Index: /trunk/src/series/civ2vel_3C.m =================================================================== --- /trunk/src/series/civ2vel_3C.m (revision 926) +++ /trunk/src/series/civ2vel_3C.m (revision 927) @@ -34,5 +34,5 @@ %======================================================================= -% Copyright 2008-2016, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France +% Copyright 2008-2015, LEGI UMR 5519 / CNRS UJF G-INP, Grenoble, France % http://www.legi.grenoble-inp.fr % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr @@ -52,5 +52,5 @@ function ParamOut=civ2vel_3C(Param) - +disp('test') %% set the input elements needed on the GUI series when the function is selected in the menu ActionName or InputTable refreshed if isstruct(Param) && isequal(Param.Action.RUN,0) @@ -68,4 +68,5 @@ ParamOut.OutputFileMode='NbInput';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice %check the input files + ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) first_j=[]; if size(Param.InputTable,1)<2 @@ -170,6 +171,37 @@ warning off +CheckOverwrite=1;%default +if isfield(Param,'CheckOverwrite') + CheckOverwrite=Param.CheckOverwrite; +end for index=1:NbField + update_waitbar(WaitbarHandle,index/NbField) + + + + + %% generating the name of the merged field + i1=i1_series{1}(index); + if ~isempty(i2_series{end}) + i2=i2_series{end}(index); + else + i2=i1; + end + j1=1; + j2=1; + if ~isempty(j1_series{1}) + j1=j1_series{1}(index); + if ~isempty(j2_series{end}) + j2=j2_series{end}(index); + else + j2=j1; + end + end + OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},'.nc','_1-2',i1,i2,j1,j2); + + %% + + if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') disp('program stopped by user') @@ -177,4 +209,9 @@ end + if (~CheckOverwrite && exist(OutputFile,'file')) + disp('existing output file already exists, skip to next field') + continue% skip iteration if the mode overwrite is desactivated and the result file already exists + end + %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%% Data=cell(1,NbView);%initiate the set Data @@ -185,9 +222,17 @@ clear ZItemp ZItemp=zeros(size(XI,1),size(XI,2),2); + + if index==1 + first_img=i1_series{1,1}(1,1); %id of the first image of the series + end + + idtemp=0; for indextemp=index:index+1; + idtemp=idtemp+1; if NbView==3 % if there is only 1 stereo folder, extract directly Xphys,Yphys and Zphys - - [Data{3},tild,errormsg] = nc2struct([Param.InputTable{3,1},'/',Param.InputTable{3,2},'/',Param.InputTable{3,3},'_',int2str(indextemp),'.nc']); - + + + + [Data{3},tild,errormsg] = nc2struct([Param.InputTable{3,1},'/',Param.InputTable{3,2},'/',Param.InputTable{3,3},'_',int2str(first_img+indextemp-1),'.nc']); if exist('Data{3}.Civ3_FF','var') % FF is present, remove wrong vector @@ -219,5 +264,8 @@ end - [Data{3},tild,errormsg] = nc2struct([Param.InputTable{3,1},'/',Param.InputTable{3,2},'/',Param.InputTable{3,3},'_',int2str(indextemp),'.nc']); + + + [Data{3},tild,errormsg] = nc2struct([Param.InputTable{3,1},'/',Param.InputTable{3,2},'/',Param.InputTable{3,3},'_',int2str(first_img+indextemp-1),'.nc']); + if exist('Data{3}.Civ3_FF','var') % if FF is present, remove wrong vector temp=find(Data{3}.Civ3_FF==0); @@ -241,5 +289,6 @@ - [Data{4},tild,errormsg] = nc2struct([Param.InputTable{4,1},'/',Param.InputTable{4,2},'/',Param.InputTable{4,3},'_',int2str(indextemp),'.nc']); + + [Data{4},tild,errormsg] = nc2struct([Param.InputTable{4,1},'/',Param.InputTable{4,2},'/',Param.InputTable{4,3},'_',int2str(first_img+indextemp-1),'.nc']); if exist('Data{4}.Civ3_FF','var') % if FF is present, remove wrong vector temp=find(Data{4}.Civ3_FF==0); @@ -279,5 +328,5 @@ - ZItemp(:,:,indextemp)=griddata(Xphys,Yphys,Zphys,XI,YI); %interpolation on the choosen gridd + ZItemp(:,:,idtemp)=griddata(Xphys,Yphys,Zphys,XI,YI); %interpolation on the choosen gridd end @@ -320,5 +369,5 @@ Va=griddata(X1,Y1,V1,Xa,Ya); - [Ua,Va,Xa,Ya]=Ud2U(XmlData{1}.GeometryCalib,Xa,Ya,Ua,Va); % convert Xd data to X +% [Ua,Va,Xa,Ya]=Ud2U(XmlData{1}.GeometryCalib,Xa,Ya,Ua,Va); % convert Xd data to X [A]=get_coeff(XmlData{1}.GeometryCalib,Xa,Ya,XI,YI,ZI); %get coef A~ @@ -332,5 +381,5 @@ Vb=griddata(X2,Y2,V2,Xb,Yb); - [Ub,Vb,Xb,Yb]=Ud2U(XmlData{2}.GeometryCalib,Xb,Yb,Ub,Vb); % convert Xd data to X +% [Ub,Vb,Xb,Yb]=Ud2U(XmlData{2}.GeometryCalib,Xb,Yb,Ub,Vb); % convert Xd data to X [B]=get_coeff(XmlData{2}.GeometryCalib,Xb,Yb,XI,YI,ZI); %get coef B~ @@ -369,22 +418,5 @@ - %% generating the name of the merged field - i1=i1_series{1}(index); - if ~isempty(i2_series{end}) - i2=i2_series{end}(index); - else - i2=i1; - end - j1=1; - j2=1; - if ~isempty(j1_series{1}) - j1=j1_series{1}(index); - if ~isempty(j2_series{end}) - j2=j2_series{end}(index); - else - j2=j1; - end - end - OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},'.nc','_1-2',i1,i2,j1,j2); + %% recording the merged field @@ -399,13 +431,13 @@ MergeData.coord_x=xI; MergeData.coord_y=yI; - MergeData.Z=ZI; end MergeData.U=U/Dt; MergeData.V=V/Dt; MergeData.W=W/Dt; - - mfx=(XmlData{1}.GeometryCalib.fx_fy(1)+XmlData{2}.GeometryCalib.fx_fy(1))/2; - mfy=(XmlData{1}.GeometryCalib.fx_fy(2)+XmlData{2}.GeometryCalib.fx_fy(2))/2; - MergeData.Error=(sqrt(mfx^2+mfy^2)/4).*sqrt(sum(Error.*Error,3)); + MergeData.Z=ZI; + +% mfx=(XmlData{1}.GeometryCalib.fx_fy(1)+XmlData{2}.GeometryCalib.fx_fy(1))/2; +% mfy=(XmlData{1}.GeometryCalib.fx_fy(2)+XmlData{2}.GeometryCalib.fx_fy(2))/2; + MergeData.Error=0.5*sqrt(sum(Error.^2,3)); errormsg=struct2nc(OutputFile,MergeData);%save result file if isempty(errormsg) @@ -496,5 +528,5 @@ %% result Den=(Dxb-Dxa).*(Dxb-Dxa)+(Dyb-Dya).*(Dyb-Dya); -error=((Dyb-Dya).*(-u)-(Dxb-Dxa).*(-v))./Den; +error=abs(((Dyb-Dya).*(-u)-(Dxb-Dxa).*(-v)))./Den; % ex=-error.*(Dyb-Dya); % ey=-error.*(Dxb-Dxa); Index: /trunk/src/series/stereo_civ.m =================================================================== --- /trunk/src/series/stereo_civ.m (revision 926) +++ /trunk/src/series/stereo_civ.m (revision 927) @@ -21,22 +21,20 @@ % .Patch2: % ncfile: name of a netcdf file to be created for the result (extension .nc) - -%======================================================================= -% Copyright 2008-2016, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France -% http://www.legi.grenoble-inp.fr -% Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr % -% This file is part of the toolbox UVMAT. -% +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright 2011-2015, LEGI / CNRS UJF G-INP, Joel.Sommeria@legi.grenoble-inp.fr +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This is part of the toolbox UVMAT. +% % UVMAT is free software; you can redistribute it and/or modify -% it under the terms of the GNU General Public License as published -% by the Free Software Foundation; either version 2 of the license, -% or (at your option) any later version. -% +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% % UVMAT is distributed in the hope that it will be useful, % but WITHOUT ANY WARRANTY; without even the implied warranty of % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -% GNU General Public License (see LICENSE.txt) for more details. -%======================================================================= +% GNU General Public License (open UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA function [Data,errormsg,result_conv]= stereo_civ(Param) @@ -67,4 +65,6 @@ Data.OutputSubDirMode='auto'; %select the last subDir in the input table as root of the output subdir name (option 'all'/'first'/'last', 'all' by default) Data.OutputFileMode='NbInput_i';% one output file expected per value of i index (used for waitbar) + Data.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) + return end @@ -168,5 +168,5 @@ end if isempty(i1_series_Civ1)||(~isempty(PairCiv2) && isempty(i1_series_Civ2)) - disp_uvmat('ERROR','no image pair fo civ in the input file index range',checkrun) + disp_uvmat('ERROR','no image pair for civ in the input file index range',checkrun) return end @@ -265,4 +265,9 @@ tic %%%%% MAIN LOOP %%%%%% +CheckOverwrite=1;%default +if isfield(Param,'CheckOverwrite') + CheckOverwrite=Param.CheckOverwrite; +end + for ifield=1:NbField update_waitbar(WaitbarHandle,ifield/NbField) @@ -282,4 +287,11 @@ ncfile2=fullfile_uvmat(RootPath_A,Civ1Dir,[RootFile_A,'_Light'],'.nc',NomTypeNc,i2_series_Civ1(ifield),[],... j1_series_Civ1(ifield),j2_series_Civ1(ifield)); + + if (~CheckOverwrite && exist(ncfile,'file')) || (~CheckOverwrite && exist(ncfile2,'file')) + disp('existing output file already exists, skip to next field') + result_conv=0; + continue% skip iteration if the mode overwrite is desactivated and the result file already exists + end + %% Civ1 @@ -845,7 +857,10 @@ end - end - - disp(['ellapsed time for the loop ' num2str(toc) ' s']) +end +disp(['ellapsed time for the loop ' num2str(toc) ' s']) +tic +while toc < rand(1)*10 + for i = 1:100000, sqrt(1237); end +end @@ -1099,5 +1114,5 @@ [npy,npx]=size(result_conv); result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log) -%the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ￜ Israel Institute of Technology +%the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ??? Israel Institute of Technology %http://urapiv.wordpress.com peaky = y; @@ -1136,9 +1151,9 @@ for j=-1:1 %following 15 lines based on - %H. Nobach ￜ M. Honkanen (2005) + %H. Nobach ??? M. Honkanen (2005) %Two-dimensional Gaussian regression for sub-pixel displacement %estimation in particle image velocimetry or particle position %estimation in particle tracking velocimetry - %Experiments in Fluids (2005) 38: 511ￜ515 + %Experiments in Fluids (2005) 38: 511???515 c10(j+2,i+2)=i*log(result_conv(y+j, x+i)); c01(j+2,i+2)=j*log(result_conv(y+j, x+i));