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function MSE = alignSubScansMarkers(calibrationFileName, scanDir, alnFileName)

%ALIGNSUBSCANSMARKERS Determines an exact alignment of sub scans (scans

% from e.g. one revolution of the rotation stage). 

% The method searches for circular white markers of the specified diameter.

% White frames corresponding to each sub scan must be available.

% A coarse alignment in the form of an aln-file must be provided. 

%

% 2017 Jakob Wilm, DTU

calibration = readOpenCVXML(calibrationFileName);

initialAlign = readMeshLabALN(alnFileName);

whiteFrameDirs = dir(fullfile(scanDir, 'sequence_*'));

assert(length(whiteFrameDirs) == length(initialAlign));

nSubScans = length(whiteFrameDirs);

for i=1:nSubScans

    frame0 = imread(fullfile(whiteFrameDirs(i).folder, whiteFrameDirs(i).name, 'frames0_0.png'));

    frame1 = imread(fullfile(whiteFrameDirs(i).folder, whiteFrameDirs(i).name, 'frames1_0.png'));

    %BW0 = im2bw(frame0, graythresh(frame0));

    %RP0 = regionprops(BW0, 'Area', 'Solidity', 'Eccentricity', 'Orientation', 'Centroid');

    gray0 = rgb2gray(frame0);

	[edge0, tr] = edge(gray0, 'Canny', [0.08 0.1], 2);

    %edge0 = edge0(1190:1290, 1975:2045);

    %figure; imagesc(edge0);

    ep = struct('minMajorAxis', 25, 'maxMajorAxis', 35, 'minAspectRatio', 0.4, 'numBest', 10, 'randomize', 2, 'smoothStddev', 1);

    e0 = ellipseDetection(edge0, ep);

    figure; hold('on'); imshow(edge0); ellipse(e0(:,3), e0(:,4), e0(:,5)*pi/180, e0(:,1), e0(:,2), 'r'); 

end

end