Store BSMclass work in progress
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resources/BSM_Class/BSM.m
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175
resources/BSM_Class/BSM.m
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classdef BSM<handle
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%BSM Summary of this class goes here
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% Detailed explanation goes here
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properties %public properties
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SPMs={}; %field to contain the full path of all SPM.mat files to be analysed
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Acfl %columns in SPM.xX.X to ignore
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Type=1; %BSM type 1..4 5: none
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end
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properties %private properties
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SPM_orig %temporary storage for SPM.mat file
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ActiveColumns %store the columns to be analized
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U_orig %store the U field of SPM
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TargetFolder %target folder
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% option below obsolete?
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BSMToolboxPath%store path to BSMToolbox
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SPMPath;%store path to SPM folder
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SPMIndexList=[];
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end
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properties (Dependent) %dependent properties
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NumSPMs% number of SPM.mat files to process
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end
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properties %constants
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BSMMethod={'Traditional BSM Rissman et al', 'Adapted BSM Rissman et al', 'Fast approach (Mumford et al)', 'Adapted fast approach','none'};
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end
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methods %user callable methods
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function Calc(obj,varargin)
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% obj.calc to apply calculate to all SPM.mat files
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% obj.calc(n) to calculated the nth SPM.mat file
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% obj.calc([1 3 6]) to indicate which SPM.mat file to calculate
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SPMidx=[];% will contain the index to the SPMs to work on
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if logical(numel(varargin))
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SPMidx=varargin{1};
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end
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%check number of input arguments
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if ~logical(obj.NumSPMs)%nothing to do
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fprintf('== == == Nothing to do: done == == ==\n')
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return;
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end
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if isempty(SPMidx)
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SPMidx=1:obj.NumSPMs;
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end
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if ~isnumeric(SPMidx)||~all(isfinite(SPMidx))||min(SPMidx)<1||max(SPMidx)>obj.NumSPMs
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id='BSM:Calc:InvalidIndex';
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msg='Invalid Index';
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throw(MException(id,msg));
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end
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if numel(SPMidx)>1
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obj.SPMIndexList=SPMidx;
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SPMidx=obj.SPMIndexList(end);
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end
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%% start dealing with val is a single entry
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%% do the calculation
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%% clean up
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%% make SPMIndexList one shorter, return if not possible
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%% next recursion loop.
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warning('OFF', 'MATLAB:MKDIR:DirectoryExists');
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%this try catch block will handle any errors that might ocure
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%warning will not remain off by accident
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try
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catch ME
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warning('ON', 'MATLAB:MKDIR:DirectoryExists');
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rethrow(ME);
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end
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end
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end
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methods %constructor and set/get methods
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function obj = BSM(varargin)
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%BSM Construct an instance of this class
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%option: parse the info of a matlab batch file? see
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%tbx_cf_bsm?
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%TODO:
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% set default values
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obj.SPMPath=[]; %get the SPM path
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if nargin>0
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[val,TF]=obj.MyGetVal('SPMs',varargin);if TF;obj.SPMs=val;end
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[val,TF]=obj.MyGetVal('Type',varargin);if TF;obj.Type=val;end
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[val,TF]=obj.MyGetVal('Acfl',varargin);if TF;obj.Acfl=val;end
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end
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% initialize spm job enviourment
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spm_jobman('initcfg');
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end
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function val=get.NumSPMs(obj)
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val=numel(obj.SPMs);
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end
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function set.Type(obj,val)
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%check allowed input
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if ~isnumeric(val)|| any(~ismember(val,1:5))
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id='BSM:Type:invalid';
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msg='use a value in the range 1..5';
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throw(MException(id,msg));
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end
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obj.Type=val;
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end
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function set.Acfl(obj,val)
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%allow clearing
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if isempty(val)
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obj.Acfl=[];
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end
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if ~isnumeric(val) || any(val<1) || any(~isfinite(val))
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id='BSM:Acfl:invalid';
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msg='set an array of positive integer values to the Acfl field';
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throw(MException(id,msg));
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end
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obj.Acfl=val;
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end
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function set.SPMs(obj,val)
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%set the SPMs to be analysed
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%obj.SPMs=<val>
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%possible values for <val>
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% {} : clear the SPMs field
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% {'ui'} : ask user input
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if ~iscell(val)
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fprintf('%s\n',...
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'Use any of the following options',...
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'obj.SPMs={}',...
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'obj.SPMs={''ui''}',...
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'obj.SPMs={<Ful path to SPM.mat>}');
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return
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end
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if isempty(val) %allow empty input
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return;
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end
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if strcmpi(val{1},'ui')
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[P,sts]=spm_select([1 Inf],'mat','select the SPM.mat files',obj.SPMs,pwd,'^SPM.mat');
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if ~logical(sts);return;end
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if iscell(P)
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val=P;
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else
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val=cellstr(P);
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end
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end
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% capture file not found somewhat clever
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TF=cellfun(@exist,val);
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if any(not(TF))
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id='BSM:SetSPMs:FileNotFound';
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msg=sprintf('file not found\t%s\n',val{not(TF)});
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throw(MException(id,msg));
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end
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obj.SPMs=val;
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end
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end
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methods %private functions
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function set.SPMPath(obj,~)
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SPMFound=which('spm'); %check if SPM in searchpath
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if isempty(SPMFound) %SPM not found
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error('please add SPM to your path before trying to run BSM');
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%to do add a check on spm version
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end
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obj.SPMPath=fileparts(SPMFound);
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end
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function[val,TF]=MyGetVal(~,selector,List)
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TF=strcmpi(selector,List);
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if any(TF) %spmpath is set as option
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k=find(TF, 1 );%find the first instance
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if (k+1)>numel(List)
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id='BSM:getval:ReadBeyondEndInput';
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msg=sprintf('use name value pairs\nlast entry is a name');
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throw(MException(id,msg));
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end
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val=List{k+1};
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TF=true;
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else
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val=false;
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TF=false;
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end
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end
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end
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end
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94
resources/BSM_Class/TestBSMClass.m
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94
resources/BSM_Class/TestBSMClass.m
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%% This code will check the BSM class code in a very basic way.
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%% create an instance
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B=BSM;
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%%
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clear B
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try
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B=BSM('type',3,'Acfl',[],'SPMs'); %#ok<*NASGU> %will create an error
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catch ME
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if strcmpi(ME.identifier,'BSM:getval:ReadBeyondEndInput')
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disp('error properly handled')
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disp(ME);
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else
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rethrow(ME);
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end
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end
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%%
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clear B
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B=BSM('type',1,'Acfl',[],'SPMs',{});
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%% set SPMs validity check
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B.SPMs=''; %should produce instructions on how to set SPMs
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B.SPMs={'ui'}; %get input from the user
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tmp=B.SPMs; %store for future use
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%B.SPMs={'ui'}; %calling it again will allow me to edit the list
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B.SPMs={}; %clear out SPMs
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try
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B.SPMs={'SPM.mat';'onzin.mat'}; %provides an error if file does not exist
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catch ME
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if strcmpi(ME.identifier,'BSM:SetSPMs:FileNotFound')
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disp('error properly handled')
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disp(ME);
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else
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rethrow(ME)
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end
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end
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B.SPMs=tmp;
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%% set Type check
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try
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B.Type='onzin'; %gives an error
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catch ME
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if strcmpi(ME.identifier,'BSM:Type:invalid')
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disp('error properly handled')
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disp(ME);
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else
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rethrow(ME)
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end
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end
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%%
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try
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B.Type=0; %gives an error
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catch ME
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if strcmpi(ME.identifier,'BSM:Type:invalid')
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disp('error properly handled')
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disp(ME);
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else
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rethrow(ME)
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end
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end
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%%
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B.Type=1; % correct call
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%% set Acfl check
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try
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B.Acfl=0;
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catch ME
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if strcmpi(ME.identifier,'BSM:Acfl:invalid')
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disp('error properly handled')
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disp(ME);
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else
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rethrow(ME)
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end
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end
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%%
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try
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B.Acfl=-5;
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catch ME
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if strcmpi(ME.identifier,'BSM:Acfl:invalid')
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disp('error properly handled')
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disp(ME);
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else
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rethrow(ME)
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end
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end
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%%
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try
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B.Acfl='test';
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catch ME
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if strcmpi(ME.identifier,'BSM:Acfl:invalid')
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disp('error properly handled')
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disp(ME);
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else
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rethrow(ME)
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end
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end
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%%
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B.Acfl=[];
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