(mask1_crop))/(numel(subrange1_y)*numel(subrange1_x));%size of the masked part relative to the correlation sub-image |
---|
| 1048 | if sizemask > 1/2% eliminate point if more than half of the correlation box is masked |
---|
| 1049 | F(ivec)=3; % |
---|
[910] | 1050 | utable(ivec)=0; |
---|
| 1051 | vtable(ivec)=0; |
---|
[879] | 1052 | else |
---|
| 1053 | image1_crop=image1_crop.*~mask1_crop;% put to zero the masked pixels (mask1_crop='true'=1) |
---|
| 1054 | image2_crop=image2_crop.*~mask2_crop; |
---|
| 1055 | image1_mean=mean(mean(image1_crop))/(1-sizemask); |
---|
| 1056 | image2_mean=mean(mean(image2_crop))/(1-sizemask); |
---|
| 1057 | end |
---|
[873] | 1058 | else |
---|
[879] | 1059 | image1_mean=mean(mean(image1_crop)); |
---|
| 1060 | image2_mean=mean(mean(image2_crop)); |
---|
[856] | 1061 | end |
---|
[879] | 1062 | %threshold on image minimum |
---|
[856] | 1063 | if F(ivec)~=3 |
---|
[880] | 1064 | if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma) |
---|
| 1065 | F(ivec)=3; |
---|
| 1066 | %threshold on image maximum |
---|
| 1067 | elseif check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma) |
---|
| 1068 | F(ivec)=3; |
---|
[879] | 1069 | end |
---|
[910] | 1070 | if F(ivec)==3 |
---|
| 1071 | utable(ivec)=0; |
---|
| 1072 | vtable(ivec)=0; |
---|
| 1073 | else |
---|
[880] | 1074 | %mask |
---|
| 1075 | if checkmask |
---|
| 1076 | image1_crop=(image1_crop-image1_mean).*~mask1_crop;%substract the mean, put to zero the masked parts |
---|
| 1077 | image2_crop=(image2_crop-image2_mean).*~mask2_crop; |
---|
| 1078 | else |
---|
| 1079 | image1_crop=(image1_crop-image1_mean); |
---|
| 1080 | image2_crop=(image2_crop-image2_mean); |
---|
| 1081 | end |
---|
| 1082 | %deformation |
---|
| 1083 | if CheckDeformation |
---|
| 1084 | xi=(1:mesh:size(image1_crop,2)); |
---|
| 1085 | yi=(1:mesh:size(image1_crop,1))'; |
---|
| 1086 | [XI,YI]=meshgrid(xi-ceil(size(image1_crop,2)/2),yi-ceil(size(image1_crop,1)/2)); |
---|
[883] | 1087 | XIant=XI-par_civ.DUDX(ivec)*XI+par_civ.DUDY(ivec)*YI+ceil(size(image1_crop,2)/2); |
---|
| 1088 | YIant=YI+par_civ.DVDX(ivec)*XI-par_civ.DVDY(ivec)*YI+ceil(size(image1_crop,1)/2); |
---|
[880] | 1089 | image1_crop=interp2(image1_crop,XIant,YIant); |
---|
| 1090 | image1_crop(isnan(image1_crop))=0; |
---|
| 1091 | xi=(1:mesh:size(image2_crop,2)); |
---|
| 1092 | yi=(1:mesh:size(image2_crop,1))'; |
---|
| 1093 | image2_crop=interp2(image2_crop,xi,yi,'*spline'); |
---|
| 1094 | image2_crop(isnan(image2_crop))=0; |
---|
| 1095 | end |
---|
| 1096 | sum_square=sum(sum(image1_crop.*image1_crop)); |
---|
| 1097 | %reference: Oliver Pust, PIV: Direct Cross-Correlation |
---|
| 1098 | result_conv= conv2(image2_crop,flipdim(flipdim(image1_crop,2),1),'valid'); |
---|
| 1099 | corrmax= max(max(result_conv)); |
---|
| 1100 | result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255 |
---|
| 1101 | %Find the correlation max, at 255 |
---|
| 1102 | [y,x] = find(result_conv==255,1); |
---|
| 1103 | subimage2_crop=image2_crop(y:y+2*iby2/mesh,x:x+2*ibx2/mesh);%subimage of image 2 corresponding to the optimum displacement of first image |
---|
| 1104 | sum_square=sum_square*sum(sum(subimage2_crop.*subimage2_crop));% product of variances of image 1 and 2 |
---|
| 1105 | sum_square=sqrt(sum_square);% srt of the variance product to normalise correlation |
---|
| 1106 | if ~isempty(y) && ~isempty(x) |
---|
| 1107 | try |
---|
| 1108 | if par_civ.CorrSmooth==1 |
---|
| 1109 | [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y); |
---|
| 1110 | elseif par_civ.CorrSmooth==2 |
---|
| 1111 | [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y); |
---|
| 1112 | else |
---|
| 1113 | [vector,F(ivec)] = quadr_fit(result_conv,x,y); |
---|
| 1114 | end |
---|
| 1115 | utable(ivec)=vector(1)*mesh+shiftx(ivec); |
---|
| 1116 | vtable(ivec)=vector(2)*mesh+shifty(ivec); |
---|
| 1117 | xtable(ivec)=iref+utable(ivec)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2) |
---|
| 1118 | ytable(ivec)=jref+vtable(ivec)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge) |
---|
[911] | 1119 | iref=round(xtable(ivec)+0.5);% nearest image index for the middle of the vector |
---|
| 1120 | jref=round(ytable(ivec)+0.5); |
---|
[880] | 1121 | % eliminate vectors located in the mask |
---|
[911] | 1122 | if checkmask && (iref<1 || jref<1 ||iref>npx_ima || jref>npy_ima ||( par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100)) |
---|
[880] | 1123 | utable(ivec)=0; |
---|
| 1124 | vtable(ivec)=0; |
---|
| 1125 | F(ivec)=3; |
---|
| 1126 | end |
---|
| 1127 | ctable(ivec)=corrmax/sum_square;% correlation value |
---|
| 1128 | catch ME |
---|
[856] | 1129 | F(ivec)=3; |
---|
[910] | 1130 | disp(ME.message) |
---|
[856] | 1131 | end |
---|
[880] | 1132 | else |
---|
[598] | 1133 | F(ivec)=3; |
---|
| 1134 | end |
---|
[597] | 1135 | end |
---|
| 1136 | end |
---|
[598] | 1137 | end |
---|
| 1138 | end |
---|
| 1139 | result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output |
---|
| 1140 | |
---|
| 1141 | %------------------------------------------------------------------------ |
---|
| 1142 | % --- Find the maximum of the correlation function after interpolation |
---|
[862] | 1143 | % OUPUT: |
---|
| 1144 | % vector = optimum displacement vector with subpixel correction |
---|
| 1145 | % F =flag: =0 OK |
---|
| 1146 | % =-2 , warning: max too close to the edge of the search box (1 pixel margin) |
---|
| 1147 | % INPUT: |
---|
| 1148 | % x,y: position of the maximum correlation at integer values |
---|
| 1149 | |
---|
[598] | 1150 | function [vector,F] = SUBPIXGAUSS (result_conv,x,y) |
---|
| 1151 | %------------------------------------------------------------------------ |
---|
[862] | 1152 | % vector=[0 0]; %default |
---|
[598] | 1153 | F=0; |
---|
| 1154 | [npy,npx]=size(result_conv); |
---|
[911] | 1155 | result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (=0 by discretisation, to avoid divergence in the log) |
---|
[731] | 1156 | %the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ï¿œ Israel Institute of Technology |
---|
| 1157 | %http://urapiv.wordpress.com |
---|
| 1158 | peaky = y; |
---|
[911] | 1159 | if y < npy && y > 1 |
---|
[731] | 1160 | f0 = log(result_conv(y,x)); |
---|
| 1161 | f1 = log(result_conv(y-1,x)); |
---|
| 1162 | f2 = log(result_conv(y+1,x)); |
---|
| 1163 | peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2); |
---|
| 1164 | else |
---|
| 1165 | F=-2; % warning flag for vector truncated by the limited search box |
---|
| 1166 | end |
---|
| 1167 | peakx=x; |
---|
[911] | 1168 | if x < npx-1 && x > 1 |
---|
[731] | 1169 | f0 = log(result_conv(y,x)); |
---|
| 1170 | f1 = log(result_conv(y,x-1)); |
---|
| 1171 | f2 = log(result_conv(y,x+1)); |
---|
| 1172 | peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2); |
---|
| 1173 | else |
---|
| 1174 | F=-2; % warning flag for vector truncated by the limited search box |
---|
| 1175 | end |
---|
| 1176 | vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; |
---|
[598] | 1177 | |
---|
| 1178 | %------------------------------------------------------------------------ |
---|
| 1179 | % --- Find the maximum of the correlation function after interpolation |
---|
| 1180 | function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y) |
---|
| 1181 | %------------------------------------------------------------------------ |
---|
[862] | 1182 | % vector=[0 0]; %default |
---|
[598] | 1183 | F=-2; |
---|
| 1184 | peaky=y; |
---|
| 1185 | peakx=x; |
---|
[731] | 1186 | result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log) |
---|
[598] | 1187 | [npy,npx]=size(result_conv); |
---|
[911] | 1188 | if (x < npx) && (y < npy) && (x > 1) && (y > 1) |
---|
[598] | 1189 | F=0; |
---|
| 1190 | for i=-1:1 |
---|
| 1191 | for j=-1:1 |
---|
| 1192 | %following 15 lines based on |
---|
| 1193 | %H. Nobach ï¿œ M. Honkanen (2005) |
---|
| 1194 | %Two-dimensional Gaussian regression for sub-pixel displacement |
---|
| 1195 | %estimation in particle image velocimetry or particle position |
---|
| 1196 | %estimation in particle tracking velocimetry |
---|
| 1197 | %Experiments in Fluids (2005) 38: 511ï¿œ515 |
---|
| 1198 | c10(j+2,i+2)=i*log(result_conv(y+j, x+i)); |
---|
| 1199 | c01(j+2,i+2)=j*log(result_conv(y+j, x+i)); |
---|
| 1200 | c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i)); |
---|
| 1201 | c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i)); |
---|
| 1202 | c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i)); |
---|
| 1203 | end |
---|
| 1204 | end |
---|
| 1205 | c10=(1/6)*sum(sum(c10)); |
---|
| 1206 | c01=(1/6)*sum(sum(c01)); |
---|
| 1207 | c11=(1/4)*sum(sum(c11)); |
---|
| 1208 | c20=(1/6)*sum(sum(c20)); |
---|
[859] | 1209 | c02=(1/6)*sum(sum(c02)); |
---|
[598] | 1210 | deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2); |
---|
| 1211 | deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2); |
---|
| 1212 | if abs(deltax)<1 |
---|
| 1213 | peakx=x+deltax; |
---|
| 1214 | end |
---|
| 1215 | if abs(deltay)<1 |
---|
| 1216 | peaky=y+deltay; |
---|
| 1217 | end |
---|
| 1218 | end |
---|
| 1219 | vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; |
---|
| 1220 | |
---|
[876] | 1221 | %------------------------------------------------------------------------ |
---|
| 1222 | % --- Find the maximum of the correlation function after quadratic interpolation |
---|
| 1223 | function [vector,F] = quadr_fit(result_conv,x,y) |
---|
| 1224 | [npy,npx]=size(result_conv); |
---|
| 1225 | if x<4 || y<4 || npx-x<4 ||npy-y <4 |
---|
| 1226 | F=-2; |
---|
| 1227 | vector=[x y]; |
---|
| 1228 | else |
---|
| 1229 | F=0; |
---|
| 1230 | x_ind=x-4:x+4; |
---|
| 1231 | y_ind=y-4:y+4; |
---|
| 1232 | x_vec=0.25*(x_ind-x); |
---|
| 1233 | y_vec=0.25*(y_ind-y); |
---|
| 1234 | [X,Y]=meshgrid(x_vec,y_vec); |
---|
| 1235 | coord=[reshape(X,[],1) reshape(Y,[],1)]; |
---|
| 1236 | result_conv=reshape(result_conv(y_ind,x_ind),[],1); |
---|
| 1237 | |
---|
| 1238 | |
---|
| 1239 | % n=numel(X); |
---|
| 1240 | % x=[X Y]; |
---|
| 1241 | % X=X-0.5; |
---|
| 1242 | % Y=Y+0.5; |
---|
| 1243 | % y = (X.*X+2*Y.*Y+X.*Y+6) + 0.1*rand(n,1); |
---|
| 1244 | p = polyfitn(coord,result_conv,2); |
---|
| 1245 | A(1,1)=2*p.Coefficients(1); |
---|
| 1246 | A(1,2)=p.Coefficients(2); |
---|
| 1247 | A(2,1)=p.Coefficients(2); |
---|
| 1248 | A(2,2)=2*p.Coefficients(4); |
---|
| 1249 | vector=[x y]'-A\[p.Coefficients(3) p.Coefficients(5)]'; |
---|
| 1250 | vector=vector'-[floor(npx/2) floor(npy/2)]-1 ; |
---|
| 1251 | % zg = polyvaln(p,coord); |
---|
| 1252 | % figure |
---|
| 1253 | % surf(x_vec,y_vec,reshape(zg,9,9)) |
---|
| 1254 | % hold on |
---|
| 1255 | % plot3(X,Y,reshape(result_conv,9,9),'o') |
---|
| 1256 | % hold off |
---|
| 1257 | end |
---|
| 1258 | |
---|
[598] | 1259 | %'RUN_FIX': function for fixing velocity fields: |
---|
| 1260 | %----------------------------------------------- |
---|
| 1261 | % RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref) |
---|
| 1262 | % |
---|
| 1263 | %filename: name of the netcdf file (used as input and output) |
---|
| 1264 | %field: structure specifying the names of the fields to fix (depending on civ1 or civ2) |
---|
[859] | 1265 | %.vel_type='civ1' or 'civ2'; |
---|
| 1266 | %.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1); |
---|
| 1267 | %.fixflag=name of fix flag variable ('vec_FixFlag' for civ1) |
---|
| 1268 | %flagindex: flag specifying which values of vec_f are removed: |
---|
| 1269 | % if flagindex(1)=1: vec_f=-2 vectors are removed |
---|
| 1270 | % if flagindex(2)=1: vec_f=3 vectors are removed |
---|
| 1271 | % if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2) |
---|
[598] | 1272 | %iter=1 for civ1 fields and iter=2 for civ2 fields |
---|
| 1273 | %thresh_vecC: threshold in the image correlation vec_C |
---|
| 1274 | %flag_mask: =1 mask used to remove vectors (0 else) |
---|
| 1275 | %maskname: name of the mask image file for fix |
---|
| 1276 | %thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists |
---|
| 1277 | %inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold |
---|
| 1278 | %fileref: .nc file name for a reference velocity (='': refrence 0 used) |
---|
| 1279 | %fieldref: 'civ1','filter1'...feld used in fileref |
---|
| 1280 | |
---|
| 1281 | function FF=fix(Param,F,C,U,V,X,Y) |
---|
| 1282 | FF=zeros(size(F));%default |
---|
| 1283 | |
---|
| 1284 | %criterium on warn flags |
---|
| 1285 | FlagName={'CheckFmin2','CheckF2','CheckF3','CheckF4'}; |
---|
| 1286 | FlagVal=[-2 2 3 4]; |
---|
| 1287 | for iflag=1:numel(FlagName) |
---|
| 1288 | if isfield(Param,FlagName{iflag}) && Param.(FlagName{iflag}) |
---|
| 1289 | FF=(FF==1| F==FlagVal(iflag)); |
---|
| 1290 | end |
---|
| 1291 | end |
---|
| 1292 | %criterium on correlation values |
---|
| 1293 | if isfield (Param,'MinCorr') |
---|
| 1294 | FF=FF==1 | C<Param.MinCorr; |
---|
| 1295 | end |
---|
| 1296 | if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)) |
---|
| 1297 | Umod= U.*U+V.*V; |
---|
| 1298 | if isfield (Param,'MinVel')&&~isempty(Param.MinVel) |
---|
| 1299 | FF=FF==1 | Umod<(Param.MinVel*Param.MinVel); |
---|
| 1300 | end |
---|
| 1301 | if isfield (Param,'MaxVel')&&~isempty(Param.MaxVel) |
---|
| 1302 | FF=FF==1 | Umod>(Param.MaxVel*Param.MaxVel); |
---|
| 1303 | end |
---|
| 1304 | end |
---|
| 1305 | |
---|
| 1306 | |
---|
| 1307 | %------------------------------------------------------------------------ |
---|
| 1308 | % --- determine the list of index pairs of processing file |
---|
| 1309 | function [i1_series,i2_series,j1_series,j2_series,check_bounds,NomTypeNc]=... |
---|
[635] | 1310 | find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j) |
---|
[598] | 1311 | %------------------------------------------------------------------------ |
---|
[610] | 1312 | i1_series=i_series;% set of first image indexes |
---|
[598] | 1313 | i2_series=i_series; |
---|
[819] | 1314 | j1_series=j_series;%ones(size(i_series));% set of first image numbers |
---|
| 1315 | j2_series=j_series;%ones(size(i_series)); |
---|
[610] | 1316 | r=regexp(str_civ,'^\D(?<ind>[i|j])=( -| )(?<num1>\d+)\|(?<num2>\d+)','names'); |
---|
[598] | 1317 | if ~isempty(r) |
---|
| 1318 | mode=['D' r.ind]; |
---|
| 1319 | ind1=str2num(r.num1); |
---|
| 1320 | ind2=str2num(r.num2); |
---|
| 1321 | else |
---|
[668] | 1322 | mode='j1-j2'; |
---|
[598] | 1323 | r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names'); |
---|
| 1324 | if ~isempty(r) |
---|
| 1325 | NomTypeNc='_1ab'; |
---|
| 1326 | else |
---|
| 1327 | r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names'); |
---|
| 1328 | if ~isempty(r) |
---|
| 1329 | NomTypeNc='_1AB'; |
---|
[597] | 1330 | else |
---|
[598] | 1331 | r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names'); |
---|
| 1332 | if ~isempty(r) |
---|
| 1333 | NomTypeNc='_1_1-2'; |
---|
[859] | 1334 | end |
---|
[597] | 1335 | end |
---|
| 1336 | end |
---|
[598] | 1337 | if isempty(r) |
---|
| 1338 | display('wrong pair mode input option') |
---|
| 1339 | else |
---|
[859] | 1340 | ind1=stra2num(r.num1); |
---|
| 1341 | ind2=stra2num(r.num2); |
---|
[598] | 1342 | end |
---|
[597] | 1343 | end |
---|
[819] | 1344 | switch mode |
---|
| 1345 | case 'Di' |
---|
| 1346 | i1_series=i_series-ind1;% set of first image numbers |
---|
| 1347 | i2_series=i_series+ind2; |
---|
| 1348 | check_bounds=i1_series<MinIndex_i | i2_series>MaxIndex_i; |
---|
| 1349 | if isempty(j_series) |
---|
| 1350 | NomTypeNc='_1-2'; |
---|
| 1351 | else |
---|
| 1352 | j1_series=j_series; |
---|
| 1353 | j2_series=j_series; |
---|
| 1354 | NomTypeNc='_1-2_1'; |
---|
| 1355 | end |
---|
| 1356 | case 'Dj' |
---|
| 1357 | j1_series=j_series-ind1; |
---|
| 1358 | j2_series=j_series+ind2; |
---|
| 1359 | check_bounds=j1_series<MinIndex_j | j2_series>MaxIndex_j; |
---|
| 1360 | NomTypeNc='_1_1-2'; |
---|
| 1361 | otherwise %bursts |
---|
| 1362 | i1_series=i_series(1,:);% do not sweep the j index |
---|
| 1363 | i2_series=i_series(1,:); |
---|
| 1364 | j1_series=ind1*ones(1,size(i_series,2));% j index is fixed by pair choice |
---|
| 1365 | j2_series=ind2*ones(1,size(i_series,2)); |
---|
| 1366 | check_bounds=zeros(size(i1_series));% no limitations due to min-max indices |
---|
[598] | 1367 | end |
---|
[597] | 1368 | |
---|
[598] | 1369 | |
---|
| 1370 | |
---|
| 1371 | |
---|