Mask Orientation Process - depends on Janas MITK-Version or else

[MatthiasWeinhold]

IMPORTANT!
The default Mask Orientation Process with permute and flip etc. is not always right
The framework needs a adaptive Code which "sees" the right orientation of the mask to the dcm/ima Files
All Datas which are created befor 02.02.2018 maybe calculated wrong!

[thomaskuestner]

You may include an orientation-dependent flipping by reading the orientation from the DICOM header SInfo:

dOrient = reshape(SInfo(1).STag.ImageOrientationPatient, [3, 2])';
dPixelSpacing = SInfo(1).STag.PixelSpacing;
dPosition = zeros(length(SInfo), 3);
for iI = 1:length(SInfo)
    dPosition(iI, :) = SInfo(iI).STag.ImagePositionPatient';
end
dOrientIndicator = sum(abs(dOrient));
[dVal, iInd] = min(dOrientIndicator);
switch(iInd)
    case 1 % sag
    case 2 % cor
    case 3 % tra
end

For the masks the orientation should be included in:
SInfo.PerFrameFunctionalGroupsSequence(1).Item_1(1).PlanePositionSequence.Item_1.ImagePositionPatient

[MatthiasWeinhold]

Not corrected but also not hard coded transformation:
Advice: pipeline Testdata with known values