source: trunk/src/series/relabel_i_j.m @ 71

Last change on this file since 71 was 71, checked in by sommeria, 11 years ago

civ3D updated: introduction of image size
imadoc2struct: reding of image size from the xml file
set_object, view_field and related functions: improvement of projection object editing
mouse: possibility of adjusting the calibrations points with the mouse

File size: 4.4 KB
Line 
1% relabel_i_j: relabel an image series with two indices, according to the time matrix given by ImaDoc
2%----------------------------------------------------------------------
3function GUI_input=relabel_i_j(num_i1,num_i2,num_j1,num_j2,Series)
4%requests for the visibility of input windows in the GUI series  (activated directly by the selection in the menu ACTION)
5if ~exist('num_i1','var')
6    GUI_input={};
7    return %exit the function
8end
9
10%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%enable waitbar
11hseries=guidata(Series.hseries);%handles of the GUI series
12WaitbarPos=get(hseries.waitbar_frame,'Position');
13%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
14
15basename=fullfile(Series.RootPath,Series.RootFile) ;
16
17%create dir of the new images
18[dir_images,namebase]=fileparts(basename);
19[path,subdir_ima]=fileparts(dir_images);
20curdir=pwd;
21cd(path);
22mkdir([subdir_ima '_ij']);
23cd(curdir);
24basename_new=fullfile(path,[subdir_ima '_ij'],namebase);
25
26% read imadoc
27[XmlData,warntext]=imadoc2struct([basename '.xml']);
28nbfield1=size(XmlData.Time,1)
29nbfield2=size(XmlData.Time,2)
30
31answer=msgbox_uvmat('INPUT_Y-N','apply image rescaling function levels.m')
32test_level=isequal(answer,'Yes')
33
34%copy the xml file
35if exist([basename '.xml'],'file')
36    copyfile([basename '.xml'],[basename_new '.xml']);% copy the .civ file
37    t=xmltree([basename_new '.xml']);
38   
39    %update information on the first image name in the series
40    uid_Heading=find(t,'ImaDoc/Heading');
41    if isempty(uid_Heading)
42        [t,uid_Heading]=add(t,1,'element','Heading');
43    end   
44    uid_ImageName=find(t,'ImaDoc/Heading/ImageName');
45    ImageName=name_generator(basename_new,num_i1(1),num_j1(1),'.png','_i_j');
46    [pth,ImageName]=fileparts(ImageName);
47    ImageName=[ImageName '.png']
48    if isempty(uid_ImageName)
49       [t,uid_ImageName]=add(t,uid_Heading,'element','ImageName');
50    end
51    uid_value=children(t,uid_ImageName);
52    if isempty(uid_value)
53        t=add(t,uid_ImageName,'chardata',ImageName)%indicate  name of the first image, with ;png extension
54    else
55        t=set(t,uid_value(1),'value',ImageName)%indicate  name of the first image, with ;png extension
56    end 
57
58%     %add information about image transform
59%     [t,new_uid]=add(t,1,'element','ImageTransform');
60%     [t,NameFunction_uid]=add(t,new_uid,'element','NameFunction');
61%     [t]=add(t,NameFunction_uid,'chardata','sub_background');     
62%     [t,NbSlice_uid]=add(t,new_uid,'element','NbSlice');
63%     [t]=add(t,new_uid,'chardata',num2str(nbslice_i));
64%     [t,NbSlidingImages_uid]=add(t,new_uid,'element','NbSlidingImages');
65%     [t]=add(t,NbSlidingImages_uid,'chardata',num2str(nbaver));
66%     [t,LuminosityRank_uid]=add(t,new_uid,'element','RankBackground');
67%     [t]=add(t,LuminosityRank_uid,'chardata',num2str(rank));% luminosity rank almong the nbaver sliding images
68    save(t,[basename_new '.xml'])
69end
70
71%main loop
72for ifile=1:nbfield1*nbfield2
73    update_waitbar(hseries.waitbar,WaitbarPos,ifile/(nbfield1*nbfield2))
74    filename=name_generator(basename,ifile-1,1,Series.FileExt,Series.NomType);
75    num_j=mod(ifile-1,nbfield2)+1;
76    num_i=floor((ifile-1)/nbfield2)+1;
77    filename_new=name_generator(basename_new,num_i,num_j,'.png','_i_j');
78    if test_level
79        A=imread(filename);
80        C=levels(A);
81        imwrite(C,filename_new)
82    else
83        copyfile(filename,filename_new);
84    end   
85end
86
87
88
89function C=levels(A)
90%whos A;
91B=double(A(:,:,1));
92windowsize=round(min(size(B,1),size(B,2))/20);
93windowsize=floor(windowsize/2)*2+1;
94ix=[1/2-windowsize/2:-1/2+windowsize/2];%
95%del=np/3;
96%fct=exp(-(ix/del).^2);
97fct2=cos(ix/(windowsize-1)/2*pi/2);
98%Mfiltre=(ones(5,5)/5^2);
99%Mfiltre=fct2';
100Mfiltre=fct2'*fct2;
101Mfiltre=Mfiltre/(sum(sum(Mfiltre)));
102
103C=filter2(Mfiltre,B);
104C(:,1:windowsize)=C(:,windowsize)*ones(1,windowsize);
105C(:,end-windowsize+1:end)=C(:,end-windowsize+1)*ones(1,windowsize);
106C(1:windowsize,:)=ones(windowsize,1)*C(windowsize,:);
107C(end-windowsize+1:end,:)=ones(windowsize,1)*C(end-windowsize,:);
108C=tanh(B./(2*C));
109[n,c]=hist(reshape(C,1,[]),100);
110% figure;plot(c,n);
111
112[m,i]=max(n);
113c_max=c(i);
114[dummy,index]=sort(abs(c-c(i)));
115n=n(index);
116c=c(index);
117i_select = find(cumsum(n)<0.95*sum(n));
118if isempty(i_select)
119    i_select = 1:length(c);
120end
121c_select=c(i_select);
122n_select=n(i_select);
123cmin=min(c_select);
124cmax=max(c_select);
125C=(C-cmin)/(cmax-cmin)*256;
126C=uint8(C);
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