1 | %'ima2vol': concatene image series to form a 'volume' image .vol used for 3D PIV
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2 | %------------------------------------------------------------------------
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3 | % function GUI_input=ima2vol(num_i1,num_i2,num_j1,num_j2,Series)
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4 | %
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5 | %OUTPUT
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6 | % GUI_input=list of options in the GUI series.fig needed for the function
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7 | %
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8 | %INPUT:
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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)
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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)
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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 )
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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)
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13 | %Series: Matlab structure containing information set by the series interface
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14 | %
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15 | %----------------------------------------------------------------------
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16 |
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17 | %=======================================================================
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18 | % Copyright 2008-2015, LEGI UMR 5519 / CNRS UJF G-INP, Grenoble, France
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19 | % http://www.legi.grenoble-inp.fr
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20 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
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21 | %
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22 | % This file is part of the toolbox UVMAT.
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23 | %
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24 | % UVMAT is free software; you can redistribute it and/or modify
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25 | % it under the terms of the GNU General Public License as published
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26 | % by the Free Software Foundation; either version 2 of the license,
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27 | % or (at your option) any later version.
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28 | %
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29 | % UVMAT is distributed in the hope that it will be useful,
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30 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
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31 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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32 | % GNU General Public License (see LICENSE.txt) for more details.
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33 | %=======================================================================
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34 |
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35 | function GUI_input=ima2vol(num_i1,num_i2,num_j1,num_j2,Series)
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36 | %requests for the visibility of input windows in the GUI series (activated directly by the selection in the menu ACTION)
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37 | if ~exist('num_i1','var')
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38 | GUI_input={};
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39 | return %exit the function
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40 | end
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41 |
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42 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%enable waitbar
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43 | hseries=guidata(Series.hseries);%handles of the GUI series
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44 | WaitbarPos=get(hseries.waitbar_frame,'Position');
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45 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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46 |
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47 | basename=fullfile(Series.RootPath,Series.RootFile) ;
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48 |
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49 | %create dir of the new images
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50 | [dir_images,namebase]=fileparts(basename);
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51 | [path,subdir_ima]=fileparts(dir_images);
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52 | curdir=pwd;
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53 | cd(path);
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54 | mkdir([subdir_ima '_vol']);
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55 | cd(curdir);
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56 | basename_new=fullfile(path,[subdir_ima '_vol'],namebase);
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57 |
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58 | % read imadoc
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59 | [XmlData,warntext]=imadoc2struct([basename '.xml']);
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60 | nbfield1=size(XmlData.Time,1)
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61 | nbfield2=size(XmlData.Time,2)
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62 |
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63 | answer=msgbox_uvmat('INPUT_Y-N','apply image rescaling function levels.m')
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64 | test_level=isequal(answer,'Yes')
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65 |
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66 | %copy the xml file
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67 | if exist([basename '.xml'],'file')
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68 | copyfile([basename '.xml'],[basename_new '.xml']);% copy the .civ file
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69 | t=xmltree([basename_new '.xml']);
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70 |
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71 | %update information on the first image name in the series
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72 | uid_Heading=find(t,'ImaDoc/Heading');
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73 | if isempty(uid_Heading)
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74 | [t,uid_Heading]=add(t,1,'element','Heading');
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75 | end
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76 | uid_ImageName=find(t,'ImaDoc/Heading/ImageName');
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77 | ImageName=name_generator(basename_new,num_i1(1),num_j1(1),'.png','_i_j');
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78 | [pth,ImageName]=fileparts(ImageName);
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79 | ImageName=[ImageName '.png']
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80 | if isempty(uid_ImageName)
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81 | [t,uid_ImageName]=add(t,uid_Heading,'element','ImageName');
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82 | end
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83 | uid_value=children(t,uid_ImageName);
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84 | if isempty(uid_value)
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85 | t=add(t,uid_ImageName,'chardata',ImageName)%indicate name of the first image, with ;png extension
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86 | else
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87 | t=set(t,uid_value(1),'value',ImageName)%indicate name of the first image, with ;png extension
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88 | end
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89 | save(t,[basename_new '.xml'])
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90 | end
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91 |
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92 | %main loop
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93 | vol=[];
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94 | for ifile=1:nbfield1*nbfield2
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95 | update_waitbar(hseries.waitbar,WaitbarPos,ifile/(nbfield1*nbfield2))
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96 | stopstate=get(hseries.RUN,'BusyAction');
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97 | if isequal(stopstate,'queue') % enable STOP command
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98 | filename=name_generator(basename,ifile-1,1,Series.FileExt,Series.NomType);
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99 | num_j=mod(ifile-1,nbfield2)+1;
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100 | num_i=floor((ifile-1)/nbfield2)+1;
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101 | A=imread(filename);
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102 | Atype=class(A);
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103 | if test_level
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104 | A=levels(A,16);
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105 | display(num2str(num_i))
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106 | end
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107 | vol=[vol;A];%concacene along y
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108 | if num_j==nbfield2
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109 | filename_new=name_generator(basename_new,num_i,1,'.vol','_i');
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110 | imwrite(vol,filename_new,'png','BitDepth',16)% WRITE IN 16 bits: needed for the current version of civ3C3D
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111 | display([filename_new 'written (16bits image)'])
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112 | vol=[];
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113 | end
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114 | end
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115 | end
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116 |
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117 |
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118 |
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119 | function C=levels(A,bitdepth)
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120 | %whos A;
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121 | B=double(A(:,:,1));
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122 | windowsize=round(min(size(B,1),size(B,2))/20);
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123 | windowsize=floor(windowsize/2)*2+1;
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124 | ix=[1/2-windowsize/2:-1/2+windowsize/2];%
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125 | %del=np/3;
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126 | %fct=exp(-(ix/del).^2);
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127 | fct2=cos(ix/(windowsize-1)/2*pi/2);
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128 | %Mfiltre=(ones(5,5)/5^2);
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129 | %Mfiltre=fct2';
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130 | Mfiltre=fct2'*fct2;
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131 | Mfiltre=Mfiltre/(sum(sum(Mfiltre)));
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132 |
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133 | C=filter2(Mfiltre,B);
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134 | C(:,1:windowsize)=C(:,windowsize)*ones(1,windowsize);
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135 | C(:,end-windowsize+1:end)=C(:,end-windowsize+1)*ones(1,windowsize);
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136 | C(1:windowsize,:)=ones(windowsize,1)*C(windowsize,:);
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137 | C(end-windowsize+1:end,:)=ones(windowsize,1)*C(end-windowsize,:);
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138 | C=tanh(B./(2*C));
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139 | [n,c]=hist(reshape(C,1,[]),100);
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140 | % figure;plot(c,n);
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141 |
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142 | [m,i]=max(n);
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143 | c_max=c(i);
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144 | [dummy,index]=sort(abs(c-c(i)));
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145 | n=n(index);
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146 | c=c(index);
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147 | i_select = find(cumsum(n)<0.95*sum(n));
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148 | if isempty(i_select)
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149 | i_select = 1:length(c);
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150 | end
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151 | c_select=c(i_select);
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152 | n_select=n(i_select);
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153 | cmin=min(c_select);
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154 | cmax=max(c_select);
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155 | if isequal(bitdepth,16)
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156 | C=((C-cmin)/(cmax-cmin))*256*256;
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157 | C=uint16(C);
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158 | else
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159 | C=((C-cmin)/(cmax-cmin))*256;
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160 | C=uint8(C);
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161 | end
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