build_ops3.m

function ops = build_ops3(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);
    
    hh=header{1};
    
    verStr = ['SI.VERSION_MAJOR = ',char(39),'2016b',char(39)];
    
    if strfind(hh, verStr) % For scanimage 2016b, SF
        str = hh(strfind(hh,'channelSave = '):end);
        ind = strfind(str, 'SI');
        ch = str2num(str(15 : ind(1)-1));
        ops.nchannels = length(ch);
        
        fastZEnable = sscanf(hh(strfind(hh,'hFastZ.enable = '):end), 'hFastZ.enable = %s');
        fastZEnable = strcmp(fastZEnable,'true');
        fastZDiscardFlybackFrames = sscanf(hh(strfind(hh, 'hFastZ.discardFlybackFrames = '):end), 'hFastZ.discardFlybackFrames = %s');
        fastZDiscardFlybackFrames = strcmp(fastZDiscardFlybackFrames,'true');
        stackNumSlices = sscanf(hh(strfind(hh, 'hStackManager.numSlices = '):end), 'hStackManager.numSlices = %d');
        
        ops.nplanes = 1;
        
        if fastZEnable
            ops.nplanes = stackNumSlices+fastZDiscardFlybackFrames;
        end
        
        str = hh(strfind(hh, 'scanZoomFactor = '):end);
        ind = strfind(str, 'SI');
        ops.zoomMicro = str2double(str(18 : ind(1)-1));
        
        ops.imageRate = sscanf(hh(strfind(hh, 'scanFrameRate = '):end), 'scanFrameRate = %f');
        
        if isfield(db, 'expred') && ~isempty(db.expred) && ...
            (~isfield(db, 'nchannels_red') || isempty(db.nchannels_red))
        [~, header] = loadFramesBuff(ops.fsred(1).name, 1, 1, 1);
        hh=header{1};
        str = hh(strfind(hh, 'channelSave = '):end);
        ind = strfind(str, 'SI');
        ch = str2num(str(15 : ind(1)-1));
        ops.nchannels_red = length(ch);
        end
        
    end
        
    % Old scanimage
    
    str = hh(strfind(hh, 'channelsSave = '):end);
    ind = strfind(str, 'scanimage');
    ch = str2num(str(16 : ind(1)-1));
    ops.nchannels = length(ch);
    
    fastZEnable = sscanf(hh(strfind(hh, 'fastZEnable = '):end), 'fastZEnable = %d');
    fastZDiscardFlybackFrames = sscanf(hh(strfind(hh, 'fastZDiscardFlybackFrames = '):end), 'fastZDiscardFlybackFrames = %d');
    if isempty(fastZDiscardFlybackFrames)
        fastZDiscardFlybackFrames = 0;
    end
    stackNumSlices = sscanf(hh(strfind(hh, 'stackNumSlices = '):end), 'stackNumSlices = %d');
    
    ops.nplanes = 1;
    if fastZEnable
        ops.nplanes = stackNumSlices+fastZDiscardFlybackFrames;
    end
    
    str = hh(strfind(hh, 'scanZoomFactor = '):end);
    ind = strfind(str, 'scanimage');
    ops.zoomMicro = str2double(str(18 : ind(1)-1));
    
    ops.imageRate = sscanf(hh(strfind(hh, 'scanFrameRate = '):end), 'scanFrameRate = %f');
    
    % get number of channels of red experiment
    if isfield(db, 'expred') && ~isempty(db.expred) && ...
            (~isfield(db, 'nchannels_red') || isempty(db.nchannels_red))
        [~, header] = loadFramesBuff(ops.fsred(1).name, 1, 1, 1);
        hh=header{1};
        str = hh(strfind(hh, 'channelsSave = '):end);
        ind = strfind(str, 'scanimage');
        ch = str2num(str(16 : ind(1)-1));
        ops.nchannels_red = length(ch);
    end
catch
    % for Scanimage 2015 -- extracting SI metadata SK 17/02/28
    info = imfinfo(fullfile(ops.RootDirRaw,ops.rawMovies(1).name));
    temp = info.Software;
    ind = strfind(temp,'SI.');
    temp(ind(2:end)-1) = ';';
    temp(end) = ';';
    eval(temp);
    
    fZ              = SI.hFastZ.enable;
    ops.nchannels   = length(SI.hChannels.channelSave);
    
    if fZ
        stackNumSlices = SI.hFastZ.numFramesPerVolume;
        fastZDiscardFlybackFrames = SI.hFastZ.discardFlybackFrames;
        ops.nplanes = stackNumSlices+fastZDiscardFlybackFrames;
    else
        stackNumSlices = 1;
        ops.nplanes = 1;
    end
    ops.zoomMicro = SI.hRoiManager.scanZoomFactor;
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