build_ops_RunOnly.m

function ops = build_ops_RunOnly(db, ops)

ops.nplanes = getOr(ops, 'nplanes', 1);
ops.nchannels = getOr(ops, 'nchannels', 1);

ops = addfields(ops, db);

for k = 1:length(db.expts)
    ops.SubDirs{k}    = num2str(db.expts(k));
end

if ops.doRegistration
    ops.RootDir = fullfile(ops.RootStorage, ops.mouse_name, ops.date);
else
    ops.RootDir = fullfile(ops.RootStorage, ops.mouse_name, ops.date,'Corrected');
    ops.RootDirRaw = fullfile(ops.RootStorage, ops.mouse_name, ops.date);
end
disp(ops.RootDir);

% build file list
ops.fsroot = [];
overview_ind = [];
for j = 1:ops.nplanes %length(ops.SubDirs) % changed on 16/11/25 by SK
    ops.fsroot{j} = dir(fullfile(ops.RootDir,sprintf('*Slice%02d*.tif',j)));
    if j==1
        ops.rawMovies = dir(fullfile(ops.RootDirRaw,'FOV1_0*.tif'));
        for k = 1:length(ops.rawMovies)
            % Do not include overview image
            if isfinite(strfind(ops.rawMovies(k).name,'overview'));
                overview_ind = k;
            end
        end
        if ~isempty(overview_ind)
            pick_ind = (1:length(ops.rawMovies))~=overview_ind;
            ops.rawMovies = ops.rawMovies(pick_ind);
        end
    end
    % ops.fsroot{j} = dir(fullfile(ops.RootDir,sprintf('*Slice%02d*_File001.tif',j)));
    for k = 1:length(ops.fsroot{j})
        % Do not include overview image
        if isempty(strfind(ops.fsroot{j}(k).name,'overview'));
            ops.fsroot{j}(k).name = fullfile(ops.RootDir, ops.fsroot{j}(k).name);
        else
            ops.fsroot{j}(k).name = [];
        end
    end
    % ops.fsroot{j} = ops.fsroot{j}(1:20); % select some fraction of files
end

try    
     % MK code for automatically determining number of planes and channels
    [~, header] = loadFramesBuff(fullfile(ops.RootDirRaw,ops.rawMovies(1).name), 1, 1, 1);
    % [~, header] = loadFramesBuff(ops.fsroot{1}(1).name, 1, 1, 1);
    [~, scanImageMetadata] = bigTiffRead(fullfile(ops.RootDirRaw,ops.rawMovies(1).name));
    % [mov, scanImageMetadata] = obj.readRaw(movNum,'single');
    
    hh=header{1};
    
    assert(strcmp(scanImageMetadata.VERSION_MAJOR, '2017b')) % For scanimage 2017b
    ops.nchannels = scanImageMetadata.hChannels.channelSave;

    fastZEnable = scanImageMetadata.hFastZ.enable;
    fastZDiscardFlybackFrames = scanImageMetadata.hFastZ.discardFlybackFrames;
    stackNumSlices = scanImageMetadata.hStackManager.numSlices;

    ops.nplanes = 1;
    ops.zoomMicro = scanImageMetadata.hRoiManager.scanZoomFactor;
    ops.imageRate = scanImageMetadata.hRoiManager.scanVolumeRate;        
        
catch
    error('Error in parsing scanImageMetadata.')
end

if ~(isfield(ops, 'planesToProcess') && ~isempty(ops.planesToProcess))
    % ops.planesToProcess = 1:ops.nplanes;
    ops.planesToProcess = 1:stackNumSlices; % changed by SK 16/12/14
else
    % planesToProcess is not working right now
    ops.planesToProcess = 1:ops.nplanes;
end

CharSubDirs = '';
for i = 1:length(ops.SubDirs)
    CharSubDirs = [CharSubDirs ops.SubDirs{i} '_'];
end
CharSubDirs = CharSubDirs(1:end-1);
ops.CharSubDirs = CharSubDirs;

ops.ResultsSavePath = sprintf('%s\\%s\\%s\\%s\\', ops.ResultsSavePath, ops.mouse_name, ops.date);
% ops.ResultsSavePath = sprintf('%s\\%s\\%s\\%s\\', ops.ResultsSavePath, ops.mouse_name, ops.date, CharSubDirs);

end