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