1 | % 'ima_remove_background': removes backgound from an image (using the local minimum)
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2 | % requires the Matlab image processing toolbox
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3 | %------------------------------------------------------------------------
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4 | %%%% Use the general syntax for transform fields with a single input %%%%
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5 | % OUTPUT:
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6 | % DataOut: output field structure
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7 | %
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8 | %INPUT:
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9 | % DataIn: first input field structure
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10 |
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11 | %=======================================================================
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12 | % Copyright 2008-2020, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
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13 | % http://www.legi.grenoble-inp.fr
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14 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
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15 | %
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16 | % This file is part of the toolbox UVMAT.
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17 | %
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18 | % UVMAT is free software; you can redistribute it and/or modify
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19 | % it under the terms of the GNU General Public License as published
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20 | % by the Free Software Foundation; either version 2 of the license,
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21 | % or (at your option) any later version.
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22 | %
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23 | % UVMAT is distributed in the hope that it will be useful,
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24 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
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25 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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26 | % GNU General Public License (see LICENSE.txt) for more details.
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27 | %=======================================================================
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28 |
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29 | function DataOut=remove_background(DataIn,Param)
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30 | %------------------------------------------------------------------------
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31 | %% request input parameters
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32 | if isfield(DataIn,'Action') && isfield(DataIn.Action,'RUN') && isequal(DataIn.Action.RUN,0)
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33 | prompt = {'radius'};
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34 | dlg_title = 'get the disk radius (pixels) used to calculate the regional minimum';
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35 | num_lines= 1;
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36 | def = { '4'};
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37 | if isfield(Param,'TransformInput')&&isfield(Param.TransformInput,'DiskRadius')
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38 | def={num2str(Param.TransformInput.DiskRadius)};
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39 | end
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40 | answer = inputdlg(prompt,dlg_title,num_lines,def);
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41 | DataOut.TransformInput.DiskRadius=str2num(answer{1});
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42 | return
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43 | end
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44 | if ~isfield(DataIn,'A')
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45 | DataOut.Txt='remove_particles only valid for input images';
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46 | return
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47 | end
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48 | if ~exist('imerode','file');
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49 | DataOut.Txt='the function imerode from the image processing toolbox is needed';
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50 | return
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51 | end
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52 |
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53 | SE=strel('disk',Param.TransformInput.DiskRadius);
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54 | %---------------------------------------------------------
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55 | DataOut=DataIn;%default
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56 |
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57 | [npy,npx]=size(DataIn.A);
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58 | [X,Y]=meshgrid(1:npx,1:npy);
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59 |
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60 | %BACKGROUND LEVEL
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61 | Atype=class(DataIn.A);
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62 | Aerode=imerode(DataIn.A,SE);
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63 | Aflagmin=find(DataIn.A==Aerode);
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64 | Xmin=X(Aflagmin);
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65 | Ymin=Y(Aflagmin);
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66 | Amin=double(DataIn.A(Aflagmin));
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67 | F = TriScatteredInterp([Xmin Ymin], Amin);
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68 | DataOut.A=double(DataOut.A)-F(X,Y);
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69 | DataOut.A=feval(Atype,DataOut.A);
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70 |
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71 | %BACKGROUND LEVEL
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72 | % Atype=class(DataIn.A);
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73 | % A=double(DataIn.A);
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74 | % Backg=zeros(size(A));
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75 | % Aflagmin=sparse(imregionalmin(A));%Amin=1 for local image minima
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76 | % Amin=A.*Aflagmin;%values of A at local minima
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77 | % % local background: find all the local minima in image subblocks
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78 | % sumblock= inline('sum(sum(x(:)))');
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79 | % Backg=blkproc(Amin,[nblock_y nblock_x],sumblock);% take the sum in blocks
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80 | % Bmin=blkproc(Aflagmin,[nblock_y nblock_x],sumblock);% find the number of minima in blocks
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81 | % Backg=Backg./Bmin; % find the average of minima in blocks
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82 | % B=imresize(Backg,size(A),'bilinear');% interpolate to the initial size image
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83 | % ImPart=(A-B);
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84 | % DataOut.A=ImPart;
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85 | % %DataOut.A=ImPart.*(ImPart>threshold);
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86 | % DataOut.A=feval(Atype,DataOut.A);
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