% 'ima_remove_background': removes backgound from an image (using the local minimum) % requires the Matlab image processing toolbox %------------------------------------------------------------------------ %%%% Use the general syntax for transform fields with a single input %%%% % OUTPUT: % DataOut: output field structure % %INPUT: % DataIn: first input field structure %======================================================================= % Copyright 2008-2019, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France % http://www.legi.grenoble-inp.fr % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr % % This file is part of the toolbox UVMAT. % % UVMAT is free software; you can redistribute it and/or modify % it under the terms of the GNU General Public License as published % by the Free Software Foundation; either version 2 of the license, % or (at your option) any later version. % % UVMAT is distributed in the hope that it will be useful, % but WITHOUT ANY WARRANTY; without even the implied warranty of % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the % GNU General Public License (see LICENSE.txt) for more details. %======================================================================= function DataOut=remove_background(DataIn,Param) %------------------------------------------------------------------------ %% request input parameters if isfield(DataIn,'Action') && isfield(DataIn.Action,'RUN') && isequal(DataIn.Action.RUN,0) prompt = {'radius'}; dlg_title = 'get the disk radius (pixels) used to calculate the regional minimum'; num_lines= 1; def = { '4'}; if isfield(Param,'TransformInput')&&isfield(Param.TransformInput,'DiskRadius') def={num2str(Param.TransformInput.DiskRadius)}; end answer = inputdlg(prompt,dlg_title,num_lines,def); DataOut.TransformInput.DiskRadius=str2num(answer{1}); return end if ~isfield(DataIn,'A') DataOut.Txt='remove_particles only valid for input images'; return end if ~exist('imerode','file'); DataOut.Txt='the function imerode from the image processing toolbox is needed'; return end SE=strel('disk',Param.TransformInput.DiskRadius); %--------------------------------------------------------- DataOut=DataIn;%default [npy,npx]=size(DataIn.A); [X,Y]=meshgrid(1:npx,1:npy); %BACKGROUND LEVEL Atype=class(DataIn.A); Aerode=imerode(DataIn.A,SE); Aflagmin=find(DataIn.A==Aerode); Xmin=X(Aflagmin); Ymin=Y(Aflagmin); Amin=double(DataIn.A(Aflagmin)); F = TriScatteredInterp([Xmin Ymin], Amin); DataOut.A=double(DataOut.A)-F(X,Y); DataOut.A=feval(Atype,DataOut.A); %BACKGROUND LEVEL % Atype=class(DataIn.A); % A=double(DataIn.A); % Backg=zeros(size(A)); % Aflagmin=sparse(imregionalmin(A));%Amin=1 for local image minima % Amin=A.*Aflagmin;%values of A at local minima % % local background: find all the local minima in image subblocks % sumblock= inline('sum(sum(x(:)))'); % Backg=blkproc(Amin,[nblock_y nblock_x],sumblock);% take the sum in blocks % Bmin=blkproc(Aflagmin,[nblock_y nblock_x],sumblock);% find the number of minima in blocks % Backg=Backg./Bmin; % find the average of minima in blocks % B=imresize(Backg,size(A),'bilinear');% interpolate to the initial size image % ImPart=(A-B); % DataOut.A=ImPart; % %DataOut.A=ImPart.*(ImPart>threshold); % DataOut.A=feval(Atype,DataOut.A);