% 'ima_remove_particles': removes particles from an image (keeping 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
%------------------------------------------------------------------------
function DataOut=ima_remove_particles(DataIn)
%------------------------------------------------------------------------
DataOut=[];  %default  output field
if strcmp(DataIn,'*')
    return
end

%parameters
threshold=200;
nblock_x=30;%size of image subblocks for analysis
nblock_y=30;
%--------------------------------------------------------- 
DataOut=DataIn;%default

if ~isfield(DataIn,'A')
    DataOut.Txt='remove_particles only valid for input images';
    return
end

%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);
ImPart=ImPart.*(ImPart>threshold);
DataOut.A=A-ImPart;%
DataOut.A=feval(Atype,DataOut.A);