SliceFinder.m

function SliceFinder(varargin)
	%SliceFinder Multi-species histology slice alignment program
	
	%% add subfolders
	if ~isdeployed
		%check version
		PF_AssertVersion();
		
		%disable buttons
		global sUPF_ChooseGui %#ok<TLEV>
		UPF_DisableButtons(sUPF_ChooseGui);
		
		%add folders
		strFullpath = mfilename('fullpath');
		strPath = fileparts(strFullpath);
		sDir=dir([strPath filesep '**' filesep]);
		%remove git folders
		sDir(contains({sDir.folder},[filesep '.git'])) = [];
		cellFolders = unique({sDir.folder});
		for intFolder=1:numel(cellFolders)
			addpath(cellFolders{intFolder});
		end
		
		%enable buttons
		UPF_EnableButtons(sUPF_ChooseGui);
	end
	
	%% try using Acquipix variables
	try
		sRP = RP_populateStructure();
		strDefaultPath = sRP.strProbeLocPath;
	catch
		sRP = struct; %#ok<NASGU>
		strDefaultPath=cd();
	end
	
	%% ask for folder & meta data (if any)
	sSliceData = SH_LoadSlicePath(strDefaultPath);
	if isempty(sSliceData),return;end
	
	%% load atlas
	sAtlasParams = PF_getAtlasIni();
	
	%select which atlas to use
	cellAtlases = {sAtlasParams.name};
	[intSelectAtlas,boolContinue] = listdlg('ListSize',[200 100],'Name','Atlas Selection','PromptString','Select Atlas:',...
		'SelectionMode','single','ListString',cellAtlases);
	if ~boolContinue,return;end
	
	%load atlas
	strAtlasName = sAtlasParams(intSelectAtlas).name; %#ok<NASGU>
	strPathVar = sAtlasParams(intSelectAtlas).pathvar;
	fLoader = sAtlasParams(intSelectAtlas).loader;
	
	%get path
	strAtlasPath = PF_getIniVar(strPathVar);
	
	%load & prep atlas
	sAtlas = feval(fLoader,strAtlasPath);
	if isempty(sAtlas),return;end
	if isfield(sAtlasParams(intSelectAtlas),'downsample') && ~isempty(sAtlasParams(intSelectAtlas).downsample)
		sAtlas.Downsample = round(sAtlasParams(intSelectAtlas).downsample);
	else
		sAtlas.Downsample = 1;
	end
	
	%% run slice aligner
	SF_GenSliceFinderGUI(sAtlas,sSliceData);
end