SM_BatchDff.m

function SM_BatchDff(DIR, varargin)

%run thorough directory and make DfF movies in AVI format
% WALIII
% 09.05.15


mat_dir='DFF_MOVIES';
counter = 1;


if exist(mat_dir,'dir') rmdir(mat_dir,'s'); end


mkdir(mat_dir);





outlier_flag=0;
if nargin<1 | isempty(DIR), DIR=pwd; end

mov_listing=dir(fullfile(DIR,'*.mat'));
mov_listing={mov_listing(:).name};



filenames=mov_listing;


disp('Creating Dff movies');

[nblanks formatstring]=fb_progressbar(100);
fprintf(1,['Progress:  ' blanks(nblanks)]);

for i=1:length(mov_listing)

    [path,file,ext]=fileparts(filenames{i});

    
	fprintf(1,formatstring,round((i/length(mov_listing))*100));

	load(fullfile(DIR,mov_listing{i}),'video');
	
    %create DFF
    figure, set(gcf, 'Color','white')
 axis tight
set(gca, 'nextplot','replacechildren', 'Visible','off');

%# create AVI object

save_filename=[ fullfile(mat_dir,file) ];

vidObj = VideoWriter(save_filename);
vidObj.Quality = 30;
vidObj.FrameRate = 30;
open(vidObj);
colormap(bone);


mov_data = video.frames;
%%%%
for i=1:(length(mov_data))
%    mov_data3 = single(rgb2gray(mov_data(i).cdata));
%    mov_data4 = single(rgb2gray(mov_data(i+1).cdata));
%    %mov_data5 = single(rgb2gray(mov_data(i+2).cdata));
   mov_data2(:,:,i) = uint8(mov_data(i).cdata/256);
end

test2=(mov_data2);
% test=imresize((test),1);
% 
% h=fspecial('disk',1);
% bground=imfilter(test,h);
% % bground=smooth3(bground,[1 1 5]);
% test=test-bground;
% 
% 
% h=fspecial('disk',1);
% test2=imfilter(test,h);

%%%%%
LinKat =  cat(1,test2(:,1,10)); % initilaize linkat
for i = 2:size(test2,2)
Lin = cat(1,test2(:,i,10));
LinKat = cat(1,LinKat,Lin);
end


H = prctile(LinKat,95)+10 % take the pixel value equal to the 70th percentile value
L = prctile(LinKat,5)

test2=imresize(test2,1);

[optimizer, metric] = imregconfig('multimodal');
%# create movie
for i=1:(length(mov_data)-2);
    %test3(:,:,i) = imregister(test2(:,:,i),test2(:,:,1),'rigid',optimizer,metric);
   image(test2(:,:,i),'CDataMapping','scaled');
  caxis([double(L),double(H)])%caxis([0,70]) % change caxis
   writeVideo(vidObj, getframe(gca));
end
close(gcf)

%# save as AVI file, and open it using system video player
close(vidObj);

FrameInfo = max(test2,[],3);
%figure();
colormap(bone)
imagesc(FrameInfo);
%set(gca,'ydir','normal'); % Otherwise the y-axis would be flipped
X = mat2gray(FrameInfo);
X = im2uint8(X);
imwrite(X,save_filename,'png')

TotalX(:,:,counter) = X;
TotalX2{counter} = X;

    counter = counter+1;

end
fprintf(1,'\n');
%%

% [optimizer, metric] = imregconfig('multimodal');
% for g = 1:size(TotalX,3)
%     tiledImage(:,:,g) = imregister(TotalX(:,:,g), TotalX(:,:,1),'rigid',optimizer, metric);
% end
%  


FrameInfo2 = max(TotalX,[],3);
imwrite(FrameInfo2,'Dff_composite','png')
% Test = TotalX2;
% %mov_data = video.frames;
% im_resize = 1;
% 
% save(save_filename,'Test','mov_data','im_resize','-v7.3')