fMRI_scripts/GIFT_Clean/GiftIcaReport.m

classdef GiftIcaReport<handle
    %GIFTICAREPORT 
    % This Class will be a little tool to print to file images and timecourses
    % to quickly inspect the result of GIFT for a cleanup of fMRI data
    % some guidlines can be found below!
    % https://doi.org/10.1016/j.neuroimage.2016.12.036
    
    properties
        ICAfile     = {};   % .nii file containing the ICA images
        TCfile      = {};   % .nii file containing the TimeCourse data
        Orientation = 'sag';% orientation of images to create
        SliceNumbers = [];   % slice numbers to plot
        
    end
    
    properties (Access=private)
        OrientationOptions={'tra','sag','cor','all'};
        SPMPath
    end
    
    methods %constructor, set and get functions
        function obj = GiftIcaReport()
            %GIFTICAREPORT Construct an instance of this class
            %   Detailed explanation goes here
            obj.SPMPath=[]; %check if SPM is in the path
        end
        
        function set.SPMPath(obj,~)
            SPMFound=which('spm'); %check if SPM in searchpath
            if isempty(SPMFound) %SPM not found
                id='GiftIcaReport:set_SPMPath:SPM_not_found';
                msg='SPM not found';
                throw(MException(id,msg));               
            end
            %to do add a check on spm version
            obj.SPMPath=fileparts(SPMFound);
        end
        
        function set.TCfile(obj,val)
           obj.TCfile=obj.setfile(val);
        end
        
        function set.ICAfile(obj,val)
           obj.ICAfile=obj.setfile(val);
        end
        
        function set.Orientation(obj,val)
            switch lower(val)
                case obj.OrientationOptions %#ok<MCSUP>
                    obj.Orientation=val;
                otherwise
                    id = 'GiftIcaReport:set_orientation:invalid_orientation';
                    msg = sprintf('%s\n%s\n%s\t%s\t%s\n',...
                        'invalid option for orientation',...
                        'pick one of the following options',...
                        obj.OrientationOptions{:}); %#ok<MCSUP>
                    throw(MException(id,msg));
            end
        end
        
        function set.SliceNumbers(obj,val)
            if isnumeric(val) && ~any(val<1)
                   obj.SliceNumbers=val;
            else
                id = 'GiftIcaReport:set_slicenumbers:invalid_input';
                msg = sprintf('invalid input for slicenumbers');
                throw(MException(id,msg));
            end
                
        end
    end
    methods %private methods
       function out = setfile(~,val)
             if isempty(val)
                out={};
                return
            end
            if strcmpi('ui',val)
                out={spm_select(1,'image','select ICA file, first frame')};
                return
            end
            if iscell(val)
                if ~exist(val{1},'file')
                    id='GiftICAReport:setfile:FileNotFound';
                    msg='File not Found';
                    throw(MException(id,msg));
                else
                    out=val(1);
                    return
                end
            else
                if ~exist(val,'file')
                    id='GiftICAReport:setfile:FileNotFound';
                    msg='File not Found';
                    throw(MException(id,msg));
                else
                    out={val};
                    return
                end
            end
       end
    end
end