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function MSE = alignSubScansMarkers(calibrationFileName, scanDir, alnFileName)
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function MSE = alignSubScansMarkers(calibrationFileName, scanDir, alnFileName)
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%ALIGNSUBSCANSMARKERS Determines an exact alignment of sub scans (scans
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%ALIGNSUBSCANSMARKERS Determines an exact alignment of sub scans (scans
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% from e.g. one revolution of the rotation stage).
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% from e.g. one revolution of the rotation stage).
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% The method searches for circular white markers of the specified diameter.
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% The method searches for circular white markers of the specified diameter.
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% White frames corresponding to each sub scan must be available.
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% White frames corresponding to each sub scan must be available.
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% A coarse alignment in the form of an aln-file must be provided.
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% A coarse alignment in the form of an aln-file must be provided.
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%
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%
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% 2017 Jakob Wilm, DTU
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% 2017 Jakob Wilm, DTU
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calibration = readOpenCVXML(calibrationFileName);
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calibration = readOpenCVXML(calibrationFileName);
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initialAlign = readMeshLabALN(alnFileName);
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initialAlign = readMeshLabALN(alnFileName);
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whiteFrameDirs = dir(fullfile(scanDir, 'sequence_*'));
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whiteFrameDirs = dir(fullfile(scanDir, 'sequence_*'));
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assert(length(whiteFrameDirs) == length(initialAlign));
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assert(length(whiteFrameDirs) == length(initialAlign));
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nSubScans = length(whiteFrameDirs);
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nSubScans = length(whiteFrameDirs);
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for i=1:nSubScans
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for i=1:nSubScans
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    frame0 = imread(fullfile(whiteFrameDirs(i).folder, whiteFrameDirs(i).name, 'frames0_0.png'));
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    frame0 = imread(fullfile(whiteFrameDirs(i).folder, whiteFrameDirs(i).name, 'frames0_0.png'));
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    frame1 = imread(fullfile(whiteFrameDirs(i).folder, whiteFrameDirs(i).name, 'frames1_0.png'));
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    frame1 = imread(fullfile(whiteFrameDirs(i).folder, whiteFrameDirs(i).name, 'frames1_0.png'));
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    %BW0 = im2bw(frame0, graythresh(frame0));
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    %BW0 = im2bw(frame0, graythresh(frame0));
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    %RP0 = regionprops(BW0, 'Area', 'Solidity', 'Eccentricity', 'Orientation', 'Centroid');
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    %RP0 = regionprops(BW0, 'Area', 'Solidity', 'Eccentricity', 'Orientation', 'Centroid');
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    gray0 = rgb2gray(frame0);
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    gray0 = rgb2gray(frame0);
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	[edge0, tr] = edge(gray0, 'Canny', [0.08 0.1], 2);
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	[edge0, tr] = edge(gray0, 'Canny', [0.08 0.1], 2);
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    %edge0 = edge0(1190:1290, 1975:2045);
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    %figure; imagesc(edge0);
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    %figure; imagesc(edge0);
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    ep = struct('minMajorAxis', 15, 'maxMajorAxis', 25, 'minAspectRatio', 0.3, 'numBest', 50);
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    ep = struct('minMajorAxis', 25, 'maxMajorAxis', 35, 'minAspectRatio', 0.4, 'numBest', 10, 'randomize', 2, 'smoothStddev', 1);
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    e0 = ellipseDetection(edge0, ep);
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    e0 = ellipseDetection(edge0, ep);
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    figure; hold('on'); imshow(edge0); ellipse(e0(:,3), e0(:,4), e0(:,5)*pi/180, e0(:,1), e0(:,2), 'r');
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    figure; hold('on'); imshow(edge0); ellipse(e0(:,3), e0(:,4), e0(:,5)*pi/180, e0(:,1), e0(:,2), 'r');
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end
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end
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end
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end
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