[171] | 1 | %'ima2vol': concatene image series to form a 'volume' image .vol used for 3D PIV
|
---|
| 2 | %------------------------------------------------------------------------
|
---|
| 3 | % function GUI_input=ima2vol(num_i1,num_i2,num_j1,num_j2,Series)
|
---|
| 4 | %
|
---|
| 5 | %OUTPUT
|
---|
| 6 | % GUI_input=list of options in the GUI series.fig needed for the function
|
---|
| 7 | %
|
---|
| 8 | %INPUT:
|
---|
| 9 | %num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
|
---|
| 10 | %num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
|
---|
| 11 | %num_j1: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ )
|
---|
| 12 | %num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ)
|
---|
| 13 | %Series: Matlab structure containing information set by the series interface
|
---|
| 14 | %
|
---|
[41] | 15 | %----------------------------------------------------------------------
|
---|
| 16 | function GUI_input=ima2vol(num_i1,num_i2,num_j1,num_j2,Series)
|
---|
| 17 | %requests for the visibility of input windows in the GUI series (activated directly by the selection in the menu ACTION)
|
---|
| 18 | if ~exist('num_i1','var')
|
---|
| 19 | GUI_input={};
|
---|
| 20 | return %exit the function
|
---|
| 21 | end
|
---|
| 22 |
|
---|
| 23 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%enable waitbar
|
---|
| 24 | hseries=guidata(Series.hseries);%handles of the GUI series
|
---|
| 25 | WaitbarPos=get(hseries.waitbar_frame,'Position');
|
---|
| 26 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
---|
| 27 |
|
---|
| 28 | basename=fullfile(Series.RootPath,Series.RootFile) ;
|
---|
| 29 |
|
---|
| 30 | %create dir of the new images
|
---|
| 31 | [dir_images,namebase]=fileparts(basename);
|
---|
| 32 | [path,subdir_ima]=fileparts(dir_images);
|
---|
| 33 | curdir=pwd;
|
---|
| 34 | cd(path);
|
---|
[72] | 35 | mkdir([subdir_ima '_vol']);
|
---|
[41] | 36 | cd(curdir);
|
---|
[72] | 37 | basename_new=fullfile(path,[subdir_ima '_vol'],namebase);
|
---|
[41] | 38 |
|
---|
| 39 | % read imadoc
|
---|
| 40 | [XmlData,warntext]=imadoc2struct([basename '.xml']);
|
---|
| 41 | nbfield1=size(XmlData.Time,1)
|
---|
| 42 | nbfield2=size(XmlData.Time,2)
|
---|
| 43 |
|
---|
| 44 | answer=msgbox_uvmat('INPUT_Y-N','apply image rescaling function levels.m')
|
---|
| 45 | test_level=isequal(answer,'Yes')
|
---|
| 46 |
|
---|
| 47 | %copy the xml file
|
---|
| 48 | if exist([basename '.xml'],'file')
|
---|
| 49 | copyfile([basename '.xml'],[basename_new '.xml']);% copy the .civ file
|
---|
| 50 | t=xmltree([basename_new '.xml']);
|
---|
| 51 |
|
---|
| 52 | %update information on the first image name in the series
|
---|
| 53 | uid_Heading=find(t,'ImaDoc/Heading');
|
---|
| 54 | if isempty(uid_Heading)
|
---|
| 55 | [t,uid_Heading]=add(t,1,'element','Heading');
|
---|
| 56 | end
|
---|
| 57 | uid_ImageName=find(t,'ImaDoc/Heading/ImageName');
|
---|
| 58 | ImageName=name_generator(basename_new,num_i1(1),num_j1(1),'.png','_i_j');
|
---|
| 59 | [pth,ImageName]=fileparts(ImageName);
|
---|
| 60 | ImageName=[ImageName '.png']
|
---|
| 61 | if isempty(uid_ImageName)
|
---|
| 62 | [t,uid_ImageName]=add(t,uid_Heading,'element','ImageName');
|
---|
| 63 | end
|
---|
| 64 | uid_value=children(t,uid_ImageName);
|
---|
| 65 | if isempty(uid_value)
|
---|
| 66 | t=add(t,uid_ImageName,'chardata',ImageName)%indicate name of the first image, with ;png extension
|
---|
| 67 | else
|
---|
| 68 | t=set(t,uid_value(1),'value',ImageName)%indicate name of the first image, with ;png extension
|
---|
| 69 | end
|
---|
| 70 | save(t,[basename_new '.xml'])
|
---|
| 71 | end
|
---|
| 72 |
|
---|
| 73 | %main loop
|
---|
| 74 | vol=[];
|
---|
[73] | 75 | for ifile=1:nbfield1*nbfield2
|
---|
| 76 | update_waitbar(hseries.waitbar,WaitbarPos,ifile/(nbfield1*nbfield2))
|
---|
| 77 | stopstate=get(hseries.RUN,'BusyAction');
|
---|
| 78 | if isequal(stopstate,'queue') % enable STOP command
|
---|
| 79 | filename=name_generator(basename,ifile-1,1,Series.FileExt,Series.NomType);
|
---|
| 80 | num_j=mod(ifile-1,nbfield2)+1;
|
---|
| 81 | num_i=floor((ifile-1)/nbfield2)+1;
|
---|
| 82 | A=imread(filename);
|
---|
| 83 | Atype=class(A);
|
---|
| 84 | if test_level
|
---|
| 85 | A=levels(A,16);
|
---|
| 86 | display(num2str(num_i))
|
---|
| 87 | end
|
---|
| 88 | vol=[vol;A];%concacene along y
|
---|
| 89 | if num_j==nbfield2
|
---|
| 90 | filename_new=name_generator(basename_new,num_i,1,'.vol','_i');
|
---|
| 91 | imwrite(vol,filename_new,'png','BitDepth',16)% WRITE IN 16 bits: needed for the current version of civ3C3D
|
---|
| 92 | display([filename_new 'written (16bits image)'])
|
---|
| 93 | vol=[];
|
---|
| 94 | end
|
---|
| 95 | end
|
---|
| 96 | end
|
---|
[41] | 97 |
|
---|
| 98 |
|
---|
| 99 |
|
---|
[73] | 100 | function C=levels(A,bitdepth)
|
---|
[41] | 101 | %whos A;
|
---|
| 102 | B=double(A(:,:,1));
|
---|
| 103 | windowsize=round(min(size(B,1),size(B,2))/20);
|
---|
| 104 | windowsize=floor(windowsize/2)*2+1;
|
---|
| 105 | ix=[1/2-windowsize/2:-1/2+windowsize/2];%
|
---|
| 106 | %del=np/3;
|
---|
| 107 | %fct=exp(-(ix/del).^2);
|
---|
| 108 | fct2=cos(ix/(windowsize-1)/2*pi/2);
|
---|
| 109 | %Mfiltre=(ones(5,5)/5^2);
|
---|
| 110 | %Mfiltre=fct2';
|
---|
| 111 | Mfiltre=fct2'*fct2;
|
---|
| 112 | Mfiltre=Mfiltre/(sum(sum(Mfiltre)));
|
---|
| 113 |
|
---|
[72] | 114 | C=filter2(Mfiltre,B);
|
---|
[41] | 115 | C(:,1:windowsize)=C(:,windowsize)*ones(1,windowsize);
|
---|
| 116 | C(:,end-windowsize+1:end)=C(:,end-windowsize+1)*ones(1,windowsize);
|
---|
| 117 | C(1:windowsize,:)=ones(windowsize,1)*C(windowsize,:);
|
---|
| 118 | C(end-windowsize+1:end,:)=ones(windowsize,1)*C(end-windowsize,:);
|
---|
| 119 | C=tanh(B./(2*C));
|
---|
| 120 | [n,c]=hist(reshape(C,1,[]),100);
|
---|
| 121 | % figure;plot(c,n);
|
---|
| 122 |
|
---|
| 123 | [m,i]=max(n);
|
---|
| 124 | c_max=c(i);
|
---|
| 125 | [dummy,index]=sort(abs(c-c(i)));
|
---|
| 126 | n=n(index);
|
---|
| 127 | c=c(index);
|
---|
| 128 | i_select = find(cumsum(n)<0.95*sum(n));
|
---|
| 129 | if isempty(i_select)
|
---|
| 130 | i_select = 1:length(c);
|
---|
| 131 | end
|
---|
| 132 | c_select=c(i_select);
|
---|
| 133 | n_select=n(i_select);
|
---|
| 134 | cmin=min(c_select);
|
---|
| 135 | cmax=max(c_select);
|
---|
[73] | 136 | if isequal(bitdepth,16)
|
---|
| 137 | C=((C-cmin)/(cmax-cmin))*256*256;
|
---|
| 138 | C=uint16(C);
|
---|
| 139 | else
|
---|
| 140 | C=((C-cmin)/(cmax-cmin))*256;
|
---|
| 141 | C=uint8(C);
|
---|
| 142 | end |
---|