add_CMOS.m

function data = add_CMOS(data,param,e_PID,e_scan_step,e_dataset,options)
	% ================================================
	% Only add if cmos cams exist.
	% ================================================
	if isfield(param,'cam_CMOS')

		% ================================================
		% Only add if cmos cams exist.
		% ================================================
		if size(param.cam_CMOS,1)>0
			% ================================================
			% Iterate for each camera
			% ================================================
			for i=1:size(param.cmos_path,2)
				% ================================================
				% Gather info
				% ================================================
				% Get camera name
				str=param.cam_CMOS{i,1};

				% Path to dir containing files
				path = param.cmos_path{i};
				stepfiles = fullfile(get_remoteprefix(),path,['*step_' sprintf('%02d',e_scan_step(1)) '*.tif']);
				filelist  = dir(stepfiles);
				n_i_shots = size(filelist,1);
				if n_i_shots == 0
					rgbvec = [1,0,0];
					printstr = ['No CMOS data found for ' str ' for path:\n' stepfiles '\n'];
					cprintf(rgbvec,printstr);
				end
				step      = zeros(1,n_i_shots);
				pID       = zeros(1,n_i_shots);
				files     = cell(1,n_i_shots);
				% ================================================
				% Iterate for each file
				% ================================================
				for j=1:n_i_shots
					file     = filelist(j).name;
					files{j} = fullfile(get_remoteprefix(),path,file);
					separ    = regexp(file,'_');
					step(j)  = str2num(file(separ(2)+1:separ(3)-1));
					pID(j)   = str2num(file(separ(4)+1:end-4));
				end
				
				% ================================================
				% Find cam background
				% ================================================

				% Pass through cam name converter (should do nothing?)
				[filestr,structstr]=cams2filenames(str,param.timestamp);
				data.raw.images.(structstr)=struct();

				prefix = get_remoteprefix();

				bgfile = dir(fullfile(prefix,path,'*background*.tif'));
				bgfile = fullfile(prefix,path,bgfile.name)

				% Only do things if bg exists
				if isfield(param,'cmos_bg_struct')
					data.raw.images.(structstr)=replace_field(data.raw.images.(structstr),...
								'background_dat'	, cell_construct(...
													bgfile,...
													1,n_i_shots),...
								'background_format'	, cell_construct('tif',1,n_i_shots));
					names=fieldnames(param.cmos_bg_struct.(str));
					for j=1:size(names,1)
						toadd=param.cmos_bg_struct.(str).(names{j});
						if iscell(toadd)
							data.raw.images.(structstr).(names{j})=cell_construct(toadd,1,n_i_shots);
						else
							data.raw.images.(structstr).(names{j})=ones(1,n_i_shots)*toadd;
						end
					end
				end
				

				% Camera type is CMOS.
				format=cell_construct('CMOS',1,n_i_shots);
	
				% ================================================
				% Write information gathered into the struct
				% ================================================
	
	
				% Get image UIDs
				option.IMAGE_PID      = pID;
				option.IMAGE_SCANSTEP = step;
				UIDs                  = assign_UID(e_PID,e_scan_step,e_dataset,option);
				i_UID                 = UIDs.image_UID;
				display('================================')
				% size(i_UID)
				% size(files)
				% size(pID)
				% size(step)
				% display(pID)
		
				data.raw.images.(structstr)=replace_field(data.raw.images.(structstr),...
								'dat'			, files, ...
								'format'		, format, ...
								'isfile'		, ones(1,n_i_shots), ...
								'bin_index'		, [1:n_i_shots], ...
								'UID'			, i_UID, ...
		                    				'PID'                   , pID,...
								'IDtype'		, 'Image');
			end
		end
	end
end