From 20b2d4f22b385379e9eefda06dcd72cc790d4bb6 Mon Sep 17 00:00:00 2001
From: p147685 <p147685@XAP029.workspace.rug.nl>
Date: Thu, 26 Mar 2020 07:10:38 +0100
Subject: [PATCH] Store BSMclass work in progress

---
 resources/BSM_Class/BSM.m          | 175 +++++++++++++++++++++++++++++
 resources/BSM_Class/TestBSMClass.m |  94 ++++++++++++++++
 2 files changed, 269 insertions(+)
 create mode 100644 resources/BSM_Class/BSM.m
 create mode 100644 resources/BSM_Class/TestBSMClass.m

diff --git a/resources/BSM_Class/BSM.m b/resources/BSM_Class/BSM.m
new file mode 100644
index 0000000..af3d638
--- /dev/null
+++ b/resources/BSM_Class/BSM.m
@@ -0,0 +1,175 @@
+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
+
diff --git a/resources/BSM_Class/TestBSMClass.m b/resources/BSM_Class/TestBSMClass.m
new file mode 100644
index 0000000..e4580e1
--- /dev/null
+++ b/resources/BSM_Class/TestBSMClass.m
@@ -0,0 +1,94 @@
+%% This code will check the BSM class code in a very basic way. 
+%% create an instance
+B=BSM;
+%% 
+clear B
+try
+    B=BSM('type',3,'Acfl',[],'SPMs'); %#ok<*NASGU> %will create an error
+catch ME
+    if strcmpi(ME.identifier,'BSM:getval:ReadBeyondEndInput')
+        disp('error properly handled')
+        disp(ME);
+    else
+        rethrow(ME);
+    end
+end
+%% 
+clear B
+B=BSM('type',1,'Acfl',[],'SPMs',{});
+%% set SPMs validity check
+B.SPMs=''; %should produce instructions on how to set SPMs
+B.SPMs={'ui'}; %get input from the user
+tmp=B.SPMs; %store for future use
+%B.SPMs={'ui'}; %calling it again will allow me to edit the list
+B.SPMs={}; %clear out SPMs
+try 
+    B.SPMs={'SPM.mat';'onzin.mat'}; %provides an error if file does not exist
+catch ME
+    if strcmpi(ME.identifier,'BSM:SetSPMs:FileNotFound')
+    disp('error properly handled')
+        disp(ME);
+    else
+        rethrow(ME)
+    end 
+end
+B.SPMs=tmp;
+%% set Type check
+try
+    B.Type='onzin'; %gives an error
+catch ME
+    if strcmpi(ME.identifier,'BSM:Type:invalid')
+        disp('error properly handled')
+        disp(ME);
+    else
+        rethrow(ME)
+    end
+end
+%% 
+try 
+    B.Type=0; %gives an error
+catch ME
+     if strcmpi(ME.identifier,'BSM:Type:invalid')
+        disp('error properly handled')
+        disp(ME);
+    else
+        rethrow(ME)
+     end
+end
+%% 
+B.Type=1; % correct call
+%% set Acfl check
+try
+    B.Acfl=0;
+catch ME
+    if strcmpi(ME.identifier,'BSM:Acfl:invalid')
+        disp('error properly handled')
+        disp(ME);
+    else
+        rethrow(ME)
+    end
+end
+%% 
+try
+    B.Acfl=-5;
+catch ME
+    if strcmpi(ME.identifier,'BSM:Acfl:invalid')
+        disp('error properly handled')
+        disp(ME);
+    else
+        rethrow(ME)
+    end
+end
+%%
+try
+    B.Acfl='test';
+catch ME
+    if strcmpi(ME.identifier,'BSM:Acfl:invalid')
+        disp('error properly handled')
+        disp(ME);
+    else
+        rethrow(ME)
+    end
+end
+%%
+B.Acfl=[];
\ No newline at end of file