fMRI_Connectivity/resources/BSM_Class/BSM.m

classdef BSM<handle
    %BSM Summary of this class goes here
    %   Detailed explanation goes here
    
    properties %public properties
        SPMs={}; %field to contain the full path of all SPM.mat files to be analysed
        Acfl %columns in SPM.xX.X to ignore
        Type=1; %BSM type 1..4 5: none
    end
    properties %private properties
        SPM_orig %temporary storage for SPM.mat file
        ActiveColumns %store the columns to be analized
        U_orig %store the U field of SPM
        TargetFolder %target folder
        % option below obsolete? 
        BSMToolboxPath%store path to BSMToolbox
        SPMPath;%store path to SPM folder
        SPMIndexList=[];
    end
    properties (Dependent) %dependent properties
        NumSPMs% number of SPM.mat files to process

    end
    properties %constants
        BSMMethod={'Traditional BSM Rissman et al', 'Adapted BSM Rissman et al', 'Fast approach (Mumford et al)', 'Adapted fast approach','none'};
    end
    
    methods %user callable methods
        function Calc(obj,varargin)
            % obj.calc to apply calculate to all SPM.mat files
            % obj.calc(n) to calculated the nth SPM.mat file
            % obj.calc([1 3 6]) to indicate which SPM.mat file to calculate
            
            
            SPMidx=[];% will contain the index to the SPMs to work on 
            if logical(numel(varargin))
                SPMidx=varargin{1};
            end
            %check number of input arguments
            if ~logical(obj.NumSPMs)%nothing to do
                fprintf('== == == Nothing to do: done == == ==\n')
                return;
            end
            if isempty(SPMidx)
                SPMidx=1:obj.NumSPMs;
            end
            if ~isnumeric(SPMidx)||~all(isfinite(SPMidx))||min(SPMidx)<1||max(SPMidx)>obj.NumSPMs
                id='BSM:Calc:InvalidIndex';
                msg='Invalid Index';
                throw(MException(id,msg));
            end
            if numel(SPMidx)>1
                obj.SPMIndexList=SPMidx;
                SPMidx=obj.SPMIndexList(end);
            end
            %% start dealing with val is a single entry
            %% do the calculation
            %% clean up
            %% make SPMIndexList one shorter, return if not possible
            %% next recursion loop. 
            warning('OFF', 'MATLAB:MKDIR:DirectoryExists');
            %this try catch block will handle any errors that might ocure
            %warning will not remain off by accident
            try
            catch ME
                warning('ON', 'MATLAB:MKDIR:DirectoryExists');
                rethrow(ME);
            end
        end
    end
    methods %constructor and set/get methods
        function obj = BSM(varargin)
            %BSM Construct an instance of this class
            %option: parse the info of a matlab batch file?  see
            %tbx_cf_bsm?
            %TODO:
            % set default values
            obj.SPMPath=[]; %get the SPM path
            if nargin>0
                [val,TF]=obj.MyGetVal('SPMs',varargin);if TF;obj.SPMs=val;end
                [val,TF]=obj.MyGetVal('Type',varargin);if TF;obj.Type=val;end
                [val,TF]=obj.MyGetVal('Acfl',varargin);if TF;obj.Acfl=val;end
            end
            %   initialize spm job enviourment
            spm_jobman('initcfg'); 
        end
        function val=get.NumSPMs(obj)
            val=numel(obj.SPMs);
        end
        function set.Type(obj,val)
            %check allowed input
            if ~isnumeric(val)|| any(~ismember(val,1:5))
                id='BSM:Type:invalid';
                msg='use a value in the range 1..5';
                throw(MException(id,msg));
            end
            obj.Type=val;
        end
        function set.Acfl(obj,val)
            %allow clearing 
            if isempty(val)
                obj.Acfl=[];
            end
            if ~isnumeric(val) || any(val<1) || any(~isfinite(val))
                id='BSM:Acfl:invalid';
                msg='set an array of positive integer values to the Acfl field';
                throw(MException(id,msg));
            end
            obj.Acfl=val;
            
        end
        function set.SPMs(obj,val)
            %set the SPMs to be analysed
            %obj.SPMs=<val>
            %possible values for <val>
            %   {}      : clear the SPMs field
            %   {'ui'}  : ask user input
            if ~iscell(val)
                fprintf('%s\n',...
                    'Use any of the following options',...
                    'obj.SPMs={}',...
                    'obj.SPMs={''ui''}',...
                    'obj.SPMs={<Ful path to SPM.mat>}');
                return
            end
            if isempty(val) %allow empty input
                return;
            end
            if strcmpi(val{1},'ui')
                [P,sts]=spm_select([1 Inf],'mat','select the SPM.mat files',obj.SPMs,pwd,'^SPM.mat');
                if ~logical(sts);return;end
                if iscell(P)
                    val=P;
                else
                    val=cellstr(P);
                end
            end
            % capture file not found somewhat clever
            TF=cellfun(@exist,val);
            if any(not(TF))
                id='BSM:SetSPMs:FileNotFound';
                msg=sprintf('file not found\t%s\n',val{not(TF)});
                throw(MException(id,msg)); 
            end
            obj.SPMs=val;
        end
    end
    methods %private functions
        function set.SPMPath(obj,~)
            SPMFound=which('spm'); %check if SPM in searchpath
            if isempty(SPMFound) %SPM not found
                error('please add SPM to your path before trying to run BSM');
                %to do add a check on spm version
            end
            obj.SPMPath=fileparts(SPMFound);
        end
        function[val,TF]=MyGetVal(~,selector,List)
            TF=strcmpi(selector,List);
            if any(TF) %spmpath is set as option
                k=find(TF, 1 );%find the first instance
                if (k+1)>numel(List)
                    id='BSM:getval:ReadBeyondEndInput';
                    msg=sprintf('use name value pairs\nlast entry is a name');
                    throw(MException(id,msg));
                end
                val=List{k+1};
                TF=true;
            else
                val=false;
                TF=false;
            end
        end
    end
end