% init (Move this file into the OMERO.matlab toolbox)
clear all;close all;

% import classes
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;

import omero.sys.ParametersI;
import omero.api.RawFileStorePrxHelper;
import omero.api.RawFileStorePrx;

% create connection
client = loadOmero(); %edit ice.config to update login credentials in the matlab toolbox
session = client.createSession();
omeroKeepAlive(client)

% plate id to download
plateId = 2285;
% target path for saving the images
targetPath = '/Users/bramalingam/Downloads/OMERO.matlab-5.3.3-ice36-b63/testDownload';

% load all wells in a plate
wellList = session.getQueryService().findAllByQuery(...
['select well from Well as well '...
'left outer join fetch well.plate as pt '...
'left outer join fetch well.wellSamples as ws '...
'left outer join fetch ws.plateAcquisition as pa '...
'left outer join fetch ws.image as img '...
'left outer join fetch img.pixels as pix '...
'left outer join fetch pix.pixelsType as pt '...
'where well.plate.id = ', num2str(plateId)], []);

% get fileset associated with the well
values = ArrayList();
for j = 0
    well = wellList.get(j);
    wellsSampleList = well.copyWellSamples();

    for i = 0:wellsSampleList.size()-1
        ws = wellsSampleList.get(i);

        image = ws.getImage();
        param = ParametersI();

        l = ArrayList();
        l.add(image.getId);
        param.add("imageIds", omero.rtypes.rlist(l));

        filesets = session.getQueryService().findAllByQuery(...
            ['select fs from Fileset as fs '...
            'join fetch fs.images as image '...
            'left outer join fetch fs.usedFiles as usedFile '...
            'join fetch usedFile.originalFile as f '...
            'join fetch f.hasher '...
            'where image.id in (:imageIds)'], param);

%         values.addAll(filesets);
        fi = filesets.iterator();
        cntr = 0;
        while (fi.hasNext)
            set = fi.next();
            entries = set.copyUsedFiles();
            fj = entries.iterator();
            while (fj.hasNext())
                fs = fj.next();
                origfile = fs.getOriginalFile();
                values.add(origfile);
                disp([i j origfile.getId().getValue()])
                cntr = cntr + 1;
            end
        end
    end
end

% download original files
i = values.iterator();
name = omero.constants.RAWFILESTORE.value;
files = ArrayList();
INC = 262144;
offset = 0;
while i.hasNext()
    of = i.next;
    store = session.createRawFileStore();
    disp(of.getId().getValue());
    store.setFileId(of.getId().getValue());

    f = File(targetPath, of.getName().getValue);
    files.add(f)

    stream = FileOutputStream(f);
    size = of.getSize().getValue();
    try
        for offset = 0:(offset+INC < size)
            stream.write(store.read(offset, INC));
            offset = offset + INC;
        end
    catch
        stream = FileOutputStream(f);
        stream.write(store.read(offset, int16(size - offset)));
    end

    stream.close();
end