From 1c93374f37bb3c928fc45ae2607fec2c4467ad73 Mon Sep 17 00:00:00 2001
From: p147685 <p147685@XAP023.workspace.rug.nl>
Date: Wed, 15 Apr 2020 14:59:21 +0200
Subject: [PATCH] step 1 basic scaffold for the unity test and object created

---
 GIFT_Clean/GiftIcaReport.m          | 41 +++++++++++++++++++++++++++++
 GIFT_Clean/UnityTestGiftIcaReport.m | 22 ++++++++++++++++
 2 files changed, 63 insertions(+)
 create mode 100644 GIFT_Clean/GiftIcaReport.m
 create mode 100644 GIFT_Clean/UnityTestGiftIcaReport.m

diff --git a/GIFT_Clean/GiftIcaReport.m b/GIFT_Clean/GiftIcaReport.m
new file mode 100644
index 0000000..5da8512
--- /dev/null
+++ b/GIFT_Clean/GiftIcaReport.m
@@ -0,0 +1,41 @@
+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
+        ICA_file    = {};   % .nii file containing the ICA images
+        TC_file     = {};   % .nii file containing the TimeCourse data
+        Orientation = 'sag';% orientation of images to create
+        SliceNumber = [];   % slice numbers to plot
+        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 outputArg = method1(obj,inputArg)
+            %METHOD1 Summary of this method goes here
+            %   Detailed explanation goes here
+            outputArg = obj.Property1 + inputArg;
+        end
+    end
+end
+
diff --git a/GIFT_Clean/UnityTestGiftIcaReport.m b/GIFT_Clean/UnityTestGiftIcaReport.m
new file mode 100644
index 0000000..060c690
--- /dev/null
+++ b/GIFT_Clean/UnityTestGiftIcaReport.m
@@ -0,0 +1,22 @@
+% this file forms the unity test for GiftIcaReport
+% it requires that SPM is on the search path
+
+%% inspect if eviourment is properly set
+if isempty(which('spm'));error('SPM not on the path, unity test not performed');end
+
+%% basic call 
+Q = GiftIcaReport;
+%% basic call with no SPM error
+try 
+    tmp=fileparts(which('spm'));
+    rmpath(tmp);
+    Q = GiftIcaReport;
+catch ME
+    addpath(tmp); %put back the path
+    if ~ strcmpi(ME.identifier,'GiftIcaReport:set_SPMPath:SPM_not_found')
+        rethrow(ME);
+    else 
+        disp('passed no SPM test')
+        disp(ME)
+    end
+end
\ No newline at end of file