source: trunk/src/series/ima2vol.m @ 41

Last change on this file since 41 was 41, checked in by sommeria, 11 years ago

-relabel_i_j: improve the question dlg box for image transform
-aver_stat,time_series,merge_proj: include modification of field transform and call of set_object.
-series: introduce a browser for set_object
-ima2vol: create volume images (png images of a slice concacened along y) for PIV 3D
-set_object: suppress TITLE, introduce Tooltip helps for parameters
-civ: fixed bug on BATCH sequences

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=ima2vol(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
72 vol=[];
73for ifile=1:nbfield1*nbfield2
74    update_waitbar(hseries.waitbar,WaitbarPos,ifile/(nbfield1*nbfield2))
75    filename=name_generator(basename,ifile-1,1,Series.FileExt,Series.NomType);
76    num_j=mod(ifile-1,nbfield2)+1;
77    num_i=floor((ifile-1)/nbfield2)+1;
78    A=imread(filename);
79    if test_level
80         A=levels(A);
81    end
82    vol=[vol;A];%concacene along y
83    if num_j==nbfield2
84         filename_new=name_generator(basename_new,num_i,1,'.vol','_i');
85         imwrite(vol,filename_new,'png')
86         vol=[];
87    end     
88end
89
90
91
92function C=levels(A)
93%whos A;
94B=double(A(:,:,1));
95windowsize=round(min(size(B,1),size(B,2))/20);
96windowsize=floor(windowsize/2)*2+1;
97ix=[1/2-windowsize/2:-1/2+windowsize/2];%
98%del=np/3;
99%fct=exp(-(ix/del).^2);
100fct2=cos(ix/(windowsize-1)/2*pi/2);
101%Mfiltre=(ones(5,5)/5^2);
102%Mfiltre=fct2';
103Mfiltre=fct2'*fct2;
104Mfiltre=Mfiltre/(sum(sum(Mfiltre)));
105
106C=filter2(ones(windowsize)/windowsize^2,B);
107C(:,1:windowsize)=C(:,windowsize)*ones(1,windowsize);
108C(:,end-windowsize+1:end)=C(:,end-windowsize+1)*ones(1,windowsize);
109C(1:windowsize,:)=ones(windowsize,1)*C(windowsize,:);
110C(end-windowsize+1:end,:)=ones(windowsize,1)*C(end-windowsize,:);
111C=tanh(B./(2*C));
112[n,c]=hist(reshape(C,1,[]),100);
113% figure;plot(c,n);
114
115[m,i]=max(n);
116c_max=c(i);
117[dummy,index]=sort(abs(c-c(i)));
118n=n(index);
119c=c(index);
120i_select = find(cumsum(n)<0.95*sum(n));
121if isempty(i_select)
122    i_select = 1:length(c);
123end
124c_select=c(i_select);
125n_select=n(i_select);
126cmin=min(c_select);
127cmax=max(c_select);
128C=(C-cmin)/(cmax-cmin)*256;
129C=uint8(C);
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