GIFT_Clean/GiftIcaReport.m

@@ -6,10 +6,15 @@ classdef GiftIcaReport<handle
     % https://doi.org/10.1016/j.neuroimage.2016.12.036
     
     properties
-        ICA_file    = {};   % .nii file containing the ICA images
+        ICAfile     = {};   % .nii file containing the ICA images
-        TC_file     = {};   % .nii file containing the TimeCourse data
+        TCfile      = {};   % .nii file containing the TimeCourse data
         Orientation = 'sag';% orientation of images to create
-        SliceNumber = [];   % slice numbers to plot
+        SliceNumbers = [];   % slice numbers to plot
+        
+    end
+    
+    properties (Access=private)
+        OrientationOptions={'tra','sag','cor','all'};
         SPMPath
     end
     
@@ -31,11 +36,69 @@ classdef GiftIcaReport<handle
             obj.SPMPath=fileparts(SPMFound);
         end
         
-        function outputArg = method1(obj,inputArg)
+        function set.TCfile(obj,val)
-            %METHOD1 Summary of this method goes here
+           obj.TCfile=obj.setfile(val);
-            %   Detailed explanation goes here
-            outputArg = obj.Property1 + inputArg;
         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
 

GIFT_Clean/UnityTestGiftIcaReport.m

@@ -3,7 +3,11 @@
 
 %% inspect if eviourment is properly set
 if isempty(which('spm'));error('SPM not on the path, unity test not performed');end
-
+%check if test files exist
+P={'X:\My Documents\MATLAB\Projects\fMRI_script\GIFT_Clean\TestData\g_sub01_component_ica_s1_.nii'};
+if not(exist(P{1},'file'));error('Test file not found,unity test not performed');end
+P2={'X:\My Documents\MATLAB\Projects\fMRI_script\GIFT_Clean\TestData\g_sub01_timecourses_ica_s1_.nii'};
+if not(exist(P2{1},'file'));error('Test file not found,unity test not performed');end
 %% basic call 
 Q = GiftIcaReport;
 %% basic call with no SPM error
@@ -19,4 +23,60 @@ catch ME
         disp('passed no SPM test')
         disp(ME)
     end
-end
+end
+%% test set ICAfile
+Q.ICAfile=[]; %set to empty
+try
+    Q.ICAfile = 'junk';
+catch ME
+    if ~strcmpi(ME.identifier,'GiftICAReport:setfile:FileNotFound')
+        rethrow(ME);
+    else
+        disp('passed file not found test')
+        disp(ME);
+    end
+end
+Q.ICAfile=P;
+Q.ICAfile=P{1};
+%Q.ICAfile='ui'; % request a user interface
+%% test set TC file
+%Q.TCfile='ui';
+Q.ICAfile=P2;
+%% test set orientation
+try
+    Q.Orientation='junk';
+catch ME
+    if ~strcmpi(ME.identifier,'GiftIcaReport:set_orientation:invalid_orientation')
+        rethrow(ME)
+    else
+        disp('passed test on Orientation error')
+        disp(ME)
+    end
+end
+Q.Orientation='tra';
+Q.Orientation='cor';
+Q.Orientation='sag';
+
+%% test setting slice numbers I
+try 
+    Q.SliceNumbers=0:5;
+catch ME
+    if ~strcmpi(ME.identifier,'GiftIcaReport:set_slicenumbers:invalid_input')
+        rethrow(ME);
+    else
+        disp('passed error test on set slicenumbers');
+        disp(ME);
+    end
+end
+%% test setting slice numbers II
+try 
+    Q.SliceNumbers='junk';
+catch ME
+    if ~strcmpi(ME.identifier,'GiftIcaReport:set_slicenumbers:invalid_input')
+        rethrow(ME);
+    else
+        disp('passed error test on set slicenumbers');
+        disp(ME);
+    end
+end
+Q.SliceNumbers=1:2:100;