recalc.m

%Copyright (c) 2018 Carlo Manzo & Marta Cullell-Dalmau

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% this software and associated documentation files (the "Software"), to deal in the 
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% The above copyright notice and this permission notice shall be included in all 
% copies or substantial portions of the Software.
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% THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, 
% INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A 
% PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT 
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function handles=recalc(handles)

h = waitbar(0,'Please wait...');

handles.thr1=get(handles.slider1,'Value');
handles.IM_mct=im2bw(handles.IM_mc,handles.thr1);
handles.IM_mct=medfilt2(handles.IM_mct,[5 5]);

handles.thr2=get(handles.slider2,'Value');
handles.IM_mct2=filledgegaps(handles.IM_mct,handles.thr2);
%[edgelist, labelededgeim] = edgelink(IM_mct, 10);
%seglist = lineseg(edgelist, 2);
handles.IM_mctfil=abs(imfill(handles.IM_mct2,'holes'));

handles.RGB=handles.IM_all;
handles.RGB(:,:,2)=handles.IM_all(:,:,2).*uint8(abs(handles.IM_mctfil-1));

% i=imfilter(handles.IM_mct,fspecial('disk',100));
% i(find(i>0))=1;
% i=abs(1-i);
% tt=(handles.IM_all);%.*uint8( i);
% imwrite(uint8(tt),'test.tiff');
%% plots
close(h)
axes(handles.axes1)
cla
imagesc(handles.IM_all)
axis image
axis off

axes(handles.axes2)
cla
imagesc(handles.IM_mct)
colormap(gray)
axis image
axis off

axes(handles.axes3)
cla
imagesc(handles.IM_mctfil)
colormap(gray)
axis image
axis off

axes(handles.axes4)
cla
imagesc(handles.RGB)
axis image
axis off