associateROIsToMovies.m

annotations = getAnnotationTypes();
objects = getObjectTypes();
defaultownerid = session.getAdminService().getEventContext().userId;
% Load existing file annotations
metadataService = session.getMetadataService();

ids = toJavaList([], 'java.lang.Long');
include = toJavaList(getLCCBOmeroNamespace, 'java.lang.String');
exclude = toJavaList([], 'java.lang.String');

parameters = omero.sys.ParametersI;
parameters.exp(rlong(defaultownerid));

% Read annotations
object = objects(strcmpi('Image', {objects.name}));
annotation = annotations(strcmpi('file', {annotations.name}));
annotations = metadataService.loadSpecifiedAnnotationsLinkedTo(...
    annotation.class, include, exclude, object.class, ids, parameters);

% Aggregate all annotations into a java.util.ArrayList
keySet = annotations.keySet;
i = keySet.iterator;
fprintf('Found %g images with analysis\n', keySet.size);
ids = [];
while (i.hasNext())
    ids = [ids i.next()];
end
    
annotationList = cell(numel(ids), 1);
for n = 1:numel(ids)
    annotationListPerId = annotations.get( ...
        java.lang.Long(ids(n)));
    if ~isempty(annotationListPerId)
        annotationList{n} = toMatlabList(annotationListPerId);
    end
end
annotations = annotationList;

%% Find images with ROIs
disp('Finding ROIs');
roiService = session.getRoiService();
roiIds = zeros(numel(ids), 1);
for i = 1 : numel(ids)
    roiResult = session.getRoiService().findByImage(ids(i), []);
    if ~isempty(roiResult.rois) && roiResult.rois.size == 1,
        roiIds(i) = roiResult.rois.get(0).getId().getValue();
    end
    progressText(i/numel(ids), 'Finding images with ROIs');
end

fprintf('Found %g images with ROI and analysis\n', sum(logical(roiIds)));

%%
validIds = ids(roiIds ~=0);
validRoiIds = roiIds(roiIds ~=0);
MD(numel(validIds)) = MovieData();

for i = 1: numel(validIds)
    fprintf(1, 'Movie %g/%g\n', i,numel(validRoiIds));
    MD(i) = MovieData.load(s, validIds(i));
    MD(i).roiOmeroId_ = validRoiIds(i);
end