source: trunk/src/transform_field/ima_levels.m @ 950

Last change on this file since 950 was 950, checked in by sommeria, 5 years ago

various updates

File size: 3.4 KB
Line 
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
7%
8%INPUT:
9% DataIn:  first input field structure
10
11%=======================================================================
12% Copyright 2008-2016, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
13%   http://www.legi.grenoble-inp.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
29function DataOut=ima_remove_background_blocks(DataIn,Param)
30%------------------------------------------------------------------------
31%% request input parameters
32if isfield(DataIn,'Action') && isfield(DataIn.Action,'RUN') && isequal(DataIn.Action.RUN,0)
33    prompt = {'block size(pixels)'};
34    dlg_title = 'get the block size (in pixels) used to calculate the local statistics';
35    num_lines= 1;
36    def     = { '100'};
37    if isfield(Param,'TransformInput')&&isfield(Param.TransformInput,'BlockSize')
38        def={num2str(Param.TransformInput.BlockSize)};
39    end
40    answer = inputdlg(prompt,dlg_title,num_lines,def);
41    DataOut.TransformInput.BlockSize=str2num(answer{1});
42    return
43end
44if ~isfield(DataIn,'A')
45    DataOut.Txt='remove_particles only valid for input images';
46    return
47end
48if ~exist('imerode','file');
49        DataOut.Txt='the function imerode from the image processing toolbox is needed';
50    return
51end
52
53%---------------------------------------------------------
54DataOut=DataIn;%default
55nblock_y=2*Param.TransformInput.BlockSize;
56nblock_x=2*Param.TransformInput.BlockSize;
57[npy,npx]=size(DataIn.A);
58[X,Y]=meshgrid(1:npx,1:npy);
59
60%BACKGROUND LEVEL
61Atype=class(DataIn.A);
62A=double(DataIn.A);
63%Backg=zeros(size(A));
64%Aflagmin=sparse(imregionalmin(A));%Amin=1 for local image minima
65%Amin=A.*Aflagmin;%values of A at local minima
66% local background: find all the local minima in image subblocks
67fctblock= inline('median(x(:))');
68Backg=blkproc(A,[nblock_y nblock_x],fctblock);% take the median in  blocks
69fctblock= inline('mean(x(:))');
70B=imresize(Backg,size(A),'bilinear');% interpolate to the initial size image
71A=(A-B);%substract background
72AMean=blkproc(A,[nblock_y nblock_x],fctblock);% take the mean in  blocks
73fctblock= inline('var(x(:))');
74AVar=blkproc(A,[nblock_y nblock_x],fctblock);% take the mean in  blocks
75Avalue=AVar./AMean% typical value of particle luminosity
76Avalue=imresize(Avalue,size(A),'bilinear');% interpolate to the initial size image
77DataOut.A=uint16(1000*tanh(A./(2*Avalue)));
78%Bmin=blkproc(Aflagmin,[nblock_y nblock_x],sumblock);% find the number of minima in blocks
79%Backg=Backg./Bmin; % find the average of minima in blocks
80
81
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