selectROIFilesForZIntensityMeasure.m

function selectROIFilesForVolumeIntensityMeasure

% Copyright (C) 2013-2014 University of Dundee & Open Microscopy Environment.
% All rights reserved.
% 
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
% 
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
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% You should have received a copy of the GNU General Public License along
% with this program; if not, write to the Free Software Foundation, Inc.,
% 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

infobox = helpdlg('You are going to be asked for your username and password for Nightshade, for some information about your experimental conditions and to select the ROI files for each condition you have. Segmentation masks will be saved in the dataset of the original images, and after processing has completed you will be asked where to save the results spreadsheet.', 'Information');
uiwait(infobox);
username = inputdlg('What is your Nightsahde Username?');
password = inputdlg('What is your Nightshade Password?');
username = username{1};
password = password{1};
numConditions = inputdlg('How many experimental conditions do you have? For example "control" and "drug1" would be 2.', 'Number of conditions');
numConditions = str2double(numConditions);
dataOut = {'Original Image', 'Mask Image', 'Condition', 'Summed Intensity', 'Mean Intensity', 'Standard Deviation';};
for thisCondition = 1:numConditions
    conditionName{thisCondition} = inputdlg(['Give condition ', num2str(thisCondition), ' a name...']);
    [files{thisCondition}, paths{thisCondition}] = uigetfile('*.xml', ['Choose your ROI files for ', conditionName{thisCondition}{1}], 'MultiSelect', 'on');
end

for thisCondition = 1:numConditions
    if iscell(files{thisCondition})
        numFiles{thisCondition} = length(files{thisCondition});
        for thisFile = 1:numFiles{thisCondition}
            [ROIIdx{thisCondition}{thisFile} roishapeIdx{thisCondition}{thisFile}] = zIntensityMeasure(paths{thisCondition}, files{thisCondition}{thisFile}, username, password, thisFile, numFiles{thisCondition}, thisCondition, numConditions);
            numROI = length(ROIIdx{thisCondition}{thisFile});
            for thisROI = 1:numROI
                dataOut = [dataOut; {roishapeIdx{thisCondition}{thisFile}{thisROI}.origName roishapeIdx{thisCondition}{thisFile}{thisROI}.name conditionName{thisCondition}{1} roishapeIdx{thisCondition}{thisFile}{thisROI}.sum roishapeIdx{thisCondition}{thisFile}{thisROI}.mean roishapeIdx{thisCondition}{thisFile}{thisROI}.stdev}];
            end
        end
    else
        thisFile = 1;
        numFiles = 1;
        [ROIIdx{thisCondition}{thisFile} roishapeIdx{thisCondition}{thisFile}] = zIntensityMeasure(paths{thisCondition}, files{thisCondition}, username, password, thisFile, numFiles, thisCondition, numConditions);
        numROI = length(ROIIdx{thisCondition}{thisFile});
        for thisROI = 1:numROI
            dataOut = [dataOut; {roishapeIdx{thisCondition}{thisFile}{thisROI}.origName roishapeIdx{thisCondition}{thisFile}{thisROI}.name conditionName{thisCondition}{1} roishapeIdx{thisCondition}{thisFile}{thisROI}.sum roishapeIdx{thisCondition}{thisFile}{thisROI}.mean roishapeIdx{thisCondition}{thisFile}{thisROI}.stdev}];
        end
    end
end

[saveFile savePath] = uiputfile('*.xls','Save Results','IntensityMeasurements.xls');
xlswrite([savePath saveFile], dataOut);

end