[574]  1  % 'ima_remove_background': removes backgound from an image (using the local minimum)


 2  % requires the Matlab image processing toolbox


 3  %


 4  %%%% Use the general syntax for transform fields with a single input %%%%


 5  % OUTPUT:


 6  % DataOut: output field structure


[810]  7  %


[574]  8  %INPUT:


 9  % DataIn: first input field structure


[810]  10 


 11  %=======================================================================


[1071]  12  % Copyright 20082020, LEGI UMR 5519 / CNRS UGA GINP, Grenoble, France


[810]  13  % http://www.legi.grenobleinp.fr


 14  % Joel.Sommeria  Joel.Sommeria (A) legi.cnrs.fr


 15  %


 16  % This file is part of the toolbox UVMAT.


 17  %


 18  % UVMAT is free software; you can redistribute it and/or modify


 19  % it under the terms of the GNU General Public License as published


 20  % by the Free Software Foundation; either version 2 of the license,


 21  % or (at your option) any later version.


 22  %


 23  % UVMAT is distributed in the hope that it will be useful,


 24  % but WITHOUT ANY WARRANTY; without even the implied warranty of


 25  % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the


 26  % GNU General Public License (see LICENSE.txt) for more details.


 27  %=======================================================================


 28 


[906]  29  function DataOut=remove_background(DataIn,Param)


[574]  30  %


[906]  31  %% request input parameters


 32  if isfield(DataIn,'Action') && isfield(DataIn.Action,'RUN') && isequal(DataIn.Action.RUN,0)


 33  prompt = {'radius'};


 34  dlg_title = 'get the disk radius (pixels) used to calculate the regional minimum';


 35  num_lines= 1;


 36  def = { '4'};


 37  if isfield(Param,'TransformInput')&&isfield(Param.TransformInput,'DiskRadius')


 38  def={num2str(Param.TransformInput.DiskRadius)};


 39  end


 40  answer = inputdlg(prompt,dlg_title,num_lines,def);


 41  DataOut.TransformInput.DiskRadius=str2num(answer{1});


[574]  42  return


 43  end


[906]  44  if ~isfield(DataIn,'A')


 45  DataOut.Txt='remove_particles only valid for input images';


 46  return


 47  end


 48  if ~exist('imerode','file');


 49  DataOut.Txt='the function imerode from the image processing toolbox is needed';


 50  return


 51  end


[574]  52 


[906]  53  SE=strel('disk',Param.TransformInput.DiskRadius);


 54  %


[574]  55  DataOut=DataIn;%default


 56 


[906]  57  [npy,npx]=size(DataIn.A);


 58  [X,Y]=meshgrid(1:npx,1:npy);


 59 


[574]  60  %BACKGROUND LEVEL


 61  Atype=class(DataIn.A);


[906]  62  Aerode=imerode(DataIn.A,SE);


 63  Aflagmin=find(DataIn.A==Aerode);


 64  Xmin=X(Aflagmin);


 65  Ymin=Y(Aflagmin);


 66  Amin=double(DataIn.A(Aflagmin));


 67  F = TriScatteredInterp([Xmin Ymin], Amin);


 68  DataOut.A=double(DataOut.A)F(X,Y);


[810]  69  DataOut.A=feval(Atype,DataOut.A);


[906]  70 


 71  %BACKGROUND LEVEL


 72  % Atype=class(DataIn.A);


 73  % A=double(DataIn.A);


 74  % Backg=zeros(size(A));


 75  % Aflagmin=sparse(imregionalmin(A));%Amin=1 for local image minima


 76  % Amin=A.*Aflagmin;%values of A at local minima


 77  % % local background: find all the local minima in image subblocks


 78  % sumblock= inline('sum(sum(x(:)))');


 79  % Backg=blkproc(Amin,[nblock_y nblock_x],sumblock);% take the sum in blocks


 80  % Bmin=blkproc(Aflagmin,[nblock_y nblock_x],sumblock);% find the number of minima in blocks


 81  % Backg=Backg./Bmin; % find the average of minima in blocks


 82  % B=imresize(Backg,size(A),'bilinear');% interpolate to the initial size image


 83  % ImPart=(AB);


 84  % DataOut.A=ImPart;


 85  % %DataOut.A=ImPart.*(ImPart>threshold);


 86  % DataOut.A=feval(Atype,DataOut.A);

