[1089] | 1 | %'civ_3D': PIV function activated by the general GUI series |
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| 2 | % --- call the sub-functions: |
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| 3 | % civ: PIV function itself |
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| 4 | % fix: removes false vectors after detection by various criteria |
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| 5 | % filter_tps: make interpolation-smoothing |
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| 6 | %------------------------------------------------------------------------ |
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| 7 | % function [Data,errormsg,result_conv]= civ_series(Param) |
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| 8 | % |
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| 9 | %OUTPUT |
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| 10 | % Data=structure containing the PIV results and information on the processing parameters |
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| 11 | % errormsg=error message char string, decd ..fault='' |
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| 12 | % resul_conv: image inter-correlation function for the last grid point (used for tests) |
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| 13 | % |
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| 14 | %INPUT: |
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| 15 | % Param: 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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| 22 | % Param.ActionInput: substructure with the parameters provided by the GUI civ_input |
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| 23 | % .Civ1: parameters for civ1 |
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| 24 | % .Fix1: parameters for fix1 |
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| 25 | % .Patch1: |
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| 26 | % .Civ2: for civ2 |
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| 27 | % .Fix2: |
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| 28 | % .Patch2: |
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| 29 | |
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| 30 | %======================================================================= |
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[1093] | 31 | % Copyright 2008-2021, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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[1089] | 32 | % http://www.legi.grenoble-inp.fr |
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| 33 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr |
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| 34 | % |
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| 35 | % This file is part of the toolbox UVMAT. |
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| 36 | % |
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| 37 | % UVMAT is free software; you can redistribute it and/or modify |
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| 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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| 41 | % |
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| 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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| 45 | % GNU General Public License (see LICENSE.txt) for more details. |
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| 46 | %======================================================================= |
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| 47 | |
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| 48 | function [Data,errormsg,result_conv]= civ_3D(Param) |
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| 49 | errormsg=''; |
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| 50 | |
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| 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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| 52 | if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN |
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| 53 | path_series=fileparts(which('series')); |
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| 54 | addpath(fullfile(path_series,'series')) |
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| 55 | Data=civ_input_3D(Param);% introduce the civ parameters using the GUI civ_input |
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| 56 | %Data=civ_input_App(Param);% introduce the civ parameters using the GUI |
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| 57 | %civ_input %%%% TO MOVE |
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| 58 | if isempty(Data) |
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| 59 | Data=Param;% if civ_input has been cancelled, keep previous parameters |
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| 60 | end |
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| 61 | Data.Program=mfilename;%gives the name of the current function |
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| 62 | Data.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
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| 63 | Data.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
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| 64 | Data.NbSlice='off'; %nbre of slices ('off' by default) |
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| 65 | Data.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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| 66 | Data.FieldName='on';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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| 67 | Data.FieldTransform = 'off';%can use a transform function |
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| 68 | Data.ProjObject='off';%can use projection object(option 'off'/'on', |
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| 69 | Data.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) |
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| 70 | Data.OutputDirExt='.civ';%set the output dir extension |
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| 71 | 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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| 72 | Data.OutputFileMode='NbInput_i';% one output file expected per value of i index (used for waitbar) |
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| 73 | Data.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) |
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| 74 | if isfield(Data.ActionInput,'PairIndices') && strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2') |
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| 75 | if isfield(Data.ActionInput.PairIndices,'ListPairCiv2') |
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| 76 | str_civ=Data.ActionInput.PairIndices.ListPairCiv2; |
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| 77 | else |
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| 78 | str_civ=Data.ActionInput.PairIndices.ListPairCiv1; |
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| 79 | end |
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| 80 | r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names'); |
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| 81 | if isempty(r) |
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| 82 | r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names'); |
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| 83 | if isempty(r) |
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| 84 | r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names'); |
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| 85 | end |
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| 86 | end |
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| 87 | if ~isempty(r) |
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| 88 | Data.j_index_1=stra2num(r.num1); |
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| 89 | Data.j_index_2=stra2num(r.num2); |
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| 90 | end |
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| 91 | end |
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| 92 | % estimated CPUTime |
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| 93 | CPUtime_unit=0.01;%estimated time for a multiplication (in microsecond) |
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| 94 | if isfield(Param.SeriesData,'FileInfo')&&isfield(Param.SeriesData.FileInfo{1},'Height')&&isfield(Param.SeriesData.FileInfo{1},'Width') |
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| 95 | pixnbre=Param.SeriesData.FileInfo{1}.Height*Param.SeriesData.FileInfo{1}.Width; % total number of pxels for input images |
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| 96 | CPUtime=0; |
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| 97 | if isfield(Data.ActionInput,'Civ1') |
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| 98 | %BoxSize=Data.ActionInput.Civ1.CorrBoxSize(1)*Data.ActionInput.Civ1.CorrBoxSize(2); |
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| 99 | tic |
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| 100 | testboxa=rand(Data.ActionInput.Civ1.CorrBoxSize(1),Data.ActionInput.Civ1.CorrBoxSize(2)); |
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| 101 | testboxb=rand(Data.ActionInput.Civ1.SearchBoxSize(1),Data.ActionInput.Civ1.SearchBoxSize(2)); |
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| 102 | anss=conv2(testboxa,testboxb); |
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| 103 | CPUtime_unit=toc; |
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| 104 | nb_box=pixnbre/(Data.ActionInput.Civ1.Dx*Data.ActionInput.Civ1.Dy); |
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| 105 | %nbpos=Data.ActionInput.Civ1.SearchBoxSize-Data.ActionInput.Civ1.CorrBoxSize; |
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| 106 | CPUtime=2*CPUtime_unit*nb_box%*BoxSize*nbpos(1)*nbpos(2);% adjustement factor 2 used |
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| 107 | end |
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| 108 | if isfield(Data.ActionInput,'Patch1') |
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| 109 | CPUtime=2*CPUtime; |
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| 110 | end |
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| 111 | if isfield(Data.ActionInput,'Civ2') |
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| 112 | tic |
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| 113 | testboxa=rand(Data.ActionInput.Civ2.CorrBoxSize(1),Data.ActionInput.Civ2.CorrBoxSize(2)); |
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| 114 | testboxb=rand(Data.ActionInput.Civ2.SearchBoxSize(1),Data.ActionInput.Civ2.SearchBoxSize(2)); |
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| 115 | anss=conv2(testboxa,testboxb); |
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| 116 | CPUtime_unit=toc; |
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| 117 | nb_box=pixnbre/(Data.ActionInput.Civ2.Dx*Data.ActionInput.Civ2.Dy); |
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| 118 | %BoxSize=Data.ActionInput.Civ2.CorrBoxSize(1)*Data.ActionInput.Civ2.CorrBoxSize(2); |
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| 119 | %nbpos=Data.ActionInput.Civ2.SearchBoxSize-Data.ActionInput.Civ2.CorrBoxSize; |
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| 120 | CPUtime=CPUtime+2*CPUtime_unit*nb_box;%*BoxSize*nbpos(1)*nbpos(2); |
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| 121 | end |
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| 122 | if isfield(Data.ActionInput,'Patch2') |
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| 123 | CPUtime=(4/3)*CPUtime; |
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| 124 | end |
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| 125 | Data.CPUTime=ceil(CPUtime/6); % estimated CPU time per field pair in minute |
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| 126 | Data.CPUTime=Data.CPUTime/10; % displqy CPU time with 1 digit beyond dot |
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| 127 | end |
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| 128 | return |
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| 129 | end |
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| 130 | |
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| 131 | %% read input parameters from an xml file if input is a file name (batch mode) |
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| 132 | checkrun=1; |
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| 133 | if ischar(Param) |
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| 134 | Param=xml2struct(Param);% read Param as input file (batch case) |
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| 135 | checkrun=0; |
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| 136 | end |
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| 137 | |
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| 138 | %% test input |
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| 139 | if ~isfield(Param,'ActionInput') |
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| 140 | disp_uvmat('ERROR','no parameter set for PIV',checkrun) |
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| 141 | return |
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| 142 | end |
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| 143 | iview_A=0;%default values |
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| 144 | NbField=1; |
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| 145 | RUNHandle=[]; |
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| 146 | CheckInputFile=isfield(Param,'InputTable');%= 1 in test use for TestCiv (no nc file involved) |
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| 147 | CheckOutputFile=isfield(Param,'OutputSubDir');%= 1 in test use for TestPatch (no nc file produced) |
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| 148 | |
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| 149 | %% input files and indexing (skipped in Test mode) |
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| 150 | if CheckInputFile |
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| 151 | hseries=findobj(allchild(0),'Tag','series'); |
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| 152 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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| 153 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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| 154 | MaxIndex_i=Param.IndexRange.MaxIndex_i; |
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| 155 | MinIndex_i=Param.IndexRange.MinIndex_i; |
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| 156 | MaxIndex_j=ones(size(MaxIndex_i));MinIndex_j=ones(size(MinIndex_i)); |
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| 157 | if isfield(Param.IndexRange,'MaxIndex_j')&& isfield(Param.IndexRange,'MinIndex_j') |
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| 158 | MaxIndex_j=Param.IndexRange.MaxIndex_j; |
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| 159 | MinIndex_j=Param.IndexRange.MinIndex_j; |
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| 160 | end |
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| 161 | if isfield(Param,'InputTable') |
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| 162 | [tild,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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| 163 | iview_A=0;% series index (iview) for the first image series |
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| 164 | 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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| 165 | if Param.ActionInput.CheckCiv1 |
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| 166 | iview_A=1;% usual PIV, the image series is on the first line of the table |
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| 167 | elseif Param.ActionInput.CheckCiv2 % civ2 is performed without Civ1, a netcdf file series is needed in the first table line |
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| 168 | iview_A=2;% the second line is used for the input images of Civ2 |
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| 169 | end |
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| 170 | % if strcmp(Param.ActionInput.ListCompareMode,'shift') |
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| 171 | % iview_B=iview_A+1; % the second image series is on the next line of the input table |
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| 172 | % end |
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| 173 | if iview_A~=0 |
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| 174 | RootPath_A=Param.InputTable{iview_A,1}; |
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| 175 | RootFile_A=Param.InputTable{iview_A,3}; |
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| 176 | SubDir_A=Param.InputTable{iview_A,2}; |
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| 177 | NomType_A=Param.InputTable{iview_A,4}; |
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| 178 | FileExt_A=Param.InputTable{iview_A,5}; |
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| 179 | if iview_B==0 |
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| 180 | iview_B=iview_A;% the second image series is the same as the first |
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| 181 | end |
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| 182 | RootPath_B=Param.InputTable{iview_B,1}; |
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| 183 | RootFile_B=Param.InputTable{iview_B,3}; |
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| 184 | SubDir_B=Param.InputTable{iview_B,2}; |
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| 185 | NomType_B=Param.InputTable{iview_B,4}; |
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| 186 | FileExt_B=Param.InputTable{iview_B,5}; |
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| 187 | end |
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| 188 | |
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| 189 | PairCiv2=''; |
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| 190 | switch Param.ActionInput.ListCompareMode |
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| 191 | case 'PIV' |
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| 192 | PairCiv1=Param.ActionInput.PairIndices.ListPairCiv1; |
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| 193 | if isfield(Param.ActionInput.PairIndices,'ListPairCiv2') |
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| 194 | PairCiv2=Param.ActionInput.PairIndices.ListPairCiv2;%string which determines the civ2 pair |
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| 195 | end |
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| 196 | if iview_A==1% if Civ1 is performed |
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| 197 | [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=... |
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| 198 | find_pair_indices(PairCiv1,i1_series{1},j1_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j); |
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| 199 | if ~isempty(PairCiv2) |
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| 200 | [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds_Civ2]=... |
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| 201 | 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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| 202 | check_bounds=check_bounds | check_bounds_Civ2; |
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| 203 | end |
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| 204 | else% we start from an existing Civ1 file |
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| 205 | i1_series_Civ1=i1_series{1}; |
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| 206 | i2_series_Civ1=i2_series{1}; |
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| 207 | j1_series_Civ1=j1_series{1}; |
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| 208 | j2_series_Civ1=j2_series{1}; |
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| 209 | NomTypeNc=Param.InputTable{1,4}; |
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| 210 | if ~isempty(PairCiv2) |
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| 211 | [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds,NomTypeNc]=... |
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| 212 | 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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| 213 | end |
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| 214 | end |
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| 215 | case 'displacement' |
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| 216 | if isfield(Param.ActionInput,'OriginIndex') |
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| 217 | i1_series_Civ1=Param.ActionInput.OriginIndex*ones(size(i1_series{1})); |
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| 218 | else |
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| 219 | i1_series_Civ1=ones(size(i1_series{1})); |
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| 220 | end |
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| 221 | i1_series_Civ2=i1_series_Civ1; |
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| 222 | i2_series_Civ1=i1_series{1}; |
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| 223 | i2_series_Civ2=i1_series{1}; |
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| 224 | j1_series_Civ1=[];% no j index variation for the ref image |
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| 225 | j1_series_Civ2=[]; |
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| 226 | if isempty(j1_series{1}) |
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| 227 | j2_series_Civ1=ones(size(i1_series_Civ1)); |
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| 228 | else |
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| 229 | j2_series_Civ1=j1_series{1};% if j index exist |
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| 230 | end |
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| 231 | j2_series_Civ2=j2_series_Civ1; |
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| 232 | NomTypeNc='_1'; |
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| 233 | case 'PIV volume' |
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| 234 | % TODO, TODO |
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| 235 | end |
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| 236 | %determine frame indices for input with movie or other multiframe input file |
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| 237 | if isempty(j1_series_Civ1)% simple movie with index i |
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| 238 | FrameIndex_A_Civ1=i1_series_Civ1; |
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| 239 | FrameIndex_B_Civ1=i2_series_Civ1; |
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| 240 | j1_series_Civ1=ones(size(i1_series_Civ1)); |
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| 241 | if strcmp(Param.ActionInput.ListCompareMode,'PIV') |
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| 242 | j2_series_Civ1=ones(size(i1_series_Civ1)); |
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| 243 | end |
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| 244 | else % movie for each burst or volume (index j) |
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| 245 | FrameIndex_A_Civ1=j1_series_Civ1; |
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| 246 | FrameIndex_B_Civ1=j2_series_Civ1; |
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| 247 | end |
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| 248 | if isempty(PairCiv2) |
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| 249 | FrameIndex_A_Civ2=FrameIndex_A_Civ1; |
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| 250 | FrameIndex_B_Civ2=FrameIndex_B_Civ1; |
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| 251 | else |
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| 252 | if isempty(j1_series_Civ2) |
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| 253 | FrameIndex_A_Civ2=i1_series_Civ2; |
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| 254 | FrameIndex_B_Civ2=i2_series_Civ2; |
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| 255 | j1_series_Civ2=ones(size(i1_series_Civ2)); |
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| 256 | if strcmp(Param.ActionInput.ListCompareMode,'PIV') |
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| 257 | j2_series_Civ2=ones(size(i1_series_Civ2)); |
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| 258 | end |
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| 259 | else |
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| 260 | FrameIndex_A_Civ2=j1_series_Civ2; |
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| 261 | FrameIndex_B_Civ2=j2_series_Civ2; |
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| 262 | end |
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| 263 | end |
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| 264 | if isempty(i1_series_Civ1)||(~isempty(PairCiv2) && isempty(i1_series_Civ2)) |
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| 265 | disp_uvmat('ERROR','no image pair for civ in the input file index range',checkrun) |
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| 266 | return |
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| 267 | end |
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| 268 | end |
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| 269 | |
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| 270 | %% check the first image pair |
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| 271 | if Param.ActionInput.CheckCiv1% Civ1 is performed |
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| 272 | NbField=numel(i1_series_Civ1); |
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| 273 | elseif Param.ActionInput.CheckCiv2 % Civ2 is performed without Civ1 |
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| 274 | NbField=numel(i1_series_Civ2); |
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| 275 | else |
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| 276 | NbField=numel(i1_series_Civ1);% no image used (only fix or patch) TO CHECK |
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| 277 | end |
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| 278 | |
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| 279 | %% Output directory |
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| 280 | OutputDir=''; |
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| 281 | if CheckOutputFile |
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| 282 | OutputDir=[Param.OutputSubDir Param.OutputDirExt]; |
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| 283 | end |
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| 284 | end |
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| 285 | |
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| 286 | %% prepare output Data |
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| 287 | ListGlobalAttribute={'Conventions','Program','CivStage'}; |
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| 288 | Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes |
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| 289 | Data.Program='civ_series'; |
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| 290 | Data.CivStage=0;%default |
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| 291 | check_civx=0;%default |
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| 292 | |
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| 293 | %% get timing from the ImaDoc file or input video |
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| 294 | if iview_A~=0 |
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| 295 | XmlFileName=find_imadoc(RootPath_A,SubDir_A,RootFile_A,FileExt_A); |
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| 296 | Time=[]; |
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| 297 | if ~isempty(XmlFileName) |
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| 298 | XmlData=imadoc2struct(XmlFileName); |
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| 299 | if isfield(XmlData,'Time') |
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| 300 | Time=XmlData.Time; |
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| 301 | end |
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| 302 | if isfield(XmlData,'Camera') |
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| 303 | if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice) |
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| 304 | NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform |
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| 305 | if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) |
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| 306 | msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); |
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| 307 | end |
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| 308 | end |
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| 309 | if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit) |
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| 310 | TimeUnit=XmlData.Camera.TimeUnit; |
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| 311 | end |
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| 312 | end |
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| 313 | end |
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| 314 | end |
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| 315 | |
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| 316 | %%%%% MAIN LOOP %%%%%% |
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| 317 | maskoldname='';% initiate the mask name |
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| 318 | FileType_A=''; |
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| 319 | FileType_B=''; |
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| 320 | CheckOverwrite=1;%default |
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| 321 | if isfield(Param,'CheckOverwrite') |
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| 322 | CheckOverwrite=Param.CheckOverwrite; |
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| 323 | end |
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| 324 | for ifield=1:NbField |
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| 325 | tic |
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| 326 | if ~isempty(RUNHandle)% update the waitbar in interactive mode with GUI series (checkrun=1) |
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| 327 | update_waitbar(WaitbarHandle,ifield/NbField) |
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| 328 | if checkrun && ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
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| 329 | disp('program stopped by user') |
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| 330 | break |
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| 331 | end |
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| 332 | end |
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| 333 | if CheckInputFile |
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| 334 | if iview_A==0 % no nc file has been entered |
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| 335 | ncfile=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},... |
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| 336 | NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),j1_series_Civ1(ifield),j2_series_Civ1(ifield)); |
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| 337 | else% an existing nc file has been entered |
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| 338 | if iview_A==1% if Civ1 is performed |
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| 339 | Civ1Dir=OutputDir; |
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| 340 | else |
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| 341 | Civ1Dir=Param.InputTable{1,2}; |
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| 342 | end |
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| 343 | if strcmp(Param.ActionInput.ListCompareMode,'PIV') |
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| 344 | ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),... |
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| 345 | j1_series_Civ1(ifield),j2_series_Civ1(ifield)); |
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| 346 | else |
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| 347 | ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],... |
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| 348 | j1_series_Civ1(ifield),j2_series_Civ1(ifield)); |
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| 349 | end |
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| 350 | end |
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| 351 | ncfile_out=ncfile;% by default |
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| 352 | if isfield (Param.ActionInput,'Civ2') |
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| 353 | i1_civ2=i1_series_Civ2(ifield); |
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| 354 | i2_civ2=i1_civ2; |
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| 355 | if ~isempty(i2_series_Civ2) |
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| 356 | i2_civ2=i2_series_Civ2(ifield); |
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| 357 | end |
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| 358 | j1_civ2=1; |
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| 359 | if ~isempty(j1_series_Civ2) |
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| 360 | j1_civ2=j1_series_Civ2(ifield); |
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| 361 | end |
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| 362 | j2_civ2=i1_civ2; |
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| 363 | if ~isempty(j2_series_Civ2) |
---|
| 364 | j2_civ2=j2_series_Civ2(ifield); |
---|
| 365 | end |
---|
| 366 | if strcmp(Param.ActionInput.ListCompareMode,'PIV') |
---|
| 367 | ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1_civ2,i2_civ2,j1_civ2,j2_civ2); |
---|
| 368 | else % displacement |
---|
| 369 | ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i2_civ2,[],j2_civ2); |
---|
| 370 | end |
---|
| 371 | end |
---|
| 372 | if ~CheckOverwrite && exist(ncfile_out,'file') |
---|
| 373 | disp(['existing output file ' ncfile_out ' already exists, skip to next field']) |
---|
| 374 | continue% skip iteration if the mode overwrite is desactivated and the result file already exists |
---|
| 375 | end |
---|
| 376 | end |
---|
| 377 | %% Civ1 |
---|
| 378 | % if Civ1 computation is requested |
---|
| 379 | if isfield (Param.ActionInput,'Civ1') |
---|
| 380 | if CheckInputFile |
---|
| 381 | disp('civ1 started') |
---|
| 382 | end |
---|
| 383 | par_civ1=Param.ActionInput.Civ1;% parameters for civ1 |
---|
| 384 | if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) |
---|
| 385 | try |
---|
| 386 | if strcmp(Param.ActionInput.ListCompareMode,'displacement') |
---|
| 387 | ImageName_A=Param.ActionInput.RefFile; |
---|
| 388 | else |
---|
| 389 | ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield)); |
---|
| 390 | end |
---|
| 391 | if strcmp(FileExt_A,'.nc')% case of input images in format netcdf |
---|
| 392 | FieldName_A=Param.InputFields.FieldName; |
---|
| 393 | [DataIn,tild,tild,errormsg]=nc2struct(ImageName_A,{FieldName_A}); |
---|
| 394 | par_civ1.ImageA=DataIn.(FieldName_A); |
---|
| 395 | else % usual image formats for image A |
---|
| 396 | if isempty(FileType_A)% open the image object if not already done in case of movie input |
---|
| 397 | [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A); |
---|
| 398 | FileType_A=FileInfo_A.FileType; |
---|
| 399 | if isempty(Time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video','cine_phantom'})))% case of video input |
---|
| 400 | Time=zeros(FileInfo_A.NumberOfFrames+1,2); |
---|
| 401 | Time(:,2)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate)'; |
---|
| 402 | end |
---|
| 403 | if ~isempty(FileType_A) && isempty(Time)% Time = index i +0.001 index j by default |
---|
| 404 | MaxIndex_i=max(i2_series_Civ1); |
---|
| 405 | MaxIndex_j=max(j2_series_Civ1); |
---|
| 406 | Time=(1:MaxIndex_i)'*ones(1,MaxIndex_j); |
---|
| 407 | Time=Time+0.001*ones(MaxIndex_i,1)*(1:MaxIndex_j); |
---|
| 408 | Time=[zeros(1,MaxIndex_j);Time];% insert a first line of zeros |
---|
| 409 | Time=[zeros(MaxIndex_i+1,1) Time];% insert a first column of zeros |
---|
| 410 | end |
---|
| 411 | end |
---|
| 412 | if ~exist(ImageName_A,'file') |
---|
| 413 | disp([ImageName_A ' missing']) |
---|
| 414 | continue |
---|
| 415 | end |
---|
| 416 | [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield)); |
---|
| 417 | end |
---|
| 418 | ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield)); |
---|
| 419 | if strcmp(FileExt_B,'.nc') % case of input images in format netcdf |
---|
| 420 | FieldName_B=Param.InputFields.FieldName; |
---|
| 421 | [DataIn,tild,tild,errormsg]=nc2struct(ImageName_B,{FieldName_B}); |
---|
| 422 | par_civ1.ImageB=DataIn.(FieldName_B); |
---|
| 423 | else % usual image formats for image B |
---|
| 424 | if isempty(FileType_B) |
---|
| 425 | [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B); |
---|
| 426 | FileType_B=FileInfo_B.FileType; |
---|
| 427 | end |
---|
| 428 | if ~exist(ImageName_B,'file') |
---|
| 429 | disp([ImageName_B ' missing']) |
---|
| 430 | continue |
---|
| 431 | end |
---|
| 432 | [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield)); |
---|
| 433 | end |
---|
| 434 | catch ME % display errors in reading input images |
---|
| 435 | if ~isempty(ME.message) |
---|
| 436 | disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun) |
---|
| 437 | continue |
---|
| 438 | end |
---|
| 439 | end |
---|
| 440 | par_civ1.ImageWidth=size(par_civ1.ImageA,2); |
---|
| 441 | par_civ1.ImageHeight=size(par_civ1.ImageA,1); |
---|
| 442 | list_param=(fieldnames(Param.ActionInput.Civ1))'; |
---|
| 443 | list_param(strcmp('TestCiv1',list_param))=[];% remove the parameter TestCiv1 from the list |
---|
| 444 | Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before each string in list_param |
---|
| 445 | Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images |
---|
| 446 | %indicate the values of all the global attributes in the output data |
---|
| 447 | Data.Civ1_ImageA=ImageName_A; |
---|
| 448 | Data.Civ1_ImageB=ImageName_B; |
---|
| 449 | i1=i1_series_Civ1(ifield); |
---|
| 450 | i2=i1; |
---|
| 451 | if ~isempty(i2_series_Civ1) |
---|
| 452 | i2=i2_series_Civ1(ifield); |
---|
| 453 | end |
---|
| 454 | j1=1; |
---|
| 455 | if ~isempty(j1_series_Civ1) |
---|
| 456 | j1=j1_series_Civ1(ifield); |
---|
| 457 | end |
---|
| 458 | j2=j1; |
---|
| 459 | if ~isempty(j2_series_Civ1) |
---|
| 460 | j2=j2_series_Civ1(ifield); |
---|
| 461 | end |
---|
| 462 | if strcmp(Param.ActionInput.ListCompareMode,'displacement') |
---|
| 463 | Data.Civ1_Time=Time(i2+1,j2+1);% the Time is the Time of the secodn image |
---|
| 464 | Data.Civ1_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading |
---|
| 465 | else |
---|
| 466 | 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 |
---|
| 467 | Data.Civ1_Dt=Time(i2+1,j2+1)-Time(i1+1,j1+1); |
---|
| 468 | end |
---|
| 469 | for ilist=1:length(list_param) |
---|
| 470 | Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist}); |
---|
| 471 | end |
---|
| 472 | Data.ListGlobalAttribute=[ListGlobalAttribute Civ1_param]; |
---|
| 473 | Data.CivStage=1; |
---|
| 474 | end |
---|
| 475 | % set the list of variables |
---|
| 476 | Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_F','Civ1_C'};% cell array containing the names of the fields to record |
---|
| 477 | Data.VarDimName={'nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1'}; |
---|
| 478 | Data.VarAttribute{1}.Role='coord_x'; |
---|
| 479 | Data.VarAttribute{2}.Role='coord_y'; |
---|
| 480 | Data.VarAttribute{3}.Role='vector_x'; |
---|
| 481 | Data.VarAttribute{4}.Role='vector_y'; |
---|
| 482 | Data.VarAttribute{5}.Role='warnflag'; |
---|
| 483 | % case of mask |
---|
| 484 | if par_civ1.CheckMask&&~isempty(par_civ1.Mask) |
---|
| 485 | if isfield(par_civ1,'NbSlice') |
---|
| 486 | [RootPath_mask,SubDir_mask,RootFile_mask,i1_mask,i2_mask,j1_mask,j2_mask,Ext_mask]=fileparts_uvmat(Param.ActionInput.Civ1.Mask); |
---|
| 487 | i1_mask=mod(i1-1,par_civ1.NbSlice)+1; |
---|
| 488 | maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',i1_mask); |
---|
| 489 | else |
---|
| 490 | maskname=Param.ActionInput.Civ1.Mask; |
---|
| 491 | end |
---|
| 492 | if strcmp(maskoldname,maskname)% mask exist, not already read in civ1 |
---|
| 493 | par_civ1.Mask=mask; %use mask already opened |
---|
| 494 | else |
---|
| 495 | if exist(maskname,'file') |
---|
| 496 | try |
---|
| 497 | par_civ1.Mask=imread(maskname);%update the mask, an store it for future use |
---|
| 498 | catch ME |
---|
| 499 | if ~isempty(ME.message) |
---|
| 500 | errormsg=['error reading input image: ' ME.message]; |
---|
| 501 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
| 502 | return |
---|
| 503 | end |
---|
| 504 | end |
---|
| 505 | else |
---|
| 506 | par_civ1.Mask=[]; |
---|
| 507 | end |
---|
| 508 | mask=par_civ1.Mask; |
---|
| 509 | maskoldname=maskname; |
---|
| 510 | end |
---|
| 511 | end |
---|
| 512 | if strcmp(Param.ActionInput.ListCompareMode, 'PIV volume') |
---|
| 513 | Data.ListVarName=[Data.ListVarName 'Civ1_Z']; |
---|
| 514 | Data.Civ1_X=[];Data.Civ1_Y=[];Data.Civ1_Z=[]; |
---|
| 515 | Data.Civ1_U=[];Data.Civ1_V=[];Data.Civ1_C=[];Data.Civ1_F=[]; |
---|
| 516 | for ivol=1:NbSlice |
---|
| 517 | % caluclate velocity data (y and v in indices, reverse to y component) |
---|
| 518 | [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1); |
---|
| 519 | if ~isempty(errormsg) |
---|
| 520 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
| 521 | return |
---|
| 522 | end |
---|
| 523 | Data.Civ1_X=[Data.Civ1_X reshape(xtable,[],1)]; |
---|
| 524 | Data.Civ1_Y=[Data.Civ1_Y reshape(Param.Civ1.ImageHeight-ytable+1,[],1)]; |
---|
| 525 | Data.Civ1_Z=[Data.Civ1_Z ivol*ones(numel(xtable),1)];% z=image index in image coordinates |
---|
| 526 | Data.Civ1_U=[Data.Civ1_U reshape(utable,[],1)]; |
---|
| 527 | Data.Civ1_V=[Data.Civ1_V reshape(-vtable,[],1)]; |
---|
| 528 | Data.Civ1_C=[Data.Civ1_C reshape(ctable,[],1)]; |
---|
| 529 | Data.Civ1_F=[Data.Civ1_C reshape(F,[],1)]; |
---|
| 530 | end |
---|
| 531 | else %usual PIV |
---|
| 532 | % caluclate velocity data (y and v in indices, reverse to y component) |
---|
| 533 | [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1); |
---|
| 534 | if ~isempty(errormsg) |
---|
| 535 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
| 536 | return |
---|
| 537 | end |
---|
| 538 | Data.Civ1_X=reshape(xtable,[],1); |
---|
| 539 | Data.Civ1_Y=reshape(par_civ1.ImageHeight-ytable+1,[],1); |
---|
| 540 | Data.Civ1_U=reshape(utable,[],1); |
---|
| 541 | Data.Civ1_V=reshape(-vtable,[],1); |
---|
| 542 | Data.Civ1_C=reshape(ctable,[],1); |
---|
| 543 | Data.Civ1_F=reshape(F,[],1); |
---|
| 544 | end |
---|
| 545 | else% we use existing Civ1 data |
---|
| 546 | if exist('ncfile','var') |
---|
| 547 | CivFile=ncfile; |
---|
| 548 | [Data,tild,tild,errormsg]=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format |
---|
| 549 | if ~isempty(errormsg) |
---|
| 550 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
| 551 | return |
---|
| 552 | end |
---|
| 553 | [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file |
---|
| 554 | elseif isfield(Param,'Civ1_X') |
---|
| 555 | Data.ListGlobalAttribute={}; |
---|
| 556 | Data.ListVarName={}; |
---|
| 557 | Data.VarDimName={}; |
---|
| 558 | Data.Civ1_X=Param.Civ1_X; |
---|
| 559 | Data.Civ1_Y=Param.Civ1_Y; |
---|
| 560 | Data.Civ1_U=Param.Civ1_U; |
---|
| 561 | Data.Civ1_V=Param.Civ1_V; |
---|
| 562 | Data.Civ1_FF=Param.Civ1_FF; |
---|
| 563 | end |
---|
| 564 | end |
---|
| 565 | |
---|
| 566 | %% Fix1 |
---|
| 567 | if isfield (Param.ActionInput,'Fix1') |
---|
| 568 | disp('fix1 started') |
---|
| 569 | if ~isfield (Param.ActionInput,'Civ1')% if we use existing Civ1, remove previous data beyond Civ1 |
---|
| 570 | Fix1_attr=find(strcmp('Fix1',Data.ListGlobalAttribute)); |
---|
| 571 | Data.ListGlobalAttribute(Fix1_attr)=[]; |
---|
| 572 | for ilist=1:numel(Fix1_attr) |
---|
| 573 | Data=rmfield(Data,Data.ListGlobalAttribute{Fix1_attr(ilist)}); |
---|
| 574 | end |
---|
| 575 | end |
---|
| 576 | list_param=fieldnames(Param.ActionInput.Fix1)'; |
---|
| 577 | Fix1_param=regexprep(list_param,'^.+','Fix1_$0');% insert 'Fix1_' before each string in ListFixParam |
---|
| 578 | %indicate the values of all the global attributes in the output data |
---|
| 579 | for ilist=1:length(list_param) |
---|
| 580 | Data.(Fix1_param{ilist})=Param.ActionInput.Fix1.(list_param{ilist}); |
---|
| 581 | end |
---|
| 582 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix1_param]; |
---|
| 583 | Data.ListVarName=[Data.ListVarName {'Civ1_FF'}]; |
---|
| 584 | Data.VarDimName=[Data.VarDimName {'nb_vec_1'}]; |
---|
| 585 | nbvar=length(Data.ListVarName); |
---|
| 586 | Data.VarAttribute{nbvar}.Role='errorflag'; |
---|
| 587 | Data.Civ1_FF=int8(fix(Param.ActionInput.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V)); |
---|
| 588 | Data.CivStage=2; |
---|
| 589 | end |
---|
| 590 | %% Patch1 |
---|
| 591 | if isfield (Param.ActionInput,'Patch1') |
---|
| 592 | disp('patch1 started') |
---|
| 593 | if check_civx |
---|
| 594 | errormsg='Civ Matlab input needed for patch'; |
---|
| 595 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
| 596 | return |
---|
| 597 | end |
---|
| 598 | |
---|
| 599 | % record the processing parameters of Patch1 as global attributes in the result nc file |
---|
| 600 | list_param=fieldnames(Param.ActionInput.Patch1)'; |
---|
| 601 | list_param(strcmp('TestPatch1',list_param))=[];% remove 'TestPatch1' from the list of parameters |
---|
| 602 | Patch1_param=regexprep(list_param,'^.+','Patch1_$0');% insert 'Patch1_' before each parameter name |
---|
| 603 | for ilist=1:length(list_param) |
---|
| 604 | Data.(Patch1_param{ilist})=Param.ActionInput.Patch1.(list_param{ilist}); |
---|
| 605 | end |
---|
| 606 | Data.CivStage=3;% record the new state of processing |
---|
| 607 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch1_param]; |
---|
| 608 | |
---|
| 609 | % list the variables to record |
---|
| 610 | nbvar=length(Data.ListVarName); |
---|
| 611 | Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbCentres','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}]; |
---|
| 612 | Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},'nb_subdomain_1',... |
---|
| 613 | {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}]; |
---|
| 614 | Data.VarAttribute{nbvar+1}.Role='vector_x'; |
---|
| 615 | Data.VarAttribute{nbvar+2}.Role='vector_y'; |
---|
| 616 | Data.VarAttribute{nbvar+5}.Role='coord_tps'; |
---|
| 617 | Data.VarAttribute{nbvar+6}.Role='vector_x'; |
---|
| 618 | Data.VarAttribute{nbvar+7}.Role='vector_y'; |
---|
| 619 | Data.Civ1_U_smooth=Data.Civ1_U; % zeros(size(Data.Civ1_X)); |
---|
| 620 | Data.Civ1_V_smooth=Data.Civ1_V; %zeros(size(Data.Civ1_X)); |
---|
| 621 | if isfield(Data,'Civ1_FF') |
---|
| 622 | ind_good=find(Data.Civ1_FF==0); |
---|
| 623 | else |
---|
| 624 | ind_good=1:numel(Data.Civ1_X); |
---|
| 625 | end |
---|
| 626 | |
---|
| 627 | % perform Patch calculation using the UVMAT fct 'filter_tps' |
---|
| 628 | [Data.Civ1_SubRange,Data.Civ1_NbCentres,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=... |
---|
| 629 | 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); |
---|
| 630 | Data.Civ1_U_smooth(ind_good)=Ures;% take the interpolated (smoothed) velocity values for good vectors, keep civ1 data for the other |
---|
| 631 | Data.Civ1_V_smooth(ind_good)=Vres; |
---|
| 632 | Data.Civ1_FF(ind_good)=int8(FFres); |
---|
| 633 | disp('patch1 performed') |
---|
| 634 | end |
---|
| 635 | |
---|
| 636 | %% Civ2 |
---|
| 637 | if isfield (Param.ActionInput,'Civ2') |
---|
| 638 | disp('civ2 started') |
---|
| 639 | par_civ2=Param.ActionInput.Civ2; |
---|
| 640 | if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) |
---|
| 641 | par_civ2.ImageA=[]; |
---|
| 642 | par_civ2.ImageB=[]; |
---|
| 643 | if strcmp(Param.ActionInput.ListCompareMode,'displacement') |
---|
| 644 | ImageName_A_Civ2=Param.ActionInput.RefFile; |
---|
| 645 | else |
---|
| 646 | ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_civ2,[],j1_civ2); |
---|
| 647 | end |
---|
| 648 | if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield)) |
---|
| 649 | par_civ2.ImageA=par_civ1.ImageA; |
---|
| 650 | else |
---|
| 651 | [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield)); |
---|
| 652 | end |
---|
| 653 | ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_civ2,[],j2_civ2); |
---|
| 654 | if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2) |
---|
| 655 | par_civ2.ImageB=par_civ1.ImageB; |
---|
| 656 | else |
---|
| 657 | [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield)); |
---|
| 658 | end |
---|
| 659 | par_civ2.ImageWidth=FileInfo_A.Width; |
---|
| 660 | par_civ2.ImageHeight=FileInfo_A.Height; |
---|
| 661 | if isfield(par_civ2,'Grid')% grid points set as input file |
---|
| 662 | if ischar(par_civ2.Grid)%read the grid file if the input is a file name |
---|
| 663 | par_civ2.Grid=dlmread(par_civ2.Grid); |
---|
| 664 | par_civ2.Grid(1,:)=[];%the first line must be removed (heading in the grid file) |
---|
| 665 | end |
---|
| 666 | else% automatic grid |
---|
| 667 | minix=floor(par_civ2.Dx/2)-0.5; |
---|
| 668 | maxix=minix+par_civ2.Dx*floor((par_civ2.ImageWidth-1)/par_civ2.Dx); |
---|
| 669 | miniy=floor(par_civ2.Dy/2)-0.5; |
---|
| 670 | maxiy=minix+par_civ2.Dy*floor((par_civ2.ImageHeight-1)/par_civ2.Dy); |
---|
| 671 | [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy); |
---|
| 672 | par_civ2.Grid(:,1)=reshape(GridX,[],1); |
---|
| 673 | par_civ2.Grid(:,2)=reshape(GridY,[],1); |
---|
| 674 | end |
---|
| 675 | end |
---|
| 676 | |
---|
| 677 | % get the guess from patch1 or patch2 (case 'CheckCiv3') |
---|
| 678 | if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) |
---|
| 679 | if isfield (par_civ2,'CheckCiv3') && par_civ2.CheckCiv3 %get the guess from patch2 |
---|
| 680 | SubRange= Data.Civ2_SubRange; |
---|
| 681 | NbCentres=Data.Civ2_NbCentres; |
---|
| 682 | Coord_tps=Data.Civ2_Coord_tps; |
---|
| 683 | U_tps=Data.Civ2_U_tps; |
---|
| 684 | V_tps=Data.Civ2_V_tps; |
---|
| 685 | CivStage=Data.CivStage;%store the current CivStage |
---|
| 686 | Civ1_Dt=Data.Civ2_Dt; |
---|
| 687 | Data=[];%reinitialise the result structure Data |
---|
| 688 | Data.ListGlobalAttribute={'Conventions','Program','CivStage'}; |
---|
| 689 | Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes |
---|
| 690 | Data.Program='civ_series'; |
---|
| 691 | Data.CivStage=CivStage+1;%update the current civStage after reinitialisation of Data |
---|
| 692 | Data.ListVarName={}; |
---|
| 693 | Data.VarDimName={}; |
---|
| 694 | else % get the guess from patch1 |
---|
| 695 | SubRange= Data.Civ1_SubRange; |
---|
| 696 | NbCentres=Data.Civ1_NbCentres; |
---|
| 697 | Coord_tps=Data.Civ1_Coord_tps; |
---|
| 698 | U_tps=Data.Civ1_U_tps; |
---|
| 699 | V_tps=Data.Civ1_V_tps; |
---|
| 700 | Civ1_Dt=Data.Civ1_Dt; |
---|
| 701 | Data.CivStage=4; |
---|
| 702 | end |
---|
| 703 | else |
---|
| 704 | SubRange= par_civ2.Civ1_SubRange; |
---|
| 705 | NbCentres=par_civ2.Civ1_NbCentres; |
---|
| 706 | Coord_tps=par_civ2.Civ1_Coord_tps; |
---|
| 707 | U_tps=par_civ2.Civ1_U_tps; |
---|
| 708 | V_tps=par_civ2.Civ1_V_tps; |
---|
| 709 | Civ1_Dt=par_civ2.Civ1_Dt; |
---|
| 710 | Civ2_Dt=par_civ2.Civ1_Dt; |
---|
| 711 | Data.ListVarName={}; |
---|
| 712 | Data.VarDimName={}; |
---|
| 713 | end |
---|
| 714 | Shiftx=zeros(size(par_civ2.Grid,1),1);% shift expected from civ1 data |
---|
| 715 | Shifty=zeros(size(par_civ2.Grid,1),1); |
---|
| 716 | nbval=zeros(size(par_civ2.Grid,1),1);% nbre of interpolated values at each grid point (from the different patch subdomains) |
---|
| 717 | if par_civ2.CheckDeformation |
---|
| 718 | DUDX=zeros(size(par_civ2.Grid,1),1); |
---|
| 719 | DUDY=zeros(size(par_civ2.Grid,1),1); |
---|
| 720 | DVDX=zeros(size(par_civ2.Grid,1),1); |
---|
| 721 | DVDY=zeros(size(par_civ2.Grid,1),1); |
---|
| 722 | end |
---|
| 723 | NbSubDomain=size(SubRange,3); |
---|
| 724 | for isub=1:NbSubDomain% for each sub-domain of Patch1 |
---|
| 725 | nbvec_sub=NbCentres(isub);% nbre of Civ vectors in the subdomain |
---|
| 726 | ind_sel=find(par_civ2.Grid(:,1)>=SubRange(1,1,isub) & par_civ2.Grid(:,1)<=SubRange(1,2,isub) &... |
---|
| 727 | par_civ2.Grid(:,2)>=SubRange(2,1,isub) & par_civ2.Grid(:,2)<=SubRange(2,2,isub));% grid points in the subdomain |
---|
| 728 | if ~isempty(ind_sel) |
---|
| 729 | epoints = par_civ2.Grid(ind_sel,:);% coordinates of interpolation sites (measurement grids) |
---|
| 730 | ctrs=Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs |
---|
| 731 | nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for each interpolation point (in case of subdomain overlap) |
---|
| 732 | EM = tps_eval(epoints,ctrs);% thin plate spline (tps) coefficient |
---|
| 733 | Shiftx(ind_sel)=Shiftx(ind_sel)+EM*U_tps(1:nbvec_sub+3,isub);%velocity shift estimated by tps from civ1 |
---|
| 734 | Shifty(ind_sel)=Shifty(ind_sel)+EM*V_tps(1:nbvec_sub+3,isub); |
---|
| 735 | if par_civ2.CheckDeformation |
---|
| 736 | [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs |
---|
| 737 | DUDX(ind_sel)=DUDX(ind_sel)+EMDX*U_tps(1:nbvec_sub+3,isub); |
---|
| 738 | DUDY(ind_sel)=DUDY(ind_sel)+EMDY*U_tps(1:nbvec_sub+3,isub); |
---|
| 739 | DVDX(ind_sel)=DVDX(ind_sel)+EMDX*V_tps(1:nbvec_sub+3,isub); |
---|
| 740 | DVDY(ind_sel)=DVDY(ind_sel)+EMDY*V_tps(1:nbvec_sub+3,isub); |
---|
| 741 | end |
---|
| 742 | end |
---|
| 743 | end |
---|
| 744 | if par_civ2.CheckMask&&~isempty(par_civ2.Mask) |
---|
| 745 | if isfield(par_civ2,'NbSlice') |
---|
| 746 | [RootPath_mask,SubDir_mask,RootFile_mask,i1_mask,i2_mask,j1_mask,j2_mask,Ext_mask]=fileparts_uvmat(Param.ActionInput.Civ2.Mask); |
---|
| 747 | i1_mask=mod(i1-1,par_civ2.NbSlice)+1; |
---|
| 748 | maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',i1_mask); |
---|
| 749 | else |
---|
| 750 | maskname=Param.ActionInput.Civ2.Mask; |
---|
| 751 | end |
---|
| 752 | if strcmp(maskoldname,maskname)% mask exist, not already read in civ1 |
---|
| 753 | par_civ2.Mask=mask; %use mask already opened |
---|
| 754 | else |
---|
| 755 | if exist(maskname,'file') |
---|
| 756 | try |
---|
| 757 | par_civ2.Mask=imread(maskname);%update the mask, an store it for future use |
---|
| 758 | catch ME |
---|
| 759 | if ~isempty(ME.message) |
---|
| 760 | errormsg=['error reading input image: ' ME.message]; |
---|
| 761 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
| 762 | return |
---|
| 763 | end |
---|
| 764 | end |
---|
| 765 | else |
---|
| 766 | par_civ2.Mask=[]; |
---|
| 767 | end |
---|
| 768 | mask=par_civ2.Mask; |
---|
| 769 | maskoldname=maskname; |
---|
| 770 | end |
---|
| 771 | end |
---|
| 772 | |
---|
| 773 | if CheckInputFile % else Dt given by par_civ2 |
---|
| 774 | if strcmp(Param.ActionInput.ListCompareMode,'displacement') |
---|
| 775 | Civ1_Dt=1; |
---|
| 776 | Civ2_Dt=1; |
---|
| 777 | else |
---|
| 778 | Civ2_Dt=Time(i2_civ2+1,j2_civ2+1)-Time(i1_civ2+1,j1_civ2+1); |
---|
| 779 | end |
---|
| 780 | end |
---|
| 781 | par_civ2.SearchBoxShift=(Civ2_Dt/Civ1_Dt)*[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)]; |
---|
| 782 | % shift the grid points by half the expected shift to provide the correlation box position in image A |
---|
| 783 | 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]; |
---|
| 784 | if par_civ2.CheckDeformation |
---|
| 785 | par_civ2.DUDX=DUDX(nbval>=1)./nbval(nbval>=1); |
---|
| 786 | par_civ2.DUDY=DUDY(nbval>=1)./nbval(nbval>=1); |
---|
| 787 | par_civ2.DVDX=DVDX(nbval>=1)./nbval(nbval>=1); |
---|
| 788 | par_civ2.DVDY=DVDY(nbval>=1)./nbval(nbval>=1); |
---|
| 789 | end |
---|
| 790 | |
---|
| 791 | % calculate velocity data (y and v in image indices, reverse to y component) |
---|
| 792 | [xtable, ytable, utable, vtable, ctable, F,result_conv,errormsg] = civ (par_civ2); |
---|
| 793 | |
---|
| 794 | list_param=(fieldnames(Param.ActionInput.Civ2))'; |
---|
| 795 | list_param(strcmp('TestCiv2',list_param))=[];% remove the parameter TestCiv2 from the list |
---|
| 796 | Civ2_param=regexprep(list_param,'^.+','Civ2_$0');% insert 'Civ2_' before each string in list_param |
---|
| 797 | Civ2_param=[{'Civ2_ImageA','Civ2_ImageB','Civ2_Time','Civ2_Dt'} Civ2_param]; %insert the names of the two input images |
---|
| 798 | %indicate the values of all the global attributes in the output data |
---|
| 799 | if exist('ImageName_A','var') |
---|
| 800 | Data.Civ2_ImageA=ImageName_A; |
---|
| 801 | Data.Civ2_ImageB=ImageName_B; |
---|
| 802 | if strcmp(Param.ActionInput.ListCompareMode,'displacement') |
---|
| 803 | Data.Civ2_Time=Time(i2_civ2+1,j2_civ2+1);% the Time is the Time of the secodn image |
---|
| 804 | Data.Civ2_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading |
---|
| 805 | else |
---|
| 806 | Data.Civ2_Time=(Time(i2_civ2+1,j2_civ2+1)+Time(i1_civ2+1,j1_civ2+1))/2; |
---|
| 807 | Data.Civ2_Dt=Civ2_Dt; |
---|
| 808 | end |
---|
| 809 | end |
---|
| 810 | for ilist=1:length(list_param) |
---|
| 811 | Data.(Civ2_param{4+ilist})=Param.ActionInput.Civ2.(list_param{ilist}); |
---|
| 812 | end |
---|
| 813 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param]; |
---|
| 814 | |
---|
| 815 | nbvar=numel(Data.ListVarName); |
---|
| 816 | % define the Civ2 variable (if Civ2 data are not replaced from previous calculation) |
---|
| 817 | if isempty(find(strcmp('Civ2_X',Data.ListVarName),1)) |
---|
| 818 | 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 |
---|
| 819 | Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}]; |
---|
| 820 | Data.VarAttribute{nbvar+1}.Role='coord_x'; |
---|
| 821 | Data.VarAttribute{nbvar+2}.Role='coord_y'; |
---|
| 822 | Data.VarAttribute{nbvar+3}.Role='vector_x'; |
---|
| 823 | Data.VarAttribute{nbvar+4}.Role='vector_y'; |
---|
| 824 | Data.VarAttribute{nbvar+5}.Role='warnflag'; |
---|
| 825 | end |
---|
| 826 | Data.Civ2_X=reshape(xtable,[],1); |
---|
| 827 | Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1); |
---|
| 828 | Data.Civ2_U=reshape(utable,[],1); |
---|
| 829 | Data.Civ2_V=reshape(-vtable,[],1); |
---|
| 830 | Data.Civ2_C=reshape(ctable,[],1); |
---|
| 831 | Data.Civ2_F=reshape(F,[],1); |
---|
| 832 | disp('civ2 performed') |
---|
| 833 | elseif ~isfield(Data,'ListVarName') % we start there, using existing Civ2 data |
---|
| 834 | if exist('ncfile','var') |
---|
| 835 | CivFile=ncfile; |
---|
| 836 | [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file |
---|
| 837 | if ~isempty(errormsg) |
---|
| 838 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
| 839 | return |
---|
| 840 | end |
---|
| 841 | elseif isfield(Param,'Civ2_X')% use Civ2 data as input in Param (test mode) |
---|
| 842 | Data.ListGlobalAttribute={}; |
---|
| 843 | Data.ListVarName={}; |
---|
| 844 | Data.VarDimName={}; |
---|
| 845 | Data.Civ2_X=Param.Civ2_X; |
---|
| 846 | Data.Civ2_Y=Param.Civ2_Y; |
---|
| 847 | Data.Civ2_U=Param.Civ2_U; |
---|
| 848 | Data.Civ2_V=Param.Civ2_V; |
---|
| 849 | Data.Civ2_FF=Param.Civ2_FF; |
---|
| 850 | end |
---|
| 851 | end |
---|
| 852 | |
---|
| 853 | %% Fix2 |
---|
| 854 | if isfield (Param.ActionInput,'Fix2') |
---|
| 855 | disp('fix2 started') |
---|
| 856 | list_param=fieldnames(Param.ActionInput.Fix2)'; |
---|
| 857 | Fix2_param=regexprep(list_param,'^.+','Fix2_$0');% insert 'Fix1_' before each string in ListFixParam |
---|
| 858 | %indicate the values of all the global attributes in the output data |
---|
| 859 | for ilist=1:length(list_param) |
---|
| 860 | Data.(Fix2_param{ilist})=Param.ActionInput.Fix2.(list_param{ilist}); |
---|
| 861 | end |
---|
| 862 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix2_param]; |
---|
| 863 | % |
---|
| 864 | % ListFixParam=fieldnames(Param.ActionInput.Fix2); |
---|
| 865 | % for ilist=1:length(ListFixParam) |
---|
| 866 | % ParamName=ListFixParam{ilist}; |
---|
| 867 | % ListName=['Fix2_' ParamName]; |
---|
| 868 | % eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];']) |
---|
| 869 | % eval(['Data.' ListName '=Param.ActionInput.Fix2.' ParamName ';']) |
---|
| 870 | % end |
---|
| 871 | if check_civx |
---|
| 872 | if ~isfield(Data,'fix2') |
---|
| 873 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix2']; |
---|
| 874 | Data.fix2=1; |
---|
| 875 | Data.ListVarName=[Data.ListVarName {'vec2_FixFlag'}]; |
---|
| 876 | Data.VarDimName=[Data.VarDimName {'nb_vectors2'}]; |
---|
| 877 | end |
---|
| 878 | Data.vec_FixFlag=fix(Param.Fix2,Data.vec2_F,Data.vec2_C,Data.vec2_U,Data.vec2_V,Data.vec2_X,Data.vec2_Y); |
---|
| 879 | else |
---|
| 880 | Data.ListVarName=[Data.ListVarName {'Civ2_FF'}]; |
---|
| 881 | Data.VarDimName=[Data.VarDimName {'nb_vec_2'}]; |
---|
| 882 | nbvar=length(Data.ListVarName); |
---|
| 883 | Data.VarAttribute{nbvar}.Role='errorflag'; |
---|
| 884 | Data.Civ2_FF=double(fix(Param.ActionInput.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V)); |
---|
| 885 | Data.CivStage=Data.CivStage+1; |
---|
| 886 | end |
---|
| 887 | end |
---|
| 888 | |
---|
| 889 | %% Patch2 |
---|
| 890 | if isfield (Param.ActionInput,'Patch2') |
---|
| 891 | disp('patch2 started') |
---|
| 892 | list_param=fieldnames(Param.ActionInput.Patch2)'; |
---|
| 893 | list_param(strcmp('TestPatch2',list_param))=[];% remove the parameter TestCiv1 from the list |
---|
| 894 | Patch2_param=regexprep(list_param,'^.+','Patch2_$0');% insert 'Fix1_' before each string in ListFixParam |
---|
| 895 | %indicate the values of all the global attributes in the output data |
---|
| 896 | for ilist=1:length(list_param) |
---|
| 897 | Data.(Patch2_param{ilist})=Param.ActionInput.Patch2.(list_param{ilist}); |
---|
| 898 | end |
---|
| 899 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch2_param]; |
---|
| 900 | |
---|
| 901 | nbvar=length(Data.ListVarName); |
---|
| 902 | Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbCentres','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}]; |
---|
| 903 | Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},... |
---|
| 904 | {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}]; |
---|
| 905 | |
---|
| 906 | Data.VarAttribute{nbvar+1}.Role='vector_x'; |
---|
| 907 | Data.VarAttribute{nbvar+2}.Role='vector_y'; |
---|
| 908 | Data.VarAttribute{nbvar+5}.Role='coord_tps'; |
---|
| 909 | Data.VarAttribute{nbvar+6}.Role='vector_x'; |
---|
| 910 | Data.VarAttribute{nbvar+7}.Role='vector_y'; |
---|
| 911 | Data.Civ2_U_smooth=Data.Civ2_U; |
---|
| 912 | Data.Civ2_V_smooth=Data.Civ2_V; |
---|
| 913 | if isfield(Data,'Civ2_FF') |
---|
| 914 | ind_good=find(Data.Civ2_FF==0); |
---|
| 915 | else |
---|
| 916 | ind_good=1:numel(Data.Civ2_X); |
---|
| 917 | end |
---|
| 918 | [Data.Civ2_SubRange,Data.Civ2_NbCentres,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures,Vres,tild,FFres]=... |
---|
| 919 | 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); |
---|
| 920 | Data.Civ2_U_smooth(ind_good)=Ures; |
---|
| 921 | Data.Civ2_V_smooth(ind_good)=Vres; |
---|
| 922 | Data.Civ2_FF(ind_good)=FFres; |
---|
| 923 | Data.CivStage=Data.CivStage+1; |
---|
| 924 | disp('patch2 performed') |
---|
| 925 | end |
---|
| 926 | |
---|
| 927 | %% write result in a netcdf file if requested |
---|
| 928 | if CheckOutputFile |
---|
| 929 | errormsg=struct2nc(ncfile_out,Data); |
---|
| 930 | if isempty(errormsg) |
---|
| 931 | disp([ncfile_out ' written']) |
---|
| 932 | %[success,msg] = fileattrib(ncfile_out ,'+w','g');% done in struct2nc |
---|
| 933 | else |
---|
| 934 | disp(errormsg) |
---|
| 935 | end |
---|
| 936 | disp(['ellapsed time ' num2str(toc/60,2) ' minutes']) |
---|
| 937 | end |
---|
| 938 | end |
---|
| 939 | |
---|
| 940 | |
---|
| 941 | % 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/ |
---|
| 942 | %-------------------------------------------------------------------------- |
---|
| 943 | % function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi) |
---|
| 944 | % |
---|
| 945 | % OUTPUT: |
---|
| 946 | % xtable: set of x coordinates |
---|
| 947 | % ytable: set of y coordiantes |
---|
| 948 | % utable: set of u displacements (along x) |
---|
| 949 | % vtable: set of v displacements (along y) |
---|
| 950 | % ctable: max image correlation for each vector |
---|
| 951 | % typevector: set of flags, =1 for good, =0 for NaN vectors |
---|
| 952 | % |
---|
| 953 | %INPUT: |
---|
| 954 | % par_civ: structure of input parameters, with fields: |
---|
| 955 | % .ImageA: first image for correlation (matrix) |
---|
| 956 | % .ImageB: second image for correlation(matrix) |
---|
| 957 | % .CorrBoxSize: 1,2 vector giving the size of the correlation box in x and y |
---|
| 958 | % .SearchBoxSize: 1,2 vector giving the size of the search box in x and y |
---|
| 959 | % .SearchBoxShift: 1,2 vector or 2 column matrix (for civ2) giving the shift of the search box in x and y |
---|
| 960 | % .CorrSmooth: =1 or 2 determines the choice of the sub-pixel determination of the correlation max |
---|
| 961 | % .ImageWidth: nb of pixels of the image in x |
---|
| 962 | % .Dx, Dy: mesh for the PIV calculation |
---|
| 963 | % .Grid: grid giving the PIV calculation points (alternative to .Dx .Dy): centres of the correlation boxes in Image A |
---|
| 964 | % .Mask: name of a mask file or mask image matrix itself |
---|
| 965 | % .MinIma: thresholds for image luminosity |
---|
| 966 | % .MaxIma |
---|
| 967 | % .CheckDeformation=1 for subpixel interpolation and image deformation (linear transform) |
---|
| 968 | % .DUDX: matrix of deformation obtained from patch at each grid point |
---|
| 969 | % .DUDY |
---|
| 970 | % .DVDX: |
---|
| 971 | % .DVDY |
---|
| 972 | |
---|
| 973 | function [xtable,ytable,utable,vtable,ctable,F,result_conv,errormsg] = civ (par_civ) |
---|
| 974 | |
---|
| 975 | %% prepare measurement grid |
---|
| 976 | if isfield(par_civ,'Grid')% grid points set as input, central positions of the sub-images in image A |
---|
| 977 | if ischar(par_civ.Grid)%read the grid file if the input is a file name (grid in x, y image coordinates) |
---|
| 978 | par_civ.Grid=dlmread(par_civ.Grid); |
---|
| 979 | par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file) |
---|
| 980 | end |
---|
| 981 | % else par_civ.Grid is already an array, no action here |
---|
| 982 | else% automatic grid in x, y image coordinates |
---|
| 983 | minix=floor(par_civ.Dx/2)-0.5; |
---|
| 984 | maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx); |
---|
| 985 | miniy=floor(par_civ.Dy/2)-0.5;% first automatic grid point at half the mesh Dy |
---|
| 986 | maxiy=minix+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy); |
---|
| 987 | [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy); |
---|
| 988 | par_civ.Grid(:,1)=reshape(GridX,[],1); |
---|
| 989 | par_civ.Grid(:,2)=reshape(GridY,[],1);% increases with array index |
---|
| 990 | end |
---|
| 991 | nbvec=size(par_civ.Grid,1); |
---|
| 992 | |
---|
| 993 | %% prepare correlation and search boxes |
---|
| 994 | ibx2=floor(par_civ.CorrBoxSize(1)/2); |
---|
| 995 | iby2=floor(par_civ.CorrBoxSize(2)/2); |
---|
| 996 | isx2=floor(par_civ.SearchBoxSize(1)/2); |
---|
| 997 | isy2=floor(par_civ.SearchBoxSize(2)/2); |
---|
| 998 | shiftx=round(par_civ.SearchBoxShift(:,1));%use the input shift estimate, rounded to the next integer value |
---|
| 999 | shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases |
---|
| 1000 | if numel(shiftx)==1% case of a unique shift for the whole field( civ1) |
---|
| 1001 | shiftx=shiftx*ones(nbvec,1); |
---|
| 1002 | shifty=shifty*ones(nbvec,1); |
---|
| 1003 | end |
---|
| 1004 | |
---|
| 1005 | %% Array initialisation and default output if par_civ.CorrSmooth=0 (just the grid calculated, no civ computation) |
---|
| 1006 | xtable=round(par_civ.Grid(:,1)+0.5)-0.5; |
---|
| 1007 | ytable=round(par_civ.ImageHeight-par_civ.Grid(:,2)+0.5)-0.5;% y index corresponding to the position in image coordiantes |
---|
| 1008 | utable=shiftx;%zeros(nbvec,1); |
---|
| 1009 | vtable=shifty;%zeros(nbvec,1); |
---|
| 1010 | ctable=zeros(nbvec,1); |
---|
| 1011 | F=zeros(nbvec,1); |
---|
| 1012 | result_conv=[]; |
---|
| 1013 | errormsg=''; |
---|
| 1014 | |
---|
| 1015 | %% prepare mask |
---|
| 1016 | if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) |
---|
| 1017 | if strcmp(par_civ.Mask,'all') |
---|
| 1018 | return % get the grid only, no civ calculation |
---|
| 1019 | elseif ischar(par_civ.Mask) |
---|
| 1020 | par_civ.Mask=imread(par_civ.Mask);% read the mask if not allready done |
---|
| 1021 | end |
---|
| 1022 | end |
---|
| 1023 | check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold |
---|
| 1024 | check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma); |
---|
| 1025 | |
---|
| 1026 | par_civ.ImageA=sum(double(par_civ.ImageA),3);%sum over rgb component for color images |
---|
| 1027 | par_civ.ImageB=sum(double(par_civ.ImageB),3); |
---|
| 1028 | [npy_ima npx_ima]=size(par_civ.ImageA); |
---|
| 1029 | if ~isequal(size(par_civ.ImageB),[npy_ima npx_ima]) |
---|
| 1030 | errormsg='image pair with unequal size'; |
---|
| 1031 | return |
---|
| 1032 | end |
---|
| 1033 | |
---|
| 1034 | %% Apply mask |
---|
| 1035 | % Convention for mask IDEAS TO IMPLEMENT ? |
---|
| 1036 | % mask >200 : velocity calculated |
---|
| 1037 | % 200 >=mask>150;velocity not calculated, interpolation allowed (bad spots) |
---|
| 1038 | % 150>=mask >100: velocity not calculated, nor interpolated |
---|
| 1039 | % 100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries) |
---|
| 1040 | % 20>=mask: velocity=0 |
---|
| 1041 | checkmask=0; |
---|
| 1042 | MinA=min(min(par_civ.ImageA)); |
---|
| 1043 | %MinB=min(min(par_civ.ImageB)); |
---|
| 1044 | %check_undefined=false(size(par_civ.ImageA)); |
---|
| 1045 | if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) |
---|
| 1046 | checkmask=1; |
---|
| 1047 | if ~isequal(size(par_civ.Mask),[npy_ima npx_ima]) |
---|
| 1048 | errormsg='mask must be an image with the same size as the images'; |
---|
| 1049 | return |
---|
| 1050 | end |
---|
| 1051 | check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 ); |
---|
| 1052 | % par_civ.ImageA(check_undefined)=0;% put image A to zero (i.e. the min image value) in the undefined area |
---|
| 1053 | % par_civ.ImageB(check_undefined)=0;% put image B to zero (i.e. the min image value) in the undefined area |
---|
| 1054 | end |
---|
| 1055 | |
---|
| 1056 | %% compute image correlations: MAINLOOP on velocity vectors |
---|
| 1057 | corrmax=0; |
---|
| 1058 | sum_square=1;% default |
---|
| 1059 | mesh=1;% default |
---|
| 1060 | CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1; |
---|
| 1061 | if CheckDeformation |
---|
| 1062 | mesh=0.25;%mesh in pixels for subpixel image interpolation (x 4 in each direction) |
---|
| 1063 | par_civ.CorrSmooth=2;% use SUBPIX2DGAUSS (take into account more points near the max) |
---|
| 1064 | end |
---|
| 1065 | |
---|
| 1066 | if par_civ.CorrSmooth~=0 % par_civ.CorrSmooth=0 implies no civ computation (just input image and grid points given) |
---|
| 1067 | for ivec=1:nbvec |
---|
| 1068 | iref=round(par_civ.Grid(ivec,1)+0.5);% xindex on the image A for the middle of the correlation box |
---|
| 1069 | 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 |
---|
| 1070 | F(ivec)=0; |
---|
| 1071 | subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage |
---|
| 1072 | subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage |
---|
| 1073 | subrange2_x=iref+shiftx(ivec)-isx2:iref+shiftx(ivec)+isx2;%x indices defining the second subimage |
---|
| 1074 | subrange2_y=jref+shifty(ivec)-isy2:jref+shifty(ivec)+isy2;%y indices defining the second subimage |
---|
| 1075 | image1_crop=MinA*ones(numel(subrange1_y),numel(subrange1_x));% default value=min of image A |
---|
| 1076 | image2_crop=MinA*ones(numel(subrange2_y),numel(subrange2_x));% default value=min of image A |
---|
| 1077 | check1_x=subrange1_x>=1 & subrange1_x<=par_civ.ImageWidth;% check which points in the subimage 1 are contained in the initial image 1 |
---|
| 1078 | check1_y=subrange1_y>=1 & subrange1_y<=par_civ.ImageHeight; |
---|
| 1079 | check2_x=subrange2_x>=1 & subrange2_x<=par_civ.ImageWidth;% check which points in the subimage 2 are contained in the initial image 2 |
---|
| 1080 | check2_y=subrange2_y>=1 & subrange2_y<=par_civ.ImageHeight; |
---|
| 1081 | 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 |
---|
| 1082 | 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 |
---|
| 1083 | if checkmask |
---|
| 1084 | mask1_crop=ones(numel(subrange1_y),numel(subrange1_x));% default value=1 for mask |
---|
| 1085 | mask2_crop=ones(numel(subrange2_y),numel(subrange2_x));% default value=1 for mask |
---|
| 1086 | 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 |
---|
| 1087 | 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 |
---|
| 1088 | sizemask=sum(sum(mask1_crop))/(numel(subrange1_y)*numel(subrange1_x));%size of the masked part relative to the correlation sub-image |
---|
| 1089 | if sizemask > 1/2% eliminate point if more than half of the correlation box is masked |
---|
| 1090 | F(ivec)=3; % |
---|
| 1091 | utable(ivec)=0; |
---|
| 1092 | vtable(ivec)=0; |
---|
| 1093 | else |
---|
| 1094 | image1_crop=image1_crop.*~mask1_crop;% put to zero the masked pixels (mask1_crop='true'=1) |
---|
| 1095 | image2_crop=image2_crop.*~mask2_crop; |
---|
| 1096 | image1_mean=mean(mean(image1_crop))/(1-sizemask); |
---|
| 1097 | image2_mean=mean(mean(image2_crop))/(1-sizemask); |
---|
| 1098 | end |
---|
| 1099 | else |
---|
| 1100 | image1_mean=mean(mean(image1_crop)); |
---|
| 1101 | image2_mean=mean(mean(image2_crop)); |
---|
| 1102 | end |
---|
| 1103 | %threshold on image minimum |
---|
| 1104 | if F(ivec)~=3 |
---|
| 1105 | if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma) |
---|
| 1106 | F(ivec)=3; |
---|
| 1107 | %threshold on image maximum |
---|
| 1108 | elseif check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma) |
---|
| 1109 | F(ivec)=3; |
---|
| 1110 | end |
---|
| 1111 | if F(ivec)==3 |
---|
| 1112 | utable(ivec)=0; |
---|
| 1113 | vtable(ivec)=0; |
---|
| 1114 | else |
---|
| 1115 | %mask |
---|
| 1116 | if checkmask |
---|
| 1117 | image1_crop=(image1_crop-image1_mean).*~mask1_crop;%substract the mean, put to zero the masked parts |
---|
| 1118 | image2_crop=(image2_crop-image2_mean).*~mask2_crop; |
---|
| 1119 | else |
---|
| 1120 | image1_crop=(image1_crop-image1_mean); |
---|
| 1121 | image2_crop=(image2_crop-image2_mean); |
---|
| 1122 | end |
---|
| 1123 | %deformation |
---|
| 1124 | if CheckDeformation |
---|
| 1125 | xi=(1:mesh:size(image1_crop,2)); |
---|
| 1126 | yi=(1:mesh:size(image1_crop,1))'; |
---|
| 1127 | [XI,YI]=meshgrid(xi-ceil(size(image1_crop,2)/2),yi-ceil(size(image1_crop,1)/2)); |
---|
| 1128 | XIant=XI-par_civ.DUDX(ivec)*XI+par_civ.DUDY(ivec)*YI+ceil(size(image1_crop,2)/2); |
---|
| 1129 | YIant=YI+par_civ.DVDX(ivec)*XI-par_civ.DVDY(ivec)*YI+ceil(size(image1_crop,1)/2); |
---|
| 1130 | image1_crop=interp2(image1_crop,XIant,YIant); |
---|
| 1131 | image1_crop(isnan(image1_crop))=0; |
---|
| 1132 | xi=(1:mesh:size(image2_crop,2)); |
---|
| 1133 | yi=(1:mesh:size(image2_crop,1))'; |
---|
| 1134 | image2_crop=interp2(image2_crop,xi,yi,'*spline'); |
---|
| 1135 | image2_crop(isnan(image2_crop))=0; |
---|
| 1136 | end |
---|
| 1137 | sum_square=sum(sum(image1_crop.*image1_crop)); |
---|
| 1138 | %reference: Oliver Pust, PIV: Direct Cross-Correlation |
---|
| 1139 | result_conv= conv2(image2_crop,flipdim(flipdim(image1_crop,2),1),'valid'); |
---|
| 1140 | corrmax= max(max(result_conv)); |
---|
| 1141 | result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255 |
---|
| 1142 | %Find the correlation max, at 255 |
---|
| 1143 | [y,x] = find(result_conv==255,1); |
---|
| 1144 | 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 |
---|
| 1145 | sum_square=sum_square*sum(sum(subimage2_crop.*subimage2_crop));% product of variances of image 1 and 2 |
---|
| 1146 | sum_square=sqrt(sum_square);% srt of the variance product to normalise correlation |
---|
| 1147 | if ~isempty(y) && ~isempty(x) |
---|
| 1148 | try |
---|
| 1149 | if par_civ.CorrSmooth==1 |
---|
| 1150 | [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y); |
---|
| 1151 | elseif par_civ.CorrSmooth==2 |
---|
| 1152 | [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y); |
---|
| 1153 | else |
---|
| 1154 | [vector,F(ivec)] = quadr_fit(result_conv,x,y); |
---|
| 1155 | end |
---|
| 1156 | utable(ivec)=vector(1)*mesh+shiftx(ivec); |
---|
| 1157 | vtable(ivec)=vector(2)*mesh+shifty(ivec); |
---|
| 1158 | xtable(ivec)=iref+utable(ivec)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2) |
---|
| 1159 | ytable(ivec)=jref+vtable(ivec)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge) |
---|
| 1160 | iref=round(xtable(ivec)+0.5);% nearest image index for the middle of the vector |
---|
| 1161 | jref=round(ytable(ivec)+0.5); |
---|
| 1162 | % eliminate vectors located in the mask |
---|
| 1163 | if checkmask && (iref<1 || jref<1 ||iref>npx_ima || jref>npy_ima ||( par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100)) |
---|
| 1164 | utable(ivec)=0; |
---|
| 1165 | vtable(ivec)=0; |
---|
| 1166 | F(ivec)=3; |
---|
| 1167 | end |
---|
| 1168 | ctable(ivec)=corrmax/sum_square;% correlation value |
---|
| 1169 | catch ME |
---|
| 1170 | F(ivec)=3; |
---|
| 1171 | disp(ME.message) |
---|
| 1172 | end |
---|
| 1173 | else |
---|
| 1174 | F(ivec)=3; |
---|
| 1175 | end |
---|
| 1176 | end |
---|
| 1177 | end |
---|
| 1178 | end |
---|
| 1179 | end |
---|
| 1180 | result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output |
---|
| 1181 | |
---|
| 1182 | %------------------------------------------------------------------------ |
---|
| 1183 | % --- Find the maximum of the correlation function after interpolation |
---|
| 1184 | % OUPUT: |
---|
| 1185 | % vector = optimum displacement vector with subpixel correction |
---|
| 1186 | % F =flag: =0 OK |
---|
| 1187 | % =-2 , warning: max too close to the edge of the search box (1 pixel margin) |
---|
| 1188 | % INPUT: |
---|
| 1189 | % x,y: position of the maximum correlation at integer values |
---|
| 1190 | |
---|
| 1191 | function [vector,F] = SUBPIXGAUSS (result_conv,x,y) |
---|
| 1192 | %------------------------------------------------------------------------ |
---|
| 1193 | % vector=[0 0]; %default |
---|
| 1194 | F=0; |
---|
| 1195 | [npy,npx]=size(result_conv); |
---|
| 1196 | result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (=0 by discretisation, to avoid divergence in the log) |
---|
| 1197 | %the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ??? Israel Institute of Technology |
---|
| 1198 | %http://urapiv.wordpress.com |
---|
| 1199 | peaky = y; |
---|
| 1200 | if y < npy && y > 1 |
---|
| 1201 | f0 = log(result_conv(y,x)); |
---|
| 1202 | f1 = log(result_conv(y-1,x)); |
---|
| 1203 | f2 = log(result_conv(y+1,x)); |
---|
| 1204 | peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2); |
---|
| 1205 | else |
---|
| 1206 | F=-2; % warning flag for vector truncated by the limited search box |
---|
| 1207 | end |
---|
| 1208 | peakx=x; |
---|
| 1209 | if x < npx-1 && x > 1 |
---|
| 1210 | f0 = log(result_conv(y,x)); |
---|
| 1211 | f1 = log(result_conv(y,x-1)); |
---|
| 1212 | f2 = log(result_conv(y,x+1)); |
---|
| 1213 | peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2); |
---|
| 1214 | else |
---|
| 1215 | F=-2; % warning flag for vector truncated by the limited search box |
---|
| 1216 | end |
---|
| 1217 | vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; |
---|
| 1218 | |
---|
| 1219 | %------------------------------------------------------------------------ |
---|
| 1220 | % --- Find the maximum of the correlation function after interpolation |
---|
| 1221 | function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y) |
---|
| 1222 | %------------------------------------------------------------------------ |
---|
| 1223 | % vector=[0 0]; %default |
---|
| 1224 | F=-2; |
---|
| 1225 | peaky=y; |
---|
| 1226 | peakx=x; |
---|
| 1227 | result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log) |
---|
| 1228 | [npy,npx]=size(result_conv); |
---|
| 1229 | if (x < npx) && (y < npy) && (x > 1) && (y > 1) |
---|
| 1230 | F=0; |
---|
| 1231 | for i=-1:1 |
---|
| 1232 | for j=-1:1 |
---|
| 1233 | %following 15 lines based on |
---|
| 1234 | %H. Nobach ??? M. Honkanen (2005) |
---|
| 1235 | %Two-dimensional Gaussian regression for sub-pixel displacement |
---|
| 1236 | %estimation in particle image velocimetry or particle position |
---|
| 1237 | %estimation in particle tracking velocimetry |
---|
| 1238 | %Experiments in Fluids (2005) 38: 511???515 |
---|
| 1239 | c10(j+2,i+2)=i*log(result_conv(y+j, x+i)); |
---|
| 1240 | c01(j+2,i+2)=j*log(result_conv(y+j, x+i)); |
---|
| 1241 | c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i)); |
---|
| 1242 | c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i)); |
---|
| 1243 | c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i)); |
---|
| 1244 | end |
---|
| 1245 | end |
---|
| 1246 | c10=(1/6)*sum(sum(c10)); |
---|
| 1247 | c01=(1/6)*sum(sum(c01)); |
---|
| 1248 | c11=(1/4)*sum(sum(c11)); |
---|
| 1249 | c20=(1/6)*sum(sum(c20)); |
---|
| 1250 | c02=(1/6)*sum(sum(c02)); |
---|
| 1251 | deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2); |
---|
| 1252 | deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2); |
---|
| 1253 | if abs(deltax)<1 |
---|
| 1254 | peakx=x+deltax; |
---|
| 1255 | end |
---|
| 1256 | if abs(deltay)<1 |
---|
| 1257 | peaky=y+deltay; |
---|
| 1258 | end |
---|
| 1259 | end |
---|
| 1260 | vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; |
---|
| 1261 | |
---|
| 1262 | %------------------------------------------------------------------------ |
---|
| 1263 | % --- Find the maximum of the correlation function after quadratic interpolation |
---|
| 1264 | function [vector,F] = quadr_fit(result_conv,x,y) |
---|
| 1265 | [npy,npx]=size(result_conv); |
---|
| 1266 | if x<4 || y<4 || npx-x<4 ||npy-y <4 |
---|
| 1267 | F=-2; |
---|
| 1268 | vector=[x y]; |
---|
| 1269 | else |
---|
| 1270 | F=0; |
---|
| 1271 | x_ind=x-4:x+4; |
---|
| 1272 | y_ind=y-4:y+4; |
---|
| 1273 | x_vec=0.25*(x_ind-x); |
---|
| 1274 | y_vec=0.25*(y_ind-y); |
---|
| 1275 | [X,Y]=meshgrid(x_vec,y_vec); |
---|
| 1276 | coord=[reshape(X,[],1) reshape(Y,[],1)]; |
---|
| 1277 | result_conv=reshape(result_conv(y_ind,x_ind),[],1); |
---|
| 1278 | |
---|
| 1279 | |
---|
| 1280 | % n=numel(X); |
---|
| 1281 | % x=[X Y]; |
---|
| 1282 | % X=X-0.5; |
---|
| 1283 | % Y=Y+0.5; |
---|
| 1284 | % y = (X.*X+2*Y.*Y+X.*Y+6) + 0.1*rand(n,1); |
---|
| 1285 | p = polyfitn(coord,result_conv,2); |
---|
| 1286 | A(1,1)=2*p.Coefficients(1); |
---|
| 1287 | A(1,2)=p.Coefficients(2); |
---|
| 1288 | A(2,1)=p.Coefficients(2); |
---|
| 1289 | A(2,2)=2*p.Coefficients(4); |
---|
| 1290 | vector=[x y]'-A\[p.Coefficients(3) p.Coefficients(5)]'; |
---|
| 1291 | vector=vector'-[floor(npx/2) floor(npy/2)]-1 ; |
---|
| 1292 | % zg = polyvaln(p,coord); |
---|
| 1293 | % figure |
---|
| 1294 | % surf(x_vec,y_vec,reshape(zg,9,9)) |
---|
| 1295 | % hold on |
---|
| 1296 | % plot3(X,Y,reshape(result_conv,9,9),'o') |
---|
| 1297 | % hold off |
---|
| 1298 | end |
---|
| 1299 | |
---|
| 1300 | %'RUN_FIX': function for fixing velocity fields: |
---|
| 1301 | %----------------------------------------------- |
---|
| 1302 | % RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref) |
---|
| 1303 | % |
---|
| 1304 | %filename: name of the netcdf file (used as input and output) |
---|
| 1305 | %field: structure specifying the names of the fields to fix (depending on civ1 or civ2) |
---|
| 1306 | %.vel_type='civ1' or 'civ2'; |
---|
| 1307 | %.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1); |
---|
| 1308 | %.fixflag=name of fix flag variable ('vec_FixFlag' for civ1) |
---|
| 1309 | %flagindex: flag specifying which values of vec_f are removed: |
---|
| 1310 | % if flagindex(1)=1: vec_f=-2 vectors are removed |
---|
| 1311 | % if flagindex(2)=1: vec_f=3 vectors are removed |
---|
| 1312 | % if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2) |
---|
| 1313 | %iter=1 for civ1 fields and iter=2 for civ2 fields |
---|
| 1314 | %thresh_vecC: threshold in the image correlation vec_C |
---|
| 1315 | %flag_mask: =1 mask used to remove vectors (0 else) |
---|
| 1316 | %maskname: name of the mask image file for fix |
---|
| 1317 | %thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists |
---|
| 1318 | %inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold |
---|
| 1319 | %fileref: .nc file name for a reference velocity (='': refrence 0 used) |
---|
| 1320 | %fieldref: 'civ1','filter1'...feld used in fileref |
---|
| 1321 | |
---|
| 1322 | function FF=fix(Param,F,C,U,V,X,Y) |
---|
| 1323 | FF=zeros(size(F));%default |
---|
| 1324 | |
---|
| 1325 | %criterium on warn flags |
---|
| 1326 | FlagName={'CheckFmin2','CheckF2','CheckF3','CheckF4'}; |
---|
| 1327 | FlagVal=[-2 2 3 4]; |
---|
| 1328 | for iflag=1:numel(FlagName) |
---|
| 1329 | if isfield(Param,FlagName{iflag}) && Param.(FlagName{iflag}) |
---|
| 1330 | FF=(FF==1| F==FlagVal(iflag)); |
---|
| 1331 | end |
---|
| 1332 | end |
---|
| 1333 | %criterium on correlation values |
---|
| 1334 | if isfield (Param,'MinCorr') |
---|
| 1335 | FF=FF==1 | C<Param.MinCorr; |
---|
| 1336 | end |
---|
| 1337 | if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)) |
---|
| 1338 | Umod= U.*U+V.*V; |
---|
| 1339 | if isfield (Param,'MinVel')&&~isempty(Param.MinVel) |
---|
| 1340 | FF=FF==1 | Umod<(Param.MinVel*Param.MinVel); |
---|
| 1341 | end |
---|
| 1342 | if isfield (Param,'MaxVel')&&~isempty(Param.MaxVel) |
---|
| 1343 | FF=FF==1 | Umod>(Param.MaxVel*Param.MaxVel); |
---|
| 1344 | end |
---|
| 1345 | end |
---|
| 1346 | |
---|
| 1347 | |
---|
| 1348 | %------------------------------------------------------------------------ |
---|
| 1349 | % --- determine the list of index pairs of processing file |
---|
| 1350 | function [i1_series,i2_series,j1_series,j2_series,check_bounds,NomTypeNc]=... |
---|
| 1351 | find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j) |
---|
| 1352 | %------------------------------------------------------------------------ |
---|
| 1353 | i1_series=i_series;% set of first image indexes |
---|
| 1354 | i2_series=i_series; |
---|
| 1355 | j1_series=j_series;%ones(size(i_series));% set of first image numbers |
---|
| 1356 | j2_series=j_series;%ones(size(i_series)); |
---|
| 1357 | r=regexp(str_civ,'^\D(?<ind>[i|j])=( -| )(?<num1>\d+)\|(?<num2>\d+)','names'); |
---|
| 1358 | if ~isempty(r) |
---|
| 1359 | mode=['D' r.ind]; |
---|
| 1360 | ind1=str2num(r.num1); |
---|
| 1361 | ind2=str2num(r.num2); |
---|
| 1362 | else |
---|
| 1363 | mode='j1-j2'; |
---|
| 1364 | r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names'); |
---|
| 1365 | if ~isempty(r) |
---|
| 1366 | NomTypeNc='_1ab'; |
---|
| 1367 | else |
---|
| 1368 | r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names'); |
---|
| 1369 | if ~isempty(r) |
---|
| 1370 | NomTypeNc='_1AB'; |
---|
| 1371 | else |
---|
| 1372 | r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names'); |
---|
| 1373 | if ~isempty(r) |
---|
| 1374 | NomTypeNc='_1_1-2'; |
---|
| 1375 | end |
---|
| 1376 | end |
---|
| 1377 | end |
---|
| 1378 | if isempty(r) |
---|
| 1379 | display('wrong pair mode input option') |
---|
| 1380 | else |
---|
| 1381 | ind1=stra2num(r.num1); |
---|
| 1382 | ind2=stra2num(r.num2); |
---|
| 1383 | end |
---|
| 1384 | end |
---|
| 1385 | switch mode |
---|
| 1386 | case 'Di' |
---|
| 1387 | i1_series=i_series-ind1;% set of first image numbers |
---|
| 1388 | i2_series=i_series+ind2; |
---|
| 1389 | check_bounds=i1_series<MinIndex_i | i2_series>MaxIndex_i; |
---|
| 1390 | if isempty(j_series) |
---|
| 1391 | NomTypeNc='_1-2'; |
---|
| 1392 | else |
---|
| 1393 | j1_series=j_series; |
---|
| 1394 | j2_series=j_series; |
---|
| 1395 | NomTypeNc='_1-2_1'; |
---|
| 1396 | end |
---|
| 1397 | case 'Dj' |
---|
| 1398 | j1_series=j_series-ind1; |
---|
| 1399 | j2_series=j_series+ind2; |
---|
| 1400 | check_bounds=j1_series<MinIndex_j | j2_series>MaxIndex_j; |
---|
| 1401 | NomTypeNc='_1_1-2'; |
---|
| 1402 | otherwise %bursts |
---|
| 1403 | i1_series=i_series(1,:);% do not sweep the j index |
---|
| 1404 | i2_series=i_series(1,:); |
---|
| 1405 | j1_series=ind1*ones(1,size(i_series,2));% j index is fixed by pair choice |
---|
| 1406 | j2_series=ind2*ones(1,size(i_series,2)); |
---|
| 1407 | check_bounds=zeros(size(i1_series));% no limitations due to min-max indices |
---|
| 1408 | end |
---|
| 1409 | |
---|
| 1410 | |
---|
| 1411 | |
---|
| 1412 | |
---|