build_ops3.m

function ops = build_ops3(db, ops)

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


% ops = db;
if ~iscell(db.mouse_name)
    % this is the usual case where we have a simple single session recording
    ops = addfields(ops, db);
    
    for k = 1:length(db.expts)
        ops.SubDirs{k}    = num2str(db.expts(k));
    end
    if isempty(db.expts)
        ops.SubDirs{1} = [];
    end
    
    if ~isfield(ops, 'RootDir')
        ops.RootDir = fullfile(ops.RootStorage, ops.mouse_name, ops.date);
    end
    
    % build file list
    ops.fsroot = [];
    for j = 1:length(ops.SubDirs)
        ops.fsroot{j} = dir(fullfile(ops.RootDir, ops.SubDirs{j}, '*.tif'));
        ops.fsroot{j} = cat(1, ops.fsroot{j}, ...
            dir(fullfile(ops.RootDir, ops.SubDirs{j}, '*.tiff')));
        for k = 1:length(ops.fsroot{j})
            ops.fsroot{j}(k).name = fullfile(ops.RootDir, ops.SubDirs{j}, ops.fsroot{j}(k).name);
        end
    end
    
    if isfield(db, 'expred') && ~isempty(db.expred) && ...
            (~isfield(db, 'nchannels_red') || isempty(db.nchannels_red))
        ops.fsred = dir(fullfile(ops.RootDir, num2str(db.expred), '*.tif'));
        for k = 1:length(ops.fsroot{j})
            ops.fsred(k).name = fullfile(ops.RootDir, num2str(db.expred), ops.fsred(k).name);
        end
    end
else
    % here we might have multiple sessions, which we want to be analyzed
    % together (exactly the same FOV)
    nSessions = length(db.mouse_name);
    % a backwards compatible version of db
    dbCompat = db;
    dbCompat.mouse_name = db.mouse_name{1};
    dbCompat.date = db.date{1};
    dbCompat.expts = cell2mat(db.expts(:)');
    ops = addfields(ops, dbCompat);
    ops.db_orig = db;
    
    ops.fsroot = cell(0);
    ops.SubDirs = cell(0);
    for iSession = 1:nSessions
        ops.RootDir = fullfile(ops.RootStorage, db.mouse_name{iSession}, db.date{iSession});
        for iExp = 1:length(db.expts{iSession})
            ops.SubDirs{end+1} = num2str(db.expts{iSession}(iExp));
            ops.fsroot{end+1} = dir(fullfile(ops.RootDir, ops.SubDirs{end}, '*.tif'));
            for iFile = 1:length(ops.fsroot{end})
                ops.fsroot{end}(iFile).name = fullfile(ops.RootDir, ops.SubDirs{end}, ops.fsroot{end}(iFile).name);
            end
        end
    end
    % this line to be backward compatible (just in case)
    ops.RootDir = fullfile(ops.RootStorage, ops.mouse_name, ops.date);
end

if ops.readTiffHeader
    try
        % MK code for automatically determining number of planes and channels
        [~, header] = loadFramesBuff(ops.fsroot{1}(1).name, 1, 1, 1);
        
        hh=header{1};
        
        verStr = ['SI.VERSION_MAJOR = ',char(39),'2016b',char(39)];
        
        if contains(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
    end
end
if isfield(ops, 'zoomMicro')
    ops.zoom = getOr(ops, 'zoom', ops.zoomMicro);
else
    ops.zoom = getOr(ops, 'zoom', 1);
end


if ~(isfield(ops, 'planesToProcess') && ~isempty(ops.planesToProcess))
    ops.planesToProcess = 1:ops.nplanes;
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, ...
    CharSubDirs);