fread_Tsm_redshirt.m

% alternative approach to read out binary data 

% fullframe loading

ind1 = NaN(1,256*256/2);
ind2 = NaN(1,256*256/2);
for c = 1:256
    ind1( [1:128]+128*(c-1) ) = [1:128] + 256*(c-1);
    ind2( [1:128]+128*(c-1) ) = fliplr([129:256] + 256*(c-1));
end

n_frames = 100;
pixel_interval = 256*256;
frames_skip = 2000;
bit_depth = info.PrimaryData.Keywords{2,2};
byte_conversion = bit_depth/8;

fid = fopen(filename,'r');
fseek(fid,offset,'bof')
% skip to the end of frame_skip and start reading from the following frame
fseek(fid, pixel_interval * byte_conversion * frames_skip, 'cof')

datatemp = fread(fid,[256*256,n_frames],'int16');
data1 = datatemp(ind1,:);
data1 = reshape(data1,128,256,n_frames);
data2 = datatemp(ind2,:);
data2 = reshape(data2,128,256,n_frames);
dataout = cat(1,data1,data2);

fclose(fid);

% reading pixels from ROIs, ROIs should be rectangles of pixels

% ROIs given as [rows , cols]; transform into pixel linear indices

fid = fopen(filename,'r');
frame_pxl = prod(rec_dim(1:2));  % pixels per frame

pix_linear = reshape(1:rec_dim(1)*rec_dim(2),rec_dim(1),rec_dim(2)); %linear indices pixels in final de-interleaved matrix
ind1 = NaN(1,256*256/2);
ind2 = NaN(1,256*256/2);
n_frames = 100; %input function
for c = 1:256
    ind1( [1:128]+128*(c-1) ) = [1:128] + 256*(c-1);
    ind2( [1:128]+128*(c-1) ) = fliplr([129:256] + 256*(c-1));
end
pix_linear_interleaved = cat(1,reshape(ind1,128,256),reshape(ind2,128,256));

% sort out ROIs based on the linear indices of the first pixel (top-left
% corner)
[ROIs_first_pxl ROIs_indices] = sort(diag(pix_linear(ROIs(:,1),ROIs(:,2))));
ROIs = ROIs(ROIs_indices,:);

for r = 1:size(ROIs,1)
    
    rows = ROIs(r,1):ROIs(r,1)+ROIs(r,3);
    cols = ROIs(r,2):ROIs(r,2)+ROIs(r,4);
    pixels = pix_linear(rows,cols);
        pixels_read = []; precision = []; skip = [];    
    dataout = NaN(numel(rows),numel(cols),n_frames);    
    
    % extract data for pixels belonging to first channel 
    pixels_read = pixels(ismember(pixels,ind1));
    if ~isempty(pixels_read)
        pixels_read = reshape(pixels_read,numel(find(rows <= 128)),numel(cols));
        precision = [num2str(size(pixels_read,1)),'*','int16'];
        skip = frame_pxl - size(pixels_read,1) * byte_conversion;
        % generate vector of offsets to move the beginning of a new column
        for cc = 1:length(cols)
            fseek(fid,offset + pix_linear(rows(1)-1,cols(cc))*byte_conversion,'bof');
            temp = fread(fid, [size(pixels_read,1) n_frames], precision, skip);
            dataout(find(rows <= 128),cc,:) = temp;
        end
    end
    
    % extract data for pixels belonging to second channel 
    pixels_read = pix_linear_interleaved(pixels(ismember(pixels,ind2)));
    if ~isempty(pixels_read)
        pixels_read = reshape(pixels_read,numel(find(rows > 128)),numel(cols));
        
        precision = [num2str(size(pixels_read,1)),'*','int16'];
        skip = frame_pxl - size(pixels_read,1) * byte_conversion;
        
        % generate vector of offsets to move the beginning of a new column
        for cc = 1:length(cols)
            fseek(fid,offset + (pixels_read(end,cc)-1)*byte_conversion,'bof');
            temp = fread(fid, [size(pixels_read,1) n_frames], precision, skip);
            dataout(find(rows > 128),cc,:) =  flipdim(temp,1);
        end
    end
    
end